Single-cell and multivariate approaches in genetic perturbation screens

A Hierarchical Map of Regulatory Genetic Interactions in Membrane Trafficking

(2014) Prisca Liberali et al.   CELL

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

(2014) Luke A. Gilbert et al.   CELL

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT

(2014) Ralf Jungmann et al.   NATURE METHODS

Cancer Cell Profiling by Barcoding Allows Multiplexed Protein Analysis in Fine-Needle Aspirates

(2014) A. V. Ullal et al.   Science Translational Medicine

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

(2013) Lei S. Qi et al.   CELL

A Systematic Mammalian Genetic Interaction Map Reveals Pathways Underlying Ricin Susceptibility

(2013) Michael C. Bassik et al.   CELL

Dynamics extracted from fixed cells reveal feedback linking cell growth to cell cycle

(2013) Ran Kafri et al.   NATURE

A screen for morphological complexity identifies regulators of switch-like transitions between discrete cell shapes

(2013) Zheng Yin et al.   NATURE CELL BIOLOGY

Predicting functional gene interactions with the hierarchical interaction score

(2013) Berend Snijder et al.   NATURE METHODS

Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping

(2013) Christina Laufer et al.   NATURE METHODS

Quantitative genetic-interaction mapping in mammalian cells

(2013) Assen Roguev et al.   NATURE METHODS

Image-based transcriptomics in thousands of single human cells at single-molecule resolution

(2013) Nico Battich et al.   NATURE METHODS

A reversible gene trap collection empowers haploid genetics in human cells

(2013) Tilmann Bürckstümmer et al.   NATURE METHODS

Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue

(2013) M. J. Gerdes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Quantum dot imaging platform for single-cell molecular profiling

(2013) Pavel Zrazhevskiy et al.   Nature Communications

Inference of gene regulatory networks from genome-wide knockout fitness data

(2012) L. Wang et al.   BIOINFORMATICS

Cell Differentiation within a Yeast Colony: Metabolic and Regulatory Parallels with a Tumor-Affected Organism

(2012) Michal Čáp et al.   MOLECULAR CELL

Dissection of DNA Damage Responses Using Multiconditional Genetic Interaction Maps

(2012) Aude Guénolé et al.   MOLECULAR CELL

Single-cell analysis of population context advances RNAi screening at multiple levels

(2012) Berend Snijder et al.   Molecular Systems Biology

Differential network biology

(2012) Trey Ideker et al.   Molecular Systems Biology

RNAi screening reveals a large signaling network controlling the Golgi apparatus in human cells

(2012) Joanne Chia et al.   Molecular Systems Biology

Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators

(2012) Bernd Bodenmiller et al.   NATURE BIOTECHNOLOGY

Genome-wide RNAi screening identifies human proteins with a regulatory function in the early secretory pathway

(2012) Jeremy C. Simpson et al.   NATURE CELL BIOLOGY

Unsupervised modeling of cell morphology dynamics for time-lapse microscopy

(2012) Qing Zhong et al.   NATURE METHODS

Biological imaging software tools

(2012) Kevin W Eliceiri et al.   NATURE METHODS

Single-cell systems biology by super-resolution imaging and combinatorial labeling

(2012) Eric Lubeck et al.   NATURE METHODS

Using Cell-to-Cell Variability--A New Era in Molecular Biology

(2012) L. Pelkmans   SCIENCE

Using Gene Expression Noise to Understand Gene Regulation

(2012) B. Munsky et al.   SCIENCE

Genetic Interactions in Cancer Progression and Treatment

(2011) Alan Ashworth et al.   CELL

Cell-to-Cell Variability in PI3K Protein Level Regulates PI3K-AKT Pathway Activity in Cell Populations

(2011) Tina L. Yuan et al.   CURRENT BIOLOGY

Robust selection of sensory organ precursors by the Notch–Delta pathway

(2011) Omer Barad et al.   CURRENT OPINION IN CELL BIOLOGY

Mouse library set to be knockout

(2011) Elie Dolgin   NATURE

Derivation of haploid embryonic stem cells from mouse embryos

(2011) Martin Leeb et al.   NATURE

A conditional knockout resource for the genome-wide study of mouse gene function

(2011) William C. Skarnes et al.   NATURE

Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE

(2011) Peng Qiu et al.   NATURE BIOTECHNOLOGY

Mapping of signaling networks through synthetic genetic interaction analysis by RNAi

(2011) Thomas Horn et al.   NATURE METHODS

Imaging the coordination of multiple signalling activities in living cells

(2011) Christopher M. Welch et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Origins of regulated cell-to-cell variability

(2011) Berend Snijder et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

From the stochasticity of molecular processes to the variability of synaptic transmission

(2011) Claire Ribrault et al.   NATURE REVIEWS NEUROSCIENCE

A haploid genetic screen identifies the major facilitator domain containing 2A (MFSD2A) transporter as a key mediator in the response to tunicamycin

(2011) J. H. Reiling et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging

(2011) A. M. Valm et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

(2011) S. C. Bendall et al.   SCIENCE

Genomic Screening with RNAi: Results and Challenges

(2010) Stephanie Mohr et al.   Annual Review of Biochemistry

Decision Making at a Subcellular Level Determines the Outcome of Bacteriophage Infection

(2010) Lanying Zeng et al.   CELL

Cellular Heterogeneity: Do Differences Make a Difference?

(2010) Steven J. Altschuler et al.   CELL

Phenotypic Landscape of a Bacterial Cell

(2010) Robert J. Nichols et al.   CELL

Patterns of basal signaling heterogeneity can distinguish cellular populations with different drug sensitivities

(2010) Dinesh Kumar Singh et al.   Molecular Systems Biology

Automated identification of pathways from quantitative genetic interaction data

(2010) Alexis Battle et al.   Molecular Systems Biology

Pre-dispositions and epigenetic inheritance in the Escherichia coli lactose operon bistable switch

(2010) Lydia Robert et al.   Molecular Systems Biology

Systems survey of endocytosis by multiparametric image analysis

(2010) Claudio Collinet et al.   NATURE

Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome

(2010) Heinz Neumann et al.   NATURE

Variability in gene expression underlies incomplete penetrance

(2010) Arjun Raj et al.   NATURE

Functional roles for noise in genetic circuits

(2010) Avigdor Eldar et al.   NATURE

A mouse knockout library for secreted and transmembrane proteins

(2010) Tracy Tang et al.   NATURE BIOTECHNOLOGY

Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe

(2010) Dong-Uk Kim et al.   NATURE BIOTECHNOLOGY

A TALE nuclease architecture for efficient genome editing

(2010) Jeffrey C Miller et al.   NATURE BIOTECHNOLOGY

Actin and serum response factor transduce physical cues from the microenvironment to regulate epidermal stem cell fate decisions

(2010) John T. Connelly et al.   NATURE CELL BIOLOGY

A mammalian functional-genetic approach to characterizing cancer therapeutics

(2010) Hai Jiang et al.   Nature Chemical Biology

Computational solutions to large-scale data management and analysis

(2010) Eric E. Schadt et al.   NATURE REVIEWS GENETICS

Genome editing with engineered zinc finger nucleases

(2010) Fyodor D. Urnov et al.   NATURE REVIEWS GENETICS

Network medicine: a network-based approach to human disease

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

Spatial organization of intracellular communication: insights from imaging

(2010) Leif Dehmelt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

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

Rewiring of Genetic Networks in Response to DNA Damage

(2010) S. Bandyopadhyay et al.   SCIENCE

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

How to Understand the Cell by Breaking It: Network Analysis of Gene Perturbation Screens

(2010) Florian Markowetz   PLoS Computational Biology

Mass Cytometry: Technique for Real Time Single Cell Multitarget Immunoassay Based on Inductively Coupled Plasma Time-of-Flight Mass Spectrometry

(2009) Dmitry R. Bandura et al.   ANALYTICAL CHEMISTRY

CellClassifier: supervised learning of cellular phenotypes

(2009) Pauli Rämö et al.   BIOINFORMATICS

Functional Organization of the S. cerevisiae Phosphorylation Network

(2009) Dorothea Fiedler et al.   CELL

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE

Population context determines cell-to-cell variability in endocytosis and virus infection

(2009) Berend Snijder et al.   NATURE

Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis

(2009) Sabrina L. Spencer et al.   NATURE

An approach for extensibly profiling the molecular states of cellular subpopulations

(2009) Lit-Hsin Loo et al.   NATURE METHODS

Statistical methods for analysis of high-throughput RNA interference screens

(2009) Amanda Birmingham et al.   NATURE METHODS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

A Direct Phenotypic Comparison of siRNA Pools and Multiple Individual Duplexes in a Functional Assay

(2009) Brendon D. Parsons et al.   PLoS One

Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning

(2009) Thouis R. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Haploid Genetic Screens in Human Cells Identify Host Factors Used by Pathogens

(2009) J. E. Carette et al.   SCIENCE

Systematic Mapping of Genetic Interaction Networks

(2008) Scott J. Dixon et al.   Annual Review of Genetics

CellProfiler Analyst: data exploration and analysis software for complex image-based screens

(2008) Thouis R Jones et al.   BMC BIOINFORMATICS

Control of cell fate by the formation of an architecturally complex bacterial community

(2008) H. Vlamakis et al.   GENES & DEVELOPMENT

Mechanism of shape determination in motile cells

(2008) Kinneret Keren et al.   NATURE

The art and design of genetic screens: RNA interference

(2008) Michael Boutros et al.   NATURE REVIEWS GENETICS

Characterizing heterogeneous cellular responses to perturbations

(2008) M. D. Slack et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Determination of cell fate selection during phage lambda infection

(2008) F. St-Pierre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Feedback Loops Shape Cellular Signals in Space and Time

(2008) O. Brandman et al.   SCIENCE

Phosphorylation Networks Regulating JNK Activity in Diverse Genetic Backgrounds

(2008) C. Bakal et al.   SCIENCE

Profiling Essential Genes in Human Mammary Cells by Multiplex RNAi Screening

(2008) J. M. Silva et al.   SCIENCE