Journal Publications

    2013

  1. Xie B, Jankovic BR, Bajic VB, Song L, Gao X (Apr 2013). Poly(A) motif prediction using spectral latent features from human DNA sequences. Bioinformatics, 2013, accepted

  2. Kuwahara H, Fan M, Wang S, Gao X (Apr 2013). A framework for scalable parameter estimation of gene circuit models using structural information. Bioinformatics, accepted

  3. Cannistraci CV, Lobato GA, Ravasi T (April 2013) Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding, Bioinfiormatics, accepted

  4. Wang JJ, Wang X, Gao X. Non-negative matrix factorization by maximizing correntropy for cancer clustering. BMC Bioinformatics. 2013 Mar 24;14(1):107. doi:10.1186/1471-2105-14-107

  5. Kalkatawi M, Rangkuti F, Schramm M, Jankovic BR, Kamau A, Chowdhary R, Archer JAC, Bajic VB (April 2013) Dragon PolyA Spotter: predictor of poly(A) motifs within human genomic DNA sequences (Letter to the Editor) Bioinformatics, 2013 doi:10.1093/bioinformatics/btt161

  6. Esack M, Radovanovic A, Bajic VB (April 2013) Information Exploration System for Sickle Cell Disease and Repurposing of Hydroxyfasudil, PLoS One, accepted

  7. Chowdhary R, Zhang J, Tan SL, Osborne DE, Bajic VB, Liu JS (April 2013) PIMiner: a web tool for extraction of Protein Interactions from biomedical literature, Int. J. Data Mining and Bioinformatics, 7(4):450-462, 2013

  8. Ma L, Bajic VB, Zhang Z (April 2013) On the classification of long non-coding RNAs. RNA Biology, accepted

  9. Cannistraci CV, Alanis-Lobato G, Ravasi T (April 2013) From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks. Scientific Reports, 2013, 3:1613 doi:10.1038/srep01613

  10. Pardo LM, Rizzu P, Francescatto M, Vitezic M, Leday GG, Sanchez JS, Khamis A, Takahashi H, van de Berg WD, Medvedeva YA, van de Wiel MA, Daub CO, Carninci P, Heutink P. (Mar 2013) Regional differences in gene expression and promoter usage in aged human brains. Neurobiol Aging. 2013 Feb 18. doi:pii: S0197-4580(13)00023-7. 10.1016/j.neurobiolaging.2013.01.005.

  11. Chandramouli KH, Sun J, Mok FS, Liu L, Qiu JW, Ravasi T, Qian PY (Mar 2013) Transcriptome and Quantitative Proteome Analysis Reveals Molecular Processes Associated with Larval Metamorphosis in the Polychaete Pseudopolydora vexillosa. J Proteome Res. 2013 Mar 1;12(3):1344-58. doi: 10.1021/pr3010088.

  12. Sepúlveda N, Campino SG, Assefa SA, Sutherland CJ, Pain A, Clark TG. (Feb 2013) A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data. BMC Genomics. 2013 Feb 26;14(1):128.

  13. Tichy J, Gardian Z, Bina D, Konik P, Litvin R, Herbstova M, Pain A, Vacha F. (Feb 2103) Light harvesting complexes of Chromera velia, photosynthetic relative of apicomplexan parasites. Biochim Biophys Acta. 2013 Feb 18. doi:pii: S0005-2728(13)00028-5. 10.1016/j.bbabio.2013.02.002.

  14. Chandramouli KH, Sun J, Mok FS, Liu L, Qiu JW, Ravasi T, Qian PY (Mar 2013) Transcriptome and Quantitative Proteome Analysis Reveals Molecular Processes Associated with Larval Metamorphosis in the Polychaete Pseudopolydora vexillosa. J Proteome Res. 2013 Mar 1;12(3):1344-58. doi: 10.1021/pr3010088.

  15. Wang J, Bensmail H, Gao X. Multiple graph regularized nonnegative matrix factorization. Pattern Recognition. Accepted.

  16. Chen P, Li J, Wong L, Kuwahara H, Huang J, Gao X. (Mar 2013) Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences. Proteins. 2013 Mar 16. doi: 10.1002/prot.24278.

  17. Gao X. (Feb 2013) Recent advances in computational methods for nuclear magnetic resonance data processing. Genomics Proteomics Bioinformatics. 2013 Feb;11(1):29-33. doi: 10.1016/j.gpb.2012.12.003.

  18. Abbas A, Kong XB, Liu Z, Jing BY, Gao X. (Jan 2013) Automatic peak selection by a Benjamini-Hochberg-based algorithm. PLoS One. 2013;8(1):e53112. doi: 10.1371/journal.pone.0053112.

  19. Stabler RA, Negus D, Pain A, Taylor PW. (Jan 2013) Draft Genome Sequences of Pseudomonas fluorescens BS2 and Pusillimonas noertemannii BS8, Soil Bacteria That Cooperate To Degrade the Poly-γ-d-Glutamic Acid Anthrax Capsule. Genome Announc. 2013 Jan;1(1). doi:pii: e00057-12. 10.1128/genomeA.00057-12. Epub 2013 Jan 24.

  20. Cannistraci CV, Ogorevc J, Zorc M, Ravasi T, Dovc P, Kunej T. (Feb 2013) Pivotal role of the muscle-contraction pathway in cryptorchidism and evidence for genomic connections with cardiomyopathy pathways in RASopathies. BMC Med Genomics. 2013 Feb 14;6(1):5. [Epub ahead of print]

  21. Holert J, Alam I, Larsen M, Antunes A, Bajic VB, Stingl U, Philipp B. (Jan 2013) Genome Sequence of Pseudomonas sp. Strain Chol1, a Model Organism for the Degradation of Bile Salts and Other Steroid Compounds. Genome Announc. 2013 Jan;1(1). doi:pii: e00014-12. 10.1128/genomeA.00014-12. Epub 2013 Jan 15.

  22. Sagar S, Kaur M, Radovanovic A, Bajic VB (Feb 2013) Dragon Exploration System on Marine Sponge Compounds Interactions, Journal of Cheminformatics, 2013 Feb 16;5(1):11. [Epub ahead of print]

  23. Sagar S, Esau L, Hikmawan T, Antunes A, Holtermann K, Stingl U, Bajic VB, Kaur M (Feb 2013) Cytotoxic and apoptotic evaluations of marine bacteria isolated from brine-seawater interface of the Red Sea, BMC Complementary and Alternative Medicine, 2013 Feb 6;13:29. doi: 10.1186/1472-6882-13-29.

  24. Narasimhan K, Lin SL, Tong T, Baig S, Ho S, Sukumar P, Biswas A, Hahn S, Bajic VB, Choolani M (Feb 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, 2013, 33(3):223-231. doi: 10.1002/pd.4047. [Epub ahead of print]

  25. Marondedze C, Turek I, Parrott B, Thomas L, Jankovic B, Lilley KS, Gehring C (Jan 2013) Structural and functional characteristics of cGMP-dependent methionine oxidation in Arabidopsis thaliana proteins. Cell Commun Signal. 2013 Jan 5;11(1):1.

