Independent component analysis recovers consistent regulatory signals from disparate datasets

The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function

(2019) Sankha Ghatak et al.   NUCLEIC ACIDS RESEARCH

Genome-wide effects on Escherichia coli transcription from ppGpp binding to its two sites on RNA polymerase

(2019) Patricia Sanchez-Vazquez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extracting Pathway-Level Signatures from Proteogenomic data in Breast Cancer Using Independent Component Analysis

(2019) Wenke Liu et al.   MOLECULAR & CELLULAR PROTEOMICS

Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets

(2019) Nicolas Sompairac et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration

(2019) Amitesh Anand et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Escherichia coli transcriptome mostly consists of independently regulated modules

(2019) Anand V. Sastry et al.   Nature Communications

A comprehensive evaluation of module detection methods for gene expression data

(2018) Wouter Saelens et al.   Nature Communications

Antibiotic-resistant bacteria show widespread collateral sensitivity to antimicrobial peptides

(2018) Viktória Lázár et al.   Nature Microbiology

A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0

(2018) Alberto Santos-Zavaleta et al.   BMC BIOLOGY

Enter the Matrix: Factorization Uncovers Knowledge from Omics

(2018) Genevieve L. Stein-O’Brien et al.   TRENDS IN GENETICS

Large-scale investigation of the reasons why potentially important genes are ignored

(2018) Thomas Stoeger et al.   PLOS BIOLOGY

ArrayExpress update – from bulk to single-cell expression data

(2018) Awais Athar et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow

(2018) Elizabeth Brunk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Why Batch Effects Matter in Omics Data, and How to Avoid Them

(2017) Wilson Wen Bin Goh et al.   TRENDS IN BIOTECHNOLOGY

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

The EcoCyc database: reflecting new knowledge aboutEscherichia coliK-12

(2016) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution

(2016) Jose Utrilla et al.   Cell Systems

Cooperative regulation of the common target genes between H2O2-sensing YedVW and Cu2+-sensing CusSR in Escherichia coli

(2015) Hiroyuki Urano et al.   MICROBIOLOGY-SGM

Repairing oxidized proteins in the bacterial envelope using respiratory chain electrons

(2015) Alexandra Gennaris et al.   NATURE

COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses: Table 1.

(2015) Marco Moretto et al.   NUCLEIC ACIDS RESEARCH

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Microbial Forensics: Predicting Phenotypic Characteristics and Environmental Conditions from Large-Scale Gene Expression Profiles

(2015) Minseung Kim et al.   PLoS Computational Biology

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

(2014) Katherine A. Hoadley et al.   CELL

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

(2014)   NATURE BIOTECHNOLOGY

Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells

(2014) Shanrong Zhao et al.   PLoS One

Quickly Finding Orthologs as Reciprocal Best Hits with BLAT, LAST, and UBLAST: How Much Do We Miss?

(2014) Natalie Ward et al.   PLoS One

Independent Component Analysis Uncovers the Landscape of the Bladder Tumor Transcriptome and Reveals Insights into Luminal and Basal Subtypes

(2014) Anne Biton et al.   Cell Reports

Determining the Control Circuitry of Redox Metabolism at the Genome-Scale

(2014) Stephen Federowicz et al.   PLoS Genetics

Coherent Functional Modules Improve Transcription Factor Target Identification, Cooperativity Prediction, and Disease Association

(2014) Konrad J. Karczewski et al.   PLoS Genetics

A comparison of methods for differential expression analysis of RNA-seq data

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

Lon protease inactivation, or translocation of thelongene, potentiate bacterial evolution to antibiotic resistance

(2013) Hervé Nicoloff et al.   MOLECULAR MICROBIOLOGY

Bacterial evolution of antibiotic hypersensitivity

(2013) V. Lazar et al.   Molecular Systems Biology

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

(2013) Peter A C 't Hoen et al.   NATURE BIOTECHNOLOGY

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Molybdenum enzymes, their maturation and molybdenum cofactor biosynthesis in Escherichia coli

(2012) Chantal Iobbi-Nivol et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Network Context and Selection in the Evolution to Enzyme Specificity

(2012) H. Nam et al.   SCIENCE

The PurR regulon in Escherichia coli K-12 MG1655

(2011) Byung-Kwan Cho et al.   NUCLEIC ACIDS RESEARCH

Deletion of Genes Encoding Cytochrome Oxidases and Quinol Monooxygenase Blocks the Aerobic-Anaerobic Shift in Escherichia coli K-12 MG1655

(2010) V. A. Portnoy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Polymyxins and their novel derivatives

(2010) Martti Vaara   CURRENT OPINION IN MICROBIOLOGY

Independent component analysis: Mining microarray data for fundamental human gene expression modules

(2010) Jesse M. Engreitz et al.   JOURNAL OF BIOMEDICAL INFORMATICS

RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media

(2010) T. M. Conrad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

A review of independent component analysis application to microarray gene expression data

(2008) Wei Kong et al.   BIOTECHNIQUES

Control of bacterial transcription, translation and replication by (p)ppGpp

(2008) Anjana Srivatsan et al.   CURRENT OPINION IN MICROBIOLOGY

Regulation of Pyrimidine Biosynthetic Gene Expression in Bacteria: Repression without Repressors

(2008) C. L. Turnbough et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH