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

The fractured landscape of RNA-seq alignment: the default in our STARs

(2018) Sara Ballouz et al.   NUCLEIC ACIDS RESEARCH

Mutant phenotypes for thousands of bacterial genes of unknown function

(2018) Morgan N. Price et al.   NATURE

Genomewide landscape of gene–metabolome associations in Escherichia coli

(2017) Tobias Fuhrer et al.   Molecular Systems Biology

Long range chromosome organization in Escherichia coli: The position of the replication origin defines the non-structured regions and the Right and Left macrodomains

(2017) Stéphane Duigou et al.   PLoS Genetics

Nontargeted in vitro metabolomics for high-throughput identification of novel enzymes in Escherichia coli

(2016) Daniel C Sévin et al.   NATURE METHODS

Determinants of tRNA Recognition by the Radical SAM Enzyme RlmN

(2016) Christina M. Fitzsimmons et al.   PLoS One

Design and synthesis of a minimal bacterial genome

(2016) C. A. Hutchison et al.   SCIENCE

Unknown unknowns: essential genes in quest for function

(2016) Antoine Danchin et al.   Microbial Biotechnology

The quantitative and condition-dependent Escherichia coli proteome

(2015) Alexander Schmidt et al.   NATURE BIOTECHNOLOGY

COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps

(2015) Yi-Chien Chang et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond

(2015) Socorro Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

Model-driven discovery of underground metabolic functions inEscherichia coli

(2015) Gabriela I. Guzmán et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Why Build Whole-Cell Models?

(2015) Javier Carrera et al.   TRENDS IN CELL BIOLOGY

EcoliNet: a database of cofunctional gene network for Escherichia coli

(2015) Hanhae Kim et al.   Database-The Journal of Biological Databases and Curation

Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale

(2014) Joanne K Liu et al.   BMC Systems Biology

The Disulfide Bonding System Suppresses CsgD-Independent Cellulose Production in Escherichia coli

(2014) D. A. Hufnagel et al.   JOURNAL OF BACTERIOLOGY

In silico assessment of the metabolic capabilities of an engineered functional reversal of the β-oxidation cycle for the synthesis of longer-chain (C≥4) products

(2014) Angela Cintolesi et al.   METABOLIC ENGINEERING

Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations

(2014) Troy E. Sandberg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

Chromosome position effects on gene expression in Escherichia coli K-12

(2014) Jack A. Bryant et al.   NUCLEIC ACIDS RESEARCH

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

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

(2014) Sang Woo Seo et al.   Nature Communications

TFpredict and SABINE: Sequence-Based Prediction of Structural and Functional Characteristics of Transcription Factors

(2013) Johannes Eichner et al.   PLoS One

Towards revealing the functions of all genes in plants

(2013) Seung Yon Rhee et al.   TRENDS IN PLANT SCIENCE

The COMBREX Project: Design, Methodology, and Initial Results

(2013) Brian P. Anton et al.   PLOS BIOLOGY

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions

(2012) Jeffrey D Orth et al.   BMC Systems Biology

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

EcoGene 3.0

(2012) Jindan Zhou et al.   NUCLEIC ACIDS RESEARCH

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

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

Engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals

(2011) Clementina Dellomonaco et al.   NATURE

Phenotypic Landscape of a Bacterial Cell

(2010) Robert J. Nichols et al.   CELL

COMBREX: a project to accelerate the functional annotation of prokaryotic genomes

(2010) R. J. Roberts et al.   NUCLEIC ACIDS RESEARCH

From complete genome sequence to ‘complete’ understanding?

(2010) Michael Y. Galperin et al.   TRENDS IN BIOTECHNOLOGY

Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins

(2009) Pingzhao Hu et al.   PLOS BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS