Vladimir Vacic

[VLAH-dee-meer VAH-tzich]

Postdoctoral Research Scientist
Columbia University
Department of Computer Science
523 Computer Science Building
500 W 120th Street, Mailcode: 0401
New York, NY 10027-7003

Telephone: (646) 775-6083
E-mail: [my first name] @cs.columbia.edu

I'm a postdoc in the Itsik Pe'er Lab of Computational Genetics. My research focus areas are neuropsychiatric genetics and functional genomics.

Education and Training

• 2010-, Postdoctoral Research Scientist, Columbia University, New York, NY
• 2008-2010, Postdoctoral Fellow, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
• 2008, Ph.D. Computer Science (Bioinformatics), University of California, Riverside, CA
• 2004, M.S. Computer and Information Sciences (Machine Learning and Data Mining), Temple University, Philadelphia, PA
• 2002, B.S. Computer Science and Mathematics (double major) Summa Cum Laude, University of Bridgeport, Brindgeport, CT

Publications

2012

[18] Vacic V, Iakoucheva LM. Disease mutations in disordered regions - exception to the rule? Molecular BioSystems (themed issue on intrinsically disordered proteins). 8(1):27-32. (2012)

2011

[17] Malhotra D, McCarthy S, Michaelson JJ, Vacic V, Burdick KE, Yoon S, Cichon S, Corvin A, Gary S, Gershon ES, Gill M, Karayiorgou M, Kelsoe JR, Krastoshevsky O, Krause V, Leibenluft E, Levy DL, Makarov V, Bhandari A, Malhotra AK, McMahon FJ, Nothen MM, Potash JB, Rietschel M, Schulze TG, Sebat J. High frequencies of de novo CNVs in bipolar disorder and schizophrenia. Neuron. 72(6):951-63. (2011)

[16] Vacic V, McCarthy SE, Malhotra D, Murray F, Cho HH, Peoples A, Makarov V, Yoon S, Bhandari A, Corominas R, Iakoucheva LM, Krastoshevsky O, Krause V, Larach Walters V, Welsh DK, Craig D, Kelsoe JR, Gershon ES, Leal SM, Dell Aquila M, Morris DW, Gill M, Corvin A, Insel PA, McClellan J, King MC, Karayiorgou M, Levy DL, DeLisi LE, Sebat J. Duplications of the neuropeptide receptor VIPR2 confer significant risk for schizophrenia. Nature. 471(7339):499-503. (2011) Featured on cover page, GenomeWeb, Science Daily

2010

[15] Radivojac P, Vacic V, Haynes C, Cocklin RR, Mohan A, Heyen JW, Goebl MG, Iakoucheva LM. Identification, analysis and prediction of protein ubiquitination sites. Proteins: Structure, Function, and Bioinformatics. 78(2):365-380. (2010) web site

[14] Vacic V, Iakoucheva LM, Lonardi S, Radivojac P. Graphlet kernels for prediction of functional residues in protein structures. Journal of Computational Biology. 17(1):55-72. (2010) web site

2009

[13] Bogunovic D, O’Neill DW, Belitskaya-Levy I, Vacic V, Yu Y-L, Adams S, Darvishian F, Berman R, Shapiro R, Pavlick AC, Lonardi S, Zavadil J, Osman I, Bhardwaj N. Immune profile and mitotic index of metastatic melanoma lesions enhance clinical staging in predicting patient survival. Proceedings of the National Academy of Sciences. 106(48):20429-34. (2009) Featured in U.S. News & World Report

[12] McCarthy SE, Makarov V, Kirov G, Addington A, McClellan J, Yoon S, Perkins D, Dickel DE, Kusenda M, Krastoshevsky O, Krause V, Kumar RA, Grozeva D, Malhotra D, Walsh T, Zackai EH, Kaplan P, Ganesh J, Krantz ID, Spinner NB, Roccanova P, Bhandari A, Pavon K, Lakshmi B, Leotta A, Kendall J, Lee Y, Vacic V, Gary S, Iakoucheva L, Crow TJ, Christian SL, Lieberman J, Stroup S, Lehtimäki T, Puura K, Haldeman-Englert C, Pearl J, Goodell M, Willour VL, DeRosse P, Steele J, Kassem L, Wolff J, Chitkara N, McMahon F, Malhotra AK, Potash JB, Schulze T, Nöthen MM, Cichon S, Rietschel M, Leibenluft E, Kustanovich V, Lajonchere CM, Sutcliffe JS, Skuse D, Gill M, Gallagher L, Mendell NR, Wellcome Trust Case Control Consortium, Craddock N, Owen MJ, O’Donovan MC, Shaikh TH, Susser E, DeLisi LE, Sullivan PF, Deutsch CK, Rapoport J, Levy DL, King MC, Sebat J. Microduplications of 16p11.2 are associated with schizophrenia. Nature Genetics. 41:1223-7. (2009) Featured on GenomeWeb

2008

[11] Dunker AK, Oldfield CJ, Meng J, Romero P, Yang JY, Chen JW, Vacic V, Obradovic Z, Uversky VN. The unfoldomics decade: an update on intrinsically disordered proteins. BMC Genomics. 9(S2):S1. (2008)

[10] Jin H, Vacic V, Girke T, Lonardi S, Zhu J-K. Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis. BMC Molecular Biology. 9:6. (2008)

[9] Vacic V, Jin H, Zhu J-K, Lonardi S. A probabilistic method for small RNA flowgram matching. Pacific Symposium on Biocomputing, PSB'08, 13:75-86. (2008) slides   web site

2007

[8] Fu Z, Chen X, Vacic V, Nan P, Zhong Y, Jiang T. MSOAR: a high-throughput ortholog assignment system based on genome rearrangement. Journal of Computational Biology. 14(9):1160-75. (2007) web site

[7] Vacic V, Uversky VN, Dunker AK, Lonardi S. Composition Profiler: a tool for discovery and visualization of amino acid composition differences. BMC Bioinformatics. 8:211. (2007) web site

[6] Vacic V, Oldfield CJ, Mohan A, Radivojac P, Cortese MS, Uversky VN, Dunker AK. Characterization of molecular recognition features, MoRFs, and their binding partners. Journal of Proteome Research. 6(6):2351-66. (2007)

[5] Sickmeier M, Hamilton JA, LeGall T, Vacic V, Cortese MS, Tantos A, Szabo B, Tompa P, Chen J, Uversky VN, Obradovic Z, Dunker AK. DisProt: the database of disordered proteins. Nucleic Acids Research. 35:D786-93. (2007). web site

2006

[4] Mohan A, Oldfield CJ, Radivojac P, Vacic V, Cortese MS, Dunker AK, Uversky VN. Analysis of molecular recognition features (MoRFs). Journal of Molecular Biology, 362(5):1043-59. (2006)

[3] Vacic V, Iakoucheva LM, Radivojac P. Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments. Bioinformatics, 22(12):1536-7. (2006) web site

[2] Fu Z, Chen X, Vacic V, Nan P, Zhong Y, Jiang T. A parsimony approach to genome-wide ortholog assignment. ACM Annual Conference on Research in Computational Molecular Biology, RECOMB'06, Venice, Italy. (2006)

2005

[1] Vucetic S, Obradovic Z, Vacic V, Radivojac P, Peng K, Iakoucheva LM, Cortese MS, Lawson JD, Brown CJ, Sikes JG, Newton CD, Dunker AK. Disprot: a database of protein disorder. Bioinformatics, 21(1): 137-140. (2005)

Software

• Graphlet kernel is a graph classification method based on efficient enumeration of small local subgraphs (graphlets).
• UbPred is a sequence-based predictor of protein ubiquitination sites.
• Composition Profiler is a web-based tool that automates detection of enrichment or depletion patterns of individual amino acids or groups of amino acids classified by several physico-chemical and structural properties.
• Two Sample Logo is a procedure for discovery of statistically significant position-specific differences in residue compositions between two multiple sequence alignments, as well as for graphical representation of those differences.