Cole Trapnell
#52,303
Most Influential Person Now
Assistant Professor in the Department of Genome Sciences at the University of Washington
Why Is Cole Trapnell Influential?
(Suggest an Edit or Addition)According to Wikipedia, Bruce Colston Trapnell Jr. is an assistant professor in the Department of Genome Sciences at the University of Washington. He was awarded the Overton Prize by the International Society for Computational Biology for “outstanding accomplishment in the early to mid stage of his career” in 2018.
Cole Trapnell's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome (2009) (19739)
- Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. (2010) (11813)
- TopHat: discovering splice junctions with RNA-Seq (2009) (11345)
- TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions (2013) (11019)
- Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks (2012) (10622)
- Differential analysis of gene regulation at transcript resolution with RNA-seq (2012) (3221)
- Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. (2011) (3061)
- The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells (2014) (2866)
- Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms (2010) (2281)
- Reversed graph embedding resolves complex single-cell trajectories (2017) (1906)
- The single cell transcriptional landscape of mammalian organogenesis (2019) (1522)
- Pseudo-temporal ordering of individual cells reveals dynamics and regulators of cell fate decisions (2014) (1211)
- Improving RNA-Seq expression estimates by correcting for fragment bias (2011) (1167)
- Computational methods for transcriptome annotation and quantification using RNA-seq (2011) (1010)
- Identification of novel transcripts in annotated genomes using RNA-Seq (2011) (929)
- Single-cell mRNA quantification and differential analysis with Census (2017) (914)
- Comprehensive single-cell transcriptional profiling of a multicellular organism (2017) (879)
- Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing (2015) (857)
- Defining cell types and states with single-cell genomics (2015) (568)
- Joint profiling of chromatin accessibility and gene expression in thousands of single cells (2018) (523)
- Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre (2014) (491)
- Targeted RNA sequencing reveals the deep complexity of the human transcriptome (2011) (462)
- A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility (2018) (452)
- Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells (2013) (409)
- Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data. (2018) (397)
- Long noncoding RNAs regulate adipogenesis (2013) (372)
- Multiplexed RNA structure characterization with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) (2011) (366)
- How to map billions of short reads onto genomes (2009) (351)
- High-throughput sequence alignment using Graphics Processing Units (2007) (338)
- A human cell atlas of fetal gene expression (2020) (306)
- A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens (2019) (302)
- Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A (2008) (286)
- The human body at cellular resolution: the NIH Human Biomolecular Atlas Program (2019) (265)
- The cis-regulatory dynamics of embryonic development at single cell resolution (2017) (263)
- Supervised classification enables rapid annotation of cell atlases (2019) (257)
- LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency. (2016) (244)
- Pulmonary Macrophage Transplantation Therapy (2014) (234)
- Single-cell transcriptome sequencing: recent advances and remaining challenges (2016) (203)
- Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species (2010) (197)
- Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency (2015) (187)
- Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis (2015) (174)
- Two New Complete Genome Sequences Offer Insight into Host and Tissue Specificity of Plant Pathogenic Xanthomonas spp (2011) (173)
- A human cell atlas of fetal chromatin accessibility (2020) (169)
- Extreme heterogeneity of influenza virus infection in single cells (2017) (165)
- Highly scalable generation of DNA methylation profiles in single cells (2018) (162)
- A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution (2019) (162)
- A lineage-resolved molecular atlas of C. elegans embryogenesis at single cell resolution (2019) (157)
- Massively multiplex chemical transcriptomics at single-cell resolution (2019) (146)
- On the design of CRISPR-based single cell molecular screens (2018) (131)
- Single-Cell Transcriptomic Comparison of Human Fetal Retina, hPSC-Derived Retinal Organoids, and Long-Term Retinal Cultures (2020) (130)
- A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition (2019) (120)
- Modeling and automation of sequencing-based characterization of RNA structure (2011) (119)
- Optimizing data intensive GPGPU computations for DNA sequence alignment (2009) (105)
- Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana (2019) (104)
- Topological Organization of Multi-chromosomal Regions by Firre (2014) (99)
- Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv . oryzae PXO 99 A (2008) (99)
- Dimensionality reduction by UMAP to visualize physical and genetic interactions (2019) (93)
- RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome (2014) (84)
- Embryo-scale, single-cell spatial transcriptomics (2021) (84)
- Reversed graph embedding resolves complex single-cell developmental trajectories (2017) (78)
- Wnt Signaling Separates the Progenitor and Endocrine Compartments during Pancreas Development. (2019) (78)
- A Peninsular Structure Coordinates Asynchronous Differentiation with Morphogenesis to Generate Pancreatic Islets (2019) (77)
- Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana. (2019) (77)
- Sequence analysis TopHat : discovering splice junctions with RNA-Seq (2009) (75)
- Thyroid hormone regulates distinct paths to maturation in pigment cell lineages (2019) (74)
- SHAPE–Seq: High‐Throughput RNA Structure Analysis (2012) (73)
- Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation. (2018) (72)
- Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe. (2020) (69)
- What Is Your Conceptual Definition of "Cell Type" in the Context of a Mature Organism? (2017) (66)
- Sci-fate characterizes the dynamics of gene expression in single cells (2020) (61)
- Faculty Opinions recommendation of Decoding the regulatory network of early blood development from single-cell gene expression measurements. (2016) (57)
- Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A (2008) (56)
- Fast Exact String Matching on the GPU (2011) (53)
- Aligning Single-Cell Developmental and Reprogramming Trajectories Identifies Molecular Determinants of Myogenic Reprogramming Outcome. (2018) (52)
- A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens (2019) (51)
- The accessible chromatin landscape of the murine hippocampus at single-cell resolution (2019) (46)
- Systematic reconstruction of cellular trajectories across mouse embryogenesis (2022) (39)
- A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development. (2018) (35)
- Trajectory analysis quantifies transcriptional plasticity during macrophage polarization (2020) (34)
- BMC Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99 A (2008) (32)
- iPSC-Derived Macrophages Effectively Treat Pulmonary Alveolar Proteinosis in Csf2rb-Deficient Mice (2018) (30)
- High‐throughput, microscope‐based sorting to dissect cellular heterogeneity (2020) (30)
- TECHNICAL BRIEF: (2001) (30)
- The anatomy of successful computational biology software (2013) (29)
- Towards inferring causal gene regulatory networks from single cell expression Measurements (2018) (29)
- Targeting TWIST1 through loss of function inhibits tumorigenicity of human glioblastoma (2018) (28)
- Multipotent progenitors and hematopoietic stem cells arise independently from hemogenic endothelium in the mouse embryo (2021) (26)
- SUN-LB55 Connect-seq to Superimpose Molecular on Anatomical Neural Circuit Maps (2018) (24)
- IL2 enhances ex-vivo expanded regulatory T cell persistence after adoptive transfer (2019) (21)
- Chromatin accessibility dynamics of myogenesis at single cell resolution (2017) (20)
- Neural G0: a quiescent-like state found in neuroepithelial-derived cells and glioma (2018) (19)
- The promise of single-cell genomics in plants. (2020) (17)
- Engineering a niche supporting hematopoietic stem cell development using integrated single-cell transcriptomics (2021) (15)
- Scalable and efficient single-cell DNA methylation sequencing by combinatorial indexing (2017) (13)
- Faculty Opinions recommendation of Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. (2016) (12)
- Developmental and conditional dynamics of gene expression in single root cells of A. thaliana (2018) (11)
- Dynamics of gene expression in single root cells ofA. thaliana (2018) (11)
- The continuum of Drosophila embryonic development at single-cell resolution (2022) (11)
- Activated CARD11 accelerates germinal center kinetics, promoting mTORC1 and terminal differentiation (2018) (10)
- A-kinase-anchoring protein 1 (dAKAP1)-based signaling complexes coordinate local protein synthesis at the mitochondrial surface (2020) (9)
- Aligning single-cell developmental and reprogramming trajectories identifies molecular determinants of reprogramming outcome (2017) (9)
- Characterizing the temporal dynamics of gene expression in single cells with sci-fate (2019) (8)
- Monocle : Differential expression and time-series analysis for single-cell RNA-Seq and qPCR experiments (2014) (8)
- Optimized single-nucleus transcriptional profiling by combinatorial indexing (2022) (7)
- An optimized protocol for single cell transcriptional profiling by combinatorial indexing (2021) (7)
- Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation (2020) (6)
- Neural G0: a quiescent‐like state found in neuroepithelial‐derived cells and glioma (2021) (6)
- Single-cell analyses reveal early thymic progenitors and pre-B cells in zebrafish (2022) (6)
- Airway epithelial interferon response to SARS-CoV-2 is inferior to rhinovirus and heterologous rhinovirus infection suppresses SARS-CoV-2 replication (2021) (5)
- Systematic reconstruction of the cellular trajectories of mammalian embryogenesis (2021) (5)
- TransMPRA: A framework for assaying the role of many trans-acting factors at many enhancers (2020) (5)
- Airway epithelial interferon response to SARS-CoV-2 is inferior to rhinovirus and heterologous rhinovirus infection suppresses SARS-CoV-2 replication (2022) (5)
- CRISPR-Cas9 Screens Reveal Genes Regulating a G0-like State in Human Neural Progenitors (2018) (4)
- Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters (2022) (3)
- Deep molecular, cellular and temporal phenotyping of developmental perturbations at whole organism scale (2022) (3)
- Faculty Opinions recommendation of High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin. (2016) (3)
- crisprQTL mapping as a genome-wide association framework for cellular genetic screens (2018) (3)
- Single cell, whole embryo phenotyping of pleiotropic disorders of mammalian development (2022) (2)
- Visual Cell Sorting: A High-throughput, Microscope-based Method to Dissect Cellular Heterogeneity (2019) (2)
- Single-cell transcriptomic profiling of the zebrafish inner ear reveals molecularly distinct hair cell and supporting cell subtypes (2022) (2)
- The accessible chromatin landscape of the hippocampus at single-cell resolution (2018) (2)
- reveals global properties and specific subclasses Integrative annotation of human large intergenic noncoding RNAs Material (2011) (1)
- Erratum: The anatomy of successful computational biology software (2014) (1)
- Single cell biology—a Keystone Symposia report (2021) (1)
- LIN 28 Regulates Stem Cel l Metabolism and Conversion to Primed Pluripotency Graphical (1)
- RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome (2014) (1)
- Single Cell Transcriptomics Maps the Embryonic Emergence of HSC and Identifies Intercellular Interactions Regulating HSC Genesis (2018) (1)
- Faculty Opinions recommendation of Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics. (2016) (1)
- Single-cell analysis of chromatin and expression reveals age- and sex-associated alterations in the human heart (2022) (1)
- TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions (2013) (1)
- Proteostasis governs differential temperature sensitivity across embryonic cell types (2022) (1)
- Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin (2023) (1)
- Faculty Opinions recommendation of Integrated genome and transcriptome sequencing of the same cell. (2016) (1)
- Integrated Single Cell Transcriptomics Defines an Engineered Niche Supporting Hematopoietic Stem Cell Development Ex Vivo (2019) (1)
- Principles of Systems Biology, No. 21. (2017) (0)
- Faculty of 1000 evaluation for Computational and analytical challenges in single-cell transcriptomics. (2016) (0)
- 3063 – DISTINCT POPULATIONS OF MULTIPOTENT PROGENITORS AND HEMATOPOIETIC STEM CELLS EMERGE FROM HEMOGENIC ENDOTHELIUM IN THE MURINE EMBRYO (2020) (0)
- Sci-fate characterizes the dynamics of gene expression in single cells (2020) (0)
- Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies (2023) (0)
- IL2 and Rapamycin Enhance Persistence of Adoptively-Transferred Ex-Vivo Expanded T Regulatory Cells (2018) (0)
- GM-CSF Signaling Deficiency Causes the Arrest of Alveolar Macrophage Differentiation and Perturbs Pulmonary Lymphocyte Homeostasis (2022) (0)
- Clonal Analysis Reveals Functional and Transcriptional Heterogeneity of Self-Renewing Fetal Liver Hematopoietic Stem Cells (2022) (0)
- BIOINFORMATICS ORIGINAL PAPER (2009) (0)
- A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup (2023) (0)
- Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation (2021) (0)
- Faculty Opinions recommendation of Spatial reconstruction of single-cell gene expression data. (2016) (0)
- Faculty Opinions recommendation of Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis. (2016) (0)
- The single-cell transcriptional landscape of mammalian organogenesis (2019) (0)
- Systematic reconstruction of cellular trajectories across mouse embryogenesis (2022) (0)
- Multipotent progenitors and hematopoietic stem cells arise independently during the endothelial to hematopoietic transition in the early mouse embryo (2021) (0)
- High-Capacity Sample Multiplexing for Single Cell Chromatin Accessibility Profiling (2023) (0)
- Resource Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells (2013) (0)
- Distinct Transcriptional Signatures Distinguish the Emergence of Multipotent Progenitors and Hematopoietic Stem Cells from Endothelial Precursors in the Murine Embryo (2020) (0)
- Resource A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens Graphical (2019) (0)
- Transcriptional Activation of Regenerative Hematopoiesis via Vascular Niche Sensing (2023) (0)
- Pulmonary osteoclast-like cells in silica induced pulmonary fibrosis (2023) (0)
- Nuclear oligo hashing improves differential analysis of single-cell RNA-seq (2022) (0)
- sci-RNA-seq2 Pipeline for the Human Biomolecular Atlas Program (HuBMAP) v1 (2020) (0)
- Faculty Opinions recommendation of Counting absolute numbers of molecules using unique molecular identifiers. (2016) (0)
- Wnt Signaling Separates t he Progenitor and Endocrine Compartments during Pancreas Development Graphical (2019) (0)
- Faculty Opinions recommendation of Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes. (2016) (0)
- Single Cell Transcriptomics Reconstructs the Embryonic Emergence of HSC and Identifies Ligand-Receptor Interactions Regulating HSC Genesis in the Aorta-Gonad-Mesonephros Vascular Niche (2018) (0)
- Faculty Opinions recommendation of Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. (2016) (0)
- 3104 – TRANSCRIPTIONAL AND FUNCTIONAL ANALYSIS OF MURINE FETAL LIVER HEMATOPOIETIC STEM CELLS AT SINGLE CELL RESOLUTION (2022) (0)
- Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy (2023) (0)
- Early Career Investigators Meeting on Quantitative Problems in Human Health and Genetics (2016) (0)
- Xanthomonas spp. Specificity of Plant Pathogenic Offer Insight into Host and Tissue Two New Complete Genome Sequences (2011) (0)
- LOCAS : A new low coverage assembler for short reads (2009) (0)
- Faculty Opinions recommendation of Image-based transcriptomics in thousands of single human cells at single-molecule resolution. (2016) (0)
- 2013 – DISSECTING THE UNIQUE TRANSCRIPTOME OF HEMATOPOIETIC STEM CELL-COMPETENT HEMOGENIC ENDOTHELIUM IN THE EARLY MOUSE EMBRYO (2021) (0)
- Faculty Opinions recommendation of Measurement of the number of molecules of a single mRNA species in a complex mRNA preparation. (2016) (0)
- Dimensionality reduction by UMAP to visualize physical and genetic interactions (2020) (0)
- Faculty Opinions recommendation of Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. (2016) (0)
- Abstract IA4: Linking RNA to human health and disease (2012) (0)
This paper list is powered by the following services:
Other Resources About Cole Trapnell
What Schools Are Affiliated With Cole Trapnell?
Cole Trapnell is affiliated with the following schools:
