Sequencing-based methods and resources to study antimicrobial resistance
Antimicrobial resistance extracts high morbidity, mortality and economic costs yearly by
rendering bacteria immune to antibiotics. Identifying and understanding antimicrobial …
rendering bacteria immune to antibiotics. Identifying and understanding antimicrobial …
Shotgun metagenomics, from sampling to analysis
Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes
have crucial roles in the environment and in human health. However, microbes are …
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 …
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 …
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 …
natural populations. Here we report the whole-genome sequencing and phenotyping of …
[PDF][PDF] Comprehensive molecular characterization of muscle-invasive bladder cancer
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 …
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 …
therapeutic options. We analyzed 363 hepatocellular carcinoma (HCC) cases by whole …
A chromosome conformation capture ordered sequence of the barley genome
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 …
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
The Illumina DNA sequencing platform generates accurate but short reads, which can be
used to produce accurate but fragmented genome assemblies. Pacific Biosciences and …
used to produce accurate but fragmented genome assemblies. Pacific Biosciences and …
[PDF][PDF] A comprehensive pan-cancer molecular study of gynecologic and breast cancers
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 …
four gynecological types plus breast. Our aims were to identify shared and unique molecular …