A comprehensive library of human transcription factors for cell fate engineering

[1]  A. Sharov,et al.  Generation and Profiling of 2,135 Human ESC Lines for the Systematic Analyses of Cell States Perturbed by Inducing Single Transcription Factors. , 2020, Cell reports.

[2]  Dan Zhang,et al.  Construction of a human cell landscape at single-cell level , 2020, Nature.

[3]  F. Hyder,et al.  Development of human brain organoids with functional vascular-like system , 2019, Nature Methods.

[4]  Jason Tchieu,et al.  SPECIFICATION OF POSITIONAL IDENTITY IN FOREBRAIN ORGANOIDS , 2019, Nature Biotechnology.

[5]  John R. Huguenard,et al.  Differentiation and Maturation of Oligodendrocytes in Human Three-Dimensional Neural Cultures , 2018, Nature Neuroscience.

[6]  Judith A. Blake,et al.  Mouse Genome Database (MGD) 2019 , 2018, Nucleic Acids Res..

[7]  T. Dawson,et al.  Synthetic mRNAs Drive Highly Efficient iPS Cell Differentiation to Dopaminergic Neurons , 2018, Stem cells translational medicine.

[8]  M. J. Moore,et al.  Comparison of visible and UVA phototoxicity in neural culture systems micropatterned with digital projection photolithography. , 2018, Journal of biomedical materials research. Part A.

[9]  Kun Zhang,et al.  Mapping Cellular Reprogramming via Pooled Overexpression Screens with Paired Fitness and Single-Cell RNA-Sequencing Readout. , 2018, Cell systems.

[10]  Endre Kiss,et al.  Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease , 2018, Nature Communications.

[11]  Principal Investigators,et al.  Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris , 2018 .

[12]  Michael J Moore,et al.  Methods for fabrication and evaluation of a 3D microengineered model of myelinated peripheral nerve. , 2018, Journal of neural engineering.

[13]  Peter F. Stadler,et al.  Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis , 2018, Cell systems.

[14]  T. Hughes,et al.  The Human Transcription Factors , 2018, Cell.

[15]  James T. Webber,et al.  Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris , 2018, Nature.

[16]  Henrik Ahlenius,et al.  Rapid and efficient induction of functional astrocytes from human pluripotent stem cells , 2018, Nature Methods.

[17]  William S. DeWitt,et al.  A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility , 2018, Cell.

[18]  Daniel C. Factor,et al.  Induction of Myelinating Oligodendrocytes in Human Cortical Spheroids , 2018, Nature Methods.

[19]  H. Blau,et al.  NKX3-1 is required for induced pluripotent stem cell reprogramming and can replace OCT4 in mouse and human iPSC induction , 2018, Nature Cell Biology.

[20]  A. Torkamani,et al.  Diverse reprogramming codes for neuronal identity , 2018, Nature.

[21]  Hao Li,et al.  An in vivo model of functional and vascularized human brain organoids , 2018, Nature Biotechnology.

[22]  Gordana Vunjak-Novakovic,et al.  Organs-on-a-Chip: A Fast Track for Engineered Human Tissues in Drug Development. , 2018, Cell stem cell.

[23]  T. Hughes,et al.  The Human Transcription Factors , 2018, Cell.

[24]  S. Kushner,et al.  SOX10 Single Transcription Factor-Based Fast and Efficient Generation of Oligodendrocytes from Human Pluripotent Stem Cells , 2018, Stem cell reports.

[25]  Fabian J Theis,et al.  SCANPY: large-scale single-cell gene expression data analysis , 2018, Genome Biology.

[26]  Michael J. T. Stubbington,et al.  The Human Cell Atlas: from vision to reality , 2017, Nature.

[27]  G. Govindaiah,et al.  Fusion of Regionally Specified hPSC-Derived Organoids Models Human Brain Development and Interneuron Migration. , 2017, Cell stem cell.