  26. Kulakovskiy IV, Medvedeva YA, Schaefer U, Kasianov AS, Vorontsov IE, Bajic VB, Makeev VJ. (Jan 2013) HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. Nucleic Acids Res. 2013 Jan 1;41(D1):D195-D202.

  27. Mora AM, Ashoor H, Jankovic BR, Kamau A, Awara K, Chowdhary R, Archer JA, Bajic VB. (Jan 2013) Dragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants. Bioinformatics. 2013 Jan 1;29(1):117-8. doi: 10.1093/bioinformatics/bts638.

    28. 2012

  28. Fanucchi F, Alpi E, Olivieri S, Cannistraci CV, Bachi A, Alpi A, Alessio M (Jun 2012) Acclimation increases freezing stress response of Arabidopsis thaliana at proteome level. Biochim Biophys Acta. 2012 Jun;1824(6):813-25. doi: 10.1016/j.bbapap.2012.03.015.

  29. Moon RW, Hall J, Rangkuti F, Ho YS, Almond N, Mitchell GH, Pain A, Holder AA, Blackman MJ. (Dec 2012) Adaptation of the genetically tractable malaria pathogen Plasmodium knowlesi to continuous culture in human erythrocytes. Proc Natl Acad Sci U S A. 2012 Dec 24. [Epub ahead of print]

  30. Oakes RD, Kurian D, Bromley E, Ward C, Lal K, Blake DP, Reid AJ, Pain A, Sinden RE, Wastling JM, Tomley FM. (Dec 2012) The rhoptry proteome of Eimeria tenella sporozoites. Int J Parasitol. 2012 Dec 19. doi:pii: S0020-7519(12)00313-X. 10.1016/j.ijpara.2012.10.024. [Epub ahead of print]

  31. Malas TB, Ravasi T. (Dec 2012) Computational Tools for Genome-Wide miRNA Prediction and Study, The Open Biology Journal , 2012, 5, 23-30

  32. Ryu T, Seridi L, Ravasi T. (Dec 2012) The evolution of ultraconserved elements with different phylogenetic origins. BMC Evol Biol. 2012 Dec 5;12(1):236. [Epub ahead of print]

  33. Kumar K, Sagar S, Esau L, Kaur M, Kumar V. (Dec 2012) Synthesis of novel 1H-1,2,3-triazole tethered C-5 substituted uracil-isatin conjugates and their cytotoxic evaluation. Eur J Med Chem. 2012 Dec;58:153-9. doi: 10.1016/j.ejmech.2012.10.008.

  34. Naeem R, Rashid M, Pain A. (Nov 2012) READSCAN: A fast and scalable pathogen discovery program with accurate genome relative abundance estimation. Bioinformatics. 2012 Nov 28. [Epub ahead of print]

  35. Haywood AF, Merner ND, Hodgkinson KA, Houston J, Syrris P, Booth V, Connors S, Pantazis A, Quarta G, Elliott P, McKenna W, Young TL. (Nov 2012) Recurrent missense mutations in TMEM43 (ARVD5) due to founder effects cause arrhythmogenic cardiomyopathies in the UK and Canada. Eur Heart J. 2012 Nov 15. [Epub ahead of print]

  36. Ho YS, Adroub SA, Abadi M, Al Alwan B, Alkhateeb R, Gao G, Ragab A, Ali S, van Soolingen D, Bitter W, Pain A, Abdallah AM (Nov 2012) Complete Genome Sequence of Mycobacterium vaccae Type Strain ATCC 25954. J Bacteriol. 2012 Nov;194(22):6339-40. doi: 10.1128/JB.01462-12.

  37. Ho YS, Adroub SA, Aleisa F, Mahmood H, Othoum G, Rashid F, Zaher M, Ali S, Bitter W, Pain A, Abdallah AM (Nov 2012) Complete Genome Sequence of Mycobacterium fortuitum subsp. fortuitum Type Strain DSM46621.J Bacteriol. 2012 Nov;194(22):6337-8. doi: 10.1128/JB.01461-12.

  38. Ammirati E, Cannistraci CV, Cristell NA, Vecchio V, Palini AG, Tornvall P, Paganoni AM, Miendlarzewska EA, Sangalli LM, Monello A, Pernow J, Bj??rnstedt Bennermo M, Marenzi G, Hu D, Uren NG, Cianflone D, Ravasi T, Manfredi AA, Maseri A (Oct. 2012) Identification and Predictive Value of Interleukin-6+ Interleukin-10+ and Interleukin-6- Interleukin-10+ Cytokine Patterns in ST-Elevation Acute Myocardial Infarction. Circ Res. 2012 Oct 26;111(10):1336-48. doi: 10.1161/CIRCRESAHA.111.262477.

  39. Essack M, Macpherson CR, Schmeier S, Bajic VB. (Oct 2012) Identification of estrogen responsive genes using esophageal squamous cell carcinoma (ESCC) as a model. BMC Syst Biol. 2012 Oct 26;6(1):135. [Epub ahead of print]

  40. Hayashida K, Hara Y, Abe T, Yamasaki C, Toyoda A, Kosuge T, Suzuki Y, Sato Y, Kawashima S, Katayama T, Wakaguri H, Inoue N, Homma K, Tada-Umezaki M, Yagi Y, Fujii Y, Habara T, Kanehisa M, Watanabe H, Ito K, Gojobori T, Sugawara H, Imanishi T, Weir W, Gardner M, Pain A, Shiels B, Hattori M, Nene V, Sugimoto C (Sep 2012) Comparative genome analysis of three eukaryotic parasites with differing abilities to transform leukocytes reveals key mediators of Theileria-induced leukocyte transformation., MBio. 2012 Sep 4;3(5):e00204-12. doi: 10.1128/mBio.00204-12. Print 2012.

  41. Köser CU, Feuerriegel S, Summers DK, Archer JA, Niemann S (Sep 2012) Importance of the genetic diversity within the Mycobacterium tuberculosis complex for the development of novel antibiotics and diagnostic tests of drug resistance, Antimicrob Agents Chemother 2012 Sep 24. [Epub ahead of print]

  42. Messih MA, Chitale M, Bajic VB, Kihara D, Gao X (Sep 2012) Protein domain recurrence and order can enhance prediction of protein functions, Bioinformatics 2012 Sep 15;28(18):i444-i450. doi: 10.1093/bioinformatics/bts398.

  43. Giles EC, Kamke J, Moitinho-Silva L, Taylor MW, Hentschel U, Ravasi T, Schmitt S (Aug 2012) Bacterial community profiles in low microbial abundance sponges. FEMS Microbiol Ecol. 2012 Aug 11. doi: 10.1111/j.1574-6941.2012.01467.x.

  44. Siam R, Mustafa GA, Sharaf H, Moustafa A, Ramadan AR, Antunes A, Bajic VB, Stingl U, Marsis NG, Coolen MJ, Sogin M, Ferreira AJ, Dorry HE (Aug 2012) Unique prokaryotic consortia in geochemically distinct sediments from Red Sea Atlantis II and discovery deep brine pools, PLoS One 2012;7(8):e42872. doi: 10.1371/journal.pone.0042872. Epub 2012 Aug 20.

  45. Fan M, Wong KC, Ryu T, Ravasi T, Gao X. (Jun 2012) SECOM: A Novel Hash Seed and Community Detection Based-Approach for Genome-Scale Protein Domain Identification. PLoS One. 2012;7(6):e39475.

  46. Zelman AK, Dawe A, Gehring C, Berkowitz GA. (May 2012) Evolutionary and structural perspectives of plant cyclic nucleotide-gated cation channels. Front Plant Sci. 2012;3:95.

  47. Essack M, Bajic VB, Archer JAC (June 2012) Conotoxins that Confer Therapeutic Possibilities. Mar. Drugs 10(6):1244-1265

  48. Kamanu FK, Medvedeva YA, Schaefer U, Jankovic BR, Archer JAC, Bajic VB (June 2012) Mutations and binding sites of human transcription factors. Front. Gene. 3:100. doi: 10.3389/fgene.2012.00100

  49. Abdallah AM, Rashid M, Adroub SA, Arnoux M, Ali S, van Soolingen D, Bitter W, Pain A. (June, 2012) Complete Genome Sequence of Mycobacterium phlei Type Strain RIVM601174 J Bacteriol. 194(12):3284-5.

  50. Abdallah AM, Rashid M, Adroub SA, Elabdalaoui H, Ali S, van Soolingen D, Bitter W, Pain A. (Jun, 2012) Complete Genome Sequence of Mycobacterium xenopi Type Strain RIVM700367. J Bacteriol. 194(12):3282-3.

  51. [Most accessed] Woo J, MacPherson CR, Liu J, Wang H, Kiba T, Hannah M, Wang XJ, Bajic VB, Chua NH, (May, 2012) The response and recovery of Arabidopsis thaliana transcriptome to phosphate starvation, BMC Plant Biology, 12(1):62.

  52. Chowdhary R, Tan SL, Zhang J, Karnik S, Bajic VB, Liu JS, (April 6, 2012) Context-specific Protein Network Miner - an online system for exploring context-specific protein interaction networks from the literature, PLoS One, 7(4):e34480. doi:10.1371/journal.pone.0034480

  53. Lawton J, Brugat T, Yam XY, Reid AJ, Boehme U, Otto TD, Pain A, Jackson A, Berriman M, Cunningham D, Preiser P, Langhorne J (Mar 2012) Characterization and gene expression analysis of the cir multi-gene family of Plasmodium chabaudi chabaudi (AS). BMC Genomics. 2012 Mar 29;13(1):125.

  54. [Highly accessed] Zhang Z, Li J, Cui P, Ding F, Li A, Townsend JP, Yu J. (March 2012) Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance. BMC Bioinformatics. 13(1):43.

  55. Reid AJ, Vermont SJ, Cotton JA, Harris D, Hill-Cawthorne GA, K??nen-Waisman S, Latham SM, Mourier T, Norton R, Quail MA, Sanders M, Shanmugam D, Sohal A, Wasmuth JD, Brunk B, Grigg ME, Howard JC, Parkinson J, Roos DS, Trees AJ, Berriman M, Pain A, Wastling JM (Mar 2012) Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy. PLoS Pathog. 2012 Mar;8(3):e1002567. doi: 10.1371/journal.ppat.1002567.

  56. Wong YH, Wang H, Ravasi T, Qian PY. Involvement of Wnt signaling pathways in the metamorphosis of the bryozoan Bugula neritina. PLoS One. 2012;7(3):e33323

  57. [Most read article in March 2012] Chowdhary R, Tan SL, Pavesi G, Jin J, Dong D, Mathur SK, Burkart A, Narang V, Glurich I, Raby BA, Weiss ST, Wong L, Liu JS, Bajic VB. A database of annotated promoters of genes associated with common respiratory and related diseases. Am J Respir Cell Mol Biol. 2012 Mar 1. [Epub ahead of print] PubMed PMID: 22383585; http://ajrcmb.atsjournals.org/reports/most-read.

  58. Seshadri Sundararajan V, Gabere MN, Pretorius A, Adam S, Christoffels A, Lehv??slaiho M, Archer JAC, Bajic VB. (Jan 2012) DAMPD: A manually curated antimicrobial peptide database. Nucleic Acids Research 2012 Jan;40(Database issue):D1108-12. doi: 10.1093/nar/gkr1063.

  59. Kalkatawi M, Rangkuti F, Schramm M, Jankovic BR, Kamau A, Chowdhary R, Archer JAC, Bajic VB (November 2011) Dragon PolyA Spotter: predictor of poly(A) motifs within human genomic DNA sequences. Bioinformatics 2012 Jan 1;28(1):127-9

    60. 2011

  60. Olivieri S, Conti A, Iannaccone S, Cannistraci CV, Campanella A, Barbariga M, Codazzi F, Pelizzoni I, Magnani G, Pesca M, Franciotta D, Cappa SF, Alessio M. (Dec 2011) Ceruloplasmin oxidation, a feature of Parkinson''s disease CSF, inhibits ferroxidase activity and promotes cellular iron retention. J Neurosci 31(50):18568-77. doi: 10.1523/???JNEUROSCI.3768-11.2011.
  61. Dawe AS, Radovanovic A, Kaur M, Sagar S, Seshadri SV, Schaefer U, Kamau AA, Christoffels A, Bajic VB (Dec 2011) DESTAF: A database of text-mined associations for reproductive toxins potentially affecting human fertility. Reprod Toxicol 33(1):99-105. Epub 2011 Dec 17. PMID:22198179
  62. Ramaprasad A, Pain A, Ravasi T. (Dec 2011) Defining the protein interaction network of human malaria parasite Plasmodium falciparum. Genomics 99(2):69-75.Dec 08. Epub 2011 Dec 8. PMID:22178265
  63. Pretorius A, Kaur M, Wamalwa M, February MF, Essack M, Bajic VB, Rees DJG (Dec 2011) 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. The GSTF Journal on Bioinformatics and Biotechnology 1(1).
  64. Feuerriegel S, Köser CU, Baù D, Rüsch-Gerdes S, Summers DK, Archer JA, Marti-Renom MA, Niemann S. (December 2011) Impact of fgd1 and ddn diversity in Mycobacterium tuberculosis complex on in vitro susceptibility to PA-824. Antimicrob Agents Chemother 55(12):5718-22. Epub 2011 Sep 19. doi: 10.1128/AAC.05500-11.
  65. [Highly Accessed] Schmeier S, Schaefer U, Essack M, Bajic VB (November 2011) Network analysis of microRNAs and their regulation in human ovarian cancer. BMC Systems Biology 5(1):183. doi:10.1186/1752-0509-5-183.
  66. Jankovic B, Seoighe C, Alqurashi M, Gehring C (November 2011) Is there evidence of optimisation for carbon efficiency in plant proteomes? Plant Biology 13(6):831-834. doi: 10.1111/j.1438-8677.2011.00494.x.
  67. Bokil NJ, Totsika M, Carey AJ, Stacey KJ, Hancock V, Saunders BM, Ravasi T, Ulett GC, Schembri MA, Sweet MJ (November 2011) Intramacrophage survival of uropathogenic Escherichia coli: Differences between diverse clinical isolates and between mouse and human macrophages. Immunobiology 216(11):1164-71. doi:10.1016/j.imbio.2011.05.011.
  68. Kulakovskiy IV, Belostotsky AA, Kasianov AS, Esipova NG, Medvedeva YA, Eliseeva IA, Makeev VJ (Ocotober 2011) A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites. Bioinformatics 27(19):2621-4. doi:10.1093/bioinformatics/btr453.
  69. Pfander C, Anar B, SchwachF, Otto TD, Brochet M, Volkmann K, Quail MA, Pain A, Rosen B, Skarnes W, Rayner JC, Billker O. (October 2011) A scalable pipeline for highly effective genetic modification of a malaria parasite. Nature Methods [Epub ahead of print]. doi: 10.1038/nmeth.1742.
  70. Essack M, Bajic VB, Archer JAC (September 2011) Recently Confirmed Apoptosis-Inducing Lead Compounds Isolated from Marine Sponge of Potential Relevance in Cancer Treatment. Mar. Drugs 9(9):1580-1606. doi:10.3390/md9091580.
  71. Projahn M, Köser CU, Homolka S, Summers DK, Archer JA, Niemann S (September 2011) Polymorphisms in isoniazid and prothionamide resistance genes of the Mycobacterium tuberculosis complex. Antimicrob Agents Chemother 55(9):4408-11. Epub 2011 Jun 27. doi: 10.1128/AAC.00555-11.
  72. Kaur M, Macpherson CR, Schmeier S, Narasimhan K, Choolani M, Bajic VB. (September 2011) In Silico discovery of transcription factors as potential diagnostic biomarkers of ovarian cancer. BMC Systems Biology 5(1):144. doi:10.1186/1752-0509-5-144.
  73. Kwofie SK, Schaefer U, Sundararajan VS, Bajic VB, Christoffels A. (September 2011) HCVpro: Hepatitis C virus protein interaction database. Infect Genet Evol [Epub ahead of print]. doi:10.1016/j.meegid.2011.09.001.
  74. Antunes A, Alam I, El Dorry H, Siam R, Robertson A, Bajic VB, Stingl U. (September 2011) Genome sequence of Haloplasma contractile, an unusual contractile bacterium from a deep-sea anoxic brine lake. J Bacteriol 193(17):4551-2. doi: 10.1128/???JB.05461-11.
  75. Antunes A, Alam I, Bajic VB, Stingl U. (September 2011) Genome sequence of Halorhabdus tiamatea, the first archaeon isolated from a deep-sea anoxic brine lake. J Bacteriol 193(17):4553-4. doi: 10.1128/???JB.05462-11.
  76. Antunes A, Alam I, Bajic VB, Stingl U. (September 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. J Bacteriol 193(17):4555-6. doi: 10.1128/???JB.05459-11.
  77. Romeo G, Materia L, Modica MN, Pittal?? V, Salerno L, Siracusa MA, Manetti M, Botta M, Minneman KP (July 2011) Novel 4-Phenylpiperidine-2,6-dione Derivatives. Ligands for alpha1-adrenoceptor subtypes. Eur. J. Medicinal Chem. 2011, 46: 2676-2690.
  78. Chen ZF, Matsumura K, Wang H, Arellano SM, Yan X, Alam I, Archer JA, Bajic VB, Qian PY. (July 2011) Toward an understanding of the molecular mechanisms of barnacle larval settlement: a comparative transcriptomic approach. PLoS One 6(7):e22913. Epub 2011 Jul 29. doi. 10.1371/journal.pone.0022913.
  79. Schmeier S, Jankovic B, Bajic VB. (July 2011) Simplified method to predict mutual interactions of human transcription factors based on their primary structure. PLoS One 6(7):e21887. Epub 2011 Jul 5. doi: 10.1371/journal.pone.0021887.
  80. Köser CU, Niemann S, Summers DK, Archer JA (June 2011) Overview of errors in the reference sequence and annotation of Mycobacterium tuberculosis H37Rv, and variation amongst its isolates. Infect Genet Evol [Epub ahead of print]. doi:10.1016/j.meegid.2011.06.011.
  81. Kwofie SK, Radovanovic A, Sundararajan VS, Maqungo M, Christoffels A, Bajic VB (June 2011)Dragon Exploratory System on Hepatitis C Virus (DESHCV). Infect Genet Evol 11(4):734-9. doi:10.1016/j.meegid.2010.12.006.
  82. Gomes-Santos CS, Braks J, Prud??ncio M, Carret C, Gomes AR, Pain A, Feltwell T, Khan S, Waters A, Janse C, Mair GR, Mota MM. (May 2011) Transition of Plasmodium sporozoites into liver stage-like forms is regulated by the RNA binding protein Pumilio. PLoS Pathog 7(5):e1002046. Epub 2011 May 19. doi:10.1371/journal.ppat.1002046.
  83. Köser CU, Summers DK, Archer JA (April 2011) Thr270Ile in embC (Rv3793) is not a marker for ethambutol resistance in the Mycobacterium tuberculosis complex. Antimicrob Agents Chemother 55(4):1825. doi: 10.1128/???AAC.01607-10.
  84. [Highly Accessed] Ryu T, Mavromatis CH, Bayer T, Voolstra CR, Ravasi T (April 2011) Unexpected complexity of the reef-building coral Acropora millepora transcription factor network. BMC Systems Biology 5(1):58. doi:10.1186/1752-0509-5-58.
  85. Lee OO, Wang Y, Yang J, Lafi FF, Al-Suwailem A, Qian PY (April 2011) Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea. ISME J 5(4):650-664. doi:10.1038/ismej.2010.165.
  86. D''''Amato ME, Bajic VB, Davison S (March 2011) Design and validation of a highly discriminatory 10-locus Y-chromosome STR multiplex system. Forensic Sci Int Genet 5(2):122-125. doi:10.1016/j.fsigen.2010.08.015.
  87. Qian PY, Wang Y, Lee OO, Lau SC, Yang J, Lafi FF, Al-Suwailem A, Wong TY (March 2011) Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing. ISME J 5(3):507-518. doi:10.1038/ismej.2010.112.
  88. Köser CU, Summers DK, Archer JA (March 2011) Comment on: Isoniazid and rifampicin resistance-associated mutations in Mycobacterium tuberculosis isolates from Yangon, Myanmar: implications for rapid molecular testing. J Antimicrob Chemother 66(3):686-687. doi: 10.1093/jac/dkq492
  89. Ogun SA, Tewari R, Otto TD, Howell SA, Knuepfer E, Cunningham DA, Xu Z, Pain A, Holder AA. (February 2011) Targeted disruption of py235ebp-1: invasion of erythrocytes by Plasmodium yoelii using an alternative Py235 erythrocyte binding protein. PLoS Pathog 7(2):e1001288. Epub 2011 Feb 17. doi:10.1371/journal.ppat.1001288
  90. Schmeier S, Schaefer U, MacPherson CR, Bajic VB (February 2011) dPORE-miRNA: polymorphic regulation of microRNA genes PLoS One 6(2):e16657. Epub 2011 Feb 4. doi:10.1371/journal.pone.0016657.
  91. Zhang H, Wong YH, Wang H, Chen Z, Arellano SM, Ravasi T, Qian PY (January 2011) Quantitative Proteomics Identify Molecular Targets That Are Crucial in Larval Settlement and Metamorphosis of Bugula neritina. J. Proteome Res 10(1):349-60. doi: 10.1021/pr100817v.
  92. Schaefer U, Schmeier S, Bajic VB (January 2011) TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. Nucleic Acids Res 39(1):D106-110. doi: 10.1093/nar/gkq945.
  93. Maqungo M, Kaur M, Kwofie SK, Radovanovic A, Schaefer U, Schmeier S, Oppon E, Christoffels A, Bajic VB (January 2011) DDPC: Dragon Database of Genes associated with Prostate Cancer. Nucleic Acids Res 39(1): D980-985. doi: 10.1093/nar/gkq849.
  94. Sha DH, Bajic VB (2011) An optimized recursive learning algorithm for three-layer feedforward neural networks for MIMO nonlinear system identification. Intelligent Automation and Soft Computing 17(2):133-147.

