Mammalian Transcription Factor Networks: Recent Advances in Interrogating Biological Complexity.

[1]  G. Biagi.  Defining the Essential , 2018, Sculpture Review.

[2]  I. Amit,et al.  Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq , 2016, Cell.

[3]  Claude Preudhomme,et al.  A 17-gene stemness score for rapid determination of risk in acute leukaemia , 2016, Nature.

[4]  Thomas M. Norman,et al.  Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens , 2016, Cell.

[5]  J. Wysocka,et al.  Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution , 2016, Cell.

[6]  Jonathan M. Cairns,et al.  Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters , 2016, Cell.

[7]  Anthony D. Schmitt,et al.  A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. , 2016, Cell reports.

[8]  M. Brent.  Past Roadblocks and New Opportunities in Transcription Factor Network Mapping. , 2016, Trends in genetics : TIG.

[9]  Julio Saez-Rodriguez,et al.  A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic Targets in Acute Myeloid Leukemia , 2016, Cell reports.

[10]  Max A. Horlbeck,et al.  Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation , 2016, eLife.

[11]  Bruce J. Aronow,et al.  Single-cell analysis of mixed-lineage states leading to a binary cell fate choice , 2016, Nature.

[12]  Carsten Marr,et al.  Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios , 2016, Nature.

[13]  L. Pennacchio,et al.  Genetic dissection of the α-globin super-enhancer in vivo , 2016, Nature Genetics.

[14]  Nicola K. Wilson,et al.  Resolving Early Mesoderm Diversification through Single Cell Expression Profiling , 2016, Nature.

[15]  Hao Yuan Kueh,et al.  Asynchronous combinatorial action of four regulatory factors activates Bcl11b for T cell commitment , 2016, Nature Immunology.

[16]  Nicola K. Wilson,et al.  Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model. , 2016, Blood.

[17]  Salam A. Assi,et al.  Dynamic Gene Regulatory Networks Drive Hematopoietic Specification and Differentiation , 2016, Developmental cell.

[18]  J. Fisher,et al.  Processing, visualising and reconstructing network models from single‐cell data , 2016, Immunology and cell biology.

[19]  Nicola K. Wilson,et al.  An experimentally validated network of nine haematopoietic transcription factors reveals mechanisms of cell state stability , 2016, eLife.

[20]  Yoshihide Hayashizaki,et al.  A predictive computational framework for direct reprogramming between human cell types , 2016, Nature Genetics.

[21]  J. Sklar,et al.  Genome-wide Detection of DNase I Hypersensitive Sites in Single Cells and FFPE Samples , 2015, Nature.

[22]  A. Jolma,et al.  DNA-dependent formation of transcription factor pairs alters their binding specificity , 2015, Nature.

[23]  Aleksandra A. Kolodziejczyk,et al.  Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation , 2015, Cell stem cell.

[24]  D. Weitz,et al.  Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state , 2015, Nature Biotechnology.

[25]  Fabian J. Theis,et al.  Network plasticity of pluripotency transcription factors in embryonic stem cells , 2015, Nature Cell Biology.

[26]  Matthew C. Canver,et al.  BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis , 2015, Nature.

[27]  R. Shiekhattar,et al.  Architectural and Functional Commonalities between Enhancers and Promoters , 2015, Cell.

[28]  C. Myers,et al.  Transcription Factor Activity Mapping of a Tissue-Specific in vivo Gene Regulatory Network. , 2015, Cell systems.

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

[30]  Howard Y. Chang,et al.  Single-cell chromatin accessibility reveals principles of regulatory variation , 2015, Nature.

[31]  Fabian J. Theis,et al.  Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations , 2015, Cell stem cell.

[32]  Andrew C. Adey,et al.  Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing , 2015, Science.

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

[34]  B. Göttgens.  Regulatory network control of blood stem cells. , 2015, Blood.

[35]  Marc Vidal,et al.  Human Gene-Centered Transcription Factor Networks for Enhancers and Disease Variants , 2015, Cell.

[36]  A. Visel,et al.  Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility , 2015, Epigenetics & Chromatin.

[37]  A. Pombo,et al.  Three-dimensional genome architecture: players and mechanisms , 2015, Nature Reviews Molecular Cell Biology.

[38]  Laura Buttitta,et al.  How the cell cycle impacts chromatin architecture and influences cell fate , 2015, Front. Genet..

[39]  N. Novère.  Quantitative and logic modelling of molecular and gene networks , 2015, Nature Reviews Genetics.

[40]  J. T. Erichsen,et al.  Enhancer Evolution across 20 Mammalian Species , 2015, Cell.

[41]  Fabian J Theis,et al.  Decoding the Regulatory Network for Blood Development from Single-Cell Gene Expression Measurements , 2015, Nature Biotechnology.

[42]  D. Sabatini,et al.  Nutrient-sensing mechanisms and pathways , 2015, Nature.

[43]  Wesley R. Legant,et al.  3D imaging of Sox2 enhancer clusters in embryonic stem cells , 2014, eLife.

[44]  Berthold Göttgens,et al.  Transcriptional network control of normal and leukaemic haematopoiesis , 2014, Experimental cell research.

[45]  Z. Weng,et al.  Principles of regulatory information conservation between mouse and human , 2014, Nature.

[46]  Elhanan Borenstein,et al.  Conservation of trans-acting circuitry during mammalian regulatory evolution , 2014, Nature.

[47]  R. Young,et al.  An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element , 2014, Science.

[48]  J. Fisher,et al.  Single-cell analyses of regulatory network perturbations using enhancer-targeting TALEs suggest novel roles for PU.1 during haematopoietic specification , 2014, Development.

[49]  Philipp S. Hoppe,et al.  Single-cell technologies sharpen up mammalian stem cell research , 2014, Nature Cell Biology.

[50]  Samantha A. Morris,et al.  Dissecting Engineered Cell Types and Enhancing Cell Fate Conversion via CellNet , 2014, Cell.

[51]  Samantha A. Morris,et al.  CellNet: Network Biology Applied to Stem Cell Engineering , 2014, Cell.

[52]  Avi Ma'ayan,et al.  Construction and Validation of a Regulatory Network for Pluripotency and Self-Renewal of Mouse Embryonic Stem Cells , 2014, PLoS Comput. Biol..

[53]  Peter J. Bickel,et al.  Comparative analysis of regulatory information and circuits across distant species , 2014, Nature.

[54]  V. Sandler,et al.  Reprogramming Human Endothelial to Hematopoietic Cells Requires Vascular Induction , 2014, Nature.

[55]  Neville E. Sanjana,et al.  Improved vectors and genome-wide libraries for CRISPR screening , 2014, Nature Methods.

[56]  S. Emmott,et al.  Defining an essential transcription factor program for naïve pluripotency , 2014, Science.

[57]  Alex K. Shalek,et al.  Heterogeneity in immune responses: from populations to single cells. , 2014, Trends in immunology.

[58]  Matthew A. Hibbs,et al.  Novel Insights into Embryonic Stem Cell Self‐Renewal Revealed Through Comparative Human and Mouse Systems Biology Networks , 2014, Stem cells.

[59]  S. Orkin,et al.  Reprogramming Committed Murine Blood Cells to Induced Hematopoietic Stem Cells with Defined Factors , 2014, Cell.

[60]  Morgan C. Giddings,et al.  Defining functional DNA elements in the human genome , 2014, Proceedings of the National Academy of Sciences.

[61]  J. D. Engel,et al.  A remote GATA2 hematopoietic enhancer drives leukemogenesis in inv(3)(q21;q26) by activating EVI1 expression. , 2014, Cancer cell.

[62]  Britta A. M. Bouwman,et al.  A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia , 2014, Cell.

[63]  Ludovic Vallier,et al.  The Cell-Cycle State of Stem Cells Determines Cell Fate Propensity , 2014, Cell.

[64]  P. Rigby,et al.  Gene regulatory networks and transcriptional mechanisms that control myogenesis. , 2014, Developmental cell.

[65]  T. Filtz,et al.  Regulation of transcription factor activity by interconnected post-translational modifications. , 2014, Trends in pharmacological sciences.

[66]  I. Macaulay,et al.  Single Cell Genomics: Advances and Future Perspectives , 2014, PLoS genetics.

[67]  R. Young,et al.  Super-Enhancers in the Control of Cell Identity and Disease , 2013, Cell.

[68]  Howard Y. Chang,et al.  Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position , 2013, Nature Methods.

[69]  A. Tanay,et al.  Single cell Hi-C reveals cell-to-cell variability in chromosome structure , 2013, Nature.

[70]  Åsa K. Björklund,et al.  Smart-seq2 for sensitive full-length transcriptome profiling in single cells , 2013, Nature Methods.

[71]  H. Nakauchi,et al.  Clonal Analysis Unveils Self-Renewing Lineage-Restricted Progenitors Generated Directly from Hematopoietic Stem Cells , 2013, Cell.

[72]  M. Elowitz,et al.  Positive Feedback Between PU.1 and the Cell Cycle Controls Myeloid Differentiation , 2013, Science.

[73]  J. Skotheim,et al.  Control of cell cycle transcription during G1 and S phases , 2013, Nature Reviews Molecular Cell Biology.

[74]  J. C. Tsang,et al.  Reprogramming to Pluripotency Using Designer TALE Transcription Factors Targeting Enhancers , 2013, Stem cell reports.

[75]  Ioannis Xenarios,et al.  Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model , 2013, Bioinform..

[76]  David A. Orlando,et al.  Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes , 2013, Cell.

[77]  Fabian J. Theis,et al.  Characterisation of transcriptional networks in blood stem and progenitor cells using high-throughput single cell gene expression analysis , 2013, Nature Cell Biology.

[78]  Łukasz M. Boryń,et al.  Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq , 2013, Science.

[79]  James E. DiCarlo,et al.  RNA-Guided Human Genome Engineering via Cas9 , 2013, Science.

[80]  B. Hendrich,et al.  Transcriptional repressors: multifaceted regulators of gene expression , 2013, Development.

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

[82]  Seung Woo Cho,et al.  Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease , 2013, Nature Biotechnology.

[83]  Juan M. Vaquerizas,et al.  DNA-Binding Specificities of Human Transcription Factors , 2013, Cell.

[84]  M. Sigvardsson.  Transcription factor dose links development to disease. , 2012, Blood.

[85]  J. Massagué.  TGFβ signalling in context , 2012, Nature Reviews Molecular Cell Biology.

[86]  M. Pellegrini,et al.  Scl Represses Cardiomyogenesis in Prospective Hemogenic Endothelium and Endocardium , 2012, Cell.

[87]  Veronica Sanchez-Freire,et al.  Microfluidic single-cell real-time PCR for comparative analysis of gene expression patterns , 2012, Nature Protocols.

[88]  David A. Orlando,et al.  Enhancer decommissioning by LSD1 during embryonic stem cell differentiation , 2012, Nature.

[89]  G. Ammerer,et al.  Controlling gene expression in response to stress , 2011, Nature Reviews Genetics.

[90]  David A. Orlando,et al.  Master Transcription Factors Determine Cell-Type-Specific Responses to TGF-β Signaling , 2011, Cell.

[91]  L. Zon,et al.  Lineage Regulators Direct BMP and Wnt Pathways to Cell-Specific Programs during Differentiation and Regeneration , 2011, Cell.

[92]  M. Crossley,et al.  PU.1 and Haematopoietic Cell Fate: Dosage Matters , 2011, International journal of cell biology.

[93]  Samuel Aparicio,et al.  High-throughput microfluidic single-cell RT-qPCR , 2011, Proceedings of the National Academy of Sciences.

[94]  Erin F. Simonds,et al.  Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum , 2011, Science.

[95]  H. Ng,et al.  The transcriptional and signalling networks of pluripotency , 2011, Nature Cell Biology.

[96]  Ryan A. Flynn,et al.  A unique chromatin signature uncovers early developmental enhancers in humans , 2011, Nature.

[97]  E. Davidson.  Emerging properties of animal gene regulatory networks , 2010, Nature.

[98]  R. Young,et al.  Histone H3K27ac separates active from poised enhancers and predicts developmental state , 2010, Proceedings of the National Academy of Sciences.

[99]  Sohail Malik,et al.  The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation , 2010, Nature Reviews Genetics.

[100]  A. McCallion,et al.  Genomics of long-range regulatory elements. , 2010, Annual review of genomics and human genetics.

[101]  Emery H. Bresnick,et al.  GATA Switches as Developmental Drivers* , 2010, The Journal of Biological Chemistry.

[102]  T. Stopka,et al.  The role of PU.1 and GATA-1 transcription factors during normal and leukemogenic hematopoiesis , 2010, Leukemia.

[103]  Catalin C. Barbacioru,et al.  RNA-Seq analysis to capture the transcriptome landscape of a single cell , 2010, Nature Protocols.

[104]  T. Enver,et al.  Forcing cells to change lineages , 2009, Nature.

[105]  Albertha J. M. Walhout,et al.  The interplay between transcription factors and microRNAs in genome‐scale regulatory networks , 2009, BioEssays : news and reviews in molecular, cellular and developmental biology.

[106]  Juan M. Vaquerizas,et al.  A census of human transcription factors: function, expression and evolution , 2009, Nature Reviews Genetics.

[107]  William Stafford Noble,et al.  Global mapping of protein-DNA interactions in vivo by digital genomic footprinting , 2009, Nature Methods.

[108]  G. Daley,et al.  Mesodermal patterning activity of SCL. , 2008, Experimental hematology.

[109]  Sheng Ding,et al.  Induction of pluripotent stem cells from mouse embryonic fibroblasts by Oct4 and Klf4 with small-molecule compounds. , 2008, Cell stem cell.

[110]  Gordon Keller,et al.  Differentiation of Embryonic Stem Cells to Clinically Relevant Populations: Lessons from Embryonic Development , 2008, Cell.

[111]  A. Mortazavi,et al.  Genome-Wide Mapping of in Vivo Protein-DNA Interactions , 2007, Science.

[112]  U. Alon.  Network motifs: theory and experimental approaches , 2007, Nature Reviews Genetics.

[113]  Ryoichiro Kageyama,et al.  The Hes gene family: repressors and oscillators that orchestrate embryogenesis , 2007, Development.

[114]  Nathaniel D. Heintzman,et al.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome , 2007, Nature Genetics.

[115]  T. Kouzarides.  Chromatin Modifications and Their Function , 2007, Cell.

[116]  C. Nusbaum,et al.  Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. , 2006, Genome research.

[117]  S. Yamanaka,et al.  Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors , 2006, Cell.

[118]  T. Anthony,et al.  Coping with stress: eIF2 kinases and translational control. , 2006, Biochemical Society transactions.

[119]  A. Blais,et al.  Constructing transcriptional regulatory networks. , 2005, Genes & development.

[120]  S. Tapscott,et al.  The circuitry of a master switch: Myod and the regulation of skeletal muscle gene transcription , 2005, Development.

[121]  Chris Wiggins,et al.  ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context , 2004, BMC Bioinformatics.

[122]  T. Graf,et al.  Stepwise Reprogramming of B Cells into Macrophages , 2004, Cell.

[123]  Hiromitsu Nakauchi,et al.  Long-Term Lymphohematopoietic Reconstitution by a Single CD34-Low/Negative Hematopoietic Stem Cell , 1996, Science.

[124]  R. Müller,et al.  Transcriptional regulation during the mammalian cell cycle. , 1995, Trends in genetics : TIG.

[125]  S. Tapscott,et al.  MyoD1: a nuclear phosphoprotein requiring a Myc homology region to convert fibroblasts to myoblasts. , 1988, Science.

[126]  H. Weintraub,et al.  Expression of a single transfected cDNA converts fibroblasts to myoblasts , 1987, Cell.

[127]  T. Maniatis,et al.  Regulation of inducible and tissue-specific gene expression. , 1987, Science.

[128]  Berthold Göttgens,et al.  Transcriptional regulation of haematopoietic stem cells. , 2013, Advances in experimental medicine and biology.

[129]  J. Chu,et al.  The transcriptional network controlling pluripotency in ES cells. , 2008, Cold Spring Harbor symposia on quantitative biology.

[130]  D. Latchman.  Regulation of Transcription Factor Activity , 2004 .