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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

BMC bioinformatics, 2011-08, Vol.12 (1), p.323-323, Article 323

2011

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Genome-wide effects on Escherichia coli transcription from ppGpp binding to its two sites on RNA polymerase

Proceedings of the National Academy of Sciences - PNAS, 2019-04, Vol.116 (17), p.8310-8319

2019

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Evaluation of de novo transcriptome assemblies from RNA-Seq data

Genome biology, 2014-12, Vol.15 (12), p.553-553, Article 553

2014

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MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive

Bioinformatics (Oxford, England), 2017-09, Vol.33 (18), p.2914-2923

2017

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De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

Nature protocols, 2013-08, Vol.8 (8), p.1494-1512

2013

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RNA-Seq gene expression estimation with read mapping uncertainty

Bioinformatics, 2010-02, Vol.26 (4), p.493-500

2010

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Whole-Genome Alignment

Methods in molecular biology (Clifton, N.J.), 2019, Vol.1910, p.121

Dewey, Colin N

2019

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Rbm20 regulates titin alternative splicing as a splicing repressor

Nucleic acids research, 2013-02, Vol.41 (4), p.2659-2672

2013

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Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema

PLoS computational biology, 2013-03, Vol.9 (3), p.e1002936-e1002936

2013

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BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis

Bioinformatics, 2010-11, Vol.26 (22), p.2910-2911

2010

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Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans

PLoS biology, 2007-11, Vol.5 (11), p.e310-e310

2007

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Gata2 cis-element is required for hematopoietic stem cell generation in the mammalian embryo

The Journal of experimental medicine, 2013-12, Vol.210 (13), p.2833-2842

2013

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Positional orthology: putting genomic evolutionary relationships into context

Briefings in bioinformatics, 2011-09, Vol.12 (5), p.401-412

Dewey, Colin N.

2011

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Zebrafish zic2 controls formation of periocular neural crest and choroid fissure morphogenesis

Developmental biology, 2017-09, Vol.429 (1), p.92-104

2017

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RNA-regulatory exosome complex confers cellular survival to promote erythropoiesis

Nucleic acids research, 2021-09, Vol.49 (16), p.9007-9025

2021

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Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome

Molecular cell, 2015-07, Vol.59 (1), p.62-74

2015

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Mechanism governing heme synthesis reveals a GATA factor/heme circuit that controls differentiation

EMBO reports, 2016-02, Vol.17 (2), p.249-265

2016

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EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments

Bioinformatics, 2015-08, Vol.31 (16), p.2614-2622

2015

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Merging short and stranded long reads improves transcript assembly

PLoS computational biology, 2023-10, Vol.19 (10), p.e1011576-e1011576

2023

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Fine-scale phylogenetic discordance across the house mouse genome

PLoS genetics, 2009-11, Vol.5 (11), p.e1000729-e1000729

2009

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Fast statistical alignment

PLoS computational biology, 2009-05, Vol.5 (5), p.e1000392-e1000392

2009

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CellO: comprehensive and hierarchical cell type classification of human cells with the Cell Ontology

iScience, 2021-01, Vol.24 (1), p.101913-101913, Article 101913

2021

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Genomic variation in natural populations of Drosophila melanogaster

Genetics (Austin), 2012-10, Vol.192 (2), p.533-598

2012

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PLK1 and NOTCH Positively Correlate in Melanoma and Their Combined Inhibition Results in Synergistic Modulations of Key Melanoma Pathways

Molecular cancer therapeutics, 2021-01, Vol.20 (1), p.161-172

2021

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Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability

Developmental biology, 2017-06, Vol.426 (2), p.143-154

2017

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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Genome-wide effects on Escherichia coli transcription from ppGpp binding to its two sites on RNA polymerase

Evaluation of de novo transcriptome assemblies from RNA-Seq data

MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

RNA-Seq gene expression estimation with read mapping uncertainty

Whole-Genome Alignment

Rbm20 regulates titin alternative splicing as a splicing repressor

Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema

BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis

Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans

Gata2 cis-element is required for hematopoietic stem cell generation in the mammalian embryo

Positional orthology: putting genomic evolutionary relationships into context

Zebrafish zic2 controls formation of periocular neural crest and choroid fissure morphogenesis

RNA-regulatory exosome complex confers cellular survival to promote erythropoiesis

Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome

Mechanism governing heme synthesis reveals a GATA factor/heme circuit that controls differentiation

EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments

Merging short and stranded long reads improves transcript assembly

Fine-scale phylogenetic discordance across the house mouse genome

Fast statistical alignment

CellO: comprehensive and hierarchical cell type classification of human cells with the Cell Ontology

Genomic variation in natural populations of Drosophila melanogaster

PLK1 and NOTCH Positively Correlate in Melanoma and Their Combined Inhibition Results in Synergistic Modulations of Key Melanoma Pathways

Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability

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