OSU Department of Biomedical Informatics

Ilya Ioschikhes Ph.D.

phone: (614) 292-8929
fax: (614) 688-6600

email:


mailing address
3172-C Graves Hall
333 W. 10th Ave.
Columbus, OH 43210


Dr. Ioshikhes received a M.Sc degree from the Department of Physics, Tadjik State University, Dushanbe, USSR, and a Ph.D. degree from the Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel. He did postdoctoral training at the Cold Spring Harbor Laboratory in New York.

Dr. Ioshikhes has been an Assistant Professor at BMI since 2002. Prior, he was an Instructor in the Department of Molecular Genetics at the Albert Einstein College of Medicine in New York and a Visiting Researcher in the School of Biology at the Geogia Institute of Technology in Atlanta. He has had research fellowships at the College of Judea and Samaria, Ariel, Israel, and held different academic and industrial positions in Dushanbe, USSR.

Research

The major focus of my research is on bioinformatics analysis of gene regulation involving chromatin, transcription factor (TF) interactions with DNA, promoter analysis, and other related topics.

My chromatin research originated from my Ph.D. studies and was initially focused on gathering of a nucleosome sequences database and its sequence analysis by multiple sequence alignment and other approaches. Now I and my lab focus mostly on computer structural modeling of single nucleosome particles and their short arrays by normal mode analysis supplemented by atomic-level basic modeling.

My interest in promoters started from my postdoctoral training and involved study of CpG islands as promoter markers in vertebrates (see my CpG_promoter program) and analysis of promoter-chromatin correlations. At OSU we focused first on studying the DNA core promoter and the synergistic action of its elements. We are currently expanding this project, considering the possible synergistic action of other promoter elements, with a goal to develop a novel promoter recognition algorithm and software on that basis. That should also explore improved position weight matrices for TF binding sites. Calculation of the latter and development of respective methodology is another of our targets.

Our ultimate goal is molecular modeling of the promoter and transcription machinery taking into account all the aforementioned regulatory elements in their appropriate positions (also predicted by us in significant extent).

Our research also involves collaborations with other research labs concerning additional aspects of gene regulation and other subjects.

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Grant Highlights


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Publications

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Amutha Ramaswamy, Ilya Ioschikhes, "Global dynamics of newly constructed nucleosome arrays of ordinary and variant H2A.Z histone", BMC Structural Biology, 7 (1) : pp. 76, November, 2007.

Ilya Ioschikhes, Sashwati Roy, Chandan K. Sen, "Algorithms for mapping of mRNA targets for microRNA", DNA Cell Biology, 4 (26) : pp. 265-272, April, 2007.

N. Gershenzon, Edward N. Trifonov, Ilya Ioschikhes, "The Features of Drosophila Core Promoters Revealed by Statistical Analysis", BMC Genomics, 7 (161) : pp. 161, June, 2006.

Ilya Ioschikhes, I. Albert, SJ Zanton, BF Pugh, "Nucleosome positions predicted through comparative genomics", Nature Genetics, 38 (10) : pp. 1210-1215, January, 2006.

D. H. Lee, N. Gershenzon, M. Gupta, Ilya Ioschikhes, D. Reinberg, B. A. Lewis, "Functional Characterization of Core Promoter Elements: The Downstream Core Element Is Recognized by TAF1", Molecular and Cellular Biology, 25 (21) : pp. 9674-9686, December, 2005.

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Presentations

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B. Bohacova, A. Papp, B. Besecker, Ilya Ioschikhes, Wolfgang Sadee, D. Knoell, "The Role of Cis-Acting Genetic Regulation on the Human Zinc Transporter SLC39A8", in Proceedings of OSU Denman Forum, Columbus, OH, 2006

Ilya Ioschikhes, "Bioinformatics approaches for studying of gene regulation", in Proceedings of OSU Computer Information Sciences Department, Columbus, OH, 2003

Ilya Ioschikhes, "Combining of gene and promoter predictions from different programs", in Proceedings of Journal Club, 2002

Publications

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T.N. Mavrich, C. Jiang, Ilya Ioschikhes, X. Li, B.J. Venters, SJ Zanton, L.P. Tomsho, J. Qi, R. Glaser, S.C. Schuster, D.S. Gilmour, I. Albert, BF Pugh, "Nucleosome organization in the Drosophila genome", Nature, Vol. 453 : pp. 358-362, April, 2008.

DJ Smiraglia, R Kazhiur-Mannar, CC Oakes, YZ Wu, P Liang, R. Ansari, J Su, L Rush, LT Smith, L Yu, C Liu, Z Dai, SS Chen, SH Wang, J Costello, Ilya Ioschikhes, DW Dawson, JS Hong, MA Teitell, A Szafranek, M Camoriano, "Restriction Landmark Genomic Scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations", BMC Genomics, 8 (1) : pp. 446, November, 2007.

Amutha Ramaswamy, Ilya Ioschikhes, "Global dynamics of newly constructed nucleosome arrays of ordinary and variant H2A.Z histone", BMC Structural Biology, 7 (1) : pp. 76, November, 2007.

Ilya Ioschikhes, Sashwati Roy, Chandan K. Sen, "Algorithms for mapping of mRNA targets for microRNA", DNA Cell Biology, 4 (26) : pp. 265-272, April, 2007.

N. Gershenzon, Edward N. Trifonov, Ilya Ioschikhes, "The Features of Drosophila Core Promoters Revealed by Statistical Analysis", BMC Genomics, 7 (161) : pp. 161, June, 2006.

Ilya Ioschikhes, I. Albert, SJ Zanton, BF Pugh, "Nucleosome positions predicted through comparative genomics", Nature Genetics, 38 (10) : pp. 1210-1215, January, 2006.

D. H. Lee, N. Gershenzon, M. Gupta, Ilya Ioschikhes, D. Reinberg, B. A. Lewis, "Functional Characterization of Core Promoter Elements: The Downstream Core Element Is Recognized by TAF1", Molecular and Cellular Biology, 25 (21) : pp. 9674-9686, December, 2005.

L. Wang, Amutha Ramaswamy, Ilya Ioschikhes, "Global Dynamics of Nucleosome Arrays: Influence of Variant Histone H2A.Z", Proc. IEEE 5th Symposium on Bioinformatics and Bioengineering 2005, : pp. 271-275, October, 2005.

N. Gershenzon, Ilya Ioschikhes, "Promoter Classifier: Software Package for Promoter Database Analysis", Applied Bioinformatics, 4 (3) : pp. 205-209, October, 2005.

N. Gershenzon, G. Stormo, Ilya Ioschikhes, "Computational Technique for Improvement of the Position-Weight Matrices for the DNA/Protein Binding Sites", Nucleic Acids Research, 33 (7) : pp. 2290-2301, April, 2005.

N. Gershenzon, Ilya Ioschikhes, "Synergy of Human Pol II Core Promoter Elements Revealed by Statistical Sequence Analysis", Bioinformatics, 21 (8) : pp. 1295-1300, April, 2005.

Amutha Ramaswamy, Ivet Bahar, Ilya Ioschikhes, "Structural Dynamics of Nucleosome Core Particle: Comparison with Nucleosomes Containing Histone Variants", Proteins: Structure, Function, and Bioinformatics, 58 (3) : pp. 683-696, March, 2005.

M. Babcock, A. Pavlicek, E. Spiteri, C. D. Kashork, Ilya Ioschikhes, L. G. Shaffer, J. Jurka, B. E. Morrow, "Shuffling of Genes Within Low-Copy Repeats on 22q11 (LCR22) by Alu-Mediated Recombination Events During Evolution", Genome Research, 12 (13) : pp. 2519-2532, December, 2003.

Kate T. Montgomery, Eunice Lee, Ashley Miller, Stephanie Lau, Cecilia Shim, Jeremy Decker, Denise Chiu, Suzanne Emerling, Mandeep Sekhon, Rachel Kim, Jack Lenz, Jinghua Han, Ilya Ioschikhes, Beatrice Renault, Ivonne Marondel, Sung-Joo K. Yoon, Kyuyoung Song, V.V.V.S. Murty, Steven Scherer, Raluca Yonescu, Ilan R. Kirsch, Thomas Ried, John Mcpherson, Richard Gibbs, Raju Kucherlapati, "A High-Resolution Map of Human Chromosomes 12", Nature, 409 : pp. 945-946, February, 2001.

Ilya Ioschikhes, Michael Q. Zhang, "Large-Scale Human Promoter Mapping Using CpG Islands", Nature Genetics, 26 (1) : pp. 61-63, September, 2000.

Ilya Ioschikhes, Edward N. Trifonov, Michael Q. Zhang, "Periodical Distribution of Transcription Factor Sites in Promoter Regions and Connection with Chromatin Structure", Proceedings of the National Academy of Science of the United States of America, 96 (6) : pp. 2891-2895, March, 1999.

L. Lvovsky, Ilya Ioschikhes, M. C. Raja, D. Zevin-Sonkin, I. A. Sobolev, A. Liberzon, J. Shwartzburd, L. E. Ulanovsky, "Interdependence Between DNA Template Secondary Structure and Priming Efficiencies of Short Primers", Nucleic Acids Research, 26 (23) : pp. 5525-5532, December, 1998.

A. Bolshoy, K. Shapiro, Edward N. Trifonov, Ilya Ioschikhes, "Enhancement of the nucleosomal pattern in sequences of lower complexity", Nucleic Acids Research, 25 (16) : pp. 3248-3254, August, 1997.

Ilya Ioschikhes, A. Bolshoy, Konstantin Derenshteyn, Mark Borodovsky, Edward N. Trifonov, "Nucleosome DNA Sequence Pattern Revealed by Multiple Alignment of Experimentally Mapped Sequences", Journal of Molecular Biology, 262 (2) : pp. 129-139, October, 1996.

A. Bolshoy, Ilya Ioschikhes, Edward N. Trifonov, "Applicability of the Multiple Alignment Algorithm for Detection of Weak Patterns: Periodically Distributed DNA Pattern as a Study Case", Bioinformatics, 12 : pp. 383-389, October, 1996.

Ilya Ioschikhes, Edward N. Trifonov, "Nucleosomal DNA Sequence Database", Nucleic Acids Research, 21 (21) : pp. 4857-59, October, 1993.

Ilya Ioschikhes, A. Bolshoy, Edward N. Trifonov, "Preferred Positions of AA and TT Dinucleotides in Aligned Nucleosomal DNA Sequences", Journal of Biomolecular Structure and Dynamics, 9 (6) : pp. 1111-1117, June, 1992.

Presentations

click to hide (-)

B. Bohacova, A. Papp, B. Besecker, Ilya Ioschikhes, Wolfgang Sadee, D. Knoell, "The Role of Cis-Acting Genetic Regulation on the Human Zinc Transporter SLC39A8", in Proceedings of OSU Denman Forum, Columbus, OH, 2006

Ilya Ioschikhes, "Bioinformatics approaches for studying of gene regulation", in Proceedings of OSU Computer Information Sciences Department, Columbus, OH, 2003

Ilya Ioschikhes, "Combining of gene and promoter predictions from different programs", in Proceedings of Journal Club, 2002

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