2018

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
Alam, T., Alazmi, M., Naser, R., Huser, F., Momin, A. A., Walkiewicz, K. W., … Arold, S. T. (2018). Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs. https://doi.org/10.1101/278903
Anton, A., Hendriks, I. E., Marbà, N., Krause-Jensen, D., Garcias-Bonet, N., & Duarte, C. M. (2018). Iron Deficiency in Seagrasses and Macroalgae in the Red Sea Is Unrelated to Latitude and Physiological Performance. Frontiers in Marine Science, 5. https://doi.org/10.3389/fmars.2018.00074
Al Rowaihi, I. S., Kick, B., Grötzinger, S. W., Burger, C., Karan, R., Weuster-Botz, D., … Arold, S. T. (2018). A two-stage biological gas to liquid transfer process to convert carbon dioxide into bioplastic. Bioresource Technology Reports, 1, 61–68. https://doi.org/10.1016/j.biteb.2018.02.007
Sequeira, A. M. M., Rodríguez, J. P., Eguíluz, V. M., Harcourt, R., Hindell, M., Sims, D. W., … Ferreira, L. C. (2018). Convergence of marine megafauna movement patterns in coastal and open oceans. Proceedings of the National Academy of Sciences, 115(12), 3072–3077. https://doi.org/10.1073/pnas.1716137115
Hays, G. C., Alcoverro, T., Christianen, M. J. A., Duarte, C. M., Hamann, M., Macreadie, P. I., … Esteban, N. (2018). New Tools to Identify the Location of Seagrass Meadows: Marine Grazers as Habitat Indicators. Frontiers in Marine Science, 5. https://doi.org/10.3389/fmars.2018.00009
Handberg-Thorsager, M., Gutierrez-Mazariegos, J., Arold, S. T., Kumar Nadendla, E., Bertucci, P. Y., Germain, P., … Schubert, M. (2018). The ancestral retinoic acid receptor was a low-affinity sensor triggering neuronal differentiation. Science Advances, 4(2), eaao1261. https://doi.org/10.1126/sciadv.aao1261
Manzoor, S., Bilal, A., Khan, S., Ullah, R., Iftikhar, S., Emwas, A.-H., … Faisal, A. (2018). Identification and characterization of SSE15206, a microtubule depolymerizing agent that overcomes multidrug resistance. Scientific Reports, 8(1). https://doi.org/10.1038/s41598-018-21642-0
Mazarrasa, I., Samper-Villarreal, J., Serrano, O., Lavery, P. S., Lovelock, C. E., Marbà, N., … Cortés, J. (2018). Habitat characteristics provide insights of carbon storage in seagrass meadows. Marine Pollution Bulletin, 134, 106–117. https://doi.org/10.1016/j.marpolbul.2018.01.059
Thums, M., Fernández-Gracia, J., Sequeira, A. M. M., Eguíluz, V. M., Duarte, C. M., & Meekan, M. G. (2018). How Big Data Fast Tracked Human Mobility Research and the Lessons for Animal Movement Ecology. Frontiers in Marine Science, 5. https://doi.org/10.3389/fmars.2018.00021
Takahashi, M., Takahashi, E., Joudeh, L. I., Marini, M., Das, G., Elshenawy, M. M., … Hamdan, S. M. (2018). Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep‐sea brines of the Red Sea. The FASEB Journal, 32(6), 3346–3360. https://doi.org/10.1096/fj.201700862rr
Duarte, C. M., & Krause-Jensen, D. (2018). Greenland Tidal Pools as Hot Spots for Ecosystem Metabolism and Calcification. Estuaries and Coasts, 41(5), 1314–1321. https://doi.org/10.1007/s12237-018-0368-9
Villarino, E., Watson, J. R., Jönsson, B., Gasol, J. M., Salazar, G., Acinas, S. G., … Chust, G. (2018). Large-scale ocean connectivity and planktonic body size. Nature Communications, 9(1). https://doi.org/10.1038/s41467-017-02535-8
Rodríguez-García, M. Á., & Hoehndorf, R. (2018). Inferring ontology graph structures using OWL reasoning. BMC Bioinformatics, 19(1). https://doi.org/10.1186/s12859-017-1999-8
Abdel-Haleem, A. M., Hefzi, H., Mineta, K., Gao, X., Gojobori, T., Palsson, B. O., … Jamshidi, N. (2018). Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting. PLOS Computational Biology, 14(1), e1005895. https://doi.org/10.1371/journal.pcbi.1005895

2017

Jamil, M., Kountche, B. A., Haider, I., Guo, X., Ntui, V. O., Jia, K.-P., … Al-Babili, S. (2017). Methyl phenlactonoates are efficient strigolactone analogs with simple structure. Journal of Experimental Botany, 69(9), 2319–2331. https://doi.org/10.1093/jxb/erx438
Pandit, S., Ravikumar, V., Abdel-Haleem, A. M., Derouiche, A., Mokkapati, V. R. S. S., Sihlbom, C., … Mijakovic, I. (2017). Low Concentrations of Vitamin C Reduce the Synthesis of Extracellular Polymers and Destabilize Bacterial Biofilms. Frontiers in Microbiology, 8. https://doi.org/10.3389/fmicb.2017.02599
Kafkas, Ş., Sarntivijai, S., & Hoehndorf, R. (2017). Usage of cell nomenclature in biomedical literature. BMC Bioinformatics, 18(S17). https://doi.org/10.1186/s12859-017-1978-0
Rodríguez-García, M. Á., Gkoutos, G. V., Schofield, P. N., & Hoehndorf, R. (2017). Integrating phenotype ontologies with PhenomeNET. Journal of Biomedical Semantics, 8(1). https://doi.org/10.1186/s13326-017-0167-4
Grötzinger, S. W., Karan, R., Strillinger, E., Bader, S., Frank, A., Al Rowaihi, I. S., … Arold, S. T. (2017). Identification and Experimental Characterization of an Extremophilic Brine Pool Alcohol Dehydrogenase from Single Amplified Genomes. ACS Chemical Biology, 13(1), 161–170. https://doi.org/10.1021/acschembio.7b00792
Fan, M., He, T., Zhang, P., Cheng, H., Zhang, J., Gao, X., & Li, L. (2017). Diffusion-weighted imaging features of breast tumours and the surrounding stroma reflect intrinsic heterogeneous characteristics of molecular subtypes in breast cancer. NMR in Biomedicine, 31(2), e3869. https://doi.org/10.1002/nbm.3869
Mechhoud, S., & Laleg-Kirati, T.-M. (2018). Adaptive energy-based bilinear control of first-order 1-D hyperbolic PDEs: Application to a one-loop parabolic solar collector trough. Journal of the Franklin Institute, 355(2), 827–848. https://doi.org/10.1016/j.jfranklin.2017.12.003
Hoehndorf, R., & Queralt-Rosinach, N. (2017). Data Science and symbolic AI: Synergies, challenges and opportunities [JB]. Data Science, 1(1–2), 27–38. https://doi.org/10.3233/DS-170004
Suen, K. M., Lin, C. C., Seiler, C., George, R., Poncet-Montange, G., Biter, A. B., … Ladbury, J. E. (2018). Phosphorylation of threonine residues on Shc promotes ligand binding and mediates crosstalk between MAPK and Akt pathways in breast cancer cells. The International Journal of Biochemistry & Cell Biology, 94, 89–97. https://doi.org/10.1016/j.biocel.2017.11.014
Raies, A. B., & Bajic, V. B. (2017). In silico toxicology: comprehensive benchmarking of multi‐label classification methods applied to chemical toxicity data. WIREs Computational Molecular Science, 8(3). https://doi.org/10.1002/wcms.1352
Ziegler, M., Eguíluz, V. M., Duarte, C. M., & Voolstra, C. R. (2017). Rare symbionts may contribute to the resilience of coral–algal assemblages. The ISME Journal, 12(1), 161–172. https://doi.org/10.1038/ismej.2017.151
Olayan, R. S., Ashoor, H., & Bajic, V. B. (2017). DDR: efficient computational method to predict drug–target interactions using graph mining and machine learning approaches. Bioinformatics, 34(7), 1164–1173. https://doi.org/10.1093/bioinformatics/btx731
Alsemari, A., Al-Younes, B., Goljan, E., Jaroudi, D., BinHumaid, F., Meyer, B. F., … Monies, D. (2017). Recessive VARS2 mutation underlies a novel syndrome with epilepsy, mental retardation, short stature, growth hormone deficiency, and hypogonadism. Human Genomics, 11(1). https://doi.org/10.1186/s40246-017-0124-4
Alshahrani, M., Soufan, O., Magana-Mora, A., & Bajic, V. B. (2017). DANNP: an efficient artificial neural network pruning tool. PeerJ Computer Science, 3, e137. https://doi.org/10.7717/peerj-cs.137
Sowada, N., Hashem, M. O., Yilmaz, R., Hamad, M., Kakar, N., Thiele, H., … Borck, G. (2017). Mutations of PTPN23 in developmental and epileptic encephalopathy. Human Genetics, 136(11-12), 1455–1461. https://doi.org/10.1007/s00439-017-1850-3
Macreadie, P. I., Serrano, O., Maher, D. T., Duarte, C. M., & Beardall, J. (2017). Addressing calcium carbonate cycling in blue carbon accounting. Limnology and Oceanography Letters, 2(6), 195–201. https://doi.org/10.1002/lol2.10052
Abdel-Haleem, A. M., Lewis, N. E., Jamshidi, N., Mineta, K., Gao, X., & Gojobori, T. (2017). The Emerging Facets of Non-Cancerous Warburg Effect. Frontiers in Endocrinology, 8. https://doi.org/10.3389/fendo.2017.00279
Li, Y., Wang, S., Umarov, R., Xie, B., Fan, M., Li, L., & Gao, X. (2017). DEEPre: sequence-based enzyme EC number prediction by deep learning. Bioinformatics, 34(5), 760–769. https://doi.org/10.1093/bioinformatics/btx680
Han, R., Zhang, F., & Gao, X. (2017). A fast fiducial marker tracking model for fully automatic alignment in electron tomography. Bioinformatics, 34(5), 853–863. https://doi.org/10.1093/bioinformatics/btx653
Chan, K. H., Xue, B., Robinson, R. C., & Hauser, C. A. E. (2017). Systematic Moiety Variations of Ultrashort Peptides Produce Profound Effects on Self-Assembly, Nanostructure Formation, Hydrogelation, and Phase Transition. Scientific Reports, 7(1). https://doi.org/10.1038/s41598-017-12694-9
Kulmanov, M., Khan, M. A., & Hoehndorf, R. (2017). DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier. Bioinformatics, 34(4), 660–668. https://doi.org/10.1093/bioinformatics/btx624
Maddirevula, S., Coskun, S., Alhassan, S., Elnour, A., Alsaif, H. S., Ibrahim, N., … Alkuraya, F. S. (2017). Female Infertility Caused by Mutations in the Oocyte-Specific Translational Repressor PATL2. The American Journal of Human Genetics, 101(4), 603–608. https://doi.org/10.1016/j.ajhg.2017.08.009
Wang, S., Li, Z., Yu, Y., & Xu, J. (2017). Folding Membrane Proteins by Deep Transfer Learning. Cell Systems, 5(3), 202–211.e3. https://doi.org/10.1016/j.cels.2017.09.001
Anazi, S., Maddirevula, S., Salpietro, V., Asi, Y. T., Alsahli, S., Alhashem, A., … Alkuraya, F. S. (2017). Expanding the genetic heterogeneity of intellectual disability. Human Genetics, 136(11-12), 1419–1429. https://doi.org/10.1007/s00439-017-1843-2
Gadd, S., Huff, V., Walz, A. L., Ooms, A. H. A. G., Armstrong, A. E., Gerhard, D. S., … Perlman, E. J. (2017). A Children’s Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor. Nature Genetics, 49(10), 1487–1494. https://doi.org/10.1038/ng.3940
Magana-Mora, A., Kalkatawi, M., & Bajic, V. B. (2017). Omni-PolyA: a method and tool for accurate recognition of Poly(A) signals in human genomic DNA. BMC Genomics, 18(1). https://doi.org/10.1186/s12864-017-4033-7
Rapakoulia, T., Gao, X., Huang, Y., de Hoon, M., Okada-Hatakeyama, M., Suzuki, H., & Arner, E. (2017). Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment. Bioinformatics, 33(23), 3696–3700. https://doi.org/10.1093/bioinformatics/btx503
Dai, H., Umarov, R., Kuwahara, H., Li, Y., Song, L., & Gao, X. (2017). Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape. Bioinformatics, 33(22), 3575–3583. https://doi.org/10.1093/bioinformatics/btx480
Han, R., Wan, X., Wang, Z., Hao, Y., Zhang, J., Chen, Y., … Zhang, F. (2017). AuTom: A novel automatic platform for electron tomography reconstruction. Journal of Structural Biology, 199(3), 196–208. https://doi.org/10.1016/j.jsb.2017.07.008
Iftikhar, S., Khan, S., Bilal, A., Manzoor, S., Abdullah, M., Emwas, A.-H., … Saleem, R. S. Z. (2017). Synthesis and evaluation of modified chalcone based p53 stabilizing agents. Bioorganic & Medicinal Chemistry Letters, 27(17), 4101–4106. https://doi.org/10.1016/j.bmcl.2017.07.042
Shao, M., Ma, J., & Wang, S. (2017). DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields. Bioinformatics, 33(14), i267–i273. https://doi.org/10.1093/bioinformatics/btx267
Yang, P., Zhao, P., & Gao, X. (2017). Robust Online Multi-Task Learning with Correlative and Personalized Structures. IEEE Transactions on Knowledge and Data Engineering, 29(11), 2510–2521. https://doi.org/10.1109/tkde.2017.2703106