    95. 2010

  95. Park MR, Yun KY, Mohanty B, Herath V, Xu F, Wijaya E, Bajic VB, Yun SJ, De Los Reyes BG (December 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 Environ 33(12): 2209-30. doi: 10.1111/j.1365-3040.2010.02221.x.
  96. Kuo D, Licon K, Bandyopadhyay S, Chuang R, Luo C, Catalana J, Ravasi T, Tan K, Ideker T (December 2010) Coevolution within a transcriptional network by compensatory trans and cis mutations. Genome Res 20(12):1672-78. doi:10.1101/gr.111765.110.
  97. Köser CU, Summers DK, Archer JA (November 2010) Role of the dihydrofolate reductase DfrA (Rv2763c) in trimethoprim-sulfamethoxazole (co-trimoxazole) resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother 54(11): 4951-4952. doi: 10.1128/???AAC.00876-10.
  98. Feuerriegel S, Köser CU, Trube L, Archer J, Rusch Gerdes S, Richter E, Niemann S (November 2010) Thr202Ala in thyA Is a Marker for the Latin American Mediterranean Lineage of the Mycobacterium tuberculosis complex rather than para-aminosalicylic acid resistance. Antimicrob Agents Chemother 54(11): 4794-98. doi: 10.1128/???AAC.00738-10.
  99. Schaefer U, Kodzius R, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bajic VB (November 2010) High sensitivity TSS prediction: estimates of locations where TSS cannot occur. PLoS One 5(11): e13934. Epub 2010 Nov 15. doi:10.1371/journal.pone.0013934.
  100. Tewari R, Straschil U, Bateman A, Bohme U, Cherevach I, Gong P, Pain A, Billker O (October 2010) The systematic functional analysis of Plasmodium protein kinases identifies essential regulators of mosquito transmission. Cell Host Microbes 8(4): 377-387. doi:10.1016/j.chom.2010.09.006.
  101. Sagar S, Kaur M, Minneman KP (October 2010) Antiviral lead compounds from marine sponges. Mar Drugs 8(10): 2619-38. doi:10.3390/md8102619.
  102. Puglisi E, Cahill MJ, Lessard PA, Capri E, Sinskey AJ, Archer JA, Boccazzi P (October 2010) Transcriptional response of Rhodococcus aetherivorans I24 to polychlorinated biphenyl-contaminated sediments. Microb Ecol 60(3): 505-515. DOI: 10.1007/s00248-010-9650-5.
  103. Köser CU, Veerapen-Pierce RN, Summers DK, Archer JA (October 2010) Role of mutations in dihydrofolate reductase DfrA (Rv2763c) and thymidylate synthase ThyA (Rv2764c) in Mycobacterium tuberculosis drug resistance. Antimicrob Agents Chemother 54(10): 4522-4523; author reply 5423-4525. doi: 10.1128/???AAC.00422-10.
  104. Pain A, Hertz-Fowler C (September 2010) Plant killers on the spot. Nature Reviews Microbiology 8(9):615. doi:10.1038/nrmicro2433.
  105. Nygaard S, Braunstein A, Malsen G, Van Dongen S, Gardner PP, Krogh A, Otto TD, Pain A, Berriman M, McAuliffe J, Dermitzakis ET, Jeffares DC (September 2010) Long- and short-term selective forces on malaria parasite genomes. PLoS Genetics 6(9): e1001099. Epub 2010 Sep 9. doi:10.1371/journal.pgen.1001099.
  106. Cannistraci CV, Ravasi T, Montevecchi FM, Ideker T, Alessio M (September 2010) Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes. Bioinformatics 26(18): i531-539. doi:10.1093/bioinformatics/btq376.
  107. [Highly accessed] Hunt P, Martinelli A, Modrzynska K, Borges S, Creasey A, Rodrigues L, Beraldi D, Loewe L, Fawcett R, Kumar S, Thomson M, Trivedi U, Otto TD, Pain A, Blaxter M, Cravo P (September 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. doi:10.1186/1471-2164-11-499.
  108. [Top 25 hottest articles in July to September 2010] Sagar S, Kaur M, Minneman KP, Bajic VB (September 2010) Anti-cancer activities of diospyrin, its derivatives and analogues. Eur J Med Chem 45(9): 3519-3530. doi:10.1016/j.ejmech.2010.06.021.
  109. Tiffin N, Meintjes A, Ramesar R, Bajic VB, Rayner B (September 2010) Computational analysis of candidate disease genes and variants for salt-sensitive hypertension in indigenous Southern Africans. PLoS One 5(9): e12989. Epub 2010 Sep 27. doi:10.1371/journal.pone.0012989.
  110. Salem M, Xiao C, Womack J, Rexroad CE, 3rd, Yao J (August 2010) A microRNA repertoire for functional genome research in rainbow trout (Oncorhynchus mykiss). Mar Biotechnol (NY) 12(4): 410-429. doi:10.1007/s10126-009-9232-z.
  111. Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, Fernandez JM, Funahashi A, Gordon PM, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas EA, Kerhornou A, Kibukawa E, Kinjo AR, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn TM, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley DM, Sugawara H, Tashiro T, Trelles O, Vos RA, Wilkinson MD, York W, Zmasek CM, Asai K, Takagi T (August 2010) The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon
  112. Zhang H, Zhao C, Li X, Zhu Y, Gan CS, Wang Y, Ravasi T, Qian PY, Wong SC, Sze SK (August 2010) Study of monocyte membrane proteome perturbation during lipopolysaccharide-induced tolerance using iTRAQ-based quantitative proteomic approach. Proteomics 10(15): 2780-2789. doi: 10.1002/pmic.201000066.
  113. Wang H, Zhang H, Wong YH, Voolstra C, Ravasi T, Bajic VB, Qian PY (August 2010) Rapid transcriptome and proteome profiling of a non-model marine invertebrate, Bugula neritina. Proteomics 10(16): 2972-81. doi: 10.1002/pmic.201000056.
  114. Tripurani SK, Xiao C, Salem M, Yao J (July 2010) Cloning and analysis of fetal ovary microRNAs in cattle. Anim Reprod Sci 120(1-4): 16-22. doi:10.1016/j.anireprosci.2010.03.001.
  115. Kuo D, Tan K, Zinman G, Ravasi T, Bar-Joseph Z, Ideker T (July 2010) Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biol 11(7):R77. doi:10.1186/gb-2010-11-7-r77.
  116. Garavaglia BS, Thomas L, Gottig N, Zimaro T, Garofalo CG, Gehring C, Ottado J (July 2010) Shedding light on the role of photosynthesis in pathogen colonization and host defense. Commun Integr Biol 3(4): 383-384. PMCID: PMC2928325
  117. Cahill MJ, Koser CU, Ross NE, Archer JA (July 2010) Read length and repeat resolution: exploring prokaryote genomes using next-generation sequencing technologies. PLoS One 5(7):e11518. Epub 2010 Jul 12. doi:10.1371/journal.pone.0011518.
  118. [Most read articles during December 2010] Shrestha R, Arnaud E, Mauleon R, Senger M, Davenport GF, Hancock D, Morrison N, Bruskiewich R, McLaren G (May 2010) Multifunctional crop trait ontology for breeders'' data: field book, annotation, data discovery and semantic enrichment of the literature. AoB Plants 2010, doi:10.1093/aobpla/plq008.
  119. Wong YH, Arellano SM, Zhang H, Ravasi T, Qian PY (May 2010) Dependency on de novo protein synthesis and proteomic changes during metamorphosis of the marine bryozoan Bugula neritina. Proteome Sci 8:25. doi:10.1186/1477-5956-8-25.
  120. Chowdhary R, Bajic VB, Dong D, Wong L, Liu JS (May 2010) Genome-wide analysis of regions similar to promoters of histone genes. BMC Syst Biol 4(Suppl 1): S4. doi:10.1186/1752-0509-4-S1-S4.
  121. [Highly Accessed] Dalgleish R, Flicek P, Cunningham F, Astashyn A, Tully RE, Proctor G, Chen Y, McLaren WM, Larsson P, Vaughan BW, Beroud C, Dobson G, Lehvaslaiho H, Taschner PE, den Dunnen JT, Devereau A, Birney E, Brookes AJ, Maglott DR (April 2010) Locus Reference Genomic sequences: an improved basis for describing human DNA variants. Genome Med 2(4): 24. doi:10.1186/gm145.
  122. [Faculty of 1000; 3 out of 5 joint first authors are from CBRC] Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, Macpherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, Tegner J, Lenhard B, Teichmann SA, Arakawa T, Ninomiya N, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitazume Y, Kawai J, Hume DA, Ideker T, Hayashizaki Y (March 2010) An atlas of combinatorial transcriptional regulation in mouse and man. Cell 140(5): 744-752. doi:10.1016/j.cell.2010.01.044. Erratum in: Cell. 2010 Apr 16;141(2):369. Kamburov, Atanas [added]; Kaur, Mandeep [added]; MacPherson, Cameron Ross [added]; Radovanovic, Aleksandar [added]; Schwartz, Ariel [added].
  123. Garavaglia BS, Thomas L, Zimaro T, Gottig N, Daurelio LD, Ndimba B, Orellano EG, Ottado J, Gehring C (March 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 Biol 10: 51. doi:10.1186/1471-2229-10-51.
  124. Bastian R, Dawe A, Meier S, Ludidi N, Bajic VB, Gehring C (March 2010) Gibberellic acid and cGMP-dependent transcriptional regulation in Arabidopsis thaliana. Plant Signal Behav 5(3): 224-232. doi: 10.4161/psb.5.3.10718.
  125. Salem M, Kenney PB, Rexroad CE, 3rd, Yao J (February 2010) Proteomic signature of muscle atrophy in rainbow trout. J Proteomics 73(4): 778-789. doi:10.1016/j.jprot.2009.10.014.
  126. Arieff Z, Kaur M, Gameeldien H, Merwe LV, Bajic VB (February 2010) 5-HTTLPR polymorphism: analysis in South African autistic individuals. Hum Biol 82(3): 291-300. doi: 10.3378/027.082.0303.
  127. Zhang X, Bocca S, Franchi A, Anderson S, Kaur M, Bajic VB, Oehninger S (February 2010) Do GnRH analogues directly affect human endometrial epithelial cell gene expression? Mol Hum Reprod 16(5): 347-360. doi: 10.1093/molehr/gaq012.
  128. Kothandaraman N, Bajic VB, Brendan PN, Huak CY, Keow PB, Razvi K, Salto-Tellez M, Choolani M (February 2010) E2F5 status significantly improves malignancy diagnosis of epithelial ovarian cancer. BMC Cancer 10: 64. doi:10.1186/1471-2407-10-64.
  129. Jung J, Ryu T, Hwang Y, Lee E, Lee D (January 2010) Prediction of extracellular matrix proteins based on distinctive sequence and domain characteristics. J Comput Biol 17(1): 97-105. doi:10.1089/cmb.2008.0236.
  130. [Highly accessed] Yun KY, Park MR, Mohanty B, Herath V, Xu F, Mauleon R, Wijaya E, Bajic VB, Bruskiewich R, de Los Reyes BG (January 2010) Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress. BMC Plant Biol 10:16. doi:10.1186/1471-2229-10-16.
  131. Meier S, Ruzvidzo O, Morse M, Donaldson L, Kwezi L, Gehring C (January 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. Epub 2010 Jan 26. doi:10.1371/journal.pone.0008904.
  132. Kim YI, Ryu T, Lee J, Heo YS, Ahnn J, Lee SJ, Yoo O (January 2010) A genetic screen for modifiers of Drosophila caspase Dcp-1 reveals caspase involvement in autophagy and novel caspase-related genes. BMC Cell Biol 11:9. doi:10.1186/1471-2121-11-9.
  133. Heckmann JM, Uwimpuhwe H, Ballo R, Kaur M, Bajic VB, Prince S (January 2010) A functional SNP in the regulatory region of the decay-accelerating factor gene associates with extraocular muscle pareses in myasthenia gravis. Genes Immun 11: 1-10. doi:10.1038/gene.2009.61.
  134. Garavaglia BS, Thomas L, Gottig N, Dunger G, Garofalo CG, Daurelio LD, Ndimba B, Orellano EG, Gehring C, Ottado J (January 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. Epub 2010 Jan 28. doi:10.1371/journal.pone.0008950.

    135. 2009

  135. Dawe AS, Bodhicharla RK, Graham NS, May ST, Reader T, Loader B, Gregory A, Swicord M, Bit-Babik G, de Pomerai DI (December 2009) Low-intensity microwave irradiation does not substantially alter gene expression in late larval and adult Caenorhabditis elegans. Bioelectromagnetics 30(8): 602-612. doi: 10.1002/bem.20515.
  136. Ryu T, Lee S, Hur CG, Lee D (December 2009) CONVIRT: a web-based tool for transcriptional regulatory site identification using a conserved virtual chromosome. BMB Rep 42(12): 823-828.
  137. [Highly accessed] Schmeier S, Macpherson CR, Essack M, Kaur M, Schaefer U, Suzuki H, Hayashizaki Y, Bajic VB (December 2009) Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation. BMC Genomics 10: 595. doi:10.1186/1471-2164-10-595.
  138. Hagg S, Skogsberg J, Lundstrom J, Noori P, Nilsson R, Zhong H, Maleki S, Shang MM, Brinne B, Bradshaw M, Bajic VB, Samnegard A, Silveira A, Kaplan LM, Gigante B, Leander K, de Faire U, Rosfors S, Lockowandt U, Liska J, Konrad P, Takolander R, Franco-Cereceda A, Schadt EE, Ivert T, Hamsten A, Tegner J, Bjorkegren J (December 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 Genet 5(12): e1000754. Epub 2009 Dec 4. doi:10.1371/journal.pgen.1000754.
  139. Sanchez CC, Smith TP, Wiedmann RT, Vallejo RL, Salem M, Yao J, Rexroad CE, 3rd (November 2009) Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library. BMC Genomics 10: 559. doi:10.1186/1471-2164-10-559.
  140. Niemann S, Koser CU, Gagneux S, Plinke C, Homolka S, Bignell H, Carter RJ, Cheetham RK, Cox A, Gormley NA, Kokko-Gonzales P, Murray LJ, Rigatti R, Smith VP, Arends FP, Cox HS, Smith G, Archer JA (October 2009) Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints. PLoS One 4(10): e7407. Epub 2009 Oct 12. doi:10.1371/journal.pone.0007407.
  141. Gersten M, Alirezaei M, Marcondes MC, Flynn C, Ravasi T, Ideker T, Fox HS (October 2009) An integrated systems analysis implicates EGR1 downregulation in simian immunodeficiency virus encephalitis-induced neural dysfunction. J Neurosci 29(40): 12467-12476. doi: 10.1523/???JNEUROSCI.3180-09.2009.
  142. RamachandraRao SP, Zhu Y, Ravasi T, McGowan TA, Toh I, Dunn SR, Okada S, Shaw MA, Sharma K (August 2009) Pirfenidone is renoprotective in diabetic kidney disease. J Am Soc Nephrol 20(8): 1765-1775. doi:10.1681/ASN.2008090931.
  143. Essack M, Radovanovic A, Schaefer U, Schmeier S, Seshadri SV, Christoffels A, Kaur M, Bajic VB (July 2009) DDEC: Dragon database of genes implicated in esophageal cancer. BMC Cancer 9: 219. doi:10.1186/1471-2407-9-219.
  144. Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D, Beckhouse AG, Bertin N, Bjorkegren J, Brombacher F, Bulger E, Chalk AM, Chiba J, Cloonan N, Dawe A, Dostie J, Engstrom PG, Essack M, Faulkner GJ, Fink JL, Fredman D, Fujimori K, Furuno M, Gojobori T, Gough J, Grimmond SM, Gustafsson M, Hashimoto M, Hashimoto T, Hatakeyama M, Heinzel S, Hide W, Hofmann O, Hornquist M, Huminiecki L, Ikeo K, Imamoto N, Inoue S, Inoue Y, Ishihara R, Iwayanagi T, Jacobsen A, Kaur M, Kawaji H, Kerr MC, Kimura R, Kimura S, Kimura Y, Kitano H, Koga H, Kojima T, Kondo S, Konno T, Krogh A, Kruger A, Kumar A, Lenhard B, Lennartsson A, Lindow M, Lizio M, Macpherson C, Maeda N, Maher CA, Maqungo M, Mar J, Matigian NA, Matsuda H, Mattick JS, Meier S, Miyamoto S, Miyamoto-Sato E, Nakabayashi K, Nakachi Y, Nakano M, Nygaard S, Okayama T, Okazaki Y, Okuda-Yabukami H, Orlando V, Otomo J, Pachkov M, Petrovsky N, Plessy C, Quackenbush J, Radovanovic A, Rehli M, Saito R, Sandelin A, Schmeier S, Schonbach C, Schwartz AS, Semple CA, Sera M, Severin J, Shirahige K, Simons C, St Laurent G, Suzuki M, Suzuki T, Sweet MJ, Taft RJ, Takeda S, Takenaka Y, Tan K, Taylor MS, Teasdale RD, Tegner J, Teichmann S, Valen E, Wahlestedt C, Waki K, Waterhouse A, Wells CA, Winther O, Wu L, Yamaguchi K, Yanagawa H, Yasuda J, Zavolan M, Hume DA, Arakawa T, Fukuda S, Imamura K, Kai C, Kaiho A, Kawashima T, Kawazu C, Kitazume Y, Kojima M, Miura H, Murakami K, Murata M, Ninomiya N, Nishiyori H, Noma S, Ogawa C, Sano T, Simon C, Tagami M, Takahashi Y, Kawai J, Hayashizaki Y (May 2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet 41: 553-562. doi:10.1038/ng.375.

