STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of omics data
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Giosuè Lo Bosco | Martin J. Aryee | Jason D. Buenrostro | Jonathan Y. Hsu | Guocheng Yuan | C. Lareau | J. Guan | M. Aryee | Shuigeng Zhou | J. Buenrostro | A. Gorban | A. Zinovyev | D. E. Bauer | L. Pinello | D. Langenau | L. Albergante | Huidong Chen | Luca Pinello | Guo-cheng Yuan | Guocheng Yuan
[1] Jing Wang,et al. MLLE: Modified Locally Linear Embedding Using Multiple Weights , 2006, NIPS.
[2] Barnett,et al. Supplementary References , 2022 .
[3] Andrei Zinovyev,et al. Principal Manifolds for Data Visualization and Dimension Reduction , 2007 .
[4] P. Cahan,et al. The transcriptional landscape of hematopoietic stem cell ontogeny. , 2012, Cell stem cell.
[5] B. Walzog,et al. Coronin 1A, a novel player in integrin biology, controls neutrophil trafficking in innate immunity. , 2017, Blood.
[6] F. Ginhoux,et al. Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development , 2016, Nature Communications.
[7] Gaël Varoquaux,et al. Scikit-learn: Machine Learning in Python , 2011, J. Mach. Learn. Res..
[8] Fabian J Theis,et al. Diffusion pseudotime robustly reconstructs lineage branching , 2016, Nature Methods.
[9] Andrew C. Adey,et al. Chromatin accessibility dynamics of myogenesis at single cell resolution , 2017, bioRxiv.
[10] Howard Y. Chang,et al. Lineage-specific and single cell chromatin accessibility charts human hematopoiesis and leukemia evolution , 2016, Nature Genetics.
[11] Cole Trapnell,et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells , 2014, Nature Biotechnology.
[12] Li Qian,et al. SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data , 2016, Genome Biology.
[13] M. Segelmark,et al. A myelopoiesis gene signature during remission in anti‐neutrophil cytoplasm antibody‐associated vasculitis does not predict relapses but seems to reflect ongoing prednisolone therapy , 2014, Clinical and experimental immunology.
[14] Alexander N. Gorban,et al. Topological grammars for data approximation , 2007, Appl. Math. Lett..
[15] William Stafford Noble,et al. Quantifying similarity between motifs , 2007, Genome Biology.
[16] Hannah A. Pliner,et al. The cis-regulatory dynamics of embryonic development at single cell resolution , 2017, Nature.
[17] William J. Greenleaf,et al. chromVAR: Inferring transcription factor-associated accessibility from single-cell epigenomic data , 2017, Nature Methods.
[18] Hannah A. Pliner,et al. Reversed graph embedding resolves complex single-cell trajectories , 2017, Nature Methods.
[19] Jun Seita,et al. Hematopoietic stem cell: self‐renewal versus differentiation , 2010, Wiley interdisciplinary reviews. Systems biology and medicine.
[20] Alexander N. Gorban,et al. Robust principal graphs for data approximation , 2016, ArXiv.
[21] 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.
[22] Emmanuel Barillot,et al. Robust and scalable learning of data manifolds with complex topologies via ElPiGraph , 2018, ArXiv.
[23] Howard Y. Chang,et al. Single-cell epigenomics maps the continuous regulatory landscape of human hematopoietic differentiation , 2017, bioRxiv.
[24] Pierre-Antoine Absil,et al. Principal Manifolds for Data Visualization and Dimension Reduction , 2007 .
[25] Manfred Nagl. Formal languages of labelled graphs , 2005, Computing.
[26] Luca Pinello,et al. Serum-Based Culture Conditions Provoke Gene Expression Variability in Mouse Embryonic Stem Cells as Revealed by Single-Cell Analysis. , 2016, Cell reports.
[27] Allon M. Klein,et al. Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells , 2015, Cell.
[28] Kevin R. Moon,et al. PHATE: A Dimensionality Reduction Method for Visualizing Trajectory Structures in High-Dimensional Biological Data , 2017 .
[29] W. Alexander,et al. Runx1 downregulates stem cell and megakaryocytic transcription programs that support niche interactions. , 2016, Blood.
[30] Alexander N. Gorban,et al. Principal Manifolds and Graphs in Practice: from Molecular Biology to Dynamical Systems , 2010, Int. J. Neural Syst..
[31] Howard Y. Chang,et al. Single-cell chromatin accessibility reveals principles of regulatory variation , 2015, Nature.
[32] Elena K. Kandror,et al. Single-cell topological RNA-Seq analysis reveals insights into cellular differentiation and development , 2017, Nature Biotechnology.
[33] Alexander N Gorban,et al. Beyond The Concept of Manifolds: Principal Trees, Metro Maps, and Elastic Cubic Complexes , 2007, 0801.0176.
[34] Cyrille F. Dunant,et al. Distinct routes of lineage development reshape the human blood hierarchy across ontogeny , 2016, Science.
[35] E. Moon,et al. Thymosin Beta-4, Actin-Sequestering Protein Regulates Vascular Endothelial Growth Factor Expression via Hypoxia-Inducible Nitric Oxide Production in HeLa Cervical Cancer Cells , 2015, Biomolecules & therapeutics.
[36] W. Vainchenker,et al. A common bipotent progenitor generates the erythroid and megakaryocyte lineages in embryonic stem cell-derived primitive hematopoiesis. , 2009, Blood.
[37] Nicola K. Wilson,et al. A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation. , 2016, Blood.
[38] Alexander N. Gorban,et al. Principal Graphs and Manifolds , 2008, ArXiv.
[39] E. Marco,et al. Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape , 2014, Proceedings of the National Academy of Sciences.
[40] Hongkai Ji,et al. TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis , 2016, Nucleic acids research.
[41] Colin N. Dewey,et al. Cis-regulatory mechanisms governing stem and progenitor cell transitions , 2015, Science Advances.
[42] S. Orkin,et al. Mapping cellular hierarchy by single-cell analysis of the cell surface repertoire. , 2013, Cell stem cell.
[43] Delbert Dueck,et al. Clustering by Passing Messages Between Data Points , 2007, Science.
[44] I. Amit,et al. Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors , 2015, Cell.
[45] McKenzie L. Shaw,et al. Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing , 2017, The Journal of experimental medicine.
[46] Song Wu,et al. BLVRB redox mutation defines heme degradation in a metabolic pathway of enhanced thrombopoiesis in humans. , 2016, Blood.
[47] Sean C. Bendall,et al. Wishbone identifies bifurcating developmental trajectories from single-cell data , 2016, Nature Biotechnology.
[48] I. Weissman,et al. Differential Expression of Novel Potential Regulators in Hematopoietic Stem Cells , 2005, PLoS genetics.
[49] Edward M. Reingold,et al. Graph drawing by force‐directed placement , 1991, Softw. Pract. Exp..
[50] D. Finkelstein,et al. Generation of hematopoietic progenitor cell lines with myeloid and lymphoid potential , 2013, Nature Methods.
[51] A. Savitzky,et al. Smoothing and Differentiation of Data by Simplified Least Squares Procedures. , 1964 .
[52] Christopher. Simons,et al. Machine learning with Python , 2017 .
[53] Bruce J. Aronow,et al. Single-cell analysis of mixed-lineage states leading to a binary cell fate choice , 2016, Nature.
[54] C. Ceol,et al. Single-cell transcriptional analysis of normal, aberrant, and malignant hematopoiesis in zebrafish , 2016, The Journal of experimental medicine.
[55] Sean R Eddy,et al. What is dynamic programming? , 2004, Nature Biotechnology.