Molecular and evolutionary processes generating variation in gene expression

MS Hill, P Vande Zande, PJ Wittkopp - Nature Reviews Genetics, 2021 - nature.com
Heritable variation in gene expression is common within and between species. This
variation arises from mutations that alter the form or function of molecular gene regulatory …

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

W Li, D Notani, MG Rosenfeld - Nature Reviews Genetics, 2016 - nature.com
Networks of regulatory enhancers dictate distinct cell identities and cellular responses to
diverse signals by instructing precise spatiotemporal patterns of gene expression. However …

WormBase in 2022—data, processes, and tools for analyzing Caenorhabditis elegans

P Davis, M Zarowiecki, V Arnaboldi, A Becerra… - Genetics, 2022 - academic.oup.com
Abstract WormBase (www. wormbase. org) is the central repository for the genetics and
genomics of the nematode Caenorhabditis elegans. We provide the research community …

The Encyclopedia of DNA elements (ENCODE): data portal update

CA Davis, BC Hitz, CA Sloan, ET Chan… - Nucleic acids …, 2018 - academic.oup.com
The Enc yclopedia of D NA E lements (ENCODE) Data Coordinating Center has developed
the ENCODE Portal database and website as the source for the data and metadata …

WormBase: a modern model organism information resource

TW Harris, V Arnaboldi, S Cain, J Chan… - Nucleic acids …, 2020 - academic.oup.com
Abstract WormBase (https://wormbase. org/) is a mature Model Organism Information
Resource supporting researchers using the nematode Caenorhabditis elegans as a model …

Comprehensive single-cell transcriptional profiling of a multicellular organism

J Cao, JS Packer, V Ramani, DA Cusanovich, C Huynh… - Science, 2017 - science.org
To resolve cellular heterogeneity, we developed a combinatorial indexing strategy to profile
the transcriptomes of single cells or nuclei, termed sci-RNA-seq (single-cell combinatorial …

Pig genome functional annotation enhances the biological interpretation of complex traits and human disease

Z Pan, Y Yao, H Yin, Z Cai, Y Wang, L Bai… - Nature …, 2021 - nature.com
The functional annotation of livestock genomes is crucial for understanding the molecular
mechanisms that underpin complex traits of economic importance, adaptive evolution and …

Spatial reconstruction of single-cell gene expression data

R Satija, JA Farrell, D Gennert, AF Schier… - Nature …, 2015 - nature.com
Spatial localization is a key determinant of cellular fate and behavior, but methods for
spatially resolved, transcriptome-wide gene expression profiling across complex tissues are …

JBrowse: a dynamic web platform for genome visualization and analysis

R Buels, E Yao, CM Diesh, RD Hayes, M Munoz-Torres… - Genome biology, 2016 - Springer
Background JBrowse is a fast and full-featured genome browser built with JavaScript and
HTML5. It is easily embedded into websites or apps but can also be served as a standalone …

The Mediator complex: a central integrator of transcription

BL Allen, DJ Taatjes - Nature reviews Molecular cell biology, 2015 - nature.com
Abstract The RNA polymerase II (Pol II) enzyme transcribes all protein-coding and most non-
coding RNA genes and is globally regulated by Mediator—a large, conformationally flexible …