2023

Wang, Y., Liu, X., Ge, R., Moretti, M., Yin, J., Zhao, Z., Valle-Pérez, A. U., Liu, H., Tian, Z., Guo, T., Zhu, Y., Hauser, C. A. E., & Alshareef, H. N. (2023). Peptide Gel Electrolytes for Stabilized Zn Metal Anodes. ACS Nano. https://doi.org/10.1021/acsnano.3c04414
Wang, J., Chistov, G., Zhang, J., Huntington, B., Salem, I., Sandholu, A., & Arold, S. T. (2023). P-NADs:PUX-basedNAnobody Degraders for Ubiquitin-Independent Degradation of Target Proteins. https://doi.org/10.1101/2023.12.20.572486
van der Zwan, F. M., Augustin, N., Petersen, S., Altalhi, S. M., Schultz, J., Peixoto, R. S., Follmann, J., Anker, A., Benzoni, F., Garcia Paredes, E. R., Al Malallah, M., Shepard, L., Ouhssain, M., Jägerup, S. B., Jones, B. H., & Rosado, A. S. (2023). Widespread diffuse venting and large microbial iron-mounds in the Red Sea. Communications Earth & Environment, 4(1). https://doi.org/10.1038/s43247-023-01169-7
Staab, S., Cardénas, A., Peixoto, R. S., Schreiber, F., & Voolstra, C. R. (2023). Coracle—A Machine Learning Framework to Identify Bacteria Associated with Continuous Variables. Bioinformatics. https://doi.org/10.1093/bioinformatics/btad749
Sait, R., Al-Jawhari, H., Ganash, A., Wustoni, S., Chen, L., Hedhili, M. N., Wehbe, N., Hussein, D., Alhowity, A., Baeesa, S., Bangash, M., Abuzenadah, A., Inal, S., & Cross, R. (2023). Electrochemical Performance of Biocompatible TiC Films Deposited through Nonreactive RF Magnetron Sputtering for Neural Interfacing. ACS Biomaterials Science & Engineering. https://doi.org/10.1021/acsbiomaterials.3c01371
Fu, C., Frappi, S., Havlik, M. N., Howe, W., Harris, S. D., Laiolo, E., Gallagher, A. J., Masqué, P., & Duarte, C. M. (2023). Substantial blue carbon sequestration in the world’s largest seagrass meadow. Communications Earth & Environment, 4(1). https://doi.org/10.1038/s43247-023-01154-0
Su, J., Xu, J., & Wang, D. (2024). PAC learning halfspaces in non-interactive local differential privacy model with public unlabeled data. Journal of Computer and System Sciences, 141, 103496. https://doi.org/10.1016/j.jcss.2023.103496
Alkuraythi, D. M., Alkhulaifi, M. M., Binjomah, A. Z., Alarwi, M., Aldakhil, H. M., Mujallad, M. I., Alharbi, S. A., Alshomrani, M., Alshahrani, S. M., Gojobori, T., & Alajel, S. M. (2023). Clonal Flux and Spread of Staphylococcus aureus Isolated from Meat and Its Genetic Relatedness to Staphylococcus aureus Isolated from Patients in Saudi Arabia. Microorganisms, 11(12), 2926. https://doi.org/10.3390/microorganisms11122926
Moretti, M., Hountondji, M., Ge, R., Emwas, A.-H., Bilalis, P., Susapto, H. H., Alrashoudi, A., Liu, X., Briola, G. R., & Hauser, C. A. E. (2023). Selectively Positioned Catechol Moiety Supports Ultrashort Self-Assembling Peptide Hydrogel Adhesion for Coral Restoration. Langmuir, 39(49), 17903–17920. https://doi.org/10.1021/acs.langmuir.3c02553
Albaradei, S., Alganmi, N., Albaradie, A., Alharbi, E., Motwalli, O., Thafar, M. A., Gojobori, T., Essack, M., & Gao, X. (2023). A deep learning model predicts the presence of diverse cancer types using circulating tumor cells. Scientific Reports, 13(1). https://doi.org/10.1038/s41598-023-47805-2
Zhong, Y., Nayak, P. D., Wustoni, S., Surgailis, J., Parrado Agudelo, J. Z., Marks, A., McCulloch, I., & Inal, S. (2023). Ionic Liquid Gated Organic Electrochemical Transistors with Broadened Bandwidth. ACS Applied Materials & Interfaces. https://doi.org/10.1021/acsami.3c11214
Bhattacharya, R., Chen, N., Shim, I., Kuwahara, H., Gao, X., Alkuraya, F. S., & Fahed, A. C. (2023). Massive underrepresentation of Arabs in genomic studies of common disease. Genome Medicine, 15(1). https://doi.org/10.1186/s13073-023-01254-8
Gou, X., Hu, L., Wang, D., & Zhang, X. (2023). A Fundamental Model with Stable Interpretability for Traffic Forecasting. Proceedings of the 1st ACM SIGSPATIAL International Workshop on Geo-Privacy and Data Utility for Smart Societies. https://doi.org/10.1145/3615889.3628510
Ramos-Mandujano, G., Grünberg, R., Zhang, Y., Bi, C., Guzmán-Vega, F. J., Shuaib, M., Gorchakov, R. V., Xu, J., Tehseen, M., Takahashi, M., Takahashi, E., Dada, A., Ahmad, A. N., Hamdan, S. M., Pain, A., Arold, S. T., & Li, M. (2023). An open-source, automated, and cost-effective platform for COVID-19 diagnosis and rapid portable genomic surveillance using nanopore sequencing. Scientific Reports, 13(1). https://doi.org/10.1038/s41598-023-47190-w
Kafkas, Ş., Abdelhakim, M., Althagafi, A., Toonsi, S., Alghamdi, M., Schofield, P. N., & Hoehndorf, R. (2023). The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients. https://doi.org/10.1101/2023.11.16.23298615
Althagafi, A., Zhapa-Camacho, F., & Hoehndorf, R. (2023). Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning. https://doi.org/10.1101/2023.11.08.566179
Modolon, F., Schultz, J., Duarte, G., Vilela, C. L., Thomas, T., & Peixoto, R. S. (2023). In situ devices can culture the microbial dark matter of corals. IScience, 108374. https://doi.org/10.1016/j.isci.2023.108374
Goto, K., Masuzawa, Y., Kohmura, M., Takumi, A., Takeyama, H., Miyazaki, S., Gojobori, T., & Mineta, K. (2023). Glutamate-Sensing Genes Are Conserved among Populations Compared to Glutamate Metabolism Genes. Annals of Nutrition and Metabolism, 1–9. Portico. https://doi.org/10.1159/000535181
Junger, P. C., Sarmento, H., Giner, C. R., Mestre, M., Sebastián, M., Morán, X. A. G., Arístegui, J., Agustí, S., Duarte, C. M., Acinas, S. G., Massana, R., Gasol, J. M., & Logares, R. (2023). Global biogeography of the smallest plankton across ocean depths. Science Advances, 9(45). https://doi.org/10.1126/sciadv.adg9763
Alhattab, D. M., Isaioglou, I., Alshehri, S., Khan, Z. N., Susapto, H. H., Li, Y., Marghani, Y., Alghuneim, A. A., Díaz-Rúa, R., Abdelrahman, S., AL-Bihani, S., Ahmed, F., Felimban, R. I., Alkhatabi, H., Alserihi, R., Abedalthagafi, M., AlFadel, A., Awidi, A., Chaudhary, A. G., … Hauser, C. A. E. (2023). Fabrication of a three-dimensional bone marrow niche-like acute myeloid Leukemia disease model by an automated and controlled process using a robotic multicellular bioprinting system. Biomaterials Research, 27(1). https://doi.org/10.1186/s40824-023-00457-9
Savva, A., Hama, A., Herrera‐López, G., Schmidt, T., Migliaccio, L., Steiner, N., Kawan, M., Fiumelli, H., Magistretti, P. J., McCulloch, I., Baran, D., Gasparini, N., Schindl, R., Głowacki, E. D., & Inal, S. (2023). Photo‐Chemical Stimulation of Neurons with Organic Semiconductors (Adv. Sci. 31/2023). Advanced Science, 10(31). Portico. https://doi.org/10.1002/advs.202370217
Wang, X., Xu, T., Yao, Y., Cheung, P. P.-H., Gao, X., & Zhang, L. (2023). SARS-CoV-2 RNA-Dependent RNA Polymerase Follows Asynchronous Translocation Pathway for Viral Transcription and Replication. The Journal of Physical Chemistry Letters, 10119–10128. https://doi.org/10.1021/acs.jpclett.3c01249
Chen, J., Ng, M. K., & Wang, D. (2023). Quantizing Heavy-tailed Data in Statistical Estimation: (Near) Minimax Rates, Covariate Quantization, and Uniform Recovery. IEEE Transactions on Information Theory, 1–1. https://doi.org/10.1109/tit.2023.3329240
Delgadillo-Ordoñez, N., Garcias-Bonet, N., Raimundo, I., García, F., Villela, H., Osman, E., Santoro, E., Curdia, J., Rosado, J., Cardoso, P., Alsaggaf, A., Barno, A., Antony, C., Bocanegra, C., Berumen, M., Voolstra, C., Benzoni, F., Carvalho, S., & Peixoto, R. (2023). Probiotics reshape the coral microbiome in situ without affecting the surrounding environment. https://doi.org/10.21203/rs.3.rs-3414265/v1
Tang, Z., Pei, S., Peng, X., Zhuang, F., Zhang, X., & Hoehndorf, R. (2023). Neural Multi-hop Logical Query Answering with Concept-Level Answers. Lecture Notes in Computer Science, 522–540. https://doi.org/10.1007/978-3-031-47240-4_28
Pei, S., Zhang, X., Eguíluz, V. M., Kienle, S. S., Robinson, P. W., Costa, D. P., & Duarte, C. M. (2023). Coherent movement patterns of female northern elephant seals across the NE Pacific Ocean. Frontiers in Marine Science, 10. https://doi.org/10.3389/fmars.2023.689953
El-Khaled, Y. C., Duarte, C. M., & Peixoto, R. S. (2023). Evidence of hawksbill turtle (Eretmochelys imbricata) depredation on fish caught in gillnets. Frontiers in Marine Science, 10. https://doi.org/10.3389/fmars.2023.1180219
El-Khaled, Y. C., Duarte, C. M., & Peixoto, R. S. (2023). Evidence of hawksbill turtle (Eretmochelys imbricata) depredation on fish caught in gillnets. Frontiers in Marine Science, 10. https://doi.org/10.3389/fmars.2023.1180219
Li, Z., Jin, J., He, W., Long, W., Yu, H., Gao, X., Nakai, K., Zou, Q., & Wei, L. (2023). CoraL: interpretable contrastive meta-learning for the prediction of cancer-associated ncRNA-encoded small peptides. Briefings in Bioinformatics, 24(6). https://doi.org/10.1093/bib/bbad352
Alsemari, A., Guzmán-Vega, F. J., Meyer, B. F., & Arold, S. T. (2024). Novel Homozygous Variants of SLC13A5 Expand the Functional Heterogeneity of a Homogeneous Syndrome of Early Infantile Epileptic Encephalopathy. Pediatric Neurology, 151, 68–72. https://doi.org/10.1016/j.pediatrneurol.2023.10.005
Shim, I., Kuwahara, H., Chen, N., Hashem, M. O., AlAbdi, L., Abouelhoda, M., Won, H.-H., Natarajan, P., Ellinor, P. T., Khera, A. V., Gao, X., Alkuraya, F. S., & Fahed, A. C. (2023). Clinical utility of polygenic scores for cardiometabolic disease in Arabs. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-41985-1
Wang, D., & Xu, J. (2024). Gradient complexity and non-stationary views of differentially private empirical risk minimization. Theoretical Computer Science, 982, 114259. https://doi.org/10.1016/j.tcs.2023.114259
Martynova, A., Genchi, L., Laptenok, S. P., Cusack, M., Stenchikov, G. L., Liberale, C., & Duarte, C. M. (2024). Atmospheric microfibrous deposition over the Eastern Red Sea coast. Science of The Total Environment, 907, 167902. https://doi.org/10.1016/j.scitotenv.2023.167902
Martynova, A., Genchi, L., Laptenok, S. P., Cusack, M., Stenchikov, G. L., Liberale, C., & Duarte, C. M. (2024). Atmospheric microfibrous deposition over the Eastern Red Sea coast. Science of The Total Environment, 907, 167902. https://doi.org/10.1016/j.scitotenv.2023.167902
Boshah, H., Samkari, F., Valle-Pérez, A. U., Alsawaf, S. M., Aldoukhi, A. H., Bilalis, P., Alshehri, S. A., Susapto, H. H., & Hauser, C. A. E. (2023). Evaluation of Potential Peptide-Based Inhibitors against SARS-CoV-2 and Variants of Concern. BioMed Research International, 2023, 1–17. https://doi.org/10.1155/2023/3892370
Zhou, J., Li, H., Liao, X., Zhang, B., He, W., Li, Z., Zhou, L., & Gao, X. (2023). A unified method to revoke the private data of patients in intelligent healthcare with audit to forget. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-41703-x
Han, R., Qi, J., Xue, Y., Sun, X., Zhang, F., Gao, X., & Li, G. (2023). HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing. Genome Biology, 24(1). https://doi.org/10.1186/s13059-023-03053-1
Ostonov, A., & Moshkov, M. (2023). On Complexity of Deterministic and Nondeterministic Decision Trees for Conventional Decision Tables from Closed Classes. Entropy, 25(10), 1411. https://doi.org/10.3390/e25101411
Knodel, M. M., Nägel, A., Herrmann, E., & Wittum, G. (2023). PDE Models of Virus Replication Coupling 2D Manifold and 3D Volume Effects Evaluated at Realistic Reconstructed Cell Geometries. Finite Volumes for Complex Applications X—Volume 1, Elliptic and Parabolic Problems, 315–323. https://doi.org/10.1007/978-3-031-40864-9_26
Chu, Y., Zhou, L., Luo, G., Qiu, Z., & Gao, X. (2023). Topology-Preserving Computed Tomography Super-Resolution Based on Dual-Stream Diffusion Model. Medical Image Computing and Computer Assisted Intervention – MICCAI 2023, 260–270. https://doi.org/10.1007/978-3-031-43999-5_25
Kulmanov, M., Guzmán-Vega, F. J., Roggli, P. D., Lane, L., Arold, S. T., & Hoehndorf, R. (2023). DeepGO-SE: Protein function prediction as Approximate Semantic Entailment. https://doi.org/10.1101/2023.09.26.559473
Samardzic, V. S., Macvanin, M. T., Zafirovic, S. S., Obradovic, M. M., Gluvic, Z. M., Grubin, J., Gao, X., Essack, M., & Isenovic, E. R. (2023). Nitric oxide, thyroglobulin, and calcitonin: unraveling the nature of thyroid nodules. Frontiers in Endocrinology, 14. https://doi.org/10.3389/fendo.2023.1241223
Bilalis, P., Alrashoudi, A. Α., Susapto, H. H., Moretti, M., Alshehri, S., Abdelrahman, S., Elsakran, A., & Hauser, C. A. E. (2023). Dipeptide-Based Photoreactive Instant Glue for Environmental and Biomedical Applications. ACS Applied Materials & Interfaces, 15(40), 46710–46720. https://doi.org/10.1021/acsami.3c10726
Malawsky, D. S., van Walree, E., Jacobs, B. M., Heng, T. H., Huang, Q. Q., Sabir, A. H., Rahman, S., Sharif, S. M., Khan, A., Mirkov, M. U., Kuwahara, H., Gao, X., Alkuraya, F. S., Posthuma, D., Newman, W. G., Griffiths, C. J., Mathur, R., van Heel, D. A., Finer, S., … Martin, H. C. (2023). Influence of autozygosity on common disease risk across the phenotypic spectrum. Cell, 186(21), 4514-4527.e14. https://doi.org/10.1016/j.cell.2023.08.028
Garcias-Bonet, N., Roik, A., Tierney, B., García, F. C., Villela, H. D. M., Dungan, A. M., Quigley, K. M., Sweet, M., Berg, G., Gram, L., Bourne, D. G., Ushijima, B., Sogin, M., Hoj, L., Duarte, G., Hirt, H., Smalla, K., Rosado, A. S., Carvalho, S., … Peixoto, R. S. (2023). Horizon scanning the application of probiotics for wildlife. Trends in Microbiology. https://doi.org/10.1016/j.tim.2023.08.012
Alsolme, E., Alqahtani, S., Fageeh, M., Barakeh, D., Sharma, N. K., Mangul, S., Robinson, H. A., Fathaddin, A., Hauser, C. A. E., & Abedalthagafi, M. (2023). The Genomic Landscape of Colorectal Cancer in the Saudi Arabian Population Using a Comprehensive Genomic Panel. Diagnostics, 13(18), 2993. https://doi.org/10.3390/diagnostics13182993
Liao, X., Zhu, W., Zhou, J., Li, H., Xu, X., Zhang, B., & Gao, X. (2023). Repetitive DNA sequence detection and its role in the human genome. Communications Biology, 6(1). https://doi.org/10.1038/s42003-023-05322-y
Guo, Y., Marin, J. M., Ashry, I., Trichili, A., Havlik, M.-N., Ng, T. K., Duarte, C. M., & Ooi, B. S. (2023). Submarine optical fiber communication provides an unrealized deep-sea observation network. Scientific Reports, 13(1). https://doi.org/10.1038/s41598-023-42748-0
Druet, V., Ohayon, D., Petoukhoff, C. E., Zhong, Y., Alshehri, N., Koklu, A., Nayak, P. D., Salvigni, L., Almulla, L., Surgailis, J., Griggs, S., McCulloch, I., Laquai, F., & Inal, S. (2023). A single n-type semiconducting polymer-based photo-electrochemical transistor. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-41313-7
Savva, A., Hama, A., Herrera‐López, G., Schmidt, T., Migliaccio, L., Steiner, N., Kawan, M., Fiumelli, H., Magistretti, P. J., McCulloch, I., Baran, D., Gasparini, N., Schindl, R., Głowacki, E. D., & Inal, S. (2023). Photo‐Chemical Stimulation of Neurons with Organic Semiconductors. Advanced Science, 10(31). Portico. https://doi.org/10.1002/advs.202300473
Sanz-Sáez, I., Sánchez, P., Salazar, G., Sunagawa, S., de Vargas, C., Bowler, C., Sullivan, M. B., Wincker, P., Karsenti, E., Pedrós-Alió, C., Agustí, S., Gojobori, T., Duarte, C. M., Gasol, J. M., Sánchez, O., & Acinas, S. G. (2023). Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation. ISME Communications, 3(1). https://doi.org/10.1038/s43705-023-00290-0
Fan, M., Huang, G., Lou, J., Gao, X., Zeng, T., & Li, L. (2023). Cross-Parametric Generative Adversarial Network-Based Magnetic Resonance Image Feature Synthesis for Breast Lesion Classification. IEEE Journal of Biomedical and Health Informatics, 27(11), 5495–5505. https://doi.org/10.1109/jbhi.2023.3311021
Li, X., Yang, Q., Luo, G., Xu, L., Dong, W., Wang, W., Dong, S., Wang, K., Xuan, P., & Gao, X. (2023). SAGDTI: self-attention and graph neural network with multiple information representations for the prediction of drug-target interactions. Bioinformatics Advances. https://doi.org/10.1093/bioadv/vbad116
Ma, J., Li, C., Zhang, Y., Wang, Z., Li, S., Guo, Y., Zhang, L., Liu, H., Gao, X., & Song, J. (2023). MULGA, a unified multi-view graph autoencoder-based approach for identifying drug–protein interaction and drug repositioning. Bioinformatics, 39(9). https://doi.org/10.1093/bioinformatics/btad524
Huang, R., He, J., Wang, N., Christakos, G., Gu, J., Song, L., Luo, J., Agusti, S., Duarte, C. M., & Wu, J. (2023). Carbon sequestration potential of transplanted mangroves and exotic saltmarsh plants in the sediments of subtropical wetlands. Science of The Total Environment, 904, 166185. https://doi.org/10.1016/j.scitotenv.2023.166185
Busbait, M., Moshkov, M., Moshkova, A., & Shevtchenko, V. (2023). Diagnosis of Extensions of Constant Faults in Circuits. Studies in Systems, Decision and Control, 53–70. https://doi.org/10.1007/978-3-031-39031-9_4
Alghamdi, S. M., & Hoehndorf, R. (2023). Improving the classification of cardinality phenotypes using collections. Journal of Biomedical Semantics, 14(1). https://doi.org/10.1186/s13326-023-00290-y
Carvalho, S., Shchepanik, H., Aylagas, E., Berumen, M. L., Costa, F. O., Costello, M. J., Duarte, S., Ferrario, J., Floerl, O., Heinle, M., Katsanevakis, S., Marchini, A., Olenin, S., Pearman, J. K., Peixoto, R. S., Rabaoui, L. J., Ruiz, G., Srėbalienė, G., Therriault, T. W., … Zaiko, A. (2023). Hurdles and opportunities in implementing marine biosecurity systems in data-poor regions. BioScience, 73(7), 494–512. https://doi.org/10.1093/biosci/biad056
Stenton, S. L., O’Leary, M., Lemire, G., VanNoy, G. E., DiTroia, S., Ganesh, V. S., Groopman, E., O’Heir, E., Mangilog, B., Osei-Owusu, I., Pais, L. S., Serrano, J., Singer-Berk, M., Weisburd, B., Wilson, M., Austin-Tse, C., Abdelhakim, M., Althagafi, A., Babbi, G., … O’Donnell-Luria, A. (2023). Critical assessment of variant prioritization methods for rare disease diagnosis within the Rare Genomes Project. https://doi.org/10.1101/2023.08.02.23293212
Guzmán‐Vega, F. J., González‐Álvarez, A. C., Peña‐Guerra, K. A., Cardona‐Londoño, K. J., & Arold, S. T. (2023). Leveraging AI Advances and Online Tools for Structure‐Based Variant Analysis. Current Protocols, 3(8). Portico. https://doi.org/10.1002/cpz1.857
Abrogueña, J. B. R., Tanita, I., Anton, A., Maquirang, J. R. H., Duarte, C., Woo, S. P., Berković, B., Roje-Busatto, R., Yacoubi, L., Doyle, A., Konji, H., Al-Johani, T., Chen, J.-L., & Rabaoui, L. J. (2023). Influence of environmental variables on the abundance of Synapta maculata (Holothuroidea: Synaptidae) in a multi-species seagrass meadow in the southern Red Sea of Saudi Arabia. Regional Studies in Marine Science, 66, 103133. https://doi.org/10.1016/j.rsma.2023.103133
Aspromonte, M. C., Conte, A. D., Zhu, S., Tan, W., Shen, Y., Zhang, Y., Li, Q., Wang, M. H., Babbi, G., Bovo, S., Martelli, P. L., Casadio, R., Althagafi, A., Toonsi, S., Kulmanov, M., Hoehndorf, R., Katsonis, P., Williams, A., Lichtarge, O., … Leonardi, E. (2023). CAGI6 ID-Challenge: Assessment of phenotype and variant predictions in 415 children with Neurodevelopmental Disorders (NDDs). https://doi.org/10.21203/rs.3.rs-3209168/v1
Villela, H., Modolon, F., Schultz, J., Delgadillo-Ordoñez, N., Carvalho, S., Soriano, A. U., & Peixoto, R. S. (2023). Genome analysis of a coral-associated bacterial consortium highlights complementary hydrocarbon degradation ability and other beneficial mechanisms for the host. Scientific Reports, 13(1). https://doi.org/10.1038/s41598-023-38512-z
Alkuraythi, D. M., Alkhulaifi, M. M., Binjomah, A. Z., Alarawi, M., Aldakhil, H. M., Mujallad, M. I., Alharbi, S. A., Alshomrani, M., Alshahrani, S. M., Gojobori, T., & Alajel, S. M. (2023). Genetic characterization and dissemination ofStaphylococcus aureusand Staphylococci genus: food and health perspective. https://doi.org/10.1101/2023.07.24.550257
Macvanin, M. T., Gluvic, Z. M., Zaric, B. L., Essack, M., Gao, X., & Isenovic, E. R. (2023). New biomarkers: prospect for diagnosis and monitoring of thyroid disease. Frontiers in Endocrinology, 14. https://doi.org/10.3389/fendo.2023.1218320
Kafkas, Șenay, Abdelhakim, M., Uludag, M., Althagafi, A., Alghamdi, M., & Hoehndorf, R. (2023). Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes. BMC Bioinformatics, 24(1). https://doi.org/10.1186/s12859-023-05406-w
Abdelrahman, S., Ge, R., Susapto, H. H., Liu, Y., Samkari, F., Moretti, M., Liu, X., Hoehndorf, R., Emwas, A.-H., Jaremko, M., Rawas, R. H., & Hauser, C. A. E. (2023). The Impact of Mechanical Cues on the Metabolomic and Transcriptomic Profiles of Human Dermal Fibroblasts Cultured in Ultrashort Self-Assembling Peptide 3D Scaffolds. ACS Nano, 17(15), 14508–14531. https://doi.org/10.1021/acsnano.3c01176
Liu, C., Zhang, Y., Gao, X., & Wang, G. (2023). Identification of cell subpopulations associated with disease phenotypes from scRNA-seq data using PACSI. BMC Biology, 21(1). https://doi.org/10.1186/s12915-023-01658-3
Petrović, N., Essack, M., Šami, A., Perry, G., Gojobori, T., Isenović, E. R., & Bajić, V. P. (2023). MicroRNA networks linked with BRCA1/2, PTEN, and common genes for Alzheimer’s disease and breast cancer share highly enriched pathways that may unravel targets for the AD/BC comorbidity treatment. Computational Biology and Chemistry, 106, 107925. https://doi.org/10.1016/j.compbiolchem.2023.107925
Lin, C.-C., Wieteska, L., Poncet-Montange, G., Suen, K. M., Arold, S. T., Ahmed, Z., & Ladbury, J. E. (2023). The combined action of the intracellular regions regulates FGFR2 kinase activity. Communications Biology, 6(1). https://doi.org/10.1038/s42003-023-05112-6
Ørberg, S. B., Duarte, C. M., Geraldi, N. R., Sejr, M. K., Wegeberg, S., Hansen, J. L. S., & Krause-Jensen, D. (2023). Prevalent fingerprint of marine macroalgae in arctic surface sediments. Science of The Total Environment, 898, 165507. https://doi.org/10.1016/j.scitotenv.2023.165507
Labra-Gayo, J. E., Waagmeester, A., Yamamoto, Y., Iglesias-Préstamo, Á., Katayama, T., Liener, T., Unni, D., Bolleman, J., Aoki-Kinoshita, K. F., Yokochi, M., Queralt-Rosinach, N., Mori, H., Álvarez, D. F., Labarga, A., Hoehndorf, R., Prud’hommeaux, E., Nanjo, C., & Thalhath, N. (2023). RDF Data integration using Shape Expressions. https://doi.org/10.37044/osf.io/md73k
Peixoto, R. S., & Voolstra, C. R. (2023). The baseline is already shifted: marine microbiome restoration and rehabilitation as essential tools to mitigate ecosystem decline. Frontiers in Marine Science, 10. https://doi.org/10.3389/fmars.2023.1218531
Garg, D., Samota, M. K., Kontis, N., Patel, N., Bala, S., & Rosado, A. S. (2023). Revolutionizing biofuel generation: Unleashing the power of CRISPR-Cas mediated gene editing of extremophiles. Microbiological Research, 274, 127443. https://doi.org/10.1016/j.micres.2023.127443
Kaidarova, A., Geraldi, N. R., Wilson, R. P., Kosel, J., Meekan, M. G., Eguíluz, V. M., Hussain, M. M., Shamim, A., Liao, H., Srivastava, M., Saha, S. S., Strano, M. S., Zhang, X., Ooi, B. S., Holton, M., Hopkins, L. W., Jin, X., Gong, X., Quintana, F., … Duarte, C. M. (2023). Wearable sensors for monitoring marine environments and their inhabitants. Nature Biotechnology. https://doi.org/10.1038/s41587-023-01827-3
Garg, D., Samota, M. K., Kontis, N., Patel, N., Bala, S., & Rosado, A. S. (2023). Revolutionizing biofuel generation: Unleashing the power of CRISPR-Cas mediated gene editing of extremophiles. Microbiological Research, 274, 127443. https://doi.org/10.1016/j.micres.2023.127443
Kuwahara, H., & Gao, X. (2023). S-leaping: an efficient downsampling method for large high-throughput sequencing data. Bioinformatics, 39(7). https://doi.org/10.1093/bioinformatics/btad399
Xu, X., Xu, T., Zhou, J., Liao, X., Zhang, R., Wang, Y., Zhang, L., & Gao, X. (2023). AB-Gen: Antibody Library Design with Generative Pre-trained Transformer and Deep Reinforcement Learning. Genomics, Proteomics & Bioinformatics. https://doi.org/10.1016/j.gpb.2023.03.004
Moradigaravand, D., Li, L., Dechesne, A., Nesme, J., de la Cruz, R., Ahmad, H., Banzhaf, M., Sørensen, S. J., Smets, B. F., & Kreft, J.-U. (2023). Plasmid permissiveness of wastewater microbiomes can be predicted from 16S rRNA sequences by machine learning. Bioinformatics, 39(7). https://doi.org/10.1093/bioinformatics/btad400
Ding, P., Wang, Y., Zhang, X., Gao, X., Liu, G., & Yu, B. (2023). DeepSTF: predicting transcription factor binding sites by interpretable deep neural networks combining sequence and shape. Briefings in Bioinformatics, 24(4). https://doi.org/10.1093/bib/bbad231
Han, W., Chen, N., Xu, X., Sahil, A., Zhou, J., Li, Z., Zhong, H., Gao, E., Zhang, R., Wang, Y., Sun, S., Cheung, P. P.-H., & Gao, X. (2023). Predicting the antigenic evolution of SARS-COV-2 with deep learning. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-39199-6
Zhang, B., & Gao, X. (2023). Publisher Correction: Deciphering DNA variant-associated aberrant splicing with the aid of RNA sequencing. Nature Genetics, 55(7), 1251–1251. https://doi.org/10.1038/s41588-023-01441-8
Genchi, L., Martin, C., Laptenok, S. P., Baalkhuyur, F., Duarte, C. M., & Liberale, C. (2023). When microplastics are not plastic: Chemical characterization of environmental microfibers using stimulated Raman microspectroscopy. Science of The Total Environment, 892, 164671. https://doi.org/10.1016/j.scitotenv.2023.164671
Wustoni, S., Ohayon, D., Hermawan, A., Nuruddin, A., Inal, S., Indartono, Y. S., & Yuliarto, B. (2023). Material Design and Characterization of Conducting Polymer-Based Supercapacitors. Polymer Reviews, 1–59. https://doi.org/10.1080/15583724.2023.2220131
Schultz, J., Modolon, F., Peixoto, R. S., & Rosado, A. S. (2023). Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles. Frontiers in Microbiology, 14. https://doi.org/10.3389/fmicb.2023.1167718
Garritano, A. N., Majzoub, M. E., Ribeiro, B., Damasceno, T., Modolon, F., Messias, C., Vilela, C., Duarte, G., Hill, L., Peixoto, R., & Thomas, T. (2023). Species-specific relationships between deep sea sponges and their symbiotic Nitrosopumilaceae. The ISME Journal, 17(9), 1517–1519. https://doi.org/10.1038/s41396-023-01439-4
Coutinho, F. H., Silveira, C. B., Sebastián, M., Sánchez, P., Duarte, C. M., Vaqué, D., Gasol, J. M., & Acinas, S. G. (2023). Water mass age structures the auxiliary metabolic gene content of free-living and particle-attached deep ocean viral communities. Microbiome, 11(1). https://doi.org/10.1186/s40168-023-01547-5
Siodmak, A., Shahul Hameed, U. F., Rayapuram, N., Völz, R., Boudsocq, M., Alharbi, S., Alhoraibi, H., Lee, Y., Blilou, I., Arold, S. T., & Hirt, H. (2023). Essential role of the CD docking motif of MPK4 in plant immunity, growth, and development. New Phytologist, 239(3), 1112–1126. Portico. https://doi.org/10.1111/nph.18989
Alshammari, M., Ahmad, A., AlKhulaifi, M., Al Farraj, D., Alsudir, S., Alarawi, M., Takashi, G., & Alyamani, E. (2023). Reduction of biofilm formation of Escherichia coli by targeting quorum sensing and adhesion genes using the CRISPR/Cas9-HDR approach, and its clinical application on urinary catheter. Journal of Infection and Public Health, 16(8), 1174–1183. https://doi.org/10.1016/j.jiph.2023.05.026
Traberg, W. C., Uribe, J., Druet, V., Hama, A., Moysidou, C., Huerta, M., McCoy, R., Hayward, D., Savva, A., Genovese, A. M. R., Pavagada, S., Lu, Z., Koklu, A., Pappa, A., Fitzgerald, R., Inal, S., Daniel, S., & Owens, R. M. (2023). Organic Electronic Platform for Real‐Time Phenotypic Screening of Extracellular‐Vesicle‐Driven Breast Cancer Metastasis. Advanced Healthcare Materials. Portico. https://doi.org/10.1002/adhm.202301194
Nakagawa, S., Sakaguchi, S., Ogura, A., Mineta, K., Endo, T., Suzuki, Y., & Gojobori, T. (2023). Current trends in RNA virus detection through metatranscriptome sequencing data. FEBS Open Bio, 13(6), 992–1000. Portico. https://doi.org/10.1002/2211-5463.13626
Schultz, J., dos Santos, A., Patel, N., & Rosado, A. S. (2023). Life on the Edge: Bioprospecting Extremophiles for Astrobiology. Journal of the Indian Institute of Science, 103(3), 721–737. https://doi.org/10.1007/s41745-023-00382-9
Zhang, B., & Gao, X. (2023). Deciphering DNA variant-associated aberrant splicing with the aid of RNA sequencing. Nature Genetics, 55(5), 732–733. https://doi.org/10.1038/s41588-023-01363-5
Kottuparambil, S., Ashok, A., Barozzi, A., Michoud, G., Cai, C., Daffonchio, D., Duarte, C. M., & Agusti, S. (2023). Tracking the early signals of crude oil in seawater and plankton after a major oil spill in the Red Sea. Environmental Science and Pollution Research. https://doi.org/10.1007/s11356-023-27111-0
Deng, R., Medico-Salsench, E., Nikoncuk, A., Ramakrishnan, R., Lanko, K., Kühn, N. A., van der Linde, H. C., Lor-Zade, S., Albuainain, F., Shi, Y., Yousefi, S., Capo, I., van den Herik, E. M., van Slegtenhorst, M., van Minkelen, R., Geeven, G., Mulder, M. T., Ruijter, G. J. G., Lütjohann, D., … Barakat, T. S. (2023). AMFR dysfunction causes autosomal recessive spastic paraplegia in human that is amenable to statin treatment in a preclinical model. Acta Neuropathologica. https://doi.org/10.1007/s00401-023-02579-9
Long, Y., Zhang, B., Tian, S., Chan, J. J., Zhou, J., Li, Z., Li, Y., An, Z., Liao, X., Wang, Y., Sun, S., Xu, Y., Tay, Y., Chen, W., & Gao, X. (2023). Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ. Genome Research. https://doi.org/10.1101/gr.277177.122
Dong, W., Yang, Q., Wang, J., Xu, L., Li, X., Luo, G., & Gao, X. (2023). Multi-modality attribute learning-based method for drug–protein interaction prediction based on deep neural network. Briefings in Bioinformatics, 24(3). https://doi.org/10.1093/bib/bbad161
Wang, Y., Wang, X., Chen, C., Gao, H., Salhi, A., Gao, X., & Yu, B. (2023). RPI-CapsuleGAN: Predicting RNA-protein interactions through an interpretable generative adversarial capsule network. Pattern Recognition, 141, 109626. https://doi.org/10.1016/j.patcog.2023.109626
Dong, W., Yang, Q., Wang, J., Xu, L., Li, X., Luo, G., & Gao, X. (2023). Multi-modality attribute learning-based method for drug–protein interaction prediction based on deep neural network. Briefings in Bioinformatics. https://doi.org/10.1093/bib/bbad161
Ribeiro, B., Lima, C., Pereira, S. E., Peixoto, R., & Klautau, M. (2023). Calcareous sponges can synthesize their skeleton under short-term ocean acidification. Scientific Reports, 13(1). https://doi.org/10.1038/s41598-023-33611-3
Jin, R., Ye, Z., Chen, S., Gu, J., He, J., Huang, L., Christakos, G., Agusti, S., Duarte, C. M., & Wu, J. (2023). Accurate mapping of seaweed farms with high-resolution imagery in China. Geocarto International, 38(1). https://doi.org/10.1080/10106049.2023.2203114
Laref, S., Harrou, F., Wang, B., Sun, Y., Laref, A., Laleg-Kirati, T.-M., Gojobori, T., & Gao, X. (2023). Synergy of Small Antiviral Molecules on a Black-Phosphorus Nanocarrier: Machine Learning and Quantum Chemical Simulation Insights. Molecules, 28(8), 3521. https://doi.org/10.3390/molecules28083521
Thafar, M. A., Albaradei, S., Uludag, M., Alshahrani, M., Gojobori, T., Essack, M., & Gao, X. (2023). OncoRTT: Predicting novel oncology-related therapeutic targets using BERT embeddings and omics features. Frontiers in Genetics, 14. https://doi.org/10.3389/fgene.2023.1139626
Doherty, H. M., Kritikos, G., Galardini, M., Banzhaf, M., & Moradigaravand, D. (2023). ChemGAPP: a tool for chemical genomics analysis and phenotypic profiling. Bioinformatics, 39(4). https://doi.org/10.1093/bioinformatics/btad171
Lesar, Ž., Alharbi, R., Bohak, C., Strnad, O., Heinzl, C., Marolt, M., & Viola, I. (2023). Volume conductor: interactive visibility management for crowded volumes. The Visual Computer. https://doi.org/10.1007/s00371-023-02828-8
Li, Y., Guo, Z., Wang, K., Gao, X., & Wang, G. (2023). End-to-end interpretable disease–gene association prediction. Briefings in Bioinformatics, 24(3). https://doi.org/10.1093/bib/bbad118
Li, Y., Guo, Z., Wang, K., Gao, X., & Wang, G. (2023). End-to-end interpretable disease–gene association prediction. Briefings in Bioinformatics. https://doi.org/10.1093/bib/bbad118
Alamro, H., Thafar, M. A., Albaradei, S., Gojobori, T., Essack, M., & Gao, X. (2023). Exploiting machine learning models to identify novel Alzheimer’s disease biomarkers and potential targets. Scientific Reports, 13(1). https://doi.org/10.1038/s41598-023-30904-5
Gao, F., Cho, W. C., Gao, X., & Wang, W. (2023). Editorial: Medical knowledge-assisted machine learning technologies in individualized medicine. Frontiers in Molecular Biosciences, 10. https://doi.org/10.3389/fmolb.2023.1167730
Li, H., Zhou, J., Li, Z., Chen, S., Liao, X., Zhang, B., Zhang, R., Wang, Y., Sun, S., & Gao, X. (2023). A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-37168-7
de Lemos, E. A., Procópio, L., da Mota, F. F., Jurelevicius, D., Rosado, A. S., & Seldin, L. (2023). Molecular characterization of Paenibacillus antarcticus IPAC21, a bioemulsifier producer isolated from Antarctic soil. Frontiers in Microbiology, 14. https://doi.org/10.3389/fmicb.2023.1142582
Gao, H., Zhang, B., Liu, L., Li, S., Gao, X., & Yu, B. (2023). A universal framework for single-cell multi-omics data integration with graph convolutional networks. Briefings in Bioinformatics, 24(3). https://doi.org/10.1093/bib/bbad081
Gao, H., Zhang, B., Liu, L., Li, S., Gao, X., & Yu, B. (2023). A universal framework for single-cell multi-omics data integration with graph convolutional networks. Briefings in Bioinformatics. https://doi.org/10.1093/bib/bbad081
Wang, X., Gao, X., Wang, G., & Li, D. (2023). miProBERT: identification of microRNA promoters based on the pre-trained model BERT. Briefings in Bioinformatics, 24(3). https://doi.org/10.1093/bib/bbad093
Wang, X., Gao, X., Wang, G., & Li, D. (2023). miProBERT: identification of microRNA promoters based on the pre-trained model BERT. Briefings in Bioinformatics. https://doi.org/10.1093/bib/bbad093
Alsanie, W. F., Abdelrahman, S., Felimban, R. I., Alkhatabi, H. A., Gaber, A., Alosimi, E. A., Alhomrani, M., Habeeballah, H., Hauser, C. A. E., S. Alamri, A., Althobaiti, A., Alsharif, A., Alzahrani, A. S., Al-Ghamdi, M. S., Raafat, B. M., Alswat, K. A., Althobaiti, Y. S., & Asiri, Y. A. (2023). The Influence of Prenatal Exposure to Methamphetamine on the Development of Dopaminergic Neurons in the Ventral Midbrain. International Journal of Molecular Sciences, 24(6), 5668. https://doi.org/10.3390/ijms24065668
Chaudhary, S., Ali, Z., Tehseen, M., Haney, E. F., Pantoja-Angles, A., Alshehri, S., Wang, T., Clancy, G. J., Ayach, M., Hauser, C., Hong, P.-Y., Hamdan, S. M., Hancock, R. E. W., & Mahfouz, M. (2023). Efficient in planta production of amidated antimicrobial peptides that are active against drug-resistant ESKAPE pathogens. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-37003-z
Macvanin, M. T., Gluvic, Z., Radovanovic, J., Essack, M., Gao, X., & Isenovic, E. R. (2023). Diabetic cardiomyopathy: The role of microRNAs and long non-coding RNAs. Frontiers in Endocrinology, 14. https://doi.org/10.3389/fendo.2023.1124613
Alsaedi, S. B., Mineta, K., Gao, X., & Gojobori, T. (2023). Computational network analysis of host genetic risk variants of severe COVID-19. Human Genomics, 17(1). https://doi.org/10.1186/s40246-023-00454-y
Voolstra, C. R., Peixoto, R. S., & Ferrier‐Pagès, C. (2023). Mitigating the ecological collapse of coral reef ecosystems. EMBO Reports, 24(4). Portico. https://doi.org/10.15252/embr.202356826
Pinheiro, Y., Faria da Mota, F., Peixoto, R. S., van Elsas, J. D., Lins, U., Mazza Rodrigues, J. L., & Rosado, A. S. (2023). A thermophilic chemolithoautotrophic bacterial consortium suggests a mutual relationship between bacteria in extreme oligotrophic environments. Communications Biology, 6(1). https://doi.org/10.1038/s42003-023-04617-4
Adisornkanj, P., Chanprasit, R., Eliason, S., Fons, J. M., Intachai, W., Tongsima, S., Olsen, B., Arold, S. T., Ngamphiw, C., Amendt, B. A., Tucker, A. S., & Kantaputra, P. (2023). Genetic Variants in Protein Tyrosine Phosphatase Non-Receptor Type 23 Are Responsible for Mesiodens Formation. Biology, 12(3), 393. https://doi.org/10.3390/biology12030393
Zhou, W., Liu, Y., Li, Y., Kong, S., Wang, W., Ding, B., Han, J., Mou, C., Gao, X., & Liu, J. (2023). TriNet: A tri-fusion neural network for the prediction of anticancer and antimicrobial peptides. Patterns, 4(3), 100702. https://doi.org/10.1016/j.patter.2023.100702
Rachid, C. T. C. C., Balieiro, F. C., Peixoto, R. S., Fonseca, E. S., Jesus, H. E., Novotny, E. H., Chaer, G. M., Santos, F. M., Tiedje, J. M., & Rosado, A. S. (2023). Mycobiome structure does not affect field litter decomposition in Eucalyptus and Acacia plantations. Frontiers in Microbiology, 14. https://doi.org/10.3389/fmicb.2023.1106422
Haider, I., Yunmeng, Z., White, F., Li, C., Incitti, R., Alam, I., Gojobori, T., Ruyter‐Spira, C., Al‐Babili, S., & Bouwmeester, H. J. (2023). Transcriptome analysis of the phosphate starvation response sheds light on strigolactone biosynthesis in rice. The Plant Journal, 114(2), 355–370. Portico. https://doi.org/10.1111/tpj.16140
Inal, S. (2023). Turning tissues into conducting matter. Science, 379(6634), 758–759. https://doi.org/10.1126/science.adg4761
AlHargan, A., AlMuhaizea, M. A., Almass, R., Alwadei, A. H., Daghestani, M., Arold, S. T., & Kaya, N. (2023). SHQ1-associated neurodevelopmental disorder: Report of the first homozygous variant in unrelated patients and review of the literature. Human Genome Variation, 10(1). https://doi.org/10.1038/s41439-023-00234-z
Moshkov, M. (2023). Decision Trees for Binary Subword-Closed Languages. Entropy, 25(2), 349. https://doi.org/10.3390/e25020349
Assaad, S., Dov, D., Davis, R., Kovalsky, S., Lee, W. T., Kahmke, R., Rocke, D., Cohen, J., Henao, R., Carin, L., & Range, D. E. (2023). Thyroid Cytopathology Cancer Diagnosis from Smartphone Images Using Machine Learning. Modern Pathology, 36(6), 100129. https://doi.org/10.1016/j.modpat.2023.100129
Bohlega, S., Abusrair, A. H., Al-Qahtani, Z., Guzmán-Vega, F. J., Ramakrishnan, R., Aldosari, H., Aldakheel, A., Al-Qahtani, S., Monies, D., & Arold, S. T. (2023). Expanding the genotype-phenotype landscape of PDE10A-associated movement disorders. Parkinsonism & Related Disorders, 108, 105323. https://doi.org/10.1016/j.parkreldis.2023.105323
Wang, J., Nitsche, J. M., Kasting, G. B., Wittum, G., & Nägel, A. (2023). Transdermal and lateral effective diffusivities for drug transport in stratum corneum from a microscopic anisotropic diffusion model. European Journal of Pharmaceutics and Biopharmaceutics, 188, 271–286. https://doi.org/10.1016/j.ejpb.2023.01.025
Wang, J., Nitsche, J. M., Kasting, G. B., Wittum, G., & Nägel, A. (2023). Transdermal and lateral effective diffusivities for drug transport in stratum corneum from a microscopic anisotropic diffusion model. European Journal of Pharmaceutics and Biopharmaceutics. https://doi.org/10.1016/j.ejpb.2023.01.025
Macvanin, M., Gluvic, Z., Radovanovic, J., Essack, M., Gao, X., & Isenovic, E. R. (2023). New insights on the cardiovascular effects of IGF-1. Frontiers in Endocrinology, 14. https://doi.org/10.3389/fendo.2023.1142644
Ohayon, D., Renn, D., Wustoni, S., Guo, K., Druet, V., Hama, A., Chen, X., Maria, I. P., Singh, S., Griggs, S., Schroeder, B. C., Rueping, M., McCulloch, I., & Inal, S. (2023). Interactions of Catalytic Enzymes with n-Type Polymers for High-Performance Metabolite Sensors. ACS Applied Materials & Interfaces. https://doi.org/10.1021/acsami.2c20502
de León, E. H.-P., Valle-Pérez, A. U., Khan, Z. N., & Hauser, C. A. E. (2023). Intelligent and Smart Biomaterials for Sustainable 3D Printing Applications. Current Opinion in Biomedical Engineering, 100450. https://doi.org/10.1016/j.cobme.2023.100450
Rosado, P. M., Cardoso, P. M., Rosado, J. G., Schultz, J., Nunes da Rocha, U., Keller-Costa, T., & Peixoto, R. S. (2023). Exploring the Potential Molecular Mechanisms of Interactions between a Probiotic Consortium and Its Coral Host. MSystems, 8(1). https://doi.org/10.1128/msystems.00921-22
Alamro, H., Bajic, V., Macvanin, M. T., Isenovic, E. R., Gojobori, T., Essack, M., & Gao, X. (2023). Type 2 Diabetes Mellitus and its comorbidity, Alzheimer’s disease: Identifying critical microRNA using machine learning. Frontiers in Endocrinology, 13. https://doi.org/10.3389/fendo.2022.1084656
Li, Z., Gao, E., Zhou, J., Han, W., Xu, X., & Gao, X. (2023). Applications of deep learning in understanding gene regulation. Cell Reports Methods, 3(1), 100384. https://doi.org/10.1016/j.crmeth.2022.100384
Laref, S., Wang, B., Gao, X., & Gojobori, T. (2023). Computational Studies of Auto-Active van der Waals Interaction Molecules on Ultra-Thin Black-Phosphorus Film. Molecules, 28(2), 681. https://doi.org/10.3390/molecules28020681
Wang, Y., Zhu, G., Zeglio, E., Castillo, T. C. H., Haseena, S., Ravva, M. K., Cong, S., Chen, J., Lan, L., Li, Z., Herland, A., McCulloch, I., Inal, S., & Yue, W. (2023). n-Type Organic Electrochemical Transistors with High Transconductance and Stability. Chemistry of Materials. https://doi.org/10.1021/acs.chemmater.2c02447
Macvanin, M. T., Gluvic, Z., Zafirovic, S., Gao, X., Essack, M., & Isenovic, E. R. (2023). The protective role of nutritional antioxidants against oxidative stress in thyroid disorders. Frontiers in Endocrinology, 13. https://doi.org/10.3389/fendo.2022.1092837
Ohayon, D., Druet, V., & Inal, S. (2023). A guide for the characterization of organic electrochemical transistors and channel materials. Chemical Society Reviews, 52(3), 1001–1023. https://doi.org/10.1039/d2cs00920j
Wu, Y., Zhou, X., Tao, Y., & Wang, D. (2023). On Private and Robust Bandits (Version 1). arXiv. https://doi.org/10.48550/ARXIV.2302.02526
Inal, S. (2023). Conducting gels for wearable bioelectronic devices. Journal of Materials Chemistry B, 11(4), 699–701. https://doi.org/10.1039/d2tb90199d
Wu, Y., Guan, C., Aggarwal, V., & Wang, D. (2023). Quantum Heavy-tailed Bandits (Version 1). arXiv. https://doi.org/10.48550/ARXIV.2301.09680

2022

Li, Z., Cong, Y., Chen, X., Qi, J., Sun, J., Yan, T., Yang, H., Liu, J., Lu, E., Wang, L., Li, J., Hu, H., Zhang, C., Yang, Q., Yao, J., Yao, P., Jiang, Q., Liu, W., Song, J., … Gao, X. (2023). Vision transformer-based weakly supervised histopathological image analysis of primary brain tumors. IScience, 26(1), 105872. https://doi.org/10.1016/j.isci.2022.105872
Slater, L. T., Williams, J. A., Schofield, P. N., Russell, S., Pendleton, S. C., Karwath, A., Fanning, H., Ball, S., Hoehndorf, R., & Gkoutos, G. V. (2023). Klarigi: Characteristic explanations for semantic biomedical data. Computers in Biology and Medicine, 153, 106425. https://doi.org/10.1016/j.compbiomed.2022.106425
Zhapa-Camacho, F., Kulmanov, M., & Hoehndorf, R. (2022). mOWL: Python library for machine learning with biomedical ontologies. Bioinformatics, 39(1). https://doi.org/10.1093/bioinformatics/btac811
Ramirez, J. R., Rautek, P., Bohak, C., Strnad, O., Zhang, Z., Li, S., Viola, I., & Heidrich, W. (2022). GPU Accelerated 3D Tomographic Reconstruction and Visualization from Noisy Electron Microscopy Tilt-Series. IEEE Transactions on Visualization and Computer Graphics, 1–15. https://doi.org/10.1109/tvcg.2022.3230445
AlTassan, R., AlQudairy, H., Alromayan, R., Alfalah, A., AlHarbi, O. A., González-Álvarez, A. C., Arold, S. T., & Kaya, N. (2022). Clinical, Radiological, and Genetic Characterization of a Patient with a Novel Homoallelic Loss-of-Function Variant in DNM1. Genes, 13(12), 2252. https://doi.org/10.3390/genes13122252
Zhong, Y., Koklu, A., Villalva, D. R., Zhang, Y., Hernandez, L. H., Moser, M., Hallani, R. K., McCulloch, I., Baran, D., & Inal, S. (2022). An Organic Electrochemical Transistor Integrated Photodetector for High Quality Photoplethysmogram Signal Acquisition. Advanced Functional Materials, 33(6), 2211479. Portico. https://doi.org/10.1002/adfm.202211479
Delgadillo-Ordoñez, N., Raimundo, I., Barno, A. R., Osman, E. O., Villela, H., Bennett-Smith, M., Voolstra, C. R., Benzoni, F., & Peixoto, R. S. (2022). Red Sea Atlas of Coral-Associated Bacteria Highlights Common Microbiome Members and Their Distribution across Environmental Gradients—A Systematic Review. Microorganisms, 10(12), 2340. https://doi.org/10.3390/microorganisms10122340
Azad, M., Chikalov, I., Hussain, S., Moshkov, M., & Zielosko, B. (2022). Infinite Families of Concepts. Synthesis Lectures on Intelligent Technologies, 113–136. https://doi.org/10.1007/978-3-031-08585-7_9
Azad, M., Chikalov, I., Hussain, S., Moshkov, M., & Zielosko, B. (2022). Infinite Binary Information Systems. Decision Trees of Types 1, 2, and 3. Synthesis Lectures on Intelligent Technologies, 83–98. https://doi.org/10.1007/978-3-031-08585-7_7
Azad, M., Chikalov, I., Hussain, S., Moshkov, M., & Zielosko, B. (2022). Main Notions. Synthesis Lectures on Intelligent Technologies, 13–17. https://doi.org/10.1007/978-3-031-08585-7_2
Azad, M., Chikalov, I., Hussain, S., Moshkov, M., & Zielosko, B. (2022). Dynamic Programming Algorithms for Minimization of Decision Tree Complexity. Synthesis Lectures on Intelligent Technologies, 19–40. https://doi.org/10.1007/978-3-031-08585-7_3
Azad, M., Chikalov, I., Hussain, S., Moshkov, M., & Zielosko, B. (2022). Construction of Optimal Decision Trees and Deriving Decision Rules from Them. Synthesis Lectures on Intelligent Technologies, 41–53. https://doi.org/10.1007/978-3-031-08585-7_4
Azad, M., Chikalov, I., Hussain, S., Moshkov, M., & Zielosko, B. (2022). Decision Trees with Hypotheses for Recognition of Monotone Boolean Functions and for Sorting. Synthesis Lectures on Intelligent Technologies, 73–80. https://doi.org/10.1007/978-3-031-08585-7_6
Azad, M., Chikalov, I., Hussain, S., Moshkov, M., & Zielosko, B. (2022). Greedy Algorithms for Construction of Decision Trees with Hypotheses. Synthesis Lectures on Intelligent Technologies, 55–72. https://doi.org/10.1007/978-3-031-08585-7_5
Bajaffer, A., Mineta, K., Magistretti, P., & Gojobori, T. (2022). Lactate-mediated neural plasticity genes emerged during the evolution of memory systems. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-23784-8
Rogers, A. D., Appeltans, W., Assis, J., Ballance, L. T., Cury, P., Duarte, C., Favoretto, F., Hynes, L. A., Kumagai, J. A., Lovelock, C. E., Miloslavich, P., Niamir, A., Obura, D., O’Leary, B. C., Ramirez-Llodra, E., Reygondeau, G., Roberts, C., Sadovy, Y., Steeds, O., … Aburto-Oropeza, O. (2022). Discovering marine biodiversity in the 21st century. Advances in Marine Biology, 23–115. https://doi.org/10.1016/bs.amb.2022.09.002
Pérez-Pedroza, R., Al-Jalih, F., Xu, J., Moretti, M., R. Briola, G., & A. E. Hauser, C. (2022). Fabrication of lumen-forming colorectal cancer organoids using a newly designed lamininderived bioink. International Journal of Bioprinting, 9(1). https://doi.org/10.18063/ijb.v9i1.633
Gallagher, A. J., Brownscombe, J. W., Alsudairy, N. A., Casagrande, A. B., Fu, C., Harding, L., Harris, S. D., Hammerschlag, N., Howe, W., Huertas, A. D., Kattan, S., Kough, A. S., Musgrove, A., Payne, N. L., Phillips, A., Shea, B. D., Shipley, O. N., Sumaila, U. R., Hossain, M. S., & Duarte, C. M. (2022). Tiger sharks support the characterization of the world’s largest seagrass ecosystem. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-33926-1
Lehmann, R., Schunter, C., Welch, M. J., Arold, S. T., Nilsson, G. E., Tegner, J. N., Munday, P. L., & Ravasi, T. (2022). Genetic architecture of behavioural resilience to ocean acidification. https://doi.org/10.1101/2022.10.18.512656
Hurtado-McCormick, V., Trevathan-Tackett, S. M., Bowen, J. L., Connolly, R. M., Duarte, C. M., & Macreadie, P. I. (2022). Pathways for Understanding Blue Carbon Microbiomes with Amplicon Sequencing. Microorganisms, 10(11), 2121. https://doi.org/10.3390/microorganisms10112121
He, Y., Yu, H., Huffman, A., Lin, A. Y., Natale, D. A., Beverley, J., Zheng, L., Perl, Y., Wang, Z., Liu, Y., Ong, E., Wang, Y., Huang, P., Tran, L., Du, J., Shah, Z., Shah, E., Desai, R., Huang, H., … Smith, B. (2022). A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology. Journal of Biomedical Semantics, 13(1). https://doi.org/10.1186/s13326-022-00279-z
Madhaiyan, M., Saravanan, V. S., See-Too, W.-S., Volpiano, C. G., Sant’Anna, F. H., Faria da Mota, F., Sutcliffe, I., Sangal, V., Passaglia, L. M. P., & Rosado, A. S. (2022). Genomic and phylogenomic insights into the family Streptomycetaceae lead to the proposal of six novel genera. International Journal of Systematic and Evolutionary Microbiology, 72(10). https://doi.org/10.1099/ijsem.0.005570
Xiong, L., Tian, K., Li, Y., Ning, W., Gao, X., & Zhang, Q. C. (2022). Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-33758-z
Alsanie, W. F., Abdelrahman, S., Alhomrani, M., Gaber, A., Alosimi, E. A., Habeeballah, H., Alkhatabi, H. A., Felimban, R. I., Hauser, C. A. E., Tayeb, H. H., Alamri, A. S., Alamri, A., Raafat, B. M., Alswat, K. A., Althobaiti, Y. S., & Asiri, Y. A. (2022). The Influence of Prenatal Exposure to Quetiapine Fumarate on the Development of Dopaminergic Neurons in the Ventral Midbrain of Mouse Embryos. International Journal of Molecular Sciences, 23(20), 12352. https://doi.org/10.3390/ijms232012352
Eckardt, N. A., Ainsworth, E. A., Bahuguna, R. N., Broadley, M. R., Busch, W., Carpita, N. C., Castrillo, G., Chory, J., DeHaan, L. R., Duarte, C. M., Henry, A., Jagadish, S. V. K., Langdale, J., Leakey, A. D. B., Liao, J. C., Lu, K.-J., McCann, M. C., McKay, J. K., Odeny, D. A., … Zhang, X. (2022). Climate change challenges, plant science solutions. The Plant Cell. https://doi.org/10.1093/plcell/koac303
Aldosary, M., Alsagob, M., AlQudairy, H., González-Álvarez, A. C., Arold, S. T., Dababo, M. A., Alharbi, O. A., Almass, R., AlBakheet, A., AlSarar, D., Qari, A., Al-Ansari, M. M., Oláhová, M., Al-Shahrani, S. A., AlSayed, M., Colak, D., Taylor, R. W., AlOwain, M., & Kaya, N. (2022). A Novel Homozygous Founder Variant of RTN4IP1 in Two Consanguineous Saudi Families. Cells, 11(19), 3154. https://doi.org/10.3390/cells11193154
Moshkov, M., Zielosko, B., & Tetteh, E. T. (2022). Selected Data Mining Tools for Data Analysis in Distributed Environment. Entropy, 24(10), 1401. https://doi.org/10.3390/e24101401
Maria, I. P., Griggs, S., Rashid, R. B., Paulsen, B. D., Surgailis, J., Thorley, K., Le, V. N., Harrison, G. T., Combe, C., Hallani, R., Giovannitti, A., Paterson, A. F., Inal, S., Rivnay, J., & McCulloch, I. (2022). Enhancing the Backbone Coplanarity of n-Type Copolymers for Higher Electron Mobility and Stability in Organic Electrochemical Transistors. Chemistry of Materials, 34(19), 8593–8602. https://doi.org/10.1021/acs.chemmater.2c01552
Pessarrodona, A., Assis, J., Filbee-Dexter, K., Burrows, M. T., Gattuso, J.-P., Duarte, C. M., Krause-Jensen, D., Moore, P. J., Smale, D. A., & Wernberg, T. (2022). Global seaweed productivity. Science Advances, 8(37). https://doi.org/10.1126/sciadv.abn2465
Han, W., Cheng, Y., Chen, J., Zhong, H., Hu, Z., Chen, S., Zong, L., Hong, L., Chan, T.-F., King, I., Gao, X., & Li, Y. (2022). Self-supervised contrastive learning for integrative single cell RNA-seq data analysis. Briefings in Bioinformatics, 23(5). https://doi.org/10.1093/bib/bbac377
Li, H., Li, H., Zhou, J., & Gao, X. (2022). SD2: spatially resolved transcriptomics deconvolution through integration of dropout and spatial information. Bioinformatics. https://doi.org/10.1093/bioinformatics/btac605