[28]  J. Bagley,et al.  Fused cerebral organoids model interactions between brain regions , 2017, Nature Methods.

[29]  F. Baralle,et al.  Alternative splicing as a regulator of development and tissue identity , 2017, Nature Reviews Molecular Cell Biology.

[30]  Jeesoo Kim,et al.  Assessment of engineered cells using CellNet and RNA-seq , 2017, Nature Protocols.

[31]  Jonathan A. Bernstein,et al.  Assembly of functionally integrated human forebrain spheroids , 2017, Nature.

[32]  Jennifer M. Bolin,et al.  A Genome-wide Analysis of Human Pluripotent Stem Cell-Derived Endothelial Cells in 2D or 3D Culture , 2017, Stem cell reports.

[33]  Axel Schambach,et al.  Rapid and efficient generation of oligodendrocytes from human induced pluripotent stem cells using transcription factors , 2017, Proceedings of the National Academy of Sciences.

[34]  Gita Kiaee,et al.  Development and characterization of a bioglass/chitosan composite as an injectable bone substitute. , 2017, Carbohydrate polymers.

[35]  Andrea Califano,et al.  Identification of an NKX3.1-G9a-UTY transcriptional regulatory network that controls prostate differentiation , 2016, Science.

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

[37]  M. Diekhans,et al.  The ORFeome Collaboration: a genome-scale human ORF-clone resource , 2016, Nature Methods.

[38]  Linda G. Griffith,et al.  Genetically engineering self-organization of human pluripotent stem cells into a liver bud-like tissue using Gata6 , 2016, Nature Communications.

[39]  F. Dick,et al.  Whole-Brain In-vivo Measurements of the Axonal G-Ratio in a Group of 37 Healthy Volunteers , 2015, Front. Neurosci..

[40]  J. Rinn,et al.  A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs , 2015, Nature Biotechnology.

[41]  Sally Temple,et al.  A Systematic Approach to Identify Candidate Transcription Factors that Control Cell Identity , 2015, Stem cell reports.

[42]  V. Fossati,et al.  Generation and isolation of oligodendrocyte progenitor cells from human pluripotent stem cells , 2015, Nature Protocols.

[43]  Dmitri D. Pervouchine,et al.  The human transcriptome across tissues and individuals , 2015, Science.

[44]  M. J. Moore,et al.  Photoreactive interpenetrating network of hyaluronic acid and Puramatrix as a selectively tunable scaffold for neurite growth. , 2015, Acta biomaterialia.

[45]  Elspeth A. Bruford,et al.  Genenames.org: the HGNC resources in 2015 , 2014, Nucleic Acids Res..

[46]  Nana Shimizu,et al.  ETS transcription factor ETV2 directly converts human fibroblasts into functional endothelial cells , 2014, Proceedings of the National Academy of Sciences.

[47]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[48]  Ron Weiss,et al.  Rapid neurogenesis through transcriptional activation in human stem cells , 2014, Molecular systems biology.

[49]  T. Maniatis,et al.  An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex , 2014, The Journal of Neuroscience.

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

[51]  T. Dawson,et al.  Tissue-Specific Progenitor and Stem Cells Proneural Transcription Factor Atoh 1 Drives Highly Efficient Differentiation of Human Pluripotent Stem Cells Into Dopaminergic Neurons , 2014 .

[52]  Seung Woo Jung,et al.  Generation of Induced Neuronal Cells by the Single Reprogramming Factor ASCL1 , 2014, Stem cell reports.

[53]  J. Leek.  svaseq: removing batch effects and other unwanted noise from sequencing data , 2014, bioRxiv.

[54]  R. Stewart,et al.  Direct Induction of Hematoendothelial Programs in Human Pluripotent Stem Cells by Transcriptional Regulators , 2014, Nature Communications.

[55]  Amit Sharma,et al.  DNASU plasmid and PSI:Biology-Materials repositories: resources to accelerate biological research , 2013, Nucleic Acids Res..

