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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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Convergent transcriptional specializations in the brains of humans and song-learning birds

Science (American Association for the Advancement of Science), 2014-12, Vol.346 (6215), p.1333-1333

2014

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Synergistic and tunable human gene activation by combinations of synthetic transcription factors

Nature methods, 2013-03, Vol.10 (3), p.239

2013

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RoboCOP: jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data

Nucleic acids research, 2021-08, Vol.49 (14), p.7925

2021

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Genome-wide chromatin footprinting reveals changes in replication origin architecture induced by pre-RC assembly

Genes & development, 2015-01, Vol.29 (2), p.212-224

2015

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Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding

Genome research, 2018-09, Vol.28 (9), p.1272

2018

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Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading

Genome research, 2010-02, Vol.20 (2), p.201

2010

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Advances to Bayesian network inference for generating causal networks from observational biological data

Bioinformatics, 2004-12, Vol.20 (18), p.3594-3603

2004

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Computational and experimental identification of novel human imprinted genes

Genome Research, 2007-12, Vol.17 (12), p.1723-1730

2007

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Core and region-enriched networks of behaviorally regulated genes and the singing genome

Science (American Association for the Advancement of Science), 2014-12, Vol.346 (6215), p.1334-1334

2014

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Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors

Developmental cell, 2016-12, Vol.39 (5), p.585-596

2016

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Genome-wide prediction of imprinted murine genes

Genome research, 2005-06, Vol.15 (6), p.875

2005

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Mapping nucleosome positions using DNase-seq

Genome research, 2016-03, Vol.26 (3), p.351

2016

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Global control of cell-cycle transcription by coupled CDK and network oscillators

Nature, 2008-06, Vol.453 (7197), p.944-947

2008

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Computational inference of neural information flow networks

PLoS computational biology, 2006-11, Vol.2 (11), p.e161-e161

2006

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Cell-Cycle-Dependent Chromatin Dynamics at Replication Origins

Genes, 2021-12, Vol.12 (12), p.1998

2021

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A nucleosome-guided map of transcription factor binding sites in yeast

PLoS computational biology, 2007-11, Vol.3 (11), p.e215-e215

2007

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Sparse multinomial logistic regression: fast algorithms and generalization bounds

IEEE transactions on pattern analysis and machine intelligence, 2005-06, Vol.27 (6), p.957-968

2005

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An ensemble model of competitive multi-factor binding of the genome

Genome research, 2009-11, Vol.19 (11), p.2101

2009

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ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Genome research, 2012-09, Vol.22 (9), p.1813

2012

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Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis

Nature genetics, 2024-04, Vol.56 (4), p.627-3

2024

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Branching process deconvolution algorithm reveals a detailed cell-cycle transcription program

Proceedings of the National Academy of Sciences - PNAS, 2013-03, Vol.110 (10), p.E968-E977

2013

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Distinguishing direct versus indirect transcription factor-DNA interactions

Genome research, 2009-11, Vol.19 (11), p.2090

2009

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Linking the dynamics of chromatin occupancy and transcription with predictive models

Genome research, 2021-06, Vol.31 (6), p.1035

2021

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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

Convergent transcriptional specializations in the brains of humans and song-learning birds

Synergistic and tunable human gene activation by combinations of synthetic transcription factors

RoboCOP: jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data

Genome-wide chromatin footprinting reveals changes in replication origin architecture induced by pre-RC assembly

Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding

Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading

Advances to Bayesian network inference for generating causal networks from observational biological data

Computational and experimental identification of novel human imprinted genes

Core and region-enriched networks of behaviorally regulated genes and the singing genome

Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors

Genome-wide prediction of imprinted murine genes

Mapping nucleosome positions using DNase-seq

Global control of cell-cycle transcription by coupled CDK and network oscillators

Computational inference of neural information flow networks

Cell-Cycle-Dependent Chromatin Dynamics at Replication Origins

A nucleosome-guided map of transcription factor binding sites in yeast

Sparse multinomial logistic regression: fast algorithms and generalization bounds

An ensemble model of competitive multi-factor binding of the genome

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis

Branching process deconvolution algorithm reveals a detailed cell-cycle transcription program

Distinguishing direct versus indirect transcription factor-DNA interactions

Linking the dynamics of chromatin occupancy and transcription with predictive models

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