2015

Chen, P., Hu, S., Zhang, J., Gao, X., Li, J., Xia, J., & Wang, B. (2016). A Sequence-Based Dynamic Ensemble Learning System for Protein Ligand-Binding Site Prediction. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 13(5), 901–912. https://doi.org/10.1109/tcbb.2015.2505286
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
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
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
Kulakovskiy, I. V., Vorontsov, I. E., Yevshin, I. S., Soboleva, A. V., Kasianov, A. S., Ashoor, H., … Makeev, V. J. (2015). HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. Nucleic Acids Research, 44(D1), D116–D125. https://doi.org/10.1093/nar/gkv1249
Ohyanagi, H., Ebata, T., Huang, X., Gong, H., Fujita, M., Mochizuki, T., … Kurata, N. (2015). OryzaGenome: Genome Diversity Database of WildOryzaSpecies. Plant and Cell Physiology, 57(1), e1–e1. https://doi.org/10.1093/pcp/pcv171
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
Kuwahara, H., Arold, S. T., & Gao, X. (2015). Beyond initiation-limited translational bursting: the effects of burst size distributions on the stability of gene expression. Integrative Biology, 7(12), 1622–1632. https://doi.org/10.1039/c5ib00107b
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
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
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
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
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
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
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
Behzad, H., Ibarra, M. A., Mineta, K., & Gojobori, T. (2016). Metagenomic studies of the Red Sea. Gene, 576(2), 717–723. https://doi.org/10.1016/j.gene.2015.10.034
Nakamura, Y., Yasuike, M., Nishiki, I., Iwasaki, Y., Fujiwara, A., Kawato, Y., … Ototake, M. (2016). V-GAP: Viral genome assembly pipeline. Gene, 576(2), 676–680. https://doi.org/10.1016/j.gene.2015.10.029
Kodzius, R., & Gojobori, T. (2016). Single-cell technologies in environmental omics. Gene, 576(2), 701–707. https://doi.org/10.1016/j.gene.2015.10.031
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
Abdallah, A. M., Hill-Cawthorne, G. A., Otto, T. D., Coll, F., Guerra-Assunção, J. A., Gao, G., … Pain, A. (2015). Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations. Scientific Reports, 5(1). https://doi.org/10.1038/srep15443
Abdel-Haleem, A. M., Rchiad, Z., Khan, B. K., Abdallah, A. M., Naeem, R., Nikhat Sheerin, S., … Pain, A. (2015). Genome Sequence of a Multidrug-Resistant Strain of Stenotrophomonas maltophilia with Carbapenem Resistance, Isolated from King Abdullah Medical City, Makkah, Saudi Arabia. Genome Announcements, 3(5). https://doi.org/10.1128/genomea.01166-15
Eisha, H. A., Chikalov, I., Moshkov, M., & Jankovic, B. (2015). A Simple Decision Rule for Recognition of Poly(A) Tail Signal Motifs in Human Genome. Journal of Advances in Information Technology, 71–74. https://doi.org/10.12720/jait.6.2.71-74
Strillinger, E., Grötzinger, S. W., Allers, T., Eppinger, J., & Weuster-Botz, D. (2015). Production of halophilic proteins using Haloferax volcanii H1895 in a stirred-tank bioreactor. Applied Microbiology and Biotechnology, 100(3), 1183–1195. https://doi.org/10.1007/s00253-015-7007-1
Ashoor, H., Kleftogiannis, D., Radovanovic, A., & Bajic, V. B. (2015). DENdb: database of integrated human enhancers. Database, 2015, bav085. https://doi.org/10.1093/database/bav085
Chandramouli, K. H., Reish, D., Zhang, H., Qian, P.-Y., & Ravasi, T. (2015). Proteomic Changes Associated with Successive Reproductive Periods in Male Polychaetous Neanthes arenaceodentata. Scientific Reports, 5(1). https://doi.org/10.1038/srep13561
Kaur, M., & Esau, L. (2015). Two-step protocol for preparing adherent cells for high-throughput flow cytometry. BioTechniques, 59(3). https://doi.org/10.2144/000114325
Naveed, H., Hameed, U. S., Harrus, D., Bourguet, W., Arold, S. T., & Gao, X. (2015). An integrated structure- and system-based framework to identify new targets of metabolites and known drugs. Bioinformatics, btv477. https://doi.org/10.1093/bioinformatics/btv477
Kalkatawi, M., Alam, I., & Bajic, V. B. (2015). BEACON: automated tool for Bacterial GEnome Annotation ComparisON. BMC Genomics, 16(1). https://doi.org/10.1186/s12864-015-1826-4
Batool, F., Parveen, S., Emwas, A.-H., Sioud, S., Gao, X., Munawar, M. A., & Chotana, G. A. (2015). Synthesis of Fluoroalkoxy Substituted Arylboronic Esters by Iridium-Catalyzed Aromatic C–H Borylation. Organic Letters, 17(17), 4256–4259. https://doi.org/10.1021/acs.orglett.5b02050
Zhang, W., Wang, Y., Bougouffa, S., Tian, R., Cao, H., Li, Y., … Qian, P.-Y. (2015). Synchronized dynamics of bacterial niche-specific functions during biofilm development in a cold seep brine pool. Environmental Microbiology, 17(10), 4089–4104. https://doi.org/10.1111/1462-2920.12978
Kodzius, R., & Gojobori, T. (2015). Marine metagenomics as a source for bioprospecting. Marine Genomics, 24, 21–30. https://doi.org/10.1016/j.margen.2015.07.001
Cheung, L. W., Walkiewicz, K. W., Besong, T. M., Guo, H., Hawke, D. H., Arold, S. T., & Mills, G. B. (2015). Regulation of the PI3K pathway through a p85α monomer–homodimer equilibrium. eLife, 4. https://doi.org/10.7554/elife.06866
Gkoutos, G. V., Hoehndorf, R., Tsaprouni, L., & Schofield, P. N. (2015). Best behaviour? Ontologies and the formal description of animal behaviour. Mammalian Genome, 26(9-10), 540–547. https://doi.org/10.1007/s00335-015-9590-y
Hrabě de Angelis, M., Nicholson, G., Selloum, M., White, J. K., Morgan, H., … Fuchs, H. (2015). Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics. Nature Genetics, 47(9), 969–978. https://doi.org/10.1038/ng.3360
Ritho, J., Arold, S. T., & Yeh, E. T. H. (2015). A Critical SUMO1 Modification of LKB1 Regulates AMPK Activity during Energy Stress. Cell Reports, 12(5), 734–742. https://doi.org/10.1016/j.celrep.2015.07.002
Copetti, D., Zhang, J., El Baidouri, M., Gao, D., Wang, J., Barghini, E., … Wing, R. A. (2015). RiTE database: a resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics, 16(1). https://doi.org/10.1186/s12864-015-1762-3
Guan, Y., Hikmawan, T., Antunes, A., Ngugi, D., & Stingl, U. (2015). Diversity of methanogens and sulfate-reducing bacteria in the interfaces of five deep-sea anoxic brines of the Red Sea. Research in Microbiology, 166(9), 688–699. https://doi.org/10.1016/j.resmic.2015.07.002
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
Meller, S., Di Domizio, J., Voo, K. S., Friedrich, H. C., Chamilos, G., Ganguly, D., … Gilliet, M. (2015). TH17 cells promote microbial killing and innate immune sensing of DNA via interleukin 26. Nature Immunology, 16(9), 970–979. https://doi.org/10.1038/ni.3211
Shahmuradov, I. A., & Solovyev, V. V. (2015). Nsite, NsiteH and NsiteM computer tools for studying transcription regulatory elements: Fig. 1. Bioinformatics, 31(21), 3544–3545. https://doi.org/10.1093/bioinformatics/btv404
Gavelis, G. S., Hayakawa, S., White III, R. A., Gojobori, T., Suttle, C. A., Keeling, P. J., & Leander, B. S. (2015). Eye-like ocelloids are built from different endosymbiotically acquired components. Nature, 523(7559), 204–207. https://doi.org/10.1038/nature14593
Roy, S., Schmeier, S., Arner, E., Alam, T., Parihar, S. P., Ozturk, M., … Suzuki, H. (2015). Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics. Nucleic Acids Research, 43(14), 6969–6982. https://doi.org/10.1093/nar/gkv646
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
Gao, Z.-M., Wang, Y., Tian, R.-M., Lee, O. O., Wong, Y. H., Batang, Z. B., … Qian, P.-Y. (2015). Pyrosequencing revealed shifts of prokaryotic communities between healthy and disease-like tissues of the Red Sea spongeCrella cyathophora. PeerJ, 3, e890. https://doi.org/10.7717/peerj.890
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
Behzad, H., Gojobori, T., & Mineta, K. (2015). Challenges and Opportunities of Airborne Metagenomics. Genome Biology and Evolution, 7(5), 1216–1226. https://doi.org/10.1093/gbe/evv064
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
Hoehndorf, R., Schofield, P. N., & Gkoutos, G. V. (2015). The role of ontologies in biological and biomedical research: a functional perspective. Briefings in Bioinformatics, 16(6), 1069–1080. https://doi.org/10.1093/bib/bbv011
Shenton, M. R., Ohyanagi, H., Wang, Z.-X., Toyoda, A., Fujiyama, A., Nagata, T., … Kurata, N. (2015). Rapid turnover of antimicrobial-type cysteine-rich protein genes in closely related Oryza genomes. Molecular Genetics and Genomics, 290(5), 1753–1770. https://doi.org/10.1007/s00438-015-1028-4
Fan, M., Kuwahara, H., Wang, X., Wang, S., & Gao, X. (2015). Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study. Briefings in Bioinformatics, 16(6), 987–999. https://doi.org/10.1093/bib/bbv015
Gottlieb, A., Hoehndorf, R., Dumontier, M., & Altman, R. B. (2015). Ranking Adverse Drug Reactions With Crowdsourcing. Journal of Medical Internet Research, 17(3), e80. https://doi.org/10.2196/jmir.3962
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
Hou, X., Liu, Y., Liu, H., Chen, X., Liu, M., Che, H., … Zhao, S. (2015). PERK silence inhibits glioma cell growth under low glucose stress by blockage of p-AKT and subsequent HK2’s mitochondria translocation. Scientific Reports, 5(1). https://doi.org/10.1038/srep09065
Kleftogiannis, D., Wong, L., Archer, J. A. C., & Kalnis, P. (2015). Hi-Jack: a novel computational framework for pathway-based inference of host–pathogen interactions. Bioinformatics, 31(14), 2332–2339. https://doi.org/10.1093/bioinformatics/btv138
Mineta, K., Matsumoto, T., Osada, N., & Araki, H. (2015). Population genetics of non-genetic traits: Evolutionary roles of stochasticity in gene expression. Gene, 562(1), 16–21. https://doi.org/10.1016/j.gene.2015.03.011
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
Oellrich, A., Walls, R. L., Cannon, E., Cannon, S. B., Cooper, L., Gardiner, J., … Huala, E. (2015). An ontology approach to comparative phenomics in plants. Plant Methods, 11(1), 10. https://doi.org/10.1186/s13007-015-0053-y
Hoehndorf, R., Gruenberger, M., Gkoutos, G. V., & Schofield, P. N. (2015). Similarity-based search of model organism, disease and drug effect phenotypes. Journal of Biomedical Semantics, 6(1), 6. https://doi.org/10.1186/s13326-015-0001-9
Wang, J. J.-Y., Wang, Y., Jing, B.-Y., & Gao, X. (2015). Regularized maximum correntropy machine. Neurocomputing, 160, 85–92. https://doi.org/10.1016/j.neucom.2014.09.080
Hoehndorf, R., Slater, L., Schofield, P. N., & Gkoutos, G. V. (2015). Aber-OWL: a framework for ontology-based data access in biology. BMC Bioinformatics, 16(1). https://doi.org/10.1186/s12859-015-0456-9
Cannistraci, C. V., Abbas, A., & Gao, X. (2015). Median Modified Wiener Filter for nonlinear adaptive spatial denoising of protein NMR multidimensional spectra. Scientific Reports, 5(1). https://doi.org/10.1038/srep08017
Wakuta, S., Mineta, K., Amano, T., Toyoda, A., Fujiwara, T., Naito, S., & Takano, J. (2015). Evolutionary Divergence of Plant Borate Exporters and Critical Amino Acid Residues for the Polar Localization and Boron-Dependent Vacuolar Sorting of AtBOR1. Plant and Cell Physiology, 56(5), 852–862. https://doi.org/10.1093/pcp/pcv011
Chen, L., Sun, J., Zhang, H., Au, D. W. T., Lam, P. K. S., Zhang, W., … Qian, P.-Y. (2015). Hepatic Proteomic Responses in Marine Medaka (Oryzias melastigma) Chronically Exposed to Antifouling Compound Butenolide [5-octylfuran-2(5H)-one] or 4,5-Dichloro-2-N-Octyl-4-Isothiazolin-3-One (DCOIT). Environmental Science & Technology, 49(3), 1851–1859. https://doi.org/10.1021/es5046748
Tian, R.-M., Lee, O. O., Wang, Y., Cai, L., Bougouffa, S., Chiu, J. M. Y., … Qian, P.-Y. (2015). Effect of polybrominated diphenyl ether (PBDE) treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis. Frontiers in Microbiology, 5. https://doi.org/10.3389/fmicb.2014.00799

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
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
Wang, X., Kuwahara, H., & Gao, X. (2014). Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels. BMC Systems Biology, 8(Suppl 5), S5. https://doi.org/10.1186/1752-0509-8-s5-s5
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
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
Boulbes, D. R., Arold, S. T., Chauhan, G. B., Blachno, K. V., Deng, N., Chang, W.-C., … Esteva, F. J. (2014). HER family kinase domain mutations promote tumor progression and can predict response to treatment in human breast cancer. Molecular Oncology, 9(3), 586–600. https://doi.org/10.1016/j.molonc.2014.10.011
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
Khamis, A. M., Essack, M., Gao, X., & Bajic, V. B. (2014). Distinct profiling of antimicrobial peptide families. Bioinformatics, 31(6), 849–856. https://doi.org/10.1093/bioinformatics/btu738
Sasaki, M., Orba, Y., Ueno, K., Ishii, A., Moonga, L., Hang’ombe, B. M., … Sawa, H. (2015). Metagenomic analysis of the shrew enteric virome reveals novel viruses related to human stool-associated viruses. Journal of General Virology, 96(2), 440–452. https://doi.org/10.1099/vir.0.071209-0
Kleftogiannis, D., Kalnis, P., & Bajic, V. B. (2014). DEEP: a general computational framework for predicting enhancers. Nucleic Acids Research, 43(1), e6–e6. https://doi.org/10.1093/nar/gku1058
Tian, R.-M., Wang, Y., Bougouffa, S., Gao, Z.-M., Cai, L., Zhang, W.-P., … Qian, P.-Y. (2014). Effect of Copper Treatment on the Composition and Function of the Bacterial Community in the Sponge Haliclona cymaeformis. mBio, 5(6). https://doi.org/10.1128/mbio.01980-14
Bastian, R., Dawe, A., Meier, S., Ludidi, N., Bajic, V. B., & Gehring, C. (2010). Gibberellic acid and cGMP-dependent transcriptional regulation inArabidopsis thaliana. Plant Signaling & Behavior, 5(3), 224–232. https://doi.org/10.4161/psb.5.3.10718
Essack, M., Alzubaidy, H., Bajic, V., & Archer, J. (2014). Chemical Compounds Toxic to Invertebrates Isolated from Marine Cyanobacteria of Potential Relevance to the Agricultural Industry. Toxins, 6(11), 3058–3076. https://doi.org/10.3390/toxins6113058
Ma, L., Bajic, V. B., & Zhang, Z. (2013). On the classification of long non-coding RNAs. RNA Biology, 10(6), 924–933. https://doi.org/10.4161/rna.24604
Wang, J. J.-Y., & Gao, X. (2015). Max–min distance nonnegative matrix factorization. Neural Networks, 61, 75–84. https://doi.org/10.1016/j.neunet.2014.10.006
Zhang, W. P., Wang, Y., Tian, R. M., Bougouffa, S., Yang, B., Cao, H. L., … Qian, P.-Y. (2014). Species sorting during biofilm assembly by artificial substrates deployed in a cold seep system. Scientific Reports, 4(1). https://doi.org/10.1038/srep06647
Wong, Y. H., Ryu, T., Seridi, L., Ghosheh, Y., Bougouffa, S., Qian, P.-Y., & Ravasi, T. (2014). Transcriptome analysis elucidates key developmental components of bryozoan lophophore development. Scientific Reports, 4(1). https://doi.org/10.1038/srep06534
Bougouffa, S., Radovanovic, A., Essack, M., & Bajic, V. B. (2014). DEOP: a database on osmoprotectants and associated pathways. Database, 2014. https://doi.org/10.1093/database/bau100
Behzad, H., Tsai, S.-H., Nassab, P., Mousavizadeh, R., McCormack, R. G., & Scott, A. (2014). Mechanism of mast cell adhesion to human tenocytes in vitro. Journal of Orthopaedic Research, 33(1), 9–16. https://doi.org/10.1002/jor.22742
Chen, L., Zhang, H., Sun, J., Wong, Y.-H., Han, Z., Au, D. W. T., … Qian, P.-Y. (2014). Proteomic changes in brain tissues of marine medaka (Oryzias melastigma) after chronic exposure to two antifouling compounds: Butenolide and 4,5-dichloro-2-n-octyl-4-isothiazolin-3-one (DCOIT). Aquatic Toxicology, 157, 47–56. https://doi.org/10.1016/j.aquatox.2014.09.010
Alam, T., Medvedeva, Y. A., Jia, H., Brown, J. B., Lipovich, L., & Bajic, V. B. (2014). Promoter Analysis Reveals Globally Differential Regulation of Human Long Non-Coding RNA and Protein-Coding Genes. PLoS ONE, 9(10), e109443. https://doi.org/10.1371/journal.pone.0109443
Earl, D., Nguyen, N., Hickey, G., Harris, R. S., Fitzgerald, S., Beal, K., … Paten, B. (2014). Alignathon: a competitive assessment of whole-genome alignment methods. Genome Research, 24(12), 2077–2089. https://doi.org/10.1101/gr.174920.114
Wang, J., Almasri, I., Shi, Y., & Gao, X. (2014). Semi-Supervised Transductive Hot Spot Predictor Working on Multiple Assumptions. Current Bioinformatics, 9(3), 258–267. https://doi.org/10.2174/1574893609999140523124421
Abdallah, R. Z., Adel, M., Ouf, A., Sayed, A., Ghazy, M. A., Alam, I., … Siam, R. (2014). Aerobic methanotrophic communities at the Red Sea brine-seawater interface. Frontiers in Microbiology, 5. https://doi.org/10.3389/fmicb.2014.00487
Islam, A. (2014). Contextual Distance Refining for Image Retrieval. The Open Cybernetics & Systemics Journal, 8(1), 40–43. https://doi.org/10.2174/1874110x01408010040
Wang, J. J.-Y., Huang, J. Z., Sun, Y., & Gao, X. (2015). Feature selection and multi-kernel learning for adaptive graph regularized nonnegative matrix factorization. Expert Systems with Applications, 42(3), 1278–1286. https://doi.org/10.1016/j.eswa.2014.09.008
Wang, J. J.-Y., Wang, Y., Zhao, S., & Gao, X. (2015). Maximum mutual information regularized classification. Engineering Applications of Artificial Intelligence, 37, 1–8. https://doi.org/10.1016/j.engappai.2014.08.009
Tian, R.-M., Wang, Y., Bougouffa, S., Gao, Z.-M., Cai, L., Bajic, V., & Qian, P.-Y. (2014). Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge. Environmental Microbiology, 16(11), 3548–3561. https://doi.org/10.1111/1462-2920.12586
Kamanda Ngugi, D., Blom, J., Alam, I., Rashid, M., Ba-Alawi, W., Zhang, G., … Stingl, U. (2014). Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea. The ISME Journal, 9(2), 396–411. https://doi.org/10.1038/ismej.2014.137
Komiyama, T., Iwama, H., Osada, N., Nakamura, Y., Kobayashi, H., Tateno, Y., & Gojobori, T. (2014). Dopamine Receptor Genes and Evolutionary Differentiation in the Domestication of Fighting Cocks and Long-Crowing Chickens. PLoS ONE, 9(7), e101778. https://doi.org/10.1371/journal.pone.0101778
Abd El Ghany, M., Chander, J., Mutreja, A., Rashid, M., Hill-Cawthorne, G. A., Ali, S., … Pain, A. (2014). The Population Structure of Vibrio cholerae from the Chandigarh Region of Northern India. PLoS Neglected Tropical Diseases, 8(7), e2981. https://doi.org/10.1371/journal.pntd.0002981
Reid, A. J., Blake, D. P., Ansari, H. R., Billington, K., Browne, H. P., Bryant, J., … Pain, A. (2014). Genomic analysis of the causative agents of coccidiosis in domestic chickens. Genome Research, 24(10), 1676–1685. https://doi.org/10.1101/gr.168955.113
Moitinho-Silva, L., Seridi, L., Ryu, T., Voolstra, C. R., Ravasi, T., & Hentschel, U. (2014). Revealing microbial functional activities in the Red Sea spongeStylissa carteriby metatranscriptomics. Environmental Microbiology, 16(12), 3683–3698. https://doi.org/10.1111/1462-2920.12533
Guttery, D. S., Poulin, B., Ramaprasad, A., Wall, R. J., Ferguson, D. J. P., Brady, D., … Tewari, R. (2014). Genome-wide Functional Analysis of Plasmodium Protein Phosphatases Reveals Key Regulators of Parasite Development and Differentiation. Cell Host & Microbe, 16(1), 128–140. https://doi.org/10.1016/j.chom.2014.05.020
Hill-Cawthorne, G. A., Hudson, L. O., El Ghany, M. F. A., Piepenburg, O., Nair, M., Dodgson, A., … Pain, A. (2014). Recombinations in Staphylococcal Cassette Chromosome mec Elements Compromise the Molecular Detection of Methicillin Resistance in Staphylococcus aureus. PLoS ONE, 9(6), e101419. https://doi.org/10.1371/journal.pone.0101419
Liu, Q.-X., Wang, X.-F., Ikeo, K., Hirose, S., Gehring, W. J., & Gojobori, T. (2014). Evolutionarily conserved transcription factor Apontic controls the G1/S progression by inducingcyclin Eduring eye development. Proceedings of the National Academy of Sciences, 111(26), 9497–9502. https://doi.org/10.1073/pnas.1407145111
Preston, M. D., Campino, S., Assefa, S. A., Echeverry, D. F., Ocholla, H., Amambua-Ngwa, A., … Clark, T. G. (2014). A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains. Nature Communications, 5(1). https://doi.org/10.1038/ncomms5052
Ferreira, A. J. S., Siam, R., Setubal, J. C., Moustafa, A., Sayed, A., Chambergo, F. S., … El-Dorry, H. (2014). Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses. PLoS ONE, 9(6), e97338. https://doi.org/10.1371/journal.pone.0097338
Alam, T., Alazmi, M., Gao, X., & Arold, S. T. (2014). How to find a leucine in a haystack? Structure, ligand recognition and regulation of leucine–aspartic acid (LD) motifs. Biochemical Journal, 460(3), 317–329. https://doi.org/10.1042/bj20140298
Jimenez-Infante, F., Ngugi, D. K., Alam, I., Rashid, M., Baalawi, W., Kamau, A. A., … Stingl, U. (2014). Genomic differentiation among two strains of the PS1 clade isolated from geographically separated marine habitats. FEMS Microbiology Ecology, 89(1), 181–197. https://doi.org/10.1111/1574-6941.12348
Moroz, L. L., Kocot, K. M., Citarella, M. R., Dosung, S., Norekian, T. P., Povolotskaya, I. S., … Kohn, A. B. (2014). The ctenophore genome and the evolutionary origins of neural systems. Nature, 510(7503), 109–114. https://doi.org/10.1038/nature13400
Mousavizadeh, R., Khosravi, S., Behzad, H., McCormack, R. G., Duronio, V., & Scott, A. (2014). Cyclic Strain Alters the Expression and Release of Angiogenic Factors by Human Tendon Cells. PLoS ONE, 9(5), e97356. https://doi.org/10.1371/journal.pone.0097356
Abdelmohsen, U., Yang, C., Horn, H., Hajjar, D., Ravasi, T., & Hentschel, U. (2014). Actinomycetes from Red Sea Sponges: Sources for Chemical and Phylogenetic Diversity. Marine Drugs, 12(5), 2771–2789. https://doi.org/10.3390/md12052771
Monma, N., Gojobori, T., & Ikeo, K. (2014). Human Genome Network Platform: A Resource for TFRN Analysis. Methods in Molecular Biology, 147–162. https://doi.org/10.1007/978-1-4939-0805-9_12
Yu, Q., Li, X.-T., Zhao, X., Liu, X.-L., Ikeo, K., Gojobori, T., & Liu, Q.-X. (2014). Coevolution of Axon Guidance Molecule Slit and Its Receptor Robo. PLoS ONE, 9(5), e94970. https://doi.org/10.1371/journal.pone.0094970
Jackson, A. P., Otto, T. D., Darby, A., Ramaprasad, A., Xia, D., Echaide, I. E., … Pain, A. (2014). The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction. Nucleic Acids Research, 42(11), 7113–7131. https://doi.org/10.1093/nar/gku322
Gao, Z.-M., Wang, Y., Lee, O. O., Tian, R.-M., Wong, Y. H., Bougouffa, S., … Qian, P.-Y. (2014). Pyrosequencing Reveals the Microbial Communities in the Red Sea Sponge Carteriospongia foliascens and Their Impressive Shifts in Abnormal Tissues. Microbial Ecology, 68(3), 621–632. https://doi.org/10.1007/s00248-014-0419-0
Abbas, A., Guo, X., Jing, B.-Y., & Gao, X. (2014). An automated framework for NMR resonance assignment through simultaneous slice picking and spin system forming. Journal of Biomolecular NMR, 59(2), 75–86. https://doi.org/10.1007/s10858-014-9828-0
Wang, J. J.-Y., Sun, Y., & Gao, X. (2014). Sparse structure regularized ranking. Multimedia Tools and Applications, 74(2), 635–654. https://doi.org/10.1007/s11042-014-1939-9
Zhang, W., Bougouffa, S., Wang, Y., Lee, O. O., Yang, J., Chan, C., … Qian, P.-Y. (2014). Toward Understanding the Dynamics of Microbial Communities in an Estuarine System. PLoS ONE, 9(4), e94449. https://doi.org/10.1371/journal.pone.0094449
Virzonis, D., Vanagas, G., Ramanaviciene, A., Makaraviciute, A., Barauskas, D., Ramanavicius, A., … Kodzius, R. (2014). Resonant gravimetric immunosensing based on capacitive micromachined ultrasound transducers. Microchimica Acta, 181(13-14), 1749–1757. https://doi.org/10.1007/s00604-014-1244-3
S.Grötzinger, S. W., Alam, I., Ba Alawi, W., Bajic, V. B., Stingl, U., & J. Eppinger. (2014). Mining a database of single amplified genomes from Red Sea brine pool extremophiles-improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA). Frontiers in Microbiology, 5. https://doi.org/10.3389/fmicb.2014.00134
Naeem, R., Hidayah, L., Preston, M. D., Clark, T. G., & Pain, A. (2014). SVAMP: sequence variation analysis, maps and phylogeny. Bioinformatics, 30(15), 2227–2229. https://doi.org/10.1093/bioinformatics/btu176
Gao, Z.-M., Wang, Y., Tian, R.-M., Wong, Y. H., Batang, Z. B., Al-Suwailem, A. M., … Qian, P.-Y. (2014). Symbiotic Adaptation Drives Genome Streamlining of the Cyanobacterial Sponge Symbiont “Candidatus Synechococcus spongiarum.” mBio, 5(2). https://doi.org/10.1128/mbio.00079-14
Li, F., Kodzius, R., Gooneratne, C. P., Foulds, I. G., & Kosel, J. (2014). Magneto-mechanical trapping systems for biological target detection. Microchimica Acta, 181(13-14), 1743–1748. https://doi.org/10.1007/s00604-014-1241-6
Medvedeva, Y. A., Khamis, A. M., Kulakovskiy, I. V., Ba-Alawi, W., Bhuyan, M. S. I., … Kawaji, H. (2014). Effects of cytosine methylation on transcription factor binding sites. BMC Genomics, 15(1), 119. https://doi.org/10.1186/1471-2164-15-119
(2014). A promoter-level mammalian expression atlas. Nature, 507(7493), 462–470. https://doi.org/10.1038/nature13182
Harjes, J., Ryu, T., Abdelmohsen, U. R., Moitinho-Silva, L., Horn, H., Ravasi, T., & Hentschel, U. (2014). Draft Genome Sequence of the Antitrypanosomally Active Sponge-Associated Bacterium Actinokineospora sp. Strain EG49. Genome Announcements, 2(2). https://doi.org/10.1128/genomea.00160-14
Cotton, J. A., Lilley, C. J., Jones, L. M., Kikuchi, T., Reid, A. J., Thorpe, P., … Urwin, P. E. (2014). The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome Biology, 15(3), R43. https://doi.org/10.1186/gb-2014-15-3-r43
Coll, F., Preston, M., Guerra-Assunção, J. A., Hill-Cawthorn, G., Harris, D., Perdigão, J., … Clark, T. G. (2014). PolyTB: A genomic variation map for Mycobacterium tuberculosis. Tuberculosis, 94(3), 346–354. https://doi.org/10.1016/j.tube.2014.02.005
Chen, Z.-F., Zhang, H., Wang, H., Matsumura, K., Wong, Y. H., Ravasi, T., & Qian, P.-Y. (2014). Quantitative Proteomics Study of Larval Settlement in the Barnacle Balanus amphitrite. PLoS ONE, 9(2), e88744. https://doi.org/10.1371/journal.pone.0088744
Rasmussen, M., Anzick, S. L., Waters, M. R., Skoglund, P., DeGiorgio, M., Stafford, T. W., … Willerslev, E. (2014). The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature, 506(7487), 225–229. https://doi.org/10.1038/nature13025
Juneja, P., Osei-Poku, J., Ho, Y. S., Ariani, C. V., Palmer, W. J., Pain, A., & Jiggins, F. M. (2014). Assembly of the Genome of the Disease Vector Aedes aegypti onto a Genetic Linkage Map Allows Mapping of Genes Affecting Disease Transmission. PLoS Neglected Tropical Diseases, 8(1), e2652. https://doi.org/10.1371/journal.pntd.0002652
Elsik, C. G., Worley, K. C., Bennett, A. K., Beye, M., Camara, F., … Childers, C. P. (2014). Finding the missing honey bee genes: lessons learned from a genome upgrade. BMC Genomics, 15(1), 86. https://doi.org/10.1186/1471-2164-15-86
Brami-Cherrier, K., Gervasi, N., Arsenieva, D., Walkiewicz, K., Boutterin, M.-C., Ortega, A., … Arold, S. T. (2014). FAK dimerization controls its kinase-dependent functions at focal adhesions. The EMBO Journal, 33(4), 356–370. https://doi.org/10.1002/embj.201386399
Zhang, D., Yang, G., Chen, X., Li, C., Wang, L., Liu, Y., … Zhao, S. (2014). mir-300 Promotes Self-Renewal and Inhibits the Differentiation of Glioma Stem-Like Cells. Journal of Molecular Neuroscience, 53(4), 637–644. https://doi.org/10.1007/s12031-014-0230-x
Yang, G., Han, D., Chen, X., Zhang, D., Wang, L., Shi, C., … Zhao, S. (2014). MiR-196a exerts its oncogenic effect in glioblastoma multiforme by inhibition of IκBα both in vitro and in vivo. Neuro-Oncology, 16(5), 652–661. https://doi.org/10.1093/neuonc/not307
Sagar, S., Esau, L., Moosa, B., Khashab, N., Bajic, V., & Kaur, M. (2014). Cytotoxicity and Apoptosis Induced by a Plumbagin Derivative in Estrogen Positive MCF-7 Breast Cancer Cells. Anti-Cancer Agents in Medicinal Chemistry, 14(1), 170–180. https://doi.org/10.2174/18715206113136660369
Lee, O. O., Wang, Y., Tian, R., Zhang, W., Shek, C. S., Bougouffa, S., … Qian, P.-Y. (2014). In situ environment rather than substrate type dictates microbial community structure of biofilms in a cold seep system. Scientific Reports, 4(1). https://doi.org/10.1038/srep03587
Takaku, Y., Hwang, J. S., Wolf, A., Böttger, A., Shimizu, H., David, C. N., & Gojobori, T. (2014). Innexin gap junctions in nerve cells coordinate spontaneous contractile behavior in Hydra polyps. Scientific Reports, 4(1). https://doi.org/10.1038/srep03573

2013

Wu, J., Kodzius, R., Cao, W., & Wen, W. (2013). Extraction, amplification and detection of DNA in microfluidic chip-based assays. Microchimica Acta, 181(13-14), 1611–1631. https://doi.org/10.1007/s00604-013-1140-2
Bougot-Robin, K., Kodzius, R., Yue, W., Chen, L., Li, S., Zhang, X. X., … Wen, W. (2013). Real time hybridization studies by resonant waveguide gratings using nanopattern imaging for Single Nucleotide Polymorphism detection. Biomedical Microdevices, 16(2), 287–299. https://doi.org/10.1007/s10544-013-9832-2
Wang, J. J.-Y., & Gao, X. (2014). Beyond cross-domain learning: Multiple-domain nonnegative matrix factorization. Engineering Applications of Artificial Intelligence, 28, 181–189. https://doi.org/10.1016/j.engappai.2013.11.002
(2013). The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes. Journal of Heredity, 105(1), 1–18. https://doi.org/10.1093/jhered/est084
Alam, I., Antunes, A., Kamau, A. A., Ba alawi Wail, Kalkatawi, M., Stingl, U., & Bajic, V. B. (2013). INDIGO – INtegrated Data Warehouse of MIcrobial GenOmes with Examples from the Red Sea Extremophiles. PLoS ONE, 8(12), e82210. https://doi.org/10.1371/journal.pone.0082210
Sagar, S., Esau, L., Holtermann, K., Hikmawan, T., Zhang, G., Stingl, U., … Kaur, M. (2013). Induction of apoptosis in cancer cell lines by the Red Sea brine pool bacterial extracts. BMC Complementary and Alternative Medicine, 13(1). https://doi.org/10.1186/1472-6882-13-344
Nozawa, M., Fukuda, N., Ikeo, K., & Gojobori, T. (2013). Tissue- and Stage-Dependent Dosage Compensation on the Neo-X Chromosome in Drosophila pseudoobscura. Molecular Biology and Evolution, 31(3), 614–624. https://doi.org/10.1093/molbev/mst239
Wang, J. J.-Y., Bensmail, H., & Gao, X. (2014). Feature selection and multi-kernel learning for sparse representation on a manifold. Neural Networks, 51, 9–16. https://doi.org/10.1016/j.neunet.2013.11.009
Sayed, A., Ghazy, M. A., Ferreira, A. J. S., Setubal, J. C., Chambergo, F. S., Ouf, A., … El-Dorry, H. (2014). A Novel Mercuric Reductase from the Unique Deep Brine Environment of Atlantis II in the Red Sea. Journal of Biological Chemistry, 289(3), 1675–1687. https://doi.org/10.1074/jbc.m113.493429
Tchekmedyian, A., Amos, C. I., Bale, S. J., Zhu, D., Arold, S., Berrueta, J., … McGarrity, T. (2013). Findings from the Peutz-Jeghers Syndrome Registry of Uruguay. PLoS ONE, 8(11), e79639. https://doi.org/10.1371/journal.pone.0079639
Steijger, T., Abril, J. F., Engström, P. G., Kokocinski, F., Hubbard, T. J., … Bertone, P. (2013). Assessment of transcript reconstruction methods for RNA-seq. Nature Methods, 10(12), 1177–1184. https://doi.org/10.1038/nmeth.2714
Engström, P. G., Steijger, T., Sipos, B., Grant, G. R., Kahles, A., … Bertone, P. (2013). Systematic evaluation of spliced alignment programs for RNA-seq data. Nature Methods, 10(12), 1185–1191. https://doi.org/10.1038/nmeth.2722
Cheng, Y., Gao, X., & Liang, F. (2014). Bayesian Peak Picking for NMR Spectra. Genomics, Proteomics & Bioinformatics, 12(1), 39–47. https://doi.org/10.1016/j.gpb.2013.07.003
Conti, A., Riva, N., Pesca, M., Iannaccone, S., Cannistraci, C. V., Corbo, M., … Alessio, M. (2014). Increased expression of Myosin binding protein H in the skeletal muscle of amyotrophic lateral sclerosis patients. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 1842(1), 99–106. https://doi.org/10.1016/j.bbadis.2013.10.013
Bin Raies, A., Mansour, H., Incitti, R., & Bajic, V. B. (2013). Combining Position Weight Matrices and Document-Term Matrix for Efficient Extraction of Associations of Methylated Genes and Diseases from Free Text. PLoS ONE, 8(10), e77848. https://doi.org/10.1371/journal.pone.0077848
Kamanu, T. K. K., Radovanovic, A., Archer, J. A. C., & Bajic, V. B. (2013). Exploration of miRNA families for hypotheses generation. Scientific Reports, 3(1). https://doi.org/10.1038/srep02940
Kleftogiannis, D., Kalnis, P., & Bajic, V. B. (2013). Comparing Memory-Efficient Genome Assemblers on Stand-Alone and Cloud Infrastructures. PLoS ONE, 8(9), e75505. https://doi.org/10.1371/journal.pone.0075505
Wang, J. J.-Y., Bensmail, H., Yao, N., & Gao, X. (2013). Discriminative sparse coding on multi-manifolds. Knowledge-Based Systems, 54, 199–206. https://doi.org/10.1016/j.knosys.2013.09.004
Ashoor, H., Hérault, A., Kamoun, A., Radvanyi, F., Bajic, V. B., Barillot, E., & Boeva, V. (2013). HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data. Bioinformatics, 29(23), 2979–2986. https://doi.org/10.1093/bioinformatics/btt524
Janouškovec, J., Sobotka, R., Lai, D.-H., Flegontov, P., Koník, P., Komenda, J., … Keeling, P. J. (2013). Split Photosystem Protein, Linear-Mapping Topology, and Growth of Structural Complexity in the Plastid Genome of Chromera velia. Molecular Biology and Evolution, 30(11), 2447–2462. https://doi.org/10.1093/molbev/mst144
Moitinho-Silva, L., Bayer, K., Cannistraci, C. V., Giles, E. C., Ryu, T., Seridi, L., … Hentschel, U. (2013). Specificity and transcriptional activity of microbiota associated with low and high microbial abundance sponges from the Red Sea. Molecular Ecology, 23(6), 1348–1363. https://doi.org/10.1111/mec.12365
Breuer, S. (2013). A Biochemical/Biophysical Assay Dyad for HTS-Compatible Triaging of Inhibitors of the HIV-1 Nef/Hck SH3 Interaction. Current Chemical Genomics and Translational Medicine, 7, 16–20. https://doi.org/10.2174/2213988501307010016
Kuwahara, H., & Gao, X. (2013). Stochastic effects as a force to increase the complexity of signaling networks. Scientific Reports, 3(1). https://doi.org/10.1038/srep02297
Alanis-Lobato, G., Cannistraci, C. V., & Ravasi, T. (2013). Exploitation of genetic interaction network topology for the prediction of epistatic behavior. Genomics, 102(4), 202–208. https://doi.org/10.1016/j.ygeno.2013.07.010
Takenaka, Y., Noda-Ogura, A., Imanishi, T., Yamaguchi, A., Gojobori, T., & Shigeri, Y. (2013). Computational analysis and functional expression of ancestral copepod luciferase. Gene, 528(2), 201–205. https://doi.org/10.1016/j.gene.2013.07.011
Chen, P., Li, J., Wong, L., Kuwahara, H., Huang, J. Z., & Gao, X. (2013). Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences. Proteins: Structure, Function, and Bioinformatics, 81(8), 1351–1362. https://doi.org/10.1002/prot.24278
Piatek, M. J., Schramm, M. C., Burra, D. D., binShbreen, A., Jankovic, B. R., Chowdhary, R., … Bajic, V. B. (2013). Simplified Method for Predicting a Functional Class of Proteins in Transcription Factor Complexes. PLoS ONE, 8(7), e68857. https://doi.org/10.1371/journal.pone.0068857
Chandramouli, K. H., Dash, S., Zhang, Y., Ravasi, T., & Qian, P.-Y. (2013). Proteomic and metabolomic profiles of marineVibriosp. 010 in response to an antifoulant challenge. Biofouling, 29(7), 789–802. https://doi.org/10.1080/08927014.2013.805209
Xie, B., Jankovic, B. R., Bajic, V. B., Song, L., & Gao, X. (2013). Poly(A) motif prediction using spectral latent features from human DNA sequences. Bioinformatics, 29(13), i316–i325. https://doi.org/10.1093/bioinformatics/btt218
Cannistraci, C. V., Alanis-Lobato, G., & Ravasi, T. (2013). Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding. Bioinformatics, 29(13), i199–i209. https://doi.org/10.1093/bioinformatics/btt208
Kuwahara, H., Fan, M., Wang, S., & Gao, X. (2013). A framework for scalable parameter estimation of gene circuit models using structural information. Bioinformatics, 29(13), i98–i107. https://doi.org/10.1093/bioinformatics/btt232
Nakamura, Y., Mori, K., Saitoh, K., Oshima, K., Mekuchi, M., Sugaya, T., … Inouye, K. (2013). Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna. Proceedings of the National Academy of Sciences, 110(27), 11061–11066. https://doi.org/10.1073/pnas.1302051110
Essack, M., Radovanovic, A., & Bajic, V. B. (2013). Information Exploration System for Sickle Cell Disease and Repurposing of Hydroxyfasudil. PLoS ONE, 8(6), e65190. https://doi.org/10.1371/journal.pone.0065190
Chowdhary, R., Zhang, J., Tan, S. L., Osborne, D. E., Bajic, V. B., & Liu, J. S. (2013). PIMiner: a web tool for extraction of protein interactions from biomedical literature. International Journal of Data Mining and Bioinformatics, 7(4), 450. https://doi.org/10.1504/ijdmb.2013.054232
Wang, J. J.-Y., Bensmail, H., & Gao, X. (2013). Joint learning and weighting of visual vocabulary for bag-of-feature based tissue classification. Pattern Recognition, 46(12), 3249–3255. https://doi.org/10.1016/j.patcog.2013.05.001
Woods, K. L., Theiler, R., Mühlemann, M., Segiser, A., Huber, S., Ansari, H. R., … Dobbelaere, D. A. E. (2013). Recruitment of EB1, a Master Regulator of Microtubule Dynamics, to the Surface of the Theileria annulata Schizont. PLoS Pathogens, 9(5), e1003346. https://doi.org/10.1371/journal.ppat.1003346
Ammirati, E., Cristell, N., Cianflone, D., Vermi, A.-C., Marenzi, G., De Metrio, M., … Cannistraci, C. V. (2013). Questing for Circadian Dependence in ST-Segment–Elevation Acute Myocardial Infarction. Circulation Research, 112(10). https://doi.org/10.1161/circresaha.112.300778
Suen, K. M., Lin, C.-C., George, R., Melo, F. A., Biggs, E. R., Ahmed, Z., … Ladbury, J. E. (2013). Interaction with Shc prevents aberrant Erk activation in the absence of extracellular stimuli. Nature Structural & Molecular Biology, 20(5), 620–627. https://doi.org/10.1038/nsmb.2557
Cannistraci, C. V., Alanis-Lobato, G., & Ravasi, T. (2013). From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks. Scientific Reports, 3(1). https://doi.org/10.1038/srep01613
Wang, J. J.-Y., Wang, X., & Gao, X. (2013). Non-negative matrix factorization by maximizing correntropy for cancer clustering. BMC Bioinformatics, 14(1), 107. https://doi.org/10.1186/1471-2105-14-107
Wang, J. J.-Y., Bensmail, H., & Gao, X. (2013). Multiple graph regularized nonnegative matrix factorization. Pattern Recognition, 46(10), 2840–2847. https://doi.org/10.1016/j.patcog.2013.03.007
Nakamura, Y., Sasaki, N., Kobayashi, M., Ojima, N., Yasuike, M., Shigenobu, Y., … Ikeo, K. (2013). The First Symbiont-Free Genome Sequence of Marine Red Alga, Susabi-nori (Pyropia yezoensis). PLoS ONE, 8(3), e57122. https://doi.org/10.1371/journal.pone.0057122
Sha, D., & Bajic, V. B. (2011). An Optimized Recursive Learning Algorithm for Three-Layer Feedforward Neural Networks For Mimo Nonlinear System Identifications. Intelligent Automation & Soft Computing, 17(2), 133–147. https://doi.org/10.1080/10798587.2011.10643137
Sepúlveda, N., Campino, S. G., Assefa, S. A., Sutherland, C. J., Pain, A., & Clark, T. G. (2013). A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data. BMC Genomics, 14(1), 128. https://doi.org/10.1186/1471-2164-14-128
Pardo, L. M., Rizzu, P., Francescatto, M., Vitezic, M., Leday, G. G. R., Sanchez, J. S., … Heutink, P. (2013). Regional differences in gene expression and promoter usage in aged human brains. Neurobiology of Aging, 34(7), 1825–1836. https://doi.org/10.1016/j.neurobiolaging.2013.01.005
Tichy, J., Gardian, Z., Bina, D., Konik, P., Litvin, R., Herbstova, M., … Vacha, F. (2013). Light harvesting complexes of Chromera velia, photosynthetic relative of apicomplexan parasites. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1827(6), 723–729. https://doi.org/10.1016/j.bbabio.2013.02.002
Sagar, S., Kaur, M., Radovanovic, A., & Bajic, V. B. (2013). Dragon exploration system on marine sponge compounds interactions. Journal of Cheminformatics, 5(1). https://doi.org/10.1186/1758-2946-5-11
Cannistraci, C. V., Ogorevc, J., Zorc, M., Ravasi, T., Dovc, P., & Kunej, T. (2013). Pivotal role of the muscle-contraction pathway in cryptorchidism and evidence for genomic connections with cardiomyopathy pathways in RASopathies. BMC Medical Genomics, 6(1). https://doi.org/10.1186/1755-8794-6-5
Sagar, S., Esau, L., Hikmawan, T., Antunes, A., Holtermann, K., Stingl, U., … Kaur, M. (2013). Cytotoxic and apoptotic evaluations of marine bacteria isolated from brine-seawater interface of the Red Sea. BMC Complementary and Alternative Medicine, 13(1). https://doi.org/10.1186/1472-6882-13-29
Narasimhan, K., Lin, S. L., Tong, T., Baig, S., Ho, S., Sukumar, P., … Choolani, M. (2013). Maternal serum protein profile and immune response protein subunits as markers for non-invasive prenatal diagnosis of trisomy 21, 18, and 13. Prenatal Diagnosis, 33(3), 223–231. https://doi.org/10.1002/pd.4047
Chandramouli, K. H., Sun, J., Mok, F. S., Liu, L., Qiu, J.-W., Ravasi, T., & Qian, P.-Y. (2013). Transcriptome and Quantitative Proteome Analysis Reveals Molecular Processes Associated with Larval Metamorphosis in the Polychaete Pseudopolydora vexillosa. Journal of Proteome Research, 12(3), 1344–1358. https://doi.org/10.1021/pr3010088
Stabler, R. A., Negus, D., Pain, A., & Taylor, P. W. (2013). Draft Genome Sequences of Pseudomonas fluorescens BS2 and Pusillimonas noertemannii BS8, Soil Bacteria That Cooperate To Degrade the Poly- -D-Glutamic Acid Anthrax Capsule. Genome Announcements, 1(1). https://doi.org/10.1128/genomea.00057-12
Asato, R., Yoshida, S., Ogura, A., Nakama, T., Ishikawa, K., Nakao, S., … Ishibashi, T. (2013). Comparison of Gene Expression Profile of Epiretinal Membranes Obtained from Eyes with Proliferative Vitreoretinopathy to That of Secondary Epiretinal Membranes. PLoS ONE, 8(1), e54191. https://doi.org/10.1371/journal.pone.0054191
Nakagawa, S., Bai, H., Sakurai, T., Nakaya, Y., Konno, T., Miyazawa, T., … Imakawa, K. (2013). Dynamic Evolution of Endogenous Retrovirus-Derived Genes Expressed in Bovine Conceptuses during the Period of Placentation. Genome Biology and Evolution, 5(2), 296–306. https://doi.org/10.1093/gbe/evt007