Belkhatir, Z., & Laleg-Kirati, T.-M. (2018). Estimation of Multiple Point Sources for Linear Fractional Order Systems Using Modulating Functions. IEEE Control Systems Letters, 2(1), 7–12. https://doi.org/10.1109/lcsys.2017.2720681
Wang, J. J.-Y., Cui, X., Yu, G., Guo, L., & Gao, X. (2017). When sparse coding meets ranking: a joint framework for learning sparse codes and ranking scores. Neural Computing and Applications, 31(3), 701–710. https://doi.org/10.1007/s00521-017-3102-9
Jimenez-Infante, F., Ngugi, D. K., Vinu, M., Blom, J., Alam, I., Bajic, V. B., & Stingl, U. (2017). Genomic characterization of two novel SAR11 isolates from the Red Sea, including the first strain of the SAR11 Ib clade. FEMS Microbiology Ecology, 93(7). https://doi.org/10.1093/femsec/fix083
Magana-Mora, A., & Bajic, V. B. (2017). OmniGA: Optimized Omnivariate Decision Trees for Generalizable Classification Models. Scientific Reports, 7(1). https://doi.org/10.1038/s41598-017-04281-9
Guan, Y., Haroon, M. F., Alam, I., Ferry, J. G., & Stingl, U. (2017). Single-cell genomics reveals pyrrolysine-encoding potential in members of uncultivated archaeal candidate division MSBL1. Environmental Microbiology Reports, 9(4), 404–410. https://doi.org/10.1111/1758-2229.12545
Salhi, A., Essack, M., Alam, T., Bajic, V. P., Ma, L., Radovanovic, A., … Bajic, V. B. (2017). DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. RNA Biology, 14(7), 963–971. https://doi.org/10.1080/15476286.2017.1312243
Wu, S., Wang, D., Liu, J., Feng, Y., Weng, J., Li, Y., … Wang, W. (2017). The Dynamic Multisite Interactions between Two Intrinsically Disordered Proteins. Angewandte Chemie International Edition, 56(26), 7515–7519. https://doi.org/10.1002/anie.201701883
Nielsen, J., Archer, J., Essack, M., Bajic, V. B., Gojobori, T., & Mijakovic, I. (2017). Building a bio-based industry in the Middle East through harnessing the potential of the Red Sea biodiversity. Applied Microbiology and Biotechnology, 101(12), 4837–4851. https://doi.org/10.1007/s00253-017-8310-9
Costa, R. M., Rauf, S., & Hauser, C. A. E. (2017). Towards biologically relevant synthetic designer matrices in 3D bioprinting for tissue engineering and regenerative medicine. Current Opinion in Biomedical Engineering, 2, 90–98. https://doi.org/10.1016/j.cobme.2017.05.001
Kobayashi, M., Ohyanagi, H., Takanashi, H., Asano, S., Kudo, T., Kajiya-Kanegae, H., … Yano, K. (2017). Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data. DNA Research, 24(4), 397–405. https://doi.org/10.1093/dnares/dsx012
Komatsu, S., Wang, X., Yin, X., Nanjo, Y., Ohyanagi, H., & Sakata, K. (2017). Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database. Journal of Proteomics, 163, 52–66. https://doi.org/10.1016/j.jprot.2017.05.009
Alshahrani, M., Khan, M. A., Maddouri, O., Kinjo, A. R., Queralt-Rosinach, N., & Hoehndorf, R. (2017). Neuro-symbolic representation learning on biological knowledge graphs. Bioinformatics, 33(17), 2723–2730. https://doi.org/10.1093/bioinformatics/btx275
Arae, T., Isai, S., Sakai, A., Mineta, K., Yokota Hirai, M., Suzuki, Y., … Chiba, Y. (2017). Co-ordinated Regulations of mRNA Synthesis and Decay during Cold Acclimation in Arabidopsis Cells. Plant and Cell Physiology, 58(6), 1090–1102. https://doi.org/10.1093/pcp/pcx059
Boudellioua, I., Mahamad Razali, R. B., Kulmanov, M., Hashish, Y., Bajic, V. B., Goncalves-Serra, E., … Hoehndorf, R. (2017). Semantic prioritization of novel causative genomic variants. PLOS Computational Biology, 13(4), e1005500. https://doi.org/10.1371/journal.pcbi.1005500
Zambri, B., Djellouli, R., & Laleg-Kirati, T.-M. (2017). An efficient multistage algorithm for full calibration of the hemodynamic model from BOLD signal responses. International Journal for Numerical Methods in Biomedical Engineering, 33(11), e2875. https://doi.org/10.1002/cnm.2875
