Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

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

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

Single-cell imaging and RNA sequencing reveal patterns of gene expression heterogeneity during fission yeast growth and adaptation

(2019) Malika Saint et al.   Nature Microbiology

A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory

(2019) Rodoniki Athanasiadou et al.   PLoS Computational Biology

Multi-study inference of regulatory networks for more accurate models of gene regulation

(2019) Dayanne M. Castro et al.   PLoS Computational Biology

Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells

(2019) Emily R. Miraldi et al.   GENOME RESEARCH

Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data

(2018) Shuonan Chen et al.   BMC BIOINFORMATICS

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

Bias, robustness and scalability in single-cell differential expression analysis

(2018) Charlotte Soneson et al.   NATURE METHODS

An accurate and robust imputation method scImpute for single-cell RNA-seq data

(2018) Wei Vivian Li et al.   Nature Communications

Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks

(2018) Konstantine Tchourine et al.   Cell Reports

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

(2018) Darach Miller et al.   PLoS Genetics

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae

(2017) Miguel C Teixeira et al.   NUCLEIC ACIDS RESEARCH

The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan

(2017) Nitish Mittal et al.   Nature Communications

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

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

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

Homeostatic control of START through negative feedback between Cln3-Cdk1 and Rim15/Greatwall kinase in budding yeast

(2017) Nicolas Talarek et al.   eLife

Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures

(2017) Thalia E. Chan et al.   Cell Systems

Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast

(2017) Petri-Jaan Lahtvee et al.   Cell Systems

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

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

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

Single-cell barcoding and sequencing using droplet microfluidics

(2016) Rapolas Zilionis et al.   Nature Protocols

Network biology concepts in complex disease comorbidities

(2016) Jessica Xin Hu et al.   NATURE REVIEWS GENETICS

A prior-based integrative framework for functional transcriptional regulatory network inference

(2016) Alireza F. Siahpirani et al.   NUCLEIC ACIDS RESEARCH

EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments

(2016) Olivia Wilkins et al.   PLANT CELL

Fused Regression for Multi-source Gene Regulatory Network Inference

(2016) Kari Y. Lam et al.   PLoS Computational Biology

Elucidation of Genetic Interactions in the Yeast GATA-Factor Network Using Bayesian Model Selection

(2016) Andreas Milias-Argeitis et al.   PLoS Computational Biology

Identification of cell types from single-cell transcriptomes using a novel clustering method

(2015) Chen Xu et al.   BIOINFORMATICS

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network

(2015) M. L. Arrieta-Ortiz et al.   Molecular Systems Biology

Glucose- and nitrogen sensing and regulatory mechanisms inSaccharomyces cerevisiae

(2014) Steven V. Rødkaer et al.   FEMS YEAST RESEARCH

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

De-Novo Learning of Genome-Scale Regulatory Networks in S. cerevisiae

(2014) Sisi Ma et al.   PLoS One

Uncoupling reproduction from metabolism extends chronological lifespan in yeast

(2014) S. Nagarajan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of transcription factor activity by interconnected post-translational modifications

(2014) Theresa M. Filtz et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks

(2013) Alex Greenfield et al.   BIOINFORMATICS

Extensive transcriptional heterogeneity revealed by isoform profiling

(2013) Vicent Pelechano et al.   NATURE

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

A Validated Regulatory Network for Th17 Cell Specification

(2012) Maria Ciofani et al.   CELL

Regulation of Histone Gene Expression in Budding Yeast

(2012) P. R. Eriksson et al.   GENETICS

The Hog1 SAPK controls the Rtg1/Rtg3 transcriptional complex activity by multiple regulatory mechanisms

(2012) Clàudia Ruiz-Roig et al.   MOLECULAR BIOLOGY OF THE CELL

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

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

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

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

Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities

(2011) Yao Fu et al.   BMC BIOINFORMATICS

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Target of Rapamycin (TOR) in Nutrient Signaling and Growth Control

(2011) Robbie Loewith et al.   GENETICS

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

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

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities

(2011) C. G. de Boer et al.   NUCLEIC ACIDS RESEARCH

Cell death in yeast: growing applications of a dying buddy

(2010) D Carmona-Gutierrez et al.   CELL DEATH AND DIFFERENTIATION

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

DREAM3: Network Inference Using Dynamic Context Likelihood of Relatedness and the Inferelator

(2010) Aviv Madar et al.   PLoS One

DREAM4: Combining Genetic and Dynamic Information to Identify Biological Networks and Dynamical Models

(2010) Alex Greenfield et al.   PLoS One

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

Amino-acid-induced signalling via the SPS-sensing pathway in yeast

(2009) Per O. Ljungdahl   BIOCHEMICAL SOCIETY TRANSACTIONS

The Yeast GATA Factor Gat1 Occupies a Central Position in Nitrogen Catabolite Repression-Sensitive Gene Activation

(2009) I. Georis et al.   MOLECULAR AND CELLULAR BIOLOGY

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences

(2008) Lucas D. Ward et al.   BIOINFORMATICS

Extended Bayesian information criteria for model selection with large model spaces

(2008) J. Chen et al.   BIOMETRIKA

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

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

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