The functional proteome landscape of Escherichia coli

Thermal proteome profiling for interrogating protein interactions

(2020) André Mateus et al.   Molecular Systems Biology

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

(2019) Sankha Ghatak et al.   NUCLEIC ACIDS RESEARCH

Global Genetic Networks and the Genotype-to-Phenotype Relationship

(2019) Michael Costanzo et al.   CELL

Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals

(2019) Natalie Romanov et al.   CELL

Rapid accumulation of motility-activating mutations in resting liquid culture of Escherichia coli

(2019) Darren J. Parker et al.   JOURNAL OF BACTERIOLOGY

High throughput discovery of functional protein modifications by Hotspot Thermal Profiling

(2019) Jun X. Huang et al.   NATURE METHODS

Co-regulation map of the human proteome enables identification of protein functions

(2019) Georg Kustatscher et al.   NATURE BIOTECHNOLOGY

Evolutionary Convergence of Pathway-Specific Enzyme Expression Stoichiometry

(2018) Jean-Benoît Lalanne et al.   CELL

Pervasive Protein Thermal Stability Variation during the Cell Cycle

(2018) Isabelle Becher et al.   CELL

Thermal proteome profiling in bacteria: probing protein state in vivo

(2018) André Mateus et al.   Molecular Systems Biology

Thermal proximity coaggregation for system-wide profiling of protein complex dynamics in cells

(2018) Chris Soon Heng Tan et al.   SCIENCE

Mutant phenotypes for thousands of bacterial genes of unknown function

(2018) Morgan N. Price et al.   NATURE

Single-pot, solid-phase-enhanced sample preparation for proteomics experiments

(2018) Christopher S. Hughes et al.   Nature Protocols

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors

(2018) François Rousset et al.   PLoS Genetics

In situ genotyping of a pooled strain library after characterizing complex phenotypes

(2017) Michael J Lawson et al.   Molecular Systems Biology

High‐throughput CRISPRi phenotyping identifies new essential genes in Streptococcus pneumoniae

(2017) Xue Liu et al.   Molecular Systems Biology

Global landscape of cell envelope protein complexes in Escherichia coli

(2017) Mohan Babu et al.   NATURE BIOTECHNOLOGY

Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis

(2017) Byoung-Mo Koo et al.   Cell Systems

A tool named Iris for versatile high-throughput phenotyping in microorganisms

(2017) George Kritikos et al.   Nature Microbiology

A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria

(2016) Jason M. Peters et al.   CELL

Thermal profiling reveals phenylalanine hydroxylase as an off-target of panobinostat

(2016) Isabelle Becher et al.   Nature Chemical Biology

The EcoCyc database: reflecting new knowledge aboutEscherichia coliK-12

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

Thermal proteome profiling: unbiased assessment of protein state through heat-induced stability changes

(2016) André Mateus et al.   Proteome Science

A global genetic interaction network maps a wiring diagram of cellular function

(2016) M. Costanzo et al.   SCIENCE

A Chemical-Genomic Screen of Neglected Antibiotics Reveals Illicit Transport of Kasugamycin and Blasticidin S

(2016) Anthony L. Shiver et al.   PLoS Genetics

Panorama of ancient metazoan macromolecular complexes

(2015) Cuihong Wan et al.   NATURE

Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry

(2015) Holger Franken et al.   Nature Protocols

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Coordination of peptidoglycan synthesis and outer membrane constriction during Escherichia coli cell division

(2015) Andrew N Gray et al.   eLife

Ion Coalescence of Neutron Encoded TMT 10-Plex Reporter Ions

(2014) Thilo Werner et al.   ANALYTICAL CHEMISTRY

Proteome-wide Subcellular Topologies ofE. coliPolypeptides Database (STEPdb)

(2014) Georgia Orfanoudaki et al.   MOLECULAR & CELLULAR PROTEOMICS

Ultrasensitive proteome analysis using paramagnetic bead technology

(2014) C. S. Hughes et al.   Molecular Systems Biology

GenoBase: comprehensive resource database of Escherichia coli K-12

(2014) Yuta Otsuka et al.   NUCLEIC ACIDS RESEARCH

Tracking cancer drugs in living cells by thermal profiling of the proteome

(2014) M. M. Savitski et al.   SCIENCE

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

A Lipid E-MAP Identifies Ubx2 as a Critical Regulator of Lipid Saturation and Lipid Bilayer Stress

(2013) Michal A. Surma et al.   MOLECULAR CELL

Monitoring Drug Target Engagement in Cells and Tissues Using the Cellular Thermal Shift Assay

(2013) D. M. Molina et al.   SCIENCE

Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present

(2012) Marcus Bantscheff et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

A Census of Human Soluble Protein Complexes

(2012) Pierre C. Havugimana et al.   CELL

The twin-arginine translocation (Tat) protein export pathway

(2012) Tracy Palmer et al.   NATURE REVIEWS MICROBIOLOGY

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

Quantitative Genetic Interactions Reveal Biological Modularity

(2010) Pedro Beltrao et al.   CELL

Regulation of Peptidoglycan Synthesis by Outer-Membrane Proteins

(2010) Athanasios Typas et al.   CELL

Phenotypic Landscape of a Bacterial Cell

(2010) Robert J. Nichols et al.   CELL

Contact-dependent growth inhibition requires the essential outer membrane protein BamA (YaeT) as the receptor and the inner membrane transport protein AcrB

(2008) Stephanie K. Aoki et al.   MOLECULAR MICROBIOLOGY