de Barros, C. R., Baethgen, L. F., Mastrobuono, G., Peixoto, R. S., Miranda, K. R., da Silva Carvalho, A. C., da Silva Dias, R. C., Rosado, A. S., & Duarte, R. S. (2022). Mycobacterial diversity in soil samples from King George Island, Antarctica. Polar Science, 34, 100890. https://doi.org/10.1016/j.polar.2022.100890
Zheng, K., Zhao, H., Zhao, Q., Wang, B., Gao, X., & Wang, J. (2022). NASMDR: a framework for miRNA-drug resistance prediction using efficient neural architecture search and graph isomorphism networks. Briefings in Bioinformatics, 23(5). https://doi.org/10.1093/bib/bbac338
Rehman, Z. U., Momin, A. A., Aldehaiman, A., Irum, T., Grünberg, R., & Arold, S. T. (2022). The exceptionally efficient quorum quenching enzyme LrsL suppresses Pseudomonas aeruginosa biofilm production. Frontiers in Microbiology, 13. https://doi.org/10.3389/fmicb.2022.977673
Schultz, J., Parise, M. T. D., Parise, D., Medeiros, L. G., Sousa, T. J., Kato, R. B., Uetanabaro, A. P. T., Araújo, F., Ramos, R. T. J., de Castro Soares, S., Brenig, B., de Carvalho Azevedo, V. A., Góes-Neto, A., & Rosado, A. S. (2022). Unraveling the Genomic Potential of the Thermophilic Bacterium Anoxybacillus flavithermus from an Antarctic Geothermal Environment. Microorganisms, 10(8), 1673. https://doi.org/10.3390/microorganisms10081673
Mafra, D., Ribeiro, M., Fonseca, L., Regis, B., Cardozo, L. F. M. F., Fragoso dos Santos, H., Emiliano de Jesus, H., Schultz, J., Shiels, P. G., Stenvinkel, P., & Rosado, A. (2022). Archaea from the gut microbiota of humans: Could be linked to chronic diseases? Anaerobe, 77, 102629. https://doi.org/10.1016/j.anaerobe.2022.102629
Li, C., Zheng, H., Xiong, J., Huang, Y., Li, H., Jin, H., Ai, S., Wang, Y., Su, T., Sun, G., Xiao, X., Fu, T., Wang, Y., Gao, X., & Liang, P. (2022). miR-596-3p suppresses brain metastasis of non-small cell lung cancer by modulating YAP1 and IL-8. Cell Death & Disease, 13(8). https://doi.org/10.1038/s41419-022-05062-7
Momin, A. A., Mendes, T., Barthe, P., Faure, C., Hong, S., Yu, P., Kadaré, G., Jaremko, M., Girault, J.-A., Jaremko, Ł., & Arold, S. T. (2022). PYK2 senses calcium through a disordered dimerization and calmodulin-binding element. Communications Biology, 5(1). https://doi.org/10.1038/s42003-022-03760-8
Cui, H., Yi, H., Bao, H., Tan, Y., Tian, C., Shi, X., Gan, D., Zhang, B., Liang, W., Chen, R., Zhu, Q., Fang, L., Gao, X., Huang, H., Tian, R., Sperling, S. R., Hu, Y., & Chen, W. (2022). The SWI/SNF chromatin remodeling factor DPF3 regulates metastasis of ccRCC by modulating TGF-β signaling. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-32472-0
Alghamdi, S. M., Schofield, P. N., & Hoehndorf, R. (2022). Contribution of model organism phenotypes to the computational identification of human disease genes. Disease Models & Mechanisms, 15(7). https://doi.org/10.1242/dmm.049441
Luo, X., Wang, X., Yao, Y., Gao, X., & Zhang, L. (2022). Unveiling the “Template-Dependent” Inhibition on the Viral Transcription of SARS-CoV-2. The Journal of Physical Chemistry Letters, 7197–7205. https://doi.org/10.1021/acs.jpclett.2c01314
Luo, X., Wang, X., Yao, Y., Gao, X., & Zhang, L. (2022). Unveiling the “Template-Dependent” Inhibition on the Viral Transcription of SARS-CoV-2. The Journal of Physical Chemistry Letters, 13(31), 7197–7205. https://doi.org/10.1021/acs.jpclett.2c01314
Santos Correa, S., Schultz, J., Lauersen, K. J., & Soares Rosado, A. (2022). Natural carbon fixation and advances in synthetic engineering for redesigning and creating new fixation pathways. Journal of Advanced Research. https://doi.org/10.1016/j.jare.2022.07.011
Garrison, L. A., Kolesar, I., Viola, I., Hauser, H., & Bruckner, S. (2022). Trends & Opportunities in Visualization for Physiology: A Multiscale Overview. Computer Graphics Forum, 41(3), 609–643. Portico. https://doi.org/10.1111/cgf.14575
Arab, W. T., Susapto, H. H., Alhattab, D., & Hauser, C. A. E. (2022). Peptide nanogels as a scaffold for fabricating dermal grafts and 3D vascularized skin models. Journal of Tissue Engineering, 13, 204173142211118. https://doi.org/10.1177/20417314221111868
Koklu, A., Wustoni, S., Guo, K., Silva, R., Salvigni, L., Hama, A., Diaz‐Galicia, E., Moser, M., Marks, A., McCulloch, I., Grünberg, R., Arold, S. T., & Inal, S. (2022). Convection Driven Ultrarapid Protein Detection via Nanobody‐Functionalized Organic Electrochemical Transistors. Advanced Materials, 2202972. Portico. https://doi.org/10.1002/adma.202202972
Hidalgo Castillo, T. C., Moser, M., Cendra, C., Nayak, P. D., Salleo, A., McCulloch, I., & Inal, S. (2022). Simultaneous Performance and Stability Improvement of a p-Type Organic Electrochemical Transistor through Additives. Chemistry of Materials, 34(15), 6723–6733. https://doi.org/10.1021/acs.chemmater.2c00632
Bajic, V. P., Salhi, A., Lakota, K., Radovanovic, A., Razali, R., Zivkovic, L., Spremo-Potparevic, B., Uludag, M., Tifratene, F., Motwalli, O., Marchand, B., Bajic, V. B., Gojobori, T., Isenovic, E. R., & Essack, M. (2022). DES-Amyloidoses “Amyloidoses through the looking-glass”: A knowledgebase developed for exploring and linking information related to human amyloid-related diseases. PLOS ONE, 17(7), e0271737. https://doi.org/10.1371/journal.pone.0271737
Albaradei, S., Albaradei, A., Alsaedi, A., Uludag, M., Thafar, M. A., Gojobori, T., Essack, M., & Gao, X. (2022). MetastaSite: Predicting metastasis to different sites using deep learning with gene expression data. Frontiers in Molecular Biosciences, 9. https://doi.org/10.3389/fmolb.2022.913602
Alsanie, W. F., Abdelrahman, S., Alhomrani, M., Gaber, A., Habeeballah, H., Alkhatabi, H. A., Felimban, R. I., Hauser, C. A. E., Tayeb, H. H., Alamri, A. S., Raafat, B. M., Anwar, S., Alswat, K. A., Althobaiti, Y. S., & Asiri, Y. A. (2022). Prenatal Exposure to Gabapentin Alters the Development of Ventral Midbrain Dopaminergic Neurons. Frontiers in Pharmacology, 13. https://doi.org/10.3389/fphar.2022.923113
Peixoto, R. S., Voolstra, C. R., Sweet, M., Duarte, C. M., Carvalho, S., Villela, H., Lunshof, J. E., Gram, L., Woodhams, D. C., Walter, J., Roik, A., Hentschel, U., Thurber, R. V., Daisley, B., Ushijima, B., Daffonchio, D., Costa, R., Keller-Costa, T., Bowman, J. S., … Berg, G. (2022). Harnessing the microbiome to prevent global biodiversity loss. Nature Microbiology. https://doi.org/10.1038/s41564-022-01173-1
Abdelrahman, S., Alsanie, W. F., Khan, Z. N., Albalawi, H. I., Felimban, R. I., Moretti, M., Steiner, N., Chaudhary, A. G., & Hauser, C. A. E. (2022). A Parkinson’s disease model composed of 3D bioprinted dopaminergic neurons within a biomimetic peptide scaffold. Biofabrication, 14(4), 044103. https://doi.org/10.1088/1758-5090/ac7eec
Wustoni, S., Nikiforidis, G., Ohayon, D., Inal, S., Indartono, Y. S., Suendo, V., & Yuliarto, B. (2022). Performance of PEDOTOH/PEO‐based Supercapacitors in Agarose Gel Electrolyte. Chemistry – An Asian Journal, 17(17). Portico. https://doi.org/10.1002/asia.202200427
Wesselmann, M., Geraldi, N. R., Marbà, N., Hendriks, I. E., Díaz-Rúa, R., & Duarte, C. M. (2022). eDNA Reveals the Associated Metazoan Diversity of Mediterranean Seagrass Sediments. Diversity, 14(7), 549. https://doi.org/10.3390/d14070549
Moshkov, M. (2022). Rough analysis of computation trees. Discrete Applied Mathematics, 321, 90–108. https://doi.org/10.1016/j.dam.2022.06.032
Blanco-Sacristán, J., Johansen, K., Duarte, C. M., Daffonchio, D., Hoteit, I., & McCabe, M. F. (2022). Mangrove distribution and afforestation potential in the Red Sea. Science of The Total Environment, 843, 157098. https://doi.org/10.1016/j.scitotenv.2022.157098
Blanco-Sacristán, J., Johansen, K., Duarte, C. M., Daffonchio, D., Hoteit, I., & McCabe, M. F. (2022). Mangrove distribution and afforestation potential in the Red Sea. Science of The Total Environment, 843, 157098. https://doi.org/10.1016/j.scitotenv.2022.157098
Laref, S., Wang, B., Inal, S., Al-Ghamdi, S., Gao, X., & Gojobori, T. (2022). A Peculiar Binding Characterization of DNA (RNA) Nucleobases at MoOS-Based Janus Biosensor: Dissimilar Facets Role on Selectivity and Sensitivity. Biosensors, 12(7), 442. https://doi.org/10.3390/bios12070442
Koklu, A., Guo, K., Wustoni, S., Grunberg, R., Arold, S., & Inal, S. (2022). Pathogen and Protein Detection using Organic Electronics. 2022 6th IEEE Electron Devices Technology & Manufacturing Conference (EDTM). https://doi.org/10.1109/edtm53872.2022.9798008
Huntington, B., Zhao, L., Bron, P., Shahul Hameed, U. F., Arold, S. T., & Qureshi, B. M. (2022). Thicker Ice Improves the Integrity and Angular Distribution of CDC48A Hexamers on Cryo-EM Grids. Frontiers in Molecular Biosciences, 9. https://doi.org/10.3389/fmolb.2022.890390
Khan, A., Bruno, L. P., Alomar, F., Umair, M., Pinto, A. M., Khan, A. A., Khan, A., Saima, Fabbiani, A., Zguro, K., Furini, S., Mencarelli, M. A., Renieri, A., Resciniti, S., Peña-Guerra, K. A., Guzmán-Vega, F. J., Arold, S. T., Ariani, F., & Khan, S. N. (2022). SPTBN5, Encoding the βV-Spectrin Protein, Leads to a Syndrome of Intellectual Disability, Developmental Delay, and Seizures. Frontiers in Molecular Neuroscience, 15. https://doi.org/10.3389/fnmol.2022.877258
Zhang, J., Vancea, A. I., & Arold, S. T. (2022). Targeting plant UBX proteins: AI-enhanced lessons from distant cousins. Trends in Plant Science. https://doi.org/10.1016/j.tplants.2022.05.012
Druet, V., Nayak, P. D., Koklu, A., Ohayon, D., Hama, A., Chen, X., Moser, M., McCulloch, I., & Inal, S. (2022). Operation Mechanism of n‐Type Organic Electronic Metabolite Sensors. Advanced Electronic Materials, 8(10), 2200065. Portico. https://doi.org/10.1002/aelm.202200065
Moshkov, M. (2022). Decision trees for regular factorial languages. Array, 15, 100203. https://doi.org/10.1016/j.array.2022.100203
Alshehri, S., Karan, R., Ghalayini, S., Kahin, K., Khan, Z., Renn, D., Mathew, S., Rueping, M., & Hauser, C. A. E. (2022). Air-loaded Gas Vesicle Nanoparticles Promote Cell Growth in Three-dimensional Bioprinted Tissue Constructs. International Journal of Bioprinting, 8(3). https://doi.org/10.18063/ijb.v8i3.489
Peng, X., Wang, X., Guo, Y., Ge, Z., Li, F., Gao, X., & Song, J. (2022). RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins. Briefings in Bioinformatics, 23(4). https://doi.org/10.1093/bib/bbac215
Fusi, M., Booth, J. M., Marasco, R., Merlino, G., Garcias-Bonet, N., Barozzi, A., Garuglieri, E., Mbobo, T., Diele, K., Duarte, C. M., & Daffonchio, D. (2022). Bioturbation Intensity Modifies the Sediment Microbiome and Biochemistry and Supports Plant Growth in an Arid Mangrove System. Microbiology Spectrum, 10(3). https://doi.org/10.1128/spectrum.01117-22
Fusi, M., Booth, J. M., Marasco, R., Merlino, G., Garcias-Bonet, N., Barozzi, A., Garuglieri, E., Mbobo, T., Diele, K., Duarte, C. M., & Daffonchio, D. (2022). Bioturbation Intensity Modifies the Sediment Microbiome and Biochemistry and Supports Plant Growth in an Arid Mangrove System. Microbiology Spectrum, 10(3). https://doi.org/10.1128/spectrum.01117-22
Alma’abadi, A., Behzad, H., Alarawi, M., Conchouso, D., Saito, Y., Hosokawa, M., Nishikawa, Y., Kogawa, M., Takeyama, H., Mineta, K., & Gojobori, T. (2022). Identification of lipolytic enzymes using high-throughput single-cell screening and sorting of a metagenomic library. New Biotechnology, 70, 102–108. https://doi.org/10.1016/j.nbt.2022.05.006
Marbà, N., Jordà, G., Bennett, S., & Duarte, C. M. (2022). Seagrass Thermal Limits and Vulnerability to Future Warming. Frontiers in Marine Science, 9. https://doi.org/10.3389/fmars.2022.860826
Guan, R., Pang, H., Liang, Y., Shao, Z., Gao, X., Xu, D., & Feng, X. (2022). Discovering trends and hotspots of biosafety and biosecurity research via machine learning. Briefings in Bioinformatics, 23(5). https://doi.org/10.1093/bib/bbac194
Martin, C., Young, C. A., Valluzzi, L., & Duarte, C. M. (2022). Ocean sediments as the global sink for marine micro‐ and mesoplastics. Limnology and Oceanography Letters, 7(3), 235–243. Portico. https://doi.org/10.1002/lol2.10257
Macreadie, P. I., Robertson, A. I., Spinks, B., Adams, M. P., Atchison, J. M., Bell-James, J., Bryan, B. A., Chu, L., Filbee-Dexter, K., Drake, L., Duarte, C. M., Friess, D. A., Gonzalez, F., Grafton, R. Q., Helmstedt, K. J., Kaebernick, M., Kelleway, J., Kendrick, G. A., Kennedy, H., … Rogers, K. (2022). Operationalizing marketable blue carbon. One Earth, 5(5), 485–492. https://doi.org/10.1016/j.oneear.2022.04.005
Stanimirovic, J., Radovanovic, J., Banjac, K., Obradovic, M., Essack, M., Zafirovic, S., Gluvic, Z., Gojobori, T., & Isenovic, E. R. (2022). Role of C-Reactive Protein in Diabetic Inflammation. Mediators of Inflammation, 2022, 1–15. https://doi.org/10.1155/2022/3706508
Aboheimed, G. I., AlRasheed, M. M., Almudimeegh, S., Peña-Guerra, K. A., Cardona-Londoño, K. J., Salih, M. A., Seidahmed, M. Z., Al-Mohanna, F., Colak, D., Harvey, R. J., Harvey, K., Arold, S. T., Kaya, N., & Ruiz, A. J. (2022). Clinical, genetic, and functional characterization of the glycine receptor β-subunit A455P variant in a family affected by hyperekplexia syndrome. Journal of Biological Chemistry, 298(7), 102018. https://doi.org/10.1016/j.jbc.2022.102018
Herrera, M., Tubío, A., Pita, P., Vázquez, E., Olabarria, C., Duarte, C. M., & Villasante, S. (2022). Trade-Offs and Synergies Between Seagrass Ecosystems and Fishing Activities: A Global Literature Review. Frontiers in Marine Science, 9. https://doi.org/10.3389/fmars.2022.781713
Duarte, C. M., Ketcheson, D. I., Eguíluz, V. M., Agustí, S., Fernández-Gracia, J., Jamil, T., Laiolo, E., Gojobori, T., & Alam, I. (2022). Rapid evolution of SARS-CoV-2 challenges human defenses. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-10097-z
Bank, M. S., Duarte, C. M., & Sonne, C. (2022). Intergovernmental Panel on Blue Foods in Support of Sustainable Development and Nutritional Security. Environmental Science & Technology, 56(9), 5302–5305. https://doi.org/10.1021/acs.est.2c00119
Naser, R., Momin, A. A., Ali, A. J., Merzaban, J., & Arold, S. T. (2022). The purified recombinant FAT domain of the Focal Adhesion Kinase does not bind directly to recombinant Talin or MBD2 in vitro. https://doi.org/10.1101/2022.04.06.487260
Behzad, H., Ohyanagi, H., Alharbi, B., Ibarra, M., Alarawi, M., Saito, Y., Duarte, C. M., Bajic, V., Mineta, K., & Gojobori, T. (2022). A cautionary signal from the Red Sea on the impact of increased dust activity on marine microbiota. BMC Genomics, 23(1). https://doi.org/10.1186/s12864-022-08485-w
Alshahrani, M., Almansour, A., Alkhaldi, A., Thafar, M. A., Uludag, M., Essack, M., & Hoehndorf, R. (2022). Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications. PeerJ, 10, e13061. Portico. https://doi.org/10.7717/peerj.13061
Vanni, C., Schechter, M. S., Acinas, S. G., Barberán, A., Buttigieg, P. L., Casamayor, E. O., Delmont, T. O., Duarte, C. M., Eren, A. M., Finn, R. D., Kottmann, R., Mitchell, A., Sánchez, P., Siren, K., Steinegger, M., Gloeckner, F. O., & Fernàndez-Guerra, A. (2022). Unifying the known and unknown microbial coding sequence space. ELife, 11. CLOCKSS. https://doi.org/10.7554/elife.67667
Sierra, A. M. R., Arold, S. T., & Grünberg, R. (2022). Efficient multi-gene expression in cell-free droplet microreactors. PLOS ONE, 17(3), e0260420. https://doi.org/10.1371/journal.pone.0260420
Zorzi, G., Giustolisi, B., Aristodemo, V., Cecchetto, C., Hauser, C., Quer, J., Sánchez Amat, J., & Donati, C. (2022). On the Reliability of the Notion of Native Signer and Its Risks. Frontiers in Psychology, 13. https://doi.org/10.3389/fpsyg.2022.716554
Alsanie, W. F., Alhomrani, M., Gaber, A., Habeeballah, H., Alkhatabi, H. A., Felimban, R. I., Abdelrahman, S., Hauser, C. A. E., Chaudhary, A. G., Alamri, A. S., Raafat, B. M., Alamri, A., Anwar, S., Alswat, K. A., Althobaiti, Y. S., & Asiri, Y. A. (2022). The Effects of Prenatal Exposure to Pregabalin on the Development of Ventral Midbrain Dopaminergic Neurons. Cells, 11(5), 852. https://doi.org/10.3390/cells11050852
Alsanie, W. F., Alhomrani, M., Gaber, A., Habeeballah, H., Alkhatabi, H. A., Felimban, R. I., Abdelrahman, S., Hauser, C. A. E., Chaudhary, A. G., Alamri, A. S., Raafat, B. M., Alamri, A., Anwar, S., Alswat, K. A., Althobaiti, Y. S., & Asiri, Y. A. (2022). The Effects of Prenatal Exposure to Pregabalin on the Development of Ventral Midbrain Dopaminergic Neurons. Cells, 11(5), 852. https://doi.org/10.3390/cells11050852
Savva, A., Hama, A., Herrera-López, G., Gasparini, N., Migliaccio, L., Kawan, M., Steiner, N., McCulloch, I., Baran, D., Fiumelli, H., Magistretti, P., Głowacki, E. D., & Inal, S. (2022). Photo-Electrochemical Stimulation of Neurons with Organic Donor-Acceptor Heterojunctions. https://doi.org/10.1101/2022.02.17.480608
Jankovic, B., & Gojobori, T. (2022). From shallow to deep: some lessons learned from application of machine learning for recognition of functional genomic elements in human genome. Human Genomics, 16(1). https://doi.org/10.1186/s40246-022-00376-1
Yu, B., Zhang, Y., Wang, X., Gao, H., Sun, J., & Gao, X. (2022). Identification of DNA modification sites based on elastic net and bidirectional gated recurrent unit with convolutional neural network. Biomedical Signal Processing and Control, 75, 103566. https://doi.org/10.1016/j.bspc.2022.103566
Klein, S. G., Alsolami, S. M., Arossa, S., Ramos-Mandujano, G., Parry, A. J., Steckbauer, A., Duarte, C. M., & Li, M. (2022). In situ monitoring reveals cellular environmental instabilities in human pluripotent stem cell culture. Communications Biology, 5(1). https://doi.org/10.1038/s42003-022-03065-w
Inal, S. (2022). Fast and sensitive electromechanical sensing. Nature Biomedical Engineering, 6(3), 223–224. https://doi.org/10.1038/s41551-021-00841-7
Slater, L. T., Russell, S., Makepeace, S., Carberry, A., Karwath, A., Williams, J. A., Fanning, H., Ball, S., Hoehndorf, R., & Gkoutos, G. V. (2022). Evaluating semantic similarity methods for comparison of text-derived phenotype profiles. BMC Medical Informatics and Decision Making, 22(1). https://doi.org/10.1186/s12911-022-01770-4
Pfeifer, L., van Erven, G., Sinclair, E. A., Duarte, C. M., Kabel, M. A., & Classen, B. (2022). Profiling the cell walls of seagrasses from A (Amphibolis) to Z (Zostera). BMC Plant Biology, 22(1). https://doi.org/10.1186/s12870-022-03447-6
Pantoja Angles, A., Valle-Pérez, A. U., Hauser, C., & Mahfouz, M. M. (2022). Microbial Biocontainment Systems for Clinical, Agricultural, and Industrial Applications. Frontiers in Bioengineering and Biotechnology, 10. https://doi.org/10.3389/fbioe.2022.830200
Chen, S., Wang, J., Gao, X., & Li, Y. (2022). HiC-LDNet: A general and robust deep learning framework for accurate chromatin loop detection in genome-wide contact maps. https://doi.org/10.1101/2022.01.30.478367
Chen, S., Wang, J., Gao, X., & Li, Y. (2022). HiC-LDNet: A general and robust deep learning framework for accurate chromatin loop detection in genome-wide contact maps. https://doi.org/10.1101/2022.01.30.478367
Ouyang, X., Duarte, C. M., Cheung, S.-G., Tam, N. F.-Y., Cannicci, S., Martin, C., Lo, H. S., & Lee, S. Y. (2022). Fate and Effects of Macro- and Microplastics in Coastal Wetlands. Environmental Science & Technology, 56(4), 2386–2397. https://doi.org/10.1021/acs.est.1c06732
Gazulla, C. R., Auladell, A., Ruiz‐González, C., Junger, P. C., Royo‐Llonch, M., Duarte, C. M., Gasol, J. M., Sánchez, O., & Ferrera, I. (2022). Global diversity and distribution of aerobic anoxygenic phototrophs in the tropical and subtropical oceans. Environmental Microbiology, 24(5), 2222–2238. Portico. https://doi.org/10.1111/1462-2920.15835
Chandra, S., Gourisaria, M. K., Gm, H., Konar, D., Gao, X., Wang, T., & Xu, M. (2022). Prolificacy Assessment of Spermatozoan via State-of-the-Art Deep Learning Frameworks. IEEE Access, 10, 13715–13727. https://doi.org/10.1109/access.2022.3146334
Díaz-Galicia, E., Grünberg, R., & Arold, S. T. (2022). How to Find the Right RNA-Sensing CRISPR-Cas System for an In Vitro Application. Biosensors, 12(2), 53. https://doi.org/10.3390/bios12020053
Kulmanov, M., & Hoehndorf, R. (2022). DeepGOZero: Improving protein function prediction from sequence and zero-shot learning based on ontology axioms. https://doi.org/10.1101/2022.01.14.476325
Moshkov, M. (2022). On the Depth of Decision Trees with Hypotheses. Entropy, 24(1), 116. https://doi.org/10.3390/e24010116
Abbas, M., Susapto, H. H., & Hauser, C. A. E. (2022). Synthesis and Organization of Gold-Peptide Nanoparticles for Catalytic Activities. ACS Omega, 7(2), 2082–2090. https://doi.org/10.1021/acsomega.1c05546
Peng, X., Tang, Z., Kulmanov, M., Niu, K., & Hoehndorf, R. (2022). Description Logic EL++ Embeddings with Intersectional Closure (Version 1). arXiv. https://doi.org/10.48550/ARXIV.2202.14018
Chen, J., Ng, M. K., & Wang, D. (2022). Quantizing Heavy-tailed Data in Statistical Estimation: (Near) Minimax Rates, Covariate Quantization, and Uniform Recovery (Version 1). arXiv. https://doi.org/10.48550/ARXIV.2212.14562
Moshkov, M. (2022). Exact learning and test theory (Version 1). arXiv. https://doi.org/10.48550/ARXIV.2201.04506
Tang, Z., Pei, S., Zhang, Z., Zhu, Y., Zhuang, F., Hoehndorf, R., & Zhang, X. (2022). Positive-Unlabeled Learning with Adversarial Data Augmentation for Knowledge Graph Completion (Version 3). arXiv. https://doi.org/10.48550/ARXIV.2205.00904
Moser, M., Wang, Y., Hidalgo, T. C., Liao, H., Yu, Y., Chen, J., Duan, J., Moruzzi, F., Griggs, S., Marks, A., Gasparini, N., Wadsworth, A., Inal, S., McCulloch, I., & Yue, W. (2022). Propylene and butylene glycol: new alternatives to ethylene glycol in conjugated polymers for bioelectronic applications. Materials Horizons, 9(3), 973–980. https://doi.org/10.1039/d1mh01889b

2021

Aldhalaan, H., AlBakheet, A., AlRuways, S., AlMutairi, N., AlNakiyah, M., AlGhofaili, R., Cardona-Londoño, K. J., Alahmadi, K. O., AlQudairy, H., AlRasheed, M. M., Colak, D., Arold, S. T., & Kaya, N. (2021). A Novel GEMIN4 Variant in a Consanguineous Family Leads to Neurodevelopmental Impairment with Severe Microcephaly, Spastic Quadriplegia, Epilepsy, and Cataracts. Genes, 13(1), 92. https://doi.org/10.3390/genes13010092
Alsaif, H. S., Alshehri, A., Sulaiman, R. A., Al‐Hindi, H., Guzmán‐Vega, F. J., Arold, S. T., & Alkuraya, F. S. (2021). MYH1 is a candidate gene for recurrent rhabdomyolysis in humans. American Journal of Medical Genetics Part A. https://doi.org/10.1002/ajmg.a.62188
Wei, J., Chen, S., Zong, L., Gao, X., & Li, Y. (2021). Protein–RNA interaction prediction with deep learning: structure matters. Briefings in Bioinformatics, 23(1). https://doi.org/10.1093/bib/bbab540
Conchouso, D., Al-Ma’abadi, A., Behzad, H., Alarawi, M., Hosokawa, M., Nishikawa, Y., Takeyama, H., Mineta, K., & Gojobori, T. (2021). Integration of Droplet Microfluidic Tools for Single-cell Functional Metagenomics: An Engineering Head Start. Genomics, Proteomics & Bioinformatics, 19(3), 504–518. https://doi.org/10.1016/j.gpb.2021.03.010
Farhat, N., Kim, L., Mineta, K., Alarawi, M., Gojobori, T., Saikaly, P., & Vrouwenvelder, J. (2022). Seawater desalination based drinking water: Microbial characterization during distribution with and without residual chlorine. Water Research, 210, 117975. https://doi.org/10.1016/j.watres.2021.117975
He, W., Jiang, Y., Jin, J., Li, Z., Zhao, J., Manavalan, B., Su, R., Gao, X., & Wei, L. (2021). Accelerating bioactive peptide discovery via mutual information-based meta-learning. Briefings in Bioinformatics, 23(1). https://doi.org/10.1093/bib/bbab499
Alharbi, R., Strnad, O., Luidolt, L. R., Waldner, M., Kouril, D., Bohak, C., Klein, T., Groller, E., & Viola, I. (2023). Nanotilus: Generator of Immersive Guided-Tours in Crowded 3D Environments. IEEE Transactions on Visualization and Computer Graphics, 29(3), 1860–1875. https://doi.org/10.1109/tvcg.2021.3133592
Stoikov, D., Ivanov, A., Shurpik, D., Stoikov, I., & Evtugyn, G. (2021). Flow-Through Electrochemical Biosensor with a Replaceable Enzyme Reactor and Screen-Printed Electrode for the Determination of Uric Acid and Tyrosine. Analytical Letters, 1–15. https://doi.org/10.1080/00032719.2021.2000621
Fan, M., Cui, Y., You, C., Liu, L., Gu, Y., Peng, W., Bai, Q., Gao, X., & Li, L. (2022). Radiogenomic Signatures of Oncotype DX Recurrence Score Enable Prediction of Survival in Estrogen Receptor–Positive Breast Cancer: A Multicohort Study. Radiology, 302(3), 516–524. https://doi.org/10.1148/radiol.2021210738
Fan, M., Cui, Y., You, C., Liu, L., Gu, Y., Peng, W., Bai, Q., Gao, X., & Li, L. (2022). Radiogenomic Signatures of Oncotype DX Recurrence Score Enable Prediction of Survival in Estrogen Receptor–Positive Breast Cancer: A Multicohort Study. Radiology, 302(3), 516–524. https://doi.org/10.1148/radiol.2021210738
Zarban, R. A., Hameed, U. F. S., Jamil, M., Ota, T., Wang, J. Y., Arold, S. T., Asami, T., & Al-Babili, S. (2021). Rational design of Striga hermonthica-specific seed germination inhibitors. Plant Physiology, 188(2), 1369–1384. https://doi.org/10.1093/plphys/kiab547
Kouril, D., Strnad, O., Mindek, P., Halladjian, S., Isenberg, T., Groller, M. E., & Viola, I. (2023). Molecumentary: Adaptable Narrated Documentaries Using Molecular Visualization. IEEE Transactions on Visualization and Computer Graphics, 29(3), 1733–1747. https://doi.org/10.1109/tvcg.2021.3130670
Vogeley, C., Sondermann, N. C., Woeste, S., Momin, A. A., Gilardino, V., Hartung, F., Heinen, M., Maaß, S. K., Mescher, M., Pollet, M., Rolfes, K. M., Vogel, C. F. A., Rossi, A., Lang, D., Arold, S. T., Nakamura, M., & Haarmann-Stemmann, T. (2022). Unraveling the differential impact of PAHs and dioxin-like compounds on AKR1C3 reveals the EGFR extracellular domain as a critical determinant of the AHR response. Environment International, 158, 106989. https://doi.org/10.1016/j.envint.2021.106989
Hammerman, N. M., Roff, G., Rodriguez-Ramirez, A., Leonard, N., Staples, T. L., Eyal, G., Rossbach, S., Havlik, M. N., Saderne, V., Zhao, J., Duarte, C. M., & Pandolfi, J. M. (2022). Reef accumulation is decoupled from recent degradation in the central and southern Red Sea. Science of The Total Environment, 809, 151176. https://doi.org/10.1016/j.scitotenv.2021.151176
Huang, N., Nie, F., Ni, P., Gao, X., Luo, F., & Wang, J. (2021). BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer. Briefings in Bioinformatics, 23(1). https://doi.org/10.1093/bib/bbab405
Wu, X., Stephen, M., Hidalgo, T. C., Salim, T., Surgailis, J., Surendran, A., Su, X., Li, T., Inal, S., & Leong, W. L. (2021). Ionic‐Liquid Induced Morphology Tuning of PEDOT:PSS for High‐Performance Organic Electrochemical Transistors. Advanced Functional Materials, 32(1), 2108510. Portico. https://doi.org/10.1002/adfm.202108510
Yamamoto, N., Nishida, N., Yamamoto, R., Gojobori, T., Shimotohno, K., Mizokami, M., & Ariumi, Y. (2021). Angiotensin–Converting Enzyme (ACE) 1 Gene Polymorphism and Phenotypic Expression of COVID-19 Symptoms. Genes, 12(10), 1572. https://doi.org/10.3390/genes12101572
Yamamoto, N., Nishida, N., Yamamoto, R., Gojobori, T., Shimotohno, K., Mizokami, M., & Ariumi, Y. (2021). Angiotensin–Converting Enzyme (ACE) 1 Gene Polymorphism and Phenotypic Expression of COVID-19 Symptoms. Genes, 12(10), 1572. https://doi.org/10.3390/genes12101572
Fatani, S., Saito, Y., Alarawi, M., Gojobori, T., & Mineta, K. (2021). Genome sequencing and identification of cellulase genes in Bacillus paralicheniformis strains from the Red Sea. BMC Microbiology, 21(1). https://doi.org/10.1186/s12866-021-02316-w
Thafar, M. A., Olayan, R. S., Albaradei, S., Bajic, V. B., Gojobori, T., Essack, M., & Gao, X. (2021). DTi2Vec: Drug–target interaction prediction using network embedding and ensemble learning. Journal of Cheminformatics, 13(1). https://doi.org/10.1186/s13321-021-00552-w
Jia, K.-P., Mi, J., Ali, S., Ohyanagi, H., Moreno, J. C., Ablazov, A., Balakrishna, A., Berqdar, L., Fiore, A., Diretto, G., Martínez, C., de Lera, A. R., Gojobori, T., & Al-Babili, S. (2022). An alternative, zeaxanthin epoxidase-independent abscisic acid biosynthetic pathway in plants. Molecular Plant, 15(1), 151–166. https://doi.org/10.1016/j.molp.2021.09.008
Azad, M., Chikalov, I., Hussain, S., & Moshkov, M. (2021). Minimizing Depth of Decision Trees with Hypotheses. Lecture Notes in Computer Science, 123–133. https://doi.org/10.1007/978-3-030-87334-9_11
Calich, H. J., Rodríguez, J. P., Eguíluz, V. M., Hammerschlag, N., Pattiaratchi, C., Duarte, C. M., & Sequeira, A. M. M. (2021). Comprehensive analytical approaches reveal species‐specific search strategies in sympatric apex predatory sharks. Ecography, 44(10), 1544–1556. https://doi.org/10.1111/ecog.05953
Li, X., Lau, A. Y. T., Ng, A. S. N., Aldehaiman, A., Zhou, Y., Ng, P. K. S., … Cheung, L. W. T. (2021). Cancer-associated mutations in the p85α N-terminal SH2 domain activate a spectrum of receptor tyrosine kinases. Proceedings of the National Academy of Sciences, 118(37), e2101751118. https://doi.org/10.1073/pnas.2101751118
Hopkins, L. W., Geraldi, N. R., Pope, E. C., Holton, M. D., Lurgi, M., Duarte, C. M., & Wilson, R. P. (2021). Testing angular velocity as a new metric for metabolic demands of slow-moving marine fauna: a case study with Giant spider conchs Lambis truncata. Animal Biotelemetry, 9(1). https://doi.org/10.1186/s40317-021-00255-x
Albaradei, S., Thafar, M., Alsaedi, A., Van Neste, C., Gojobori, T., Essack, M., & Gao, X. (2021). Machine Learning and Deep Learning Methods that use Omics Data for Metastasis Prediction. Computational and Structural Biotechnology Journal. https://doi.org/10.1016/j.csbj.2021.09.001
Ziegler, M., Anton, A., Klein, S. G., Rädecker, N., Geraldi, N. R., Schmidt‐Roach, S., Saderne, V., Mumby, P. J., Cziesielski, M. J., Martin, C., Frölicher, T. L., Pandolfi, J. M., Suggett, D. J., Aranda, M., Duarte, C. M., & Voolstra, C. R. (2021). Integrating environmental variability to broaden the research on coral responses to future ocean conditions. Global Change Biology, 27(21), 5532–5546. Portico. https://doi.org/10.1111/gcb.15840
Ziegler, M., Anton, A., Klein, S. G., Rädecker, N., Geraldi, N. R., Schmidt‐Roach, S., Saderne, V., Mumby, P. J., Cziesielski, M. J., Martin, C., Frölicher, T. L., Pandolfi, J. M., Suggett, D. J., Aranda, M., Duarte, C. M., & Voolstra, C. R. (2021). Integrating environmental variability to broaden the research on coral responses to future ocean conditions. Global Change Biology, 27(21), 5532–5546. Portico. https://doi.org/10.1111/gcb.15840
Ziegler, M., Anton, A., Klein, S. G., Rädecker, N., Geraldi, N. R., Schmidt‐Roach, S., … Voolstra, C. R. (2021). Integrating environmental variability to broaden the research on coral responses to future ocean conditions. Global Change Biology, 27(21), 5532–5546. https://doi.org/10.1111/gcb.15840
Albalawi, H. I., Khan, Z. N., Valle-Pérez, A. U., Kahin, K. M., Hountondji, M., Alwazani, H., … Hauser, C. A. E. (2021). Sustainable and Eco-Friendly Coral Restoration through 3D Printing and Fabrication. ACS Sustainable Chemistry & Engineering, 9(37), 12634–12645. https://doi.org/10.1021/acssuschemeng.1c04148
Klein, S. G., Geraldi, N. R., Anton, A., Schmidt‐Roach, S., Ziegler, M., Cziesielski, M. J., … Duarte, C. M. (2021). Projecting coral responses to intensifying marine heatwaves under ocean acidification. Global Change Biology. https://doi.org/10.1111/gcb.15818
Klein, S. G., Geraldi, N. R., Anton, A., Schmidt‐Roach, S., Ziegler, M., Cziesielski, M. J., Martin, C., Rädecker, N., Frölicher, T. L., Mumby, P. J., Pandolfi, J. M., Suggett, D. J., Voolstra, C. R., Aranda, M., & Duarte, Carlos. M. (2021). Projecting coral responses to intensifying marine heatwaves under ocean acidification. Global Change Biology, 28(5), 1753–1765. Portico. https://doi.org/10.1111/gcb.15818
Kobiyama, A., Rashid, J., Reza, M. S., Ikeda, Y., Yamada, Y., Kudo, T., … Watabe, S. (2021). Seasonal and annual changes in the microbial communities of Ofunato Bay, Japan, based on metagenomics. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-96641-9
Kafkas, Ş., Althubaiti, S., Gkoutos, G. V., Hoehndorf, R., & Schofield, P. N. (2021). Linking common human diseases to their phenotypes; development of a resource for human phenomics. Journal of Biomedical Semantics, 12(1). htttps://doi:10.1186/s13326-021-00249-x
Alalwan, A., Albalawi, F., & Laleg-Kirati, T. M. (2021). Tracking Model Predictive Control Paradigm for Underwater Optical Communication. IEEE Open Journal of the Communications Society, 1–1. https://doi.org/10.1109/ojcoms.2021.3104929
Klein, S. G., Alsolami, S. M., Steckbauer, A., Arossa, S., Parry, A. J., Ramos Mandujano, G., Alsayegh, K., Izpisua Belmonte, J. C., Li, M., & Duarte, C. M. (2021). A prevalent neglect of environmental control in mammalian cell culture calls for best practices. Nature Biomedical Engineering, 5(8), 787–792. https://doi.org/10.1038/s41551-021-00775-0
Klein, S. G., Alsolami, S. M., Steckbauer, A., Arossa, S., Parry, A. J., Ramos Mandujano, G., … Duarte, C. M. (2021). A prevalent neglect of environmental control in mammalian cell culture calls for best practices. Nature Biomedical Engineering, 5(8), 787–792. https://doi.org/10.1038/s41551-021-00775-0
Zhao, X., Remington, J. M., Schneebeli, S. T., Arold, S. T., & Li, J. (2021). Molecular Basis for Environment Sensing by a Nucleoid-Structuring Bacterial Protein Filament. The Journal of Physical Chemistry Letters, 12(32), 7878–7884. https://doi.org/10.1021/acs.jpclett.1c01710
Abouelhoda, M., Mohty, D., Alayary, I., Meyer, B. F., Arold, S. T., Fadel, B. M., & Monies, D. (2021). Established and candidate transthyretin amyloidosis variants identified in the Saudi population by data mining. Human Genomics, 15(1). https://doi.org/10.1186/s40246-021-00351-2
Queralt-Rosinach, N., Schofield, P., Hoehndorf, R., Weiland, C., Schultes, E. A., Bernabé, C. H., & Roos, M. (2021). The COVID-19 epidemiology and monitoring ontology. https://doi.org/10.37044/osf.io/n6tcz
Salsench, E. M., Maroofian, R., Deng, R., Lanko, K., Nikoncuk, A., Pérez, B., … Barakat, T. S. (2021). Expanding the mutational landscape and clinical phenotype of the YIF1B related brain disorder. Brain. https://doi.org/10.1093/brain/awab297
Albaradei, S., Napolitano, F., Thafar, M. A., Gojobori, T., Essack, M., & Gao, X. (2021). MetaCancer: A deep learning-based pan-cancer metastasis prediction model developed using multi-omics data. Computational and Structural Biotechnology Journal, 19, 4404–4411. https://doi.org/10.1016/j.csbj.2021.08.006
