University at Buffalo - The State University of New York
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Jianxin Wang, PhD

Bioinformatics Computational Scientist

Dr. Wang joined the Center for Computational Research in 2015.   He has a PhD in Biological Sciences and a Master of Science in Computer Science both from the State University of New York at Buffalo.

Areas of Support:

  • Buffalo Institute for Genomics
  • NGS data analysis
  • Development of pipelines/workflows for high dimensional –omics data.
  • Pathway analysis
  • Databases

Research Interests:

•    Biomarker discovery for personalized medicine.
•    Development of work flows and pipelines for Next-generation sequencing (NGS) data analysis.
•    Development of bioinformatics tools for high dimensional -omics data analysis.
•    Development of data visualization tools for high dimensional -omics data.
•    Integrated analysis of high dimensional -omics data using statistics and machine learning approaches.

Publications:

Boutros PC1 and Fraser M2, et. al.,  Spatial genomic heterogeneity within localized, multifocal prostate cancer. Nat Genet. 2015 Jul;47(7):736-45
 

Weinreb I. and Piscuoglio S. et. al., Hotsport activationg PRKD1 somatic mutations in polymorphous low-grade adenocarcinomas of the salivary glands.  Nature Genetics, 2014, doi:10.1038/ng.3096
 

Coschi HC., Ishak C., Gallo D., Marshall ST. Wang J. Cecchini M., Martens A., Percy V. Welch I., Boutros PC., Brown GW. and Dick FA.  Haploinsufficiency of an RB-E2F1-Condensin II Complex Leads to Aberrant Replication and Aneuploidy. Cancer Discovery, 4(7), 840-53, 2014.
 

Peltekova VD and Lemire M. et al. Identification of genes expressed by immune cells of the colon that are regulated by colorecal cancer-associated variants. Int J Cancer, 134(10), 2330-41, 2013.
 

Zhang J, Baran J, Cros A, Guberman JM, Haider S, Hsu J, Liang Y, Rivkin E, Wang J, Whitty B, Wong-Erasmus M, Yao L, Kasprzyk A. (2011) International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data. Database (Oxford). 2011 Sep 19.


Guberman JM, et al. (2011) BioMart Central Portal: an open database network for the biological community. Database (Oxford). 2011 Sep 18.

The International Cancer Genome Consortium. (2010) International network of cancer genome projects. Nature, 464, 993-998.


Lee J, Cordaux R, Han K, Wang J. Hedges DF. Liang P, Batzer MA. (2007) Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons. Gene, 390(1-2), 18-27.
 

Konkel MK, Wang J, Liang P, Batzer MA. (2007) Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies. Gene. 390(1-2), 28-38.
 

Han K., Lee J., Meyer T., Wang J., Sen S.K., Sirkanta D., Liang P. and Batzer M.A. (2007) Alu recombination-mediated structural deletions in the chimpanzee genome. PloS Genet 3(10), 1939-1949.


Zhou J, Beermann F, Wang J, Kawakami K, Wei X. (2006) The Fugu tyrp1 promoter directs specific GFP expression in zebrafish: tools to study the RPE and the neural crest-derived melanophores. Pigment Cell Res. 19(6), 615-27.


Burhans DT, Ramachandran L, Wang J, Liang P, Patterton H, Breitenbach M and Burhans WC. (2006) Non-random clustering of stress-related genes during evolution of the S. cerevisiae genome. BMC Evolutionary Biology. 21, 6-58.


Wang J
, Song L, Grover D, Azrak S, Batzer MA, Liang P. (2006) dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans. Hum Mutat. 27(4), 323-9.


Wang J
, Song L, Gonder MK, Azrak S, Ray DA, Batzer MA, Tishkoff SA, Liang P. (2006) Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms. Gene. 365, 11-20.


Ramachandran L, Burhans DT, Laun P, Wang J, Liang P, Weinberger M, Wissing S, Jarolim S, Suter B, Madeo F, Breitenbach M, Burhans W. (2006) Evidence for ORC-dependent repression of budding yeast genes induced by starvation and other stresses. FEMS Yeast Res. 6(5), 763-76.


Han K*, Sen SK*, Wang J*, Callinan PA, Lee J, Cordaux R, Liang P, Batzer MA. (2005) Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages. Nucleic Acids Res. 33(13), 4040-52, 2005. (*co-first authors)


Sen SK, Han K, Wang J, Lee J, Wang H, Callinan PA, Dyer M, Cordaux R, Liang P, Batzer MA. (2006) Human genomic deletions mediated by recombination bwtween Alu elements. Am J Hum Genet 79, 41-53.


Callinan* PA, Wang J*, Herke SW, Garber RK, Liang P, Batzer MA. (2005) Alu retrotransposition-mediated deletion. J. Mol. Biol. 348(4), 791-800. (*co-first authors)


Laun P, Ramachandran L, Jarolim S, Herker E, Liang P, Wang J, Weinberger W, Burhans DT, Suter B, Madeo F, Burhans WC, Breitenbach M. (2005) A comparison of the aging and apoptotic transcriptome of Saccharomyces cerevisiae. FEMS Yeast Res. 5, 1262-1271.


Chen H, Wang J, Liang P, Karsay-Klein M, James AA, Brazeau D, Yan G. (2003) Microarray Analysis for Identification of Plasmodium Refractoriness Candidate Genes in Mosquitoes. Genome. 47(6), 1061-70, 2004.


Wang J
and Liang P. (2003) DigiNorthern, digital expression analysis of query genes based on ESTs. Bioinformatics 19 (5), 653-654.


Wang J
, Block A, Wang Y and Liang P. KaryoReader: (2003) Parsing karyotypic data and calculating detailed chromosomal changes to facilitate systematic analysis of cancer cytogenetic data. 94th Annual Meeting of American Association for Cancer Research. Washington D.C., USA.


McCormac DJ, Litz H, Wang J, Gollnick PD and Berry JO. (2001) Light-associated and processing-dependent protein binding to 5' regions of rbcL mRNA in the chloroplasts of a C4 plant. J. Bio. Chem., 276, 3476-3483.