20 Result(s)

Article

Annotating and prioritizing human non-coding variants with RegulomeDB v.2

Shengcheng Dong, Nanxiang Zhao, Emma Spragins, Meenakshi S. Kagda… in Nature Genetics (2023)

Article

SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions

Aberrant DNA methylation in transcription factor binding sites has been shown to lead to anomalous gene regulation that is strongly associated with human disease. However, the majority of methylation-sensitive...

Sierra S. Nishizaki, Alan P. Boyle in BMC Bioinformatics (2022)

Article

Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data

Revealing the gene targets of distal regulatory elements is challenging yet critical for interpreting regulome data. Experiment-derived enhancer-gene links are restricted to a small set of enhancers and/or cel...

Tingting Qin, Christopher Lee, Shiting Li, Raymond G. Cavalcante… in Genome Biology (2022)

Article

SquiggleNet: real-time, direct classification of nanopore signals

We present SquiggleNet, the first deep-learning model that can classify nanopore reads directly from their electrical signals. SquiggleNet operates faster than DNA passes through the pore, allowing real-time c...

Yuwei Bao, Jack Wadden, John R. Erb-Downward, Piyush Ranjan, Weichen Zhou… in Genome Biology (2021)

Article

Cas9 targeted enrichment of mobile elements using nanopore sequencing

Mobile element insertions (MEIs) are repetitive genomic sequences that contribute to genetic variation and can lead to genetic disorders. Targeted and whole-genome approaches using short-read sequencing have b...

Torrin L. McDonald, Weichen Zhou, Christopher P. Castro… in Nature Communications (2021)

Article

MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony

Comparative genomics studies are growing in number partly because of their unique ability to provide insight into shared and divergent biology between species. Of particular interest is the use of phylogenetic...

Adam G. Diehl, Alan P. Boyle in BMC Bioinformatics (2020)

Article

Transposable elements contribute to cell and species-specific chromatin loo** and gene regulation in mammalian genomes

Chromatin loo** is important for gene regulation, and studies of 3D chromatin structure across species and cell types have improved our understanding of the principles governing chromatin loo**. However, 3...

Adam G. Diehl, Ningxin Ouyang, Alan P. Boyle in Nature Communications (2020)

Article

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

Functional genomics assays based on high-throughput sequencing greatly expand our ability to understand the genome. Here, we define the ENCODE blacklist- a comprehensive set of regions in the human, mouse, wor...

Haley M. Amemiya, Anshul Kundaje, Alan P. Boyle in Scientific Reports (2019)

Article

A proximity-based graph clustering method for the identification and application of transcription factor clusters

Transcription factors (TFs) form a complex regulatory network within the cell that is crucial to cell functioning and human health. While methods to establish where a TF binds to DNA are well established, thes...

Maxwell Spadafore, Kayvan Najarian, Alan P. Boyle in BMC Bioinformatics (2017)

Article

Protein-altering and regulatory genetic variants near GATA4 implicated in bicuspid aortic valve

Bicuspid aortic valve (BAV) is a heritable congenital heart defect and an important risk factor for valvulopathy and aortopathy. Here we report a genome-wide association scan of 466 BAV cases and 4,660 age, se...

Bo Yang, Wei Zhou, Jiao Jiao, Jonas B. Nielsen, Michael R. Mathis… in Nature Communications (2017)

Article

Correction: Corrigendum: Regulatory analysis of the C. elegans genome with spatiotemporal resolution

Nature 512, 400–405 (2014); doi:10.1038/nature13497 In this Article, when processing C. elegans ChIP-seq libraries, the gene label ZK337.2 (KLU-1, a C2H2 Zn-finger protein) was mis-transcribed to ZK377.2 (SAX-...

Carlos L. Araya, Trupti Kawli, Anshul Kundaje, Lixia Jiang, Bei**g Wu… in Nature (2015)

Article

Principles of regulatory information conservation between mouse and human

To broaden our understanding of the evolution of gene regulation mechanisms, we generated occupancy profiles for 34 orthologous transcription factors (TFs) in human–mouse erythroid progenitor, lymphoblast and ...

Yong Cheng, Zhihai Ma, Bong-Hyun Kim, Weisheng Wu, Philip Cayting, Alan P. Boyle… in Nature (2014)

Article

A comparative encyclopedia of DNA elements in the mouse genome

The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater in...

Feng Yue, Yong Cheng, Alessandra Breschi, Jeff Vierstra, Weisheng Wu, Tyrone Ryba… in Nature (2014)

Article

Regulatory analysis of the C. elegans genome with spatiotemporal resolution

Discovering the structure and dynamics of transcriptional regulatory events in the genome with cellular and temporal resolution is crucial to understanding the regulatory underpinnings of development and disea...

Carlos L. Araya, Trupti Kawli, Anshul Kundaje, Lixia Jiang, Bei**g Wu… in Nature (2014)

Article

Comparative analysis of regulatory information and circuits across distant species

A map of genome-wide binding locations of 165 human, 93 worm and 52 fly transcription-regulatory factors (almost 50% presented for the first time) from diverse cell types, developmental stages, or conditions r...

Alan P. Boyle, Carlos L. Araya, Cathleen Brdlik, Philip Cayting, Chao Cheng… in Nature (2014)

Article

Architecture of the human regulatory network derived from ENCODE data

Transcription factors bind in a combinatorial fashion to specify the on-and-off states of genes; the ensemble of these binding events forms a regulatory network, constituting the wiring diagram for a cell. To ...

Mark B. Gerstein, Anshul Kundaje, Manoj Hariharan, Stephen G. Landt, Koon-Kiu Yan… in Nature (2012)

Article

Evidence-ranked motif identification

cERMIT is a computationally efficient motif discovery tool based on analyzing genome-wide quantitative regulatory evidence. Instead of pre-selecting promising candidate sequences, it utilizes information acros...

Stoyan Georgiev, Alan P Boyle, Karthik Jayasurya, Xuan Ding… in Genome Biology (2010)