Abdelrahman, S., Alghrably, M., Campagna, M., Hauser, C. A. E., Jaremko, M., & Lachowicz, J. I. (2021). Metal Complex Formation and Anticancer Activity of Cu(I) and Cu(II) Complexes with Metformin. Molecules, 26(16), 4730. https://doi.org/10.3390/molecules26164730
Shimada, T., Meekan, M. G., Baldwin, R., Al-Suwailem, A. M., Clarke, C., Santillan, A. S., & Duarte, C. M. (2021). Distribution and temporal trends in the abundance of nesting sea turtles in the Red Sea. Biological Conservation, 261, 109235. https://doi.org/10.1016/j.biocon.2021.109235
Li, X., Sindihebura, T. T., Zhou, L., Duarte, C. M., Costa, D. P., Hindell, M. A., … Peng, C. (2021). A prediction and imputation method for marine animal movement data. PeerJ Computer Science, 7, e656. https://doi.org/10.7717/peerj-cs.656
Agulles, M., Jordà, G., Hoteit, I., Agustí, S., & Duarte, C. M. (2021). Assessment of Red Sea temperatures in CMIP5 models for present and future climate. PLOS ONE, 16(7), e0255505. https://doi.org/10.1371/journal.pone.0255505
Gallagher, A. J., Alsudairy, N. A., Shea, B. D., Payne, N. L., & Duarte, C. M. (2021). First Application of 360-Degree Camera Technology to Marine Predator Bio-Logging. Frontiers in Marine Science, 8. https://doi.org/10.3389/fmars.2021.707376
Britten, G. L., Duarte, C. M., & Worm, B. (2021). Recovery of assessed global fish stocks remains uncertain. Proceedings of the National Academy of Sciences, 118(31). https://doi.org/10.1073/pnas.2108532118
Britten, G. L., Duarte, C. M., & Worm, B. (2021). Recovery of assessed global fish stocks remains uncertain. Proceedings of the National Academy of Sciences, 118(31). https://doi.org/10.1073/pnas.2108532118
Britten, G. L., Duarte, C. M., & Worm, B. (2021). Recovery of assessed global fish stocks remains uncertain. Proceedings of the National Academy of Sciences, 118(31), e2108532118. https://doi.org/10.1073/pnas.2108532118
Arossa, S., Barozzi, A., Callegari, M., Klein, S. G., Parry, A. J., Hung, S.-H., … Duarte, C. M. (2021). The Internal Microenvironment of the Symbiotic Jellyfish Cassiopea sp. From the Red Sea. Frontiers in Marine Science, 8. https://doi.org/10.3389/fmars.2021.705915
Wang, Q., Duarte, C., Song, L., Christakos, G., Agusti, S., & Wu, J. (2021). Effects of Ecological Restoration Using Non-Native Mangrove Kandelia obovata to Replace Invasive Spartina alterniflora on Intertidal Macrobenthos Community in Maoyan Island (Zhejiang, China). Journal of Marine Science and Engineering, 9(8), 788. https://doi.org/10.3390/jmse9080788
Moshkov, M. (2021). Decision trees based on 1-consequences. Discrete Applied Mathematics, 302, 208–214. https://doi.org/10.1016/j.dam.2021.07.017
Alshukairi, A. N., El-Kafrawy, S. A., Dada, A., Yasir, M., Yamani, A. H., Saeedi, M. F., … Azhar, E. I. (2021). Re-infection with a different SARS-CoV-2 clade and prolonged viral shedding in a hematopoietic stem cell transplantation patient. International Journal of Infectious Diseases, 110, 267–271. https://doi.org/10.1016/j.ijid.2021.07.036
Rolandi, M., Noy, A., Inal, S., & Rivnay, J. (2021). Advances in bioelectronics: Materials, devices, and translational applications. APL Materials, 9(7), 070402. https://doi.org/10.1063/5.0060323
Deutschmann, I. M., Delage, E., Giner, C. R., Sebastián, M., Poulain, J., Arístegui, J., … Logares, R. (2021). Disentangling marine microbial networks across space. https://doi.org/10.1101/2021.07.12.451729
AlSaieedi, A., Salhi, A., Tifratene, F., Raies, A. B., Hungler, A., Uludag, M., … Essack, M. (2021). DES-Tcell is a knowledgebase for exploring immunology-related literature. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-93809-1
Queiroz, N., Humphries, N. E., Couto, A., Vedor, M., da Costa, I., Sequeira, A. M. M., … Abercrombie, D. L. (2021). Reply to: Shark mortality cannot be assessed by fishery overlap alone. Nature, 595(7866), E8–E16. https://doi.org/10.1038/s41586-021-03397-3
Queiroz, N., Humphries, N. E., Couto, A., Vedor, M., da Costa, I., Sequeira, A. M. M., … Abercrombie, D. L. (2021). Reply to: Caution over the use of ecological big data for conservation. Nature, 595(7866), E20–E28. https://doi.org/10.1038/s41586-021-03464-9
Queiroz, N., Humphries, N. E., Couto, A., Vedor, M., da Costa, I., Sequeira, A. M. M., … Abercrombie, D. L. (2021). Reply to: Caution over the use of ecological big data for conservation. Nature, 595(7866), E20–E28. https://doi.org/10.1038/s41586-021-03464-9
L Ghaffour, TML Kirati, (2021). Reference Tracking AND Observer Design for Space-Fractional Partial Differential Equation Modeling Gas Pressures in Fractured Media. arXiv.2107.02042
Liao, X., Li, M., Hu, K., Wu, F.-X., Gao, X., & Wang, J. (2021). A sensitive repeat identification framework based on short and long reads. Nucleic Acids Research. https://doi.org/10.1093/nar/gkab563
Gunner, R. M., Holton, M. D., Scantlebury, M. D., van Schalkwyk, O. L., English, H. M., Williams, H. J., … Wilson, R. P. (2021). Dead-reckoning animal movements in R: a reappraisal using Gundog.Tracks. Animal Biotelemetry, 9(1). https://doi.org/10.1186/s40317-021-00245-z
Gunner, R. M., Holton, M. D., Scantlebury, M. D., van Schalkwyk, O. L., English, H. M., Williams, H. J., … Wilson, R. P. (2021). Dead-reckoning animal movements in R: a reappraisal using Gundog.Tracks. Animal Biotelemetry, 9(1). https://doi.org/10.1186/s40317-021-00245-z
Azad, M., Chikalov, I., Hussain, S., & Moshkov, M. (2021). Optimization of Decision Trees with Hypotheses for Knowledge Representation. Electronics, 10(13), 1580. https://doi.org/10.3390/electronics10131580
Gu, J., Jin, R., Chen, G., Ye, Z., Li, Q., Wang, H., … Wu, J. (2021). Areal Extent, Species Composition, and Spatial Distribution of Coastal Saltmarshes in China. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, 14, 7085–7094. https://doi.org/10.1109/jstars.2021.3093673
Yu, G., Huang, Q., Zhang, X., Guo, M., & Wang, J. (2021). Tissue Specificity based Isoform Function Prediction. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1–1. https://doi.org/10.1109/tcbb.2021.3093167
Bajaffer, A., Mineta, K., & Gojobori, T. (2021). Evolution of memory system‐related genes. FEBS Open Bio. https://doi.org/10.1002/2211-5463.13224
Nayak, P. D., Ohayon, D., Wustoni, S., & Inal, S. (2021). Tailoring Electropolymerized Poly(3,4‐ethylenedioxythiophene) Films for Oxygen Reduction Reaction. Advanced Materials Technologies, 7(2), 2100277. Portico. https://doi.org/10.1002/admt.202100277
Azad, M., Chikalov, I., Hussain, S., & Moshkov, M. (2021). Entropy-Based Greedy Algorithm for Decision Trees Using Hypotheses. Entropy, 23(7), 808. https://doi.org/10.3390/e23070808
Pörtner, H.-O., Scholes, R. J., Agard, J., Archer, E., Bai, X., Barnes, D., Burrows, M., Chan, L., Cheung, W. L. (W., Diamond, S., Donatti, C., Duarte, C., Eisenhauer, N., Foden, W., Gasalla, M. A., Handa, C., Hickler, T., Hoegh-Guldberg, O., Ichii, K., … Ngo, H. (2021). IPBES-IPCC co-sponsored workshop report on biodiversity and climate change (Version 2). Zenodo. https://doi.org/10.5281/ZENODO.4782538
Li, H., Zhou, J., Zhou, Y., Chen, Q., She, Y., Gao, F., … Gao, X. (2021). An Interpretable Computer-Aided Diagnosis Method for Periodontitis From Panoramic Radiographs. Frontiers in Physiology, 12. https://doi.org/10.3389/fphys.2021.655556
Zhou, J., zhang, bin, Li, H., Zhou, L., Li, Z., Long, Y., … Gao, X. (2021). DeeReCT-TSS: A novel meta-learning-based method annotates TSS in multiple cell types based on DNA sequences and RNA-seq data. https://doi.org/10.21203/rs.3.rs-640669/v1
Ramirez-Calderon, G., Susapto, H. H., & Hauser, C. A. E. (2021). Delivery of Endothelial Cell-Laden Microgel Elicits Angiogenesis in Self-Assembling Ultrashort Peptide Hydrogels In Vitro. ACS Applied Materials & Interfaces, 13(25), 29281–29292. https://doi.org/10.1021/acsami.1c03787
Gajdzik, L., DeCarlo, T. M., Aylagas, E., Coker, D. J., Green, A. L., Majoris, J. E., … Berumen, M. L. (2021). A portfolio of climate‐tailored approaches to advance the design of marine protected areas in the Red Sea. Global Change Biology, 27(17), 3956–3968. https://doi.org/10.1111/gcb.15719
Duarte, C. M., Jamil, T., Gojobori, T., & Alam, I. (2021). Detection of SARS-CoV-2 variants requires urgent global coordination. International Journal of Infectious Diseases, 109, 50–53. https://doi.org/10.1016/j.ijid.2021.06.027
Duarte, C. M., Jamil, T., Gojobori, T., & Alam, I. (2021). Detection of SARS-CoV-2 variants requires urgent global coordination. International Journal of Infectious Diseases, 109, 50–53. https://doi.org/10.1016/j.ijid.2021.06.027
Duarte, C. M., Jamil, T., Gojobori, T., & Alam, I. (2021). Detection of SARS-CoV-2 variants requires urgent global coordination. International Journal of Infectious Diseases, 109, 50–53. https://doi.org/10.1016/j.ijid.2021.06.027
Makita, Y., Suzuki, S., Fushimi, K., Shimada, S., Suehisa, A., Hirata, M., … Matsui, M. (2021). Identification of a dual orange/far-red and blue light photoreceptor from an oceanic green picoplankton. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-23741-5
Gunner, R. M., Wilson, R. P., Holton, M. D., Hopkins, P., Bell, S. H., Marks, N. J., … Scantlebury, D. M. (2021). Decision rules for determining terrestrial movement and the consequences for filtering high-resolution GPS tracks – A case study using the African Lion (Panthera leo). https://doi.org/10.21203/rs.3.rs-600317/v1
Slater, L. T., Williams, J. A., Karwath, A., Russell, S., Pendleton, S. C., Fanning, H., … Gkoutos, G. V. (2021). Klarigi: Explanations for Semantic Groupings. https://doi.org/10.1101/2021.06.14.448423
López‐Sandoval, D. C., Duarte, C. M., & Agustí, S. (2021). Nutrient and temperature constraints on primary production and net phytoplankton growth in a tropical ecosystem. Limnology and Oceanography, 66(7), 2923–2935. https://doi.org/10.1002/lno.11849
López‐Sandoval, D. C., Duarte, C. M., & Agustí, S. (2021). Nutrient and temperature constraints on primary production and net phytoplankton growth in a tropical ecosystem. Limnology and Oceanography, 66(7), 2923–2935. https://doi.org/10.1002/lno.11849
Mazarrasa, I., Lavery, P., Duarte, C. M., Lafratta, A., Lovelock, C. E., Macreadie, P. I., … Serrano, O. (2021). Factors Determining Seagrass Blue Carbon Across Bioregions and Geomorphologies. Global Biogeochemical Cycles, 35(6). https://doi.org/10.1029/2021gb006935
Conchouso, D., Al-Ma’abadi, A., Behzad, H., Alarawi, M., Hosokawa, M., Nishikawa, Y., … Gojobori, T. (2021). Integration of Droplet Microfluidic Tools for Single-cell Functional Metagenomics: An Engineering Head Start. https://doi.org/10.36227/techrxiv.14760726.v1
Mazarrasa, I., Lavery, P., Duarte, C. M., Lafratta, A., Lovelock, C. E., Macreadie, P. I., … Serrano, O. (2021). Factors Determining Seagrass Blue Carbon Across Bioregions and Geomorphologies. Global Biogeochemical Cycles, 35(6). https://doi.org/10.1029/2021gb006935
Morales-Caselles, C., Viejo, J., Martí, E., González-Fernández, D., Pragnell-Raasch, H., González-Gordillo, J. I., … Cózar, A. (2021). An inshore–offshore sorting system revealed from global classification of ocean litter. Nature Sustainability, 4(6), 484–493. https://doi.org/10.1038/s41893-021-00720-8
Pei, S., Yu, L., & Zhang, X. (2021). Set-aware Entity Synonym Discovery with Flexible Receptive Fields. IEEE Transactions on Knowledge and Data Engineering, 1–1. https://doi.org/10.1109/tkde.2021.3087532
Yoshitake, K., Kimura, G., Sakami, T., Watanabe, T., Taniuchi, Y., Kakehi, S., … Gojobori, T. (2021). Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-91615-3
Primack, R. B., Bates, A. E., & Duarte, C. M. (2021). The conservation and ecological impacts of the COVID-19 pandemic. Biological Conservation, 260, 109204. https://doi.org/10.1016/j.biocon.2021.109204
Alam, I., Kamau, A. A., Ngugi, D. K., Gojobori, T., Duarte, C. M., & Bajic, V. B. (2021). KAUST Metagenomic Analysis Platform (KMAP), enabling access to massive analytics of re-annotated metagenomic data. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-90799-y
Slater, L. T., Williams, J. A., Karwath, A., Fanning, H., Ball, S., Schofield, P., … Gkoutos, G. V. (2021). Multi-faceted Semantic Clustering With Text-derived Phenotypes. https://doi.org/10.1101/2021.05.26.21257830
Guo, K., Wustoni, S., Koklu, A., Díaz-Galicia, E., Moser, M., Hama, A., … Inal, S. (2021). Rapid single-molecule detection of COVID-19 and MERS antigens via nanobody-functionalized organic electrochemical transistors. Nature Biomedical Engineering. https://doi.org/10.1038/s41551-021-00734-9
Noro, Y., Shimizu, H., Mineta, K., & Gojobori, T. (2021). A single neuron subset governs a single coactive neuron circuit in Hydra vulgaris, representing a possible ancestral feature of neural evolution. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-89325-x
Noro, Y., Shimizu, H., Mineta, K., & Gojobori, T. (2021). A single neuron subset governs a single coactive neuron circuit in Hydra vulgaris, representing a possible ancestral feature of neural evolution. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-89325-x
Bank, M. S., Swarzenski, P. W., Duarte, C. M., Rillig, M. C., Koelmans, A. A., Metian, M., Wright, S., Provencher, J. F., Sanden, M., Jordaan, A., Wagner, M., Thiel, M., & Ok, Y. S. (2021). Global Plastic Pollution Observation System to Aid Policy. Environmental Science & Technology, 55(12), 7770–7775. https://doi.org/10.1021/acs.est.1c00818
Magbool, A., Bahloul, M. A., Ballal, T., Al-Naffouri, T. Y., & Laleg-Kirati, T.-M. (2021). Aortic blood pressure estimation: A hybrid machine-learning and cross-relation approach. Biomedical Signal Processing and Control, 68, 102762. https://doi.org/10.1016/j.bspc.2021.102762
Acinas, S. G., Sánchez, P., Salazar, G., Cornejo-Castillo, F. M., Sebastián, M., Logares, R., … Gasol, J. M. (2021). Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Communications Biology, 4(1). https://doi.org/10.1038/s42003-021-02112-2
Kulmanov, M., Zhapa-Camacho, F., & Hoehndorf, R. (2021). DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web. Nucleic Acids Research, 49(W1), W140–W146. https://doi.org/10.1093/nar/gkab373
Bates, A. E., Primack, R. B., Biggar, B. S., Bird, T. J., Clinton, M. E., Command, R. J., Richards, C., Shellard, M., Geraldi, N. R., Vergara, V., Acevedo-Charry, O., Colón-Piñeiro, Z., Ocampo, D., Ocampo-Peñuela, N., Sánchez-Clavijo, L. M., Adamescu, C. M., Cheval, S., Racoviceanu, T., Adams, M. D., … Duarte, C. M. (2021). Global COVID-19 lockdown highlights humans as both threats and custodians of the environment. Biological Conservation, 263, 109175. https://doi.org/10.1016/j.biocon.2021.109175
Bates, A. E., Primack, R. B., & Duarte, C. M. (2021). Global COVID-19 lockdown highlights humans as both threats and custodians of the environment. Biological Conservation, 109175. https://doi.org/10.1016/j.biocon.2021.109175
Chen, S., Li, Y., Zhang, T., Zhu, X., Sun, S., & Gao, X. (2021). Lunar features detection for energy discovery via deep learning. Applied Energy, 296, 117085. https://doi.org/10.1016/j.apenergy.2021.117085
Obradovic, M., Sudar-Milovanovic, E., Soskic, S., Essack, M., Arya, S., Stewart, A. J., … Isenovic, E. R. (2021). Leptin and Obesity: Role and Clinical Implication. Frontiers in Endocrinology, 12. https://doi.org/10.3389/fendo.2021.585887
Zhang, X., Yang, Q., Albaradei, S., Lyu, X., Alamro, H., Salhi, A., … Gao, X. (2021). Rise and fall of the global conversation and shifting sentiments during the COVID-19 pandemic. Humanities and Social Sciences Communications, 8(1). https://doi.org/10.1057/s41599-021-00798-7
Zhang, J., Vancea, A. I., Shahul Hameed, U. F., & Arold, S. T. (2021). Versatile control of the CDC48 segregase by the plant UBX-containing (PUX) proteins. Computational and Structural Biotechnology Journal, 19, 3125–3132. https://doi.org/10.1016/j.csbj.2021.05.025
Bahloul, M. A., & Laleg Kirati, T.-M. (2021). Fractional-order model representations of apparent vascular compliance as an alternative in the analysis of arterial stiffness: an in-silico study. Physiological Measurement, 42(4), 045008. https://doi.org/10.1088/1361-6579/abf1b1
Konovalov, K. A., Wang, W., Wang, G., Goonetilleke, E. C., Gao, X., Wang, D., & Huang, X. (2021). A comprehensive mechanism for 5-carboxylcytosine-induced transcriptional pausing revealed by Markov state models. Journal of Biological Chemistry, 296, 100735. https://doi.org/10.1016/j.jbc.2021.100735
Huang, N., Nie, F., Ni, P., Luo, F., Gao, X., & Wang, J. (2021). NeuralPolish: a novel Nanopore polishing method based on alignment matrix construction and orthogonal Bi-GRU Networks. Bioinformatics. https://doi.org/10.1093/bioinformatics/btab354
Roth, F., El-Khaled, Y. C., Karcher, D. B., Rädecker, N., Carvalho, S., Duarte, C. M., … Wild, C. (2021). Nutrient pollution enhances productivity and framework dissolution in algae- but not in coral-dominated reef communities. Marine Pollution Bulletin, 168, 112444. https://doi.org/10.1016/j.marpolbul.2021.112444
