Genome-wide base editor screen identifies regulators of protein abundance in yeast

Massively parallel assessment of human variants with base editor screens

(2021) Ruth E. Hanna et al.   CELL

Functional interrogation of DNA damage response variants with base editing screens

(2021) Raquel Cuella-Martin et al.   CELL

A Robust Method for Packing High Resolution C18 RP-nano-HPLC Columns

(2021) Yasaman Jami-Alahmadi et al.   Jove-Journal of Visualized Experiments

A new era in functional genomics screens

(2021) Laralynne Przybyla et al.   NATURE REVIEWS GENETICS

Towards a comprehensive catalogue of validated and target-linked human enhancers

(2020) Molly Gasperini et al.   NATURE REVIEWS GENETICS

Multiple Alternative Carbon Pathways Combine To Promote Candida albicans Stress Resistance, Immune Interactions, and Virulence

(2020) Robert B. Williams et al.   mBio

Perturbing proteomes at single residue resolution using base editing

(2020) Philippe C. Després et al.   Nature Communications

Determinants of Base Editing Outcomes from Target Library Analysis and Machine Learning

(2020) Mandana Arbab et al.   CELL

Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors

(2020) Andrew V. Anzalone et al.   NATURE BIOTECHNOLOGY

Sequence-specific prediction of the efficiencies of adenine and cytosine base editors

(2020) Myungjae Song et al.   NATURE BIOTECHNOLOGY

mRNAs, proteins and the emerging principles of gene expression control

(2020) Christopher Buccitelli et al.   NATURE REVIEWS GENETICS

The BioGRID database: A comprehensive biomedical resource of curated protein, genetic and chemical interactions

(2020) Rose Oughtred et al.   PROTEIN SCIENCE

The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets

(2020) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

CRISPResso2 provides accurate and rapid genome editing sequence analysis

(2019) Kendell Clement et al.   NATURE BIOTECHNOLOGY

Massively Parallel Assays and Quantitative Sequence–Function Relationships

(2019) Justin B. Kinney et al.   Annual Review of Genomics and Human Genetics

DNA variants affecting the expression of numerous genes in trans have diverse mechanisms of action and evolutionary histories

(2019) Sheila Lutz et al.   PLoS Genetics

The formation of hybrid complexes between isoenzymes of glyceraldehyde‐3‐phosphate dehydrogenase regulates its aggregation state, the glycolytic activity and sphingolipid status inSaccharomyces cerevisiae

(2019) Francisca Randez‐Gil et al.   Microbial Biotechnology

Highly parallel genome variant engineering with CRISPR–Cas9

(2018) Meru J. Sadhu et al.   NATURE GENETICS

Genetics of trans-regulatory variation in gene expression

(2018) Frank Wolfgang Albert et al.   eLife

Unification of Protein Abundance Datasets Yields a Quantitative Saccharomyces cerevisiae Proteome

(2018) Brandon Ho et al.   Cell Systems

Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data

(2018) Nadezhda T. Doncheva et al.   JOURNAL OF PROTEOME RESEARCH

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening

(2017) Julia Joung et al.   Nature Protocols

Fructose-1,6-bisphosphate couples glycolytic flux to activation of Ras

(2017) Ken Peeters et al.   Nature Communications

Deconstruction of the Ras switching cycle through saturation mutagenesis

(2017) Pradeep Bandaru et al.   eLife

CRISPRpred: A flexible and efficient tool for sgRNAs on-target activity prediction in CRISPR/Cas9 systems

(2017) Md. Khaledur Rahman et al.   PLoS One

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

(2016) Diego Adhemar Jaitin et al.   CELL

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

(2016) Britt Adamson et al.   CELL

On the Dependency of Cellular Protein Levels on mRNA Abundance

(2016) Yansheng Liu et al.   CELL

A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy

(2016) Rohith Srivas et al.   MOLECULAR CELL

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

(2016) Alexis C. Komor et al.   NATURE

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

(2016) M. Costanzo et al.   SCIENCE

Robust Extracellular pH Modulation by Candida albicans during Growth in Carboxylic Acids

(2016) Heather A. Danhof et al.   mBio

Lollipops in the Clinic: Information Dense Mutation Plots for Precision Medicine

(2016) Jeremy J. Jay et al.   PLoS One

Targeting cellular mRNAs translation by CRISPR-Cas9

(2016) Yuchen Liu et al.   Scientific Reports

Quantitative Analysis of Proteome and Lipidome Dynamics Reveals Functional Regulation of Global Lipid Metabolism

(2015) Albert Casanovas et al.   CHEMISTRY & BIOLOGY

Comprehensive Temporal Protein Dynamics during the Diauxic Shift inSaccharomyces cerevisiae

(2015) J. Patrick Murphy et al.   MOLECULAR & CELLULAR PROTEOMICS

GFP Loss-of-Function Mutations in Arabidopsis thaliana

(2015) Jason L. Fu et al.   G3-Genes Genomes Genetics

MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments

(2014) Meena Choi et al.   BIOINFORMATICS

Large-Scale Genetic Perturbations Reveal Regulatory Networks and an Abundance of Gene-Specific Repressors

(2014) Patrick Kemmeren et al.   CELL

Subunit Architecture and Functional Modular Rearrangements of the Transcriptional Mediator Complex

(2014) Kuang-Lei Tsai et al.   CELL

Genetics of single-cell protein abundance variation in large yeast populations

(2014) Frank W. Albert et al.   NATURE

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

A sentinel protein assay for simultaneously quantifying cellular processes

(2014) Martin Soste et al.   NATURE METHODS

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

(2013) Lei S. Qi et al.   CELL

Regulation of histone gene transcription in yeast

(2013) Christoph F. Kurat et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

A conserved Mediator–CDK8 kinase module association regulates Mediator–RNA polymerase II interaction

(2013) Kuang-Lei Tsai et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems

(2013) James E. DiCarlo et al.   NUCLEIC ACIDS RESEARCH

Yeast Tdh3 (Glyceraldehyde 3-Phosphate Dehydrogenase) Is a Sir2-Interacting Factor That Regulates Transcriptional Silencing and rDNA Recombination

(2013) Alison E. Ringel et al.   PLoS Genetics

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics

(2011) R. Costenoble et al.   Molecular Systems Biology

Systems Genetics

(2011) J. H. Nadeau et al.   SCIENCE

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

Nutrient signals driving cell growth

(2008) Reinhard Dechant et al.   CURRENT OPINION IN CELL BIOLOGY

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

A One Pot, One Step, Precision Cloning Method with High Throughput Capability

(2008) Carola Engler et al.   PLoS One

Gene–Environment Interaction in Yeast Gene Expression

(2008) Erin N Smith et al.   PLOS BIOLOGY

The role of the yeast plasma membrane SPS nutrient sensor in the metabolic response to extracellular amino acids

(2003) Hanna Forsberg et al.   MOLECULAR MICROBIOLOGY