2023

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
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
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
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

2022

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). 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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

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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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: 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: 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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., 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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, 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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

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
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
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
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
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
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
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
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
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
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
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
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
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,
Ghaffour, Lilia & Noack, Matti & Reger, Johann & Laleg-Kirati, Taous-Meriem. (2020). Non-asymptotic State Estimation of Linear Reaction Diffusion Equation using Modulating Functions.
Yamamoto, N., Ariumi, Y., Nishida, N., Yamamoto, R., Bauer, G., Gojobori, T., … Mizokami, M. (2020). SARS-CoV-2 infections and COVID-19 mortalities strongly correlate with ACE1 I/D genotype. Gene, 758, 144944. https://doi.org/10.1016/j.gene.2020.144944
Ni, M., Tresset, G., Iliescu, C., & Hauser, C. A. E. (2020). Ultrashort Peptide Theranostic Nanoparticles by Microfluidic-Assisted Rapid Solvent Exchange. IEEE Transactions on NanoBioscience, 19(4), 627–632. https://doi.org/10.1109/tnb.2020.3007103
Albalawi, F., Alshehri, S., Chahid, A., & Laleg-Kirati, T.-M. (2020). Voxel Weight Matrix-Based Feature Extraction for Biomedical Applications. IEEE Access, 8, 121451–121459. https://doi.org/10.1109/access.2020.3006521
Yu, G., Wang, Y., Wang, J., Domeniconi, C., Guo, M., & Zhang, X. (2020). Attributed heterogeneous network fusion via collaborative matrix tri-factorization. Information Fusion, 63, 153–165. https://doi.org/10.1016/j.inffus.2020.06.012
Yu, G., Chen, X., Domeniconi, C., Wang, J., Li, Z., Zhang, Z., & Zhang, X. (2020). CMAL: Cost-effective Multi-label Active Learning by Querying Subexamples. IEEE Transactions on Knowledge and Data Engineering, 1–1. https://doi.org/10.1109/tkde.2020.3003899
Queralt-Rosinach, N., Bello, S. M., Hoehndorf, R., Weiland, C., Rocca-Serra, P., & Schofield, P. N. (2020). Modeling quantitative traits for COVID-19 case reports. https://doi.org/10.1101/2020.06.18.20135103
Vu, T.-D., Iwasaki, Y., Shigenobu, S., Maruko, A., Oshima, K., Iioka, E., … Okada, N. (2020). Behavioral and brain- transcriptomic synchronization between the two opponents of a fighting pair of the fish Betta splendens. PLOS Genetics, 16(6), e1008831. https://doi.org/10.1371/journal.pgen.1008831
Abdelhakim, M., McMurray, E., Syed, A. R., Kafkas, S., Kamau, A. A., Schofield, P. N., & Hoehndorf, R. (2020). DDIEM: drug database for inborn errors of metabolism. Orphanet Journal of Rare Diseases, 15(1). https://doi.org/10.1186/s13023-020-01428-2
Zhou, L., Li, Z., Zhou, J., Li, H., Chen, Y., Huang, Y., … Gao, X. (2020). A Rapid, Accurate and Machine-Agnostic Segmentation and Quantification Method for CT-Based COVID-19 Diagnosis. IEEE Transactions on Medical Imaging, 39(8), 2638–2652. https://doi.org/10.1109/tmi.2020.3001810
S. Asiri, D. Liu and T. Laleg-Kirati, (2020) Selection of Modulating Functions' Design Parameters for Estimation Problems, IEEE Control Systems Letters, vol. 5, no. 1, pp. 277-282, doi: 10.1109/LCSYS.2020.3000849.
Moraga, P., Ketcheson, D. I., Ombao, H. C., & Duarte, C. M. (2020). Assessing the age- and gender-dependence of the severity and case fatality rates of COVID-19 disease in Spain. Wellcome Open Research, 5, 117. https://doi.org/10.12688/wellcomeopenres.15996.1
Friis, G., Vizueta, J., Nelson, D. R., Khraiwesh, B., Qudeimat, E., Salehi-Ashtiani, K., … Burt, J. A. (2020). A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina. https://doi.org/10.1101/2020.05.30.124800
Zhang, Y., Liu, G., Liu, A., Zhang, Y., Li, Z., Zhang, X., & Li, Q. (2020). Personalized Geographical Influence Modeling for POI Recommendation. IEEE Intelligent Systems, 35(5), 18–27. https://doi.org/10.1109/mis.2020.2998040
Zhang, D., N’Doye, I., Ballal, T., Al-Naffouri, T. Y., Alouini, M.-S., & Laleg-Kirati, T.-M. (2020). Localization and Tracking Control Using Hybrid Acoustic–Optical Communication for Autonomous Underwater Vehicles. IEEE Internet of Things Journal, 7(10), 10048–10060. https://doi.org/10.1109/jiot.2020.2995799
Slater, L. T., Gkoutos, G. V., & Hoehndorf, R. (2020). Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies. https://doi.org/10.1101/2020.05.16.099309
Ketcheson, D. I., Ombao, H. C., Moraga, P., Ballal, T., & Duarte, C. M. (2020). Estimating and forecasting COVID-19 attack rates and mortality. https://doi.org/10.1101/2020.05.11.20097972
Albaradei, S., Magana-Mora, A., Thafar, M., Uludag, M., Bajic, V. B., Gojobori, T., … Jankovic, B. R. (2020). Splice2Deep: An ensemble of deep convolutional neural networks for improved splice site prediction in genomic DNA. Gene: X, 5, 100035. https://doi.org/10.1016/j.gene.2020.100035
Chen, H., Ballal, T., Muqaibel, A. H., Zhang, X., & Al-Naffouri, T. Y. (2020). Air-writing via Receiver Array Based Ultrasonic Source Localization. IEEE Transactions on Instrumentation and Measurement, 1–1. https://doi.org/10.1109/tim.2020.2991573
Mankowski, M., & Moshkov, M. (2020). Dynamic programming bi-criteria combinatorial optimization. Discrete Applied Mathematics, 284, 513–533. https://doi.org/10.1016/j.dam.2020.04.016
Liu-Wei, W., Kafkas, Ş., Chen, J., Dimonaco, N., Tegnér, J., & Hoehndorf, R. (2020). DeepViral: infectious disease phenotypes improve prediction of novel virus–host interactions. https://doi.org/10.1101/2020.04.22.055095
Bahloul, M. A., & Laleg-Kirati, T.-M. (2020). Assessment of Fractional-Order Arterial Windkessel as a Model of Aortic Input Impedance. IEEE Open Journal of Engineering in Medicine and Biology, 1, 123–132. https://doi.org/10.1109/ojemb.2020.2988179
Han, Y., & Zhang, X. (2020). Robust Federated Learning via Collaborative Machine Teaching. Proceedings of the AAAI Conference on Artificial Intelligence, 34(04), 4075–4082. https://doi.org/10.1609/aaai.v34i04.5826
Essack, M., Salhi, A., Van Neste, C., Raies, A. B., Tifratene, F., Uludag, M., … Bajic, V. P. (2020). DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases. Oxidative Medicine and Cellular Longevity, 2020, 1–13. https://doi.org/10.1155/2020/5904315
Wang, K., Wang, J., Domeniconi, C., Zhang, X., & Yu, G. (2019). Differentiating isoform functions with collaborative matrix factorization. Bioinformatics. https://doi.org/10.1093/bioinformatics/btz847
Moshkov, M. (2020). Comparative Analysis of Deterministic and Nondeterministic Decision Trees. Intelligent Systems Reference Library. https://doi.org/10.1007/978-3-030-41728-4
Gentry, S., Mankowski, M. A., & Michael, T. S. (2020). Maximum matchings in graphs for allocating kidney paired donation. Operations Research for Health Care, 25, 100246. https://doi.org/10.1016/j.orhc.2020.100246
Nishikawa, Y., Kogawa, M., Hosokawa, M., Mineta, K., Takahashi, K., Sakanashi, C., … Takeyama, H. (2020). Massively parallel single-cell genome sequencing enables high-resolution analysis of soil and marine microbiome. https://doi.org/10.1101/2020.03.05.962001
Chen, Y., Pu, J., Liu, X., & Zhang, X. (2019). Gaussian mixture embedding of multiple node roles in networks. World Wide Web. doi:10.1007/s11280-019-00743-4
Vos, R. A., Katayama, T., Mishima, H., Kawano, S., Kawashima, S., Kim, J.-D., … Yamamoto, Y. (2020). BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000Research, 9, 136. https://doi.org/10.12688/f1000research.18236.1
alam, I., Kamau, A., Kulmanov, M., Arold, S. T., Pain, A., Gojobori, T., & Duarte, C. M. (2020). Functional pangenome analysis suggests inhibition of the protein E as a readily available therapy for COVID-2019. https://doi.org/10.1101/2020.02.17.952895
Elkhalil, K., Kammoun, A., Zhang, X., Alouini, M.-S., & Al-Naffouri, T. Y. (2020). Risk Convergence of Centered Kernel Ridge Regression with Large Dimensional Data. ICASSP 2020 - 2020 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP). doi:10.1109/icassp40776.2020.9053349
Baalkhuyur, F. M., Qurban, M. A., Panickan, P., & Duarte, C. M. (2020). Microplastics in fishes of commercial and ecological importance from the Western Arabian Gulf. Marine Pollution Bulletin, 152, 110920. https://doi.org/10.1016/j.marpolbul.2020.110920
Chahid, A., Albalawi, F., Alotaiby, T. N., Al-Hameed, M. H., Alshebeili, S., & Laleg-Kirati, T.-M. (2020). QuPWM: Feature Extraction Method for Epileptic Spike Classification. IEEE Journal of Biomedical and Health Informatics, 24(10), 2814–2824. https://doi.org/10.1109/jbhi.2020.2972286
AlMuhaizea, M., AlMass, R., AlHargan, A., AlBader, A., Medico Salsench, E., Howaidi, J., … Kaya, N. (2020). Truncating mutations in YIF1B cause a progressive encephalopathy with various degrees of mixed movement disorder, microcephaly, and epilepsy. Acta Neuropathologica, 139(4), 791–794. https://doi.org/10.1007/s00401-020-02128-8
Guo, X., Albalawi, F., & Laleg-Kirati, T.-M. (2020). Observer-based Economic Model Predictive Control for Direct Contact Membrane Distillation. Chemical Engineering Research and Design, 156, 86–99. https://doi.org/10.1016/j.cherd.2020.01.027
Baldry, K., Saderne, V., McCorkle, D. C., Churchill, J. H., Agusti, S., & Duarte, C. M. (2020). Anomalies in the carbonate system of Red Sea coastal habitats. Biogeosciences, 17(2), 423–439. https://doi.org/10.5194/bg-17-423-2020
Bajic, V. P., Essack, M., Zivkovic, L., Stewart, A., Zafirovic, S., Bajic, V. B., … Spremo-Potparevic, B. (2020). The X Files: “The Mystery of X Chromosome Instability in Alzheimer’s Disease.” Frontiers in Genetics, 10. https://doi.org/10.3389/fgene.2019.01368
Meng, Z., Liang, S., Zhang, X., McCreadie, R., & Ounis, I. (2020). Jointly Learning Representations of Nodes and Attributes for Attributed Networks. ACM Transactions on Information Systems, 38(2), 1–32. https://doi.org/10.1145/3377850
Ren, X., Yin, H., Chen, T., Wang, H., Hung, N. Q. V., Huang, Z., & Zhang, X. (2020). CRSAL. ACM Transactions on Information Systems, 38(4), 1–40. https://doi.org/10.1145/3394592
Gluvic, Z. M., Obradovic, M. M., Sudar-Milovanovic, E. M., Zafirovic, S. S., Radak, D. J., Essack, M. M., … Isenovic, E. R. (2020). Regulation of nitric oxide production in hypothyroidism. Biomedicine & Pharmacotherapy, 124, 109881. https://doi.org/10.1016/j.biopha.2020.109881
Agulles, M., Jordà, G., Jones, B., Agustí, S., & Duarte, C. M. (2020). Temporal evolution of temperatures in the Red Sea and the Gulf of Aden based on in situ observations (1958–2017). Ocean Science, 16(1), 149–166. https://doi.org/10.5194/os-16-149-2020
Geraldi, N. R., Klein, S. G., Anton, A., & Duarte, C. M. (2020). A framework for experimental scenarios of global change in marine systems using coral reefs as a case study. Royal Society Open Science, 7(1), 191118. https://doi.org/10.1098/rsos.191118
Ding, L., Liao, S., Liu, Y., Liu, L., Zhu, F., Yao, Y., … Gao, X. (2020). Approximate Kernel Selection via Matrix Approximation. IEEE Transactions on Neural Networks and Learning Systems, 31(11), 4881–4891. https://doi.org/10.1109/tnnls.2019.2958922
Bhaduri, S., Chahid, A., Achten, E., Laleg-Kirati, T.-M., & Serrai, H. (2020). SCSA based MATLAB pre-processing toolbox for 1H MR spectroscopic water suppression and denoising. Informatics in Medicine Unlocked, 18, 100294. https://doi.org/10.1016/j.imu.2020.100294
Duarte, C. M., Rodriguez-Navarro, A. B., Delgado-Huertas, A., & Krause-Jensen, D. (2020). Dense Mytilus Beds Along Freshwater-Influenced Greenland Shores: Resistance to Corrosive Waters Under High Food Supply. Estuaries and Coasts, 43(2), 387–395. https://doi.org/10.1007/s12237-019-00682-3
El-Araby, M. E., Omar, A. M., Soror, S. H., Arold, S. T., Khayat, M. T., Asfour, H. Z., … Elfaky, M. A. (2020). Synthetic bulky NS4A peptide variants bind to and inhibit HCV NS3 protease. Journal of Advanced Research, 24, 251–259. https://doi.org/10.1016/j.jare.2020.01.003
Agustí, S., Krause, J. W., Marquez, I. A., Wassmann, P., Kristiansen, S., & Duarte, C. M. (2020). Arctic (Svalbard islands) active and exported diatom stocks and cell health status. Biogeosciences, 17(1), 35–45. https://doi.org/10.5194/bg-17-35-2020

2019

Momin, A. A., Hameed, U. F. S., & Arold, S. T. (2019). Passenger sequences can promote interlaced dimers in a common variant of the maltose-binding protein. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-56718-y
Jorda, G., Marbà, N., Bennett, S., Santana-Garcon, J., Agusti, S., & Duarte, C. M. (2019). Ocean warming compresses the three-dimensional habitat of marine life. Nature Ecology & Evolution, 4(1), 109–114. https://doi.org/10.1038/s41559-019-1058-0
Geraldi, N. R., Anton, A., Santana‐Garcon, J., Bennett, S., Marbà, N., Lovelock, C. E., … Duarte, C. M. (2019). Ecological effects of non‐native species in marine ecosystems relate to co‐occurring anthropogenic pressures. Global Change Biology, 26(3), 1248–1258. https://doi.org/10.1111/gcb.14930
Eguíluz, V. M., Salazar, G., Fernández-Gracia, J., Pearman, J. K., Gasol, J. M., Acinas, S. G., … Duarte, C. M. (2019). Scaling of species distribution explains the vast potential marine prokaryote diversity. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-54936-y
Siuly, S., & Zhang, X. (2019). Guest Editorial: Special issue on “Application of artificial intelligence in health research.” Health Information Science and Systems, 8(1). https://doi.org/10.1007/s13755-019-0089-x
Jia, G., Li, Y., Zhang, H., Chattopadhyay, I., Boeck Jensen, A., Blair, D. R., … Rzhetsky, A. (2019). Estimating heritability and genetic correlations from large health datasets in the absence of genetic data. Nature Communications, 10(1). https://doi.org/10.1038/s41467-019-13455-0
Naveed, H., Reglin, C., Schubert, T., Gao, X., Arold, S. T., & Maitland, M. L. (2019). Identifying Novel Targets by using Drug-binding Site Signature: A Case Study of Kinase Inhibitors. https://doi.org/10.1101/860510
Boumenir, A., Ghattassi, M., & Laleg‐Kirati, T. M. (2019). Monitoring the temperature of a direct contact membrane distillation. Mathematical Methods in the Applied Sciences, 43(3), 1399–1408. https://doi.org/10.1002/mma.5966
Sola, J., Klein, S. G., Martin, C., Agustí, S., & Duarte, C. M. (2019). Gelatinous Zooplankton in the Surface Layers of the Coastal Central Red Sea. Frontiers in Marine Science, 6. https://doi.org/10.3389/fmars.2019.00726
Alghamdi, M., Al Khalifah, R., Al Homyani, D. K., Alkhamis, W. H., Arold, S. T., Ekhzaimy, A., … Halwani, R. (2019). A Novel TBX1 Variant Causing Hypoparathyroidism and Deafness. Journal of the Endocrine Society, 4(2). https://doi.org/10.1210/jendso/bvz028
Chen, Y., Pu, J., Liu, X., & Zhang, X. (2019). Gaussian mixture embedding of multiple node roles in networks. World Wide Web, 23(2), 927–950. https://doi.org/10.1007/s11280-019-00743-4
Rossbach, S., Cardenas, A., Perna, G., Duarte, C. M., & Voolstra, C. R. (2019). Tissue-Specific Microbiomes of the Red Sea Giant Clam Tridacna maxima Highlight Differential Abundance of Endozoicomonadaceae. Frontiers in Microbiology, 10. https://doi.org/10.3389/fmicb.2019.02661
Garrabou, J., Gómez-Gras, D., Ledoux, J.-B., Linares, C., Bensoussan, N., López-Sendino, P., … Grimes, S. (2019). Collaborative Database to Track Mass Mortality Events in the Mediterranean Sea. Frontiers in Marine Science, 6. https://doi.org/10.3389/fmars.2019.00707
Althubaiti, S., Karwath, A., Dallol, A., Noor, A., Alkhayyat, S. S., Alwassia, R., … Hoehndorf, R. (2019). Ontology-based prediction of cancer driver genes. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-53454-1
Rabaoui, L., Cusack, M., Saderne, V., Krishnakumar, P. K., Lin, Y.-J., Shemsi, A. M., … Qurban, M. A. (2020). Anthropogenic-induced acceleration of elemental burial rates in blue carbon repositories of the Arabian Gulf. Science of The Total Environment, 719, 135177. https://doi.org/10.1016/j.scitotenv.2019.135177
Qashqari, M. S., Garcias-Bonet, N., Fusi, M., Booth, J. M., Daffonchio, D., & Duarte, C. M. (2020). High temperature and crab density reduce atmospheric nitrogen fixation in Red Sea mangrove sediments. Estuarine, Coastal and Shelf Science, 232, 106487. https://doi.org/10.1016/j.ecss.2019.106487
Klein, S. G., Steckbauer, A., & Duarte, C. M. (2019). Defining CO2and O2syndromes of marine biomes in the Anthropocene. Global Change Biology, 26(2), 355–363. https://doi.org/10.1111/gcb.14879
Tan, Q., Yu, G., Wang, J., Domeniconi, C., & Zhang, X. (2021). Individuality- and Commonality-Based Multiview Multilabel Learning. IEEE Transactions on Cybernetics, 51(3), 1716–1727. https://doi.org/10.1109/tcyb.2019.2950560
Koutsaviti, A., Daskalaki, M. G., Agusti, S., Kampranis, S. C., Tsatsanis, C., Duarte, C. M., … Ioannou, E. (2019). Thuwalallenes A–E and Thuwalenynes A–C: New C15 Acetogenins with Anti-Inflammatory Activity from a Saudi Arabian Red Sea Laurencia sp. Marine Drugs, 17(11), 644. https://doi.org/10.3390/md17110644
Bendevis, P., Karam, A., & Laleg-Kirati, T.-M. (2020). Optimal model-free control of solar thermal membrane distillation system. Computers & Chemical Engineering, 133, 106622. https://doi.org/10.1016/j.compchemeng.2019.106622
Mourier, T., de Alvarenga, D. A. M., Kaushik, A., de Pina-Costa, A., Douvropoulou, O., Guan, Q., … Pain, A. (2019). The genome of the zoonotic malaria parasite Plasmodium simium reveals adaptations to host-switching. https://doi.org/10.1101/841171
Wang, K., Wang, J., Domeniconi, C., Zhang, X., & Yu, G. (2019). Differentiating isoform functions with collaborative matrix factorization. Bioinformatics. https://doi.org/10.1093/bioinformatics/btz847
Kulmanov, M., & Hoehndorf, R. (2019). DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier. https://doi.org/10.1101/839332
Fischer, J., Renn, D., Quitterer, F., Radhakrishnan, A., Liu, M., Makki, A., … Eppinger, J. (2019). Robust and Versatile Host Protein for the Design and Evaluation of Artificial Metal Centers. ACS Catalysis, 9(12), 11371–11380. https://doi.org/10.1021/acscatal.9b02896
Saderne, V., Baldry, K., Anton, A., Agustí, S., & Duarte, C. M. (2019). Characterization of the CO 2 System in a Coral Reef, a Seagrass Meadow, and a Mangrove Forest in the Central Red Sea. Journal of Geophysical Research: Oceans, 124(11), 7513–7528. https://doi.org/10.1029/2019jc015266
Aldoghaither, A., & Laleg-Kirati, T.-M. (2020). Parameter and differentiation order estimation for a two dimensional fractional partial differential equation. Journal of Computational and Applied Mathematics, 369, 112570. https://doi.org/10.1016/j.cam.2019.112570
Liu, H., Wen, J., Jing, L., Yu, J., Zhang, X., & Zhang, M. (2019). In2Rec. Proceedings of the 28th ACM International Conference on Information and Knowledge Management. https://doi.org/10.1145/3357384.3358017
Geraldi, N. R., Díaz‐Rúa, R., Shea, L. A., & Duarte, C. M. (2019). Performance of extraction methods for extracellular DNA from sediments across marine habitats. Environmental DNA, 2(1), 91–98. https://doi.org/10.1002/edn3.48
Sequeira, A. M. M., Hays, G. C., Sims, D. W., Eguíluz, V. M., Rodríguez, J. P., Heupel, M. R., … Duarte, C. M. (2019). Overhauling Ocean Spatial Planning to Improve Marine Megafauna Conservation. Frontiers in Marine Science, 6. https://doi.org/10.3389/fmars.2019.00639
Lam, J. H., Li, Y., Zhu, L., Umarov, R., Jiang, H., Héliou, A., … Gao, X. (2019). A deep learning framework to predict binding preference of RNA constituents on protein surface. Nature Communications, 10(1). https://doi.org/10.1038/s41467-019-12920-0
Chen, Y., Sun, K., Pu, J., Xiong, Z., & Zhang, X. (2020). GraPASA: Parametric graph embedding via siamese architecture. Information Sciences, 512, 1442–1457. https://doi.org/10.1016/j.ins.2019.10.027
Chen, Y., Sun, K., Pu, J., Xiong, Z., & Zhang, X. (2019). GraPASA: Parametric Graph Embedding via Siamese Architecture. Information Sciences. https://doi.org/10.1016/j.ins.2019.10.027
Fernández de Puelles, Gazá, Cabanellas-Reboredo, Santandreu, Irigoien, González-Gordillo, & Duarte. (2019). Zooplankton Abundance and Diversity in the Tropical and Subtropical Ocean. Diversity, 11(11), 203. https://doi.org/10.3390/d11110203
Giner, C. R., Pernice, M. C., Balagué, V., Duarte, C. M., Gasol, J. M., Logares, R., & Massana, R. (2019). Marked changes in diversity and relative activity of picoeukaryotes with depth in the world ocean. The ISME Journal, 14(2), 437–449. https://doi.org/10.1038/s41396-019-0506-9
Xiao, X., Agusti, S., Lin, F., Xu, C., Yu, Y., Pan, Y., … Duarte, C. M. (2019). Resource (Light and Nitrogen) and Density-Dependence of Seaweed Growth. Frontiers in Marine Science, 6. https://doi.org/10.3389/fmars.2019.00618
Han, R., Li, L., Yang, P., Zhang, F., & Gao, X. (2019). A novel constrained reconstruction model towards high-resolution subtomogram averaging. Bioinformatics. https://doi.org/10.1093/bioinformatics/btz787
Xiao, X., Agustí, S., Pan, Y., Yu, Y., Li, K., Wu, J., & Duarte, C. M. (2019). Warming Amplifies the Frequency of Harmful Algal Blooms with Eutrophication in Chinese Coastal Waters. Environmental Science & Technology, 53(22), 13031–13041. https://doi.org/10.1021/acs.est.9b03726
Han, R., Wang, S., & Gao, X. (2019). Novel algorithms for efficient subsequence searching and mapping in nanopore raw signals towards targeted sequencing. Bioinformatics. https://doi.org/10.1093/bioinformatics/btz742
Obradovic, M., Zafirovic, S., Essack, M., Dimitrov, J., Zivkovic, L., Spremo-Potparevic, B., … Isenovic, E. R. (2020). Antioxidant enzymes expression in lymphocytes of patients undergoing carotid endarterectomy. Medical Hypotheses, 134, 109419. https://doi.org/10.1016/j.mehy.2019.109419
Serrano, O., Lovelock, C. E., B. Atwood, T., Macreadie, P. I., Canto, R., Phinn, S., … Duarte, C. M. (2019). Australian vegetated coastal ecosystems as global hotspots for climate change mitigation. Nature Communications, 10(1). https://doi.org/10.1038/s41467-019-12176-8
Lee, M. A., Duarte, C. M., Eguíluz, V. M., Heller, D. A., Langer, R., Meekan, M. G., … Wilson, R. P. (2019). Can Fish and Cell Phones Teach Us about Our Health? ACS Sensors, 4(10), 2566–2570. https://doi.org/10.1021/acssensors.9b00947
Yang, Z., Yu, G., Guo, M., Yu, J., Zhang, X., & Wang, J. (2019). CDPath: Cooperative driver pathways discovery using integer linear programming and Markov clustering. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1–1. https://doi.org/10.1109/tcbb.2019.2945029
Zhao, Y., Wang, J., Guo, M., Zhang, X., & Yu, G. (2019). Cross-Species Protein Function Prediction with Asynchronous-Random Walk. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1–1. https://doi.org/10.1109/tcbb.2019.2943342
Aalismail, N. A., Ngugi, D. K., Díaz-Rúa, R., Alam, I., Cusack, M., & Duarte, C. M. (2019). Functional metagenomic analysis of dust-associated microbiomes above the Red Sea. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-50194-0
Martin, C., Corona, E., Mahadik, G. A., & Duarte, C. M. (2019). Adhesion to coral surface as a potential sink for marine microplastics. Environmental Pollution, 255, 113281. https://doi.org/10.1016/j.envpol.2019.113281
Karimi, M. A., Zhang, Q., Kuo, Y. H., Shaikh, S. F., Kaidarova, A., Geraldi, N., … Shamim, A. (2019). Flexible tag design for semi-continuous wireless data acquisition from marine animals. Flexible and Printed Electronics, 4(3), 035006. https://doi.org/10.1088/2058-8585/ab423f
Nagai, S., Chen, H., Kawakami, Y., Yamamoto, K., Sildever, S., Kanno, N., … Gojobori, T. (2019). Monitoring of the toxic dinoflagellate Alexandrium catenella in Osaka Bay, Japan using a massively parallel sequencing (MPS)-based technique. Harmful Algae, 89, 101660. https://doi.org/10.1016/j.hal.2019.101660
Macreadie, P. I., Anton, A., Raven, J. A., Beaumont, N., Connolly, R. M., Friess, D. A., … Duarte, C. M. (2019). The future of Blue Carbon science. Nature Communications, 10(1). https://doi.org/10.1038/s41467-019-11693-w
Giomi, F., Barausse, A., Duarte, C. M., Booth, J., Agusti, S., Saderne, V., … Fusi, M. (2019). Oxygen supersaturation protects coastal marine fauna from ocean warming. Science Advances, 5(9), eaax1814. https://doi.org/10.1126/sciadv.aax1814
Obradovic, M., Essack, M., Zafirovic, S., Sudar‐Milovanovic, E., Bajic, V. P., Van Neste, C., … Isenovic, E. R. (2020). Redox control of vascular biology. BioFactors, 46(2), 246–262. https://doi.org/10.1002/biof.1559
Hawerkamp, H. C., Kislat, A., Gerber, P. A., Pollet, M., Rolfes, K. M., Soshilov, A. A., … Meller, S. (2019). Vemurafenib acts as an aryl hydrocarbon receptor antagonist: Implications for inflammatory cutaneous adverse events. Allergy, 74(12), 2437–2448. https://doi.org/10.1111/all.13972
Othoum, G., Bougouffa, S., Bokhari, A., Lafi, F. F., Gojobori, T., Hirt, H., … Essack, M. (2019). Mining biosynthetic gene clusters in Virgibacillus genomes. BMC Genomics, 20(1). https://doi.org/10.1186/s12864-019-6065-7
Sanada, T., Tsukiyama-Kohara, K., Shin-I, T., Yamamoto, N., Kayesh, M. E. H., Yamane, D., … Kohara, M. (2019). Construction of complete Tupaia belangeri transcriptome database by whole-genome and comprehensive RNA sequencing. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-48867-x
Kaidarova, A., Almoudi, A., Allagani, R. M., Marengo, M., Khan, M. A., Buttner, U., … Kosel, J. (2019). Flexible and Multi-Functional Graphene Sensor Platform. 2019 IEEE International Conference on Flexible and Printable Sensors and Systems (FLEPS). https://doi.org/10.1109/fleps.2019.8792302
Kaidarova, A., Almoudi, A., Allagani, R. M., Marengo, M., Khan, M. A., Buttner, U., … Kosel, J. (2019). Flexible and Multi-Functional Graphene Sensor Platform. 2019 IEEE International Conference on Flexible and Printable Sensors and Systems (FLEPS). https://doi.org/10.1109/fleps.2019.8792302
Kaidaorva, A., Marengo, M., Marinaro, G., Geraldi, N. R., Wilson, R., Duarte, C. M., & Kosel, J. (2019). Flexible, four-electrode conductivity cell for biologging applications. Results in Materials, 1, 100009. https://doi.org/10.1016/j.rinma.2019.100009
Ortega, A., Geraldi, N. R., Alam, I., Kamau, A. A., Acinas, S. G., Logares, R., … Duarte, C. M. (2019). Important contribution of macroalgae to oceanic carbon sequestration. Nature Geoscience, 12(9), 748–754. https://doi.org/10.1038/s41561-019-0421-8
Sanz-Martín, M., Vernet, M., Cape, M. R., Mesa, E., Delgado-Huertas, A., Reigstad, M., … Duarte, C. M. (2019). Relationship Between Carbon- and Oxygen-Based Primary Productivity in the Arctic Ocean, Svalbard Archipelago. Frontiers in Marine Science, 6. https://doi.org/10.3389/fmars.2019.00468
López-Sandoval, D. C., Rowe, K., Carillo-de-Albonoz, P., Duarte, C. M., & Agustí, S. (2019). Rates and drivers of Red Sea plankton community metabolism. Biogeosciences, 16(15), 2983–2995. https://doi.org/10.5194/bg-16-2983-2019
Kaidarova, A., Khan, M. A., Marengo, M., Swanepoel, L., Przybysz, A., Muller, C., … Kosel, J. (2019). Wearable multifunctional printed graphene sensors. Npj Flexible Electronics, 3(1). https://doi.org/10.1038/s41528-019-0061-5
López-Sandoval, D. C., Rowe, K., Carillo-de-Albonoz, P., Duarte, C. M., & Agustí, S. (2019). Rates and drivers of Red Sea plankton community metabolism. Biogeosciences, 16(15), 2983–2995. https://doi.org/10.5194/bg-16-2983-2019
Chen, X., Yu, G., Wang, J., Domeniconi, C., Li, Z., & Zhang, X. (2019). ActiveHNE: Active Heterogeneous Network Embedding. Proceedings of the Twenty-Eighth International Joint Conference on Artificial Intelligence. https://doi.org/10.24963/ijcai.2019/294
Yao, S., Yu, G., Wang, J., Domeniconi, C., & Zhang, X. (2019). Multi-View Multiple Clustering. Proceedings of the Twenty-Eighth International Joint Conference on Artificial Intelligence. https://doi.org/10.24963/ijcai.2019/572
Pei, S., Yu, L., & Zhang, X. (2019). Improving Cross-lingual Entity Alignment via Optimal Transport. Proceedings of the Twenty-Eighth International Joint Conference on Artificial Intelligence. https://doi.org/10.24963/ijcai.2019/448
De los Santos, C. B., Krause-Jensen, D., Alcoverro, T., Marbà, N., Duarte, C. M., van Katwijk, M. M., … Santos, R. (2019). Recent trend reversal for declining European seagrass meadows. Nature Communications, 10(1). https://doi.org/10.1038/s41467-019-11340-4
Klein, S. G., Pitt, K. A., Lucas, C. H., Hung, S.-H., Schmidt-Roach, S., Aranda, M., & Duarte, C. M. (2019). Night-Time Temperature Reprieves Enhance the Thermal Tolerance of a Symbiotic Cnidarian. Frontiers in Marine Science, 6. https://doi.org/10.3389/fmars.2019.00453
Yan, R., Le, R., Song, Y., Zhang, T., Zhang, X., & Zhao, D. (2019). Interview Choice Reveals Your Preference on the Market. Proceedings of the 25th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining. https://doi.org/10.1145/3292500.3330963
Jin, P., Overmans, S., Duarte, C. M., & Agustí, S. (2019). Increasing temperature within thermal limits compensates negative ultraviolet‐B radiation effects in terrestrial and aquatic organisms. Global Ecology and Biogeography, 28(11), 1695–1711. https://doi.org/10.1111/geb.12973
Queiroz, N., Humphries, N. E., Couto, A., Vedor, M., da Costa, I., Sequeira, A. M. M., … Abercrombie, D. L. (2019). Global spatial risk assessment of sharks under the footprint of fisheries. Nature, 572(7770), 461–466. https://doi.org/10.1038/s41586-019-1444-4
Peng, C., Duarte, C. M., Costa, D. P., Guinet, C., Harcourt, R. G., Hindell, M. A., … Zhang, X. (2019). Deep Learning Resolves Representative Movement Patterns in a Marine Predator Species. Applied Sciences, 9(14), 2935. https://doi.org/10.3390/app9142935
Mazarrasa, I., Marbà, N., Krause-Jensen, D., Kennedy, H., Santos, R., Lovelock, C. E., & Duarte, C. M. (2019). Decreasing carbonate load of seagrass leaves with increasing latitude. Aquatic Botany, 159, 103147. https://doi.org/10.1016/j.aquabot.2019.103147
Zhao, J., Shang, S., Wang, P., Lui, J. C., & Zhang, X. (2019). Submodular Optimization over Streams with Inhomogeneous Decays. Proceedings of the AAAI Conference on Artificial Intelligence, 33(01), 5861-5868. https://doi.org/10.1609/aaai.v33i01.33015861
Yu, L., Zhang, C., Liang, S., & Zhang, X. (2019). Multi-Order Attentive Ranking Model for Sequential Recommendation. Proceedings of the AAAI Conference on Artificial Intelligence, 33, 5709–5716. https://doi.org/10.1609/aaai.v33i01.33015709
Mahadik, G. A., Agusti, S., & Duarte, C. M. (2019). Distribution and Characteristics of Halobates germanus Population in the Red Sea. Frontiers in Marine Science, 6. https://doi.org/10.3389/fmars.2019.00408
Sequeira, A. M. M., Heupel, M. R., Lea, M. ‐A., Eguíluz, V. M., Duarte, C. M., Meekan, M. G., … Hays, G. C. (2019). The importance of sample size in marine megafauna tagging studies. Ecological Applications, 29(6). https://doi.org/10.1002/eap.1947
Rossbach, S., Saderne, V., Anton, A., & Duarte, C. M. (2019). Light-dependent calcification in Red Sea giant clam <i>Tridacna maxima</i> Biogeosciences, 16(13), 2635–2650. https://doi.org/10.5194/bg-16-2635-2019
Han, R., Bao, Z., Zeng, X., Niu, T., Zhang, F., Xu, M., & Gao, X. (2019). A joint method for marker-free alignment of tilt series in electron tomography. Bioinformatics, 35(14), i249–i259. https://doi.org/10.1093/bioinformatics/btz323
Duffy, J. E., Benedetti-Cecchi, L., Trinanes, J., Muller-Karger, F. E., Ambo-Rappe, R., Boström, C., … Yaakub, S. M. (2019). Toward a Coordinated Global Observing System for Seagrasses and Marine Macroalgae. Frontiers in Marine Science, 6. https://doi.org/10.3389/fmars.2019.00317
Krause-Jensen, D., Sejr, M. K., Bruhn, A., Rasmussen, M. B., Christensen, P. B., Hansen, J. L. S., … Wegeberg, S. (2019). Deep Penetration of Kelps Offshore Along the West Coast of Greenland. Frontiers in Marine Science, 6. https://doi.org/10.3389/fmars.2019.00375
Wilson, R. P., Börger, L., Holton, M. D., Scantlebury, D. M., Gómez‐Laich, A., Quintana, F., … Shepard, E. L. C. (2019). Estimates for energy expenditure in free‐living animals using acceleration proxies: A reappraisal. Journal of Animal Ecology, 89(1), 161–172. https://doi.org/10.1111/1365-2656.13040
Harcourt, R., Sequeira, A. M. M., Zhang, X., Roquet, F., Komatsu, K., Heupel, M., … Carroll, G. (2019). Animal-Borne Telemetry: An Integral Component of the Ocean Observing Toolkit. Frontiers in Marine Science, 6. https://doi.org/10.3389/fmars.2019.00326
Sanz-Martín, M., Hendriks, I. E., Carstensen, J., Marbà, N., Krause-Jensen, D., Sejr, M. K., & Duarte, C. M. (2019). Continuous photoperiod of the Artic summer stimulates the photosynthetic response of some marine macrophytes. Aquatic Botany, 158, 103126. https://doi.org/10.1016/j.aquabot.2019.06.005
Ramajo, L., Lagos, N. A., & Duarte, C. M. (2019). Seagrass Posidonia oceanica diel pH fluctuations reduce the mortality of epiphytic forams under experimental ocean acidification. Marine Pollution Bulletin, 146, 247–254. https://doi.org/10.1016/j.marpolbul.2019.06.011
Ni, M., Zhuo, S., Iliescu, C., So, P. T. C., Mehta, J. S., Yu, H., & Hauser, C. A. E. (2019). Self‐assembling amyloid‐like peptides as exogenous second harmonic probes for bioimaging applications. Journal of Biophotonics, 12(12). https://doi.org/10.1002/jbio.201900065
Iuculano, F., Álverez-Salgado, X. A., Otero, J., Catalá, T. S., Sobrino, C., Duarte, C. M., & Agustí, S. (2019). Patterns and Drivers of UV Absorbing Chromophoric Dissolved Organic Matter in the Euphotic Layer of the Open Ocean. Frontiers in Marine Science, 6. https://doi.org/10.3389/fmars.2019.00320
Bennett, S., Duarte, C. M., Marbà, N., & Wernberg, T. (2019). Integrating within-species variation in thermal physiology into climate change ecology. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1778), 20180550. https://doi.org/10.1098/rstb.2018.0550
Martin, C., Agustí, S., & Duarte, C. M. (2019). Seasonality of marine plastic abundance in central Red Sea pelagic waters. Science of The Total Environment, 688, 536–541. https://doi.org/10.1016/j.scitotenv.2019.06.240
Zhao, J., Shang, S., Wang, P., Lui, J. C. S., & Zhang, X. (2019). Tracking Influential Nodes in Time-Decaying Dynamic Interaction Networks. 2019 IEEE 35th International Conference on Data Engineering (ICDE). https://doi.org/10.1109/icde.2019.00102
Siuly, S., & Zhang, X. (2019). Guest Editorial: Special issue on “Application of artificial intelligence in health research.” Health Information Science and Systems, 8(1). https://doi.org/10.1007/s13755-019-0089-x
Yahya, R. Z., Arrieta, J. M., Cusack, M., & Duarte, C. M. (2019). Airborne Prokaryote and Virus Abundance Over the Red Sea. Frontiers in Microbiology, 10. https://doi.org/10.3389/fmicb.2019.01112