Animal and translational models of SARS-CoV-2 infection and COVID-19

MD Johansen, A Irving, X Montagutelli, MD Tate… - Mucosal …, 2020 - nature.com
COVID-19 is causing a major once-in-a-century global pandemic. The scientific and clinical
community is in a race to define and develop effective preventions and treatments. The …

Intervertebral disc degeneration and how it leads to low back pain

AD Diwan, J Melrose - JOR spine, 2023 - Wiley Online Library
The purpose of this review was to evaluate data generated by animal models of
intervertebral disc (IVD) degeneration published in the last decade and show how this has …

Tertiary lymphoid structures and B cells determine clinically relevant T cell phenotypes in ovarian cancer

L Kasikova, J Rakova, M Hensler, T Lanickova… - Nature …, 2024 - nature.com
Intratumoral tertiary lymphoid structures (TLSs) have been associated with improved
outcome in various cohorts of patients with cancer, reflecting their contribution to the …

Mouse Genome Informatics: an integrated knowledgebase system for the laboratory mouse

RM Baldarelli, CL Smith, M Ringwald, JE Richardson… - Genetics, 2024 - academic.oup.com
Abstract Mouse Genome Informatics (MGI) is a federation of expertly curated information
resources designed to support experimental and computational investigations into genetic …

Single-cell RNA counting at allele and isoform resolution using Smart-seq3

M Hagemann-Jensen, C Ziegenhain, P Chen… - Nature …, 2020 - nature.com
Large-scale sequencing of RNA from individual cells can reveal patterns of gene, isoform
and allelic expression across cell types and states. However, current short-read single-cell …

Epithelial NOTCH signaling rewires the tumor microenvironment of colorectal cancer to drive poor-prognosis subtypes and metastasis

R Jackstadt, SR van Hooff, JD Leach, X Cortes-Lavaud… - Cancer cell, 2019 - cell.com
The metastatic process of colorectal cancer (CRC) is not fully understood and effective
therapies are lacking. We show that activation of NOTCH1 signaling in the murine intestinal …

Single-cell mRNA quantification and differential analysis with Census

X Qiu, A Hill, J Packer, D Lin, YA Ma, C Trapnell - Nature methods, 2017 - nature.com
Single-cell gene expression studies promise to reveal rare cell types and cryptic states, but
the high variability of single-cell RNA-seq measurements frustrates efforts to assay …

A universal SNP and small-indel variant caller using deep neural networks

R Poplin, PC Chang, D Alexander, S Schwartz… - Nature …, 2018 - nature.com
Despite rapid advances in sequencing technologies, accurately calling genetic variants
present in an individual genome from billions of short, errorful sequence reads remains …

Local regulation of gene expression by lncRNA promoters, transcription and splicing

JM Engreitz, JE Haines, EM Perez, G Munson, J Chen… - Nature, 2016 - nature.com
Mammalian genomes are pervasively transcribed, to produce thousands of long non-coding
RNAs (lncRNAs),. A few of these lncRNAs have been shown to recruit regulatory complexes …

Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity

S Shalapour, XJ Lin, IN Bastian, J Brain, AD Burt… - Nature, 2017 - nature.com
The role of adaptive immunity in early cancer development is controversial. Here we show
that chronic inflammation and fibrosis in humans and mice with non-alcoholic fatty liver …