2021

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
Yamamoto, N., Nishida, N., Yamamoto, R., Gojobori, T., Shimotohno, K., Mizokami, M., & Ariumi, Y. (2021). Angiotensin–Converting Enzyme (ACE) 1 Gene Polymorphism and Phenotypic Expression of COVID-19 Symptoms. Genes, 12(10), 1572. https://doi.org/10.3390/genes12101572
Yamamoto, N., Nishida, N., Yamamoto, R., Gojobori, T., Shimotohno, K., Mizokami, M., & Ariumi, Y. (2021). Angiotensin–Converting Enzyme (ACE) 1 Gene Polymorphism and Phenotypic Expression of COVID-19 Symptoms. Genes, 12(10), 1572. https://doi.org/10.3390/genes12101572
Fatani, S., Saito, Y., Alarawi, M., Gojobori, T., & Mineta, K. (2021). Genome sequencing and identification of cellulase genes in Bacillus paralicheniformis strains from the Red Sea. BMC Microbiology, 21(1). https://doi.org/10.1186/s12866-021-02316-w
Thafar, M. A., Olayan, R. S., Albaradei, S., Bajic, V. B., Gojobori, T., Essack, M., & Gao, X. (2021). DTi2Vec: Drug–target interaction prediction using network embedding and ensemble learning. Journal of Cheminformatics, 13(1). https://doi.org/10.1186/s13321-021-00552-w
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., … 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
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., … Duarte, C. M. (2021). A prevalent neglect of environmental control in mammalian cell culture calls for best practices. Nature Biomedical Engineering, 5(8), 787–792. https://doi.org/10.1038/s41551-021-00775-0
Zhao, X., Remington, J. M., Schneebeli, S. T., Arold, S. T., & Li, J. (2021). Molecular Basis for Environment Sensing by a Nucleoid-Structuring Bacterial Protein Filament. The Journal of Physical Chemistry Letters, 12(32), 7878–7884. https://doi.org/10.1021/acs.jpclett.1c01710
Abouelhoda, M., Mohty, D., Alayary, I., Meyer, B. F., Arold, S. T., Fadel, B. M., & Monies, D. (2021). Established and candidate transthyretin amyloidosis variants identified in the Saudi population by data mining. Human Genomics, 15(1). https://doi.org/10.1186/s40246-021-00351-2
Queralt-Rosinach, N., Schofield, P., Hoehndorf, R., Weiland, C., Schultes, E. A., Bernabé, C. H., & Roos, M. (2021). The COVID-19 epidemiology and monitoring ontology. https://doi.org/10.37044/osf.io/n6tcz
Salsench, E. M., Maroofian, R., Deng, R., Lanko, K., Nikoncuk, A., Pérez, B., … Barakat, T. S. (2021). Expanding the mutational landscape and clinical phenotype of the YIF1B related brain disorder. Brain. https://doi.org/10.1093/brain/awab297
Albaradei, S., Napolitano, F., Thafar, M. A., Gojobori, T., Essack, M., & Gao, X. (2021). MetaCancer: A deep learning-based pan-cancer metastasis prediction model developed using multi-omics data. Computational and Structural Biotechnology Journal, 19, 4404–4411. https://doi.org/10.1016/j.csbj.2021.08.006
Abdelrahman, S., Alghrably, M., Campagna, M., Hauser, C. A. E., Jaremko, M., & Lachowicz, J. I. (2021). Metal Complex Formation and Anticancer Activity of Cu(I) and Cu(II) Complexes with Metformin. Molecules, 26(16), 4730. https://doi.org/10.3390/molecules26164730
Shimada, T., Meekan, M. G., Baldwin, R., Al-Suwailem, A. M., Clarke, C., Santillan, A. S., & Duarte, C. M. (2021). Distribution and temporal trends in the abundance of nesting sea turtles in the Red Sea. Biological Conservation, 261, 109235. https://doi.org/10.1016/j.biocon.2021.109235
Li, X., Sindihebura, T. T., Zhou, L., Duarte, C. M., Costa, D. P., Hindell, M. A., … Peng, C. (2021). A prediction and imputation method for marine animal movement data. PeerJ Computer Science, 7, e656. https://doi.org/10.7717/peerj-cs.656
Agulles, M., Jordà, G., Hoteit, I., Agustí, S., & Duarte, C. M. (2021). Assessment of Red Sea temperatures in CMIP5 models for present and future climate. PLOS ONE, 16(7), e0255505. https://doi.org/10.1371/journal.pone.0255505
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
Arossa, S., Barozzi, A., Callegari, M., Klein, S. G., Parry, A. J., Hung, S.-H., … Duarte, C. M. (2021). The Internal Microenvironment of the Symbiotic Jellyfish Cassiopea sp. From the Red Sea. Frontiers in Marine Science, 8. https://doi.org/10.3389/fmars.2021.705915
Wang, Q., Duarte, C., Song, L., Christakos, G., Agusti, S., & Wu, J. (2021). Effects of Ecological Restoration Using Non-Native Mangrove Kandelia obovata to Replace Invasive Spartina alterniflora on Intertidal Macrobenthos Community in Maoyan Island (Zhejiang, China). Journal of Marine Science and Engineering, 9(8), 788. https://doi.org/10.3390/jmse9080788
Moshkov, M. (2021). Decision trees based on 1-consequences. Discrete Applied Mathematics, 302, 208–214. https://doi.org/10.1016/j.dam.2021.07.017
Alshukairi, A. N., El-Kafrawy, S. A., Dada, A., Yasir, M., Yamani, A. H., Saeedi, M. F., … Azhar, E. I. (2021). Re-infection with a different SARS-CoV-2 clade and prolonged viral shedding in a hematopoietic stem cell transplantation patient. International Journal of Infectious Diseases, 110, 267–271. https://doi.org/10.1016/j.ijid.2021.07.036
Rolandi, M., Noy, A., Inal, S., & Rivnay, J. (2021). Advances in bioelectronics: Materials, devices, and translational applications. APL Materials, 9(7), 070402. https://doi.org/10.1063/5.0060323
Deutschmann, I. M., Delage, E., Giner, C. R., Sebastián, M., Poulain, J., Arístegui, J., … Logares, R. (2021). Disentangling marine microbial networks across space. https://doi.org/10.1101/2021.07.12.451729
AlSaieedi, A., Salhi, A., Tifratene, F., Raies, A. B., Hungler, A., Uludag, M., … Essack, M. (2021). DES-Tcell is a knowledgebase for exploring immunology-related literature. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-93809-1
Queiroz, N., Humphries, N. E., Couto, A., Vedor, M., da Costa, I., Sequeira, A. M. M., … Abercrombie, D. L. (2021). Reply to: Shark mortality cannot be assessed by fishery overlap alone. Nature, 595(7866), E8–E16. https://doi.org/10.1038/s41586-021-03397-3
Queiroz, N., Humphries, N. E., Couto, A., Vedor, M., da Costa, I., Sequeira, A. M. M., … Abercrombie, D. L. (2021). Reply to: Caution over the use of ecological big data for conservation. Nature, 595(7866), E20–E28. https://doi.org/10.1038/s41586-021-03464-9
Queiroz, N., Humphries, N. E., Couto, A., Vedor, M., da Costa, I., Sequeira, A. M. M., … Abercrombie, D. L. (2021). Reply to: Caution over the use of ecological big data for conservation. Nature, 595(7866), E20–E28. https://doi.org/10.1038/s41586-021-03464-9
L Ghaffour, TML Kirati, (2021). Reference Tracking AND Observer Design for Space-Fractional Partial Differential Equation Modeling Gas Pressures in Fractured Media. arXiv.2107.02042
Liao, X., Li, M., Hu, K., Wu, F.-X., Gao, X., & Wang, J. (2021). A sensitive repeat identification framework based on short and long reads. Nucleic Acids Research. https://doi.org/10.1093/nar/gkab563
Gunner, R. M., Holton, M. D., Scantlebury, M. D., van Schalkwyk, O. L., English, H. M., Williams, H. J., … Wilson, R. P. (2021). Dead-reckoning animal movements in R: a reappraisal using Gundog.Tracks. Animal Biotelemetry, 9(1). https://doi.org/10.1186/s40317-021-00245-z
Gunner, R. M., Holton, M. D., Scantlebury, M. D., van Schalkwyk, O. L., English, H. M., Williams, H. J., … Wilson, R. P. (2021). Dead-reckoning animal movements in R: a reappraisal using Gundog.Tracks. Animal Biotelemetry, 9(1). https://doi.org/10.1186/s40317-021-00245-z
Azad, M., Chikalov, I., Hussain, S., & Moshkov, M. (2021). Optimization of Decision Trees with Hypotheses for Knowledge Representation. Electronics, 10(13), 1580. https://doi.org/10.3390/electronics10131580
Gu, J., Jin, R., Chen, G., Ye, Z., Li, Q., Wang, H., … Wu, J. (2021). Areal Extent, Species Composition, and Spatial Distribution of Coastal Saltmarshes in China. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, 14, 7085–7094. https://doi.org/10.1109/jstars.2021.3093673
Yu, G., Huang, Q., Zhang, X., Guo, M., & Wang, J. (2021). Tissue Specificity based Isoform Function Prediction. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1–1. https://doi.org/10.1109/tcbb.2021.3093167
Bajaffer, A., Mineta, K., & Gojobori, T. (2021). Evolution of memory system‐related genes. FEBS Open Bio. https://doi.org/10.1002/2211-5463.13224
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
Makita, Y., Suzuki, S., Fushimi, K., Shimada, S., Suehisa, A., Hirata, M., … Matsui, M. (2021). Identification of a dual orange/far-red and blue light photoreceptor from an oceanic green picoplankton. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-23741-5
Gunner, R. M., Wilson, R. P., Holton, M. D., Hopkins, P., Bell, S. H., Marks, N. J., … Scantlebury, D. M. (2021). Decision rules for determining terrestrial movement and the consequences for filtering high-resolution GPS tracks – A case study using the African Lion (Panthera leo). https://doi.org/10.21203/rs.3.rs-600317/v1
Slater, L. T., Williams, J. A., Karwath, A., Russell, S., Pendleton, S. C., Fanning, H., … Gkoutos, G. V. (2021). Klarigi: Explanations for Semantic Groupings. https://doi.org/10.1101/2021.06.14.448423
López‐Sandoval, D. C., Duarte, C. M., & Agustí, S. (2021). Nutrient and temperature constraints on primary production and net phytoplankton growth in a tropical ecosystem. Limnology and Oceanography, 66(7), 2923–2935. https://doi.org/10.1002/lno.11849
López‐Sandoval, D. C., Duarte, C. M., & Agustí, S. (2021). Nutrient and temperature constraints on primary production and net phytoplankton growth in a tropical ecosystem. Limnology and Oceanography, 66(7), 2923–2935. https://doi.org/10.1002/lno.11849
Mazarrasa, I., Lavery, P., Duarte, C. M., Lafratta, A., Lovelock, C. E., Macreadie, P. I., … Serrano, O. (2021). Factors Determining Seagrass Blue Carbon Across Bioregions and Geomorphologies. Global Biogeochemical Cycles, 35(6). https://doi.org/10.1029/2021gb006935
Conchouso, D., Al-Ma’abadi, A., Behzad, H., Alarawi, M., Hosokawa, M., Nishikawa, Y., … Gojobori, T. (2021). Integration of Droplet Microfluidic Tools for Single-cell Functional Metagenomics: An Engineering Head Start. https://doi.org/10.36227/techrxiv.14760726.v1
Mazarrasa, I., Lavery, P., Duarte, C. M., Lafratta, A., Lovelock, C. E., Macreadie, P. I., … Serrano, O. (2021). Factors Determining Seagrass Blue Carbon Across Bioregions and Geomorphologies. Global Biogeochemical Cycles, 35(6). https://doi.org/10.1029/2021gb006935
Morales-Caselles, C., Viejo, J., Martí, E., González-Fernández, D., Pragnell-Raasch, H., González-Gordillo, J. I., … Cózar, A. (2021). An inshore–offshore sorting system revealed from global classification of ocean litter. Nature Sustainability, 4(6), 484–493. https://doi.org/10.1038/s41893-021-00720-8
Pei, S., Yu, L., & Zhang, X. (2021). Set-aware Entity Synonym Discovery with Flexible Receptive Fields. IEEE Transactions on Knowledge and Data Engineering, 1–1. https://doi.org/10.1109/tkde.2021.3087532
Yoshitake, K., Kimura, G., Sakami, T., Watanabe, T., Taniuchi, Y., Kakehi, S., … Gojobori, T. (2021). Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-91615-3
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
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
Bank, M. S., Swarzenski, P. W., Duarte, C. M., Rillig, M. C., Koelmans, A. A., Metian, 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
Noro, Y., Shimizu, H., Mineta, K., & Gojobori, T. (2021). A single neuron subset governs a single coactive neuron circuit in Hydra vulgaris, representing a possible ancestral feature of neural evolution. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-89325-x
Bank, M. S., Swarzenski, P. W., Duarte, C. M., Rillig, M. C., Koelmans, A. A., Metian, M., … Ok, Y. S. (2021). Global Plastic Pollution Observation System to Aid Policy. Environmental Science & Technology, 55(12), 7770–7775. https://doi.org/10.1021/acs.est.1c00818
Magbool, A., Bahloul, M. A., Ballal, T., Al-Naffouri, T. Y., & Laleg-Kirati, T.-M. (2021). Aortic blood pressure estimation: A hybrid machine-learning and cross-relation approach. Biomedical Signal Processing and Control, 68, 102762. https://doi.org/10.1016/j.bspc.2021.102762
Acinas, S. G., Sánchez, P., Salazar, G., Cornejo-Castillo, F. M., Sebastián, M., Logares, R., … Gasol, J. M. (2021). Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Communications Biology, 4(1). https://doi.org/10.1038/s42003-021-02112-2
Kulmanov, M., Zhapa-Camacho, F., & Hoehndorf, R. (2021). DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web. Nucleic Acids Research, 49(W1), W140–W146. https://doi.org/10.1093/nar/gkab373
Bates, A. E., Primack, R. B., & Duarte, C. M. (2021). Global COVID-19 lockdown highlights humans as both threats and custodians of the environment. Biological Conservation, 109175. https://doi.org/10.1016/j.biocon.2021.109175
Chen, S., Li, Y., Zhang, T., Zhu, X., Sun, S., & Gao, X. (2021). Lunar features detection for energy discovery via deep learning. Applied Energy, 296, 117085. https://doi.org/10.1016/j.apenergy.2021.117085
Obradovic, M., Sudar-Milovanovic, E., Soskic, S., Essack, M., Arya, S., Stewart, A. J., … Isenovic, E. R. (2021). Leptin and Obesity: Role and Clinical Implication. Frontiers in Endocrinology, 12. https://doi.org/10.3389/fendo.2021.585887
Zhang, X., Yang, Q., Albaradei, S., Lyu, X., Alamro, H., Salhi, A., … Gao, X. (2021). Rise and fall of the global conversation and shifting sentiments during the COVID-19 pandemic. Humanities and Social Sciences Communications, 8(1). https://doi.org/10.1057/s41599-021-00798-7
Zhang, J., Vancea, A. I., Shahul Hameed, U. F., & Arold, S. T. (2021). Versatile control of the CDC48 segregase by the plant UBX-containing (PUX) proteins. Computational and Structural Biotechnology Journal, 19, 3125–3132. https://doi.org/10.1016/j.csbj.2021.05.025
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., … 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
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Zhang, L., Zhang, D., Wang, X., Yuan, C., Li, Y., Jia, X., … Huang, X. (2021). 1′-Ribose cyano substitution allows Remdesivir to effectively inhibit nucleotide addition and proofreading during SARS-CoV-2 viral RNA replication. Physical Chemistry Chemical Physics, 23(10), 5852–5863. https://doi.org/10.1039/d0cp05948j
Alzanbaki, H., Moretti, M., & Hauser, C. A. E. (2021). Engineered Microgels—Their Manufacturing and Biomedical Applications. Micromachines, 12(1), 45. https://doi.org/10.3390/mi12010045
Zhang, Y. (2021). Computation Offloading and Service Caching in Heterogeneous MEC Wireless Networks. KAUST Research Repository. https://doi.org/10.25781/KAUST-DQ447
Klevjer, T. A., Martinez, U., Boyra, G., Røstad, A., Kaartvedt, S., & Irigoien, X. (2021). Per station summaries of acoustic water column properties during MALASPINA-2010 [Data set]. PANGAEA - Data Publisher for Earth & Environmental Science. https://doi.org/10.1594/PANGAEA.926619

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
Laptenok, S. P., Martin, C., Genchi, L., Duarte, C. M., & Liberale, C. (2020). Stimulated Raman microspectroscopy as a new method to classify microfibers from environmental samples. Environmental Pollution, 267, 115640. https://doi.org/10.1016/j.envpol.2020.115640
Alghamdi, M., Bashiri, F. A., Abdelhakim, M., Adly, N., Jamjoom, D. Z., Sumaily, K. M., … Arold, S. T. (2020). Phenotypic and molecular spectrum of pyridoxamine‐5′‐phosphate oxidase deficiency: A scoping review of 87 cases of pyridoxamine‐5′‐phosphate oxidase deficiency. Clinical Genetics, 99(1), 99–110. https://doi.org/10.1111/cge.13843
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
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
Auffray, C., Balling, R., Blomberg, N., Bonaldo, M. C., Boutron, B., Brahmachari, S., … Clément, K. (2020). COVID-19 and beyond: a call for action and audacious solidarity to all the citizens and nations, it is humanity’s fight. F1000Research, 9, 1130. https://doi.org/10.12688/f1000research.26098.1
Alam, I., Aalismail, N., Martin, C., Kamau, A., Guzmán-Vega, F. J., Jamil, T., … Duarte, C. M. (2020). Rapid Evolution of Plastic-degrading Enzymes Prevalent in the Global Ocean. https://doi.org/10.1101/2020.09.07.285692
Abdel-Haleem, A. M., Ravikumar, V., Ji, B., Mineta, K., Gao, X., Nielsen, J., … Mijakovic, I. (2020). Integrated Metabolic Modeling, Culturing, and Transcriptomics Explain Enhanced Virulence of Vibrio cholerae during Coinfection with Enterotoxigenic Escherichia coli. mSystems, 5(5). https://doi.org/10.1128/msystems.00491-20
Li, P., & Laleg-Kirati, T.-M. (2020). Schrödinger Spectrum Based PPG Features for the Estimation of the Arterial Blood Pressure. 2020 42nd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC). https://doi.org/10.1109/embc44109.2020.9176849
Magbool, A., Bahloul, M. A., Ballal, T., Al-Naffouri, T. Y., & Laleg-Kirati, T.-M. (2020). Blind Estimation of Central Blood Pressure Using Least-Squares with Mean Matching and Box Constraints. 2020 42nd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC). https://doi.org/10.1109/embc44109.2020.9176258
Chahid, A., Khushaba, R., Al-Jumaily, A., & Laleg-Kirati, T.-M. (2020). A Position Weight Matrix Feature Extraction Algorithm Improves Hand Gesture Recognition. 2020 42nd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC). https://doi.org/10.1109/embc44109.2020.9176097
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
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
Guan, Q., Sadykov, M., Mfarrej, S., Hala, S., Naeem, R., Nugmanova, R., … Pain, A. (2020). A genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic. International Journal of Infectious Diseases, 100, 216–223. https://doi.org/10.1016/j.ijid.2020.08.052
Mankowski, M., & Moshkov, M. (2020). Extensions of dynamic programming for multi-stage combinatorial optimization. Theoretical Computer Science, 844, 106–132. https://doi.org/10.1016/j.tcs.2020.08.009
Schmidt-Roach, S., Duarte, C. M., Hauser, C. A. E., & Aranda, M. (2020). Beyond Reef Restoration: Next-Generation Techniques for Coral Gardening, Landscaping, and Outreach. Frontiers in Marine Science, 7. https://doi.org/10.3389/fmars.2020.00672
Alam, I., Kamau, A. A., Kulmanov, M., Jaremko, Ł., Arold, S. T., Pain, A., … Duarte, C. M. (2020). Functional Pangenome Analysis Shows Key Features of E Protein Are Preserved in SARS and SARS-CoV-2. Frontiers in Cellular and Infection Microbiology, 10. https://doi.org/10.3389/fcimb.2020.00405
Alfares, A., Alsubaie, L., Aloraini, T., Alaskar, A., Althagafi, A., Alahmad, A., … Alfadhel, M. (2020). What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations. BMC Medical Genomics, 13(1). https://doi.org/10.1186/s12920-020-00743-8
Liu, A., Zhang, Y., Zhang, X., Liu, G., Zhang, Y., Li, Z., … Zhou, X. (2020). Representation Learning with Multi-level Attention for Activity Trajectory Similarity Computation. IEEE Transactions on Knowledge and Data Engineering, 1–1. https://doi.org/10.1109/tkde.2020.3010022
Ghattassi, M., Laleg, T.-M., & Vivalda, J.-C. (2020). Analysis and output tracking design for the direct contact membrane distillation parabolic system. Journal of Mathematical Analysis and Applications, 491(2), 124367. https://doi.org/10.1016/j.jmaa.2020.124367
X. Guo, P. Hong, and T. M. Laleg-Kirati, (2020) Nonlinear Model Predictive Control Design for BSM-MBR: Benchmark of Membrane Bioreactor, IFAC World Congress, Berlin,
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
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
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
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
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
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
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
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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
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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
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
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
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
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
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
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
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
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
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
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
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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
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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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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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
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
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
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
Krause, J. W., Schulz, I. K., Rowe, K. A., Dobbins, W., Winding, M. H. S., Sejr, M. K., … Agustí, S. (2019). Silicic acid limitation drives bloom termination and potential carbon sequestration in an Arctic bloom. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-44587-4
Arossa, S., Martin, C., Rossbach, S., & Duarte, C. M. (2019). Microplastic removal by Red Sea giant clam (Tridacna maxima). Environmental Pollution, 252, 1257–1266. https://doi.org/10.1016/j.envpol.2019.05.149
Garcias-Bonet, N., Delgado-Huertas, A., Carrillo-de-Albornoz, P., Anton, A., Almahasheer, H., Marbà, N., … Duarte, C. M. (2019). Carbon and Nitrogen Concentrations, Stocks, and Isotopic Compositions in Red Sea Seagrass and Mangrove Sediments. Frontiers in Marine Science, 6. https://doi.org/10.3389/fmars.2019.00267
Mankowski, M. A., Kosztowski, M., Raghavan, S., Garonzik‐Wang, J. M., Axelrod, D., Segev, D. L., & Gentry, S. E. (2019). Accelerating kidney allocation: Simultaneously expiring offers. American Journal of Transplantation, 19(11), 3071–3078. https://doi.org/10.1111/ajt.15396
Geraldi, N. R., Ortega, A., Serrano, O., Macreadie, P. I., Lovelock, C. E., Krause-Jensen, D., … Duarte, C. M. (2019). Fingerprinting Blue Carbon: Rationale and Tools to Determine the Source of Organic Carbon in Marine Depositional Environments. Frontiers in Marine Science, 6. https://doi.org/10.3389/fmars.2019.00263
Wang, W., Zhao, M., Gao, Z., Xu, G., Xian, H., Li, Y., & Zhang, X. (2019). Constructing Features for Detecting Android Malicious Applications: Issues, Taxonomy and Directions. IEEE Access, 7, 67602–67631. https://doi.org/10.1109/access.2019.2918139
Yang, Q., Li, Z., Liu, A., Liu, G., Zhao, L., Zhang, X., … Zhou, X. (2019). A novel hybrid publication recommendation system using compound information. World Wide Web, 22(6), 2499–2517. https://doi.org/10.1007/s11280-019-00687-9
Pu, J., Wang, Y., Liu, X., & Zhang, X. (2019). STLP-OD: Spatial and Temporal Label Propagation for Traffic Outlier Detection. IEEE Access, 7, 63036–63044. https://doi.org/10.1109/access.2019.2916853
Acinas, S. G., Sánchez, P., Salazar, G., Cornejo-Castillo, F. M., Sebastián, M., Logares, R., … Gasol, J. M. (2019). Metabolic Architecture of the Deep Ocean Microbiome. https://doi.org/10.1101/635680
Acinas, S. G., Sánchez, P., Salazar, G., Cornejo-Castillo, F. M., Sebastián, M., Logares, R., … Gasol, J. M. (2019). Metabolic Architecture of the Deep Ocean Microbiome. https://doi.org/10.1101/635680
Pei, S., Yu, L., Hoehndorf, R., & Zhang, X. (2019). Semi-Supervised Entity Alignment via Knowledge Graph Embedding with Awareness of Degree Difference. The World Wide Web Conference on - WWW ’19. https://doi.org/10.1145/3308558.3313646
Berumen, M. L., Voolstra, C. R., Daffonchio, D., Agusti, S., Aranda, M., Irigoien, X., … Duarte, C. M. (2019). The Red Sea: Environmental Gradients Shape a Natural Laboratory in a Nascent Ocean. Coral Reefs of the World, 1–10. https://doi.org/10.1007/978-3-030-05802-9_1
Ruiz‐González, C., Logares, R., Sebastián, M., Mestre, M., Rodríguez‐Martínez, R., Galí, M., … Gasol, J. M. (2019). Higher contribution of globally rare bacterial taxa reflects environmental transitions across the surface ocean. Molecular Ecology, 28(8), 1930–1945. https://doi.org/10.1111/mec.15026
Ruiz‐González, C., Logares, R., Sebastián, M., Mestre, M., Rodríguez‐Martínez, R., Galí, M., … Gasol, J. M. (2019). Higher contribution of globally rare bacterial taxa reflects environmental transitions across the surface ocean. Molecular Ecology, 28(8), 1930–1945. https://doi.org/10.1111/mec.15026
Guan, Y., Ngugi, D. K., Vinu, M., Blom, J., Alam, I., Guillot, S., … Stingl, U. (2019). Comparative Genomics of the Genus Methanohalophilus, Including a Newly Isolated Strain From Kebrit Deep in the Red Sea. Frontiers in Microbiology, 10. https://doi.org/10.3389/fmicb.2019.00839
Wang, Y., Yu, G., Domeniconi, C., Wang, J., Zhang, X., & Guo, M. (2019). Selective Matrix Factorization for Multi-relational Data Fusion. Lecture Notes in Computer Science, 313–329. https://doi.org/10.1007/978-3-030-18576-3_19
Zhai, D., Liu, A., Chen, S., Li, Z., & Zhang, X. (2019). SeqST-ResNet: A Sequential Spatial Temporal ResNet for Task Prediction in Spatial Crowdsourcing. Lecture Notes in Computer Science, 260–275. https://doi.org/10.1007/978-3-030-18576-3_16
Geraldi, N. R., Anton, A., Lovelock, C. E., & Duarte, C. M. (2019). Are the ecological effects of the “worst” marine invasive species linked with scientific and media attention? PLOS ONE, 14(4), e0215691. https://doi.org/10.1371/journal.pone.0215691
Anton, A., Geraldi, N. R., Lovelock, C. E., Apostolaki, E. T., Bennett, S., Cebrian, J., … Duarte, C. M. (2019). Global ecological impacts of marine exotic species. Nature Ecology & Evolution, 3(5), 787–800. https://doi.org/10.1038/s41559-019-0851-0
Jamil, M., Kountche, B. A., Haider, I., Wang, J. Y., Aldossary, F., Zarban, R. A., … Al-Babili, S. (2019). Methylation at the C-3′ in D-Ring of Strigolactone Analogs Reduces Biological Activity in Root Parasitic Plants and Rice. Frontiers in Plant Science, 10. https://doi.org/10.3389/fpls.2019.00353
Regaudie-de-Gioux, A., Huete-Ortega, M., Sobrino, C., López-Sandoval, D. C., González, N., Fernández-Carrera, A., … Duarte, C. M. (2019). Multi-model remote sensing assessment of primary production in the subtropical gyres. Journal of Marine Systems, 196, 97–106. https://doi.org/10.1016/j.jmarsys.2019.03.007
Sun, G., & Zhang, X. (2019). A Novel Framework for Node/Edge Attributed Graph Embedding. Lecture Notes in Computer Science, 169–182. https://doi.org/10.1007/978-3-030-16142-2_14
Carstensen, J., & Duarte, C. M. (2019). Drivers of pH Variability in Coastal Ecosystems. Environmental Science & Technology, 53(8), 4020–4029. https://doi.org/10.1021/acs.est.8b03655
Vaqué, D., Lara, E., Arrieta, J. M., Holding, J., Sà, E. L., Hendriks, I. E., … Duarte, C. M. (2019). Warming and CO2 Enhance Arctic Heterotrophic Microbial Activity. Frontiers in Microbiology, 10. https://doi.org/10.3389/fmicb.2019.00494
