Reconstruction of a Global Transcriptional Regulatory Network for Control of Lipid Metabolism in Yeast by Using Chromatin Immunoprecipitation with Lambda Exonuclease Digestion

Global transcriptional regulatory network forEscherichia colirobustly connects gene expression to transcription factor activities

(2017) Xin Fang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering of synthetic, stress-responsive yeast promoters

(2016) Arun S. Rajkumar et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Mapping of Binding Sites Reveals Multiple Biological Functions of the Transcription Factor Cst6p in Saccharomyces cerevisiae

(2016) Guodong Liu et al.   mBio

Production of fatty acid-derived oleochemicals and biofuels by synthetic yeast cell factories

(2016) Yongjin J. Zhou et al.   Nature Communications

Controllability analysis of transcriptional regulatory networks reveals circular control patterns among transcription factors

(2015) Tobias Österlund et al.   Integrative Biology

Microbial acetyl-CoA metabolism and metabolic engineering

(2015) Anastasia Krivoruchko et al.   METABOLIC ENGINEERING

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Deep learning for regulatory genomics

(2015) Yongjin Park et al.   NATURE BIOTECHNOLOGY

Spurious transcription factor binding: Non-functional or genetically redundant?

(2014) Mikhail Spivakov   BIOESSAYS

Inactivation of Yeast Isw2 Chromatin Remodeling Enzyme Mimics Longevity Effect of Calorie Restriction via Induction of Genotoxic Stress Response

(2014) Weiwei Dang et al.   Cell Metabolism

Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli

(2014) Sang Woo Seo et al.   Nature Communications

Integrated analysis, transcriptome-lipidome, reveals the effects of INO-level (INO2 and INO4) on lipid metabolism in yeast

(2013) Pramote Chumnanpuen et al.   BMC Systems Biology

Mapping Yeast Transcriptional Networks

(2013) T. R. Hughes et al.   GENETICS

Genomic Reconstruction of the Transcriptional Regulatory Network in Bacillus subtilis

(2013) S. A. Leyn et al.   JOURNAL OF BACTERIOLOGY

Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods

(2013) Leif Väremo et al.   NUCLEIC ACIDS RESEARCH

Nucleosome Free Regions in Yeast Promoters Result from Competitive Binding of Transcription Factors That Interact with Chromatin Modifiers

(2013) Evgeniy A. Ozonov et al.   PLoS Computational Biology

Fast and accurate preparation fatty acid methyl esters by microwave-assisted derivatization in the yeast Saccharomyces cerevisiae

(2012) Sakda Khoomrung et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Metabolism and Regulation of Glycerolipids in the Yeast Saccharomyces cerevisiae

(2012) Susan A. Henry et al.   GENETICS

Integrated analysis of transcriptome and lipid profiling reveals the co-influences of inositol–choline and Snf1 in controlling lipid biosynthesis in yeast

(2012) Pramote Chumnanpuen et al.   MOLECULAR GENETICS AND GENOMICS

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints

(2012) Yuchun Guo et al.   PLoS Computational Biology

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities

(2011) C. G. de Boer et al.   NUCLEIC ACIDS RESEARCH

Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights

(2011) Raluca Gordân et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Backup in gene regulatory networks explains differences between binding and knockout results

(2009) Anthony Gitter et al.   Molecular Systems Biology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Yeast transcription factor Oaf1 forms homodimer and induces some oleate-responsive genes in absence of Pip2

(2008) Joanna Trzcinska-Danielewicz et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Comparative analysis of the complex transcription-factor gene regulatory networks of E. coli and S. cerevisiae

(2008) Lev Guzman-Vargas et al.   BMC Systems Biology

Binding Characteristics and Regulatory Mechanisms of the Transcription Factors Controlling Oleate-responsive Genes inSaccharomyces cerevisiae

(2008) Igor V. Karpichev et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY