Single-cell topological RNA-Seq analysis reveals insights into cellular differentiation and development
暂无分享,去创建一个
[1] M. Poincaré. Cinquième complément à l’Analysis situs , 1904 .
[2] S. Gaunt,et al. Temporal colinearity in expression of anterior hox genes in developing chick embryos , 1996, Developmental dynamics : an official publication of the American Association of Anatomists.
[3] David J. Anderson,et al. neurogenins,a Novel Family ofatonal-Related bHLH Transcription Factors, Are Putative Mammalian Neuronal Determination Genes That Reveal Progenitor Cell Heterogeneity in the Developing CNS and PNS , 1996, Molecular and Cellular Neuroscience.
[4] T. Jessell. Neuronal specification in the spinal cord: inductive signals and transcriptional codes , 2000, Nature Reviews Genetics.
[5] H. Wichterle,et al. Directed Differentiation of Embryonic Stem Cells into Motor Neurons , 2002, Cell.
[6] Herbert Edelsbrunner,et al. Topological Persistence and Simplification , 2000, Proceedings 41st Annual Symposium on Foundations of Computer Science.
[7] R. Blomhoff,et al. Gene expression regulation by retinoic acid Published, JLR Papers in Press, August 16, 2002. DOI 10.1194/jlr.R100015-JLR200 , 2002, Journal of Lipid Research.
[8] Afra Zomorodian,et al. Computing Persistent Homology , 2004, SCG '04.
[9] Paulo P. Amaral,et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. , 2008, Genome research.
[10] John A. Calarco,et al. Regulation of Vertebrate Nervous System Alternative Splicing and Development by an SR-Related Protein , 2009, Cell.
[11] Lior Pachter,et al. Sequence Analysis , 2020, Definitions.
[12] Todd C McDevitt,et al. Engineering the embryoid body microenvironment to direct embryonic stem cell differentiation , 2009, Biotechnology progress.
[13] Gunnar E. Carlsson,et al. Topology and data , 2009 .
[14] Herbert Edelsbrunner,et al. Computational Topology - an Introduction , 2009 .
[15] Rachael P. Huntley,et al. QuickGO: a web-based tool for Gene Ontology searching , 2009, Bioinform..
[16] G. Carlsson,et al. Topology based data analysis identifies a subgroup of breast cancers with a unique mutational profile and excellent survival , 2011, Proceedings of the National Academy of Sciences.
[17] D. Zheng,et al. RNA-Seq of Human Neurons Derived from iPS Cells Reveals Candidate Long Non-Coding RNAs Involved in Neurogenesis and Neuropsychiatric Disorders , 2011, PloS one.
[18] P. Dollé,et al. Retinoic acid signalling during development , 2012, Development.
[19] T. Hashimshony,et al. CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. , 2012, Cell reports.
[20] Aleksandra A. Kolodziejczyk,et al. Accounting for technical noise in single-cell RNA-seq experiments , 2013, Nature Methods.
[21] G. Carlsson,et al. Topology of viral evolution , 2013, Proceedings of the National Academy of Sciences.
[22] C. Alonso,et al. The regulation of Hox gene expression during animal development , 2013, Development.
[23] Anushya Muruganujan,et al. Large-scale gene function analysis with the PANTHER classification system , 2013, Nature Protocols.
[24] R. Myers,et al. Intricate interplay between astrocytes and motor neurons in ALS , 2013, Proceedings of the National Academy of Sciences.
[25] Robert B Darnell,et al. RNA protein interaction in neurons. , 2013, Annual review of neuroscience.
[26] Shmuel Weinberger,et al. The Complexity of Some Topological Inference Problems , 2014, Found. Comput. Math..
[27] P. Kharchenko,et al. Bayesian approach to single-cell differential expression analysis , 2014, Nature Methods.
[28] Sean C. Bendall,et al. Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development , 2014, Cell.
[29] Cole Trapnell,et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells , 2014, Nature Biotechnology.
[30] A. Oudenaarden,et al. Validation of noise models for single-cell transcriptomics , 2014, Nature Methods.
[31] N. Neff,et al. Reconstructing lineage hierarchies of the distal lung epithelium using single cell RNA-seq , 2014, Nature.
[32] Rona S. Gertner,et al. Single cell RNA Seq reveals dynamic paracrine control of cellular variation , 2014, Nature.
[33] E. Marco,et al. Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape , 2014, Proceedings of the National Academy of Sciences.
[34] S. Weissman,et al. Long intergenic non-coding RNA HOTAIRM1 regulates cell cycle progression during myeloid maturation in NB4 human promyelocytic leukemia cells , 2014, RNA biology.
[35] P. Linsley,et al. MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data , 2015, Genome Biology.
[36] María Martín,et al. UniProt: A hub for protein information , 2015 .
[37] The Uniprot Consortium,et al. UniProt: a hub for protein information , 2014, Nucleic Acids Res..
[38] B. Blencowe,et al. Essential roles for the splicing regulator nSR100/SRRM4 during nervous system development , 2015, Genes & development.
[39] Paul Theodor Pyl,et al. HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.
[40] S. Teichmann,et al. Computational and analytical challenges in single-cell transcriptomics , 2015, Nature Reviews Genetics.
[41] Benjamin S. Glicksberg,et al. Identification of type 2 diabetes subgroups through topological analysis of patient similarity , 2015, Science Translational Medicine.
[42] A. Regev,et al. Spatial reconstruction of single-cell gene expression data , 2015 .
[43] Fabian J Theis,et al. Diffusion pseudotime robustly reconstructs lineage branching , 2016, Nature Methods.
[44] Li Qian,et al. SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data , 2016, Genome Biology.
[45] J. D. Macklis,et al. Modeling ALS with motor neurons derived from human induced pluripotent stem cells , 2016, Nature Neuroscience.
[46] Alvaro Plaza Reyes,et al. Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos , 2016, Cell.
[47] Kevin J. Emmett,et al. Topological Data Analysis Generates High-Resolution, Genome-wide Maps of Human Recombination. , 2016, Cell systems.
[48] Fabian J. Theis,et al. destiny: diffusion maps for large-scale single-cell data in R , 2015, Bioinform..
[49] Pablo G. Cámara,et al. Inference of Ancestral Recombination Graphs through Topological Data Analysis , 2015, PLoS Comput. Biol..
[50] Greg Finak,et al. The contribution of cell cycle to heterogeneity in single-cell RNA-seq data , 2016, Nature Biotechnology.
[51] Wei Wu,et al. NONCODE 2016: an informative and valuable data source of long non-coding RNAs , 2015, Nucleic Acids Res..
[52] Bei Wang,et al. Convergence between Categorical Representations of Reeb Space and Mapper , 2015, SoCG.
[53] Julien Prados,et al. Sequential transcriptional waves direct the differentiation of newborn neurons in the mouse neocortex , 2016, Science.
[54] Sean C. Bendall,et al. Wishbone identifies bifurcating developmental trajectories from single-cell data , 2016, Nature Biotechnology.
[55] R. Ho. Algebraic Topology , 2022 .