Explanipedia

Systematic cell-type resolved transcriptomes of 8 tissues in 8 lab and wild-derived mouse strains captures global and local expression variation Open

Elisabeth Rebboah, Ryan Weber, Elnaz Abdollahzadeh, Nikhila Swarna, Delaney K. Sullivan , et al. · 2025

Mapping the impact of genomic variation on gene expression facilitates an understanding of the molecular basis of complex phenotypic traits and disease predisposition. Mouse models provide a controlled and reproducible framework for captur…

Data sharing ethics toolkit: The Human Cell Atlas Open

Emily Kirby, Alexander Bernier, Roderic Guigó, B Wold, Fabiana Arzuaga , et al. · 2024

Striving to build an exhaustive guidebook of the types and properties of human cells, the Human Cell Atlas’ (HCA) success relies on the sampling of diverse populations, developmental stages, and tissue types. Its open science philosophy pr…

The commitment of the human cell atlas to humanity Open

Ido Amit, Kristin Ardlie, Fabiana Arzuaga, Gordon A. Awandare, Gary D. Bader , et al. · 2024

Empowering Large Scale Quantum Circuit Development: Effective Simulation of Sycamore Circuits Open

Venkateswaran Kasirajan, Torey Battelle, B Wold · 2024

Simulating quantum systems using classical computing equipment has been a significant research focus. This work demonstrates that circuits as large and complex as the random circuit sampling (RCS) circuits published as a part of Google's p…

Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease Open

Michal Polonsky, Louisa M.S. Gerhardt, Jina Yun, Kari Koppitch, Katsuya Lex Colón , et al. · 2024

Long-read sequencing transcriptome quantification with lr-kallisto Open

Rebekah K. Loving, Delaney K. Sullivan, Fairlie Reese, Elisabeth Rebboah, Jasmine Sakr , et al. · 2024

RNA abundance quantification has become routine and affordable thanks to high-throughput “short-read” technologies that provide accurate molecule counts at the gene level. Similarly accurate and affordable quantification of definitive full…

The ENCODE mouse postnatal developmental time course identifies regulatory programs of cell types and cell states Open

Elisabeth Rebboah, Narges Rezaie, Brian A. Williams, Annika K. Weimer, Minyi Shi , et al. · 2024

Postnatal genomic regulation significantly influences tissue and organ maturation but is under-studied relative to existing genomic catalogs of adult tissues or prenatal development in mouse. The ENCODE4 consortium generated the first comp…

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification Open

Francisco J. Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark Diekhans, Sílvia Carbonell Sala , et al. · 2024

Identification of robust cellular programs using reproducible LDA that impact sex-specific disease progression in different genotypes of a mouse model of AD Open

Narges Rezaie, Elisabeth Rebboah, Brian A. Williams, Heidi Yahan Liang, Fairlie Reese , et al. · 2024

The gene expression profiles of distinct cell types reflect complex genomic interactions among multiple simultaneous biological processes within each cell that can be altered by disease progression as well as genetic background. The identi…

A human embryonic limb cell atlas resolved in space and time Open

Bao Zhang, Peng He, John E. Lawrence, Shuaiyu Wang, Elizabeth Tuck , et al. · 2023

Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells Open

Belle A. Moyers, E. Christopher Partridge, Mark Mackiewicz, Michael J. Betti, Roshan Darji , et al. · 2023

Transcription factors (TFs) are trans -acting proteins that bind cis -regulatory elements (CREs) in DNA to control gene expression. Here, we analyzed the genomic localization profiles of 529 sequence-specific TFs and 151 cofactors and chro…

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification Open

Francisco J. Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark Diekhans, Sílvia Carbonell Sala , et al. · 2023

The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from …

The ENCODE Uniform Analysis Pipelines Open

Benjamin C. Hitz, Jin-Wook Lee, Otto Jolanki, Meenakshi S. Kagda, Keenan Graham , et al. · 2023

The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity Open

Fairlie Reese, Brian A. Williams, Gabriela Balderrama-Gutierrez, Dana Wyman, Muhammed Hasan Çelik , et al. · 2023

The majority of mammalian genes encode multiple transcript isoforms that result from differential promoter use, changes in exonic splicing, and alternative 3’ end choice. Detecting and quantifying transcript isoforms across tissues, cell t…

ENCSR876VXR Open

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ENCSR398OAO Open

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ENCSR051YOP Open

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ENCSR309QSV Open

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ENCSR970EPL Open

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The ENCODE Uniform Analysis Pipelines Open

Benjamin C. Hitz, Jin-Wook Lee, Otto Jolanki, Meenakshi S. Kagda, Keenan Graham , et al. · 2023

The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across…

RNAget: an API to securely retrieve RNA quantifications Open

Sean Upchurch, Emilio Palumbo, Jeremy Adams, David Bujold, Guillaume Bourque , et al. · 2023

Summary Large-scale sharing of genomic quantification data requires standardized access interfaces. In this Global Alliance for Genomics and Health project, we developed RNAget, an API for secure access to genomic quantification data in ma…

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models Open

Joel Rozowsky, Jiahao Gao, Beatrice Borsari, Yucheng Yang, Timur R. Galeev , et al. · 2023

Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of 1,635 open-access datasets fr…

ENCSR681ARR Open

B Wold · 2023

ENCSR727DPU Open

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ENCSR619DQO Open

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ENCSR828JSJ Open

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ENCSR131FDP Open

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ENCSR441IDG Open

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ENCSR570DQR Open

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ENCSR568UGZ Open

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