2017

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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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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Jiang, H., Sheong, F. K., Zhu, L., Gao, X., Bernauer, J., & Huang, X. (2015). Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement. PLOS Computational Biology, 11(7), e1004404. https://doi.org/10.1371/journal.pcbi.1004404
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Walkiewicz, K. W., Girault, J.-A., & Arold, S. T. (2015). How to awaken your nanomachines: Site-specific activation of focal adhesion kinases through ligand interactions. Progress in Biophysics and Molecular Biology, 119(1), 60–71. https://doi.org/10.1016/j.pbiomolbio.2015.06.001
Khamis, A. M., Hamilton, A. R., Medvedeva, Y. A., Alam, T., Alam, I., Essack, M., … Bajic, V. B. (2015). Insights into the Transcriptional Architecture of Behavioral Plasticity in the Honey Bee Apis mellifera. Scientific Reports, 5(1). https://doi.org/10.1038/srep11136
Cui, X., Naveed, H., & Gao, X. (2015). Finding optimal interaction interface alignments between biological complexes. Bioinformatics, 31(12), i133–i141. https://doi.org/10.1093/bioinformatics/btv242
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Hoehndorf, R., Schofield, P. N., & Gkoutos, G. V. (2015). Analysis of the human diseasome using phenotype similarity between common, genetic and infectious diseases. Scientific Reports, 5(1). https://doi.org/10.1038/srep10888
Roperch, J.-P., Benzekri, K., Mansour, H., & Incitti, R. (2015). Improved amplification efficiency on stool samples by addition of spermidine and its use for non-invasive detection of colorectal cancer. BMC Biotechnology, 15(1). https://doi.org/10.1186/s12896-015-0148-6
Sasaki, M., Orba, Y., Anindita, P. D., Ishii, A., Ueno, K., Hang’ombe, B. M., … Sawa, H. (2015). Distinct Lineages of Bufavirus in Wild Shrews and Nonhuman Primates. Emerging Infectious Diseases, 21(7), 1230–1233. https://doi.org/10.3201/eid2107.141969
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Baran, J., Durgahee, B. S. B., Eilbeck, K., Antezana, E., Hoehndorf, R., & Dumontier, M. (2015). GFVO: the Genomic Feature and Variation Ontology. PeerJ, 3, e933. https://doi.org/10.7717/peerj.933
Ates, L. S., Ummels, R., Commandeur, S., van der Weerd, R., Sparrius, M., Weerdenburg, E., … Houben, E. N. G. (2015). Essential Role of the ESX-5 Secretion System in Outer Membrane Permeability of Pathogenic Mycobacteria. PLOS Genetics, 11(5), e1005190. https://doi.org/10.1371/journal.pgen.1005190
Ramaprasad, A., Mourier, T., Naeem, R., Malas, T. B., Moussa, E., Panigrahi, A., … Pain, A. (2015). Comprehensive Evaluation of Toxoplasma gondii VEG and Neospora caninum LIV Genomes with Tachyzoite Stage Transcriptome and Proteome Defines Novel Transcript Features. PLOS ONE, 10(4), e0124473. https://doi.org/10.1371/journal.pone.0124473
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Huang, C.-L., Pu, P.-H., Huang, H.-J., Sung, H.-M., Liaw, H.-J., Chen, Y.-M., … Chiang, T.-Y. (2015). Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts. BMC Genomics, 16(1). https://doi.org/10.1186/s12864-015-1369-8
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Hayakawa, S., Takaku, Y., Hwang, J. S., Horiguchi, T., Suga, H., Gehring, W., … Gojobori, T. (2015). Function and Evolutionary Origin of Unicellular Camera-Type Eye Structure. PLOS ONE, 10(3), e0118415. https://doi.org/10.1371/journal.pone.0118415
Soufan, O., Kleftogiannis, D., Kalnis, P., & Bajic, V. B. (2015). DWFS: A Wrapper Feature Selection Tool Based on a Parallel Genetic Algorithm. PLOS ONE, 10(2), e0117988. https://doi.org/10.1371/journal.pone.0117988
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2014

Marondedze, C., Wong, A., Groen, A., Serrano, N., Jankovic, B., Lilley, K., … Thomas, L. (2014). Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage. International Journal of Molecular Sciences, 16(1), 857–870. https://doi.org/10.3390/ijms16010857
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Grewal, N., Thornton, G. M., Behzad, H., Sharma, A., Lu, A., Zhang, P., … Scott, A. (2014). Accumulation of Oxidized LDL in the Tendon Tissues of C57BL/6 or Apolipoprotein E Knock-Out Mice That Consume a High Fat Diet: Potential Impact on Tendon Health. PLoS ONE, 9(12), e114214. https://doi.org/10.1371/journal.pone.0114214
Chen, P., Huang, J. Z., & Gao, X. (2014). LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone. BMC Bioinformatics, 15(Suppl 15), S4. https://doi.org/10.1186/1471-2105-15-s15-s4
Ishii, A., Ueno, K., Orba, Y., Sasaki, M., Moonga, L., Hang’ombe, B. M., … Sawa, H. (2014). A nairovirus isolated from African bats causes haemorrhagic gastroenteritis and severe hepatic disease in mice. Nature Communications, 5(1). https://doi.org/10.1038/ncomms6651
Liu, K., Smith, R. L., Nguyen-Vu, T., Candelaria, N. R., Rogerson, C. M., Johnson, W. E., … Lin, C.-Y. (2013). Abstract 3107: Runt-related transcription factor 1 (RUNX1) is involved in transcriptional repression by estrogen receptor and breast cancer cell proliferation. Molecular and Cellular Biology. https://doi.org/10.1158/1538-7445.am2013-3107
Ma, L., Li, A., Zou, D., Xu, X., Xia, L., Yu, J., … Zhang, Z. (2014). LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs. Nucleic Acids Research, 43(D1), D187–D192. https://doi.org/10.1093/nar/gku1167
Raies, A. B., Mansour, H., Incitti, R., & Bajic, V. B. (2014). DDMGD: the database of text-mined associations between genes methylated in diseases from different species. Nucleic Acids Research, 43(D1), D879–D886. https://doi.org/10.1093/nar/gku1168
Kadaré, G., Gervasi, N., Brami-Cherrier, K., Blockus, H., El Messari, S., Arold, S. T., & Girault, J.-A. (2015). Conformational Dynamics of the Focal Adhesion Targeting Domain Control Specific Functions of Focal Adhesion Kinase in Cells. Journal of Biological Chemistry, 290(1), 478–491. https://doi.org/10.1074/jbc.m114.593632
Huang, C.-L., Ho, C.-W., Chiang, Y.-C., Shigemoto, Y., Hsu, T.-W., Hwang, C.-C., … Chiang, T.-Y. (2014). Adaptive divergence with gene flow in incipient speciation ofMiscanthus floridulus/sinensiscomplex (Poaceae). The Plant Journal, 80(5), 834–847. https://doi.org/10.1111/tpj.12676
Oliver, P. G., Vestheim, H., Antunes, A., & Kaartvedt, S. (2014). Systematics, functional morphology and distribution of a bivalve (Apachecorbula muriatica gen. et sp. nov.) from the rim of the “Valdivia Deep” brine pool in the Red Sea. Journal of the Marine Biological Association of the United Kingdom, 95(3), 523–535. https://doi.org/10.1017/s0025315414001234
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