Multi-omic measurements of heterogeneity in HeLa cells across laboratories

Genetic and transcriptional evolution alters cancer cell line drug response

(2018) Uri Ben-David et al.   NATURE

Stem cells: the new “model organism”

(2017) David G. Drubin et al.   MOLECULAR BIOLOGY OF THE CELL

Can we predict protein from mRNA levels?

(2017) Nikolaus Fortelny et al.   NATURE

Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses

(2017) George Rosenberger et al.   NATURE METHODS

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells

(2017) Yansheng Liu et al.   Nature Communications

A novel RNA sequencing data analysis method for cell line authentication

(2017) Erik Fasterius et al.   PLoS One

A Landscape of Pharmacogenomic Interactions in Cancer

(2016) Francesco Iorio et al.   CELL

On the Dependency of Cellular Protein Levels on mRNA Abundance

(2016) Yansheng Liu et al.   CELL

21st Century Cell Culture for 21st Century Toxicology

(2016) David Pamies et al.   CHEMICAL RESEARCH IN TOXICOLOGY

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics

(2016) Hannes L Röst et al.   NATURE METHODS

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Systems proteomics of liver mitochondria function

(2016) E. G. Williams et al.   SCIENCE

Genetic variability in a frozen batch of MCF-7 cells invisible in routine authentication affecting cell function

(2016) Andre Kleensang et al.   Scientific Reports

Standards for Cell Line Authentication and Beyond

(2016) Jamie L. Almeida et al.   PLOS BIOLOGY

Autophagy Proteins Promote Repair of Endosomal Membranes Damaged by the Salmonella Type Three Secretion System 1

(2015) Saskia Kreibich et al.   Cell Host & Microbe

Quantitative variability of 342 plasma proteins in a human twin population

(2015) Y. Liu et al.   Molecular Systems Biology

A resource for cell line authentication, annotation and quality control

(2015) Mamie Yu et al.   NATURE

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Dynamic profiling of the protein life cycle in response to pathogens

(2015) M. Jovanovic et al.   SCIENCE

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

Genomic Instability of Osteosarcoma Cell Lines in Culture: Impact on the Prediction of Metastasis Relevant Genes

(2015) Roman Muff et al.   PLoS One

High variability of genomic instability and gene expression profiling in different HeLa clones

(2015) Annalisa Frattini et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Guidelines for the use of cell lines in biomedical research

(2014) R J Geraghty et al.   BRITISH JOURNAL OF CANCER

iPortal: the swiss grid proteomics portal: Requirements and new features based on experience and usability considerations

(2014) Peter Kunszt et al.   CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Fixing problems with cell lines

(2014) Jon R. Lorsch et al.   SCIENCE

Organogenesis in a dish: Modeling development and disease using organoid technologies

(2014) M. A. Lancaster et al.   SCIENCE

Endocytosis of Viruses and Bacteria

(2014) P. Cossart et al.   Cold Spring Harbor Perspectives in Biology

Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations

(2014) Yao-Cheng Lin et al.   Nature Communications

Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast

(2014) Noah Dephoure et al.   eLife

A repository of assays to quantify 10,000 human proteins by SWATH-MS

(2014) George Rosenberger et al.   Scientific Data

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line

(2013) Andrew Adey et al.   NATURE

Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system

(2013) Ben C Collins et al.   NATURE METHODS

The Genomic and Transcriptomic Landscape of a HeLa Cell Line

(2013) Jonathan J. M. Landry et al.   G3-Genes Genomes Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Proteome Dynamics: Revisiting Turnover with a Global Perspective

(2012) Amy J. Claydon et al.   MOLECULAR & CELLULAR PROTEOMICS

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells

(2012) Silvia Stingele et al.   Molecular Systems Biology

Near Surface Swimming of Salmonella Typhimurium Explains Target-Site Selection and Cooperative Invasion

(2012) Benjamin Misselwitz et al.   PLoS Pathogens

Screening the human exome: a comparison of whole genome and whole transcriptome sequencing

(2012) Elizabeth T Cirulli et al.   GENOME BIOLOGY

Assembly and Initial Characterization of a Panel of 85 Genomically Validated Cell Lines from Diverse Head and Neck Tumor Sites

(2011) M. Zhao et al.   CLINICAL CANCER RESEARCH

Analysis of the host microRNA response toSalmonellauncovers the control of major cytokines by thelet-7family

(2011) Leon N Schulte et al.   EMBO JOURNAL

Estimation of Absolute Protein Quantities of Unlabeled Samples by Selected Reaction Monitoring Mass Spectrometry

(2011) Christina Ludwig et al.   MOLECULAR & CELLULAR PROTEOMICS

A Quantitative Spatial Proteomics Analysis of Proteome Turnover in Human Cells

(2011) François-Michel Boisvert et al.   MOLECULAR & CELLULAR PROTEOMICS

iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates

(2011) David Shteynberg et al.   MOLECULAR & CELLULAR PROTEOMICS

A Protein Epitope Signature Tag (PrEST) Library Allows SILAC-based Absolute Quantification and Multiplexed Determination of Protein Copy Numbers in Cell Lines

(2011) Marlis Zeiler et al.   MOLECULAR & CELLULAR PROTEOMICS

RNAi screen of Salmonella invasion shows role of COPI in membrane targeting of cholesterol and Cdc42

(2011) B. Misselwitz et al.   Molecular Systems Biology

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Check your cultures! A list of cross-contaminated or misidentified cell lines

(2010) Amanda Capes-Davis et al.   INTERNATIONAL JOURNAL OF CANCER

Defining the transcriptome and proteome in three functionally different human cell lines

(2010) Emma Lundberg et al.   Molecular Systems Biology

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

CORUM: the comprehensive resource of mammalian protein complexes—2009

(2009) Andreas Ruepp et al.   NUCLEIC ACIDS RESEARCH

The let-7 family of microRNAs

(2008) Sarah Roush et al.   TRENDS IN CELL BIOLOGY