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Ilya Ioshikhes - Publications

Affiliations: 
Bioinformatics University of Ottawa, Ottawa, ON, Canada 
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32 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Pranckeviciene E, Hosid S, Maziukas I, Ioshikhes I. Galaxy Dnpatterntools for Computational Analysis of Nucleosome Positioning Sequence Patterns. International Journal of Molecular Sciences. 23. PMID 35563261 DOI: 10.3390/ijms23094869  0.378
2020 Pranckeviciene E, Hosid S, Liang N, Ioshikhes I. Nucleosome positioning sequence patterns as packing or regulatory. Plos Computational Biology. 16: e1007365. PMID 31986131 DOI: 10.1371/Journal.Pcbi.1007365  0.373
2019 Mahmud AKMF, Yang D, Stenberg P, Ioshikhes I, Nandi S. Exploring a Transcription Factor Interaction Network to Identify Cis-Regulatory Modules. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 31855461 DOI: 10.1089/Cmb.2018.0160  0.359
2017 Hamed M, Khilji S, Dixon K, Blais A, Ioshikhes I, Chen J, Li Q. Insights into interplay between rexinoid signaling and myogenic regulatory factor-associated chromatin state in myogenic differentiation. Nucleic Acids Research. PMID 28981706 DOI: 10.1093/Nar/Gkx800  0.359
2016 Yang D, Ioshikhes I. Drosophila H2A and H2A.Z Nucleosome Sequences Reveal Different Nucleosome Positioning Sequence Patterns. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 27992255 DOI: 10.1089/Cmb.2016.0173  0.446
2016 Rajagopalan M, Balasubramanian S, Ioshikhes I, Ramaswamy A. Structural dynamics of nucleosome mediated by acetylations at H3K56 and H3K115,122. European Biophysics Journal : Ebj. PMID 27933430 DOI: 10.1007/S00249-016-1191-5  0.425
2016 Wight A, Yang D, Ioshikhes I, Makrigiannis AP. Nucleosome Presence at AML-1 Binding Sites Inversely Correlates with Ly49 Expression: Revelations from an Informatics Analysis of Nucleosomes and Immune Cell Transcription Factors. Plos Computational Biology. 12: e1004894. PMID 27124577 DOI: 10.1371/Journal.Pcbi.1004894  0.418
2014 Hosid S, Ioshikhes I. Apoptotic lymphocytes of H. sapiens lose nucleosomes in GC-rich promoters. Plos Computational Biology. 10: e1003760. PMID 25077608 DOI: 10.1371/Journal.Pcbi.1003760  0.441
2014 Alvarez-Saavedra M, De Repentigny Y, Lagali PS, Raghu Ram EV, Yan K, Hashem E, Ivanochko D, Huh MS, Yang D, Mears AJ, Todd MA, Corcoran CP, Bassett EA, Tokarew NJ, Kokavec J, ... ... Ioshikhes I, et al. Snf2h-mediated chromatin organization and histone H1 dynamics govern cerebellar morphogenesis and neural maturation. Nature Communications. 5: 4181. PMID 24946904 DOI: 10.1038/Ncomms5181  0.357
2013 Nandi S, Blais A, Ioshikhes I. Identification of cis-regulatory modules in promoters of human genes exploiting mutual positioning of transcription factors. Nucleic Acids Research. 41: 8822-41. PMID 23913413 DOI: 10.1093/Nar/Gkt578  0.365
2013 Ramaswamy A, Ioshikhes I. Dynamics of modeled oligonucleosomes and the role of histone variant proteins in nucleosome organization. Advances in Protein Chemistry and Structural Biology. 90: 119-49. PMID 23582203 DOI: 10.1016/B978-0-12-410523-2.00004-3  0.362
2012 Nandi S, Ioshikhes I. Optimizing the GATA-3 position weight matrix to improve the identification of novel binding sites. Bmc Genomics. 13: 416. PMID 22913572 DOI: 10.1186/1471-2164-13-416  0.334
2012 Liu Y, Nandi S, Martel A, Antoun A, Ioshikhes I, Blais A. Discovery, optimization and validation of an optimal DNA-binding sequence for the Six1 homeodomain transcription factor. Nucleic Acids Research. 40: 8227-39. PMID 22730291 DOI: 10.1093/Nar/Gks587  0.433
2011 Ioshikhes I, Hosid S, Pugh BF. Variety of genomic DNA patterns for nucleosome positioning. Genome Research. 21: 1863-71. PMID 21750105 DOI: 10.1101/gr.116228.110  0.31
2008 Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Research. 18: 1073-83. PMID 18550805 DOI: 10.1101/Gr.078261.108  0.353
2008 Mavrich TN, Jiang C, Ioshikhes IP, Li X, Venters BJ, Zanton SJ, Tomsho LP, Qi J, Glaser RL, Schuster SC, Gilmour DS, Albert I, Pugh BF. Nucleosome organization in the Drosophila genome. Nature. 453: 358-62. PMID 18408708 DOI: 10.1038/Nature06929  0.355
2007 Smiraglia DJ, Kazhiyur-Mannar R, Oakes CC, Wu YZ, Liang P, Ansari T, Su J, Rush LJ, Smith LT, Yu L, Liu C, Dai Z, Chen SS, Wang SH, Costello J, ... Ioshikhes I, et al. Restriction landmark genomic scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations. Bmc Genomics. 8: 446. PMID 18053125 DOI: 10.1186/1471-2164-8-446  0.327
2007 Ramaswamy A, Ioshikhes I. Global dynamics of newly constructed oligonucleosomes of conventional and variant H2A.Z histone Bmc Structural Biology. 7. PMID 17996059 DOI: 10.1186/1472-6807-7-76  0.39
2006 Ioshikhes IP, Albert I, Zanton SJ, Pugh BF. Nucleosome positions predicted through comparative genomics. Nature Genetics. 38: 1210-5. PMID 16964265 DOI: 10.1038/Ng1878  0.389
2005 Gershenzon NI, Ioshikhes IP. Promoter classifier: software package for promoter database analysis. Applied Bioinformatics. 4: 205-9. PMID 16231962 DOI: 10.2165/00822942-200504030-00005  0.316
2005 Gershenzon NI, Stormo GD, Ioshikhes IP. Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites. Nucleic Acids Research. 33: 2290-301. PMID 15849315 DOI: 10.1093/nar/gki519  0.3
2005 Ramaswamy A, Bahar I, Ioshikhes I. Structural dynamics of nucleosome core particle: comparison with nucleosomes containing histone variants. Proteins. 58: 683-96. PMID 15624215 DOI: 10.1002/Prot.20357  0.384
2005 Gershenzon NI, Ioshikhes IP. Synergy of human Pol II core promoter elements revealed by statistical sequence analysis. Bioinformatics (Oxford, England). 21: 1295-300. PMID 15572469 DOI: 10.1093/bioinformatics/bti172  0.337
2003 Babcock M, Pavlicek A, Spiteri E, Kashork CD, Ioshikhes I, Shaffer LG, Jurka J, Morrow BE. Shuffling of genes within low-copy repeats on 22q11 (LCR22) by Alu-mediated recombination events during evolution. Genome Research. 13: 2519-32. PMID 14656960 DOI: 10.1101/Gr.1549503  0.342
2000 Ioshikhes IP, Zhang MQ. Large-scale human promoter mapping using CpG islands. Nature Genetics. 26: 61-63. PMID 10973249 DOI: 10.1038/79189  0.475
1999 Ioshikhes I, Trifonov EN, Zhang MQ. Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure Proceedings of the National Academy of Sciences of the United States of America. 96: 2891-2895. PMID 10077607 DOI: 10.1073/Pnas.96.6.2891  0.521
1998 Lvovsky L, Ioshikhes I, Raja MC, Zevin-Sonkin D, Sobolev IA, Liberzon A, Shwartzburd J, Ulanovsky LE. Interdependence between DNA template secondary structure and priming efficiencies of short primers Nucleic Acids Research. 26: 5525-5532. PMID 9826780 DOI: 10.1093/Nar/26.23.5525  0.347
1997 Bolshoy A, Shapiro K, Trifonov EN, Ioshikhes I. Enhancement of the nucleosomal pattern in sequences of lower complexity. Nucleic Acids Research. 25: 3248-54. PMID 9241237 DOI: 10.1093/Nar/25.16.3248  0.413
1996 Bolshoy A, Ioshikhes I, Trifonov EN. Applicability of the multiple alignment algorithm for detection of weak patterns: periodically distributed DNA pattern as a study case Bioinformatics. 12: 383-389. PMID 8996786 DOI: 10.1093/Bioinformatics/12.5.383  0.357
1996 Ioshikhes I, Bolshoy A, Derenshteyn K, Borodovsky M, Trifonov EN. Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. Journal of Molecular Biology. 262: 129-139. PMID 8831784 DOI: 10.1006/Jmbi.1996.0503  0.424
1993 Ioshikhes I, Trifonov EN. Nucleosomal DNA sequence database Nucleic Acids Research. 21: 4857-4859. PMID 8177730 DOI: 10.1093/Nar/21.21.4857  0.398
1992 Ioshikhes I, Bolshoy A, Trifonov EN. Preferred Positions of AA and TT Dinucleotides in Aligned Nucleosomal DNA Sequences Journal of Biomolecular Structure & Dynamics. 9: 1111-1117. PMID 1637505 DOI: 10.1080/07391102.1992.10507982  0.387
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