Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

[1]  E. M. DeGennaro,et al.  Multiplex gene editing by CRISPR-Cpf1 through autonomous processing of a single crRNA array , 2016, Nature Biotechnology.

[2]  Thomas M. Norman,et al.  A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response , 2016, Cell.

[3]  Y. Saeys,et al.  SCORPIUS improves trajectory inference and identifies novel modules in dendritic cell development , 2016, bioRxiv.

[4]  Adam P. Rosebrock,et al.  A global genetic interaction network maps a wiring diagram of cellular function , 2016, Science.

[5]  Angela N. Brooks,et al.  High-throughput Phenotyping of Lung Cancer Somatic Mutations. , 2016, Cancer cell.

[6]  Evan Z. Macosko,et al.  Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics , 2016, Cell.

[7]  Grace X. Y. Zheng,et al.  Massively parallel digital transcriptional profiling of single cells , 2016, Nature Communications.

[8]  Matt Thomson,et al.  Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing. , 2016, Cell systems.

[9]  Eli R. Zunder,et al.  Highly multiplexed simultaneous detection of RNAs and proteins in single cells , 2016, Nature Methods.

[10]  T. Harris,et al.  The Signal Transducer and Activator of Transcription 1 (STAT1) Inhibits Mitochondrial Biogenesis in Liver and Fatty Acid Oxidation in Adipocytes , 2015, PloS one.

[11]  E. Lander,et al.  Identification and characterization of essential genes in the human genome , 2015, Science.

[12]  E. Latz,et al.  ATF3 Is a Key Regulator of Macrophage IFN Responses , 2015, The Journal of Immunology.

[13]  Patrick Flick,et al.  GOATOOLS: Tools for Gene Ontology , 2015 .

[14]  David K. Gifford,et al.  Modular combinatorial binding among human trans-acting factors reveals direct and indirect factor binding , 2015, BMC Genomics.

[15]  Michael Poidinger,et al.  Identification of cDC1- and cDC2-committed DC progenitors reveals early lineage priming at the common DC progenitor stage in the bone marrow , 2015, Nature Immunology.

[16]  Chun Jimmie Ye,et al.  A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks , 2015, Cell.

[17]  T. Jacques,et al.  Signal transducer and activator of transcription 2 deficiency is a novel disorder of mitochondrial fission , 2015, Brain : a journal of neurology.

[18]  P. Chakravarty,et al.  GM-CSF Mouse Bone Marrow Cultures Comprise a Heterogeneous Population of CD11c(+)MHCII(+) Macrophages and Dendritic Cells. , 2015, Immunity.

[19]  Allon M. Klein,et al.  Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells , 2015, Cell.

[20]  Evan Z. Macosko,et al.  Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets , 2015, Cell.

[21]  S. Linnarsson,et al.  Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq , 2015, Science.

[22]  S. P. Fodor,et al.  Combinatorial labeling of single cells for gene expression cytometry , 2015, Science.

[23]  Fabian J Theis,et al.  Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells , 2015, Nature Biotechnology.

[24]  John D. Storey,et al.  Statistical significance of variables driving systematic variation in high-dimensional data , 2013, Bioinform..

[25]  Meagan E. Sullender,et al.  Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation , 2014, Nature Biotechnology.

[26]  Robert Langer,et al.  CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling , 2014, Cell.

[27]  Junling Wang,et al.  GABP Transcription Factor (Nuclear Respiratory Factor 2) Is Required for Mitochondrial Biogenesis , 2014, Molecular and Cellular Biology.

[28]  Rona S. Gertner,et al.  Single cell RNA Seq reveals dynamic paracrine control of cellular variation , 2014, Nature.

[29]  Mehdi M. Kashani,et al.  Large-Scale Genetic Perturbations Reveal Regulatory Networks and an Abundance of Gene-Specific Repressors , 2014, Cell.

[30]  A. Larner,et al.  Toward a new STATe: the role of STATs in mitochondrial function. , 2014, Seminars in immunology.

[31]  Kerry Bloom,et al.  Systematic triple-mutant analysis uncovers functional connectivity between pathways involved in chromosome regulation. , 2013, Cell reports.

[32]  Wolfgang Huber,et al.  Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping , 2013, Nature Methods.

[33]  Rona S. Gertner,et al.  Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells , 2013, Nature.

[34]  Luke A. Gilbert,et al.  Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression , 2013, Cell.

[35]  Michael T. McManus,et al.  A Systematic Mammalian Genetic Interaction Map Reveals Pathways Underlying Ricin Susceptibility , 2013, Cell.

[36]  Le Cong,et al.  Multiplex Genome Engineering Using CRISPR/Cas Systems , 2013, Science.

[37]  Michael S. Behnke,et al.  Compensatory dendritic cell development mediated by BATF-IRF interactions , 2012, Nature.

[38]  Nir Friedman,et al.  A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. , 2012, Molecular cell.

[39]  B. Gao,et al.  STAT proteins - key regulators of anti-viral responses, inflammation, and tumorigenesis in the liver. , 2012, Journal of hepatology.

[40]  Jacob T. Robinson,et al.  Systematic Discovery of TLR Signaling Components Delineates Viral-Sensing Circuits , 2011, Cell.

[41]  Po-Ling Loh,et al.  High-dimensional regression with noisy and missing data: Provable guarantees with non-convexity , 2011, NIPS.

[42]  N. Friedman,et al.  Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells , 2011, Nature Biotechnology.

[43]  G. Packham,et al.  The NF-κB p50:p50:HDAC-1 repressor complex orchestrates transcriptional inhibition of multiple pro-inflammatory genes , 2010, Journal of hepatology.

[44]  R. Durbin,et al.  Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes , 2010, Nature.

[45]  Zachary D. Smith,et al.  Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses , 2009 .

[46]  S. Goh,et al.  Cytokine-mediated increases in fetal hemoglobin are associated with globin gene histone modification and transcription factor reprogramming. , 2009, Blood.

[47]  N. Friedman,et al.  Structure and function of a transcriptional network activated by the MAPK Hog1 , 2008, Nature Genetics.

[48]  Ramin Homayouni,et al.  Bioinformatic analysis reveals cRel as a regulator of a subset of interferon-stimulated genes. , 2008, Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research.

[49]  Martin Rosvall,et al.  Maps of random walks on complex networks reveal community structure , 2007, Proceedings of the National Academy of Sciences.

[50]  E. Seto,et al.  Histone Deacetylase 3 Down-regulates Cholesterol Synthesis through Repression of Lanosterol Synthase Gene Expression* , 2007, Journal of Biological Chemistry.

[51]  H. Hauser,et al.  Distinct modes of action applied by transcription factors STAT1 and IRF1 to initiate transcription of the IFN-γ-inducible gbp2 gene , 2007, Proceedings of the National Academy of Sciences.

[52]  L. Pachter,et al.  EPISTASIS AND SHAPES OF FITNESS LANDSCAPES , 2006, q-bio/0603034.

[53]  Paul A Clemons,et al.  The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease , 2006, Science.

[54]  Kathleen A. Kennedy,et al.  Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4 , 2006, Nature.

[55]  H. Zou,et al.  Regularization and variable selection via the elastic net , 2005 .

[56]  E. D. Weinberger,et al.  Fourier and Taylor series on fitness landscapes , 1991, Biological Cybernetics.

[57]  R. Wiesner,et al.  Regulation and Co‐Ordination of Nuclear Gene Expression During Mitochondrial Biogenesis , 2003, Experimental physiology.

[58]  Yaniv Ziv,et al.  Revealing modular organization in the yeast transcriptional network , 2002, Nature Genetics.

[59]  Yudong D. He,et al.  Functional Discovery via a Compendium of Expression Profiles , 2000, Cell.

[60]  G. Schuler,et al.  An advanced culture method for generating large quantities of highly pure dendritic cells from mouse bone marrow. , 1999, Journal of immunological methods.

[61]  R. Lenski,et al.  Test of synergistic interactions among deleterious mutations in bacteria , 1997, Nature.

[62]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[63]  D. Du,et al.  Combinatorial Group Testing and Its Applications , 1993 .