Roth, F., El-Khaled, Y. C., Karcher, D. B., Rädecker, N., Carvalho, S., Duarte, C. M., Silva, L., Calleja, M. Ll., Morán, X. A. G., Jones, B. H., Voolstra, C. R., & Wild, C. (2021). Nutrient pollution enhances productivity and framework dissolution in algae- but not in coral-dominated reef communities. Marine Pollution Bulletin, 168, 112444. https://doi.org/10.1016/j.marpolbul.2021.112444
Aalismail, N. A., Díaz-Rúa, R., Geraldi, N., Cusack, M., & Duarte, C. M. (2021). Diversity and Sources of Airborne Eukaryotic Communities (AEC) in the Global Dust Belt over the Red Sea. Earth Systems and Environment, 5(2), 459–471. https://doi.org/10.1007/s41748-021-00219-4
Zhang, D., Yao, L., Chen, K., Yang, Z., Gao, X., & Liu, Y. (2021). Preventing Sensitive Information Leakage from Mobile Sensor Signals via IntegrativeTransformation. IEEE Transactions on Mobile Computing, 1–1. https://doi.org/10.1109/tmc.2021.3078086
Zhang, S., Yuan, B., Lam, J. H., Zhou, J., Zhou, X., Ramos-Mandujano, G., … Yang, M. (2021). Structure of the full-length human Pannexin1 channel and insights into its role in pyroptosis. Cell Discovery, 7(1). https://doi.org/10.1038/s41421-021-00259-0
Khan, F., Radovanovic, A., Gojobori, T., & Kaur, M. (2021). IBDDB: a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease. Database, 2021. https://doi.org/10.1093/database/baab022
Hinnerichs, T., & Hoehndorf, R. (2021). DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug–target interactions. https://doi.org/10.1101/2021.04.28.441733
Alshehri, S., Susapto, H. H., & Hauser, C. A. E. (2021). Scaffolds from Self-Assembling Tetrapeptides Support 3D Spreading, Osteogenic Differentiation, and Angiogenesis of Mesenchymal Stem Cells. Biomacromolecules, 22(5), 2094–2106. https://doi.org/10.1021/acs.biomac.1c00205
Wu, D., Ye, M., Lin, G., Gao, X., & Shen, J. (2021). Person Re-Identification by Context-aware Part Attention and Multi-Head Collaborative Learning. IEEE Transactions on Information Forensics and Security, 1–1. https://doi.org/10.1109/tifs.2021.3075894
Subedi, R. C., Rossbach, S., Kang, C. H., Alkhazragi, O., Sun, X., Holguin-Lerma, J. A., … Ooi, B. S. (2021). Giant clam inspired high-speed photo-conversion for ultraviolet optical wireless communication. Optical Materials Express, 11(5), 1515. https://doi.org/10.1364/ome.423432
Napolitano, F., Rapakoulia, T., Annunziata, P., Hasegawa, A., Cardon, M., Napolitano, S., … Arner, E. (2021). Automatic identification of small molecules that promote cell conversion and reprogramming. Stem Cell Reports, 16(5), 1381–1390. https://doi.org/10.1016/j.stemcr.2021.03.028
Martin, C., Zhang, Q., Zhai, D., Zhang, X., & Duarte, C. M. (2021). Anthropogenic litter density and composition data acquired flying commercial drones on sandy beaches along the Saudi Arabian Red Sea. Data in Brief, 36, 107056. https://doi.org/10.1016/j.dib.2021.107056
Unarta, I. C., Cao, S., Kubo, S., Wang, W., Cheung, P. P.-H., Gao, X., … Huang, X. (2021). Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model. Proceedings of the National Academy of Sciences, 118(17), e2024324118. https://doi.org/10.1073/pnas.2024324118
Aldehaiman, A., Momin, A. A., Restouin, A., Wang, L., Shi, X., Aljedani, S., … Arold, S. T. (2021). Synergy and allostery in ligand binding by HIV-1 Nef. Biochemical Journal, 478(8), 1525–1545. https://doi.org/10.1042/bcj20201002
Alghamdi, M., Alhumsi, T. R., Altweijri, I., Alkhamis, W. H., Barasain, O., Cardona-Londoño, K. J., … Bakhrebah, M. A. (2021). Clinical and Genetic Characterization of Craniosynostosis in Saudi Arabia. Frontiers in Pediatrics, 9. https://doi.org/10.3389/fped.2021.582816
Duarte, C. M., Agusti, S., Barbier, E., Britten, G. L., Castilla, J. C., Gattuso, J.-P., … Worm, B. (2021). Author Correction: Rebuilding marine life. Nature. https://doi.org/10.1038/s41586-021-03271-2
N’doye, I., Zhang, D., Alouini, M.-S., & Laleg-Kirati, T.-M. (2021). Establishing and Maintaining a Reliable Optical Wireless Communication in Underwater Environment. IEEE Access, 9, 62519–62531. https://doi.org/10.1109/access.2021.3073461
Bank, M. S., Swarzenski, P. W., Bianchi, G., Metian, M., Ok, Y. S., & Duarte, C. M. (2021). Reimagining aquaculture in the Global South. Science, 372(6539), 247.2–248. https://doi.org/10.1126/science.abi5015
Hickey, S. M., Radford, B., Callow, J. N., Phinn, S. R., Duarte, C. M., & Lovelock, C. E. (2021). ENSO feedback drives variations in dieback at a marginal mangrove site. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-87341-5
Goto, K., Mineta, K., Miyazaki, S., & Gojobori, T. (2021). Significant variants of type 2 diabetes in the Arabian Region through an Integration of exome databases. PLOS ONE, 16(4), e0249226. doi:10.1371/journal.pone.0249226
Wesselmann, M., Geraldi, N. R., Duarte, C. M., Garcia‐Orellana, J., Díaz‐Rúa, R., Arias‐Ortiz, A., … Marbà, N. (2021). Seagrass (Halophila stipulacea) invasion enhances carbon sequestration in the Mediterranean Sea. Global Change Biology. https://doi.org/10.1111/gcb.15589
Slater, L. T., Bradlow, W., Ball, S., Hoehndorf, R., & Gkoutos, G. V. (2021). Improved characterisation of clinical text through ontology-based vocabulary expansion. Journal of Biomedical Semantics, 12(1). https://doi.org/10.1186/s13326-021-00241-5
Abouelhoda, M., Mohty, D., Alayary, I., Meyer, B. F., Arold, S. T., Fadel, B. M., & Monies, D. (2021). Data Mining for the Identification of Known and Candidate Transthyretin Amyloidosis Variants in the Saudi Population. https://doi.org/10.21203/rs.3.rs-386081/v1
Costa, R. M., Cárdenas, A., Loussert-Fonta, C., Toullec, G., Meibom, A., & Voolstra, C. R. (2021). Surface Topography, Bacterial Carrying Capacity, and the Prospect of Microbiome Manipulation in the Sea Anemone Coral Model Aiptasia. Frontiers in Microbiology, 12. https://doi.org/10.3389/fmicb.2021.637834
Li, P., & Laleg‐Kirati, T. M. (2021). Signal denoising based on the Schrödinger operator’s eigenspectrum and a curvature constraint. IET Signal Processing, 15(3), 195–206. https://doi.org/10.1049/sil2.12023
N’Doye, I., Cai, W., Alalwan, A., Sun, X., Headary, W. G., Alouini, M.-S., … Laleg-Kirati, T.-M. (2021). Reduction of the beam pointing error for improved free-space optical communication link performance. IFAC Journal of Systems and Control, 16, 100154. https://doi.org/10.1016/j.ifacsc.2021.100154
Rosentreter, J. A., Borges, A. V., Deemer, B. R., Holgerson, M. A., Liu, S., Song, C., … Eyre, B. D. (2021). Half of global methane emissions come from highly variable aquatic ecosystem sources. Nature Geoscience, 14(4), 225–230. https://doi.org/10.1038/s41561-021-00715-2
Moshkov, M. (2021). On the depth of decision trees over infinite 1-homogeneous binary information systems. Array, 10, 100060. https://doi.org/10.1016/j.array.2021.100060
Slater, L. T., Karwath, A., Williams, J. A., Russell, S., Makepeace, S., Carberry, A., … Gkoutos, G. V. (2021). Towards similarity-based differential diagnostics for common diseases. Computers in Biology and Medicine, 133, 104360. https://doi.org/10.1016/j.compbiomed.2021.104360
Sequeira, A. M. M., O’Toole, M., Keates, T. R., McDonnell, L. H., Braun, C. D., Hoenner, X., Jaine, F. R. A., Jonsen, I. D., Newman, P., Pye, J., Bograd, S. J., Hays, G. C., Hazen, E. L., Holland, M., Tsontos, V. M., Blight, C., Cagnacci, F., Davidson, S. C., Dettki, H., … Weise, M. (2021). A standardisation framework for bio‐logging data to advance ecological research and conservation. Methods in Ecology and Evolution, 12(6), 996–1007. Portico. https://doi.org/10.1111/2041-210x.13593
Naveed, H., Reglin, C., Schubert, T., Gao, X., Arold, S. T., & Maitland, M. L. (2021). Identifying Novel Drug Targets by iDTPnd: A Case Study of Kinase Inhibitors. Genomics, Proteomics & Bioinformatics. https://doi.org/10.1016/j.gpb.2020.05.006
Sanderson, L. E., Lanko, K., Alsagob, M., Almass, R., Al-Ahmadi, N., Najafi, M., … Perenthaler, E. (2021). Bi-allelic variants in HOPS complex subunit VPS41 cause cerebellar ataxia and abnormal membrane trafficking. Brain, 144(3), 769–780. https://doi.org/10.1093/brain/awaa459
Ben Nasser, B., Djemai, M., Defoort, M., & Laleg-Kirati, T.-M. (2021). Time scale observability and constructibility of linear dynamic equations. International Journal of Control, 1–11. https://doi.org/10.1080/00207179.2021.1890823
Kuwahara, H., & Gao, X. (2021). Analysis of the effects of related fingerprints on molecular similarity using an eigenvalue entropy approach. Journal of Cheminformatics, 13(1). https://doi.org/10.1186/s13321-021-00506-2
Eldawlatly, S., Abouelhoda, M., Al-Kadi, O. S., Gojobori, T., Jankovic, B., Khalil, M., … Morsy, A. (2021). Biomedical computing in the Arab world. Communications of the ACM, 64(4), 108–113. doi:10.1145/3447746
Fan, M., Chen, H., You, C., Liu, L., Gu, Y., Peng, W., … Li, L. (2021). Radiomics of Tumor Heterogeneity in Longitudinal Dynamic Contrast-Enhanced Magnetic Resonance Imaging for Predicting Response to Neoadjuvant Chemotherapy in Breast Cancer. Frontiers in Molecular Biosciences, 8. https://doi.org/10.3389/fmolb.2021.622219
Lozin, V., & Moshkov, M. (2021). Critical Properties and Complexity Measures of Read-Once Boolean Functions. Annals of Mathematics and Artificial Intelligence, 89(5-6), 595–614. https://doi.org/10.1007/s10472-021-09734-6
Gunner, R., Wilson, R., Holton, M., Scott, R., Arkwright, A., Fahlman, A., … Eizaguirre, C. (2021). Activity of loggerhead turtles during the U-shaped dive: insights using angular velocity metrics. Endangered Species Research, 45, 1–12. https://doi.org/10.3354/esr01125
Gattuso, J.-P., Williamson, P., Duarte, C. M., & Magnan, A. K. (2021). The Potential for Ocean-Based Climate Action: Negative Emissions Technologies and Beyond. Frontiers in Climate, 2. https://doi.org/10.3389/fclim.2020.575716
Sequeira, A. M. M., O’Toole, M., Keates, T. R., McDonnell, L. H., Braun, C. D., Hoenner, X., … Weise, M. (2021). A standardisation framework for bio‐logging data to advance ecological research and conservation. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.13593
Chalastani, V. I., Tsoukala, V. K., Coccossis, H., & Duarte, C. M. (2021). A bibliometric assessment of progress in marine spatial planning. Marine Policy, 127, 104329. https://doi.org/10.1016/j.marpol.2020.104329
Bennett, S., Santana‐Garcon, J., Marbà, N., Jorda, G., Anton, A., Apostolaki, E. T., … Duarte, C. M. (2021). Climate‐driven impacts of exotic species on marine ecosystems. Global Ecology and Biogeography, 30(5), 1043–1055. https://doi.org/10.1111/geb.13283
Rossbach, S., Hume, B. C. C., Cárdenas, A., Perna, G., Voolstra, C. R., & Duarte, C. M. (2021). Flexibility in Red Sea Tridacna maxima Symbiodiniaceae associations supports environmental niche adaptation. Ecology and Evolution, 11(7), 3393–3406. https://doi.org/10.1002/ece3.7299
Li, P., & Laleg-Kirati, T.-M. (2021). Central Blood Pressure Estimation From Distal PPG Measurement Using Semiclassical Signal Analysis Features. IEEE Access, 9, 44963–44973. https://doi.org/10.1109/access.2021.3065576
Althubaiti, S., Kulmanov, M., Liu, Y., Gkoutos, G. V., Schofield, P., & Hoehndorf, R. (2021). DeepMOCCA: A pan-cancer prognostic model identifies personalized prognostic markers through graph attention and multi-omics data integration. https://doi.org/10.1101/2021.03.02.433454
Khan, Z., Kahin, K., & Hauser, C. (2021). Time-dependent pulsing of microfluidic pumps to enhance 3D bioprinting of peptide bioinks. Microfluidics, BioMEMS, and Medical Microsystems XIX. https://doi.org/10.1117/12.2578830
Liu-Wei, W., Kafkas, Ş., Chen, J., Dimonaco, N. J., Tegnér, J., & Hoehndorf, R. (2021). DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes. Bioinformatics. https://doi.org/10.1093/bioinformatics/btab147
Li, Z., Li, Y., Zhang, B., Li, Y., Long, Y., Zhou, J., … Gao, X. (2021). DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning. Genomics, Proteomics & Bioinformatics. doi:10.1016/j.gpb.2020.05.004
Rodríguez, J. P., Fernández-Gracia, J., Duarte, C. M., Irigoien, X., & Eguíluz, V. M. (2021). The global network of ports supporting high seas fishing. Science Advances, 7(9), eabe3470. https://doi.org/10.1126/sciadv.abe3470
Dasouki, M., Alaiya, A., ElAmin, T., Shinwari, Z., Monies, D., Abouelhoda, M., … Ahmed, S. O. (2021). Comprehensive multi-omics analysis of G6PC3 deficiency-related congenital neutropenia with inflammatory bowel disease. iScience, 24(3), 102214. https://doi.org/10.1016/j.isci.2021.102214
Gui, S., Zhang, X., Zhong, P., Qiu, S., Wu, M., Ye, J., … Liu, J. (2021). PINE: Universal Deep Embedding for Graph Nodes via Partial Permutation Invariant Set Functions. IEEE Transactions on Pattern Analysis and Machine Intelligence, 1–1. https://doi.org/10.1109/tpami.2021.3061162
Aldosari, M. N., Yalamanchi, K. K., Gao, X., & Sarathy, S. M. (2021). Predicting entropy and heat capacity of hydrocarbons using machine learning. Energy and AI, 4, 100054. https://doi.org/10.1016/j.egyai.2021.100054
Weerts, M. J. A., Lanko, K., Guzmán-Vega, F. J., Jackson, A., Ramakrishnan, R., Cardona-Londoño, K. J., … Kievit, A. (2021). Delineating the molecular and phenotypic spectrum of the SETD1B-related syndrome. https://doi.org/10.1101/2021.02.11.430742
Han, P., Shang, S., Sun, A., Zhao, P., Zheng, K., & Zhang, X. (2021). Point-of-Interest Recommendation with Global and Local Context. IEEE Transactions on Knowledge and Data Engineering, 1–1. https://doi.org/10.1109/tkde.2021.3059744
Martin, C., Zhang, Q., Zhai, D., Zhang, X., & Duarte, C. M. (2021). Enabling a large-scale assessment of litter along Saudi Arabian red sea shores by combining drones and machine learning. Environmental Pollution, 277, 116730. https://doi.org/10.1016/j.envpol.2021.116730
Hala, S., Antony, C. P., Momin, A. A., Alshehri, M., Ben-Rached, F., Al-Ahmadi, G., … Pain, A. (2021). Co-occurrence of mcr-1 and mcr-8 genes in multi-drug-resistant Klebsiella pneumoniae from a 2015 clinical isolate. International Journal of Antimicrobial Agents, 57(3), 106303. https://doi.org/10.1016/j.ijantimicag.2021.106303
Hoshino, K., Maeshiro, T., Nishida, N., Sugiyama, M., Fujita, J., Gojobori, T., & Mizokami, M. (2021). Transmission dynamics of SARS-CoV-2 on the Diamond Princess uncovered using viral genome sequence analysis. Gene, 779, 145496. https://doi.org/10.1016/j.gene.2021.145496
Kaidarova, B. A., Liu, W., Swanepoel, L., Almansouri, A., Geraldi, N. R., Duarte, C. M., & Kosel, J. (2021). Flexible Hall sensor made of laser-scribed graphene. Npj Flexible Electronics, 5(1). https://doi.org/10.1038/s41528-021-00100-4
Ahmed, W. W., Farhat, M., Zhang, X., & Wu, Y. (2021). Deterministic and probabilistic deep learning models for inverse design of broadband acoustic cloak. Physical Review Research, 3(1). https://doi.org/10.1103/physrevresearch.3.013142
Lim, K. K., Rossbach, S., Geraldi, N. R., Serrão, E. A., & Duarte, C. M. (2021). Phylogeographic Analysis Suggests a Recent Population Bottleneck in the Rare Red Sea Tridacna squamosina. Frontiers in Marine Science, 8. https://doi:10.3389/fmars.2021.628142
Xiao, X., Agustí, S., Yu, Y., Huang, Y., Chen, W., Hu, J., … Duarte, C. M. (2021). Seaweed farms provide refugia from ocean acidification. Science of The Total Environment, 776, 145192. https://doi.org/10.1016/j.scitotenv.2021.145192
Mankowski, M., & Moshkov, M. (2021). Dynamic Programming Multi-Objective Combinatorial Optimization. Studies in Systems, Decision and Control. https://doi.org/10.1007/978-3-030-63920-4
Alam, I., Radovanovic, A., Incitti, R., Kamau, A. A., Alarawi, M., Azhar, E. I., & Gojobori, T. (2021). CovMT: an interactive SARS-CoV-2 mutation tracker, with a focus on critical variants. The Lancet Infectious Diseases. https://doi.org/10.1016/s1473-3099(21)00078-5
Li, Y., Xu, Z., Han, W., Cao, H., Umarov, R., Yan, A., … Gao, X. (2021). HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes. Microbiome, 9(1). doi:10.1186/s40168-021-01002-3
Ben Nasser, B., Djemai, M., Defoort, M., & Laleg-Kirati, T.-M. (2021). Time scale state feedback h-stabilisation of linear systems under Lipschitz-type disturbances. International Journal of Systems Science, 52(8), 1719–1729. https://doi.org/10.1080/00207721.2020.1869345
Li, C., Gao, X., & Sun, Q. (2021). Introduction of Progress in Education under Recent Technology Revolution. Mobile Networks and Applications. https://doi.org/10.1007/s11036-021-01732-6
Vaqué, D., Boras, J. A., Arrieta, J. M., Agustí, S., Duarte, C. M., & Sala, M. M. (2021). Enhanced Viral Activity in the Surface Microlayer of the Arctic and Antarctic Oceans. Microorganisms, 9(2), 317. https://doi.org/10.3390/microorganisms9020317
Duarte, C. M., Chapuis, L., Collin, S. P., Costa, D. P., Devassy, R. P., Eguiluz, V. M., … Juanes, F. (2021). The soundscape of the Anthropocene ocean. Science, 371(6529), eaba4658. https://doi.org/10.1126/science.aba4658
De Smit, J. C., Anton, A., Martin, C., Rossbach, S., Bouma, T. J., & Duarte, C. M. (2021). Habitat-forming species trap microplastics into coastal sediment sinks. Science of The Total Environment, 145520. https://doi:10.1016/j.scitotenv.2021.145520
Shijie Zhang, Hongzhi Yin, Tong Chen, Zi Huang, Lizhen Cui, Xiangliang Zhang, (2021). Graph Embedding for Recommendation against Attribute Inference Attacks. arXiv. Doi: 2101.12549
Althagafi, A., Alsubaie, L., Kathiresan, N., Mineta, K., Aloraini, T., Almutairi, F., … Hoehndorf, R. (2021). DeepSVP: Integration of genotype and phenotype for structural variant prioritization using deep learning. https://doi.org/10.1101/2021.01.28.428557
zhu, Yongchun & Zhuang, Fuzhen & Zhang, Xiangliang & Qi, Zhiyuan & Shi, Zhiping & He, Qing. (2021). Combat Data Shift in Few-shot Learning with Knowledge Graph. Ariv. Doi: 2101.11354
Gallagher, A. J., Shipley, O. N., van Zinnicq Bergmann, M. P. M., Brownscombe, J. W., Dahlgren, C. P., Frisk, M. G., … Duarte, C. M. (2021). Spatial Connectivity and Drivers of Shark Habitat Use Within a Large Marine Protected Area in the Caribbean, The Bahamas Shark Sanctuary. Frontiers in Marine Science, 7. https://doi:10.3389/fmars.2020.608848
Albuquerque, R., Bode, A., González-Gordillo, J. I., Duarte, C. M., & Queiroga, H. (2021). Trophic Structure of Neuston Across Tropical and Subtropical Oceanic Provinces Assessed With Stable Isotopes. Frontiers in Marine Science, 7. doi:10.3389/fmars.2020.606088
Alam, I., Radovanovic, A., Incitti, R., Kamau, A., Alarawi, M., Azhar, E. I., & Gojobori, T. (2021). An interactive COVID-19 virus Mutation Tracker (CovMT) with a particular focus on critical mutations in the Receptor Binding Domain (RBD) region of the Spike protein. https://doi.org/10.1101/2021.01.22.21249716
Susapto, H. H., Alhattab, D., Abdelrahman, S., Khan, Z., Alshehri, S., Kahin, K., … Hauser, C. A. E. (2021). Ultrashort Peptide Bioinks Support Automated Printing of Large-Scale Constructs Assuring Long-Term Survival of Printed Tissue Constructs. Nano Letters, 21(7), 2719–2729. https://doi.org/10.1021/acs.nanolett.0c04426
Xiao, Lin & Zhang, Xiangliang & Jing, Liping & Huang, Chi & Song, Mingyang. (2021). Does Head Label Help for Long-Tailed Multi-Label Text Classification. arXiv. Doi: 2101.09704
Yu, Junliang & Yin, Hongzhi & Li, Jundong & Wang, Qinyong & Hung, Nguyen & Zhang, Xiangliang. (2021). Self-Supervised Multi-Channel Hypergraph Convolutional Network for Social Recommendation. arXiv. Doi: 2101.06448
Chaib-Draa, K., Zemouche, A., Bedouhene, F., Rajamani, R., Wang, Y., Karimi, H. R., & Laleg-Kirati, T. M. (2021). Finite-time estimation algorithms for LPV discrete-time systems with application to output feedback stabilization. Automatica, 125, 109436. https://doi.org/10.1016/j.automatica.2020.109436
Dennison, W. C., Bracken, M. E. S., Brown, M., Bruno, J. F., Carlton, J. T., Carpenter, R. C., … Waycott, M. (2021). Susan Lynn Williams: the Life of an Exceptional Scholar, Leader, and Friend (1951–2018). Estuaries and Coasts, 44(2), 304–311. https://doi.org/10.1007/s12237-020-00886-y
Cziesielski, M. J., Duarte, C. M., Aalismail, N., Al-Hafedh, Y., Anton, A., Baalkhuyur, F., … Aranda, M. (2021). Investing in Blue Natural Capital to Secure a Future for the Red Sea Ecosystems. Frontiers in Marine Science, 7. https://doi:10.3389/fmars.2020.603722
Guo, X.-G., Hong, P.-Y., & Laleg-Kirati, T.-M. (2021). Calibration and validation for a real-time membrane bioreactor: A sliding window approach. Journal of Process Control, 98, 92–105. https://doi.org/10.1016/j.jprocont.2020.11.013
Rossbach, S., Anton, A., & Duarte, C. M. (2021). Drivers of the Abundance of Tridacna spp. Giant Clams in the Red Sea. Frontiers in Marine Science, 7. https://doi.org/10.3389/fmars.2020.592852
Kuwahara, H., & Gao, X. (2021). Stable maintenance of hidden switches as a strategy to increase the gene expression stability. Nature Computational Science, 1(1), 62–70. https://doi.org/10.1038/s43588-020-00001-y
Kuwahara, H., & Gao, X. (2021). Stable maintenance of hidden switches as a strategy to increase the gene expression stability. Nature Computational Science, 1(1), 62–70. https://doi.org/10.1038/s43588-020-00001-y
Nasser, B., Saito, Y., Alarawi, M., Humam, A. A., Mineta, K., & Gojobori, T. (2021). Characterization of microbiologically influenced corrosion by comprehensive metagenomic analysis of an inland oil field. Gene, 145425. doi:10.1016/j.gene.2021.145425
Sampaio, E., Santos, C., Rosa, I. C., Ferreira, V., Pörtner, H.-O., Duarte, C. M., … Rosa, R. (2021). Impacts of hypoxic events surpass those of future ocean warming and acidification. Nature Ecology & Evolution, 5(3), 311–321. https://doi.org/10.1038/s41559-020-01370-3
Mineta, K., Goto, K., Gojobori, T., & Alkuraya, F. S. (2021). Population structure of indigenous inhabitants of Arabia. PLOS Genetics, 17(1), e1009210. https://doi.org/10.1371/journal.pgen.1009210
Rayapuram, N., Jarad, M., Alhoraibi, H. M., Bigeard, J., Abulfaraj, A. A., Völz, R., … Hirt, H. (2021). Chromatin phosphoproteomics unravels a function for AT-hook motif nuclear localized protein AHL13 in PAMP-triggered immunity. Proceedings of the National Academy of Sciences, 118(3), e2004670118. https://doi.org/10.1073/pnas.2004670118
Salamina, M., Montefiore, B. C., Liu, M., Wood, D. J., Heath, R., Ault, J. R., … Endicott, J. A. (2021). Discriminative SKP2 Interactions with CDK-Cyclin Complexes Support a Cyclin A-Specific Role in p27KIP1 Degradation. Journal of Molecular Biology, 433(5), 166795. https://doi.org/10.1016/j.jmb.2020.166795
Garcia-Corral, L. S., Duarte, C. M., & Agusti, S. (2021). Plankton Community Metabolism in Western Australia: Estuarine, Coastal and Oceanic Surface Waters. Frontiers in Marine Science, 7. https://doi.org/10.3389/fmars.2020.582136
Alghamdi, M. A., Mulla, J., Saheb Sharif-Askari, N., Guzmán-Vega, F. J., Arold, S. T., Abd-Alwahed, M., … Halwani, R. (2021). A Novel Biallelic STING1 Gene Variant Causing SAVI in Two Siblings. Frontiers in Immunology, 11. https://doi.org/10.3389/fimmu.2020.599564
Han, R., Li, G., & Gao, X. (2021). Robust and ultrafast fiducial marker correspondence in electron tomography by a two-stage algorithm considering local constraints. Bioinformatics, 37(1), 107–117. https://doi.org/10.1093/bioinformatics/btaa1098
Zhao, X., Shahul Hameed, U. F., Kharchenko, V., Liao, C., Huser, F., Remington, J. M., … Li, J. (2021). Molecular basis for the adaptive evolution of environment-sensing by H-NS proteins. eLife, 10. https://doi.org/10.7554/elife.57467
Ye, G., Yin, H., Chen, T., Chen, H., Cui, L., & Zhang, X. (2021). FENet: A Frequency Extraction Network for Obstructive Sleep Apnea Detection. IEEE Journal of Biomedical and Health Informatics, 1–1. https://doi.org/10.1109/jbhi.2021.3050113
Zhang, L., Fan, M., Napolitano, F., Gao, X., Xu, Y., & Li, L. (2021). Transcriptomic analysis identifies organ-specific metastasis genes and pathways across different primary sites. Journal of Translational Medicine, 19(1). https://doi.org/10.1186/s12967-020-02696-z
Zhang, L., Zhang, D., Wang, X., Yuan, C., Li, Y., Jia, X., … Huang, X. (2021). 1′-Ribose cyano substitution allows Remdesivir to effectively inhibit nucleotide addition and proofreading during SARS-CoV-2 viral RNA replication. Physical Chemistry Chemical Physics, 23(10), 5852–5863. https://doi.org/10.1039/d0cp05948j
Alzanbaki, H., Moretti, M., & Hauser, C. A. E. (2021). Engineered Microgels—Their Manufacturing and Biomedical Applications. Micromachines, 12(1), 45. https://doi.org/10.3390/mi12010045
Zhang, Y. (2021). Computation Offloading and Service Caching in Heterogeneous MEC Wireless Networks. KAUST Research Repository. https://doi.org/10.25781/KAUST-DQ447
Klevjer, T. A., Martinez, U., Boyra, G., Røstad, A., Kaartvedt, S., & Irigoien, X. (2021). Per station summaries of acoustic water column properties during MALASPINA-2010 [Data set]. PANGAEA - Data Publisher for Earth & Environmental Science. https://doi.org/10.1594/PANGAEA.926619
Zhang, Z. (2021). Improving the Self-Consistent Field Initial Guess Using a 3D Convolutional Neural Network. KAUST Research Repository. https://doi.org/10.25781/KAUST-542XY

2020

Piliouras, E., & Laleg-Kirati, T.-M. (2020). Quantum-based interval selection of the Semi-classical Signal Analysis method. 2020 28th European Signal Processing Conference (EUSIPCO). https://doi.org/10.23919/eusipco47968.2020.9287878
Zhou, G., Wang, J., Zhang, X., Guo, M., & Yu, G. (2020). Predicting functions of maize proteins using graph convolutional network. BMC Bioinformatics, 21(S16). https://doi.org/10.1186/s12859-020-03745-6
Alam, I., Kamau, A., Gugi, D., Gojobori, T., Duarte, C., & Bajic, V. (2020). KAUST Metagenomic Analysis Platform (KMAP), Enabling Access to Massive Analytics of Re-Annotated Metagenomic Data. Journal is Scientific Reports, https://doi.org/10.1038/s41598-021-90799-y
Garcias‐Bonet, N., Eguíluz, V. M., Díaz‐Rúa, R., & Duarte, C. M. (2020). Host‐association as major driver of microbiome structure and composition in Red Sea seagrass ecosystems. Environmental Microbiology. https://doi.org/10.1111/1462-2920.15334
Mineta, K., Goto, K., Gojobori, T., & Alkuraya, F. S. (2020). Indigenous Arabs have an intermediate frequency of a Neanderthal‐derived COVID ‐19 risk haplotype compared with other world populations. Clinical Genetics, 99(3), 484–485. https://doi.org/10.1111/cge.13885
Karan, R., Mathew, S., Muhammad, R., Bautista, D. B., Vogler, M., Eppinger, J., … Rueping, M. (2020). Understanding High-Salt and Cold Adaptation of a Polyextremophilic Enzyme. Microorganisms, 8(10), 1594. https://doi.org/10.3390/microorganisms8101594
Chen, J., Althagafi, A., & Hoehndorf, R. (2020). Predicting candidate genes from phenotypes, functions and anatomical site of expression. Bioinformatics. https://doi.org/10.1093/bioinformatics/btaa879
Hawerkamp, H. C., van Geelen, L., Korte, J., Di Domizio, J., Swidergall, M., Momin, A. A., … Meller, S. (2020). Interleukin-26 activates macrophages and facilitates killing of Mycobacterium tuberculosis. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-73989-y
Yu, G., Liu, X., Wang, J., Domeniconi, C., & Zhang, X. (2020). Flexible Cross-Modal Hashing. IEEE Transactions on Neural Networks and Learning Systems, 1–11. https://doi.org/10.1109/tnnls.2020.3027729
Kulmanov, M., Smaili, F. Z., Gao, X., & Hoehndorf, R. (2020). Semantic similarity and machine learning with ontologies. Briefings in Bioinformatics. https://doi.org/10.1093/bib/bbaa199
Arold, S. T. (2020). Intrinsic negative feedback as a limiting factor for the evolution of higher forms of intelligence. F1000Research, 9, 34. https://doi.org/10.12688/f1000research.22039.2
Duarte, C. M., Ngugi, D. K., Alam, I., Pearman, J., Kamau, A., Eguiluz, V. M., … Irigoien, X. (2020). Sequencing effort dictates gene discovery in marine microbial metagenomes. Environmental Microbiology, 22(11), 4589–4603. https://doi.org/10.1111/1462-2920.15182
Zaric, B. L., Radovanovic, J. N., Gluvic, Z., Stewart, A. J., Essack, M., Motwalli, O., … Isenovic, E. R. (2020). Atherosclerosis Linked to Aberrant Amino Acid Metabolism and Immunosuppressive Amino Acid Catabolizing Enzymes. Frontiers in Immunology, 11. https://doi.org/10.3389/fimmu.2020.551758
Fu, C., Li, Y., Zeng, L., Zhang, H., Tu, C., Zhou, Q., … Luo, Y. (2020). Stocks and losses of soil organic carbon from Chinese vegetated coastal habitats. Global Change Biology, 27(1), 202–214. https://doi.org/10.1111/gcb.15348
Tietbohl, M. D., Hardenstine, R. S., Tanabe, L. K., Hulver, A. M., & Berumen, M. L. (2020). Intentional partial beaching in a coral reef fish: a newly recorded hunting behaviour of titan triggerfish, Balistoides viridescens. Journal of Fish Biology, 97(5), 1569–1572. https://doi.org/10.1111/jfb.14513
Ou, G., Yu, G., Domeniconi, C., Lu, X., & Zhang, X. (2020). Multi-label zero-shot learning with graph convolutional networks. Neural Networks, 132, 333–341. https://doi.org/10.1016/j.neunet.2020.09.010
Luo, J. Y., Condon, R. H., Stock, C. A., Duarte, C. M., Lucas, C. H., Pitt, K. A., & Cowen, R. K. (2020). Gelatinous Zooplankton‐Mediated Carbon Flows in the Global Oceans: A Data‐Driven Modeling Study. Global Biogeochemical Cycles, 34(9). https://doi.org/10.1029/2020gb006704
Laptenok, S. P., Martin, C., Genchi, L., Duarte, C. M., & Liberale, C. (2020). Stimulated Raman microspectroscopy as a new method to classify microfibers from environmental samples. Environmental Pollution, 267, 115640. https://doi.org/10.1016/j.envpol.2020.115640
Alghamdi, M., Bashiri, F. A., Abdelhakim, M., Adly, N., Jamjoom, D. Z., Sumaily, K. M., … Arold, S. T. (2020). Phenotypic and molecular spectrum of pyridoxamine‐5′‐phosphate oxidase deficiency: A scoping review of 87 cases of pyridoxamine‐5′‐phosphate oxidase deficiency. Clinical Genetics, 99(1), 99–110. https://doi.org/10.1111/cge.13843
Herrera, M., Klein, S. G., Campana, S., Chen, J. E., Prasanna, A., Duarte, C. M., & Aranda, M. (2020). Temperature transcends partner specificity in the symbiosis establishment of a cnidarian. The ISME Journal, 15(1), 141–153. https://doi.org/10.1038/s41396-020-00768-y
Umair, M., Ballow, M., Asiri, A., Alyafee, Y., Tuwaijri, A., Alhamoudi, K. M., … Alfadhel, M. (2020). EMC10 homozygous variant identified in a family with global developmental delay, mild intellectual disability, and speech delay. Clinical Genetics, 98(6), 555–561. https://doi.org/10.1111/cge.13842
Auffray, C., Balling, R., Blomberg, N., Bonaldo, M. C., Boutron, B., Brahmachari, S., … Clément, K. (2020). COVID-19 and beyond: a call for action and audacious solidarity to all the citizens and nations, it is humanity’s fight. F1000Research, 9, 1130. https://doi.org/10.12688/f1000research.26098.1
Alam, I., Aalismail, N., Martin, C., Kamau, A., Guzmán-Vega, F. J., Jamil, T., … Duarte, C. M. (2020). Rapid Evolution of Plastic-degrading Enzymes Prevalent in the Global Ocean. https://doi.org/10.1101/2020.09.07.285692
Abdel-Haleem, A. M., Ravikumar, V., Ji, B., Mineta, K., Gao, X., Nielsen, J., … Mijakovic, I. (2020). Integrated Metabolic Modeling, Culturing, and Transcriptomics Explain Enhanced Virulence of Vibrio cholerae during Coinfection with Enterotoxigenic Escherichia coli. mSystems, 5(5). https://doi.org/10.1128/msystems.00491-20
Li, P., & Laleg-Kirati, T.-M. (2020). Schrödinger Spectrum Based PPG Features for the Estimation of the Arterial Blood Pressure. 2020 42nd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC). https://doi.org/10.1109/embc44109.2020.9176849
Magbool, A., Bahloul, M. A., Ballal, T., Al-Naffouri, T. Y., & Laleg-Kirati, T.-M. (2020). Blind Estimation of Central Blood Pressure Using Least-Squares with Mean Matching and Box Constraints. 2020 42nd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC). https://doi.org/10.1109/embc44109.2020.9176258
Chahid, A., Khushaba, R., Al-Jumaily, A., & Laleg-Kirati, T.-M. (2020). A Position Weight Matrix Feature Extraction Algorithm Improves Hand Gesture Recognition. 2020 42nd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC). https://doi.org/10.1109/embc44109.2020.9176097
Jamil, T., Alam, I., Gojobori, T., & Duarte, C. M. (2020). No Evidence for Temperature-Dependence of the COVID-19 Epidemic. Frontiers in Public Health, 8. https://doi.org/10.3389/fpubh.2020.00436
Bahloul, M. A., Chahid, A., & Laleg-Kirati, T.-M. (2020). Fractional-Order SEIQRDP Model for Simulating the Dynamics of COVID-19 Epidemic. IEEE Open Journal of Engineering in Medicine and Biology, 1, 249–256. https://doi.org/10.1109/ojemb.2020.3019758
Guan, Q., Sadykov, M., Mfarrej, S., Hala, S., Naeem, R., Nugmanova, R., … Pain, A. (2020). A genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic. International Journal of Infectious Diseases, 100, 216–223. https://doi.org/10.1016/j.ijid.2020.08.052
Mankowski, M., & Moshkov, M. (2020). Extensions of dynamic programming for multi-stage combinatorial optimization. Theoretical Computer Science, 844, 106–132. https://doi.org/10.1016/j.tcs.2020.08.009
Schmidt-Roach, S., Duarte, C. M., Hauser, C. A. E., & Aranda, M. (2020). Beyond Reef Restoration: Next-Generation Techniques for Coral Gardening, Landscaping, and Outreach. Frontiers in Marine Science, 7. https://doi.org/10.3389/fmars.2020.00672
Alam, I., Kamau, A. A., Kulmanov, M., Jaremko, Ł., Arold, S. T., Pain, A., … Duarte, C. M. (2020). Functional Pangenome Analysis Shows Key Features of E Protein Are Preserved in SARS and SARS-CoV-2. Frontiers in Cellular and Infection Microbiology, 10. https://doi.org/10.3389/fcimb.2020.00405
Alfares, A., Alsubaie, L., Aloraini, T., Alaskar, A., Althagafi, A., Alahmad, A., … Alfadhel, M. (2020). What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations. BMC Medical Genomics, 13(1). https://doi.org/10.1186/s12920-020-00743-8
Liu, A., Zhang, Y., Zhang, X., Liu, G., Zhang, Y., Li, Z., … Zhou, X. (2020). Representation Learning with Multi-level Attention for Activity Trajectory Similarity Computation. IEEE Transactions on Knowledge and Data Engineering, 1–1. https://doi.org/10.1109/tkde.2020.3010022
Ghattassi, M., Laleg, T.-M., & Vivalda, J.-C. (2020). Analysis and output tracking design for the direct contact membrane distillation parabolic system. Journal of Mathematical Analysis and Applications, 491(2), 124367. https://doi.org/10.1016/j.jmaa.2020.124367
X. Guo, P. Hong, and T. M. Laleg-Kirati, (2020) Nonlinear Model Predictive Control Design for BSM-MBR: Benchmark of Membrane Bioreactor, IFAC World Congress, Berlin,