Publications by authors named "Cole Trapnell"

71Publications

Trajectory analysis quantifies transcriptional plasticity during macrophage polarization.

Sci Rep 2020 Jul 23;10(1):12273. Epub 2020 Jul 23.

Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.

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http://dx.doi.org/10.1038/s41598-020-68766-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7378057PMC
July 2020

The promise of single-cell genomics in plants.

Curr Opin Plant Biol 2020 04 5;54:114-121. Epub 2020 May 5.

Department of Genome Sciences, University of Washington, Seattle, WA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.pbi.2020.04.002DOI Listing
April 2020

Sci-fate characterizes the dynamics of gene expression in single cells.

Nat Biotechnol 2020 Aug 13;38(8):980-988. Epub 2020 Apr 13.

Department of Genome Sciences, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1038/s41587-020-0480-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7416490PMC
August 2020

Dimensionality reduction by UMAP to visualize physical and genetic interactions.

Nat Commun 2020 03 24;11(1):1537. Epub 2020 Mar 24.

Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.

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http://dx.doi.org/10.1038/s41467-020-15351-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7093466PMC
March 2020

Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe.

Cell Syst 2020 03 4;10(3):265-274.e11. Epub 2020 Mar 4.

Department of Electrical Engineering, University of Washington, Seattle, WA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2020.02.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223477PMC
March 2020

Connect-seq to superimpose molecular on anatomical neural circuit maps.

Proc Natl Acad Sci U S A 2020 02 7;117(8):4375-4384. Epub 2020 Feb 7.

Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109;

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http://dx.doi.org/10.1073/pnas.1912176117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7049128PMC
February 2020

Supervised classification enables rapid annotation of cell atlases.

Nat Methods 2019 10 9;16(10):983-986. Epub 2019 Sep 9.

Department of Genome Sciences, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1038/s41592-019-0535-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6791524PMC
October 2019

A lineage-resolved molecular atlas of embryogenesis at single-cell resolution.

Science 2019 09 5;365(6459). Epub 2019 Sep 5.

Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1126/science.aax1971DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7428862PMC
September 2019

The accessible chromatin landscape of the murine hippocampus at single-cell resolution.

Genome Res 2019 05 1;29(5):857-869. Epub 2019 Apr 1.

Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA.

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http://dx.doi.org/10.1101/gr.243725.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499306PMC
May 2019

Dynamics of Gene Expression in Single Root Cells of .

Plant Cell 2019 05 28;31(5):993-1011. Epub 2019 Mar 28.

Department of Genome Sciences, University of Washington, Seattle, Washington 98195

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http://www.plantcell.org/lookup/doi/10.1105/tpc.18.00785
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http://dx.doi.org/10.1105/tpc.18.00785DOI Listing
May 2019

A Peninsular Structure Coordinates Asynchronous Differentiation with Morphogenesis to Generate Pancreatic Islets.

Cell 2019 02 17;176(4):790-804.e13. Epub 2019 Jan 17.

Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.12.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6705176PMC
February 2019

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens.

Cell 2019 01 3;176(1-2):377-390.e19. Epub 2019 Jan 3.

Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98105, USA; Howard Hughes Medical Institute, Seattle, WA 98105, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674183155
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http://dx.doi.org/10.1016/j.cell.2018.11.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6690346PMC
January 2019

Aligning Single-Cell Developmental and Reprogramming Trajectories Identifies Molecular Determinants of Myogenic Reprogramming Outcome.

Cell Syst 2018 09 5;7(3):258-268.e3. Epub 2018 Sep 5.

Molecular & Cellular Biology Program, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.07.006DOI Listing
September 2018

iPSC-Derived Macrophages Effectively Treat Pulmonary Alveolar Proteinosis in Csf2rb-Deficient Mice.

Stem Cell Reports 2018 09 9;11(3):696-710. Epub 2018 Aug 9.

Research Group Reprogramming and Gene Therapy, Hannover Medical School (MHH), Hannover, Germany; Institute of Experimental Hematology, MHH, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany; Cluster of Excellence REBIRTH, MHH, Hannover, Germany.

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http://dx.doi.org/10.1016/j.stemcr.2018.07.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6135208PMC
September 2018

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.

Mol Cell 2018 09 2;71(5):858-871.e8. Epub 2018 Aug 2.

Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2018.06.044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582963PMC
September 2018

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility.

Cell 2018 08 2;174(5):1309-1324.e18. Epub 2018 Aug 2.

Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.06.052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6158300PMC
August 2018

Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation.

Trends Genet 2018 09 11;34(9):653-665. Epub 2018 Jul 11.

Department of Genome Sciences, Room S333, Foege Building, Box 355065, Seattle, WA 98105, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2018.06.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097890PMC
September 2018

Highly scalable generation of DNA methylation profiles in single cells.

Nat Biotechnol 2018 06 9;36(5):428-431. Epub 2018 Apr 9.

Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA.

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http://dx.doi.org/10.1038/nbt.4112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5938134PMC
June 2018

A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development.

Cell Stem Cell 2018 04;22(4):575-588.e7

Stem Cell Program, Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2018.03.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5957284PMC
April 2018

Extreme heterogeneity of influenza virus infection in single cells.

Elife 2018 02 16;7. Epub 2018 Feb 16.

Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, United States.

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http://dx.doi.org/10.7554/eLife.32303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5826275PMC
February 2018

Reversed graph embedding resolves complex single-cell trajectories.

Nat Methods 2017 Oct 21;14(10):979-982. Epub 2017 Aug 21.

Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, USA.

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http://dx.doi.org/10.1038/nmeth.4402DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5764547PMC
October 2017

Single-cell mRNA quantification and differential analysis with Census.

Nat Methods 2017 03 23;14(3):309-315. Epub 2017 Jan 23.

Department of Genome Sciences, University of Washington, Seattle, Washington, USA.

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http://dx.doi.org/10.1038/nmeth.4150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5330805PMC
March 2017

LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency.

Cell Stem Cell 2016 07 16;19(1):66-80. Epub 2016 Jun 16.

Stem Cell Transplantation Program, Division of Pediatric Hematology Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2016.05.009DOI Listing
July 2016

Single-cell transcriptome sequencing: recent advances and remaining challenges.

F1000Res 2016 17;5. Epub 2016 Feb 17.

Department of Genome Sciences, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.12688/f1000research.7223.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4758375PMC
March 2016

Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis.

Science 2015 Dec 5;350(6265):1251-5. Epub 2015 Nov 5.

Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.

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https://cole-trapnell-lab.github.io/pdfs/papers/hanchate-olf
Web Search
http://www.sciencemag.org/cgi/doi/10.1126/science.aad2456
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http://dx.doi.org/10.1126/science.aad2456DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5642900PMC
December 2015

Defining cell types and states with single-cell genomics.

Authors:
Cole Trapnell

Genome Res 2015 Oct;25(10):1491-8

Department of Genome Sciences, University of Washington, Seattle, Washington 98105, USA.

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http://dx.doi.org/10.1101/gr.190595.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4579334PMC
October 2015

Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency.

Cell 2015 Jul;162(2):412-424

Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.06.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4511597PMC
July 2015

Pulmonary macrophage transplantation therapy.

Nature 2014 Oct 1;514(7523):450-4. Epub 2014 Oct 1.

1] Division of Pulmonary Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, Ohio 45229, USA [2] Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, Ohio 45229, USA [3] Division of Pulmonary, Critical Care, and Sleep Medicine, University of Cincinnati Medical Center, 3333 Burnet Avenue, Cincinnati, Ohio 45229, USA.

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http://dx.doi.org/10.1038/nature13807DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4236859PMC
October 2014

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.

Nat Biotechnol 2014 Apr 23;32(4):381-386. Epub 2014 Mar 23.

Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.2859DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4122333PMC
April 2014

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre.

Nat Struct Mol Biol 2014 Feb 26;21(2):198-206. Epub 2014 Jan 26.

1] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA. [2] Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA. [3] Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nsmb.2764DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3950333PMC
February 2014

SHAPE-Seq: High-Throughput RNA Structure Analysis.

Curr Protoc Chem Biol 2012 Dec;4(4):275-97

Department of Molecular and Cell Biology, University of California, Berkeley, California.

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http://dx.doi.org/10.1002/9780470559277.ch120019DOI Listing
December 2012

Differential analysis of gene regulation at transcript resolution with RNA-seq.

Nat Biotechnol 2013 Jan 9;31(1):46-53. Epub 2012 Dec 9.

Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.2450DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3869392PMC
January 2013

Targeted RNA sequencing reveals the deep complexity of the human transcriptome.

Nat Biotechnol 2011 Nov 13;30(1):99-104. Epub 2011 Nov 13.

Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia.

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http://dx.doi.org/10.1038/nbt.2024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3710462PMC
November 2011

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses.

Genes Dev 2011 Sep 2;25(18):1915-27. Epub 2011 Sep 2.

Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1101/gad.17446611DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3185964PMC
September 2011

Identification of novel transcripts in annotated genomes using RNA-Seq.

Bioinformatics 2011 Sep 21;27(17):2325-9. Epub 2011 Jun 21.

Department of Computer Science, UC Berkeley, Berkeley, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr355DOI Listing
September 2011

Modeling and automation of sequencing-based characterization of RNA structure.

Proc Natl Acad Sci U S A 2011 Jul 3;108(27):11069-74. Epub 2011 Jun 3.

Department of Bioengineering, University of California, Berkeley, CA 94720, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1106541108
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http://dx.doi.org/10.1073/pnas.1106541108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3131376PMC
July 2011

Computational methods for transcriptome annotation and quantification using RNA-seq.

Nat Methods 2011 Jun 27;8(6):469-77. Epub 2011 May 27.

Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nmeth.1613DOI Listing
June 2011

Improving RNA-Seq expression estimates by correcting for fragment bias.

Genome Biol 2011 16;12(3):R22. Epub 2011 Mar 16.

Department of Computer Science, 387 Soda Hall, UC Berkeley, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1186/gb-2011-12-3-r22DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129672PMC
January 2012

Optimizing Data Intensive GPGPU Computations for DNA Sequence Alignment.

Parallel Comput 2009 Aug;35(8):429-440

Center for Bioinformatics and Computational Biology, University of Maryland.

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http://linkinghub.elsevier.com/retrieve/pii/S016781910900071
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http://dx.doi.org/10.1016/j.parco.2009.05.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2749273PMC
August 2009

How to map billions of short reads onto genomes.

Nat Biotechnol 2009 May;27(5):455-7

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.

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http://dx.doi.org/10.1038/nbt0509-455DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836519PMC
May 2009

TopHat: discovering splice junctions with RNA-Seq.

Bioinformatics 2009 May 16;25(9):1105-11. Epub 2009 Mar 16.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2672628PMC
May 2009

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Genome Biol 2009 4;10(3):R25. Epub 2009 Mar 4.

Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA.

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http://dx.doi.org/10.1186/gb-2009-10-3-r25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690996PMC
July 2009

High-throughput sequence alignment using Graphics Processing Units.

BMC Bioinformatics 2007 Dec 10;8:474. Epub 2007 Dec 10.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.

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http://dx.doi.org/10.1186/1471-2105-8-474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2222658PMC
December 2007