From @leviwaldron1.bsky.social & colleagues in #OUP 's #DATABASE journal | Large-scale manual #Curation & harmonization of metadata from #MetaGenomic & #Cancer #Genomic repositories: challenges and solutions | #Bioinformatics #OpenScience #Biocuration #LLM | 🧬🖥️🧪🔓 ⬇️ doi.org/10.1093/data...

Large-scale manual curation and harmonization of metadata from metagenomic and cancer genomic repositories: challenges and solutions

Abstract. Public omics repositories contain vast amounts of valuable data, but their metadata suffers from extreme heterogeneity, unstandardized terminolog

doi.org

🥁 NEW: Commentary in @cellcellpress.bsky.social! by @msabrysarhan.bsky.social Giacomo Antonello @whansi.bsky.social @cengoni.bsky.social @dmascalzoni.bsky.social @leviwaldron1.bsky.social Nicola Segata, Christian Fuchsberger www.cell.com/cell/fulltex... 1/4

Human mitochondrial DNA in public metagenomes: Opportunity or privacy threat?

Human DNA is unavoidably present in metagenomic analyses of human microbiomes. While current protocols remove human DNA before submission to public repositories, mitochondrial DNA (mtDNA) has been ove...

cell.com

Excited to share our MicrobiomeBenchmarkData preprint, addressing compositional data analysis for microbiome DA. This Bioconductor package features 3 datasets with biological ground truths. Spoiler: simple methods like LEfSe, Wilcoxon, RNA-seq methods performed well www.biorxiv.org/content/10.1...

Commonly used compositional data analysis implementations are not advantageous in microbial differential abundance analyses benchmarked against biological ground truth

Previous benchmarking of differential abundance (DA) analysis methods in microbiome studies have employed synthetic data, simulations, and "real data" examples, but to the best of our knowledge, none ...

biorxiv.org

Today we asked our #outreachy applicants: What's the best/most fun and least fun part while BugSigDB-ing? Their answers are beautiful!

Very kind blog post from my Outreachy mentee Peace Sandy about the journey to closing her first issue on an open-source software project! peacesandy.hashnode.dev/my-outreachy...

My Outreachy Internship with Bioconductor

An Open Source Journey

peacesandy.hashnode.dev

Reported a duplicated figure to PubPeer - discovered via bugsigdb.org which re-codes published signatures in an analyzable format. Identical signatures are easy to spot as outliers as typical overlap between independently discovered signatures is nowhere near 100% pubpeer.com/publications...

So impressed by outreachy.org 's reach and competitive applicant screening that connected me with a remarkably talented and hard-working intern from Nigeria for a highly productive 3-month paid internship. Recommend to any open-source/open-science projects blog.bioconductor.org/posts/2024-0...

Microbiome Virtual International Forum is a free, monthly 3-hour mini-conference with a keynote talk, short talks, and 1-minute highlights, repeated for accessibility in all time zones. Mar. 20-22 features Curtis Huttenhower; see www.microbiome-vif.org to register and for timing in your time zone

Read a very first blog by Esther Afuape, a #BugSigDB intern: kunmiwrites.wordpress.com Much more to come from Esther and her #BugSigDB curations! #proudmentor cc @leviwaldron1.bsky.social

The everyday chronicles

kunmiwrites.wordpress.com

Chioma Onyido, an Outreachy intern, wrote about core values, how she applied for internship & why did she choose the Microbiome Study Curation project. Stay tuned for more Chioma’s stories, tips & tricks on #BugSigDB-ing! cc @leviwaldron1.bsky.social chiomaonyido.wordpress.com/2023/12/18/m...

My First Piece… Hi…

I almost did not believe this was REAL because it looked too good to be true, and as a Nigerian we've a natural instinct to question everything, especially because of the high rate of fraud and cyber ...

chiomaonyido.wordpress.com

Peace Sandy just started her Outreachy journey (together with Chioma Onyido and Afuape Esther) of contribution and growth while curating microbiome studies Read Peace's point of view on #BugSigDB-ing! cc @leviwaldron1.bsky.social peacesandy.hashnode.dev/kicking-off-...

Outreachy Blog : Introducing Myself

Kicking Off Outreachy: Week One Highlights, a Journey of Contribution and Growth

peacesandy.hashnode.dev

Two positions available at CUNY SPH working with myself & Nicola Segata to understand roles of the microbiome in Parkinson's Disease, in collab with the Michael J Fox Foundation ASAP network. $75-85K/yr, conference travel, 1 mo/yr in the Segata lab in Italy. In-person or remote work possible.

In NEW Nature Reviews Microbiology article, @fasnicar.bsky.social Andrew Maltez Thomas, Andrea Passerini @leviwaldron1.bsky.social and Nicola Segata cover the aspects that they consider most important to enable microbiologists to use machine learning. www.nature.com/articles/s41... 1/2

Machine learning for microbiologists - Nature Reviews Microbiology

In this Review, Segata, Waldron and colleagues discuss important key concepts of machine learning that are relevant to microbiologists and provide them with a set of tools essential to apply machine l...

nature.com