[56]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[57]  D. Schlessinger,et al.  Identification of Transcription Factors for Lineage-Specific ESC Differentiation , 2013, Stem cell reports.

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

[59]  Madeline A. Lancaster,et al.  Cerebral organoids model human brain development and microcephaly , 2013, Nature.

[60]  T. Südhof,et al.  Rapid Single-Step Induction of Functional Neurons from Human Pluripotent Stem Cells , 2013, Neuron.

[61]  P. Cahan,et al.  Origins and implications of pluripotent stem cell variability and heterogeneity , 2013, Nature Reviews Molecular Cell Biology.

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

[63]  K. Hochedlinger,et al.  The sox family of transcription factors: versatile regulators of stem and progenitor cell fate. , 2013, Cell stem cell.

[64]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[65]  Johannes E. Schindelin,et al.  Fiji: an open-source platform for biological-image analysis , 2012, Nature Methods.

[66]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[67]  Thomas M Green,et al.  A public genome-scale lentiviral expression library of human ORFs , 2011, Nature Methods.

[68]  Michael J. Lush,et al.  genenames.org: the HGNC resources in 2011 , 2010, Nucleic Acids Res..

[69]  S. Rennard,et al.  Differentiation of embryonic stem cells into fibroblast-like cells in three-dimensional type I collagen gel cultures , 2010, In vitro cellular & developmental biology. Animal.

[70]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[71]  Wei Wang,et al.  piggyBac transposition reprograms fibroblasts to induced pluripotent stem cells , 2009, Nature.

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

[73]  Michael P. Snyder,et al.  A high throughput embryonic stem cell screen identifies Oct-2 as a bifunctional regulator of neuronal differentiation. , 2009, Genes & development.

[74]  Lei Yuan,et al.  Engineering Robust and Functional Vascular Networks In Vivo With Human Adult and Cord Blood–Derived Progenitor Cells , 2008, Circulation research.

[75]  M. Kyba,et al.  ER71 acts downstream of BMP, Notch, and Wnt signaling in blood and vessel progenitor specification. , 2008, Cell stem cell.

[76]  D. Trono,et al.  Production and Titration of Lentiviral Vectors , 2007, Current protocols in human genetics.

[77]  G. Churchill,et al.  Characterization of human embryonic stem cell lines by the International Stem Cell Initiative , 2007, Nature Biotechnology.

[78]  C. Liang,et al.  In vitro scratch assay: a convenient and inexpensive method for analysis of cell migration in vitro , 2007, Nature Protocols.

[79]  D. Trono,et al.  Production and Titration of Lentiviral Vectors , 2006, Current protocols in neuroscience.

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

[81]  I. Lemischka,et al.  Genomewide gain-of-function genetic screen identifies functionally active genes in mouse embryonic stem cells. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[82]  P. Ngo,et al.  Collagen gel contraction assay. , 2006, Methods in molecular biology.

[83]  G. Church,et al.  The Personal Genome Project , 2005, Molecular systems biology.

[84]  Dai Fukumura,et al.  Tissue engineering: Creation of long-lasting blood vessels , 2004, Nature.

[85]  Guy McKhann,et al.  Fetal and adult human oligodendrocyte progenitor cell isolates myelinate the congenitally dysmyelinated brain , 2004, Nature Medicine.

[86]  Bassem A. Hassan,et al.  Math1: an essential gene for the generation of inner ear hair cells. , 1999, Science.

[87]  Richard R. Behringer,et al.  Sox9 is required for cartilage formation , 1999, Nature Genetics.

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

[89]  A. Groom,et al.  Capillary diameter and geometry in cardiac and skeletal muscle studied by means of corrosion casts. , 1983, Microvascular research.

[90]  E Bell,et al.  Production of a tissue-like structure by contraction of collagen lattices by human fibroblasts of different proliferative potential in vitro. , 1979, Proceedings of the National Academy of Sciences of the United States of America.