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MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics

Genome Biology, 2017-07, Vol.18 (1), p.138-138, Article 138

2017

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SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data

Genome Biology, 2016-05, Vol.17 (1), p.106-106, Article 106

2016

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Single-cell transcriptomics reconstructs fate conversion from fibroblast to cardiomyocyte

Nature (London), 2017-11, Vol.551 (7678), p.100-104

2017

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MapSplice: accurate mapping of RNA-seq reads for splice junction discovery

Nucleic acids research, 2010-10, Vol.38 (18), p.e178

2010

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Deep Sequencing Shows Multiple Oligouridylations Are Required for 3′ to 5′ Degradation of Histone mRNAs on Polyribosomes

Molecular cell, 2014-03, Vol.53 (6), p.1020-1030

2014

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EnD-Seq and AppEnD: sequencing 3' ends to identify nontemplated tails and degradation intermediates

RNA (Cambridge), 2015-07, Vol.21 (7), p.1375-1389

2015

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Single-Cell Transcriptomic Analyses of Cell Fate Transitions during Human Cardiac Reprogramming

Cell stem cell, 2019-07, Vol.25 (1), p.149-164.e9

2019

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Robust detection of alternative splicing in a population of single cells

Nucleic acids research, 2016-05, Vol.44 (8), p.e73

2016

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A probabilistic framework for aligning paired-end RNA-seq data

Bioinformatics, 2010-08, Vol.26 (16), p.1950-1957

2010

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Comparison of OpenMP 3.0 and Other Task Parallel Frameworks on Unbalanced Task Graphs

International journal of parallel programming, 2010-10, Vol.38 (5-6), p.341-360

2010

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Systematic evaluation of spliced alignment programs for RNA-seq data

Nature methods, 2013-12, Vol.10 (12), p.1185

2013

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Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects

Genome research, 2014-02, Vol.24 (2), p.241

2014

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DiffSplice: the genome-wide detection of differential splicing events with RNA-seq

Nucleic acids research, 2013-01, Vol.41 (2), p.e39

2013

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Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential

BMC genomics, 2015-02, Vol.16 (1), p.113-113, Article 113

2015

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OpenMP task scheduling strategies for multicore NUMA systems

The international journal of high performance computing applications, 2012-05, Vol.26 (2), p.110-124

2012

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Selective single cell isolation for genomics using microraft arrays

Nucleic acids research, 2016-09, Vol.44 (17), p.8292

2016

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FDM: a graph-based statistical method to detect differential transcription using RNA-seq data

Bioinformatics, 2011-10, Vol.27 (19), p.2633-2640

2011

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NeoSplice: a bioinformatics method for prediction of splice variant neoantigens

Bioinformatics advances, 2022, Vol.2 (1), p.vbac032-vbac032

2022

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BlackOPs: increasing confidence in variant detection through mappability filtering

Nucleic acids research, 2013-10, Vol.41 (19), p.e178

2013

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A robust method for transcript quantification with RNA-seq data

Journal of computational biology, 2013-03, Vol.20 (3), p.167

2013

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Comprehensive genomic characterization of head and neck squamous cell carcinomas

Nature (London), 2015-01, Vol.517 (7536), p.576-582

2015

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Integrated Genomic Characterization of Papillary Thyroid Carcinoma

Cell, 2014-10, Vol.159 (3), p.676-690

2014

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Comprehensive molecular profiling of lung adenocarcinoma

Nature (London), 2014-07, Vol.511 (7511), p.543-550

2014

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Comprehensive molecular characterization of human colon and rectal cancer

Nature (London), 2012-07, Vol.487 (7407), p.330-337

2012

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Characterizing and Mitigating Work Time Inflation in Task Parallel Programs

Scientific programming, 2013, Vol.21 (3-4), p.123-136

2013

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MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics

SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data

Single-cell transcriptomics reconstructs fate conversion from fibroblast to cardiomyocyte

MapSplice: accurate mapping of RNA-seq reads for splice junction discovery

Deep Sequencing Shows Multiple Oligouridylations Are Required for 3′ to 5′ Degradation of Histone mRNAs on Polyribosomes

EnD-Seq and AppEnD: sequencing 3' ends to identify nontemplated tails and degradation intermediates

Single-Cell Transcriptomic Analyses of Cell Fate Transitions during Human Cardiac Reprogramming

Robust detection of alternative splicing in a population of single cells

A probabilistic framework for aligning paired-end RNA-seq data

Comparison of OpenMP 3.0 and Other Task Parallel Frameworks on Unbalanced Task Graphs

Systematic evaluation of spliced alignment programs for RNA-seq data

Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects

DiffSplice: the genome-wide detection of differential splicing events with RNA-seq

Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential

OpenMP task scheduling strategies for multicore NUMA systems

Selective single cell isolation for genomics using microraft arrays

FDM: a graph-based statistical method to detect differential transcription using RNA-seq data

NeoSplice: a bioinformatics method for prediction of splice variant neoantigens

BlackOPs: increasing confidence in variant detection through mappability filtering

A robust method for transcript quantification with RNA-seq data

Comprehensive genomic characterization of head and neck squamous cell carcinomas

Integrated Genomic Characterization of Papillary Thyroid Carcinoma

Comprehensive molecular profiling of lung adenocarcinoma

Comprehensive molecular characterization of human colon and rectal cancer

Characterizing and Mitigating Work Time Inflation in Task Parallel Programs

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