Systematic identification of factors mediating accelerated mRNA degradation in response to changes in environmental nitrogen

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

The Stress Granule Transcriptome Reveals Principles of mRNA Accumulation in Stress Granules

(2017) Anthony Khong et al.   MOLECULAR CELL

Sort-seq under the hood: implications of design choices on large-scale characterization of sequence-function relations

(2016) Neil Peterman et al.   BMC GENOMICS

General Amino Acid Control and 14-3-3 Proteins Bmh1/2 Are Required for Nitrogen Catabolite Repression-Sensitive Regulation of Gln3 and Gat1 Localization

(2016) Jennifer J. Tate et al.   GENETICS

Steady-state and dynamic gene expression programs in Saccharomyces cerevisiae in response to variation in environmental nitrogen

(2016) Edoardo M. Airoldi et al.   MOLECULAR BIOLOGY OF THE CELL

Growth rate controls mRNA turnover in steady and non-steady states

(2016) José García-Martínez et al.   RNA Biology

Barcode Sequencing Screen Identifies SUB1 as a Regulator of Yeast Pheromone Inducible Genes

(2016) Anna Sliva et al.   G3-Genes Genomes Genetics

Dynamical Allocation of Cellular Resources as an Optimal Control Problem: Novel Insights into Microbial Growth Strategies

(2016) Nils Giordano et al.   PLoS Computational Biology

General Amino Acid Control and 14-3-3 Proteins Bmh1/2 Are Required for Nitrogen Catabolite Repression-Sensitive Regulation of Gln3 and Gat1 Localization

(2016) Jennifer J. Tate et al.   GENETICS

Impact of high pH stress on yeast gene expression: A comprehensive analysis of mRNA turnover during stress responses

(2015) David Canadell et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Codon Optimality Is a Major Determinant of mRNA Stability

(2015) Vladimir Presnyak et al.   CELL

Snf1-Dependent Transcription Confers Glucose-Induced Decay upon the mRNA Product

(2015) Katherine A. Braun et al.   MOLECULAR AND CELLULAR BIOLOGY

Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry

(2015) Erin E. Duffy et al.   MOLECULAR CELL

Glucose-Regulated Phosphorylation of the PUF Protein Puf3 Regulates the Translational Fate of Its Bound mRNAs and Association with RNA Granules

(2015) Chien-Der Lee et al.   Cell Reports

Genome-Wide Analysis of the TORC1 and Osmotic Stress Signaling Network in Saccharomyces cerevisiae

(2015) Jeremy Worley et al.   G3-Genes Genomes Genetics

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

The Yeast Deletion Collection: A Decade of Functional Genomics

(2014) Guri Giaever et al.   GENETICS

Transcriptional profiling of cells sorted by RNA abundance

(2014) Sandy Klemm et al.   NATURE METHODS

Genome-wide identification of transcript start and end sites by transcript isoform sequencing

(2014) Vicent Pelechano et al.   Nature Protocols

Determination of in vivo RNA kinetics using RATE-seq

(2014) Benjamin Neymotin et al.   RNA

Phosphoproteomic analysis identifies proteins involved in transcription-coupled mRNA decay as targets of Snf1 signaling

(2014) K. A. Braun et al.   Science Signaling

Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection

(2014) Benjamin VanderSluis et al.   GENOME BIOLOGY

Gene Expression Is Circular: Factors for mRNA Degradation Also Foster mRNA Synthesis

(2013) Gal Haimovich et al.   CELL

Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing

(2013) J. A. Arribere et al.   GENOME RESEARCH

Five Conditions Commonly Used to Down-regulate Tor Complex 1 Generate Different Physiological Situations Exhibiting Distinct Requirements and Outcomes

(2013) Jennifer J. Tate et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Eukaryotic mRNA Decay: Methodologies, Pathways, and Links to Other Stages of Gene Expression

(2013) José E. Pérez-Ortín et al.   JOURNAL OF MOLECULAR BIOLOGY

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Detection of Low Abundance RNA Molecules in Individual Cells by Flow Cytometry

(2013) Mary Beth Hanley et al.   PLoS One

Architecture of the Lsm1-7-Pat1 Complex: A Conserved Assembly in Eukaryotic mRNA Turnover

(2013) Humayun Sharif et al.   Cell Reports

Glucose, Nitrogen, and Phosphate Repletion in Saccharomyces cerevisiae : Common Transcriptional Responses to Different Nutrient Signals

(2013) Michael K. Conway et al.   G3-Genes Genomes Genetics

Design and Analysis of Bar-seq Experiments

(2013) David G. Robinson et al.   G3-Genes Genomes Genetics

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae

(2013) Mallory A Freeberg et al.   GENOME BIOLOGY

RNA Degradation in Saccharomyces cerevisae

(2012) Roy Parker   GENETICS

The AMP-activated Protein Kinase Snf1 Regulates Transcription Factor Binding, RNA Polymerase II Activity, and mRNA Stability of Glucose-repressed Genes inSaccharomyces cerevisiae

(2012) Elton T. Young et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Internal Amino Acids Promote Gap1 Permease Ubiquitylation via TORC1/Npr1/14-3-3-Dependent Control of the Bul Arrestin-Like Adaptors

(2012) A. Merhi et al.   MOLECULAR AND CELLULAR BIOLOGY

Scd6 Targets eIF4G to Repress Translation: RGG Motif Proteins as a Class of eIF4G-Binding Proteins

(2012) Purusharth Rajyaguru et al.   MOLECULAR CELL

Systematic discovery of structural elements governing stability of mammalian messenger RNAs

(2012) Hani Goodarzi et al.   NATURE

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

A complex ‘mRNA degradation code’ controls gene expression during animal development

(2012) Claudio R. Alonso   TRENDS IN GENETICS

DECOD: fast and accurate discriminative DNA motif finding

(2011) Peter Huggins et al.   BIOINFORMATICS

Single-Molecule mRNA Decay Measurements Reveal Promoter- Regulated mRNA Stability in Yeast

(2011) Tatjana Trcek et al.   CELL

Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay

(2011) Sarah E. Munchel et al.   MOLECULAR BIOLOGY OF THE CELL

The cAMP-Dependent Protein Kinase Signaling Pathway Is a Key Regulator of P Body Foci Formation

(2011) Vidhya Ramachandran et al.   MOLECULAR CELL

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast

(2011) C. Miller et al.   Molecular Systems Biology

Heat Shock Response in Yeast Involves Changes in Both Transcription Rates and mRNA Stabilities

(2011) Laia Castells-Roca et al.   PLoS One

Counting individual DNA molecules by the stochastic attachment of diverse labels

(2011) G. K. Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antagonistic gene transcripts regulate adaptation to new growth environments

(2011) B. L. Baumgartner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

Nutrients and the Pkh1/2 and Pkc1 Protein Kinases Control mRNA Decay and P-body Assembly in Yeast

(2010) Guangzuo Luo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cost of Unneeded Proteins in E. coli Is Reduced after Several Generations in Exponential Growth

(2010) Irit Shachrai et al.   MOLECULAR CELL

Initiation of the TORC1-Regulated G0 Program Requires Igo1/2, which License Specific mRNAs to Evade Degradation via the 5′-3′ mRNA Decay Pathway

(2010) Nicolas Talarek et al.   MOLECULAR CELL

Decapping Activators in Saccharomyces cerevisiae Act by Multiple Mechanisms

(2010) Tracy Nissan et al.   MOLECULAR CELL

Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence

(2010) J. B. Kinney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure

(2010) X. Li et al.   RNA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Quantitative phenotyping via deep barcode sequencing

(2009) A. M. Smith et al.   GENOME RESEARCH

Specific and global regulation of mRNA stability during osmotic stress in Saccharomyces cerevisiae

(2009) L. Romero-Santacreu et al.   RNA

A Genome-Wide Screen for Regulators of TORC1 in Response to Amino Acid Starvation Reveals a Conserved Npr2/3 Complex

(2009) Taavi K. Neklesa et al.   PLoS Genetics

Comprehensive Transcriptional Analysis of the Oxidative Response in Yeast

(2008) María Micaela Molina-Navarro et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation

(2008) Ophir Shalem et al.   Molecular Systems Biology

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast

(2007) Matthew J. Brauer et al.   MOLECULAR BIOLOGY OF THE CELL