Book Chapters

    2012

  1. Sagar S, Gehring C, Minneman KP. Methods to Isolate and Identify New Plant Signaling Peptides. Chapter 12 in Plant Signaling Peptides, Eds. Helen Irving and Christoph Gehring, Springer, 2012, pp.217-239.
  2. Zhang Z, Bajic VB, Yu J, Cheung KH, Townsend JP. Data Integration in Bioinformatics: Current Efforts and Challenges, Chapter in Bioinformatics - Trends and Methodologies, Mahmood A. Mahdavi (Ed.), InTech, October 2011 (ISBN 978-953-307-282-1)
  3. Ashoor H, Mora AM, Awara K, Jankovic BR, Chowdhary R, Archer JAC, Bajic VB.Recognition of Translation Initiation Sites in Arabidopsis Thaliana, Chapter 5 inSystemic Approaches in Bioinformatics and Computational Systems Biology: Recent Advances, Eds. Paola Lecca, Dan Tulpan, Kanagasabai Rajaraman, IGI Global, 2012, 105-116, DOI: 10.4018/978-1-61350-435-2.ch005
  4. Jankovic BR, Archer JAC, Chowdhary R, Schaefer U, Bajic VB. Promoter structures conserved between Homo sapiens, Mus musculus and Drosophila melanogaster, Chapter 4 inSystemic Approaches in Bioinformatics and Computational Systems Biology: Recent Advances, Eds. Paola Lecca, Dan Tulpan, Kanagasabai Rajaraman, IGI Global, 2012, 92-104, DOI: 10.4018/978-1-61350-435-2.ch004

    5. 2011

  5. Kowald A and Schmeier S. Text Mining for Systems Modelling In: Data Mining in Proteomics, edited by Michael Hamacher, Martin Eisenacher, Christian Stephan (in series:Methods in Molecular Biology, edited by John and Jane Walker), Humana Press USA, Methods Mol Biol. 2011;696:305-18

    6. 2010

  6. Gottig N, Garavaglia BS, Garofalo CG, Zimaro T, Sgro G, Ficarra FA, Dunger G, Daurelio LD, Thomas L, Gehring C, Orellano EG, Ottado J Mechanisms of infection used by Xanthomonas axonopodis pv. citri in citrus canker disease InCurrent Research Technology and Education Topics in Applied Microbiology and Microbial Biotechnology, Ed A. Mendez-Vilas, 1-10 (ISBN-13: 978-84-614-6194-3)
  7. Ma, W., Yoshioka, K., Gehring, C.A., Berkowitz, G.A. The function of cyclic nucleotide gated channels in biotic stress In Ion Channels and Plant Stress Responses; Eds.: Demidchik, V. and Maathuis, F.J.M. (Springer Publishers), 2010, 159 ??? 174. DOI: 10.1007/978-3-642-10494-7_8
  8. Dwivedi, S., Upadhyaya, H., Subudhi, P., Gehring, C., Bajic, V., Ortiz, R. Enhancing abiotic stress tolerance in cereals through breeding and transgenic interventions InPlant Breeding Reviews (John Wiley & Sons, Inc.) 2010, 33, 31- 114.
  9. Tegnéer J, Björkegren J, Ravasi T, Bajic VB. Transcription Regulatory Networks Analysis Using CAGE (Chapter 12 in Cap-Analysis of Gene Expression (CAGE): The Science of Decoding Genes Transcription, Ed. P Carninci, Pan Stanford Publishing Pte Ltd, 153-168, 2010, 978-981-4241-34-2 (eISBN: 9789814241359)
  10. Bajic VB, Schmeier S, MacPherson CR. Computational Methods to Identify Transcription Factor Binding Sites Using CAGE Information (Chapter 11 inCap-Analysis of Gene Expression (CAGE): The Science of Decoding Genes Transcription, Ed. P Carninci, Pan Stanford Publishing Pte Ltd, 137-151, 2010, 978-981-4241-34-2

Full Patent Applications

    2012

  1. Mansour H, Incitti R, Bajic V. PCT Patent Application No.: PCT/US12/60388; Entitled: COMPOSITE BIOMARKERS FOR NON-INVASIVE SCREENING, DIAGNOSIS AND PROGNOSIS OF COLORECTAL CANCER, Date Filed: October 15, 2012
  2. Magbubah E, Radovanovic A, Bajic V. PCT Patent Application No.: PCT/US12/55042; Entitled: TREATMENT OF SICKLE CELL DISEASE, Date Filed: September 13, 2012
  3. Bajic V, Kaur M. U.S. Non-Provisional Application No.: 13/415,004; Entitled: MOLECULAR BIOMARKER SET FOR EARLY DETECTION OF OVARIAN CANCER, Date Filed: March 8, 2012

Provisional Patent Applications

    2013

  1. Mansour H, Incitti R, Bajic V, US Provisional Patent Application No: 61/752,156; Entitled: METHYLATION BIOMARKERS FOR OVARIAN CANCER, Filing Date: January 14, 2013

    2. 2012

  2. Incitti R, Mansour H, Bajic V, US Provisional Patent Application No: 61/659,236; Entitled: METHYLATION BIOMARKERS FOR PROSTATE CANCER, Filing Date: June 13, 2012
  3. Sagar S, Esau L and Kaur M. US Provisional Patent Application No: 61/640,255; Entitled: ANTI-CANCER LEAD MOLECULE, Filing Date: April 30, 2012
  4. Incitti R, Mansour H, Bajic V, US Provisional Patent Application No: 61/659,239; Entitled: METHYLATION BIOMARKERS FOR BREAST CANCER, Filing Date: June 13, 2012
  5. Essack M, Bajic V. U.S. Provisional Application No.: 61/649,964; Entitled: COMBINATORIAL DRUGS FOR TREATMENT OF ALZHEIMER''S DISEASE AND OTHER NEURODEGENERATIVE DISORDERS, Filing Date: May 22, 2012

    6. 2011

  6. Mansour H, Incitti R, Bajic V. U.S. Provisional Application No.: 61/548,202; Entitled: COMPOSITE BIOMARKERS FOR NON-INVASIVE SCREENING, DIAGNOSIS AND PROGNOSIS OF COLORECTAL CANCER, Filing Date: October 17, 2011
  7. Essack M, Radovanovic A, Bajic V. U.S. Provisional Application No.: 61/534,449; Entitled: TREATMENT OF SICKLE CELL DISEASE, Filing Date: September 14, 2011
  8. Bajic V. Kaur M. U.S. Provisional Patent Application No.: 61/450,212; Entitled: MOLECULAR BIOMARKER SET FOR EARLY DETECTION OF OVARIAN CANCER. Filing Date: 08.March 2011.

Selected Conference Papers

    2013

  1. Ashoor H, Hérault A, Radvanyi F, Bajic VB, Barillot E, Boeva V. HMCan – a tool to detect chromatin modifications in cancer samples using ChIP-seq data. RECOMB 2013Accepted

    2. 2012

  2. Ashoor H, Bajic VB, Poster titled: Genome-wide prediction of transcription factor binding regions based on individual ChIP-seq experiments. ISMB 2012, Long Beach, CA, USA.

    3. 2011

  3. Marchand B, Bajic VB, Kaushik D (Nov. 2011) Highly Scalable Ab Initio Genomic Motif Identification, SuperComputing 2011 (oral presentation on Nov. 17, 2011, at The International Conference for High Performance Computing, Networking, Storage and Analysis) (acceptance rate 22%).