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

Autonomous Metabolic Oscillations Robustly Gate the Early and Late Cell Cycle

(2017) Alexandros Papagiannakis et al.   MOLECULAR CELL

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance

(2017) Sydney M. Shaffer et al.   NATURE

SCnorm: robust normalization of single-cell RNA-seq data

(2017) Rhonda Bacher et al.   NATURE METHODS

Batch effects and the effective design of single-cell gene expression studies

(2017) Po-Yuan Tung et al.   Scientific Reports

Persistence to anti-cancer treatments in the stationary to proliferating transition

(2016) Sivan Pearl Mizrahi et al.   CELL CYCLE

Encoding four gene expression programs in the activation dynamics of a single transcription factor

(2016) Anders S. Hansen et al.   CURRENT BIOLOGY

Cellular Heterogeneity: Benefits Besides Bet-Hedging

(2016) Sasha F. Levy   CURRENT BIOLOGY

Cell cycle Start is coupled to entry into the yeast metabolic cycle across diverse strains and growth rates

(2016) Anthony J. Burnetti et al.   MOLECULAR BIOLOGY OF THE CELL

Cyclin-Dependent Kinase Co-Ordinates Carbohydrate Metabolism and Cell Cycle in S. cerevisiae

(2016) Gang Zhao et al.   MOLECULAR CELL

The Yeast Cyclin-Dependent Kinase Routes Carbon Fluxes to Fuel Cell Cycle Progression

(2016) Jennifer C. Ewald et al.   MOLECULAR CELL

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

(2016) Jean Fan et al.   NATURE METHODS

Schedule-dependent interaction between anticancer treatments

(2016) Sheng-hong Chen et al.   SCIENCE

Affinity and competition for TBP are molecular determinants of gene expression noise

(2016) Charles N. J. Ravarani et al.   Nature Communications

Dynamic control of gene regulatory logic by seemingly redundant transcription factors

(2016) Zohreh AkhavanAghdam et al.   eLife

Exploiting the yeast stress-activated signaling network to inform on stress biology and disease signaling

(2015) Yi-Hsuan Ho et al.   CURRENT GENETICS

Molecular mechanisms of ribosomal protein gene coregulation

(2015) Rohit Reja et al.   GENES & DEVELOPMENT

Hog1 Targets Whi5 and Msa1 Transcription Factors To Downregulate Cyclin Expression upon Stress

(2015) Alberto González-Novo et al.   MOLECULAR AND CELLULAR BIOLOGY

Combinatorial gene regulation by modulation of relative pulse timing

(2015) Yihan Lin et al.   NATURE

Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments

(2015) Ning Leng et al.   NATURE METHODS

Slow-growing cells within isogenic populations have increased RNA polymerase error rates and DNA damage

(2015) David van Dijk et al.   Nature Communications

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression

(2015) Jong Kyoung Kim et al.   Nature Communications

cis Determinants of Promoter Threshold and Activation Timescale

(2015) Anders S. Hansen et al.   Cell Reports

Pulsatile Dynamics in the Yeast Proteome

(2014) Chiraj K. Dalal et al.   CURRENT BIOLOGY

Cell cycle population effects in perturbation studies

(2014) E. O'Duibhir et al.   Molecular Systems Biology

Pathway connectivity and signaling coordination in the yeast stress-activated signaling network

(2014) D. Chasman et al.   Molecular Systems Biology

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Msn2 Coordinates a Stoichiometric Gene Expression Program

(2013) Jacob Stewart-Ornstein et al.   CURRENT BIOLOGY

From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing

(2013) G. K. Marinov et al.   GENOME RESEARCH

Balanced Production of Ribosome Components Is Required for Proper G1/S Transition inSaccharomyces cerevisiae

(2013) Fernando Gómez-Herreros et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Noise and interlocking signaling pathways promote distinct transcription factor dynamics in response to different stresses

(2013) Natalia Petrenko et al.   MOLECULAR BIOLOGY OF THE CELL

Promoter decoding of transcription factor dynamics involves a trade-off between noise and control of gene expression

(2013) A. S. Hansen et al.   Molecular Systems Biology

Tunable Signal Processing Through Modular Control of Transcription Factor Translocation

(2013) N. Hao et al.   SCIENCE

Characterization of the p53 Cistrome – DNA Binding Cooperativity Dissects p53's Tumor Suppressor Functions

(2013) Katharina Schlereth et al.   PLoS Genetics

Dynamic Changes in Nucleosome Occupancy Are Not Predictive of Gene Expression Dynamics but Are Linked to Transcription and Chromatin Regulators

(2012) D. J. Huebert et al.   MOLECULAR AND CELLULAR BIOLOGY

Cellular Noise Regulons Underlie Fluctuations in Saccharomyces cerevisiae

(2012) Jacob Stewart-Ornstein et al.   MOLECULAR CELL

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Cdc28 kinase activity regulates the basal transcription machinery at a subset of genes

(2012) P. Chymkowitch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

p53 Dynamics Control Cell Fate

(2012) J. E. Purvis et al.   SCIENCE

Bet Hedging in Yeast by Heterogeneous, Age-Correlated Expression of a Stress Protectant

(2012) Sasha F. Levy et al.   PLOS BIOLOGY

Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L

(2011) Alexandre Huber et al.   EMBO JOURNAL

Proteasomal degradation of Sfp1 contributes to the repression of ribosome biogenesis during starvation and is mediated by the proteasome activator Blm10

(2011) Antonio Diaz Lopez et al.   MOLECULAR BIOLOGY OF THE CELL

Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast

(2011) Nikolai Slavov et al.   MOLECULAR BIOLOGY OF THE CELL

Commitment to a Cellular Transition Precedes Genome-wide Transcriptional Change

(2011) Umut Eser et al.   MOLECULAR CELL

A Comprehensive Genomic Binding Map of Gene and Chromatin Regulatory Proteins in Saccharomyces

(2011) Bryan J. Venters et al.   MOLECULAR CELL

Signal-dependent dynamics of transcription factor translocation controls gene expression

(2011) Nan Hao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

Slow-Cycling Therapy-Resistant Cancer Cells

(2011) Nathan Moore et al.   STEM CELLS AND DEVELOPMENT

Multiple Means to the Same End: The Genetic Basis of Acquired Stress Resistance in Yeast

(2011) David B. Berry et al.   PLoS Genetics

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

A Chromatin-Mediated Reversible Drug-Tolerant State in Cancer Cell Subpopulations

(2010) Sreenath V. Sharma et al.   CELL

Basal Dynamics of p53 Reveal Transcriptionally Attenuated Pulses in Cycling Cells

(2010) Alexander Loewer et al.   CELL

A Temporarily Distinct Subpopulation of Slow-Cycling Melanoma Cells Is Required for Continuous Tumor Growth

(2010) Alexander Roesch et al.   CELL

Exploiting Natural Variation in Saccharomyces cerevisiae to Identify Genes for Increased Ethanol Resistance

(2010) J. A. Lewis et al.   GENETICS

The role of physiological heterogeneity in microbial population behavior

(2010) Mary E Lidstrom et al.   Nature Chemical Biology

YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface

(2010) D. Abdulrehman et al.   NUCLEIC ACIDS RESEARCH

Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate

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

Single-Cell Analysis Reveals That Insulation Maintains Signaling Specificity Between Two Yeast MAPK Pathways with Common Components

(2010) J. C. Patterson et al.   Science Signaling

Transcriptional Regulation by P53

(2010) R. Beckerman et al.   Cold Spring Harbor Perspectives in Biology

A Systems-Level Analysis of Perfect Adaptation in Yeast Osmoregulation

(2009) Dale Muzzey et al.   CELL

Growth control and ribosome biogenesis

(2009) Harri Lempiäinen et al.   CURRENT OPINION IN CELL BIOLOGY

High-resolution DNA-binding specificity analysis of yeast transcription factors

(2009) C. Zhu et al.   GENOME RESEARCH

Quantification of the yeast transcriptome by single-molecule sequencing

(2009) Doron Lipson et al.   NATURE BIOTECHNOLOGY

Protein kinase A and TORC1 activate genes for ribosomal biogenesis by inactivating repressors encoded by Dot6 and its homolog Tod6

(2009) S. I. Lippman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The histone deacetylase Rpd3p is required for transient changes in genomic expression in response to stress

(2009) Adriana L Alejandro-Osorio et al.   GENOME BIOLOGY

Stress-activated Genomic Expression Changes Serve a Preparative Role for Impending Stress in Yeast

(2008) David B. Berry et al.   MOLECULAR BIOLOGY OF THE CELL

Slow Growth Induces Heat-Shock Resistance in Normal and Respiratory-deficient Yeast

(2008) Charles Lu et al.   MOLECULAR BIOLOGY OF THE CELL

Frequency-modulated nuclear localization bursts coordinate gene regulation

(2008) Long Cai et al.   NATURE

Chromatin decouples promoter threshold from dynamic range

(2008) Felix H. Lam et al.   NATURE

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation

(2008) Luis López-Maury et al.   NATURE REVIEWS GENETICS

Single-RNA counting reveals alternative modes of gene expression in yeast

(2008) Daniel Zenklusen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Up-to-date catalogues of yeast protein complexes

(2008) Shuye Pu et al.   NUCLEIC ACIDS RESEARCH