Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor
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Sara Ballouz | Jesse Gillis | Z Josh Huang | Anirban Paul | Megan Crow | Z. J. Huang | J. Gillis | Sara Ballouz | M. Crow | A. Paul | Z. J. Huang
[1] R. Tibshirani,et al. Repeated observation of breast tumor subtypes in independent gene expression data sets , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[2] R. Irizarry,et al. Missing data and technical variability in single‐cell RNA‐sequencing experiments , 2018, Biostatistics.
[3] Christoph Bock,et al. Single‐cell transcriptomes reveal characteristic features of human pancreatic islet cell types , 2015, EMBO reports.
[4] Z. Bar-Joseph,et al. Using neural networks for reducing the dimensions of single-cell RNA-Seq data , 2017, Nucleic acids research.
[5] Fabian J Theis,et al. The Human Cell Atlas , 2017, bioRxiv.
[6] S. Dudoit,et al. Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data , 2002 .
[7] Jason Tucciarone,et al. Strategies and Tools for Combinatorial Targeting of GABAergic Neurons in Mouse Cerebral Cortex , 2016, Neuron.
[8] Yuval Kluger,et al. Lineage specificity of gene expression patterns. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[9] Lan Bao,et al. Somatosensory neuron types identified by high-coverage single-cell RNA-sequencing and functional heterogeneity , 2016, Cell Research.
[10] D. Craig,et al. Transcriptomics , 2020, Nature Biotechnology.
[11] Samuel L. Wolock,et al. A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure. , 2016, Cell systems.
[12] Aleksandra A. Kolodziejczyk,et al. The technology and biology of single-cell RNA sequencing. , 2015, Molecular cell.
[13] J. Schug,et al. Single-Cell Transcriptomics of the Human Endocrine Pancreas , 2016, Diabetes.
[14] Cynthia C. Hession,et al. Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons , 2016, Science.
[15] Leopold Parts,et al. A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies , 2010, PLoS Comput. Biol..
[16] Evan Z. Macosko,et al. Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics , 2016, Cell.
[17] Yuchio Yanagawa,et al. Integration of electrophysiological recordings with single-cell RNA-seq data identifies novel neuronal subtypes , 2015, Nature Biotechnology.
[18] John C. Marioni,et al. Correcting batch effects in single-cell RNA sequencing data by matching mutual nearest neighbours , 2017, bioRxiv.
[19] Z. J. Huang,et al. Transcriptional Architecture of Synaptic Communication Delineates GABAergic Neuron Identity , 2017, Cell.
[20] Catalina A. Vallejos,et al. BASiCS: Bayesian Analysis of Single-Cell Sequencing Data , 2015, PLoS Comput. Biol..
[21] John C. Marioni,et al. Additional file 1 of Pooling across cells to normalize single-cell RNA sequencing data with many zero counts , 2016 .
[22] Matt Thomson,et al. Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing. , 2016, Cell systems.
[23] Fabian J Theis,et al. Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells , 2015, Nature Biotechnology.
[24] Patrick F Sullivan,et al. The Psychiatric GWAS Consortium: Big Science Comes to Psychiatry , 2010, Neuron.
[25] A. Murphy,et al. RNA Sequencing of Single Human Islet Cells Reveals Type 2 Diabetes Genes. , 2016, Cell metabolism.
[26] Roland Eils,et al. Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes , 2005, BMC Bioinformatics.
[27] Aleksandra A. Kolodziejczyk,et al. Accounting for technical noise in single-cell RNA-seq experiments , 2013, Nature Methods.
[28] S. Linnarsson,et al. Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing , 2014, Nature Neuroscience.
[29] Y. Benjamini,et al. Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .
[30] E. Marcotte,et al. Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana , 2010, Nature Biotechnology.
[31] Alexander J. Hartemink,et al. MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics , 2017, Genome Biology.
[32] E. P. Gardner,et al. Petilla terminology: nomenclature of features of GABAergic interneurons of the cerebral cortex , 2008, Nature Reviews Neuroscience.
[33] S. Linnarsson,et al. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq , 2015, Science.
[34] Emma Pierson,et al. ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis , 2015, Genome Biology.
[35] R. Fisher. Statistical methods for research workers , 1927, Protoplasma.
[36] David Venet,et al. Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome , 2011, PLoS Comput. Biol..
[37] Evan Z. Macosko,et al. Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets , 2015, Cell.
[38] Hannah Dueck,et al. Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation , 2015, Genome Biology.
[39] Allon M. Klein,et al. Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells , 2015, Cell.
[40] Mauro J. Muraro,et al. A Single-Cell Transcriptome Atlas of the Human Pancreas , 2016, Cell systems.
[41] Staci A. Sorensen,et al. Adult Mouse Cortical Cell Taxonomy Revealed by Single Cell Transcriptomics , 2016 .
[42] A. Regev,et al. Revealing the vectors of cellular identity with single-cell genomics , 2016, Nature Biotechnology.
[43] Andrew Butler,et al. Integrated analysis of single cell transcriptomic data across conditions, technologies, and species , 2017, bioRxiv.
[44] E. Hovig,et al. Methods that remove batch effects while retaining group differences may lead to exaggerated confidence in downstream analyses , 2015, Biostatistics.
[45] Lior Pachter,et al. Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis , 2015, Science.
[46] Maqc Consortium. The MicroArray Quality Control ( MAQC )-II study of common practices for the development and validation of microarray-based predictive models , 2012 .
[47] Sara Ballouz,et al. Guidance for RNA-seq co-expression network construction and analysis: safety in numbers , 2015, Bioinform..
[48] Lars E. Borm,et al. Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells , 2016, Cell.
[49] Jens Hjerling-Leffler,et al. Disentangling neural cell diversity using single-cell transcriptomics , 2016, Nature Neuroscience.
[50] Michael I. Jordan,et al. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence , 2008, Genome Biology.
[51] Martin Hemberg,et al. scmap - A tool for unsupervised projection of single cell RNA-seq data , 2017, bioRxiv.
[52] N. Neff,et al. Reconstructing lineage hierarchies of the distal lung epithelium using single cell RNA-seq , 2014, Nature.
[53] Amy V Kapp,et al. Discovery and validation of breast cancer subtypes , 2006, BMC Genomics.
[54] Sara Ballouz,et al. EGAD: Ultra-fast functional analysis of gene networks , 2016, bioRxiv.
[55] Evan Z. Macosko,et al. A Molecular Census of Arcuate Hypothalamus and Median Eminence Cell Types , 2017, Nature Neuroscience.
[56] D. M. Smith,et al. Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes , 2016, Cell metabolism.
[57] Amy V Kapp,et al. Are clusters found in one dataset present in another dataset? , 2007, Biostatistics.
[58] Yu-Jin Jung,et al. Identification of Distinct Tumor Subpopulations in Lung Adenocarcinoma via Single-Cell RNA-seq , 2015, PloS one.
[59] Hans Clevers,et al. Single-cell messenger RNA sequencing reveals rare intestinal cell types , 2015, Nature.
[60] Spyros Darmanis,et al. Single-cell RNAseq reveals cell adhesion molecule profiles in electrophysiologically defined neurons , 2016, Proceedings of the National Academy of Sciences.