2014

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
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
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
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

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
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
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
Holert, J., Alam, I., Larsen, M., Antunes, A., Bajic, V. B., Stingl, U., & Philipp, B. (2013). Genome Sequence of Pseudomonas sp. Strain Chol1, a Model Organism for the Degradation of Bile Salts and Other Steroid Compounds. Genome Announcements, 1(1). https://doi.org/10.1128/genomea.00014-12
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
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
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
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
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

2012

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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 + Interleukin-10 + and Interleukin-6 − Interleukin-10 + Cytokine Patterns in ST-Elevation Acute Myocardial Infarction. Circulation Research, 111(10), 1336–1348. https://doi.org/10.1161/circresaha.111.262477
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
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
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
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
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
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
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
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
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
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
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
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
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
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

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
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
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
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
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
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
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
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
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
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
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
Kulakovskiy, I. V., Belostotsky, A. A., Kasianov, A. S., Esipova, N. G., Medvedeva, Y. A., Eliseeva, I. A., & Makeev, V. J. (2011). A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites. Bioinformatics, 27(19), 2621–2624. https://doi.org/10.1093/bioinformatics/btr453
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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

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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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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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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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
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
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
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
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
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
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
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

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