Coby Viner

Benchmarking CUT&RUN analysis using motif enrichment

Luomeng Tan, Coby Viner, Xing Hao Li, Michael Wrana et autres

Abstract Background Cleavage under targets and release using nuclease (CUT&RUN) maps the genome-wide locations of chromatin-associated proteins and provides an improved alternative to chromatin immunoprecipitation sequencing (ChIP-seq) for profiling sequence-specific transcription factor binding sites. Identifying these binding sites plays a critical role …

ca, us (code pays fourni par la source)

Beyond statistical significance: ranking transcription factor binding motifs by effect size

Coby Viner, Scott Mastromatteo, Danielle Denisko, Jeffrey Negrea et autres

Abstract Chromatin immunoprecipitation-sequencing (ChIP-seq) has wide use in identifying transcription factor binding sites. DNA sequence motifs specific to a targeted transcription factor occur more frequently near ChIP-seq peak centres. The most common approach to quantifying relative motif enrichment ranks motifs by p-value. …

ca, us, gb (code pays fourni par la source)

Motif Ranking: Software

Coby Viner, Scott Mastromatteo, Danielle Denisko, Jeffrey Negrea et autres

Code for all statistical motif ranking work.

ca, us, gb (code pays fourni par la source)

Motif Ranking: Software

Coby Viner, Scott Mastromatteo, Danielle Denisko, Jeffrey Negrea et autres

Code for all statistical motif ranking work.

ca, us, gb (code pays fourni par la source)

Motif Ranking: Data

Coby Viner, Scott Mastromatteo, Danielle Denisko, Jeffrey Negrea et autres

CentriMo HTML and TXT files for JASPAR and de novo (MEME and DREME) motif results, as used in our paper "Beyond statistical significance: ranking transcription factor binding motifs by effect size".

ca, us, gb (code pays fourni par la source)

Motif Ranking: Data

Coby Viner, Scott Mastromatteo, Danielle Denisko, Jeffrey Negrea et autres

CentriMo HTML and TXT files for JASPAR and de novo (MEME and DREME) motif results, as used in our paper "Beyond statistical significance: ranking transcription factor binding motifs by effect size".

ca, us, gb (code pays fourni par la source)

Transcription factor regulation and epigenetic modifiers

Coby Viner

Transcription factors bind DNA in specific sequence contexts. Their binding to particular motifs, leads to downstream control of genic expression and cell fate specification. Understanding the particular motifs they bind is therefore of great importance, but is complicated by experimental artifacts, different …

Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet

Coby Viner, Charles A. Ishak, James Johnson, Nicolas J. Walker et autres

BACKGROUND: Transcription factors bind DNA in specific sequence contexts. In addition to distinguishing one nucleobase from another, some transcription factors can distinguish between unmodified and modified bases. Current models of transcription factor binding tend not to take DNA modifications into account, while …

ca, us, au, gb, cl (code pays fourni par la source)

Motif elucidation in ChIP-seq datasets with a knockout control

Danielle Denisko, Coby Viner, Michael M. Hoffman

Summary: Chromatin immunoprecipitation-sequencing is widely used to find transcription factor binding sites, but suffers from various sources of noise. Knocking out the target factor mitigates noise by acting as a negative control. Paired wild-type and knockout (KO) experiments can generate improved motifs …

ca (code pays fourni par la source)

Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet: transcription factor preferences

Coby Viner, Michael M. Hoffman

The main output of our analysis, as a raw dataset. This data was used to create the plots depicting transcription factor preferences across our paper, including for our treemaps.

ca (code pays fourni par la source)

Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet: transcription factor preferences

Coby Viner, Michael M. Hoffman

The main output of our analysis, as a raw dataset. This data was used to create the plots depicting transcription factor preferences across our paper, including for our treemaps.

ca (code pays fourni par la source)

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Heidi L. Rehm, Angela Page, Lindsay Smith, Jeremy Adams et autres

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular …

us, ca, ch, gb, es, au, qa, hk, cz, at, tw, sg, jp (code pays fourni par la source)