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Ilya Ioshikhes

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Chemicals & Drugs

Procedures

Genes & Molecular Sequences

Genome, Human

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Publications

TOP 3
Travis N Mavrich; Ilya P Ioshikhes; Bryan J Venters; Cizhong Jiang; Lynn P Tomsho; Ji Qi; Stephan C Schuster; Istvan Albert; B Franklin Pugh
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome.
Travis N Mavrich; Cizhong Jiang; Ilya P Ioshikhes; Xiaoyong Li; Bryan J Venters; Sara J Zanton; Lynn P Tomsho; Ji Qi; Robert L Glaser; Stephan C Schuster; David S Gilmour; Istvan Albert; B Franklin Pugh
Nucleosome organization in the Drosophila genome.
Ilya P Ioshikhes; Sashwati Roy; Chandan K Sen
Algorithms for mapping of mRNA targets for microRNA.

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All Publications

2008: Travis N Mavrich; Ilya P Ioshikhes; Bryan J Venters; Cizhong Jiang; Lynn P Tomsho; Ji Qi; Stephan C Schuster; Istvan Albert; B Franklin Pugh
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome.
Genome research 2008;18(7):1073-83.
2008: Travis N Mavrich; Cizhong Jiang; Ilya P Ioshikhes; Xiaoyong Li; Bryan J Venters; Sara J Zanton; Lynn P Tomsho; Ji Qi; Robert L Glaser; Stephan C Schuster; David S Gilmour; Istvan Albert; B Franklin Pugh
Nucleosome organization in the Drosophila genome.
Nature 2008;453(7193):358-62.
2007: Ilya P Ioshikhes; Sashwati Roy; Chandan K Sen
Algorithms for mapping of mRNA targets for microRNA.
DNA and cell biology 2007;26(4):265-72.
2007: Dominic J Smiraglia; Ramakrishnan Kazhiyur-Mannar; Christopher C Oakes; Yue-Zhong Wu; Ping Liang; Tahmina Ansari; Jian Su; Laura J Rush; Laura T Smith; Li Yu; Chunhui Liu; Zunyan Dai; shih-shih chen; Shu-Huei Wang; Joseph F Costello; Ilya P Ioshikhes; David W Dawson; Jason S Hong; Michael A Teitell; Angela Szafranek; Marta Camoriano; Fei Song; Rosemary Elliott; Werner Held; Jacquetta M Trasler; Christoph Plass; Rephael Wenger
Restriction landmark genomic scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations.
BMC genomics 2007;8():446.
2007: Amutha Ramaswamy; Ilya P Ioshikhes
Global dynamics of newly constructed oligonucleosomes of conventional and variant H2A.Z histone.
BMC structural biology 2007;7():76.
2006: Ilya P Ioshikhes; Istvan Albert; Sara J Zanton; B Franklin Pugh
Nucleosome positions predicted through comparative genomics.
Nature genetics 2006;38(10):1210-5.
2006: Naum I Gershenzon; Edward N Trifonov; Ilya P Ioshikhes
The features of Drosophila core promoters revealed by statistical analysis.
BMC genomics 2006;7():161.
2005: Dong-Hoon Lee; Naum I Gershenzon; Malavika Gupta; Ilya P Ioshikhes; Danny Reinberg; Brian A Lewis
Functional characterization of core promoter elements: the downstream core element is recognized by TAF1.
Molecular and cellular biology 2005;25(21):9674-86.
2005: Naum I Gershenzon; Ilya P Ioshikhes
Synergy of human Pol II core promoter elements revealed by statistical sequence analysis.
Bioinformatics (Oxford, England) 2005;21(8):1295-300.
2005: Amutha Ramaswamy; Ivet Bahar; Ilya P Ioshikhes
Structural dynamics of nucleosome core particle: comparison with nucleosomes containing histone variants.
Proteins 2005;58(3):683-96.
2005: Naum I Gershenzon; Ilya P Ioshikhes
Promoter classifier: software package for promoter database analysis.
Applied bioinformatics 2005;4(3):205-9.
2005: Naum I Gershenzon; Gary stormo; Ilya P Ioshikhes
Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites.
Nucleic acids research 2005;33(7):2290-301.
2003: Melanie Babcock; Adam Pavlicek; Elizabeth Spiteri; Catherine D Kashork; Ilya P Ioshikhes; Lisa Shaffer; Jerzy Jurka; Bernice E Morrow
Shuffling of genes within low-copy repeats on 22q11 (LCR22) by Alu-mediated recombination events during evolution.
Genome research 2003;13(12):2519-32.
2001: Kate T Montgomery; E Lee; A Miller; S Lau; C Shim; J Decker; D Chiu; S Emerling; Mandeep Sekhon; R Kim; Jack Lenz; J Han; Ilya P Ioshikhes; B Renault; I Marondel; S J Yoon; K Song; Vundavalli Murty; S Scherer; Raluca Yonescu; Ilan R Kirsch; Thomas Ried; John McPherson; Richard Gibbs; Raju Kucherlapati
A high-resolution map of human chromosome 12.
Nature 2001;409(6822):945-6.
2000: Ilya P Ioshikhes; Michael Q Zhang
Large-scale human promoter mapping using CpG islands.
Nature genetics 2000;26(1):61-3.
1999: Ilya P Ioshikhes; E 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 Sciences of the United States of America 1999;96(6):2891-5.
1997: Alexander Bolshoy; K Shapiro; Edward N Trifonov; Ilya P Ioshikhes
Enhancement of the nucleosomal pattern in sequences of lower complexity.
Nucleic acids research 1997;25(16):3248-54.
1996: Alexander Bolshoy; Ilya P Ioshikhes; Edward N Trifonov
Applicability of the multiple alignment algorithm for detection of weak patterns: periodically distributed DNA pattern as a study case.
Computer applications in the biosciences : CABIOS 1996;12(5):383-9.
1996: Ilya P Ioshikhes; Alexander Bolshoy; K Derenshteyn; Mark Borodovsky; Edward N Trifonov
Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences.
Journal of molecular biology 1996;262(2):129-39.
1993: Ilya P Ioshikhes; Edward N Trifonov
Nucleosomal DNA sequence database.
Nucleic acids research 1993;21(21):4857-9.
1992: Ilya P Ioshikhes; Alexander Bolshoy; Edward N Trifonov
Preferred positions of AA and TT dinucleotides in aligned nucleosomal DNA sequences.
Journal of biomolecular structure & dynamics 1992;9(6):1111-7.