Vladimir B Bajic

Summary

Affiliation: South African National Bioinformatics Institute
Country: South Africa

Publications

  1. pmc Co-expression and promoter content analyses assign a role in biotic and abiotic stress responses to plant natriuretic peptides
    Stuart Meier
    Department of Biotechnology, University of the Western Cape, Private Bag X17, Cape Town Bellville 7535, South Africa
    BMC Plant Biol 8:24. 2008
  2. pmc An early response regulatory cluster induced by low temperature and hydrogen peroxide in seedlings of chilling-tolerant japonica rice
    Chen Cheng
    Department of Biological Sciences, University of Maine, Orono, ME 04469, USA
    BMC Genomics 8:175. 2007
  3. pmc Computational selection and prioritization of candidate genes for fetal alcohol syndrome
    Zane Lombard
    Division of Human Genetics, National Health Laboratory Service and School of Pathology, University of the Witwatersrand, Johannesburg, 2001, South Africa
    BMC Genomics 8:389. 2007
  4. pmc Mice and men: their promoter properties
    Vladimir B Bajic
    Knowledge Extraction Laboratory, Institute for Infocomm Research, Singapore
    PLoS Genet 2:e54. 2006
  5. pmc Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment
    Vladimir B Bajic
    South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa
    Genome Biol 7:S3.1-13. 2006
  6. ncbi request reprint Dragon Promoter Mapper (DPM): a Bayesian framework for modelling promoter structures
    Rajesh Chowdhary
    Knowledge Extraction Lab, Institute for Infocomm Research 21 Heng Mui Keng Terrace, Singapore 119613, Singapore
    Bioinformatics 22:2310-2. 2006
  7. pmc KBERG: KnowledgeBase for Estrogen Responsive Genes
    Suisheng Tang
    Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
    Nucleic Acids Res 35:D732-6. 2007
  8. pmc Database for exploration of functional context of genes implicated in ovarian cancer
    Mandeep Kaur
    South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Modderdam Road, Bellville, Cape Town, South Africa
    Nucleic Acids Res 37:D820-3. 2009
  9. pmc Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes
    Manisha Brahmachary
    Knowledge Extraction Laboratory, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore
    BMC Bioinformatics 7:S8. 2006
  10. pmc Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation
    Sebastian Schmeier
    South African National Bioinformatics Institute, University of the Western Cape, Modderdam Road, Bellville, South Africa
    BMC Genomics 10:595. 2009

Collaborators

Detail Information

Publications42

  1. pmc Co-expression and promoter content analyses assign a role in biotic and abiotic stress responses to plant natriuretic peptides
    Stuart Meier
    Department of Biotechnology, University of the Western Cape, Private Bag X17, Cape Town Bellville 7535, South Africa
    BMC Plant Biol 8:24. 2008
    ....
  2. pmc An early response regulatory cluster induced by low temperature and hydrogen peroxide in seedlings of chilling-tolerant japonica rice
    Chen Cheng
    Department of Biological Sciences, University of Maine, Orono, ME 04469, USA
    BMC Genomics 8:175. 2007
    ..In this study, the wide contrast in chilling sensitivity between indica and japonica rice was used as model to identify other regulatory clusters by integrative analysis of promoter architecture (ab initio) and gene expression profiles...
  3. pmc Computational selection and prioritization of candidate genes for fetal alcohol syndrome
    Zane Lombard
    Division of Human Genetics, National Health Laboratory Service and School of Pathology, University of the Witwatersrand, Johannesburg, 2001, South Africa
    BMC Genomics 8:389. 2007
    ..No genome-wide association or linkage studies have been performed for FAS, making computational selection and -prioritization of candidate disease genes an attractive approach...
  4. pmc Mice and men: their promoter properties
    Vladimir B Bajic
    Knowledge Extraction Laboratory, Institute for Infocomm Research, Singapore
    PLoS Genet 2:e54. 2006
    ....
  5. pmc Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment
    Vladimir B Bajic
    South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa
    Genome Biol 7:S3.1-13. 2006
    ..The systems analyzed operate on various principles and we assessed the effectiveness of different conceptual strategies used to correlate produced promoter predictions with the manually annotated 5' gene ends...
  6. ncbi request reprint Dragon Promoter Mapper (DPM): a Bayesian framework for modelling promoter structures
    Rajesh Chowdhary
    Knowledge Extraction Lab, Institute for Infocomm Research 21 Heng Mui Keng Terrace, Singapore 119613, Singapore
    Bioinformatics 22:2310-2. 2006
    ..i2r.a-star.edu.sg/projects/BayesPromoter/ CONTACT: vlad@sanbi.ac.za SUPPLEMENTARY INFORMATION: Manual for using DPM web server is provided at http://defiant.i2r.a-star.edu.sg/projects/BayesPromoter/html/manual/manual.htm...
  7. pmc KBERG: KnowledgeBase for Estrogen Responsive Genes
    Suisheng Tang
    Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
    Nucleic Acids Res 35:D732-6. 2007
    ..KBERG database can be accessed at http://research.i2r.a-star.edu.sg/kberg...
  8. pmc Database for exploration of functional context of genes implicated in ovarian cancer
    Mandeep Kaur
    South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Modderdam Road, Bellville, Cape Town, South Africa
    Nucleic Acids Res 37:D820-3. 2009
    ..Access is free for academic and non-profit users and database can be accessed at http://apps.sanbi.ac.za/ddoc/...
  9. pmc Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes
    Manisha Brahmachary
    Knowledge Extraction Laboratory, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore
    BMC Bioinformatics 7:S8. 2006
    ..For many AMPcgs the promoter elements and transcription factors that control their tissue cell-specific expression have yet to be fully identified and characterized...
  10. pmc Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation
    Sebastian Schmeier
    South African National Bioinformatics Institute, University of the Western Cape, Modderdam Road, Bellville, South Africa
    BMC Genomics 10:595. 2009
    ..We focus on getting insights into the transcriptional circuitry regulating miRNA genes expressed during monocytic differentiation...
  11. pmc Computational method for discovery of estrogen responsive genes
    Suisheng Tang
    Knowledge Extraction Lab, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
    Nucleic Acids Res 32:6212-7. 2004
    ..We believe this method can significantly reduce the number of testing potential estrogen target genes and provide functional clues for annotating part of genes that lack functional information...
  12. pmc Dragon gene start finder: an advanced system for finding approximate locations of the start of gene transcriptional units
    Vladimir B Bajic
    Knowledge Extraction Lab, Institute for Infocomm Research, Singapore 119613
    Genome Res 13:1923-9. 2003
    ..Comparison of abilities to predict TSS with the two other systems on human chromosomes 4, 21, and 22 reveals that our system has superior accuracy and overall provides the most confident predictions...
  13. ncbi request reprint Finding functional promoter motifs by computational methods: a word of caution
    Rajesh Chowdhary
    Institute for Infocomm Research, 21 Heng Mui Kung Terrace, Singapore
    Int J Bioinform Res Appl 2:282-8. 2006
    ..We illustrate these issues using the example of histones H2A and H2B and show how such analysis could be misleading if care is not exercised to eliminate coding regions from the presumed promoter sequences...
  14. doi request reprint HCVpro: hepatitis C virus protein interaction database
    Samuel K Kwofie
    South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Modderdam Road, Bellville 7535, Cape Town, South Africa
    Infect Genet Evol 11:1971-7. 2011
    ..The use of HCVpro is free and the resource can be accessed via http://apps.sanbi.ac.za/hcvpro/ or http://cbrc.kaust.edu.sa/hcvpro/...
  15. ncbi request reprint Promoter modeling: the case study of mammalian histone promoters
    Rajesh Chowdhary
    Knowledge Extraction Lab, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
    Bioinformatics 21:2623-8. 2005
    ....
  16. pmc Dragon Plant Biology Explorer. A text-mining tool for integrating associations between genetic and biochemical entities with genome annotation and biochemical terms lists
    Vladimir B Bajic
    Knowledge Extraction Lab, Institute for Infocomm Research, Singapore 119613
    Plant Physiol 138:1914-25. 2005
    ..Last, DPBE can be helpful for beginning researchers and graduate students to summarize vast information in an unfamiliar area. DPBE is freely available for academic and nonprofit users at http://research.i2r.a-star.edu.sg/DRAGON/ME2/...
  17. pmc Dragon TF Association Miner: a system for exploring transcription factor associations through text-mining
    Hong Pan
    Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
    Nucleic Acids Res 32:W230-4. 2004
    ..DTFAM summarizes information from a large volume of documents saving time and making analysis simpler for individual users. DTFAM is freely available for academic and non-profit users at http://research.i2r.a-star.edu.sg/DRAGON/TFAM/...
  18. doi request reprint Dragon exploratory system on hepatitis C virus (DESHCV)
    Samuel K Kwofie
    South African National Bioinformatics Institute, University of the Western Cape, Modderdam Road, Bellville, Cape Town, South Africa
    Infect Genet Evol 11:734-9. 2011
    ..DESHCV thus represents online literature-based discovery resource freely accessible for academic and non-profit users via http://apps.sanbi.ac.za/DESHCV/ and its mirror site http://cbrc.kaust.edu.sa/deshcv/...
  19. pmc DDEC: Dragon database of genes implicated in esophageal cancer
    Magbubah Essack
    South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
    BMC Cancer 9:219. 2009
    ....
  20. ncbi request reprint Content analysis of the core promoter region of human genes
    Vladimir B Bajic
    Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore
    In Silico Biol 4:109-25. 2004
    ..It was also observed that a number of promoter elements show strong preference either for the GC-rich or the GC-poor core promoters...
  21. ncbi request reprint Promoter profiling and coexpression data analysis identifies 24 novel genes that are coregulated with AMPA receptor genes, GRIAs
    Allen Chong
    Molecular Bioinformatics Group, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore
    Genomics 89:378-84. 2007
    ..Using microarray expression data, we found 24 (of the 47) genes that share not only a similar promoter profile with GRIAs but also a well-correlated gene expression profile and, thus, we believe these to be coregulated with GRIAs...
  22. pmc DDESC: Dragon database for exploration of sodium channels in human
    Sunil Sagar
    South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Modderdam Road, Bellville, Cape Town 7535, South Africa
    BMC Genomics 9:622. 2008
    ....
  23. pmc Prioritizing genes of potential relevance to diseases affected by sex hormones: an example of myasthenia gravis
    Mandeep Kaur
    South African National Bioinformatics Institute, University of the Western Cape, Bellville, Republic of South Africa
    BMC Genomics 9:481. 2008
    ..The identification of disease-associated genes has always been challenging and to date there is no universal and effective method developed...
  24. pmc DDPC: Dragon Database of Genes associated with Prostate Cancer
    Monique Maqungo
    South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Modderdam Road, Bellville, Cape Town, South Africa
    Nucleic Acids Res 39:D980-5. 2011
    ..We believe this resource will serve as a source of useful information for research on PC. DDPC is freely accessible for academic and non-profit users via http://apps.sanbi.ac.za/ddpc/ and http://cbrc.kaust.edu.sa/ddpc/...
  25. pmc Dragon Gene Start Finder identifies approximate locations of the 5' ends of genes
    Vladimir B Bajic
    Knowledge Extraction Laboratory Discovery Systems Laboratory, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
    Nucleic Acids Res 31:3560-3. 2003
    ..lit.org.sg/promoter/dragonGSF1_0/genestart.htm; the download version of the program integrated within the TRANSPLORER package can be obtained from Biobase GmbH, at http://www.biobase.de/...
  26. pmc Gibberellic acid and cGMP-dependent transcriptional regulation in Arabidopsis thaliana
    René Bastian
    Department of Biotechnology, University of the Western Cape, Bellville, South Africa
    Plant Signal Behav 5:224-32. 2010
    ....
  27. ncbi request reprint Information for the Coordinates of Exons (ICE): a human splice sites database
    Allen Chong
    Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore
    Genomics 84:762-6. 2004
    ..It allows targeted search and presents evidence for the gene structure...
  28. pmc Integration of text- and data-mining using ontologies successfully selects disease gene candidates
    Nicki Tiffin
    South African National Bioinformatics Institute, University of the Western Cape Belville 7535, South Africa
    Nucleic Acids Res 33:1544-52. 2005
    ....
  29. pmc DAMPD: a manually curated antimicrobial peptide database
    Vijayaraghava Seshadri Sundararajan
    South African National Bioinformatics Institute, The University of the Western Cape, 7535 Bellville, South Africa
    Nucleic Acids Res 40:D1108-12. 2012
    ....
  30. pmc FIE2: A program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes
    Allen Chong
    Molecular Bioinformatics Group, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
    Nucleic Acids Res 31:3546-53. 2003
    ..FIE2 is freely available at http://sdmc.lit.org.sg/FIE2.0...
  31. doi request reprint Evolutionary genomics of Glossina morsitans immune-related CLIP domain serine proteases and serine protease inhibitors
    Sarah Mwangi
    South African National Bioinformatics Institute, University of the Western Cape, Modderdam Road, Bellville, Cape Town, South Africa
    Infect Genet Evol 11:740-5. 2011
    ..The presence of alternatively spliced variants in the G. morsitans serpins transcriptome data mirrors that of the D. melanogaster transcriptome...
  32. pmc Computational analysis of candidate disease genes and variants for salt-sensitive hypertension in indigenous Southern Africans
    Nicki Tiffin
    Division of Nephrology and Hypertension, University of Cape Town Groote Schuur Hospital, Cape Town, South Africa
    PLoS ONE 5:e12989. 2010
    ..We propose that the candidate genes identified in this study warrant further investigation as potential aetiological genes for salt-sensitive hypertension...
  33. pmc Detection and preliminary analysis of motifs in promoters of anaerobically induced genes of different plant species
    Bijayalaxmi Mohanty
    Knowledge Extraction Laboratory, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
    Ann Bot 96:669-81. 2005
    ..The aim of this study was to clarify mechanisms of transcriptional regulation of these anaerobic genes by identifying motifs shared by their promoter regions...
  34. pmc Transcriptomic analyses reveal novel genes with sexually dimorphic expression in the zebrafish gonad and brain
    Rajini Sreenivasan
    Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
    PLoS ONE 3:e1791. 2008
    ..Our knowledge on zebrafish reproduction is very limited. We generated a gonad-derived cDNA microarray from zebrafish and used it to analyze large-scale gene expression profiles in adult gonads and other organs...
  35. pmc Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map
    Jean Marc Celton
    Biotechnology Department, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa
    BMC Biol 8:155. 2010
    ....
  36. pmc Dragon ERE Finder version 2: A tool for accurate detection and analysis of estrogen response elements in vertebrate genomes
    Vladimir B Bajic
    Knowledge Extraction Laboratory, Institute for Infocomm Research, Singapore 119613
    Nucleic Acids Res 31:3605-7. 2003
    ..Dragon ERE Finder version 2 is freely available for academic and non-profit users (http://sdmc.lit.org.sg/ERE-V2/index)...
  37. doi request reprint 5-HTTLPR polymorphism: analysis in South African autistic individuals
    Zainunisha Arieff
    Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, Cape Town, South Africa
    Hum Biol 82:291-300. 2010
    ..The results of this study open new avenues for investigating the role of transmission of the L and S alleles in families with autism in South Africa...
  38. pmc eVOC: a controlled vocabulary for unifying gene expression data
    Janet Kelso
    South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
    Genome Res 13:1222-30. 2003
    ..Both the vocabularies and the vocabulary-annotated libraries can be retrieved from http://www.sanbi.ac.za/evoc/. Several groups are involved in developing this resource with the aim of unifying transcript expression information...
  39. ncbi request reprint Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes
    Samuel Aparicio
    Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore 117609
    Science 297:1301-10. 2002
    ..Conserved linkages between Fugu and human genes indicate the preservation of chromosomal segments from the common vertebrate ancestor, but with considerable scrambling of gene order...
  40. pmc Comparative genomics in cyprinids: common carp ESTs help the annotation of the zebrafish genome
    Alan Christoffels
    Computational Biology Group, Temasek Life Sciences Laboratory, Singapore
    BMC Bioinformatics 7:S2. 2006
    ..The scarcity of genomic information from other cyprinids provides the impetus to leverage EST collections to understand gene structures in this diverse teleost group...
  41. ncbi request reprint Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes
    Alan Christoffels
    Institute of Molecular and Cell Biology, Singapore
    Mol Biol Evol 21:1146-51. 2004
    ..These data strongly suggest a whole-genome duplication event early during the evolution of ray-finned fishes, probably before the origin of teleosts...
  42. pmc Extensive expansion of the claudin gene family in the teleost fish, Fugu rubripes
    Yong Hwee Loh
    Institute of Molecular and Cell Biology, Singapore 117609
    Genome Res 14:1248-57. 2004
    ....