List of works - Cole Trapnell

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

scientific article published in April 2018

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

scientific article published on 03 January 2019

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

scientific article published on 01 March 2019

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

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

scientific article

A human cell atlas of fetal chromatin accessibility

scientific article published on 01 November 2020

A human cell atlas of fetal gene expression

scientific article published on 01 November 2020

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

scientific article published on 05 September 2019

A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition

scientific article published on 02 September 2019

A-kinase-anchoring protein 1 (dAKAP1)-based signaling complexes coordinate local protein synthesis at the mitochondrial surface

scientific article published on 01 June 2020

Activated CARD11 accelerates germinal center kinetics, promoting mTORC1 and terminal differentiation

scientific article published on 20 August 2018

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

scientific article published on 05 September 2018

Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species

scientific article

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

scientific article published on 2 August 2018

Comprehensive single-cell transcriptional profiling of a multicellular organism.

scientific article

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

scientific article published on May 27, 2011

Connect-seq to superimpose molecular on anatomical neural circuit maps

scientific article published on 07 February 2020

Defining cell types and states with single-cell genomics

scientific article

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

scientific article (publication date: 2013)

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

scientific article

Dimensionality reduction by UMAP to visualize physical and genetic interactions

scientific article published on 24 March 2020

Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana

scientific article published on 28 March 2019

Embryo-scale, single-cell spatial transcriptomics

scientific article

Engineering a niche supporting hematopoietic stem cell development using integrated single-cell transcriptomics

scientific article published on 24 March 2022

Erratum: The anatomy of successful computational biology software

article

Extreme heterogeneity of influenza virus infection in single cells

scientific article published on 16 February 2018

Extreme heterogeneity of influenza virus infection in single cells

article

Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A

article

Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A.

scientific article

High-throughput sequence alignment using Graphics Processing Units

scientific article

High-throughput, microscope-based sorting to dissect cellular heterogeneity

scientific article published on 01 June 2020

Highly scalable generation of DNA methylation profiles in single cells

scientific article published on 09 April 2018

How to map billions of short reads onto genomes

scientific article (publication date: May 2009)

IL-2 enhances ex vivo-expanded regulatory T-cell persistence after adoptive transfer

scientific article published on 01 April 2020

Identification of novel transcripts in annotated genomes using RNA-Seq

scientific article published on 21 June 2011

Improving RNA-Seq expression estimates by correcting for fragment bias

scientific article

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

scientific article published on 04 March 2020

Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency

scientific article published in July 2015

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

scientific article (publication date: 15 September 2011)

Joint profiling of chromatin accessibility and gene expression in thousands of single cells.

scientific article published on 30 August 2018

LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency

scientific article

Long noncoding RNAs regulate adipogenesis

scientific article

Massively multiplex chemical transcriptomics at single-cell resolution

scientific article published on 05 December 2019

Modeling and automation of sequencing-based characterization of RNA structure

scientific article

Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing

scientific article published on 7 May 2015

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

scientific article

Nuclear oligo hashing improves differential analysis of single-cell RNA-seq

scientific article published on 13 May 2022

On the design of CRISPR-based single cell molecular screens

On the design of CRISPR-based single-cell molecular screens

scientific article published on 19 February 2018

Optimizing Data Intensive GPGPU Computations for DNA Sequence Alignment

scientific article

Pulmonary macrophage transplantation therapy

scientific article

RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome

scientific article

Reversed graph embedding resolves complex single-cell trajectories.

scientific article

SHAPE–Seq: High‐Throughput RNA Structure Analysis ⬇️

scientific article published on December 1, 2012

Scalable and efficient single-cell DNA methylation sequencing by combinatorial indexing

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

scientific article published on 13 April 2020

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

scientific article published on 11 July 2018

Single-Cell Transcriptomic Comparison of Human Fetal Retina, hPSC-Derived Retinal Organoids, and Long-Term Retinal Cultures

scientific article published on 01 February 2020

Single-cell mRNA quantification and differential analysis with Census

scientific article published on 23 January 2017

Single-cell transcriptome sequencing: recent advances and remaining challenges

scientific article

Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis

scientific article

Supervised classification enables rapid annotation of cell atlases

scientific article published on 09 September 2019

Systematic reconstruction of cellular trajectories across mouse embryogenesis

scientific article published on 14 March 2022

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

scientific article

Targeting TWIST1 through loss of function inhibits tumorigenicity of human glioblastoma.

