🥁 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...
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also has an associated Bioconductor package `benchdamic` to facilitate benchmarking against commonly used methods (Calgaro et al, Bioinformatics 2023), which we profited from in this analysis academic.oup.com/bioinformati...
A previous broad benchmarking of microbiome methods that I was part of (Calgaro et al, Genome Biology 2020) genomebiology.biomedcentral.com/articles/10....
I like your idea, and it seems promising! No snub intended, just not yet in our scope of 'commonly used' or of reviewing broad benchmarking-focused studies. FYI our benchmarking is reproducible and hopefully easily extensible w/ code from github.com/waldronlab/M...
I guess I can thank you for breaking my long sojourn from social media :D I made a thread about our preprint and referenced your post - we agree on compositional normalization, but "normalization based methods don't work well" (including for RNAseq) is a big claim! bsky.app/profile/levi...
So we agree that compositional normalization is problematic, but disagree about the simple, widely-used methods. Prove your method outperforms 17 methods in the 3 datasets we've provided, and I'll eat humble pie 🙂
Discussion! @inschool4life.bsky.social says all these methods are bad and that his new alternative to normalization improves rigor in microbiome *and* RNAseq analysis, as demonstrated by a simulation and a real-data study of each. I hope you're right! bsky.app/profile/insc...
My history on simple methods: In 2014, I benchmarked a simple prediction method (can be trained in a spreadsheet!) against penalized regression. In 27 independent microarray studies, it performed comparably or better than theoretically superior methods (incl. Lasso) academic.oup.com/bioinformati...
Disclaimer: I favor simple methods for high-dimensional data analysis. They perform well in diverse settings. I'm skeptical of hand-selected benchmarks by researchers with a "horse in the race." It's a good start but far short of showing broad utility.
Implications: Our findings suggest researchers should use widely adopted non-parametric or RNA-seq DA methods. Further development of compositional methods should include benchmarking against datasets with known biological ground truth.
Key findings: we benchmarked 17 DA approaches and found compositional methods often lack sensitivity and show increased variability. Non-parametric and RNA-seq-derived methods performed best, challenging the assumption that compositional methods are superior.
MicrobiomeBenchmarkData includes:
1) Oral microbiomes (supragingival vs. subgingival plaques)
2) Vaginal microbiomes (healthy vs. bacterial vaginosis)
3) Spike-in dataset with known absolute abundances
These datasets cover diverse complexities.
The Need for Ground Truth Data: DA method benchmarks usually rely on synthetic data, simulations, or expt'l data without a sequencing-independent biological ground truth. Our BioC package fills this gap with 3 experimental datasets with known ground truths www.bioconductor.org/packages/Mic...
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...
outreachy
outreachy
outreachy
outreachy
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...
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
Love this post!
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
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...
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-...
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...
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Retro Jane Fonda videos are my favorite
Great hook for a course title. And hi on Bluesky!
Welcome, Svetlana!