Missing Avatar

Raya Khanin

Associate Lab Member, Bioinformatics Core - Memorial Sloan-Kettering Cancer Center

A unique combination of computational skills, big data modeling, in depth knowledge of genomics, expertise in translational research with 20 years of experience working with some of the world’s leading life scientists and clinicians. Over 30 refereed publications (including Nature, NEJM, PNAS, Bioinformatics) with over 3000 citations, and numerous conference papers and presentations. I have obtained my PhD from the Weizmann Institute of Science, Israel and was a recipient of Royal Society Dorothy Hodgkin Fellowship at the University of Cambridge, England.

--Directing customized Bioinformatics & Computational Biology analyses of high-throughput genomics data (DNA/RNA sequencing, metagenomics, proteomic, microarrays)
--Leading the development of innovative computational analyses platforms
--Proven track record in biomarker identification, predictive computational modeling, pathway and systems biology analyses, data integration


Position - Company  
Research Fellow - University of Glasgow

I was working on several computational biology projects: from modeling gene regulation by transcription factors and microRNAs and reconstruction of regulatory interactions from expression data, to analysis of mass-spectrometry and expression data in microRNA mis-expression experiments.

Show details
Aug 2003 - Jul 2009
Associate Lab Member, Bioinformatics Core - Memorial Sloan-Kettering Cancer Center

Working on computational and statistical analysis of high-throughput genomics data.

Show details
Jul 2009 - Present
Degree - University  
PhD, Applied Mathematics - The Weizmann Institute of Science 1992 - 1996
MSc, MEX-MAT - Lomonosov Moscow State University 1985 - 1990
Publication Info
Induction of sarcomas by mutant IDH2. Lu C, Venneti S, Akalin A, Fang F, Ward PS, Dematteo RG, Intlekofer AM and 13 others Genes Dev. 27(18):1986-98. doi: 10.1101/gad.226753.113. September 15, 2013. View on PubMed.
Relationships between LDH-A, lactate, and metastases in 4T1 breast tumors. Rizwan A, Serganova I, Khanin R, Karabeber H, Ni X, Thakur S, Zakian KL, Blasberg R, Koutcher JA Clin Cancer Res. 19(18):5158-69. doi: 10.1158/1078-0432.CCR-12-3300. September 15, 2013. View on PubMed.
Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Rapaport F, Khanin R, Liang Y, Pirun M, Krek A, Zumbo P, Mason CE, Socci ND, Betel D Genome Biol. 14(9):R95. doi: 10.1186/gb-2013-14-9-r95. September 10, 2013. View on PubMed.
Analytic and Clinical Validation of a Prostate Cancer-Enhanced Messenger RNA Detection Assay in Whole Blood as a Prognostic Biomarker for Survival. Danila DC, Anand A, Schultz N, Heller G, Wan M, Sung CC, Dai C and 4 others Eur Urol. :. doi: 10.1016/j.eururo.2013.07.006. July 26, 2013. View on PubMed.
Identification of KIF5B-RET and GOPC-ROS1 fusions in lung adenocarcinomas through a comprehensive mRNA-based screen for tyrosine kinase fusions. Suehara Y, Arcila M, Wang L, Hasanovic A, Ang D, Ito T, Kimura Y and 8 others Clin Cancer Res. 18(24):6599-608. doi: 10.1158/1078-0432.CCR-12-0838. December 15, 2012. View on PubMed.
Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis. Scher JU, Ubeda C, Equinda M, Khanin R, Buischi Y, Viale A, Lipuma L and 7 others Arthritis Rheum. 64(10):3083-94. doi: 10.1002/art.34539. October 2012. View on PubMed.
Familial transmission rather than defective innate immunity shapes the distinct intestinal microbiota of TLR-deficient mice. Ubeda C, Lipuma L, Gobourne A, Viale A, Leiner I, Equinda M, Khanin R, Pamer EG J Exp Med. 209(8):1445-56. doi: 10.1084/jem.20120504. July 30, 2012. View on PubMed.
The miR-17-92 cluster and its target THBS1 are differentially expressed in angiosarcomas dependent on MYC amplification. Italiano A, Thomas R, Breen M, Zhang L, Crago AM, Singer S, Khanin R and 5 others Genes Chromosomes Cancer. 51(6):569-78. doi: 10.1002/gcc.21943. June 2012. View on PubMed.
Regulation of intestinal inflammation by microbiota following allogeneic bone marrow transplantation. Jenq RR, Ubeda C, Taur Y, Menezes CC, Khanin R, Dudakov JA, Liu C and 14 others J Exp Med. 209(5):903-11. doi: 10.1084/jem.20112408. May 7, 2012. View on PubMed.
IDH mutation impairs histone demethylation and results in a block to cell differentiation. Lu C, Ward PS, Kapoor GS, Rohle D, Turcan S, Abdel-Wahab O, Edwards CR and 10 others Nature. 483(7390):474-8. doi: 10.1038/nature10860. February 15, 2012. View on PubMed.
Identification of a novel, recurrent HEY1-NCOA2 fusion in mesenchymal chondrosarcoma based on a genome-wide screen of exon-level expression data. Wang L, Motoi T, Khanin R, Olshen A, Mertens F, Bridge J, Dal Cin P and 7 others Genes Chromosomes Cancer. 51(2):127-39. doi: 10.1002/gcc.20937. February 2012. View on PubMed.
Small RNA sequencing and functional characterization reveals MicroRNA-143 tumor suppressor activity in liposarcoma. Ugras S, Brill E, Jacobsen A, Hafner M, Socci ND, Decarolis PL, Khanin R and 11 others Cancer Res. 71(17):5659-69. doi: 10.1158/0008-5472.CAN-11-0890. September 1, 2011. View on PubMed.
miR-21 and miR-214 are consistently modulated during renal injury in rodent models. Denby L, Ramdas V, McBride MW, Wang J, Robinson H, McClure J, Crawford W and 7 others Am J Pathol. 179(2):661-72. doi: 10.1016/j.ajpath.2011.04.021. August 2011. View on PubMed.
Molecular classification of gastric cancer: a new paradigm. Shah MA, Khanin R, Tang L, Janjigian YY, Klimstra DS, Gerdes H, Kelsen DP Clin Cancer Res. 17(9):2693-701. doi: 10.1158/1078-0432.CCR-10-2203. May 1, 2011. View on PubMed.
Mutations in GNA11 in uveal melanoma. Van Raamsdonk CD, Griewank KG, Crosby MB, Garrido MC, Vemula S, Wiesner T, Obenauf AC and 13 others N Engl J Med. 363(23):2191-9. doi: 10.1056/NEJMoa1000584. December 2, 2010. View on PubMed.
A comparative analysis of extra-embryonic endoderm cell lines. Brown K, Legros S, Artus J, Doss MX, Khanin R, Hadjantonakis AK, Foley A PLoS One. 5(8):e12016. doi: 10.1371/journal.pone.0012016. August 6, 2010. View on PubMed.
Gene expression profiling in whole blood of patients with coronary artery disease. Taurino C, Miller WH, McBride MW, McClure JD, Khanin R, Moreno MU, Dymott JA, Delles C, Dominiczak AF Clin Sci (Lond). 119(8):335-43. doi: 10.1042/CS20100043. July 9, 2010. View on PubMed.
Dynamic changes in lung microRNA profiles during the development of pulmonary hypertension due to chronic hypoxia and monocrotaline. Caruso P, MacLean MR, Khanin R, McClure J, Soon E, Southgate M, MacDonald RA and 8 others Arterioscler Thromb Vasc Biol. 30(4):716-23. doi: 10.1161/ATVBAHA.109.202028. January 28, 2010. View on PubMed.
Widespread changes in protein synthesis induced by microRNAs. Selbach M, Schwanhäusser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N Nature. 455(7209):58-63. doi: 10.1038/nature07228. September 4, 2008. View on PubMed.
Computational modeling of post-transcriptional gene regulation by microRNAs. Khanin R, Vinciotti V J Comput Biol. 15(3):305-16. doi: 10.1089/cmb.2007.0184. April 2008. View on PubMed.
Statistical reconstruction of transcription factor activity using Michaelis-Menten kinetics. Khanin R, Vinciotti V, Mersinias V, Smith CP, Wit E Biometrics. 63(3):816-23. doi: 10.1111/j.1541-0420.2007.00757.x. September 2007. View on PubMed.
Bayesian model-based inference of transcription factor activity. Rogers S, Khanin R, Girolami M BMC Bioinformatics. 8 Suppl 2:S2. doi: 10.1186/1471-2105-8-S2-S2. May 3, 2007. View on PubMed.
Reconstructing repressor protein levels from expression of gene targets in Escherichia coli. Khanin R, Vinciotti V, Wit E Proc Natl Acad Sci U S A. 103(49):18592-6. doi: 10.1073/pnas.0603390103. December 5, 2006. View on PubMed.
On the feedback between theory and experiment in elucidating the molecular mechanisms underlying neurotransmitter release. Khanin R, Parnas I, Parnas H Bull Math Biol. 68(5):997-1009. doi: 10.1007/s11538-006-9099-3. May 23, 2006. View on PubMed.
How scale-free are biological networks. Khanin R, Wit E J Comput Biol. 13(3):810-8. doi: 10.1089/cmb.2006.13.810. April 2006. View on PubMed.
An experimental evaluation of a loop versus a reference design for two-channel microarrays. Vinciotti V, Khanin R, D'Alimonte D, Liu X, Cattini N, Hotchkiss G, Bucca G and 5 others Bioinformatics. 21(4):492-501. doi: 10.1093/bioinformatics/bti022. February 15, 2005. View on PubMed.
A probabilistic model for the establishment of neuron polarity. Khanin K, Khanin R J Math Biol. 42(1):26-40. January 2001. View on PubMed.
The diffusion of molecules in axonal plasma membranes: the sites of insertion of new membrane molecules and their distribution along the axon surface. Khanin R, Segel L, Futerman AH J Theor Biol. 193(3):371-82. doi: 10.1006/jtbi.1998.0707. August 7, 1998. View on PubMed.
"First step" negative feedback accounts for inhibition of fast neurotransmitter release. Khanin R, Parnas H, Segel L J Theor Biol. 188(3):261-76. doi: 10.1006/jtbi.1997.0480. October 7, 1997. View on PubMed.
A mechanism for discharge of charged excitatory neurotransmitter. Khanin R, Parnas H, Segel L Biophys J. 72(2 Pt 1):507-21. February 1997. View on PubMed.
Neurotransmitter discharge and postsynaptic rise times. Khanin R, Segel L, Parnas H, Ratner E Biophys J. 70(4):2030-2. doi: 10.1016/S0006-3495(96)79769-2. April 1996. View on PubMed.
Diffusion cannot govern the discharge of neurotransmitter in fast synapses. Khanin R, Parnas H, Segel L Biophys J. 67(3):966-72. doi: 10.1016/S0006-3495(94)80562-4. September 1994. View on PubMed.
Lipid diffusion in neurons. Futerman AH, Khanin R, Segel LA Nature. 362(6416):119. doi: 10.1038/362119a0. March 11, 1993. View on PubMed.
  • Raya Khanin hasn't received any ratings yet...