Gkoutos, G. V., Schofield, P. N., & Hoehndorf, R. (2017). The anatomy of phenotype ontologies: principles, properties and applications. Briefings in Bioinformatics, 19(5), 1008–1021. https://doi.org/10.1093/bib/bbx035
Monies, D., Maddirevula, S., Kurdi, W., Alanazy, M. H., Alkhalidi, H., Al-Owain, M., … Alkuraya, F. S. (2017). Autozygosity reveals recessive mutations and novel mechanisms in dominant genes: implications in variant interpretation. Genetics in Medicine, 19(10), 1144–1150. https://doi.org/10.1038/gim.2017.22
Alzahrani, M., Kuwahara, H., Wang, W., & Gao, X. (2017). Gracob: a novel graph-based constant-column biclustering method for mining growth phenotype data. Bioinformatics, 33(16), 2523–2531. https://doi.org/10.1093/bioinformatics/btx199
Sulaiman, R. A., Patel, N., Alsharif, H., Arold, S. T., & Alkuraya, F. S. (2017). A novel mutation in SLC25A46 causes optic atrophy and progressive limb spasticity, with no cerebellar atrophy or axonal neuropathy. Clinical Genetics, 92(2), 230–231. https://doi.org/10.1111/cge.12963
Lafi, F. F., Alam, I., Geurts, R., Bisseling, T., Bajic, V. B., Hirt, H., & Saad, M. M. (2017). Draft Genome Sequence of Ochrobactrum intermedium Strain SA148, a Plant Growth-Promoting Desert Rhizobacterium. Genome Announcements, 5(9). https://doi.org/10.1128/genomea.01707-16
Kuwahara, H., Umarov, R., Almasri, I., & Gao, X. (2017). ACRE: Absolute concentration robustness exploration in module-based combinatorial networks. Synthetic Biology, 2(1). https://doi.org/10.1093/synbio/ysx001
Nakagawa, S., Niimura, Y., & Gojobori, T. (2017). Comparative genomic analysis of translation initiation mechanisms for genes lacking the Shine–Dalgarno sequence in prokaryotes. Nucleic Acids Research, 45(7), 3922–3931. https://doi.org/10.1093/nar/gkx124
Lafi, F. F., Alam, I., Geurts, R., Bisseling, T., Bajic, V. B., Hirt, H., & Saad, M. M. (2017). Draft Genome Sequence of Enterobacter sp. Sa187, an Endophytic Bacterium Isolated from the Desert Plant Indigofera argentea. Genome Announcements, 5(7). https://doi.org/10.1128/genomea.01638-16
Kulmanov, M., & Hoehndorf, R. (2017). Evaluating the effect of annotation size on measures of semantic similarity. Journal of Biomedical Semantics, 8(1). https://doi.org/10.1186/s13326-017-0119-z
Najibi, S. M., Maadooliat, M., Zhou, L., Huang, J. Z., & Gao, X. (2017). Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions. Computational and Structural Biotechnology Journal, 15, 243–254. https://doi.org/10.1016/j.csbj.2017.01.011
Jarvis, D. E., Ho, Y. S., Lightfoot, D. J., Schmöckel, S. M., Li, B., Borm, T. J. A., … Tester, M. (2017). The genome of Chenopodium quinoa. Nature, 542(7641), 307–312. https://doi.org/10.1038/nature21370
Lafi, F. F., Ramirez-Prado, J. S., Alam, I., Bajic, V. B., Hirt, H., & Saad, M. M. (2017). Draft Genome Sequence of Plant Growth–Promoting Micrococcus luteus Strain K39 Isolated from Cyperus conglomeratus in Saudi Arabia. Genome Announcements, 5(4). https://doi.org/10.1128/genomea.01520-16
Kuwahara, H., Cui, X., Umarov, R., Grünberg, R., Myers, C. J., & Gao, X. (2017). SBOLme: a Repository of SBOL Parts for Metabolic Engineering. ACS Synthetic Biology, 6(4), 732–736. https://doi.org/10.1021/acssynbio.6b00278
Ling, Y., Alshareef, S., Butt, H., Lozano-Juste, J., Li, L., Galal, A. A., … Mahfouz, M. M. (2017). Pre-mRNA splicing repression triggers abiotic stress signaling in plants. The Plant Journal, 89(2), 291–309. https://doi.org/10.1111/tpj.13383
Lafi, F. F., AlBladi, M. L., Salem, N. M., Al-Banna, L., Alam, I., Bajic, V. B., … Saad, M. M. (2017). Draft Genome Sequence of the Plant Growth–Promoting Pseudomonas punonensis Strain D1-6 Isolated from the Desert Plant Erodium hirtum in Jordan. Genome Announcements, 5(2). https://doi.org/10.1128/genomea.01437-16
Motwalli, O., Essack, M., Jankovic, B. R., Ji, B., Liu, X., Ansari, H. R., … Bajic, V. B. (2017). In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria. BMC Genomics, 18(1). https://doi.org/10.1186/s12864-016-3389-4
Ashoor, H., Louis-Brennetot, C., Janoueix-Lerosey, I., Bajic, V. B., & Boeva, V. (2017). HMCan-diff: a method to detect changes in histone modifications in cells with different genetic characteristics. Nucleic Acids Research, gkw1319. https://doi.org/10.1093/nar/gkw1319
Weng, J., Gu, S., Gao, X., Huang, X., & Wang, W. (2017). Maltose-binding protein effectively stabilizes the partially closed conformation of the ATP-binding cassette transporter MalFGK2. Physical Chemistry Chemical Physics, 19(14), 9366–9373. https://doi.org/10.1039/c6cp07943a

2016

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
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
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 Pseudomonas argentinensis Strain SA190 Isolated from the Desert Plant Indigofera argentea. Genome Announcements, 4(6). https://doi.org/10.1128/genomea.01431-16
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Fisher, H. M., Hoehndorf, R., Bazelato, B. S., Dadras, S. S., King, L. E., Gkoutos, G. V., … Schofield, P. N. (2016). DermO; an ontology for the description of dermatologic disease. Journal of Biomedical Semantics, 7(1). https://doi.org/10.1186/s13326-016-0085-x
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
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
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
Nozawa, M., Fujimi, M., Iwamoto, C., Onizuka, K., Fukuda, N., Ikeo, K., & Gojobori, T. (2016). Evolutionary Transitions of MicroRNA-Target Pairs. Genome Biology and Evolution, 8(5), 1621–1633. https://doi.org/10.1093/gbe/evw092
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
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
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
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
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
Ba-alawi Wail, Soufan, O., Essack, M., Kalnis, P., & Bajic, V. B. (2016). DASPfind: new efficient method to predict drug–target interactions. Journal of Cheminformatics, 8(1). https://doi.org/10.1186/s13321-016-0128-4
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
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
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
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
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
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
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
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
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
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
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
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
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

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
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
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
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
Jimenez-Infante, F., Ngugi, D. K., Vinu, M., Alam, I., Kamau, A. A., Blom, J., … Stingl, U. (2015). Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs. Applied and Environmental Microbiology, 82(4), 1215–1226. https://doi.org/10.1128/aem.02852-15
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
Perlman, E. J., Gadd, S., Arold, S. T., Radhakrishnan, A., Gerhard, D. S., Jennings, L., … Smith, M. A. (2015). MLLT1 YEATS domain mutations in clinically distinctive Favourable Histology Wilms tumours. Nature Communications, 6(1). https://doi.org/10.1038/ncomms10013
Kleftogiannis, D., Kalnis, P., & Bajic, V. B. (2015). Progress and challenges in bioinformatics approaches for enhancer identification. Briefings in Bioinformatics, 17(6), 967–979. https://doi.org/10.1093/bib/bbv101