Hays, G. C., Bailey, H., Bograd, S. J., Bowen, W. D., Campagna, C., Carmichael, R. H., … Sequeira, A. M. M. (2019). Translating Marine Animal Tracking Data into Conservation Policy and Management. Trends in Ecology & Evolution, 34(5), 459–473. https://doi.org/10.1016/j.tree.2019.01.009
Burkholz, C., Duarte, C., & Garcias-Bonet, N. (2019). Thermal dependence of seagrass ecosystem metabolism in the Red Sea. Marine Ecology Progress Series, 614, 79–90. https://doi.org/10.3354/meps12912
Saderne, V., Geraldi, N. R., Macreadie, P. I., Maher, D. T., Middelburg, J. J., Serrano, O., … Duarte, C. M. (2019). Role of carbonate burial in Blue Carbon budgets. Nature Communications, 10(1). https://doi.org/10.1038/s41467-019-08842-6
Lovelock, C. E., & Duarte, C. M. (2019). Dimensions of Blue Carbon and emerging perspectives. Biology Letters, 15(3), 20180781. https://doi.org/10.1098/rsbl.2018.0781
Ashok, A., Cusack, M., Saderne, V., Krishnakumar, P. K., Rabaoui, L., Qurban, M. A., … Agustí, S. (2019). Accelerated burial of petroleum hydrocarbons in Arabian Gulf blue carbon repositories. Science of The Total Environment, 669, 205–212. https://doi.org/10.1016/j.scitotenv.2019.01.437
Liu, X., Liu, J., Zhu, S., Wang, W., & Zhang, X. (2020). Privacy Risk Analysis and Mitigation of Analytics Libraries in the Android Ecosystem. IEEE Transactions on Mobile Computing, 19(5), 1184–1199. https://doi.org/10.1109/tmc.2019.2903186
Liu, X., Liu, J., Zhu, S., Wang, W., & Zhang, X. (2020). Privacy Risk Analysis and Mitigation of Analytics Libraries in the Android Ecosystem. IEEE Transactions on Mobile Computing, 19(5), 1184–1199. https://doi.org/10.1109/tmc.2019.2903186
Palmer, E. E., Hong, S., Al Zahrani, F., Hashem, M. O., Aleisa, F. A., Ahmed, H. M. J., … Arold, S. T. (2019). De Novo Variants Disrupting the HX Repeat Motif of ATN1 Cause a Recognizable Non-Progressive Neurocognitive Syndrome. The American Journal of Human Genetics, 104(3), 542–552. https://doi.org/10.1016/j.ajhg.2019.01.013
Kafkas, Ş., & Hoehndorf, R. (2019). Ontology based text mining of gene-phenotype associations: application to candidate gene prediction. Database, 2019. https://doi.org/10.1093/database/baz019
Tse, C. K. M., Xu, J., Xu, L., Sheong, F. K., Wang, S., Chow, H. Y., … Huang, X. (2019). Intrinsic cleavage of RNA polymerase II adopts a nucleobase-independent mechanism assisted by transcript phosphate. Nature Catalysis, 2(3), 228–235. https://doi.org/10.1038/s41929-019-0227-5
Boudellioua, I., Kulmanov, M., Schofield, P. N., Gkoutos, G. V., & Hoehndorf, R. (2019). DeepPVP: phenotype-based prioritization of causative variants using deep learning. BMC Bioinformatics, 20(1). https://doi.org/10.1186/s12859-019-2633-8
Smaili, F. Z., Gao, X., & Hoehndorf, R. (2019). Formal axioms in biomedical ontologies improve analysis and interpretation of associated data. https://doi.org/10.1101/536649
Shaikh, S. F., Mazo-Mantilla, H. F., Qaiser, N., Khan, S. M., Nassar, J. M., Geraldi, N. R., … Hussain, M. M. (2019). Noninvasive Featherlight Wearable Compliant “Marine Skin”: Standalone Multisensory System for Deep-Sea Environmental Monitoring. Small, 15(10), 1804385. https://doi.org/10.1002/smll.201804385
Liu, X., Li, Z., Wang, J., Yu, G., Domenicon, C., & Zhang, X. (2019). Cross-Modal Zero-Shot Hashing. 2019 IEEE International Conference on Data Mining (ICDM). https://doi.org/10.1109/icdm.2019.00055
Zhang, W., Ding, W., Li, Y.-X., Tam, C., Bougouffa, S., Wang, R., … Qian, P.-Y. (2019). Marine biofilms constitute a bank of hidden microbial diversity and functional potential. Nature Communications, 10(1). https://doi.org/10.1038/s41467-019-08463-z
Akujuobi, U., Yufei, H., Zhang, Q., & Zhang, X. (2019). Collaborative Graph Walk for Semi-Supervised Multi-label Node Classification. 2019 IEEE International Conference on Data Mining (ICDM). https://doi.org/10.1109/icdm.2019.00010
Meng, Z., Liang, S., Bao, H., & Zhang, X. (2019). Co-Embedding Attributed Networks. Proceedings of the Twelfth ACM International Conference on Web Search and Data Mining. https://doi.org/10.1145/3289600.3291015
WILSON, R. P., HOLTON, M., WILSON, V. L., GUNNER, R., TYSSE, B., WILSON, G. I., … SCANTLEBURY, D. M. (2019). Towards informed metrics for examining the role of human-induced animal responses in tag studies on wild animals. Integrative Zoology, 14(1), 17–29. https://doi.org/10.1111/1749-4877.12328
Martin, C., Almahasheer, H., & Duarte, C. M. (2019). Mangrove forests as traps for marine litter. Environmental Pollution, 247, 499–508. https://doi.org/10.1016/j.envpol.2019.01.067
Garcias-Bonet, N., Vaquer-Sunyer, R., Duarte, C. M., & Marbà, N. (2019). Warming effect on nitrogen fixation in Mediterranean macrophyte sediments. Biogeosciences, 16(1), 167–175. https://doi.org/10.5194/bg-16-167-2019
Agusti, S., Lubián, L. M., Moreno-Ostos, E., Estrada, M., & Duarte, C. M. (2019). Projected Changes in Photosynthetic Picoplankton in a Warmer Subtropical Ocean. Frontiers in Marine Science, 5. https://doi.org/10.3389/fmars.2018.00506
López‐Sandoval, D. C., Delgado‐Huertas, A., Carrillo‐de‐Albornoz, P., Duarte, C. M., & Agustí, S. (2019). Use of cavity ring‐down spectrometry to quantify 13 C‐primary productivity in oligotrophic waters. Limnology and Oceanography: Methods, 17(2), 137–144. https://doi.org/10.1002/lom3.10305
N’Doye, I., Asiri, S., Aloufi, A., Asem Al-Awan, A., & Laleg-Kirati, T.-M. (2020). Intelligent Proportional–Integral–Derivative Control-Based Modulating Functions for Laser Beam Pointing and Stabilization. IEEE Transactions on Control Systems Technology, 28(3), 1001–1008. https://doi.org/10.1109/tcst.2018.2884197
Wang, G., Yin, H., Li, B., Yu, C., Wang, F., Xu, X., … Zhang, Z. (2019). Characterization and identification of long non-coding RNAs based on feature relationship. Bioinformatics, 35(17), 2949–2956. https://doi.org/10.1093/bioinformatics/btz008

2018

Shahul Hameed, U. F., Liao, C., Radhakrishnan, A. K., Huser, F., Aljedani, S. S., Zhao, X., … Arold, S. T. (2018). H-NS uses an autoinhibitory conformational switch for environment-controlled gene silencing. Nucleic Acids Research, 47(5), 2666–2680. https://doi.org/10.1093/nar/gky1299
Lei, J., Sheng, G., Cheung, P. P.-H., Wang, S., Li, Y., Gao, X., … Huang, X. (2018). Two symmetric arginine residues play distinct roles inThermus thermophilusArgonaute DNA guide strand-mediated DNA target cleavage. Proceedings of the National Academy of Sciences, 116(3), 845–853. https://doi.org/10.1073/pnas.1817041116
Alazmi, M., Kuwahara, H., Soufan, O., Ding, L., & Gao, X. (2018). Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions. Bioinformatics, 35(15), 2634–2643. https://doi.org/10.1093/bioinformatics/bty1035
Kleftogiannis, D., Ashoor, H., & Bajic, V. B. (2018). TELS: A Novel Computational Framework for Identifying Motif Signatures of Transcribed Enhancers. Genomics, Proteomics & Bioinformatics, 16(5), 332–341. https://doi.org/10.1016/j.gpb.2018.05.003
Akal, A. L., Karan, R., Hohl, A., Alam, I., Vogler, M., Grötzinger, S. W., … Rueping, M. (2018). A polyextremophilic alcohol dehydrogenase from the Atlantis II Deep Red Sea brine pool. FEBS Open Bio, 9(2), 194–205. https://doi.org/10.1002/2211-5463.12557
Dooley, D. M., Griffiths, E. J., Gosal, G. S., Buttigieg, P. L., Hoehndorf, R., Lange, M. C., … Hsiao, W. W. L. (2018). FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration. Npj Science of Food, 2(1). https://doi.org/10.1038/s41538-018-0032-6
Wang, P., Zhao, J., Zhang, X., Tao, J., & Guan, X. (2018). SNOD: a fast sampling method of exploring node orbit degrees for large graphs. Knowledge and Information Systems, 61(1), 301–326. https://doi.org/10.1007/s10115-018-1301-z
Almahasheer, H., Serrano, O., Duarte, C. M., & Irigoien, X. (2018). Remobilization of Heavy Metals by Mangrove Leaves. Frontiers in Marine Science, 5. https://doi.org/10.3389/fmars.2018.00484
Lee, M. A., Nguyen, F. T., Scott, K., Chan, N. Y. L., Bakh, N. A., Jones, K. K., … Strano, M. S. (2018). Implanted Nanosensors in Marine Organisms for Physiological Biologging: Design, Feasibility, and Species Variability. ACS Sensors, 4(1), 32–43. https://doi.org/10.1021/acssensors.8b00538
Garcias-Bonet, N., Fusi, M., Ali, M., Shaw, D. R., Saikaly, P. E., Daffonchio, D., & Duarte, C. M. (2018). High denitrification and anaerobic ammonium oxidation contributes to net nitrogen loss in a seagrass ecosystem in the central Red Sea. Biogeosciences, 15(23), 7333–7346. https://doi.org/10.5194/bg-15-7333-2018
Duarte, C. M., & Krause-Jensen, D. (2018). Intervention Options to Accelerate Ecosystem Recovery From Coastal Eutrophication. Frontiers in Marine Science, 5. https://doi.org/10.3389/fmars.2018.00470
Pitt, K. A., Lucas, C. H., Condon, R. H., Duarte, C. M., & Stewart-Koster, B. (2018). Claims That Anthropogenic Stressors Facilitate Jellyfish Blooms Have Been Amplified Beyond the Available Evidence: A Systematic Review. Frontiers in Marine Science, 5. https://doi.org/10.3389/fmars.2018.00451
Unsworth, R. K. F., McKenzie, L. J., Collier, C. J., Cullen-Unsworth, L. C., Duarte, C. M., Eklöf, J. S., … Nordlund, L. M. (2018). Global challenges for seagrass conservation. Ambio, 48(8), 801–815. https://doi.org/10.1007/s13280-018-1115-y
Arias-Ortiz, A., Masqué, P., Garcia-Orellana, J., Serrano, O., Mazarrasa, I., Marbà, N., … Duarte, C. M. (2018). Reviews and syntheses: <sup>210</sup>Pb-derived sediment and carbon accumulation rates in vegetated coastal ecosystems – setting the record straight. Biogeosciences, 15(22), 6791–6818. https://doi.org/10.5194/bg-15-6791-2018
Shashi, V., Magiera, M. M., Klein, D., Zaki, M., Schoch, K., Rudnik‐Schöneborn, S., … Yuan, X. (2018). Loss of tubulin deglutamylase CCP 1 causes infantile‐onset neurodegeneration. The EMBO Journal, 37(23). https://doi.org/10.15252/embj.2018100540
Smaili, F. Z., Gao, X., & Hoehndorf, R. (2018). OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction. Bioinformatics, 35(12), 2133–2140. https://doi.org/10.1093/bioinformatics/bty933
Smaili, F. Z., Gao, X., & Hoehndorf, R. (2018). OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction. Bioinformatics, 35(12), 2133–2140. https://doi.org/10.1093/bioinformatics/bty933
Krause, J. W., Duarte, C. M., Marquez, I. A., Assmy, P., Fernández-Méndez, M., Wiedmann, I., … Agustí, S. (2018). Biogenic silica production and diatom dynamics in the Svalbard region during spring. Biogeosciences, 15(21), 6503–6517. https://doi.org/10.5194/bg-15-6503-2018
Tovar-Sánchez, A., González-Ortegón, E., & Duarte, C. M. (2019). Trace metal partitioning in the top meter of the ocean. Science of The Total Environment, 652, 907–914. https://doi.org/10.1016/j.scitotenv.2018.10.315
Kaidarova, A., Marengo, M., Marinaro, G., Geraldi, N., Duarte, C. M., & Kosel, J. (2018). Flexible and Biofouling Independent Salinity Sensor. Advanced Materials Interfaces, 5(23), 1801110. https://doi.org/10.1002/admi.201801110
Ogura, A., Akizuki, Y., Imoda, H., Mineta, K., Gojobori, T., & Nagai, S. (2018). Comparative genome and transcriptome analysis of diatom, Skeletonema costatum, reveals evolution of genes for harmful algal bloom. BMC Genomics, 19(1). https://doi.org/10.1186/s12864-018-5144-5
Ma, L., Cao, J., Liu, L., Du, Q., Li, Z., Zou, D., … Zhang, Z. (2018). LncBook: a curated knowledgebase of human long non-coding RNAs. Nucleic Acids Research, 47(D1), D128–D134. https://doi.org/10.1093/nar/gky960
Serrano, O., Almahasheer, H., Duarte, C. M., & Irigoien, X. (2018). Carbon stocks and accumulation rates in Red Sea seagrass meadows. Scientific Reports, 8(1). https://doi.org/10.1038/s41598-018-33182-8
Steckbauer, A., Díaz-Gil, C., Alós, J., Catalán, I. A., & Duarte, C. M. (2018). Predator Avoidance in the European Seabass After Recovery From Short-Term Hypoxia and Different CO2 Conditions. Frontiers in Marine Science, 5. https://doi.org/10.3389/fmars.2018.00350
González‐Wangüemert, M., Basso, L., Balau, A., Costa, J., Renault, L., Serrão, E. A., … Hendriks, I. E. (2018). Gene pool and connectivity patterns of Pinna nobilis in the Balearic Islands (Spain, Western Mediterranean Sea): Implications for its conservation through restocking. Aquatic Conservation: Marine and Freshwater Ecosystems, 29(2), 175–188. https://doi.org/10.1002/aqc.2976
Gattuso, J.-P., Magnan, A. K., Bopp, L., Cheung, W. W. L., Duarte, C. M., Hinkel, J., … Rau, G. H. (2018). Ocean Solutions to Address Climate Change and Its Effects on Marine Ecosystems. Frontiers in Marine Science, 5. https://doi.org/10.3389/fmars.2018.00337
Razali, R., Bougouffa, S., Morton, M. J. L., Lightfoot, D. J., Alam, I., Essack, M., … Negrão, S. (2018). The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance. Frontiers in Plant Science, 9. https://doi.org/10.3389/fpls.2018.01402
Boudellioua, I., Kulmanov, M., Schofield, P. N., Gkoutos, G. V., & Hoehndorf, R. (2018). OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants. Scientific Reports, 8(1). https://doi.org/10.1038/s41598-018-32876-3
Schofield, P., Elmore, S., Cardiff, R., Cesta, M., Gkoutos, G., Helton, E., Hoehndorf, R., Keenan, C., McKerlie, C., & Sundberg, J. (2018). All in the Name: A Review of Current Standards and the Evolution of Histopathological Nomenclature for Laboratory Animals. Apollo - University of Cambridge Repository. https://doi.org/10.17863/CAM.30296
Young, M. A., Macreadie, P. I., Duncan, C., Carnell, P. E., Nicholson, E., Serrano, O., … Ierodiaconou, D. (2018). Optimal soil carbon sampling designs to achieve cost-effectiveness: a case study in blue carbon ecosystems. Biology Letters, 14(9), 20180416. https://doi.org/10.1098/rsbl.2018.0416
Marbà, N., Krause-Jensen, D., Masqué, P., & Duarte, C. M. (2018). Expanding Greenland seagrass meadows contribute new sediment carbon sinks. Scientific Reports, 8(1). https://doi.org/10.1038/s41598-018-32249-w
Gu, J., Luo, M., Zhang, X., Christakos, G., Agusti, S., Duarte, C. M., & Wu, J. (2018). Losses of salt marsh in China: Trends, threats and management. Estuarine, Coastal and Shelf Science, 214, 98–109. https://doi.org/10.1016/j.ecss.2018.09.015
Shaheen, R., Maddirevula, S., Ewida, N., Alsahli, S., Abdel-Salam, G. M. H., Zaki, M. S., … Alkuraya, F. S. (2018). Genomic and phenotypic delineation of congenital microcephaly. Genetics in Medicine, 21(3), 545–552. https://doi.org/10.1038/s41436-018-0140-3
Hayase, S., Wang, H., Ohgushi, E., Kobayashi, M., Mori, C., Horita, H., … Wada, K. (2018). Vocal practice regulates singing activity–dependent genes underlying age-independent vocal learning in songbirds. PLOS Biology, 16(9), e2006537. https://doi.org/10.1371/journal.pbio.2006537
Lehmann, R., Lightfoot, D. J., Schunter, C., Michell, C. T., Ohyanagi, H., Mineta, K., … Ravasi, T. (2018). Finding Nemo’s Genes: A chromosome‐scale reference assembly of the genome of the orange clownfish Amphiprion percula. Molecular Ecology Resources, 19(3), 570–585. https://doi.org/10.1111/1755-0998.12939
Alshahrani, M., & Hoehndorf, R. (2018). Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes. Bioinformatics, 34(17), i901–i907. https://doi.org/10.1093/bioinformatics/bty559
Kulmanov, M., Schofield, P. N., Gkoutos, G. V., & Hoehndorf, R. (2018). Ontology-based validation and identification of regulatory phenotypes. Bioinformatics, 34(17), i857–i865. https://doi.org/10.1093/bioinformatics/bty605
Kordopati, V., Salhi, A., Razali, R., Radovanovic, A., Tifratene, F., Uludag, M., … Bajic, V. B. (2018). DES-Mutation: System for Exploring Links of Mutations and Diseases. Scientific Reports, 8(1). https://doi.org/10.1038/s41598-018-31439-w
Linn, S. C., Mustonen, A. M., Silva, K. A., Kennedy, V. E., Sundberg, B. A., Bechtold, L. S., … Sundberg, J. P. (2018). Nail abnormalities identified in an ageing study of 30 inbred mouse strains. Experimental Dermatology, 28(4), 383–390. https://doi.org/10.1111/exd.13759
Sea, M. A., Garcias-Bonet, N., Saderne, V., & Duarte, C. M. (2018). Carbon dioxide and methane fluxes at the air–sea interface of Red Sea mangroves. Biogeosciences, 15(17), 5365–5375. https://doi.org/10.5194/bg-15-5365-2018
Kalkatawi, M., Magana-Mora, A., Jankovic, B., & Bajic, V. B. (2018). DeepGSR: an optimized deep-learning structure for the recognition of genomic signals and regions. Bioinformatics, 35(7), 1125–1132. https://doi.org/10.1093/bioinformatics/bty752
Rehman, Z. ur, Alam, I., Kamau, A. A., Bajic, V. B., & Leiknes, T. (2018). Genome sequence analysis of Zooshikella ganghwensis strain VG4 and its potential for the synthesis of antimicrobial metabolites. Biotechnology Reports, 19, e00278. https://doi.org/10.1016/j.btre.2018.e00278
Duarte, C. M., Delgado-Huertas, A., Anton, A., Carrillo-de-Albornoz, P., López-Sandoval, D. C., Agustí, S., … Garcias-Bonet, N. (2018). Stable Isotope (δ13C, δ15N, δ18O, δD) Composition and Nutrient Concentration of Red Sea Primary Producers. Frontiers in Marine Science, 5. https://doi.org/10.3389/fmars.2018.00298
Shahul Hameed, U. F., Sanislav, O., Lay, S. T., Annesley, S. J., Jobichen, C., Fisher, P. R., … Arold, S. T. (2018). Proteobacterial Origin of Protein Arginine Methylation and Regulation of Complex I Assembly by MidA. Cell Reports, 24(8), 1996–2004. https://doi.org/10.1016/j.celrep.2018.07.075
Krause-Jensen, D., Serrano, O., Apostolaki, E. T., Gregory, D. J., & Duarte, C. M. (2018). Seagrass sedimentary deposits as security vaults and time capsules of the human past. Ambio, 48(4), 325–335. https://doi.org/10.1007/s13280-018-1083-2
Wilson, R. P., Holton, M. D., Virgilio, A., Williams, H., Shepard, E. L. C., Lambertucci, S., … Duarte, C. M. (2018). Give the machine a hand: A Boolean time‐based decision‐tree template for rapidly finding animal behaviours in multisensor data. Methods in Ecology and Evolution, 9(11), 2206–2215. https://doi.org/10.1111/2041-210x.13069
Motwalli, O., Essack, M., Salhi, A., Hanks, J., Mijakovic, I., & Bajic, V. B. (2018). BioPS: System for screening and assessment of biofuel-production potential of cyanobacteria. PLOS ONE, 13(8), e0202002. https://doi.org/10.1371/journal.pone.0202002
Duarte, C. M., Poiner, I., & Gunn, J. (2018). Perspectives on a Global Observing System to Assess Ocean Health. Frontiers in Marine Science, 5. https://doi.org/10.3389/fmars.2018.00265
Chefaoui, R. M., Duarte, C. M., & Serrão, E. A. (2018). Dramatic loss of seagrass habitat under projected climate change in the Mediterranean Sea. Global Change Biology, 24(10), 4919–4928. https://doi.org/10.1111/gcb.14401
Khan, A. O., Patel, N., Ghazi, N. G., Alzahrani, S. S., Arold, S. T., & Alkuraya, F. S. (2018). Familial non-syndromic macular pseudocoloboma secondary to homozygous CLDN19 mutation. Ophthalmic Genetics, 39(5), 577–583. https://doi.org/10.1080/13816810.2018.1498528
Shahul Hameed, U., Haider, I., Jamil, M., Kountche, B. A., Guo, X., Zarban, R. A., … Arold, S. T. (2018). Structural basis for specific inhibition of the highly sensitive Sh HTL 7 receptor. EMBO Reports, 19(9). https://doi.org/10.15252/embr.201745619
Bermejo, R., Chefaoui, R. M., Engelen, A. H., Buonomo, R., Neiva, J., Ferreira-Costa, J., … Serrão, E. A. (2018). Marine forests of the Mediterranean-Atlantic Cystoseira tamariscifolia complex show a southern Iberian genetic hotspot and no reproductive isolation in parapatry. Scientific Reports, 8(1). https://doi.org/10.1038/s41598-018-28811-1
Sanz-Martín, M., Chierici, M., Mesa, E., Carrillo-de-Albornoz, P., Delgado-Huertas, A., Agustí, S., … Duarte, C. M. (2018). Episodic Arctic CO2 Limitation in the West Svalbard Shelf. Frontiers in Marine Science, 5. https://doi.org/10.3389/fmars.2018.00221
Mestre, M., Ruiz-González, C., Logares, R., Duarte, C. M., Gasol, J. M., & Sala, M. M. (2018). Sinking particles promote vertical connectivity in the ocean microbiome. Proceedings of the National Academy of Sciences, 115(29), E6799–E6807. https://doi.org/10.1073/pnas.1802470115
Behzad, H., Mineta, K., & Gojobori, T. (2018). Global Ramifications of Dust and Sandstorm Microbiota. Genome Biology and Evolution, 10(8), 1970–1987. https://doi.org/10.1093/gbe/evy134
Ramajo, L., Hendriks, I. E., Lagos, N. A., Krause-Jensen, D., Marbà, N., Sejr, M. K., & Duarte, C. M. (2018). Reply to “Increased food supply mitigates ocean acidification effects on calcification but exacerbates effects on growth.” Scientific Reports, 8(1). https://doi.org/10.1038/s41598-018-27670-0
Cusack, M., Saderne, V., Arias-Ortiz, A., Masqué, P., Krishnakumar, P. K., Rabaoui, L., … Duarte, C. M. (2018). Organic carbon sequestration and storage in vegetated coastal habitats along the western coast of the Arabian Gulf. Environmental Research Letters, 13(7), 074007. https://doi.org/10.1088/1748-9326/aac899
Smaili, F. Z., Gao, X., & Hoehndorf, R. (2018). Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations. Bioinformatics, 34(13), i52–i60. https://doi.org/10.1093/bioinformatics/bty259
Agusti, S., Vigoya, L., & Duarte, C. M. (2018). Annual plankton community metabolism in estuarine and coastal waters in Perth (Western Australia). PeerJ, 6, e5081. https://doi.org/10.7717/peerj.5081
Fontanini, A., Steckbauer, A., Dupont, S., & Duarte, C. M. (2018). Variable metabolic responses of Skagerrak invertebrates to low O<sub>2</sub> and high CO<sub>2</sub> scenarios. Biogeosciences, 15(12), 3717–3729. https://doi.org/10.5194/bg-15-3717-2018
Krause-Jensen, D., Lavery, P., Serrano, O., Marbà, N., Masque, P., & Duarte, C. M. (2018). Sequestration of macroalgal carbon: the elephant in the Blue Carbon room. Biology Letters, 14(6), 20180236. https://doi.org/10.1098/rsbl.2018.0236
Kaidarova, A., Khan, M. A., Amara, S., Geraldi, N. R., Karimi, M. A., Shamim, A., … Kosel, J. (2018). Tunable, Flexible Composite Magnets for Marine Monitoring Applications. Advanced Engineering Materials, 20(9), 1800229. https://doi.org/10.1002/adem.201800229
Almahasheer, H., Duarte, C. M., & Irigoien, X. (2018). Leaf Nutrient Resorption and Export Fluxes of Avicennia marina in the Central Red Sea Area. Frontiers in Marine Science, 5. https://doi.org/10.3389/fmars.2018.00204
Naser, R., Aldehaiman, A., Díaz-Galicia, E., & Arold, S. (2018). Endogenous Control Mechanisms of FAK and PYK2 and Their Relevance to Cancer Development. Cancers, 10(6), 196. https://doi.org/10.3390/cancers10060196
Pinedo-González, P., West, A. J., Tovar-Sanchez, A., Duarte, C. M., & Sañudo-Wilhelmy, S. A. (2018). Concentration and isotopic composition of dissolved Pb in surface waters of the modern global ocean. Geochimica et Cosmochimica Acta, 235, 41–54. https://doi.org/10.1016/j.gca.2018.05.005
Zheng, Y., Duarte, C. M., Chen, J., Li, D., Lou, Z., & Wu, J. (2018). Remote sensing mapping of macroalgal farms by modifying thresholds in the classification tree. Geocarto International, 34(10), 1098–1108. https://doi.org/10.1080/10106049.2018.1474272
Duarte, B., Martins, I., Rosa, R., Matos, A. R., Roleda, M. Y., Reusch, T. B. H., … Jueterbock, A. (2018). Climate Change Impacts on Seagrass Meadows and Macroalgal Forests: An Integrative Perspective on Acclimation and Adaptation Potential. Frontiers in Marine Science, 5. https://doi.org/10.3389/fmars.2018.00190
Giralt, A., de Pins, B., Cifuentes-Díaz, C., López-Molina, L., Farah, A. T., Tible, M., … Girault, J.-A. (2018). PTK2B/Pyk2 overexpression improves a mouse model of Alzheimer’s disease. Experimental Neurology, 307, 62–73. https://doi.org/10.1016/j.expneurol.2018.05.020
Saderne, V., Cusack, M., Almahasheer, H., Serrano, O., Masqué, P., Arias‐Ortiz, A., … Duarte, C. M. (2018). Accumulation of Carbonates Contributes to Coastal Vegetated Ecosystems Keeping Pace With Sea Level Rise in an Arid Region (Arabian Peninsula). Journal of Geophysical Research: Biogeosciences, 123(5), 1498–1510. https://doi.org/10.1029/2017jg004288
Martin, C., Parkes, S., Zhang, Q., Zhang, X., McCabe, M. F., & Duarte, C. M. (2018). Use of unmanned aerial vehicles for efficient beach litter monitoring. Marine Pollution Bulletin, 131, 662–673. https://doi.org/10.1016/j.marpolbul.2018.04.045
Nassar, J. M., Khan, S. M., Velling, S. J., Diaz-Gaxiola, A., Shaikh, S. F., Geraldi, N. R., … Hussain, M. M. (2018). Compliant lightweight non-invasive standalone “Marine Skin” tagging system. Npj Flexible Electronics, 2(1). https://doi.org/10.1038/s41528-018-0025-1
Rashid, J., Kobiyama, A., Reza, M. S., Yamada, Y., Ikeda, Y., Ikeda, D., … Watabe, S. (2018). Seasonal changes in the communities of photosynthetic picoeukaryotes in Ofunato Bay as revealed by shotgun metagenomic sequencing. Gene, 665, 127–132. https://doi.org/10.1016/j.gene.2018.04.071
Kobiyama, A., Ikeo, K., Reza, M. S., Rashid, J., Yamada, Y., Ikeda, Y., … Watabe, S. (2018). Metagenome-based diversity analyses suggest a strong locality signal for bacterial communities associated with oyster aquaculture farms in Ofunato Bay. Gene, 665, 149–154. https://doi.org/10.1016/j.gene.2018.04.073
Reza, M. S., Kobiyama, A., Yamada, Y., Ikeda, Y., Ikeda, D., Mizusawa, N., … Watabe, S. (2018). Taxonomic profiles in metagenomic analyses of free-living microbial communities in the Ofunato Bay. Gene, 665, 192–200. https://doi.org/10.1016/j.gene.2018.04.075
Kudo, T., Kobiyama, A., Rashid, J., Reza, M. S., Yamada, Y., Ikeda, Y., … Watabe, S. (2018). Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis. Gene, 665, 174–184. https://doi.org/10.1016/j.gene.2018.04.072
Reza, M. S., Kobiyama, A., Yamada, Y., Ikeda, Y., Ikeda, D., Mizusawa, N., … Watabe, S. (2018). Basin-scale seasonal changes in marine free-living bacterioplankton community in the Ofunato Bay. Gene, 665, 185–191. https://doi.org/10.1016/j.gene.2018.04.074
Baalkhuyur, F. M., Bin Dohaish, E.-J. A., Elhalwagy, M. E. A., Alikunhi, N. M., AlSuwailem, A. M., Røstad, A., … Duarte, C. M. (2018). Microplastic in the gastrointestinal tract of fishes along the Saudi Arabian Red Sea coast. Marine Pollution Bulletin, 131, 407–415. https://doi.org/10.1016/j.marpolbul.2018.04.040
Duarte, C. M., Riker, P., Srinivasan, M., Robinson, P. W., Gallo-Reynoso, J. P., & Costa, D. P. (2018). Sonification of Animal Tracks as an Alternative Representation of Multi-Dimensional Data: A Northern Elephant Seal Example. Frontiers in Marine Science, 5. https://doi.org/10.3389/fmars.2018.00128
Wang, W., Liu, A., Li, Z., Zhang, X., Li, Q., & Zhou, X. (2018). Protecting multi-party privacy in location-aware social point-of-interest recommendation. World Wide Web, 22(2), 863–883. https://doi.org/10.1007/s11280-018-0550-9
Arias-Ortiz, A., Serrano, O., Masqué, P., Lavery, P. S., Mueller, U., Kendrick, G. A., … Duarte, C. M. (2018). A marine heatwave drives massive losses from the world’s largest seagrass carbon stocks. Nature Climate Change, 8(4), 338–344. https://doi.org/10.1038/s41558-018-0096-y
Wesselmann, M., González-Wangüemert, M., Serrão, E. A., Engelen, A. H., Renault, L., García-March, J. R., … Hendriks, I. E. (2018). Genetic and oceanographic tools reveal high population connectivity and diversity in the endangered pen shell Pinna nobilis. Scientific Reports, 8(1). https://doi.org/10.1038/s41598-018-23004-2
Younis, S., Weiland, C., Hoehndorf, R., Dressler, S., Hickler, T., Seeger, B., & Schmidt, M. (2018). Taxon and trait recognition from digitized herbarium specimens using deep convolutional neural networks. Botany Letters, 165(3-4), 377–383. https://doi.org/10.1080/23818107.2018.1446357