scientific article

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

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

scientific article published on 01 April 2019

The anatomy of successful computational biology software

scientific article

The cis-regulatory dynamics of embryonic development at single cell resolution

article

The cis-regulatory dynamics of embryonic development at single-cell resolution

scientific article published on 14 March 2018

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

scientific article published on 23 March 2014

The promise of single-cell genomics in plants

scientific article published on 05 May 2020

The single-cell transcriptional landscape of mammalian organogenesis

scientific article published on 20 February 2019

Thyroid hormone regulates distinct paths to maturation in pigment cell lineages

scientific article published on 29 May 2019

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

scientific article

TopHat: discovering splice junctions with RNA-Seq

scientific article

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

scientific article

Trajectory analysis quantifies transcriptional plasticity during macrophage polarization

scientific article published on 23 July 2020

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

scientific article

Transcriptional and epigenetic dynamics during specification of human embryonic stem cells

scientific article published on 09 May 2013

Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp.

scientific article

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

scientific article

What Is Your Conceptual Definition of "Cell Type" in the Context of a Mature Organism? ⬇️

scientific article published on 01 March 2017

Wnt Signaling Separates the Progenitor and Endocrine Compartments during Pancreas Development

scientific article published on 01 May 2019

crisprQTL mapping as a genome-wide association framework for cellular genetic screens

cummeRbund

scholarly article

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

scientific article published on 09 August 2018

List of works by Cole Trapnell

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

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

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

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

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

A human cell atlas of fetal chromatin accessibility

A human cell atlas of fetal gene expression

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

A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition

A-kinase-anchoring protein 1 (dAKAP1)-based signaling complexes coordinate local protein synthesis at the mitochondrial surface

Activated CARD11 accelerates germinal center kinetics, promoting mTORC1 and terminal differentiation

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

Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species

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

Comprehensive single-cell transcriptional profiling of a multicellular organism.

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

Connect-seq to superimpose molecular on anatomical neural circuit maps

Defining cell types and states with single-cell genomics

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

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

Dimensionality reduction by UMAP to visualize physical and genetic interactions

Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana

Embryo-scale, single-cell spatial transcriptomics

Engineering a niche supporting hematopoietic stem cell development using integrated single-cell transcriptomics

Erratum: The anatomy of successful computational biology software

Extreme heterogeneity of influenza virus infection in single cells

Extreme heterogeneity of influenza virus infection in single cells

Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A

Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A.

High-throughput sequence alignment using Graphics Processing Units

High-throughput, microscope-based sorting to dissect cellular heterogeneity

Highly scalable generation of DNA methylation profiles in single cells

How to map billions of short reads onto genomes

IL-2 enhances ex vivo-expanded regulatory T-cell persistence after adoptive transfer

Identification of novel transcripts in annotated genomes using RNA-Seq

Improving RNA-Seq expression estimates by correcting for fragment bias

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

Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency

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

Joint profiling of chromatin accessibility and gene expression in thousands of single cells.

LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency

Long noncoding RNAs regulate adipogenesis

Massively multiplex chemical transcriptomics at single-cell resolution

Modeling and automation of sequencing-based characterization of RNA structure

Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

Nuclear oligo hashing improves differential analysis of single-cell RNA-seq

On the design of CRISPR-based single cell molecular screens

On the design of CRISPR-based single-cell molecular screens

Optimizing Data Intensive GPGPU Computations for DNA Sequence Alignment

Pulmonary macrophage transplantation therapy

RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome

Reversed graph embedding resolves complex single-cell trajectories.

SHAPE–Seq: High‐Throughput RNA Structure Analysis ⬇️

Scalable and efficient single-cell DNA methylation sequencing by combinatorial indexing

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

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

Single-Cell Transcriptomic Comparison of Human Fetal Retina, hPSC-Derived Retinal Organoids, and Long-Term Retinal Cultures

Single-cell mRNA quantification and differential analysis with Census

Single-cell transcriptome sequencing: recent advances and remaining challenges

Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis

Supervised classification enables rapid annotation of cell atlases

Systematic reconstruction of cellular trajectories across mouse embryogenesis

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

Targeting TWIST1 through loss of function inhibits tumorigenicity of human glioblastoma.

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

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

The anatomy of successful computational biology software

The cis-regulatory dynamics of embryonic development at single cell resolution

The cis-regulatory dynamics of embryonic development at single-cell resolution

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

The promise of single-cell genomics in plants

The single-cell transcriptional landscape of mammalian organogenesis

Thyroid hormone regulates distinct paths to maturation in pigment cell lineages

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

TopHat: discovering splice junctions with RNA-Seq

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

Trajectory analysis quantifies transcriptional plasticity during macrophage polarization

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation