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Tissue-specific regulation of gene expression via unproductive splicing

Nucleic acids research, 2023-04, Vol.51 (7), p.3055-3066

2023

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Exploring massive, genome scale datasets with the GenometriCorr package

PLoS computational biology, 2012-05, Vol.8 (5), p.e1002529-e1002529

2012

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Replicate sequencing libraries are important for quantification of allelic imbalance

Nature communications, 2021-06, Vol.12 (1), p.3370-3370, Article 3370

2021

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Inter-chromosomal contact networks provide insights into Mammalian chromatin organization

PloS one, 2015-05, Vol.10 (5), p.e0126125

2015

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Comparative Genomics of the Vitamin B12 Metabolism and Regulation in Prokaryotes

The Journal of biological chemistry, 2003-10, Vol.278 (42), p.41148-41159

2003

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Investigation of the Role of PUFA Metabolism in Breast Cancer Using a Rank-Based Random Forest Algorithm

Cancers, 2022-09, Vol.14 (19), p.4663

2022

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Identification of Position-Specific Correlations between DNA-Binding Domains and Their Binding Sites. Application to the MerR Family of Transcription Factors

PloS one, 2016-09, Vol.11 (9), p.e0162681-e0162681

2016

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Comparative Genomics of Bacterial Zinc Regulons: Enhanced Ion Transport, Pathogenesis, and Rearrangement of Ribosomal Proteins

Proceedings of the National Academy of Sciences - PNAS, 2003-08, Vol.100 (17), p.9912-9917

2003

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BaRDIC: robust peak calling for RNA–DNA interaction data

NAR genomics and bioinformatics, 2024-06, Vol.6 (2)

2024

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Origin of the nuclear proteome on the basis of pre-existing nuclear localization signals in prokaryotic proteins

Biology direct, 2020-04, Vol.15 (1), p.9-9, Article 9

2020

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Ectopic expression of HIV-1 Tat modifies gene expression in cultured B cells: implications for the development of B-cell lymphomas in HIV-1-infected patients

PeerJ (San Francisco, CA), 2022-10, Vol.10, p.e13986-e13986, Article e13986

2022

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Cumulative contact frequency of a chromatin region is an intrinsic property linked to its function

PeerJ (San Francisco, CA), 2020-08, Vol.8, p.e9566-e9566, Article e9566

2020

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Hidden Markov models for evolution and comparative genomics analysis

PloS one, 2013-06, Vol.8 (6), p.e65012-e65012

2013

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A Metabolic Network in the Evolutionary Context: Multiscale Structure and Modularity

Proceedings of the National Academy of Sciences - PNAS, 2006-06, Vol.103 (23), p.8774-8779

2006

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Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale

Bioinformatics (Oxford, England), 2023-06, Vol.39 (Supplement_1), p.i431-i439

2023

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Spatial proximity and similarity of the epigenetic state of genome domains

PloS one, 2012-04, Vol.7 (4), p.e33947-e33947

2012

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OrthoQuantum: visualizing evolutionary repertoire of eukaryotic proteins

Nucleic acids research, 2022-07, Vol.50 (W1), p.W534-W540

2022

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Evolution of Prokaryotic Genes by Shift of Stop Codons

Journal of molecular evolution, 2011-02, Vol.72 (2), p.138-146

2011

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Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families

Protein science, 2004-02, Vol.13 (2), p.443-456

2004

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An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies

Algorithms for molecular biology, 2010-07, Vol.5 (1), p.29-29, Article 29

2010

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Weak Negative and Positive Selection and the Drift Load at Splice Sites

Genome biology and evolution, 2014-05, Vol.6 (6), p.1437-1447

2014

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Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae)

BMC genomics, 2007-02, Vol.8 (1), p.54-54, Article 54

2007

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Compensatory reactions of B cells in response to chronic HIV-1 Tat exposure

Journal of cellular physiology, 2024-10, p.e31459

2024

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Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics

Nucleic acids research, 2020-07, Vol.48 (12), p.6699-6714

2020

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Coloc-stats: a unified web interface to perform colocalization analysis of genomic features

Nucleic acids research, 2018-07, Vol.46 (W1), p.W186-W193

2018

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Tissue-specific regulation of gene expression via unproductive splicing

Exploring massive, genome scale datasets with the GenometriCorr package

Replicate sequencing libraries are important for quantification of allelic imbalance

Inter-chromosomal contact networks provide insights into Mammalian chromatin organization

Comparative Genomics of the Vitamin B12 Metabolism and Regulation in Prokaryotes

Investigation of the Role of PUFA Metabolism in Breast Cancer Using a Rank-Based Random Forest Algorithm

Identification of Position-Specific Correlations between DNA-Binding Domains and Their Binding Sites. Application to the MerR Family of Transcription Factors

Comparative Genomics of Bacterial Zinc Regulons: Enhanced Ion Transport, Pathogenesis, and Rearrangement of Ribosomal Proteins

BaRDIC: robust peak calling for RNA–DNA interaction data

Origin of the nuclear proteome on the basis of pre-existing nuclear localization signals in prokaryotic proteins

Ectopic expression of HIV-1 Tat modifies gene expression in cultured B cells: implications for the development of B-cell lymphomas in HIV-1-infected patients

Cumulative contact frequency of a chromatin region is an intrinsic property linked to its function

Hidden Markov models for evolution and comparative genomics analysis

A Metabolic Network in the Evolutionary Context: Multiscale Structure and Modularity

Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale

Spatial proximity and similarity of the epigenetic state of genome domains

OrthoQuantum: visualizing evolutionary repertoire of eukaryotic proteins

Evolution of Prokaryotic Genes by Shift of Stop Codons

Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families

An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies

Weak Negative and Positive Selection and the Drift Load at Splice Sites

Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae)

Compensatory reactions of B cells in response to chronic HIV-1 Tat exposure

Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features

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