Levi Waldron
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leviwaldron1.bsky.social
Levi Waldron
@leviwaldron1.bsky.social
220 followers 13 following 22 posts
Professor of Biostatistics at CUNY SPH, rstat / Bioconductor enthusiast, cancer genomics/metagenomics, proud HPV OSCC cancer survivor.
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Reposted by Levi Waldron
cibiocm.bsky.social
🥁 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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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...
www.cell.com
May 16, 2025 at 10:55 AM
leviwaldron1.bsky.social
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 ...
www.biorxiv.org
February 19, 2025 at 11:53 AM
Reposted by Levi Waldron
svetlanaup.bsky.social
Today we asked our #outreachy applicants:

What's the best/most fun and least fun part while BugSigDB-ing?

Their answers are beautiful!
outreachy outreachy outreachy outreachy
March 21, 2024 at 7:27 AM
leviwaldron1.bsky.social
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
March 12, 2024 at 2:28 PM
leviwaldron1.bsky.social
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...
March 5, 2024 at 11:59 AM
leviwaldron1.bsky.social
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...
Bioconductor community blog - Journey of Growth: Our Internship experience with Bioconductor
Bioconductor participated in the Outreachy Internship program for the December 2023 cohort. Our interns share their experience working on their various projects and Bioconductor in general.
blog.bioconductor.org
March 5, 2024 at 11:38 AM
leviwaldron1.bsky.social
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
March 5, 2024 at 11:18 AM
Reposted by Levi Waldron
svetlanaup.bsky.social
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
December 18, 2023 at 1:30 PM
Reposted by Levi Waldron
svetlanaup.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...
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
December 19, 2023 at 10:13 AM
Reposted by Levi Waldron
svetlanaup.bsky.social
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
December 19, 2023 at 2:57 PM
leviwaldron1.bsky.social
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.
Search Results
www.rfcuny.org
December 21, 2023 at 9:03 PM
Reposted by Levi Waldron
cibiocm.bsky.social
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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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...
www.nature.com
November 15, 2023 at 7:33 PM