| 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 |
0.417 |
|
| 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 |
0.356 |
|
| 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 |
0.364 |
|
| 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 |
0.352 |
|
| 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 |
0.315 |
|
| 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 |
0.473 |
|
| 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 |
0.52 |
|
| 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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