John Lazar

SMARCA4, STK11, and KEAP1 co-inactivation associates with poor prognosis and upregulation of the TGF-β pathway in lung adenocarcinoma

Emily A. Costa, Barbara Vaz de Mello, Corrin Wohlhieter, Subhiksha Nandakumar et autres

BACKGROUND: Lung adenocarcinoma (LUAD) is clinically and molecularly defined by oncogenic driver mutations, identification of which has led to the development of driver-targeted therapies and substantial improvements in prognosis for subsets of LUAD patients. Recent studies assessing clinical outcomes in the context …

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The Society of Thoracic Surgeons Expert Consensus Statements on a Framework for a Standardized National Robotic Curriculum for Thoracic Surgery Trainees

Samuel S. Kim, Lana Schumacher, David T. Cooke, Elliot L. Servais et autres

OBJECTIVE: With robotic technology's rapid growth and integration, an urgent need to bridge the educational gap in thoracic surgical training has emerged. This document, a result of consensus among a group of experts in the practice and training of robotic surgery from …

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Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

Federico Abascal, Reyes Acosta, Nicholas J. Addleman, Jessika Adrian et autres

In the version of this article initially published, two members of the ENCODE Project Consortium were missing from the author list. Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in …

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Author Correction: Perspectives on ENCODE

Federi Bronwen co Abascal, Reyes Acosta, Nicholas J. Addleman, Jessika Adrian et autres

In this Article, the authors Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA) were mistakenly omitted from the ENCODE …

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Perspectives on ENCODE

Federico Abascal, Reyes Acosta, Nicholas J. Addleman, Jessika Adrian et autres

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open …

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Expanded encyclopaedias of DNA elements in the human and mouse genomes

Federico Abascal, Reyes Acosta, Nicholas J. Addleman, Veena Afzal et autres

Abstract The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis …

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Global reference mapping of human transcription factor footprints

Jeff Vierstra, John Lazar, Richard Sandstrom, Jessica Halow et autres

Abstract Combinatorial binding of transcription factors to regulatory DNA underpins gene regulation in all organisms. Genetic variation in regulatory regions has been connected with diseases and diverse phenotypic traits 1 , but it remains challenging to distinguish variants that affect regulatory function …

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Atlas and developmental dynamics of mouse DNase I hypersensitive sites

Charles E. Breeze, John Lazar, Tim R. Mercer, Jessica Halow et autres

Abstract Early mammalian development is orchestrated by genome-encoded regulatory elements populated by a changing complement of regulatory factors, creating a dynamic chromatin landscape. To define the spatiotemporal organization of regulatory DNA landscapes during mouse development and maturation, we generated nucleotide-resolution DNA accessibility …

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Global Regulatory DNA Potentiation by SMARCA4 Propagates to Selective Gene Expression Programs via Domain-Level Remodeling

John Lazar, Sandra Stehling-Sun, Vivek Nandakumar, Hao Wang et autres

(Cell Reports 31, 107676-1–107676-16.e1–e5; May 26, 2020) In the originally published version of this article, the order of authors in the author list was incorrect. The last two authors on the list should be, in this order: John A. Stamatoyannopoulos and Alister …

Global Regulatory DNA Potentiation by SMARCA4 Propagates to Selective Gene Expression Programs via Domain-Level Remodeling

John Lazar, Sandra Stehling-Sun, Vivek Nandakumar, Hao Wang et autres

The human genome encodes millions of regulatory elements, of which only a small fraction are active within a given cell type. Little is known about the global impact of chromatin remodelers on regulatory DNA landscapes and how this translates to gene expression. …

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Global reference mapping and dynamics of human transcription factor footprints

Jeff Vierstra, John Lazar, Richard Sandstrom, Jessica Halow et autres

Abstract Combinatorial binding of transcription factors to regulatory DNA underpins gene regulation in all organisms. Genetic variation in regulatory regions has been connected with diseases and diverse phenotypic traits 1 , yet it remains challenging to distinguish variants that impact regulatory function …

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eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data

Charles E. Breeze, Alex Reynolds, Jenny van Dongen, Ian Dunham et autres

SUMMARY: The Illumina Infinium EPIC BeadChip is a new high-throughput array for DNA methylation analysis, extending the earlier 450k array by over 400 000 new sites. Previously, a method named eFORGE was developed to provide insights into cell type-specific and cell-composition effects …

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