Sequencing-based methods and resources to study antimicrobial resistance

M Boolchandani, AW D'Souza, G Dantas - Nature Reviews Genetics, 2019 - nature.com
Antimicrobial resistance extracts high morbidity, mortality and economic costs yearly by
rendering bacteria immune to antibiotics. Identifying and understanding antimicrobial …

Shotgun metagenomics, from sampling to analysis

C Quince, AW Walker, JT Simpson, NJ Loman… - Nature …, 2017 - nature.com
Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes
have crucial roles in the environment and in human health. However, microbes are …

Clonal IgA and IgG autoantibodies from individuals at risk for rheumatoid arthritis identify an arthritogenic strain of Subdoligranulum

ME Chriswell, AR Lefferts, MR Clay, AR Hsu… - Science translational …, 2022 - science.org
The mucosal origins hypothesis of rheumatoid arthritis (RA) proposes a central role for
mucosal immune responses in the initiation or perpetuation of the systemic autoimmunity …

[HTML][HTML] Severe acute respiratory syndrome coronavirus 2 from patient with coronavirus disease, United States

J Harcourt, A Tamin, X Lu, S Kamili… - Emerging infectious …, 2020 - ncbi.nlm.nih.gov
The etiologic agent of an outbreak of pneumonia in Wuhan, China, was identified as severe
acute respiratory syndrome coronavirus 2 in January 2020. A patient in the United States …

Genome evolution across 1,011 Saccharomyces cerevisiae isolates

J Peter, M De Chiara, A Friedrich, JX Yue, D Pflieger… - Nature, 2018 - nature.com
Large-scale population genomic surveys are essential to explore the phenotypic diversity of
natural populations. Here we report the whole-genome sequencing and phenotyping of …

[PDF][PDF] Comprehensive molecular characterization of muscle-invasive bladder cancer

AG Robertson, J Kim, H Al-Ahmadie, J Bellmunt, G Guo… - Cell, 2017 - cell.com
We report a comprehensive analysis of 412 muscle-invasive bladder cancers characterized
by multiple TCGA analytical platforms. Fifty-eight genes were significantly mutated, and the …

[PDF][PDF] Comprehensive and integrative genomic characterization of hepatocellular carcinoma

A Ally, M Balasundaram, R Carlsen, E Chuah, A Clarke… - Cell, 2017 - cell.com
Liver cancer has the second highest worldwide cancer mortality rate and has limited
therapeutic options. We analyzed 363 hepatocellular carcinoma (HCC) cases by whole …

A chromosome conformation capture ordered sequence of the barley genome

M Mascher, H Gundlach, A Himmelbach, S Beier… - Nature, 2017 - nature.com
Cereal grasses of the Triticeae tribe have been the major food source in temperate regions
since the dawn of agriculture. Their large genomes are characterized by a high content of …

Unicycler: resolving bacterial genome assemblies from short and long sequencing reads

RR Wick, LM Judd, CL Gorrie… - PLoS computational …, 2017 - journals.plos.org
The Illumina DNA sequencing platform generates accurate but short reads, which can be
used to produce accurate but fragmented genome assemblies. Pacific Biosciences and …

[PDF][PDF] A comprehensive pan-cancer molecular study of gynecologic and breast cancers

AC Berger, A Korkut, RS Kanchi, AM Hegde, W Lenoir… - Cancer cell, 2018 - cell.com
We analyzed molecular data on 2,579 tumors from The Cancer Genome Atlas (TCGA) of
four gynecological types plus breast. Our aims were to identify shared and unique molecular …