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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Zhao, J., Shang, S., Wang, P., Lui, J. C., & Zhang, X. (2019). Submodular Optimization over Streams with Inhomogeneous Decays. Proceedings of the AAAI Conference on Artificial Intelligence, 33(01), 5861-5868. https://doi.org/10.1609/aaai.v33i01.33015861
Yu, L., Zhang, C., Liang, S., & Zhang, X. (2019). Multi-Order Attentive Ranking Model for Sequential Recommendation. Proceedings of the AAAI Conference on Artificial Intelligence, 33, 5709–5716. https://doi.org/10.1609/aaai.v33i01.33015709
Mahadik, G. A., Agusti, S., & Duarte, C. M. (2019). Distribution and Characteristics of Halobates germanus Population in the Red Sea. Frontiers in Marine Science, 6. https://doi.org/10.3389/fmars.2019.00408
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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
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10.1002/eap.1947Rossbach, 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
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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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Duffy, J. E., Benedetti-Cecchi, L., Trinanes, J., Muller-Karger, F. E., Ambo-Rappe, R., Boström, C., … Yaakub, S. M. (2019). Toward a Coordinated Global Observing System for Seagrasses and Marine Macroalgae. Frontiers in Marine Science, 6. https://doi.org/10.3389/fmars.2019.00317
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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10.1101/635680Acinas, 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
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10.1101/635680Pei, 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
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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
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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
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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
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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
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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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10.1101/536649Shaikh, 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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Akal, A. L., Karan, R., Hohl, A., Alam, I., Vogler, M., Grötzinger, S. W., … Rueping, M. (2018). A polyextremophilic alcohol dehydrogenase from the Atlantis
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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
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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
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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
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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
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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
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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
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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
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Shashi, V., Magiera, M. M., Klein, D., Zaki, M., Schoch, K., Rudnik‐Schöneborn, S., … Yuan, X. (2018). Loss of tubulin deglutamylase
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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
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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
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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
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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
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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
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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
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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
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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
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González‐Wangüemert, M., Basso, L., Balau, A., Costa, J., Renault, L., Serrão, E. A., … Hendriks, I. E. (2018). Gene pool and connectivity patterns of
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10.1002/aqc.2976Gattuso, 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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Wang, J. J.-Y., Tsang, I. W.-H., Cui, X., Lu, Z., & Gao, X. (2017). Multi-instance dictionary learning via multivariate performance measure optimization. Pattern Recognition, 66, 448–459. https://doi.org/10.1016/j.patcog.2016.12.023
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Gojobori, T., Ikeo, K., Katayama, Y., Kawabata, T., Kinjo, A. R., Kinoshita, K., … Yura, K. (2016). VaProS: a database-integration approach for protein/genome information retrieval. Journal of Structural and Functional Genomics, 17(4), 69–81. https://doi.org/10.1007/s10969-016-9211-3
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Aranda, M., Li, Y., Liew, Y. J., Baumgarten, S., Simakov, O., Wilson, M. C., … Voolstra, C. R. (2016). Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle. Scientific Reports, 6(1). https://doi.org/10.1038/srep39734
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Lafi, F. F., Alam, I., Geurts, R., Bisseling, T., Bajic, V. B., Hirt, H., & Saad, M. M. (2016). Draft Genome Sequence of the Phosphate-Solubilizing Bacterium
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Nozawa, M., Onizuka, K., Fujimi, M., Ikeo, K., & Gojobori, T. (2016). Accelerated pseudogenization on the neo-X chromosome in Drosophila miranda. Nature Communications, 7(1). https://doi.org/10.1038/ncomms13659
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Hoehndorf, R., Alshahrani, M., Gkoutos, G. V., Gosline, G., Groom, Q., Hamann, T., … Weiland, C. (2016). The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. Journal of Biomedical Semantics, 7(1). https://doi.org/10.1186/s13326-016-0107-8
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Shamseldin, H. E., Khalifa, O., Binamer, Y. M., Almutawa, A., Arold, S. T., Zaidan, H., & Alkuraya, F. S. (2016). KDF1, encoding keratinocyte differentiation factor 1, is mutated in a multigenerational family with ectodermal dysplasia. Human Genetics, 136(1), 99–105. https://doi.org/10.1007/s00439-016-1741-z
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Soufan, O., Ba-Alawi, W., Afeef, M., Essack, M., Kalnis, P., & Bajic, V. B. (2016). DRABAL: novel method to mine large high-throughput screening assays using Bayesian active learning. Journal of Cheminformatics, 8(1). https://doi.org/10.1186/s13321-016-0177-8
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Elmetennani, S., & Laleg-Kirati, T. M. (2017). Bilinear Approximate Model-Based Robust Lyapunov Control for Parabolic Distributed Collectors. IEEE Transactions on Control Systems Technology, 25(5), 1848–1855. https://doi.org/10.1109/tcst.2016.2618908
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Lafi, F. F., Ramirez-Prado, J. S., Alam, I., Bajic, V. B., Hirt, H., & Saad, M. M. (2016). Draft Genome Sequence ofHalomonas elongataStrain K4, an Endophytic Growth-Promoting Bacterium Enhancing Salinity ToleranceIn Planta. Genome Announcements, 4(6). https://doi.org/10.1128/genomea.01214-16
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Hungler, A., Momin, A., Diederichs, K., & Arold, S., T. (2016). ContaMinerand ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminants. Journal of Applied Crystallography, 49(6), 2252–2258. https://doi.org/10.1107/s1600576716014965
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Schmeier, S., Alam, T., Essack, M., & Bajic, V. B. (2016). TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions. Nucleic Acids Research, 45(D1), D145–D150. https://doi.org/10.1093/nar/gkw1007
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Kleftogiannis, D., Kalnis, P., Arner, E., & Bajic, V. B. (2016). Discriminative identification of transcriptional responses of promoters and enhancers after stimulus. Nucleic Acids Research, gkw1015. https://doi.org/10.1093/nar/gkw1015
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Alam, T., Uludag, M., Essack, M., Salhi, A., Ashoor, H., Hanks, J. B., … Bajic, V. B. (2016). FARNA: knowledgebase of inferred functions of non-coding RNA transcripts. Nucleic Acids Research, gkw973. https://doi.org/10.1093/nar/gkw973
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Feng, Y., Zhang, L., Wu, S., Liu, Z., Gao, X., Zhang, X., … Wang, W. (2016). Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis. Angewandte Chemie International Edition, 55(45), 13990–13994. https://doi.org/10.1002/anie.201606613
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Zhu, L., Jiang, H., Sheong, F. K., Cui, X., Wang, Y., Gao, X., & Huang, X. (2017). Understanding the core of RNA interference: The dynamic aspects of Argonaute-mediated processes. Progress in Biophysics and Molecular Biology, 128, 39–46. https://doi.org/10.1016/j.pbiomolbio.2016.09.008
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Shahmuradov, I. A., Mohamad Razali, R., Bougouffa, S., Radovanovic, A., & Bajic, V. B. (2016). bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria andEscherichia coli. Bioinformatics, btw629. https://doi.org/10.1093/bioinformatics/btw629
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Al-Amoudi, S., Razali, R., Essack, M., Amini, M. S., Bougouffa, S., Archer, J. A. C., … Bajic, V. B. (2016). Metagenomics as a preliminary screen for antimicrobial bioprospecting. Gene, 594(2), 248–258. https://doi.org/10.1016/j.gene.2016.09.021
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Al-Amoudi, S., Essack, M., Simões, M., Bougouffa, S., Soloviev, I., Archer, J., … Bajic, V. (2016). Bioprospecting Red Sea Coastal Ecosystems for Culturable Microorganisms and Their Antimicrobial Potential. Marine Drugs, 14(9), 165. https://doi.org/10.3390/md14090165
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Roperch, J.-P., Grandchamp, B., Desgrandchamps, F., Mongiat-Artus, P., Ravery, V., Ouzaid, I., … Incitti, R. (2016). Promoter hypermethylation of HS3ST2, SEPTIN9 and SLIT2 combined with FGFR3 mutations as a sensitive/specific urinary assay for diagnosis and surveillance in patients with low or high-risk non-muscle-invasive bladder cancer. BMC Cancer, 16(1). https://doi.org/10.1186/s12885-016-2748-5
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Cui, X., & Gao, X. (2017). K-nearest uphill clustering in the protein structure space. Neurocomputing, 220, 52–59. https://doi.org/10.1016/j.neucom.2016.04.065
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Fujii, C., Kuwahara, H., Yu, G., Guo, L., & Gao, X. (2017). Learning gene regulatory networks from gene expression data using weighted consensus. Neurocomputing, 220, 23–33. https://doi.org/10.1016/j.neucom.2016.02.087
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Smirnova, E., Kwan, J. J., Siu, R., Gao, X., Zoidl, G., Demeler, B., … Donaldson, L. W. (2016). A new mode of SAM domain mediated oligomerization observed in the CASKIN2 neuronal scaffolding protein. Cell Communication and Signaling, 14(1). https://doi.org/10.1186/s12964-016-0140-3
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Slater, L., Gkoutos, G. V., Schofield, P. N., & Hoehndorf, R. (2016). Using AberOWL for fast and scalable reasoning over BioPortal ontologies. Journal of Biomedical Semantics, 7(1). https://doi.org/10.1186/s13326-016-0090-0
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Alfadhel, M., Nashabat, M., Qahtani, H. A., Alfares, A., Mutairi, F. A., Shaalan, H. A., … Ali, Q. A. (2016). Mutation in SLC6A9 encoding a glycine transporter causes a novel form of non-ketotic hyperglycinemia in humans. Human Genetics, 135(11), 1263–1268. https://doi.org/10.1007/s00439-016-1719-x
Lafi, F. F., Bokhari, A., Alam, I., Bajic, V. B., Hirt, H., & Saad, M. M. (2016). Draft Genome Sequence of the Plant Growth-Promoting Cupriavidus gilardii Strain JZ4 Isolated from the Desert Plant Tribulus terrestris. Genome Announcements, 4(4). https://doi.org/10.1128/genomea.00678-16
Anazi, S., Maddirevula, S., Faqeih, E., Alsedairy, H., Alzahrani, F., Shamseldin, H. E., … Alkuraya, F. S. (2016). Clinical genomics expands the morbid genome of intellectual disability and offers a high diagnostic yield. Molecular Psychiatry, 22(4), 615–624. https://doi.org/10.1038/mp.2016.113
Ishikawa, M., Shimizu, H., Nozawa, M., Ikeo, K., & Gojobori, T. (2016). Two-step evolution of endosymbiosis between hydra and algae. Molecular Phylogenetics and Evolution, 103, 19–25. https://doi.org/10.1016/j.ympev.2016.07.010
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Boudellioua, I., Saidi, R., Hoehndorf, R., Martin, M. J., & Solovyev, V. (2016). Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining. PLOS ONE, 11(7), e0158896. https://doi.org/10.1371/journal.pone.0158896
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Wang, Y., Gao, Z.-M., Li, J.-T., Bougouffa, S., Tian, R. M., Bajic, V. B., & Qian, P.-Y. (2016). Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments. Science Bulletin, 61(15), 1176–1186. https://doi.org/10.1007/s11434-016-1135-6
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Ishikawa, M., Yuyama, I., Shimizu, H., Nozawa, M., Ikeo, K., & Gojobori, T. (2016). Different Endosymbiotic Interactions in Two Hydra Species Reflect the Evolutionary History of Endosymbiosis. Genome Biology and Evolution, 8(7), 2155–2163. https://doi.org/10.1093/gbe/evw142
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Cui, X., Lu, Z., Wang, S., Jing-Yan Wang, J., & Gao, X. (2016). CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction. Bioinformatics, 32(12), i332–i340. https://doi.org/10.1093/bioinformatics/btw271
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Bolleman, J. T., Mungall, C. J., Strozzi, F., Baran, J., Dumontier, M., Bonnal, R. J. P., … Cock, P. J. A. (2016). FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation. Journal of Biomedical Semantics, 7(1). https://doi.org/10.1186/s13326-016-0067-z
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Shimada, M. K., Sanbonmatsu, R., Yamaguchi-Kabata, Y., Yamasaki, C., Suzuki, Y., Chakraborty, R., … Imanishi, T. (2016). Selection pressure on human STR loci and its relevance in repeat expansion disease. Molecular Genetics and Genomics, 291(5), 1851–1869. https://doi.org/10.1007/s00438-016-1219-7
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Maadooliat, M., Zhou, L., Najibi, S. M., Gao, X., & Huang, J. Z. (2016). Collective Estimation of Multiple Bivariate Density Functions With Application to Angular-Sampling-Based Protein Loop Modeling. Journal of the American Statistical Association, 111(513), 43–56. https://doi.org/10.1080/01621459.2015.1099535
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Kuwahara, H., Alazmi, M., Cui, X., & Gao, X. (2016). MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind. Nucleic Acids Research, 44(W1), W217–W225. https://doi.org/10.1093/nar/gkw342
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Hoehndorf, R., Gkoutos, G. V., & Schofield, P. N. (2016). Datamining with Ontologies. Data Mining Techniques for the Life Sciences, 385–397. https://doi.org/10.1007/978-1-4939-3572-7_19
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Da, L.-T., Pardo-Avila, F., Xu, L., Silva, D.-A., Zhang, L., Gao, X., … Huang, X. (2016). Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue. Nature Communications, 7(1). https://doi.org/10.1038/ncomms11244
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Kim, J. J., Lorenz, R., Arold, S. T., Reger, A. S., Sankaran, B., Casteel, D. E., … Kim, C. (2016). Crystal Structure of PKG I:cGMP Complex Reveals a cGMP-Mediated Dimeric Interface that Facilitates cGMP-Induced Activation. Structure, 24(5), 710–720. https://doi.org/10.1016/j.str.2016.03.009
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Lu, Z., Fu, Z., Xiang, T., Han, P., Wang, L., & Gao, X. (2017). Learning from Weak and Noisy Labels for Semantic Segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence, 39(3), 486–500. https://doi.org/10.1109/tpami.2016.2552172
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Henkel, R., Hoehndorf, R., Kacprowski, T., Knüpfer, C., Liebermeister, W., & Waltemath, D. (2016). Notions of similarity for computational biology models. https://doi.org/10.1101/044818
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Cao, H., Dong, C., Bougouffa, S., Li, J., Zhang, W., Shao, Z., … Qian, P.-Y. (2016). Delta-proteobacterial SAR324 group in hydrothermal plumes on the South Mid-Atlantic Ridge. Scientific Reports, 6(1). https://doi.org/10.1038/srep22842
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Zhu, L., Jiang, H., Sheong, F. K., Cui, X., Gao, X., Wang, Y., & Huang, X. (2016). A Flexible Domain-Domain Hinge Promotes an Induced-fit Dominant Mechanism for the Loading of Guide-DNA into Argonaute Protein inThermus thermophilus. The Journal of Physical Chemistry B, 120(10), 2709–2720. https://doi.org/10.1021/acs.jpcb.5b12426
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Carter, B. Z., Mak, P. Y., Chen, Y., Mak, D. H., Mu, H., Jacamo, R., … Andreeff, M. (2016). Anti-apoptotic ARC protein confers chemoresistance by controlling leukemia-microenvironment interactions through a NFκB/IL1β signaling network. Oncotarget, 7(15), 20054–20067. https://doi.org/10.18632/oncotarget.7911
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Ryu, T., Seridi, L., Moitinho-Silva, L., Oates, M., Liew, Y. J., Mavromatis, C., … Ravasi, T. (2016). Hologenome analysis of two marine sponges with different microbiomes. BMC Genomics, 17(1). https://doi.org/10.1186/s12864-016-2501-0
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Lissanu Deribe, Y., Shi, Y., Rai, K., Nezi, L., Amin, S. B., Wu, C.-C., … Chin, L. (2016). Truncating PREX2 mutations activate its GEF activity and alter gene expression regulation in NRAS-mutant melanoma. Proceedings of the National Academy of Sciences, 113(9), E1296–E1305. https://doi.org/10.1073/pnas.1513801113
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Ohyanagi, H., Obayashi, T., & Yano, K. (2016). Editorial:Plant and Cell Physiology’s 2016 Online Database Issue. Plant and Cell Physiology, 57(1), 1–3. https://doi.org/10.1093/pcp/pcv205
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Emwas, A.-H., Roy, R., McKay, R. T., Ryan, D., Brennan, L., Tenori, L., … Wishart, D. S. (2016). Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis. Journal of Proteome Research, 15(2), 360–373. https://doi.org/10.1021/acs.jproteome.5b00885
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Mwirichia, R., Alam, I., Rashid, M., Vinu, M., Ba-Alawi, W., Anthony Kamau, A., … Stingl, U. (2016). Metabolic traits of an uncultured archaeal lineage -MSBL1- from brine pools of the Red Sea. Scientific Reports, 6(1). https://doi.org/10.1038/srep19181
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Kim, K., Omori, R., Ueno, K., Iida, S., & Ito, K. (2016). Host-Specific and Segment-Specific Evolutionary Dynamics of Avian and Human Influenza A Viruses: A Systematic Review. PLOS ONE, 11(1), e0147021. https://doi.org/10.1371/journal.pone.0147021
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Alabdulmohsin, I., Cisse, M., Gao, X., & Zhang, X. (2016). Large margin classification with indefinite similarities. Machine Learning, 103(2), 215–237. https://doi.org/10.1007/s10994-015-5542-8
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Raies, A. B., & Bajic, V. B. (2016). In silicotoxicology: computational methods for the prediction of chemical toxicity. Wiley Interdisciplinary Reviews: Computational Molecular Science, 6(2), 147–172. https://doi.org/10.1002/wcms.1240
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Tanaka, H., Yamamoto, Y., Kashihara, H., Yamazaki, Y., Tani, K., Fujiyoshi, Y., … Tsukita, S. (2016). Claudin-21 Has a Paracellular Channel Role at Tight Junctions. Molecular and Cellular Biology, 36(6), 954–964. https://doi.org/10.1128/mcb.00758-15
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Carpenter, M. H., Parsani, M., Nielsen, E. J., & Fisher, T. C. (2016). Towards an Entropy Stable Spectral Element Framework for Computational Fluid Dynamics. 54th AIAA Aerospace Sciences Meeting. https://doi.org/10.2514/6.2016-1058
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2015
Horiuchi, Y., Harushima, Y., Fujisawa, H., Mochizuki, T., Fujita, M., Ohyanagi, H., & Kurata, N. (2015). Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes. BMC Genomics, 16(1). https://doi.org/10.1186/s12864-015-2319-1
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Antunes, A., Stackebrandt, E., & Lima, N. (2016). Fueling the Bio-economy: European Culture Collections and Microbiology Education and Training. Trends in Microbiology, 24(2), 77–79. https://doi.org/10.1016/j.tim.2015.11.010
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Soufan, O., Ba-alawi Wail, Afeef, M., Essack, M., Rodionov, V., Kalnis, P., & Bajic, V. B. (2015). Mining Chemical Activity Status from High-Throughput Screening Assays. PLOS ONE, 10(12), e0144426. https://doi.org/10.1371/journal.pone.0144426
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Lennartsson, A., Arner, E., Fagiolini, M., Saxena, A., Andersson, R., Takahashi, H., … Carninci, P. (2015). Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors. Epigenetics & Chromatin, 8(1). https://doi.org/10.1186/s13072-015-0043-3
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Sun, S., Wang, X., Gao, X., Ren, L., Su, X., Bu, D., & Ning, K. (2015). Condensing Raman spectrum for single-cell phenotype analysis. BMC Bioinformatics, 16(Suppl 18), S15. https://doi.org/10.1186/1471-2105-16-s18-s15
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Zhao, F., & Bajic, V. B. (2015). The Value and Significance of Metagenomics of Marine Environments. Genomics, Proteomics & Bioinformatics, 13(5), 271–274. https://doi.org/10.1016/j.gpb.2015.10.002
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Matsumoto, T., Mineta, K., Osada, N., & Araki, H. (2015). An Individual-Based Diploid Model Predicts Limited Conditions Under Which Stochastic Gene Expression Becomes Advantageous. Frontiers in Genetics, 6. https://doi.org/10.3389/fgene.2015.00336
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Ueno, K., Ibarra, M., & Gojobori, T. (2016). Structural adaption of extremophile proteins to the environments with special reference to hydrophobic networks. Ecological Genetics and Genomics, 1, 1–5. https://doi.org/10.1016/j.egg.2015.10.001
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Liao, H.-W., Hsu, J.-M., Xia, W., Wang, H.-L., Wang, Y.-N., Chang, W.-C., … Hung, M.-C. (2015). PRMT1-mediated methylation of the EGF receptor regulates signaling and cetuximab response. Journal of Clinical Investigation, 125(12), 4529–4543. https://doi.org/10.1172/jci82826
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Alzubaidy, H., Essack, M., Malas, T. B., Bokhari, A., Motwalli, O., Kamanu, F. K., … Archer, J. A. C. (2016). Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea. Gene, 576(2), 626–636. https://doi.org/10.1016/j.gene.2015.10.032
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Alma’abadi, A. D., Gojobori, T., & Mineta, K. (2015). Marine Metagenome as A Resource for Novel Enzymes. Genomics, Proteomics & Bioinformatics, 13(5), 290–295. https://doi.org/10.1016/j.gpb.2015.10.001
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Simões, M. F., Antunes, A., Ottoni, C. A., Amini, M. S., Alam, I., Alzubaidy, H., … Bajic, V. B. (2015). Soil and Rhizosphere Associated Fungi in Gray Mangroves (Avicennia marina) from the Red Sea — A Metagenomic Approach. Genomics, Proteomics & Bioinformatics, 13(5), 310–320. https://doi.org/10.1016/j.gpb.2015.07.002
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Salhi, A., Essack, M., Radovanovic, A., Marchand, B., Bougouffa, S., Antunes, A., … Bajic, V. B. (2015). DESM: portal for microbial knowledge exploration systems. Nucleic Acids Research, 44(D1), D624–D633. https://doi.org/10.1093/nar/gkv1147
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Antunes, A., Alam, I., Simões, M. F., Daniels, C., Ferreira, A. J. S., Siam, R., … Bajic, V. B. (2015). First Insights into the Viral Communities of the Deep-sea Anoxic Brines of the Red Sea. Genomics, Proteomics & Bioinformatics, 13(5), 304–309. https://doi.org/10.1016/j.gpb.2015.06.004
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Akihito, Akishinonomiya, F., Ikeda, Y., Aizawa, M., Nakagawa, S., Umehara, Y., … Gojobori, T. (2016). Speciation of two gobioid species, Pterogobius elapoides and Pterogobius zonoleucus revealed by multi-locus nuclear and mitochondrial DNA analyses. Gene, 576(2), 593–602. https://doi.org/10.1016/j.gene.2015.10.014
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Mineta, K., & Gojobori, T. (2016). Databases of the marine metagenomics. Gene, 576(2), 724–728. https://doi.org/10.1016/j.gene.2015.10.035
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Nagai, S., Hida, K., Urushizaki, S., Onitsuka, G., Yasuike, M., Nakamura, Y., … Ototake, M. (2016). Influences of diurnal sampling bias on fixed-point monitoring of plankton biodiversity determined using a massively parallel sequencing-based technique. Gene, 576(2), 667–675. https://doi.org/10.1016/j.gene.2015.10.025
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