Simultaneous quantification of mRNA and protein in single cells reveals post-transcriptional effects of genetic variation

Keeping the Proportions of Protein Complex Components in Check

(2020) James Christopher Taggart et al.   Cell Systems

Gene expression networks in the Drosophila Genetic Reference Panel

(2020) Logan J. Everett et al.   GENOME RESEARCH

Pervasive phenotypic impact of a large non-recombining introgressed region in yeast

(2020) Christian Brion et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide pQTL analysis of protein expression regulatory networks in the human liver

(2020) Bing He et al.   BMC BIOLOGY

mRNAs, proteins and the emerging principles of gene expression control

(2020) Christopher Buccitelli et al.   NATURE REVIEWS GENETICS

Population-scale proteome variation in human induced pluripotent stem cells

(2020) Bogdan Andrei Mirauta et al.   eLife

Sensitive high-throughput single-cell RNA-seq reveals within-clonal transcript correlations in yeast populations

(2019) Mariona Nadal-Ribelles et al.   Nature Microbiology

Multiplex RNA single molecule FISH of inducible mRNAs in single yeast cells

(2019) Guoliang Li et al.   Scientific Data

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

Rare variants contribute disproportionately to quantitative trait variation in yeast

(2019) Joshua S Bloom et al.   eLife

Extensive impact of low-frequency variants on the phenotypic landscape at population-scale

(2019) Téo Fournier et al.   eLife

Genetics of trans-regulatory variation in gene expression

(2018) Frank Wolfgang Albert et al.   eLife

Genomic atlas of the human plasma proteome

(2018) Benjamin B. Sun et al.   NATURE

Co-regulatory networks of human serum proteins link genetics to disease

(2018) Valur Emilsson et al.   SCIENCE

Genome‐wide mapping of plasma protein QTLs identifies putatively causal genes and pathways for cardiovascular disease

(2018) Chen Yao et al.   Nature Communications

GWAS and eQTL analysis identifies a SNP associated with both residual feed intake and GFRA2 expression in beef cattle

(2018) Marc G. Higgins et al.   Scientific Reports

Non-invasive measurement of mRNA decay reveals translation initiation as the major determinant of mRNA stability

(2018) Leon Y Chan et al.   eLife

ClampFISH detects individual nucleic acid molecules using click chemistry–based amplification

(2018) Sara H Rouhanifard et al.   NATURE BIOTECHNOLOGY

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

mRNA detection in budding yeast with single fluorophores

(2017) Gable M. Wadsworth et al.   NUCLEIC ACIDS RESEARCH

RNA-guided transcriptional activation via CRISPR/dCas9 mimics overexpression phenotypes in Arabidopsis

(2017) Jong-Jin Park et al.   PLoS One

High-resolution mapping ofcis-regulatory variation in budding yeast

(2017) Ryosuke Kita et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Highly motif- and organism-dependent effects of naturally occurring hammerhead ribozyme sequences on gene expression

(2017) Lena A. Wurmthaler et al.   RNA Biology

Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress

(2017) Audrey P. Gasch et al.   PLOS BIOLOGY

Defining the consequences of genetic variation on a proteome-wide scale

(2016) Joel M. Chick et al.   NATURE

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Single-cell RNA-sequencing: The future of genome biology is now

(2016) Simone Picelli   RNA Biology

Systems proteomics of liver mitochondria function

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

Natural gene expression variation studies in yeast

(2016) Dawn A. Thompson et al.   YEAST

Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes

(2016) Yehudit Hasin-Brumshtein et al.   eLife

Regulation of transcriptionally active genes via the catalytically inactive Cas9 in C. elegans and D. rerio

(2015) Lijiang Long et al.   CELL RESEARCH

Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans

(2015) Can Cenik et al.   GENOME RESEARCH

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

(2015) Silvana Konermann et al.   NATURE

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

Genetic basis of transcriptome diversity inDrosophila melanogaster

(2015) Wen Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accounting for Experimental Noise Reveals That mRNA Levels, Amplified by Post-Transcriptional Processes, Largely Determine Steady-State Protein Levels in Yeast

(2015) Gábor Csárdi et al.   PLoS Genetics

Systematic Dissection of the Sequence Determinants of Gene 3’ End Mediated Expression Control

(2015) Ophir Shalem et al.   PLoS Genetics

Identification and Validation of Genetic Variants that Influence Transcription Factor and Cell Signaling Protein Levels

(2014) Ronald J. Hause et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RNA-seq: impact of RNA degradation on transcript quantification

(2014) Irene Gallego Romero et al.   BMC BIOLOGY

Allele-specific expression and eQTL analysis in mouse adipose tissue

(2014) Yehudit Hasin-Brumshtein et al.   BMC GENOMICS

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

Genetic Architecture of Ethanol-Responsive Transcriptome Variation in Saccharomyces cerevisiae Strains

(2014) Jeffrey A. Lewis et al.   GENETICS

Heritability and genetic basis of protein level variation in an outbred population

(2014) Leopold Parts et al.   GENOME RESEARCH

Tempo and mode of regulatory evolution in Drosophila

(2014) J. D. Coolon et al.   GENOME RESEARCH

Natural genetic variation impacts expression levels of coding, non-coding, and antisense transcripts in fission yeast

(2014) M. Clement-Ziza et al.   Molecular Systems Biology

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

(2014) Frank W. Albert et al.   NATURE

Heritability and genomics of gene expression in peripheral blood

(2014) Fred A Wright et al.   NATURE GENETICS

Impact of regulatory variation from RNA to protein

(2014) A. Battle et al.   SCIENCE

Single  -Actin mRNA Detection in Neurons Reveals a Mechanism for Regulating Its Translatability

(2014) A. R. Buxbaum et al.   SCIENCE

The new frontier of genome engineering with CRISPR-Cas9

(2014) J. A. Doudna et al.   SCIENCE

Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells

(2014) M. N. Lee et al.   SCIENCE

Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression

(2014) B. P. Fairfax et al.   SCIENCE

Genetic Influences on Translation in Yeast

(2014) Frank W. Albert et al.   PLoS Genetics

The molecular basis of phenotypic variation in yeast

(2013) Justin C Fay   CURRENT OPINION IN GENETICS & DEVELOPMENT

Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast

(2013) D. A. Skelly et al.   GENOME RESEARCH

Self-processing of ribozyme-flanked RNAs into guide RNAsin vitroandin vivofor CRISPR-mediated genome editing

(2013) Yangbin Gao et al.   Journal of Integrative Plant Biology

A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis

(2013) Paola Picotti et al.   NATURE

Variation and genetic control of protein abundance in humans

(2013) Linfeng Wu et al.   NATURE

Finding the sources of missing heritability in a yeast cross

(2013) Joshua S. Bloom et al.   NATURE

CRISPR RNA–guided activation of endogenous human genes

(2013) Morgan L Maeder et al.   NATURE METHODS

Expression of carnitine palmitoyl-CoA transferase-1B is influenced by a cis-acting eQTL in two chicken lines selected for high and low body weight

(2013) Sojeong Ka et al.   PHYSIOLOGICAL GENOMICS

RNA sequencing reveals the complex regulatory network in the maize kernel

(2013) Junjie Fu et al.   Nature Communications

Tunable and Multifunctional Eukaryotic Transcription Factors Based on CRISPR/Cas

(2013) Fahim Farzadfard et al.   ACS Synthetic Biology

Mapping cis- and trans-regulatory effects across multiple tissues in twins

(2012) Elin Grundberg et al.   NATURE GENETICS

Rare and common variants: twenty arguments

(2012) Greg Gibson   NATURE REVIEWS GENETICS

Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast

(2012) R. Scott McIsaac et al.   NUCLEIC ACIDS RESEARCH

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

THE QTN PROGRAM AND THE ALLELES THAT MATTER FOR EVOLUTION: ALL THAT'S GOLD DOES NOT GLITTER

(2011) Matthew V. Rockman   EVOLUTION

Genetic architecture of regulatory variation in Arabidopsis thaliana

(2011) X. Zhang et al.   GENOME RESEARCH

Genetic Variation Shapes Protein Networks Mainly through Non-transcriptional Mechanisms

(2011) Eric J. Foss et al.   PLOS BIOLOGY

Trait Variation in Yeast Is Defined by Population History

(2011) Jonas Warringer et al.   PLoS Genetics

Comparative Analysis of Proteome and Transcriptome Variation in Mouse

(2011) Anatole Ghazalpour et al.   PLoS Genetics

Regulatory divergence in Drosophila revealed by mRNA-seq

(2010) C. J. McManus et al.   GENOME RESEARCH

Genome-wide gene expression regulation as a function of genotype and age in C. elegans

(2010) A. Vinuela et al.   GENOME RESEARCH

Natural selection on cis and trans regulation in yeasts

(2010) J. J. Emerson et al.   GENOME RESEARCH

Dissection of genetically complex traits with extremely large pools of yeast segregants

(2010) Ian M. Ehrenreich et al.   NATURE

Genetic architecture of a complex trait and its implications for fitness and genome-wide association studies

(2010) A. Eyre-Walker   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

flowCore: a Bioconductor package for high throughput flow cytometry

(2009) Florian Hahne et al.   BMC BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

System-wide molecular evidence for phenotypic buffering in Arabidopsis

(2009) Jingyuan Fu et al.   NATURE GENETICS

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Expression Quantitative Trait Loci Are Highly Sensitive to Cellular Differentiation State

(2009) Alice Gerrits et al.   PLoS Genetics

Comparison of drug transporter gene expression and functionality in Caco-2 cells from 10 different laboratories

(2008) Rose Hayeshi et al.   EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES

Yeast Yak1 kinase, a bridge between PKA and stress-responsive transcription factors, Hsf1 and Msn2/Msn4

(2008) Peter Lee et al.   MOLECULAR MICROBIOLOGY

Gene–Environment Interaction in Yeast Gene Expression

(2008) Erin N Smith et al.   PLOS BIOLOGY