Eukaryotic Single-Cell mRNA Sequencing

[1]  H. Ueda,et al.  Erratum to: Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity , 2017, Genome Biology.

[2]  Allon M. Klein,et al.  Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells , 2015, Cell.

[3]  Nevenka Dimitrova,et al.  Optimizing sparse sequencing of single cells for highly multiplex copy number profiling , 2015, Genome research.

[4]  Evan Z. Macosko,et al.  Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets , 2015, Cell.

[5]  J. Radich,et al.  Single-cell genotyping demonstrates complex clonal diversity in acute myeloid leukemia , 2015, Science Translational Medicine.

[6]  N. Navin,et al.  SNES: single nucleus exome sequencing , 2015, Genome Biology.

[7]  Steven L Salzberg,et al.  HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.

[8]  S. Linnarsson,et al.  Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq , 2015, Science.

[9]  S. P. Fodor,et al.  Combinatorial labeling of single cells for gene expression cytometry , 2015, Science.

[10]  C. Walsh,et al.  Cell Lineage Analysis in Human Brain Using Endogenous Retroelements , 2015, Neuron.

[11]  Siddharth S. Dey,et al.  Integrated genome and transcriptome sequencing from the same cell , 2014, Nature Biotechnology.

[12]  W. Koh,et al.  Dissecting the clonal origins of childhood acute lymphoblastic leukemia by single-cell genomics , 2014, Proceedings of the National Academy of Sciences.

[13]  Michael C. Schatz,et al.  Interactive analysis and quality assessment of single-cell copy-number variations , 2014, bioRxiv.

[14]  Lana X. Garmire,et al.  Co-detection and sequencing of genes and transcripts from the same single cells facilitated by a microfluidics platform , 2014, Scientific Reports.

[15]  Annapurna Poduri,et al.  Single-Cell, Genome-wide Sequencing Identifies Clonal Somatic Copy-Number Variation in the Human Brain , 2014, Cell reports.

[16]  Charles Gawad,et al.  A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods , 2014, PloS one.

[17]  N. Navin,et al.  Clonal Evolution in Breast Cancer Revealed by Single Nucleus Genome Sequencing , 2014, Nature.

[18]  Alex A. Pollen,et al.  Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex , 2014, Nature Biotechnology.

[19]  Ryan A. Kellogg,et al.  High-throughput microfluidic single-cell analysis pipeline for studies of signaling dynamics , 2014, Nature Protocols.

[20]  Rona S. Gertner,et al.  Single cell RNA Seq reveals dynamic paracrine control of cellular variation , 2014, Nature.

[21]  J. C. Love,et al.  EGFR variant heterogeneity in glioblastoma resolved through single-nucleus sequencing. , 2014, Cancer discovery.

[22]  P. Kharchenko,et al.  Bayesian approach to single-cell differential expression analysis , 2014, Nature Methods.

[23]  A. Oudenaarden,et al.  Validation of noise models for single-cell transcriptomics , 2014, Nature Methods.

[24]  Cole Trapnell,et al.  The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells , 2014, Nature Biotechnology.

[25]  D. Cacchiarelli,et al.  Characterization of directed differentiation by high-throughput single-cell RNA-Seq , 2014, bioRxiv.

[26]  I. Amit,et al.  Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types , 2014, Science.

[27]  S. P. Fodor,et al.  Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations , 2014, Proceedings of the National Academy of Sciences.

[28]  Gioele La Manno,et al.  Quantitative single-cell RNA-seq with unique molecular identifiers , 2013, Nature Methods.

[29]  P. Nürnberg,et al.  Enrichment of target sequences for next-generation sequencing applications in research and diagnostics , 2013, Biological chemistry.

[30]  Åsa K. Björklund,et al.  Full-length RNA-seq from single cells using Smart-seq2 , 2014, Nature Protocols.

[31]  N. Neff,et al.  Quantitative assessment of single-cell RNA-sequencing methods , 2013, Nature Methods.

[32]  Eivind Hovig,et al.  Performance comparison of four exome capture systems for deep sequencing , 2014, BMC Genomics.

[33]  Rong Li,et al.  Genome Analyses of Single Human Oocytes , 2013, Cell.

[34]  X. Xie,et al.  Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients , 2013, Proceedings of the National Academy of Sciences.

[35]  Kun Zhang,et al.  Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells , 2013, Nature Biotechnology.

[36]  Åsa K. Björklund,et al.  Smart-seq2 for sensitive full-length transcriptome profiling in single cells , 2013, Nature Methods.

[37]  Ira M. Hall,et al.  Mosaic Copy Number Variation in Human Neurons , 2013, Science.

[38]  Mauricio O. Carneiro,et al.  From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.

[39]  Aleksandra A. Kolodziejczyk,et al.  Accounting for technical noise in single-cell RNA-seq experiments , 2013, Nature Methods.

[40]  Jay Shendure,et al.  Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation , 2013, Genome research.

[41]  M. Stratton,et al.  Single-cell paired-end genome sequencing reveals structural variation per cell cycle , 2013, Nucleic acids research.

[42]  P. Blainey The future is now: single-cell genomics of bacteria and archaea. , 2013, FEMS microbiology reviews.

[43]  David G Hendrickson,et al.  Differential analysis of gene regulation at transcript resolution with RNA-seq , 2012, Nature Biotechnology.

[44]  Mary Goldman,et al.  The UCSC Genome Browser database: extensions and updates 2013 , 2012, Nucleic Acids Res..

[45]  S. Gabriel,et al.  Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability , 2012, Genome research.

[46]  Andrew McDavid,et al.  Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments , 2012, Bioinform..

[47]  Stephen R Quake,et al.  Optofluidic cell selection from complex microbial communities for single-genome analysis. , 2013, Methods in enzymology.

[48]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[49]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[50]  J. Marioni,et al.  Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data , 2013, Genome Biology.

[51]  X. Xie,et al.  Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell , 2012, Science.

[52]  Michael L. Simpson,et al.  Transcriptional burst frequency and burst size are equally modulated across the human genome , 2012, Proceedings of the National Academy of Sciences.

[53]  T. Hashimshony,et al.  CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. , 2012, Cell reports.

[54]  I. Weissman,et al.  Clonal Evolution of Preleukemic Hematopoietic Stem Cells Precedes Human Acute Myeloid Leukemia , 2012, Science Translational Medicine.

[55]  Günter P. Wagner,et al.  Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples , 2012, Theory in Biosciences.

[56]  Jesse J. Salk,et al.  Detection of ultra-rare mutations by next-generation sequencing , 2012, Proceedings of the National Academy of Sciences.

[57]  Stephen R. Quake,et al.  Genome-wide Single-Cell Analysis of Recombination Activity and De Novo Mutation Rates in Human Sperm , 2012, Cell.

[58]  Xiaoqing Yu,et al.  How do alignment programs perform on sequencing data with varying qualities and from repetitive regions? , 2012, BioData Mining.

[59]  R. Sandberg,et al.  Full-Length mRNA-Seq from single cell levels of RNA and individual circulating tumor cells , 2012, Nature Biotechnology.

[60]  Michael Wigler,et al.  Genome-wide copy number analysis of single cells , 2012, Nature Protocols.

[61]  Pawel Zajac,et al.  Highly multiplexed and strand-specific single-cell RNA 5′ end sequencing , 2012, Nature Protocols.

[62]  Alexander Schliep,et al.  CLEVER: clique-enumerating variant finder , 2012, Bioinform..

[63]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[64]  Christopher A. Miller,et al.  VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. , 2012, Genome research.

[65]  David R. Kelley,et al.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.

[66]  Tony Z. Jia,et al.  Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes , 2012, Proceedings of the National Academy of Sciences.

[67]  S. Linnarsson,et al.  Counting absolute numbers of molecules using unique molecular identifiers , 2011, Nature Methods.

[68]  Benjamin J. Raphael,et al.  An integrative probabilistic model for identification of structural variation in sequencing data , 2012, Genome Biology.

[69]  J. V. Moran,et al.  Ataxia telangiectasia mutated (ATM) modulates long interspersed element-1 (L1) retrotransposition in human neural stem cells , 2011, Proceedings of the National Academy of Sciences.

[70]  P. J. van der Zaag,et al.  Targeted enrichment of genomic DNA regions for next-generation sequencing , 2011, Briefings in functional genomics.

[71]  Pradeep S Rajendran,et al.  Single-cell dissection of transcriptional heterogeneity in human colon tumors , 2011, Nature Biotechnology.

[72]  Matthew Ruffalo,et al.  Comparative analysis of algorithms for next-generation sequencing read alignment , 2011, Bioinform..

[73]  Anders Ståhlberg,et al.  Single-cell gene-expression profiling and its potential diagnostic applications , 2011, Expert review of molecular diagnostics.

[74]  M. Salit,et al.  Synthetic Spike-in Standards for Rna-seq Experiments Material Supplemental Open Access License Commons Creative , 2022 .

[75]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[76]  H. Hakonarson,et al.  SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data , 2011, Nucleic acids research.

[77]  Samuel Aparicio,et al.  High-throughput microfluidic single-cell RT-qPCR , 2011, Proceedings of the National Academy of Sciences.

[78]  M. Gerstein,et al.  CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. , 2011, Genome research.

[79]  Marcel Martin Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[80]  J. Troge,et al.  Tumour evolution inferred by single-cell sequencing , 2011, Nature.

[81]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[82]  Alison S. Devonshire,et al.  Applicability of RNA standards for evaluating RT-qPCR assays and platforms , 2011, BMC Genomics.

[83]  Robert A. Edwards,et al.  Quality control and preprocessing of metagenomic datasets , 2011, Bioinform..

[84]  K. Anderson,et al.  Genetic variegation of clonal architecture and propagating cells in leukaemia , 2011, Nature.

[85]  Thomas M. Keane,et al.  Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly , 2010, Genome Biology.

[86]  Fred H. Gage,et al.  L1 retrotransposition in neurons is modulated by MeCP2 , 2010, Nature.

[87]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[88]  Vikas Bansal,et al.  A statistical method for the detection of variants from next-generation resequencing of DNA pools , 2010, Bioinform..

[89]  J Christopher Love,et al.  Development and optimization of a process for automated recovery of single cells identified by microengraving , 2010, Biotechnology progress.

[90]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[91]  Emily H Turner,et al.  Target-enrichment strategies for next-generation sequencing , 2010, Nature Methods.

[92]  Eric T. Wang,et al.  An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data , 2009, PLoS Comput. Biol..

[93]  Ken Chen,et al.  VarScan: variant detection in massively parallel sequencing of individual and pooled samples , 2009, Bioinform..

[94]  R. Wilson,et al.  BreakDancer: An algorithm for high resolution mapping of genomic structural variation , 2009, Nature Methods.

[95]  Siu-Ming Yiu,et al.  SOAP2: an improved ultrafast tool for short read alignment , 2009, Bioinform..

[96]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[97]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[98]  Catalin C. Barbacioru,et al.  mRNA-Seq whole-transcriptome analysis of a single cell , 2009, Nature Methods.

[99]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[100]  Derek Y. Chiang,et al.  High-resolution mapping of copy-number alterations with massively parallel sequencing , 2009, Nature Methods.

[101]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[102]  Martin Hemberg,et al.  Quantification of mRNA in single cells and modelling of RT-qPCR induced noise , 2008, BMC Molecular Biology.

[103]  Kuo-Kang Liu,et al.  Optical tweezers for single cells , 2008, Journal of The Royal Society Interface.

[104]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[105]  Gideon Rechavi,et al.  Amplification of multiple genomic loci from single cells isolated by laser micro-dissection of tissues , 2008, BMC biotechnology.

[106]  Hanlee P. Ji,et al.  Multigene amplification and massively parallel sequencing for cancer mutation discovery , 2007, Proceedings of the National Academy of Sciences.

[107]  E. S. Venkatraman,et al.  A faster circular binary segmentation algorithm for the analysis of array CGH data , 2007, Bioinform..

[108]  E. Petricoin,et al.  Laser Capture Microdissection , 1996, Science.

[109]  M. Wigler,et al.  Circular binary segmentation for the analysis of array-based DNA copy number data. , 2004, Biostatistics.

[110]  H. Hug,et al.  Measurement of the number of molecules of a single mRNA species in a complex mRNA preparation. , 2003, Journal of theoretical biology.

[111]  S. Kingsmore,et al.  Comprehensive human genome amplification using multiple displacement amplification , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[112]  A. Chenchik,et al.  Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction. , 2001, BioTechniques.