Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction.
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Nir Yosef | Anat Kreimer | Tal Ashuach | Nadav Ahituv | Fumitaka Inoue | Anat Kreimer | N. Yosef | N. Ahituv | Tal Ashuach | Fumitaka Inoue | A. Kreimer
[1] M. Araúzo-Bravo,et al. FGF signalling inhibits neural induction in human embryonic stem cells , 2011, The EMBO journal.
[2] Jun S. Liu,et al. The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans , 2015, Science.
[3] Cole Trapnell,et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.
[4] H. Kalkman. A review of the evidence for the canonical Wnt pathway in autism spectrum disorders , 2012, Molecular Autism.
[5] P. Swain,et al. Gene Regulation at the Single-Cell Level , 2005, Science.
[6] T. Mikkelsen,et al. Massively Parallel Reporter Assays in Cultured Mammalian Cells , 2014, Journal of visualized experiments : JoVE.
[7] Tom H. Pringle,et al. The human genome browser at UCSC. , 2002, Genome research.
[8] Michael Wainberg,et al. Predicting gene expression in massively parallel reporter assays: A comparative study , 2017, Human mutation.
[9] A. Sandelin,et al. Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance , 2014, Nature Genetics.
[10] T. Meehan,et al. An atlas of active enhancers across human cell types and tissues , 2014, Nature.
[11] Luke A. Gilbert,et al. CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes , 2013, Cell.
[12] D. Geschwind,et al. The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis , 2018, Cell.
[13] N. Trinklein,et al. Genome-Wide Discovery of Drug-Dependent Human Liver Regulatory Elements , 2014, PLoS genetics.
[14] F. Collins,et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits , 2009, Proceedings of the National Academy of Sciences.
[15] Anna Zhukova,et al. Modeling sample variables with an Experimental Factor Ontology , 2010, Bioinform..
[16] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[17] Sarah M. Goggin,et al. High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human , 2018, Nature Communications.
[18] Data production leads,et al. An integrated encyclopedia of DNA elements in the human genome , 2012 .
[19] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[20] Andrew D. Johnson,et al. SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap , 2008, Bioinform..
[21] John P. Rice,et al. Identification of common genetic risk variants for autism spectrum disorder , 2019, Nature Genetics.
[22] U. Alon,et al. Detailed map of a cis-regulatory input function , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[23] B. Cohen,et al. High-throughput functional testing of ENCODE segmentation predictions , 2014, Genome research.
[24] Anat Kreimer,et al. Meta‐analysis of massively parallel reporter assays enables prediction of regulatory function across cell types , 2019, Human mutation.
[25] Jing Liang,et al. Chromatin architecture reorganization during stem cell differentiation , 2015, Nature.
[26] S. Chou,et al. LHX2 regulates the neural differentiation of human embryonic stem cells via transcriptional modulation of PAX6 and CER1 , 2013, Nucleic acids research.
[27] P. Gruss,et al. Identification of the vertebrate Iroquois homeobox gene family with overlapping expression during early development of the nervous system , 1997, Mechanisms of Development.
[28] N. Yosef,et al. Comparative Analysis of Immune Cells Reveals a Conserved Regulatory Lexicon. , 2018, Cell systems.
[29] A. Simeone,et al. OTX1 compensates for OTX2 requirement in regionalisation of anterior neuroectoderm. , 2003, Gene expression patterns : GEP.
[30] Michael T. McManus,et al. A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity , 2016, bioRxiv.
[31] Richard Leslie,et al. GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database , 2014, Bioinform..
[32] Kate B. Cook,et al. Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity , 2014, Cell.
[33] K. Weber,et al. Fractionation of brain microtubule-associated proteins. Isolation of two different proteins which stimulate tubulin polymerization in vitro. , 1978, European journal of biochemistry.
[34] K. Weber,et al. Fractionation of Brain Microtubule‐Associated Proteins , 1978 .
[35] M. Tomishima,et al. Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling , 2009, Nature Biotechnology.
[36] Hailiang Huang,et al. Whole genome sequencing in psychiatric disorders: the WGSPD consortium , 2017, bioRxiv.
[37] Raymond K. Auerbach,et al. An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.
[38] X. Chen,et al. Sall4 Interacts with Nanog and Co-occupies Nanog Genomic Sites in Embryonic Stem Cells* , 2006, Journal of Biological Chemistry.
[39] Christopher S. Poultney,et al. Meta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a novel locus at 10q24.32 and a significant overlap with schizophrenia , 2017, Molecular Autism.
[40] D. Volk,et al. Prenatal ontogeny as a susceptibility period for cortical GABA neuron disturbances in schizophrenia , 2013, Neuroscience.
[41] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[42] R. Jaenisch,et al. SOX2 Co-Occupies Distal Enhancer Elements with Distinct POU Factors in ESCs and NPCs to Specify Cell State , 2013, PLoS genetics.
[43] A. Regev,et al. Dynamic regulatory network controlling Th17 cell differentiation , 2013, Nature.
[44] G. Kempermann. Faculty Opinions recommendation of Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. , 2015 .
[45] Stephan J Sanders,et al. A framework for the interpretation of de novo mutation in human disease , 2014, Nature Genetics.
[46] Tao Liu,et al. Using MACS to Identify Peaks from ChIP‐Seq Data , 2011, Current protocols in bioinformatics.
[47] Y. Minami,et al. Ror family receptor tyrosine kinases regulate the maintenance of neural progenitor cells in the developing neocortex , 2012, Journal of Cell Science.
[48] Michael J. Ziller,et al. Dissecting neural differentiation regulatory networks through epigenetic footprinting , 2014, Nature.
[49] P. Robson,et al. Transcriptional Regulation of Nanog by OCT4 and SOX2* , 2005, Journal of Biological Chemistry.
[50] William Stafford Noble,et al. FIMO: scanning for occurrences of a given motif , 2011, Bioinform..
[51] H. Herschman. Primary response genes induced by growth factors and tumor promoters. , 1991, Annual review of biochemistry.
[52] Aaron R. Quinlan,et al. Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .
[53] Inna Dubchak,et al. VISTA Enhancer Browser—a database of tissue-specific human enhancers , 2006, Nucleic Acids Res..
[54] U. Alon,et al. Spontaneous evolution of modularity and network motifs. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[55] Ying Jin,et al. Pax6 is a human neuroectoderm cell fate determinant. , 2010, Cell stem cell.
[56] A. Regev,et al. Writ large: Genomic dissection of the effect of cellular environment on immune response , 2016, Science.
[57] Nir Yosef,et al. ImpulseDE: detection of differentially expressed genes in time series data using impulse models , 2016, Bioinform..
[58] Nir Friedman,et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. , 2012, Molecular cell.
[59] Shane J. Neph,et al. Systematic Localization of Common Disease-Associated Variation in Regulatory DNA , 2012, Science.
[60] Jiajie Zhang,et al. PEAR: a fast and accurate Illumina Paired-End reAd mergeR , 2013, Bioinform..
[61] Megan F. Cole,et al. Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells , 2005, Cell.
[62] Pablo Tamayo,et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[63] Sharon R Grossman,et al. Systematic dissection of genomic features determining transcription factor binding and enhancer function , 2017, Proceedings of the National Academy of Sciences.
[64] Helen E. Parkinson,et al. The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog) , 2016, Nucleic Acids Res..
[65] T. Mikkelsen,et al. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. , 2013, Genome research.
[66] Michael Q. Zhang,et al. Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells , 2013, Cell.
[67] Björn Usadel,et al. Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..
[68] Manolis Kellis,et al. Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments , 2013, Nucleic acids research.
[69] Wei Shi,et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..
[70] Christopher S. Poultney,et al. Meta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a novel locus at 10q24.32 and a significant overlap with schizophrenia , 2017, Molecular Autism.
[71] Michael J. Ziller,et al. Transcription factor binding dynamics during human ESC differentiation , 2015, Nature.
[72] C. Molony,et al. Genomic Characterization of Metformin Hepatic Response , 2016, PLoS genetics.
[73] Thomas J. Ha,et al. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells , 2015, Science.
[74] Cole Trapnell,et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.
[75] Fabian J. Theis,et al. MPRAnalyze: statistical framework for massively parallel reporter assays , 2019, Genome Biology.
[76] Jacob C. Ulirsch,et al. Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits , 2016, Cell.
[77] Nathaniel D. Heintzman,et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression , 2009, Nature.
[78] Cole Trapnell,et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.
[79] Michael J. Ziller,et al. Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells , 2013, Cell.
[80] Clifford A. Meyer,et al. Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.
[81] 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.
[82] Cory Y. McLean,et al. GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.