The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics

LK Pino, BC Searle, JG Bollinger… - Mass spectrometry …, 2020 - Wiley Online Library
Skyline is a freely available, open‐source Windows client application for accelerating
targeted proteomics experimentation, with an emphasis on the proteomics and mass …

Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future

SA Huws, CJ Creevey, LB Oyama, I Mizrahi… - Frontiers in …, 2018 - frontiersin.org
The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi,
methanogenic archaea and phages. These microbes interact closely to breakdown plant …

Sixteen facial expressions occur in similar contexts worldwide

AS Cowen, D Keltner, F Schroff, B Jou, H Adam… - Nature, 2021 - nature.com
Understanding the degree to which human facial expressions co-vary with specific social
contexts across cultures is central to the theory that emotions enable adaptive responses to …

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues

D Wang, B Eraslan, T Wieland, B Hallström… - Molecular systems …, 2019 - embopress.org
Abstract Genome‐, transcriptome‐and proteome‐wide measurements provide insights into
how biological systems are regulated. However, fundamental aspects relating to which …

Stress-triggered phase separation is an adaptive, evolutionarily tuned response

JA Riback, CD Katanski, JL Kear-Scott, EV Pilipenko… - Cell, 2017 - cell.com
In eukaryotic cells, diverse stresses trigger coalescence of RNA-binding proteins into stress
granules. In vitro, stress-granule-associated proteins can demix to form liquids, hydrogels …

Transcriptome and translatome co-evolution in mammals

ZY Wang, E Leushkin, A Liechti, S Ovchinnikova… - Nature, 2020 - nature.com
Gene-expression programs define shared and species-specific phenotypes, but their
evolution remains largely uncharacterized beyond the transcriptome layer. Here we report …

Integration of omic networks in a developmental atlas of maize

JW Walley, RC Sartor, Z Shen, RJ Schmitz, KJ Wu… - Science, 2016 - science.org
Coexpression networks and gene regulatory networks (GRNs) are emerging as important
tools for predicting functional roles of individual genes at a system-wide scale. To enable …

Unification of protein abundance datasets yields a quantitative Saccharomyces cerevisiae proteome

B Ho, A Baryshnikova, GW Brown - Cell systems, 2018 - cell.com
Protein activity is the ultimate arbiter of function in most cellular pathways, and protein
concentration is fundamentally connected to protein action. While the proteome of yeast has …

[HTML][HTML] Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation

DE Weinberg, P Shah, SW Eichhorn, JA Hussmann… - Cell reports, 2016 - cell.com
Ribosome-footprint profiling provides genome-wide snapshots of translation, but technical
challenges can confound its analysis. Here, we use improved methods to obtain ribosome …

GPCRomics: an approach to discover GPCR drug targets

PA Insel, K Sriram, MW Gorr, SZ Wiley… - Trends in …, 2019 - cell.com
G protein-coupled receptors (GPCRs) are targets for∼ 35% of approved drugs but only∼
15% of the∼ 800 human GPCRs are currently such targets. GPCRomics, the use of …