Ivan Ovcharenko

发表

Structure of Proximal and Distant Regulatory Elements in the Human Genome

Ivan Ovcharenko, 2010, ISBRA.

Enhancer reprogramming in mammalian genomes

Mario Flores, Ivan Ovcharenko, I. Ovcharenko, 2018, BMC Bioinformatics.

Identifying synonymous regulatory elements in vertebrate genomes

Ivan Ovcharenko, Marcelo A. Nobrega, M. Nóbrega, 2005, Nucleic Acids Res..

Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs

Ivan Ovcharenko, Hani Z. Girgis, I. Ovcharenko, 2012, BMC Bioinformatics.

Dcode.org anthology of comparative genomic tools

Ivan Ovcharenko, Gabriela G. Loots, I. Ovcharenko, 2005, Nucleic Acids Res..

ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes

Ivan Ovcharenko, Gabriela G. Loots, Marcelo A. Nobrega, 2004, Nucleic Acids Res..

rVISTA 2.0: evolutionary analysis of transcription factor binding sites

Ivan Ovcharenko, Gabriela G. Loots, I. Ovcharenko, 2004, Nucleic Acids Res..

Array2BIO: from microarray expression data to functional annotation of co-regulated genes

Ivan Ovcharenko, Gabriela G. Loots, Patrick S. G. Chain, 2006, BMC Bioinformatics.

DiRE: identifying distant regulatory elements of co-expressed genes

Valer Gotea, Ivan Ovcharenko, Valer Gotea, 2008, Nucleic Acids Res..

SNPDelScore: combining multiple methods to score deleterious effects of noncoding mutations in the human genome

Shan Li, David Landsman, Ivan Ovcharenko, 2018, Bioinform..

CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments

Roded Sharan, Richard M. Karp, Asa Ben-Hur, 2003, ISMB.

ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes

Ivan Ovcharenko, Gabriela G. Loots, I. Ovcharenko, 2007, Bioinform..

CREME: Cis-Regulatory Module Explorer for the human genome

Roded Sharan, Asa Ben-Hur, Ivan Ovcharenko, 2004, Nucleic Acids Res..

Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements

Ivan Ovcharenko, Leila Taher, I. Ovcharenko, 2009, Bioinform..

CLARE: Cracking the LAnguage of Regulatory Elements

Ivan Ovcharenko, Leelavati Narlikar, Leila Taher, 2012, Bioinform..

Effects of HMGN variants on the cellular transcription profile

Michael Bustin, Vladimir N. Uversky, Ivan Ovcharenko, 2011, Nucleic acids research.

Evolution and functional classification of vertebrate gene deserts.

Webb Miller, Ivan Ovcharenko, Ross C Hardison, 2005, Genome research.

Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes

Manuel Serrano, Roderic Guigó, Miguel Manzanares, 2011, Nature Structural &Molecular Biology.

Identifying causal regulatory SNPs in ChIP-seq enhancers

Ivan Ovcharenko, Di Huang, I. Ovcharenko, 2014, Nucleic acids research.

zPicture: dynamic alignment and visualization tool for analyzing conservation profiles.

Webb Miller, Ivan Ovcharenko, Ross C Hardison, 2004, Genome research.

Predicting tissue-specific enhancers in the human genome.

Ivan Ovcharenko, Len A Pennacchio, Marcelo A Nobrega, 2006, Genome research.

Machine learning classification of cell-specific cardiac enhancers uncovers developmental subnetworks regulating progenitor cell division and cell fate specification

Martha L. Bulyk, Ivan Ovcharenko, Neal Jeffries, 2014, Development.

Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes

Manuel Serrano, Roderic Guigó, Miguel Manzanares, 2011, Nature Structural &Molecular Biology.

Widespread Ultraconservation Divergence in Primates

Ivan Ovcharenko, I. Ovcharenko, 2008, Molecular biology and evolution.

Sequence signatures extracted from proximal promoters can be used to predict distal enhancers

Ivan Ovcharenko, Nadav Ahituv, Leila Taher, 2013, Genome Biology.

Generation and annotation of the DNA sequences of human chromosomes 2 and 4

Terrence S. Furey, Sean R. Eddy, Li Ding, 2005, Nature.

comparative sequence-based discovery of functional transcription factor binding sites

Lior Pachter, Inna Dubchak, Ivan Ovcharenko, 2002 .

Interpreting mammalian evolution using Fugu genome comparisons.

Ivan Ovcharenko, I. Ovcharenko, L. Stubbs, 2004, Genomics.

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

Heng Li, Leif Andersson, Caleb Webber, 2004, Nature.

The DNA sequence and biology of human chromosome 19

Terrence S. Furey, Inna Dubchak, Matt Nolan, 2004, Nature.

Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions.

Ivan Ovcharenko, Richard Crooijmans, Laurie Gordon, 2007, Genome research.

Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network

Ting Ni, Ivan Ovcharenko, Di Huang, 2012, Proceedings of the National Academy of Sciences.

Tissue-Specific and Ubiquitous Expression Patterns from Alternative Promoters of Human Genes

Valer Gotea, Edwin Jacox, Ivan Ovcharenko, 2010, PloS one.

A Machine Learning Approach for Identifying Novel Cell Type–Specific Transcriptional Regulators of Myogenesis

Ivan Ovcharenko, Leila Taher, Brian W. Busser, 2012, PLoS genetics.

Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control

Takeshi Matsui, Ivan Ovcharenko, Andrew S. McCallion, 2012, Genome research.