Prognostic and predictive enrichment in sepsis

NL Stanski, HR Wong - Nature Reviews Nephrology, 2020 - nature.com
Sepsis is a heterogeneous disease state that is both common and consequential in critically
ill patients. Unfortunately, the heterogeneity of sepsis at the individual patient level has …

Studying and modelling dynamic biological processes using time-series gene expression data

Z Bar-Joseph, A Gitter, I Simon - Nature Reviews Genetics, 2012 - nature.com
Biological processes are often dynamic, thus researchers must monitor their activity at
multiple time points. The most abundant source of information regarding such dynamic …

Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry

BC Searle, LK Pino, JD Egertson, YS Ting… - Nature …, 2018 - nature.com
Data independent acquisition (DIA) mass spectrometry is a powerful technique that is
improving the reproducibility and throughput of proteomics studies. Here, we introduce an …

Ballgown bridges the gap between transcriptome assembly and expression analysis

AC Frazee, G Pertea, AE Jaffe, B Langmead… - Nature …, 2015 - nature.com
To the Editor: Analysis of raw reads from RNA sequencing (RNA-seq) makes it possible to
reconstruct complete gene structures, including multiple splice variants, without relying on …

Genomic responses in mouse models poorly mimic human inflammatory diseases

J Seok, HS Warren, AG Cuenca, MN Mindrinos… - Proceedings of the …, 2013 - pnas.org
A cornerstone of modern biomedical research is the use of mouse models to explore basic
pathophysiological mechanisms, evaluate new therapeutic approaches, and make go or no …

Induction of pathogenic TH17 cells by inducible salt-sensing kinase SGK1

C Wu, N Yosef, T Thalhamer, C Zhu, S **ao, Y Kishi… - Nature, 2013 - nature.com
Abstract TH17 cells (interleukin-17 (IL-17)-producing helper T cells) are highly
proinflammatory cells that are critical for clearing extracellular pathogens and for inducing …

Proteome-wide solubility and thermal stability profiling reveals distinct regulatory roles for ATP

S Sridharan, N Kurzawa, T Werner, I Günthner… - Nature …, 2019 - nature.com
Adenosine triphosphate (ATP) plays fundamental roles in cellular biochemistry and was
recently discovered to function as a biological hydrotrope. Here, we use mass spectrometry …

A genomic storm in critically injured humans

W **ao, MN Mindrinos, J Seok, J Cuschieri… - Journal of Experimental …, 2011 - rupress.org
Human survival from injury requires an appropriate inflammatory and immune response. We
describe the circulating leukocyte transcriptome after severe trauma and burn injury, as well …

Dynamic regulatory network controlling TH17 cell differentiation

N Yosef, AK Shalek, JT Gaublomme, H **, Y Lee… - Nature, 2013 - nature.com
Despite their importance, the molecular circuits that control the differentiation of naive T cells
remain largely unknown. Recent studies that reconstructed regulatory networks in …

Guidelines for genome-scale analysis of biological rhythms

ME Hughes, KC Abruzzi, R Allada… - Journal of biological …, 2017 - journals.sagepub.com
Genome biology approaches have made enormous contributions to our understanding of
biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins …