I. Ioshikhes

发表

Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences.

M. Borodovsky, E. Trifonov, I. Ioshikhes, 1996, Journal of molecular biology.

Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure.

M. Q. Zhang, E. Trifonov, I. Ioshikhes, 1999, Proceedings of the National Academy of Sciences of the United States of America.

Nucleosome positions predicted through comparative genomics

I. Albert, B. Pugh, I. Ioshikhes, 2006, Nature Genetics.

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome.

Bryan J Venters, Bryan J. Venters, I. Albert, 2008, Genome research.

Nucleosome organization in the Drosophila genome

Stephan C. Schuster, Bryan J Venters, Ji Qi, 2008, Nature.

Insights into interplay between rexinoid signaling and myogenic regulatory factor-associated chromatin state in myogenic differentiation

Ilya Ioshikhes, I. Ioshikhes, A. Blais, 2017, Nucleic acids research.

Nucleosomal DNA sequence database.

E. Trifonov, I. Ioshikhes, 1993, Nucleic acids research.

Enhancement of the nucleosomal pattern in sequences of lower complexity.

E. Trifonov, I. Ioshikhes, A. Bolshoy, 1997, Nucleic acids research.

Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites

G. Stormo, I. Ioshikhes, N. Gershenzon, 2005, Nucleic acids research.

Optimizing the GATA-3 position weight matrix to improve the identification of novel binding sites

I. Ioshikhes, Soumyadeep Nandi, 2012, BMC Genomics.

Large-scale human promoter mapping using CpG islands

Michael Q. Zhang, I. Ioshikhes, 2000, Nature Genetics.

A multi-tissue analysis identifies HLA complex group 9 gene methylation differences in bipolar disorder

J. Vincent, P. Jia, J. Mill, 2012, Molecular Psychiatry.

Shuffling of genes within low-copy repeats on 22q11 (LCR22) by Alu-mediated recombination events during evolution.

L. Shaffer, J. Jurka, B. Morrow, 2003, Genome research.

Functional Characterization of Core Promoter Elements: the Downstream Core Element Is Recognized by TAF1

D. Reinberg, I. Ioshikhes, B. Lewis, 2005, Molecular and Cellular Biology.

Human milk metagenome: a functional capacity analysis

I. Ioshikhes, Tonya L. Ward, I. Altosaar, 2013, BMC Microbiology.

Galaxy Dnpatterntools for Computational Analysis of Nucleosome Positioning Sequence Patterns

I. Ioshikhes, Erinija Pranckevičienė, S. Hosid, 2022, International journal of molecular sciences.

Snf2h-mediated chromatin organization and histone H1 dynamics govern cerebellar morphogenesis and neural maturation

P. Lagali, I. Ioshikhes, E. Meshorer, 2014, Nature Communications.

Structural dynamics of nucleosome mediated by acetylations at H3K56 and H3K115,122

I. Ioshikhes, M. Rajagopalan, Sangeetha Balasubramanian, 2016, European Biophysics Journal.

Optimized Position Weight Matrices in Prediction of Novel Putative Binding Sites for Transcription Factors in the Drosophila melanogaster Genome

I. Ioshikhes, Vyacheslav Morozov, 2013, PloS one.

Applicability of the multiple alignment algorithm for detection of weak patterns: periodically distributed DNA pattern as a study case

Edward N. Trifonov, Alexander Bolshoy, I. Ioshikhes, 1996, Comput. Appl. Biosci..

Exploring a Drosophila Transcription Factor Interaction Network to Identify Cis-Regulatory Modules

I. Ioshikhes, Doo Yang, P. Stenberg, 2019, J. Comput. Biol..

A high-resolution map of human chromosome 12

R. Gibbs, J. McPherson, S. Scherer, 2001, Nature.

Identification of the conserved long non-coding RNAs in myogenesis

I. Ioshikhes, Soumyadeep Nandi, A. Bhattacharya, 2021, BMC Genomics.

Human milk metagenome: a functional capacity

I. Ioshikhes, Tonya L. Ward, I. Altosaar, 2013 .

Preferred positions of AA and TT dinucleotides in aligned nucleosomal DNA sequences.

E. Trifonov, I. Ioshikhes, A. Bolshoy, 1992, Journal of biomolecular structure & dynamics.

The features of Drosophila core promoters revealed by statistical analysis

Naum I Gershenzon, Edward N Trifonov, E. Trifonov, 2006, BMC Genomics.

Snf2h Drives Chromatin Remodeling to Prime Upper Layer Cortical Neuron Development

Teruyoshi Hirayama, T. Yagi, I. Ioshikhes, 2019, Front. Mol. Neurosci..

Apoptotic Lymphocytes of H. sapiens Lose Nucleosomes in GC-Rich Promoters

Ilya Ioshikhes, Sergey Hosid, I. Ioshikhes, 2014, PLoS Comput. Biol..

Restriction Landmark Genomic Scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations

R. Wenger, Yue-zhong Wu, C. Plass, 2007, BMC Genomics.

Promoter Classifier

Naum I Gershenzon, Ilya P Ioshikhes, I. Ioshikhes, 2005, Applied bioinformatics.

Dynamics of modeled oligonucleosomes and the role of histone variant proteins in nucleosome organization.

I. Ioshikhes, Amutha Ramaswamy, 2013, Advances in protein chemistry and structural biology.

Synergy of human Pol II core promoter elements revealed by statistical sequence analysis

Naum I. Gershenzon, Ilya P. Ioshikhes, I. Ioshikhes, 2005, Bioinform..

Drosophila H2A and H2A.Z Nucleosome Sequences Reveal Different Nucleosome Positioning Sequence Patterns

Doo Yang, Ilya Ioshikhes, I. Ioshikhes, 2017, J. Comput. Biol..

Optimizing the GATA-3 position weight matrix to improve the identification of novel binding sites

I. Ioshikhes, Soumyadeep Nandi, 2012, BMC Genomics.

Bmc Structural Biology Global Dynamics of Newly Constructed Oligonucleosomes of Conventional and Variant H2a.z Histone

I. Ioshikhes, Amutha Ramaswamy, Ilya Ioshikhes, 2022 .

Nucleosome Presence at AML-1 Binding Sites Inversely Correlates with Ly49 Expression: Revelations from an Informatics Analysis of Nucleosomes and Immune Cell Transcription Factors

Andrew Wight, Doo Yang, Ilya Ioshikhes, 2016, PLoS Comput. Biol..

Discovery, optimization and validation of an optimal DNA-binding sequence for the Six1 homeodomain transcription factor

I. Ioshikhes, A. Blais, Yubing Liu, 2012, Nucleic acids research.

Global dynamics of nucleosome arrays: influence of variant histone H2A.Z

Li Wang, Amutha Ramaswamy, Ilya P. Ioshikhes, 2005, Fifth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'05).

Structural dynamics of nucleosome core particle: Comparison with nucleosomes containing histone variants

Ilya Ioshikhes, Ivet Bahar, Amutha Ramaswamy, 2004, Proteins.

Variety of genomic DNA patterns for nucleosome positioning.

Ilya Ioshikhes, Sergey Hosid, B. Pugh, 2011, Genome research.

Identification of cis-regulatory modules in promoters of human genes exploiting mutual positioning of transcription factors

Ilya Ioshikhes, Soumyadeep Nandi, I. Ioshikhes, 2013, Nucleic acids research.

Algorithms for mapping of mRNA targets for microRNA.

Ilya Ioshikhes, Sashwati Roy, Chandan K Sen, 2007, DNA and cell biology.

Voluntary Running Triggers VGF-Mediated Oligodendrogenesis to Prolong the Lifespan of Snf2h-Null Ataxic Mice.

I. Ioshikhes, L. Racacho, D. Bulman, 2016, Cell reports.

Nucleosome positioning sequence patterns as packing or regulatory

Ilya Ioshikhes, Nathan Liang, Erinija Pranckeviciene, 2019, bioRxiv.

Variety of genomic DNA patterns for nucleosome positioning.

I. Ioshikhes, Sergey Hosid, Pugh Bf, 2011, Genome research.

NLP can help parents to understand rare diseases

Marina Sokolova, Ilya Ioshikhes, Hamid Poursepanj, 2013 .