Resource Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming Graphical

[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]  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.

[9]  Hannah A. Pliner,et al.  Reversed graph embedding resolves complex single-cell trajectories , 2017, Nature Methods.

[10]  Ziv Bar-Joseph,et al.  TASIC: determining branching models from time series single cell data , 2017, Bioinform..

[11]  Caleb Weinreb,et al.  SPRING: a kinetic interface for visualizing high dimensional single-cell expression data , 2017, bioRxiv.

[12]  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.

[13]  A. Regev,et al.  Scaling single-cell genomics from phenomenology to mechanism , 2017, Nature.

[14]  Lénaïc Chizat,et al.  Scaling Algorithms for Unbalanced Transport Problems , 2016, 1607.05816.

[15]  Zachary D. Smith,et al.  Probabilistic Modeling of Reprogramming to Induced Pluripotent Stem Cells. , 2016, Cell reports.

[16]  M. Blasco,et al.  Tissue damage and senescence provide critical signals for cellular reprogramming in vivo , 2016, Science.

[17]  Mariella G. Filbin,et al.  Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma , 2016, Nature.

[18]  M. Hemberger,et al.  From the stem of the placental tree: trophoblast stem cells and their progeny , 2016, Development.

[19]  Mesenchyme associated transcription factor PRRX1: A key regulator of IPF fibroblast , 2016 .

[20]  Dongcai Wu,et al.  CXCR2 is decreased in preeclamptic placentas and promotes human trophoblast invasion through the Akt signaling pathway. , 2016, Placenta.

[21]  Junjie Lu,et al.  MSX2 Induces Trophoblast Invasion in Human Placenta , 2016, PloS one.

[22]  Michael A. Halbisen,et al.  OSKM Induce Extraembryonic Endoderm Stem Cells in Parallel to Induced Pluripotent Stem Cells , 2016, Stem cell reports.

[23]  S. Yamanaka,et al.  A decade of transcription factor-mediated reprogramming to pluripotency , 2016, Nature Reviews Molecular Cell Biology.

[24]  Hyuk Song,et al.  SOHLH2 is essential for synaptonemal complex formation during spermatogenesis in early postnatal mouse testes , 2016, Scientific Reports.

[25]  J. Baker,et al.  Selective Amplification of the Genome Surrounding Key Placental Genes in Trophoblast Giant Cells , 2016, Current Biology.

[26]  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.

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

[28]  G. Pan,et al.  The oncogene c-Jun impedes somatic cell reprogramming , 2015, Nature Cell Biology.

[29]  Michael J. Ziller,et al.  Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency , 2015, Cell.

[30]  Zakary S. Singer,et al.  Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming. , 2015, Cell stem cell.

[31]  Filippo Santambrogio,et al.  Optimal Transport for Applied Mathematicians , 2015 .

[32]  P. Verma,et al.  Cell Reprogramming , 2015, Methods in Molecular Biology.

[33]  K. Plath,et al.  X Chromosome Reactivation Dynamics Reveal Stages of Reprogramming to Pluripotency , 2014, Cell.

[34]  E. Marco,et al.  Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape , 2014, Proceedings of the National Academy of Sciences.

[35]  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.

[36]  M. Jacomy,et al.  ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software , 2014, PloS one.

[37]  Christian L'eonard A survey of the Schr\"odinger problem and some of its connections with optimal transport , 2013, 1308.0215.

[38]  S. Linnarsson,et al.  High resolution analysis with novel cell-surface markers identifies routes to iPS cells , 2013, Nature.

[39]  Marco Cuturi,et al.  Sinkhorn Distances: Lightspeed Computation of Optimal Transportation , 2013, NIPS 2013.

[40]  S. Ramaswamy,et al.  A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells , 2012, Cell.

[41]  N. Grishin,et al.  Unexpected diversity in Shisa-like proteins suggests the importance of their roles as transmembrane adaptors. , 2012, Cellular signalling.

[42]  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.

[43]  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.

[44]  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.

[45]  R. Gronostajski,et al.  Nfix Regulates Fetal-Specific Transcription in Developing Skeletal Muscle , 2010, Cell.

[46]  J. Rossant,et al.  Gata3 regulates trophoblast development downstream of Tead4 and in parallel to Cdx2 , 2010, Development.

[47]  K. Hochedlinger,et al.  A reprogrammable mouse strain from gene-targeted embryonic stem cells , 2010, Nature Methods.

[48]  M. Parast,et al.  PPARγ Regulates Trophoblast Proliferation and Promotes Labyrinthine Trilineage Differentiation , 2009, PloS one.

[49]  Arthur Cayley,et al.  The Collected Mathematical Papers: On Monge's “Mémoire sur la théorie des déblais et des remblais” , 2009 .

[50]  C. Villani Optimal Transport: Old and New , 2008 .

[51]  T. Mikkelsen,et al.  Dissecting direct reprogramming through integrative genomic analysis , 2008, Nature.

[52]  C. Lengner,et al.  Sequential expression of pluripotency markers during direct reprogramming of mouse somatic cells. , 2008, Cell stem cell.

[53]  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.

[54]  Weiwei Zhang,et al.  Zic3 is required for maintenance of pluripotency in embryonic stem cells. , 2007, Molecular biology of the cell.

[55]  U. Bogdahn,et al.  TGF-beta in neural stem cells and in tumors of the central nervous system , 2007, Cell and Tissue Research.

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

[57]  G. Pan,et al.  Regulation of the Pluripotency Marker Rex-1 by Nanog and Sox2* , 2006, Journal of Biological Chemistry.

[58]  S. Dunwoodie,et al.  Loss of Cited2 affects trophoblast formation and vascularization of the mouse placenta. , 2006, Developmental biology.

[59]  L. Kantorovich On the Translocation of Masses , 2006 .

[60]  J. Cross,et al.  Determinants of trophoblast lineage and cell subtype specification in the mouse placenta. , 2005, Developmental biology.

[61]  L. Ambrosio,et al.  Gradient Flows: In Metric Spaces and in the Space of Probability Measures , 2005 .

[62]  Wei Yan,et al.  Obox, a family of homeobox genes preferentially expressed in germ cells. , 2002, Genomics.

[63]  M. Cybulsky,et al.  Wnt7b regulates placental development in mice. , 2001, Developmental biology.

[64]  S. Chevalier,et al.  CLF associates with CLC to form a functional heteromeric ligand for the CNTF receptor complex , 2000, Nature Neuroscience.

[65]  J. Cross,et al.  The HAND1 Basic Helix-Loop-Helix Transcription Factor Regulates Trophoblast Differentiation via Multiple Mechanisms , 2000, Molecular and Cellular Biology.

[66]  J. D. Engel,et al.  GATA-2 and GATA-3 regulate trophoblast-specific gene expression in vivo. , 1997, Development.

[67]  D. Kinderlehrer,et al.  THE VARIATIONAL FORMULATION OF THE FOKKER-PLANCK EQUATION , 1996 .

[68]  C. Waddington How animals develop / by C.H. Waddington. , 1936 .

[69]  E. Schrödinger Sur la théorie relativiste de l'électron et l'interprétation de la mécanique quantique , 1932 .