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Venn diagrams in bioinformatics
A Jia, L Xu, Y Wang - Briefings in bioinformatics, 2021 - academic.oup.com
Venn diagrams are widely used tools for graphical depiction of the unions, intersections and
distinctions among multiple datasets, and a large number of programs have been developed …
distinctions among multiple datasets, and a large number of programs have been developed …
Challenges and opportunities in sharing microbiome data and analyses
C Huttenhower, RD Finn, AC McHardy - Nature Microbiology, 2023 - nature.com
Microbiome data, metadata and analytical workflows have become 'big'in terms of volume
and complexity. Although the infrastructure and technologies to share data have been …
and complexity. Although the infrastructure and technologies to share data have been …
FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles
S Põlme, K Abarenkov, R Henrik Nilsson, BD Lindahl… - Fungal diversity, 2020 - Springer
The cryptic lifestyle of most fungi necessitates molecular identification of the guild in
environmental studies. Over the past decades, rapid development and affordability of …
environmental studies. Over the past decades, rapid development and affordability of …
Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome
VJ Carrión, J Perez-Jaramillo, V Cordovez, V Tracanna… - Science, 2019 - science.org
Microorganisms living inside plants can promote plant growth and health, but their genomic
and functional diversity remain largely elusive. Here, metagenomics and network inference …
and functional diversity remain largely elusive. Here, metagenomics and network inference …
Robustness of cancer microbiome signals over a broad range of methodological variation
GD Sepich-Poore, D McDonald, E Kopylova… - Oncogene, 2024 - nature.com
In 2020, we identified cancer-specific microbial signals in The Cancer Genome Atlas
(TCGA). Multiple peer-reviewed papers independently verified or extended our findings …
(TCGA). Multiple peer-reviewed papers independently verified or extended our findings …
Reproducible molecular networking of untargeted mass spectrometry data using GNPS
AT Aron, EC Gentry, KL McPhail, LF Nothias… - Nature protocols, 2020 - nature.com
Abstract Global Natural Product Social Molecular Networking (GNPS) is an interactive online
small molecule–focused tandem mass spectrometry (MS2) data curation and analysis …
small molecule–focused tandem mass spectrometry (MS2) data curation and analysis …
Establishing microbial composition measurement standards with reference frames
JT Morton, C Marotz, A Washburne, J Silverman… - Nature …, 2019 - nature.com
Differential abundance analysis is controversial throughout microbiome research. Gold
standard approaches require laborious measurements of total microbial load, or absolute …
standard approaches require laborious measurements of total microbial load, or absolute …
[PDF][PDF] QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
E Bolyen, JR Rideout, MR Dillon, NA Bokulich, C Abnet… - 2018 - peerj.com
We present QIIME 2, an opensource microbiome data science platform accessible to users
spanning the microbiome research ecosystem, from scientists and engineers to clinicians …
spanning the microbiome research ecosystem, from scientists and engineers to clinicians …
Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in rheumatoid arthritis
Periodontal disease is more common in individuals with rheumatoid arthritis (RA) who have
detectable anti-citrullinated protein antibodies (ACPAs), implicating oral mucosal …
detectable anti-citrullinated protein antibodies (ACPAs), implicating oral mucosal …
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
E Bolyen, JR Rideout, MR Dillon, NA Bokulich… - Nature …, 2019 - nature.com
Conclusions Because of a clear trend toward more engagement and transparency with
research participants, we should expect more research participants to exercise their HIPAA …
research participants, we should expect more research participants to exercise their HIPAA …