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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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10.1002/pd.4047Chandramouli, 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
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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
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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
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Gao, X. (2013). Recent Advances in Computational Methods for Nuclear Magnetic Resonance Data Processing. Genomics, Proteomics & Bioinformatics, 11(1), 29–33. https://doi.org/10.1016/j.gpb.2012.12.003
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Abbas, A., Kong, X.-B., Liu, Z., Jing, B.-Y., & Gao, X. (2013). Automatic Peak Selection by a Benjamini-Hochberg-Based Algorithm. PLoS ONE, 8(1), e53112. https://doi.org/10.1371/journal.pone.0053112
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Marondedze, C., Turek, I., Parrott, B., Thomas, L., Jankovic, B., Lilley, K. S., & Gehring, C. (2013). Structural and functional characteristics of cGMP-dependent methionine oxidation in Arabidopsis thaliana proteins. Cell Communication and Signaling, 11(1), 1. https://doi.org/10.1186/1478-811x-11-1
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Sarhan, A., Bocca, S., Yu, L., Anderson, S., Jacot, T., Burch, T., … Oehninger, S. (2013). Human endometrial milk fat globule-epidermal growth factor 8 (MFGE8) is up regulated by estradiol at the transcriptional level, and its secretion via microvesicles is stimulated by human chorionic gonadotropin (hCG). Cell Signalling and Trafficking, 1(1), 1. https://doi.org/10.7243/2054-1481-1-1
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Miendlarzewska, E. A., van Elswijk, G., Cannistraci, C. V., & van Ee, R. (2013). Working Memory Load Attenuates Emotional Enhancement in Recognition Memory. Frontiers in Psychology, 4. https://doi.org/10.3389/fpsyg.2013.00112
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Moon, R. W., Hall, J., Rangkuti, F., Ho, Y. S., Almond, N., Mitchell, G. H., … Blackman, M. J. (2012). Adaptation of the genetically tractable malaria pathogen Plasmodium knowlesi to continuous culture in human erythrocytes. Proceedings of the National Academy of Sciences, 110(2), 531–536. https://doi.org/10.1073/pnas.1216457110
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Oakes, R. D., Kurian, D., Bromley, E., Ward, C., Lal, K., Blake, D. P., … Tomley, F. M. (2013). The rhoptry proteome of Eimeria tenella sporozoites. International Journal for Parasitology, 43(2), 181–188. https://doi.org/10.1016/j.ijpara.2012.10.024
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Ryu, T., Seridi, L., & Ravasi, T. (2012). The evolution of ultraconserved elements with different phylogenetic origins. BMC Evolutionary Biology, 12(1), 236. https://doi.org/10.1186/1471-2148-12-236
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Dai, L., Gao, X., Guo, Y., Xiao, J., & Zhang, Z. (2012). Bioinformatics clouds for big data manipulation. Biology Direct, 7(1), 43. https://doi.org/10.1186/1745-6150-7-43
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Takeda, J., Yamasaki, C., Murakami, K., Nagai, Y., Sera, M., Hara, Y., … Imanishi, T. (2012). H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery. Nucleic Acids Research, 41(D1), D915–D919. https://doi.org/10.1093/nar/gks1245
Naeem, R., Rashid, M., & Pain, A. (2012). READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation. Bioinformatics, 29(3), 391–392. https://doi.org/10.1093/bioinformatics/bts684
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Kulakovskiy, I. V., Medvedeva, Y. A., Schaefer, U., Kasianov, A. S., Vorontsov, I. E., Bajic, V. B., & Makeev, V. J. (2012). HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. Nucleic Acids Research, 41(D1), D195–D202. https://doi.org/10.1093/nar/gks1089
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Haywood, A. F. M., Merner, N. D., Hodgkinson, K. A., Houston, J., Syrris, P., Booth, V., … Young, T.-L. (2012). Recurrent missense mutations in TMEM43 (ARVD5) due to founder effects cause arrhythmogenic cardiomyopathies in the UK and Canada. European Heart Journal, 34(13), 1002–1011. https://doi.org/10.1093/eurheartj/ehs383
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B. Malas, T., & Ravasi, T. (2012). Computational Tools for Genome-Wide miRNA Prediction and Study. The Open Biology Journal, 5(1), 23–30. https://doi.org/10.2174/1874196701205010023
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Magana-Mora, A., Ashoor, H., Jankovic, B. R., Kamau, A., Awara, K., Chowdhary, R., … Bajic, V. B. (2012). Dragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants. Bioinformatics, 29(1), 117–118. https://doi.org/10.1093/bioinformatics/bts638
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Ho, Y. S., Adroub, S. A., Aleisa, F., Mahmood, H., Othoum, G., Rashid, F., … Abdallah, A. M. (2012). Complete Genome Sequence of Mycobacterium fortuitum subsp. fortuitum Type Strain DSM46621. Journal of Bacteriology, 194(22), 6337–6338. https://doi.org/10.1128/jb.01461-12
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Essack, M., MacPherson, C., Schmeier, S., & Bajic, V. B. (2012). Identification of estrogen responsive genes using esophageal squamous cell carcinoma (ESCC) as a model. BMC Systems Biology, 6(1), 135. https://doi.org/10.1186/1752-0509-6-135
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Ho, Y. S., Adroub, S. A., Abadi, M., Al Alwan, B., Alkhateeb, R., Gao, G., … Abdallah, A. M. (2012). Complete Genome Sequence of Mycobacterium vaccae Type Strain ATCC 25954. Journal of Bacteriology, 194(22), 6339–6340. https://doi.org/10.1128/jb.01462-12
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Kumar, K., Sagar, S., Esau, L., Kaur, M., & Kumar, V. (2012). Synthesis of novel 1H-1,2,3-triazole tethered C-5 substituted uracil–isatin conjugates and their cytotoxic evaluation. European Journal of Medicinal Chemistry, 58, 153–159. https://doi.org/10.1016/j.ejmech.2012.10.008
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Köser, C. U., Feuerriegel, S., Summers, D. K., Archer, J. A. C., & Niemann, S. (2012). Importance of the Genetic Diversity within the Mycobacterium tuberculosis Complex for the Development of Novel Antibiotics and Diagnostic Tests of Drug Resistance. Antimicrobial Agents and Chemotherapy, 56(12), 6080–6087. https://doi.org/10.1128/aac.01641-12
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Hayashida, K., Hara, Y., Abe, T., Yamasaki, C., Toyoda, A., Kosuge, T., … Sugimoto, C. (2012). Comparative Genome Analysis of Three Eukaryotic Parasites with Differing Abilities To Transform Leukocytes Reveals Key Mediators of Theileria-Induced Leukocyte Transformation. mBio, 3(5). https://doi.org/10.1128/mbio.00204-12
Giles, E. C., Kamke, J., Moitinho-Silva, L., Taylor, M. W., Hentschel, U., Ravasi, T., & Schmitt, S. (2012). Bacterial community profiles in low microbial abundance sponges. FEMS Microbiology Ecology, 83(1), 232–241. https://doi.org/10.1111/j.1574-6941.2012.01467.x
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Messih, M. A., Chitale, M., Bajic, V. B., Kihara, D., & Gao, X. (2012). Protein domain recurrence and order can enhance prediction of protein functions. Bioinformatics, 28(18), i444–i450. https://doi.org/10.1093/bioinformatics/bts398
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Ammirati, E., Cannistraci, C. V., Cristell, N. A., Vecchio, V., Palini, A. G., Tornvall, P., … Maseri, A. (2012). Identification and Predictive Value of Interleukin-6
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Siam, R., Mustafa, G. A., Sharaf, H., Moustafa, A., Ramadan, A. R., Antunes, A., … Dorry, H. E. (2012). Unique Prokaryotic Consortia in Geochemically Distinct Sediments from Red Sea Atlantis II and Discovery Deep Brine Pools. PLoS ONE, 7(8), e42872. https://doi.org/10.1371/journal.pone.0042872
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Fan, M., Wong, K.-C., Ryu, T., Ravasi, T., & Gao, X. (2012). SECOM: A Novel Hash Seed and Community Detection Based-Approach for Genome-Scale Protein Domain Identification. PLoS ONE, 7(6), e39475. https://doi.org/10.1371/journal.pone.0039475
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Essack, M., Bajic, V. B., & Archer, J. A. C. (2012). Conotoxins that Confer Therapeutic Possibilities. Marine Drugs, 10(12), 1244–1265. https://doi.org/10.3390/md10061244
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Abdallah, A. M., Rashid, M., Adroub, S. A., Elabdalaoui, H., Ali, S., van Soolingen, D., … Pain, A. (2012). Complete Genome Sequence of Mycobacterium xenopi Type Strain RIVM700367. Journal of Bacteriology, 194(12), 3282–3283. https://doi.org/10.1128/jb.00482-12
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Abdallah, A. M., Rashid, M., Adroub, S. A., Arnoux, M., Ali, S., van Soolingen, D., … Pain, A. (2012). Complete Genome Sequence of Mycobacterium phlei Type Strain RIVM601174. Journal of Bacteriology, 194(12), 3284–3285. https://doi.org/10.1128/jb.00485-12
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Woo, J., MacPherson, C., Liu, J., Wang, H., Kiba, T., Hannah, M. A., … Chua, N.-H. (2012). The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation. BMC Plant Biology, 12(1), 62. https://doi.org/10.1186/1471-2229-12-62
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Chowdhary, R., Tan, S. L., Zhang, J., Karnik, S., Bajic, V. B., & Liu, J. S. (2012). Context-Specific Protein Network Miner – An Online System for Exploring Context-Specific Protein Interaction Networks from the Literature. PLoS ONE, 7(4), e34480. https://doi.org/10.1371/journal.pone.0034480
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Lawton, J., Brugat, T., Yan, Y., Reid, A., Böhme, U., Otto, T., … Langhorne, J. (2012). Characterization and gene expression analysis of the cir multi-gene family of plasmodium chabaudi chabaudi (AS). BMC Genomics, 13(1), 125. https://doi.org/10.1186/1471-2164-13-125
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Zhang, Z., Li, J., Cui, P., Ding, F., Li, A., Townsend, J. P., & Yu, J. (2012). Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance. BMC Bioinformatics, 13(1), 43. https://doi.org/10.1186/1471-2105-13-43
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Reid, A. J., Vermont, S. J., Cotton, J. A., Harris, D., Hill-Cawthorne, G. A., Könen-Waisman, S., … Wastling, J. M. (2012). Comparative Genomics of the Apicomplexan Parasites Toxoplasma gondii and Neospora caninum: Coccidia Differing in Host Range and Transmission Strategy. PLoS Pathogens, 8(3), e1002567. https://doi.org/10.1371/journal.ppat.1002567
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Wong, Y. H., Wang, H., Ravasi, T., & Qian, P.-Y. (2012). Involvement of Wnt Signaling Pathways in the Metamorphosis of the Bryozoan Bugula neritina. PLoS ONE, 7(3), e33323. https://doi.org/10.1371/journal.pone.0033323
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Chowdhary, R., Tan, S. L., Pavesi, G., Jin, J., Dong, D., Mathur, S. K., … Bajic, V. B. (2012). A Database of Annotated Promoters of Genes Associated with Common Respiratory and Related Diseases. American Journal of Respiratory Cell and Molecular Biology, 47(1), 112–119. https://doi.org/10.1165/rcmb.2011-0419oc
Liu, Z., Abbas, A., Jing, B.-Y., & Gao, X. (2012). WaVPeak: picking NMR peaks through wavelet-based smoothing and volume-based filtering. Bioinformatics, 28(7), 914–920. https://doi.org/10.1093/bioinformatics/bts078
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Zelman, A. K., Dawe, A., Gehring, C., & Berkowitz, G. A. (2012). Evolutionary and Structural Perspectives of Plant Cyclic Nucleotide-Gated Cation Channels. Frontiers in Plant Science, 3. https://doi.org/10.3389/fpls.2012.00095
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Kamanu, F. K., Medvedeva, Y. A., Schaefer, U., Jankovic, B. R., Archer, J. A. C., & Bajic, V. B. (2012). Mutations and Binding Sites of Human Transcription Factors. Frontiers in Genetics, 3. https://doi.org/10.3389/fgene.2012.00100
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2011
Dawe, A. S., Radovanovic, A., Kaur, M., Sagar, S., Seshadri, S. V., Schaefer, U., … Bajic, V. B. (2012). DESTAF: A database of text-mined associations for reproductive toxins potentially affecting human fertility. Reproductive Toxicology, 33(1), 99–105. https://doi.org/10.1016/j.reprotox.2011.12.007
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Olivieri, S., Conti, A., Iannaccone, S., Cannistraci, C. V., Campanella, A., Barbariga, M., … Alessio, M. (2011). Ceruloplasmin Oxidation, a Feature of Parkinson’s Disease CSF, Inhibits Ferroxidase Activity and Promotes Cellular Iron Retention. Journal of Neuroscience, 31(50), 18568–18577. https://doi.org/10.1523/jneurosci.3768-11.2011
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Ramaprasad, A., Pain, A., & Ravasi, T. (2012). Defining the protein interaction network of human malaria parasite Plasmodium falciparum. Genomics, 99(2), 69–75. https://doi.org/10.1016/j.ygeno.2011.11.006
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Seshadri Sundararajan, V., Gabere, M. N., Pretorius, A., Adam, S., Christoffels, A., Lehväslaiho, M., … Bajic, V. B. (2011). DAMPD: a manually curated antimicrobial peptide database. Nucleic Acids Research, 40(D1), D1108–D1112. https://doi.org/10.1093/nar/gkr1063
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Kalkatawi, M., Rangkuti, F., Schramm, M., Jankovic, B. R., Kamau, A., Chowdhary, R., … Bajic, V. B. (2011). Dragon PolyA Spotter: predictor of poly(A) motifs within human genomic DNA sequences. Bioinformatics, 28(1), 127–129. https://doi.org/10.1093/bioinformatics/btr602
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Schmeier, S., Schaefer, U., Essack, M., & Bajic, V. B. (2011). Network analysis of microRNAs and their regulation in human ovarian cancer. BMC Systems Biology, 5(1), 183. https://doi.org/10.1186/1752-0509-5-183
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Pfander, C., Anar, B., Schwach, F., Otto, T. D., Brochet, M., Volkmann, K., … Billker, O. (2011). A scalable pipeline for highly effective genetic modification of a malaria parasite. Nature Methods, 8(12), 1078–1082. https://doi.org/10.1038/nmeth.1742
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Kaur, M., MacPherson, C. R., Schmeier, S., Narasimhan, K., Choolani, M., & Bajic, V. B. (2011). In Silico discovery of transcription factors as potential diagnostic biomarkers of ovarian cancer. BMC Systems Biology, 5(1), 144. https://doi.org/10.1186/1752-0509-5-144
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Essack, M., Bajic, V. B., & Archer, J. A. C. (2011). Recently Confirmed Apoptosis-Inducing Lead Compounds Isolated from Marine Sponge of Potential Relevance in Cancer Treatment. Marine Drugs, 9(9), 1580–1606. https://doi.org/10.3390/md9091580
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Feuerriegel, S., Köser, C. U., Baù, D., Rüsch-Gerdes, S., Summers, D. K., Archer, J. A. C., … Niemann, S. (2011). Impact offgd1andddnDiversity in Mycobacterium tuberculosis Complex onIn VitroSusceptibility to PA-824. Antimicrobial Agents and Chemotherapy, 55(12), 5718–5722. https://doi.org/10.1128/aac.05500-11
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Kwofie, S. K., Schaefer, U., Sundararajan, V. S., Bajic, V. B., & Christoffels, A. (2011). HCVpro: Hepatitis C virus protein interaction database. Infection, Genetics and Evolution, 11(8), 1971–1977. https://doi.org/10.1016/j.meegid.2011.09.001
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Chen, Z.-F., Matsumura, K., Wang, H., Arellano, S. M., Yan, X., Alam, I., … Qian, P.-Y. (2011). Toward an Understanding of the Molecular Mechanisms of Barnacle Larval Settlement: A Comparative Transcriptomic Approach. PLoS ONE, 6(7), e22913. https://doi.org/10.1371/journal.pone.0022913
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Jankovic, B., Seoighe, C., Alqurashi, M., & Gehring, C. (2011). Is there evidence of optimisation for carbon efficiency in plant proteomes? Plant Biology, 13(6), 831–834. https://doi.org/10.1111/j.1438-8677.2011.00494.x
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Schmeier, S., Jankovic, B., & Bajic, V. B. (2011). Simplified Method to Predict Mutual Interactions of Human Transcription Factors Based on Their Primary Structure. PLoS ONE, 6(7), e21887. https://doi.org/10.1371/journal.pone.0021887
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Köser, C. U., Niemann, S., Summers, D. K., & Archer, J. A. C. (2012). Overview of errors in the reference sequence and annotation of Mycobacterium tuberculosis H37Rv, and variation amongst its isolates. Infection, Genetics and Evolution, 12(4), 807–810. https://doi.org/10.1016/j.meegid.2011.06.011
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Projahn, M., Köser, C. U., Homolka, S., Summers, D. K., Archer, J. A. C., & Niemann, S. (2011). Polymorphisms in Isoniazid and Prothionamide Resistance Genes of the Mycobacterium tuberculosis Complex. Antimicrobial Agents and Chemotherapy, 55(9), 4408–4411. https://doi.org/10.1128/aac.00555-11
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Antunes, A., Alam, I., El Dorry, H., Siam, R., Robertson, A., Bajic, V. B., & Stingl, U. (2011). Genome Sequence of Haloplasma contractile, an Unusual Contractile Bacterium from a Deep-Sea Anoxic Brine Lake. Journal of Bacteriology, 193(17), 4551–4552. https://doi.org/10.1128/jb.05461-11
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Antunes, A., Alam, I., Bajic, V. B., & Stingl, U. (2011). Genome Sequence of Salinisphaera shabanensis, a Gammaproteobacterium from the Harsh, Variable Environment of the Brine-Seawater Interface of the Shaban Deep in the Red Sea. Journal of Bacteriology, 193(17), 4555–4556. https://doi.org/10.1128/jb.05459-11
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Antunes, A., Alam, I., Bajic, V. B., & Stingl, U. (2011). Genome Sequence of Halorhabdus tiamatea, the First Archaeon Isolated from a Deep-Sea Anoxic Brine Lake. Journal of Bacteriology, 193(17), 4553–4554. https://doi.org/10.1128/jb.05462-11
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Bokil, N. J., Totsika, M., Carey, A. J., Stacey, K. J., Hancock, V., Saunders, B. M., … Sweet, M. J. (2011). Intramacrophage survival of uropathogenic Escherichia coli: Differences between diverse clinical isolates and between mouse and human macrophages. Immunobiology, 216(11), 1164–1171. https://doi.org/10.1016/j.imbio.2011.05.011
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Gomes-Santos, C. S. S., Braks, J., Prudêncio, M., Carret, C., Gomes, A. R., Pain, A., … Mota, M. M. (2011). Transition of Plasmodium Sporozoites into Liver Stage-Like Forms Is Regulated by the RNA Binding Protein Pumilio. PLoS Pathogens, 7(5), e1002046. https://doi.org/10.1371/journal.ppat.1002046
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Ryu, T., Mavromatis, C., Bayer, T., Voolstra, C. R., & Ravasi, T. (2011). Unexpected complexity of the Reef-Building Coral Acropora millepora transcription factor network. BMC Systems Biology, 5(1), 58. https://doi.org/10.1186/1752-0509-5-58
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Romeo, G., Materia, L., Modica, M. N., Pittalà, V., Salerno, L., Siracusa, M. A., … Minneman, K. P. (2011). Novel 4-phenylpiperidine-2,6-dione derivatives. Ligands for α1-adrenoceptor subtypes. European Journal of Medicinal Chemistry, 46(7), 2676–2690. https://doi.org/10.1016/j.ejmech.2011.03.054
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Köser, C. U., Summers, D. K., & Archer, J. A. C. (2011). Thr270Ile inembC(Rv3793) Is Not a Marker for Ethambutol Resistance in theMycobacterium tuberculosisComplex. Antimicrobial Agents and Chemotherapy, 55(4), 1825–1825. https://doi.org/10.1128/aac.01607-10
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Ogun, S. A., Tewari, R., Otto, T. D., Howell, S. A., Knuepfer, E., Cunningham, D. A., … Holder, A. A. (2011). Targeted Disruption of py235ebp-1: Invasion of Erythrocytes by Plasmodium yoelii Using an Alternative Py235 Erythrocyte Binding Protein. PLoS Pathogens, 7(2), e1001288. https://doi.org/10.1371/journal.ppat.1001288
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Schmeier, S., Schaefer, U., MacPherson, C. R., & Bajic, V. B. (2011). dPORE-miRNA: Polymorphic Regulation of MicroRNA Genes. PLoS ONE, 6(2), e16657. https://doi.org/10.1371/journal.pone.0016657
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Pretorius, A., Kaur, M., Wamalwa, M., February, M. F., Essack, M., Bajic, V. B., & Rees, D. J. G. (2013). Functional analysis and characterization of the human RBBP6 promoters based on a combination of molecular biology and in silico approaches provide additional evidence for RBBP6 role in apoptosis. J. Biosci, 1, 2251-3159. http://dl6.globalstf.org/index.php/jbio/article/view/917
2010
Kwofie, S. K., Radovanovic, A., Sundararajan, V. S., Maqungo, M., Christoffels, A., & Bajic, V. B. (2011). Dragon exploratory system on Hepatitis C Virus (DESHCV). Infection, Genetics and Evolution, 11(4), 734–739. https://doi.org/10.1016/j.meegid.2010.12.006
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Zhang, H., Wong, Y. H., Wang, H., Chen, Z., Arellano, S. M., Ravasi, T., & Qian, P.-Y. (2011). Quantitative Proteomics Identify Molecular Targets That Are Crucial in Larval Settlement and Metamorphosis ofBugula neritina. Journal of Proteome Research, 10(1), 349–360. https://doi.org/10.1021/pr100817v
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Lee, O. O., Wang, Y., Yang, J., Lafi, F. F., Al-Suwailem, A., & Qian, P.-Y. (2010). Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea. The ISME Journal, 5(4), 650–664. https://doi.org/10.1038/ismej.2010.165
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Schaefer, U., Kodzius, R., Kai, C., Kawai, J., Carninci, P., Hayashizaki, Y., & Bajic, V. B. (2010). High Sensitivity TSS Prediction: Estimates of Locations Where TSS Cannot Occur. PLoS ONE, 5(11), e13934. https://doi.org/10.1371/journal.pone.0013934
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Zhang, H., Zhao, C., Li, X., Zhu, Y., Gan, C. S., Wang, Y., … Sze, S. K. (2010). Study of monocyte membrane proteome perturbation during lipopolysaccharide-induced tolerance using iTRAQ-based quantitative proteomic approach. PROTEOMICS - Clinical Applications, 4(10-11), 860–860. https://doi.org/10.1002/prca.201090077
Kuo, D., Licon, K., Bandyopadhyay, S., Chuang, R., Luo, C., Catalana, J., … Ideker, T. (2010). Coevolution within a transcriptional network by compensatory trans and cis mutations. Genome Research, 20(12), 1672–1678. https://doi.org/10.1101/gr.111765.110
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Tewari, R., Straschil, U., Bateman, A., Böhme, U., Cherevach, I., Gong, P., … Billker, O. (2010). The Systematic Functional Analysis of Plasmodium Protein Kinases Identifies Essential Regulators of Mosquito Transmission. Cell Host & Microbe, 8(4), 377–387. https://doi.org/10.1016/j.chom.2010.09.006
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Schaefer, U., Schmeier, S., & Bajic, V. B. (2010). TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. Nucleic Acids Research, 39(Database), D106–D110. https://doi.org/10.1093/nar/gkq945
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Kowald, A., & Schmeier, S. (2010). Text Mining for Systems Modeling. Data Mining in Proteomics, 305–318. https://doi.org/10.1007/978-1-60761-987-1_19
Sagar, S., Kaur, M., & Minneman, K. P. (2010). Antiviral Lead Compounds from Marine Sponges. Marine Drugs, 8(10), 2619–2638. https://doi.org/10.3390/md8102619
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D’Amato, M. E., Bajic, V. B., & Davison, S. (2011). Design and validation of a highly discriminatory 10-locus Y-chromosome STR multiplex system. Forensic Science International: Genetics, 5(2), 122–125. https://doi.org/10.1016/j.fsigen.2010.08.015
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Maqungo, M., Kaur, M., Kwofie, S. K., Radovanovic, A., Schaefer, U., Schmeier, S., … Bajic, V. B. (2010). DDPC: Dragon Database of Genes associated with Prostate Cancer. Nucleic Acids Research, 39(Database), D980–D985. https://doi.org/10.1093/nar/gkq849
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PARK, M.-R., YUN, K.-Y., MOHANTY, B., HERATH, V., XU, F., WIJAYA, E., … DE LOS REYES, B. G. (2010). Supra-optimal expression of the cold-regulated OsMyb4 transcription factor in transgenic rice changes the complexity of transcriptional network with major effects on stress tolerance and panicle development. Plant, Cell & Environment, 33(12), 2209–2230. https://doi.org/10.1111/j.1365-3040.2010.02221.x
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Tiffin, N., Meintjes, A., Ramesar, R., Bajic, V. B., & Rayner, B. (2010). Computational Analysis of Candidate Disease Genes and Variants for Salt-Sensitive Hypertension in Indigenous Southern Africans. PLoS ONE, 5(9), e12989. https://doi.org/10.1371/journal.pone.0012989
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Koser, C. U., Veerapen-Pierce, R. N., Summers, D. K., Archer, J. A. C., Bifani, P., Wintjens, R., … Roberts, G. D. (2010). Role of Mutations in Dihydrofolate Reductase DfrA (Rv2763c) and Thymidylate Synthase ThyA (Rv2764c) in Mycobacterium tuberculosis Drug Resistance. Antimicrobial Agents and Chemotherapy, 54(10), 4522–4525. https://doi.org/10.1128/aac.00422-10
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Hunt, P., Martinelli, A., Modrzynska, K., Borges, S., Creasey, A., Rodrigues, L., … Cravo, P. (2010). Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites. BMC Genomics, 11(1), 499. https://doi.org/10.1186/1471-2164-11-499
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Nygaard, S., Braunstein, A., Malsen, G., Van Dongen, S., Gardner, P. P., Krogh, A., … Jeffares, D. C. (2010). Long- and Short-Term Selective Forces on Malaria Parasite Genomes. PLoS Genetics, 6(9), e1001099. https://doi.org/10.1371/journal.pgen.1001099
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Cannistraci, C. V., Ravasi, T., Montevecchi, F. M., Ideker, T., & Alessio, M. (2010). Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes. Bioinformatics, 26(18), i531–i539. https://doi.org/10.1093/bioinformatics/btq376
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Feuerriegel, S., Köser, C., Trübe, L., Archer, J., Rüsch Gerdes, S., Richter, E., & Niemann, S. (2010). Thr202Ala in thyA Is a Marker for the Latin American Mediterranean Lineage of the Mycobacterium tuberculosis Complex Rather than Para-Aminosalicylic Acid Resistance. Antimicrobial Agents and Chemotherapy, 54(11), 4794–4798. https://doi.org/10.1128/aac.00738-10
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Kuo, D., Tan, K., Zinman, G., Ravasi, T., Bar-Joseph, Z., & Ideker, T. (2010). Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biology, 11(7), R77. https://doi.org/10.1186/gb-2010-11-7-r77
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Katayama, T., Arakawa, K., Nakao, M., Ono, K., Aoki-Kinoshita, K. F., Yamamoto, Y., … Aerts, J. (2010). The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. Journal of Biomedical Semantics, 1(1), 8. https://doi.org/10.1186/2041-1480-1-8
Pain, A., & Hertz-Fowler, C. (2010). Plant killers on the spot. Nature Reviews Microbiology, 8(9), 615–615. https://doi.org/10.1038/nrmicro2433
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Qian, P.-Y., Wang, Y., Lee, O. O., Lau, S. C. K., Yang, J., Lafi, F. F., … Wong, T. Y. (2010). Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing. The ISME Journal, 5(3), 507–518. https://doi.org/10.1038/ismej.2010.112
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Arieff, Z., Kaur, M., Gameeldien, H., van der Merwe, L., & Bajic, V. B. (2010). 5-HTTLPR Polymorphism: Analysis in South African Autistic Individuals. Human Biology, 82(3), 291–300. https://doi.org/10.3378/027.082.0303
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Cahill, M. J., Köser, C. U., Ross, N. E., & Archer, J. A. C. (2010). Read Length and Repeat Resolution: Exploring Prokaryote Genomes Using Next-Generation Sequencing Technologies. PLoS ONE, 5(7), e11518. https://doi.org/10.1371/journal.pone.0011518
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Sagar, S., Kaur, M., Minneman, K. P., & Bajic, V. B. (2010). Anti-cancer activities of diospyrin, its derivatives and analogues. European Journal of Medicinal Chemistry, 45(9), 3519–3530. https://doi.org/10.1016/j.ejmech.2010.06.021
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Wang, H., Zhang, H., Wong, Y. H., Voolstra, C., Ravasi, T., B. Bajic, V., & Qian, P.-Y. (2010). Rapid transcriptome and proteome profiling of a non-model marine invertebrate, Bugula neritina. PROTEOMICS, 10(16), 2972–2981. https://doi.org/10.1002/pmic.201000056
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Chowdhary, R., Bajic, V. B., Dong, D., Wong, L., & Liu, J. S. (2010). Genome-wide analysis of regions similar to promoters of histone genes. BMC Systems Biology, 4(S1). https://doi.org/10.1186/1752-0509-4-s1-s4
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Wong, Y., Arellano, S. M., Zhang, H., Ravasi, T., & Qian, P.-Y. (2010). Dependency on de novo protein synthesis and proteomic changes during metamorphosis of the marine bryozoan Bugula neritina. Proteome Science, 8(1), 25. https://doi.org/10.1186/1477-5956-8-25
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Dalgleish, R., Flicek, P., Cunningham, F., Astashyn, A., Tully, R. E., Proctor, G., … Maglott, D. R. (2010). Locus Reference Genomic sequences: an improved basis for describing human DNA variants. Genome Medicine, 2(4), 24. https://doi.org/10.1186/gm145
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DOI
10.1186/gm145Puglisi, E., Cahill, M. J., Lessard, P. A., Capri, E., Sinskey, A. J., Archer, J. A. C., & Boccazzi, P. (2010). Transcriptional Response of Rhodococcus aetherivorans I24 to Polychlorinated Biphenyl-Contaminated Sediments. Microbial Ecology, 60(3), 505–515. https://doi.org/10.1007/s00248-010-9650-5
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Garavaglia, B. S., Thomas, L., Zimaro, T., Gottig, N., Daurelio, L. D., Ndimba, B., … Gehring, C. (2010). A plant natriuretic peptide-like molecule of the pathogen Xanthomonas axonopodis pv. citri causes rapid changes in the proteome of its citrus host. BMC Plant Biology, 10(1), 51. https://doi.org/10.1186/1471-2229-10-51
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Garavaglia, B. S., Thomas, L., Zimaro, T., Gottig, N., Daurelio, L. D., Ndimba, B., … Gehring, C. (2010). A plant natriuretic peptide-like molecule of the pathogen Xanthomonas axonopodis pv. citri causes rapid changes in the proteome of its citrus host. BMC Plant Biology, 10(1), 51. https://doi.org/10.1186/1471-2229-10-51
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Tripurani, S. K., Xiao, C., Salem, M., & Yao, J. (2010). Cloning and analysis of fetal ovary microRNAs in cattle. Animal Reproduction Science, 120(1-4), 16–22. https://doi.org/10.1016/j.anireprosci.2010.03.001
Ravasi, T., Suzuki, H., Cannistraci, C. V., Katayama, S., Bajic, V. B., Tan, K., … Hayashizaki, Y. (2010). An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man. Cell, 140(5), 744–752. https://doi.org/10.1016/j.cell.2010.01.044
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Zhang, X., Bocca, S., Franchi, A., Anderson, S., Kaur, M., Bajic, V. B., & Oehninger, S. (2010). Do GnRH analogues directly affect human endometrial epithelial cell gene expression? Molecular Human Reproduction, 16(5), 347–360. https://doi.org/10.1093/molehr/gaq012
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Kothandaraman, N., Bajic, V. B., Brendan, P. N., Huak, C. Y., Keow, P. B., Razvi, K., … Choolani, M. (2010). E2F5 status significantly improves malignancy diagnosis of epithelial ovarian cancer. BMC Cancer, 10(1). https://doi.org/10.1186/1471-2407-10-64
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Garavaglia, B. S., Thomas, L., Gottig, N., Dunger, G., Garofalo, C. G., Daurelio, L. D., … Ottado, J. (2010). A Eukaryotic-Acquired Gene by a Biotrophic Phytopathogen Allows Prolonged Survival on the Host by Counteracting the Shut-Down of Plant Photosynthesis. PLoS ONE, 5(1), e8950. https://doi.org/10.1371/journal.pone.0008950
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Meier, S., Ruzvidzo, O., Morse, M., Donaldson, L., Kwezi, L., & Gehring, C. (2010). The Arabidopsis Wall Associated Kinase-Like 10 Gene Encodes a Functional Guanylyl Cyclase and Is Co-Expressed with Pathogen Defense Related Genes. PLoS ONE, 5(1), e8904. https://doi.org/10.1371/journal.pone.0008904
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Yun, K.-Y., Park, M. R., Mohanty, B., Herath, V., Xu, F., Mauleon, R., … de los Reyes, B. G. (2010). Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress. BMC Plant Biology, 10(1), 16. https://doi.org/10.1186/1471-2229-10-16
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Kim, Y.-I., Ryu, T., Lee, J., Heo, Y.-S., Ahnn, J., Lee, S.-J., & Yoo, O. (2010). A genetic screen for modifiers of Drosophila caspase Dcp-1 reveals caspase involvement in autophagy and novel caspase-related genes. BMC Cell Biology, 11(1), 9. https://doi.org/10.1186/1471-2121-11-9
2009
Schmeier, S., MacPherson, C. R., Essack, M., Kaur, M., Schaefer, U., Suzuki, H., … Bajic, V. B. (2009). Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation. BMC Genomics, 10(1), 595. https://doi.org/10.1186/1471-2164-10-595
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Hägg, S., Skogsberg, J., Lundström, J., Noori, P., Nilsson, R., Zhong, H., … Björkegren, J. (2009). Multi-Organ Expression Profiling Uncovers a Gene Module in Coronary Artery Disease Involving Transendothelial Migration of Leukocytes and LIM Domain Binding 2: The Stockholm Atherosclerosis Gene Expression (STAGE) Study. PLoS Genetics, 5(12), e1000754. https://doi.org/10.1371/journal.pgen.1000754
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Salem, M., Kenney, P. B., Rexroad, C. E., & Yao, J. (2010). Proteomic signature of muscle atrophy in rainbow trout. Journal of Proteomics, 73(4), 778–789. https://doi.org/10.1016/j.jprot.2009.10.014
Niemann, S., Köser, C. U., Gagneux, S., Plinke, C., Homolka, S., Bignell, H., … Archer, J. A. C. (2009). Genomic Diversity among Drug Sensitive and Multidrug Resistant Isolates of Mycobacterium tuberculosis with Identical DNA Fingerprints. PLoS ONE, 4(10), e7407. https://doi.org/10.1371/journal.pone.0007407
Salem, M., Xiao, C., Womack, J., Rexroad, C. E., & Yao, J. (2009). A MicroRNA Repertoire for Functional Genome Research in Rainbow Trout (Oncorhynchus mykiss). Marine Biotechnology, 12(4), 410–429. https://doi.org/10.1007/s10126-009-9232-z
Gersten, M., Alirezaei, M., Marcondes, M. C. G., Flynn, C., Ravasi, T., Ideker, T., & Fox, H. S. (2009). An Integrated Systems Analysis Implicates EGR1 Downregulation in Simian Immunodeficiency Virus Encephalitis-Induced Neural Dysfunction. Journal of Neuroscience, 29(40), 12467–12476. https://doi.org/10.1523/jneurosci.3180-09.2009
Heckmann, J. M., Uwimpuhwe, H., Ballo, R., Kaur, M., Bajic, V. B., & Prince, S. (2009). A functional SNP in the regulatory region of the decay-accelerating factor gene associates with extraocular muscle pareses in myasthenia gravis. Genes & Immunity, 11(1), 1–10. https://doi.org/10.1038/gene.2009.61
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Essack, M., Radovanovic, A., Schaefer, U., Schmeier, S., Seshadri, S. V., Christoffels, A., … Bajic, V. B. (2009). DDEC: Dragon database of genes implicated in esophageal cancer. BMC Cancer, 9(1). https://doi.org/10.1186/1471-2407-9-219
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RamachandraRao, S. P., Zhu, Y., Ravasi, T., McGowan, T. A., Toh, I., Dunn, S. R., … Sharma, K. (2009). Pirfenidone Is Renoprotective in Diabetic Kidney Disease. Journal of the American Society of Nephrology, 20(8), 1765–1775. https://doi.org/10.1681/asn.2008090931
The FANTOM Consortium & Riken Omics Science Center (2009). The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics, 41(5), 553–562. https://doi.org/10.1038/ng.375