Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming
暂无分享,去创建一个
P. Rigollet | A. Regev | E. Lander | R. Jaenisch | Geoffrey Schiebinger | J. Shu | M. Tabaka | B. Cleary | Vidya Subramanian | A. Solomon | Siyan Liu | Stacie Lin | P. Berube | Lia Lee | Jenny Chen | J. Brumbaugh | K. Hochedlinger | Joshua Gould | Justin Brumbaugh
[1] A. van Oudenaarden,et al. Single-Cell Transcriptomics Meets Lineage Tracing. , 2018, Cell stem cell.
[2] Chao Tang,et al. Single-Cell RNA-Seq Reveals Dynamic Early Embryonic-like Programs during Chemical Reprogramming. , 2018, Cell stem cell.
[3] Allon M. Klein,et al. Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo , 2018, Science.
[4] A. Regev,et al. Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis , 2018, Science.
[5] Paul Hoffman,et al. Integrating single-cell transcriptomic data across different conditions, technologies, and species , 2018, Nature Biotechnology.
[6] Yvan Saeys,et al. A comparison of single-cell trajectory inference methods: towards more accurate and robust tools , 2018, bioRxiv.
[7] Sagar,et al. FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data , 2017, Nature Methods.
[8] Fabian J. Theis,et al. PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells , 2017, Genome Biology.
[9] Caleb Weinreb,et al. Fundamental limits on dynamic inference from single-cell snapshots , 2017, Proceedings of the National Academy of Sciences.
[10] Michael B. Stadler,et al. DMRTC2, PAX7, BRACHYURY/T and TERT Are Implicated in Male Germ Cell Development Following Curative Hormone Treatment for Cryptorchidism-Induced Infertility , 2017, Genes.
[11] Hannah A. Pliner,et al. Reversed graph embedding resolves complex single-cell trajectories , 2017, Nature Methods.
[12] Ziv Bar-Joseph,et al. TASIC: determining branching models from time series single cell data , 2017, Bioinform..
[13] R. Raychowdhury,et al. An Integrative Framework Reveals Signaling-to-Transcription Events in Toll-like Receptor Signaling. , 2017, Cell reports.
[14] Caleb Weinreb,et al. SPRING: a kinetic interface for visualizing high dimensional single-cell expression data , 2017, bioRxiv.
[15] Neil D. Lawrence,et al. Single-cell RNA-seq and computational analysis using temporal mixture modeling resolves TH1/TFH fate bifurcation in malaria , 2017, Science Immunology.
[16] A. Regev,et al. Scaling single-cell genomics from phenomenology to mechanism , 2017, Nature.
[17] Lénaïc Chizat,et al. Scaling Algorithms for Unbalanced Transport Problems , 2016, 1607.05816.
[18] Zachary D. Smith,et al. Probabilistic Modeling of Reprogramming to Induced Pluripotent Stem Cells. , 2016, Cell reports.
[19] M. Blasco,et al. Tissue damage and senescence provide critical signals for cellular reprogramming in vivo , 2016, Science.
[20] Mariella G. Filbin,et al. Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma , 2016, Nature.
[21] M. Hemberger,et al. From the stem of the placental tree: trophoblast stem cells and their progeny , 2016, Development.
[22] Mesenchyme associated transcription factor PRRX1: A key regulator of IPF fibroblast , 2016 .
[23] Dongcai Wu,et al. CXCR2 is decreased in preeclamptic placentas and promotes human trophoblast invasion through the Akt signaling pathway. , 2016, Placenta.
[24] Junjie Lu,et al. MSX2 Induces Trophoblast Invasion in Human Placenta , 2016, PloS one.
[25] Michael A. Halbisen,et al. OSKM Induce Extraembryonic Endoderm Stem Cells in Parallel to Induced Pluripotent Stem Cells , 2016, Stem cell reports.
[26] S. Yamanaka,et al. A decade of transcription factor-mediated reprogramming to pluripotency , 2016, Nature Reviews Molecular Cell Biology.
[27] Hyuk Song,et al. SOHLH2 is essential for synaptonemal complex formation during spermatogenesis in early postnatal mouse testes , 2016, Scientific Reports.
[28] J. Baker,et al. Selective Amplification of the Genome Surrounding Key Placental Genes in Trophoblast Giant Cells , 2016, Current Biology.
[29] Simon James Tunster,et al. The imprinted Phlda2 gene modulates a major endocrine compartment of the placenta to regulate placental demands for maternal resources , 2016, Developmental biology.
[30] Aleksandra A. Kolodziejczyk,et al. Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation , 2015, Cell stem cell.
[31] G. Pan,et al. The oncogene c-Jun impedes somatic cell reprogramming , 2015, Nature Cell Biology.
[32] Michael J. Ziller,et al. Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency , 2015, Cell.
[33] Eli R. Zunder,et al. A continuous molecular roadmap to iPSC reprogramming through progression analysis of single-cell mass cytometry. , 2015, Cell stem cell.
[34] Zakary S. Singer,et al. Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming. , 2015, Cell stem cell.
[35] Filippo Santambrogio,et al. Optimal Transport for Applied Mathematicians , 2015 .
[36] P. Verma,et al. Cell Reprogramming , 2015, Methods in Molecular Biology.
[37] K. Plath,et al. X Chromosome Reactivation Dynamics Reveal Stages of Reprogramming to Pluripotency , 2014, Cell.
[38] E. Marco,et al. Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape , 2014, Proceedings of the National Academy of Sciences.
[39] D. Salomon,et al. The multifaceted role of the embryonic gene Cripto-1 in cancer, stem cells and epithelial-mesenchymal transition. , 2014, Seminars in cancer biology.
[40] M. Jacomy,et al. ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software , 2014, PloS one.
[41] Christian L'eonard. A survey of the Schr\"odinger problem and some of its connections with optimal transport , 2013, 1308.0215.
[42] Marco Cuturi. Sinkhorn Distances: Lightspeed Computation of Optimal Transportation Distances , 2013, 1306.0895.
[43] S. Linnarsson,et al. High resolution analysis with novel cell-surface markers identifies routes to iPS cells , 2013, Nature.
[44] S. Ramaswamy,et al. A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells , 2012, Cell.
[45] N. Grishin,et al. Unexpected diversity in Shisa-like proteins suggests the importance of their roles as transmembrane adaptors. , 2012, Cellular signalling.
[46] R. Brinster,et al. The POU Domain Transcription Factor POU3F1 Is an Important Intrinsic Regulator of GDNF-Induced Survival and Self-Renewal of Mouse Spermatogonial Stem Cells1 , 2010, Biology of reproduction.
[47] C. Glass,et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.
[48] Benjamin L. Kidder,et al. Examination of transcriptional networks reveals an important role for TCFAP2C, SMARCA4, and EOMES in trophoblast stem cell maintenance. , 2010, Genome research.
[49] R. Gronostajski,et al. Nfix Regulates Fetal-Specific Transcription in Developing Skeletal Muscle , 2010, Cell.
[50] J. Rossant,et al. Gata3 regulates trophoblast development downstream of Tead4 and in parallel to Cdx2 , 2010, Development.
[51] K. Hochedlinger,et al. A reprogrammable mouse strain from gene-targeted embryonic stem cells , 2010, Nature Methods.
[52] M. Parast,et al. PPARγ Regulates Trophoblast Proliferation and Promotes Labyrinthine Trilineage Differentiation , 2009, PloS one.
[53] Arthur Cayley,et al. The Collected Mathematical Papers: On Monge's “Mémoire sur la théorie des déblais et des remblais” , 2009 .
[54] C. Villani. Optimal Transport: Old and New , 2008 .
[55] T. Mikkelsen,et al. Dissecting direct reprogramming through integrative genomic analysis , 2008, Nature.
[56] B. Doble,et al. The ground state of embryonic stem cell self-renewal , 2008, Nature.
[57] C. Lengner,et al. Sequential expression of pluripotency markers during direct reprogramming of mouse somatic cells. , 2008, Cell stem cell.
[58] T. Griffin,et al. PRR5, a Novel Component of mTOR Complex 2, Regulates Platelet-derived Growth Factor Receptor β Expression and Signaling* , 2007, Journal of Biological Chemistry.
[59] Weiwei Zhang,et al. Zic3 is required for maintenance of pluripotency in embryonic stem cells. , 2007, Molecular biology of the cell.
[60] U. Bogdahn,et al. TGF-beta in neural stem cells and in tumors of the central nervous system , 2007, Cell and Tissue Research.
[61] S. Yamanaka,et al. Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors , 2006, Cell.
[62] G. Pan,et al. Regulation of the Pluripotency Marker Rex-1 by Nanog and Sox2* , 2006, Journal of Biological Chemistry.
[63] S. Dunwoodie,et al. Loss of Cited2 affects trophoblast formation and vascularization of the mouse placenta. , 2006, Developmental biology.
[64] L. Kantorovich. On the Translocation of Masses , 2006 .
[65] J. Cross,et al. Determinants of trophoblast lineage and cell subtype specification in the mouse placenta. , 2005, Developmental biology.
[66] L. Ambrosio,et al. Gradient Flows: In Metric Spaces and in the Space of Probability Measures , 2005 .
[67] Wei Yan,et al. Obox, a family of homeobox genes preferentially expressed in germ cells. , 2002, Genomics.
[68] M. Cybulsky,et al. Wnt7b regulates placental development in mice. , 2001, Developmental biology.
[69] S. Chevalier,et al. CLF associates with CLC to form a functional heteromeric ligand for the CNTF receptor complex , 2000, Nature Neuroscience.
[70] J. Cross,et al. The HAND1 Basic Helix-Loop-Helix Transcription Factor Regulates Trophoblast Differentiation via Multiple Mechanisms , 2000, Molecular and Cellular Biology.
[71] J. D. Engel,et al. GATA-2 and GATA-3 regulate trophoblast-specific gene expression in vivo. , 1997, Development.
[72] D. Kinderlehrer,et al. THE VARIATIONAL FORMULATION OF THE FOKKER-PLANCK EQUATION , 1996 .
[73] C. Waddington,et al. The strategy of the genes , 1957 .
[74] F. H. A. MARSHALL,et al. How Animals Develop , 1936, Nature.
[75] E. Schrödinger. Sur la théorie relativiste de l'électron et l'interprétation de la mécanique quantique , 1932 .