Reposted by Moamen ElmassryScience Magazine @science.org · 21/09/2026"I realized I would need to figure out my postdoc personality on my own." #NationalPostdocAppreciationWeek scim.ag/4yb15sK 0225
Reposted by Moamen ElmassryKate Lagerstrom @kate-lagerstrom.bsky.social · 02/09/2026Really excited to see this piece out in The Microbiologist! 🐾🦠🌍 A look at how human activities are reshaping wildlife microbiomes—and when those changes may become a One Health concern. Thanks to @amiposts.bsky.social for the opportunity to contribute! 032
Reposted by Moamen ElmassryCameron Myhrvold @cambearon.bsky.social · 19/06/2026Over the past 50 years, we have learned much about how transcription factors and other DNA-binding proteins search for their targets, but we know much less about how sequence-specific RNA-binding proteins (RBPs) search for their targets. 🧵⤵️ (1/26) 184
Reposted by Moamen ElmassryAi Ing Lim @aiinglim.bsky.social · 13/05/2026LIMmunity 2nd brew: Motherhood comes with superpower: pathogen protection! 🤰🤱 www.nature.com/articles/s41... We often think moms are immunologically vulnerable during reproduction to tolerate the baby. But I always wondered: why would evolution make such a critical period of life so dangerous?nature.comEosinophils drive intestinal remodelling and innate defence in reproduction - NatureFrom pregnancy until lactation, eosinophils accumulate in the small intestine where they regulate goblet cell fate and enhance innate defences against enteric pathogens. 1184
Moamen Elmassry @elmassry.bsky.social · 28/04/2026The takeaway? If you don’t get any hits from nt, re-BLAST using refseq_genomes, before you conclude that there are no matches for your sequences. P.S. I don’t recommend BLASTing against refseq_genomes first, only because it takes longer to run on the NCBI web servers. Try nt, then refseq_genomes. 000
Moamen Elmassry @elmassry.bsky.social · 28/04/2026Nucleotide collection (nt) — The nucleotide collection consists of GenBank+EMBL+DDBJ+PDB+RefSeq sequences, but excludes EST, STS, GSS, WGS, TSA, patent sequences as well as phase 0, 1, and 2 HTGS sequences and sequences longer than 100Mb. The database is non-redundant. 100
Moamen Elmassry @elmassry.bsky.social · 28/04/2026RefSeq Genome Database (refseq_genomes) — This database contains NCBI Refseq genomes across all taxonomy groups. It contains only the top-level sequences, i.e., only the longest sequences representing any given part of the genomes are included. 100
Moamen Elmassry @elmassry.bsky.social · 28/04/2026This was surprising because nt is a larger database (126M sequences) than refseq_genomes (56M sequences). However, the curation of refseq_genomes makes it more comprehensive. This is because the collection of sequences in each database is quite different. Here is the description for each from NCBI. 100
Moamen Elmassry @elmassry.bsky.social · 28/04/2026• 41.4% matched both nt and refseq_genomes • 24.9% matched refseq_genomes ONLY • 1.3% matched nt ONLY • 32.5% had no match in either 100
Moamen Elmassry @elmassry.bsky.social · 28/04/2026Here is an important BLAST tip. TL;DR: Always search both Nucleotide collection (nt) AND RefSeq Genome (refseq_genomes) databases— don't rely on just one. I BLASTed ~10,000 nucleotide sequences (mostly gut microbiome-derived sequences) against both NCBI databases and here's what I found: 100
Reposted by Moamen ElmassryNational Microbiome Data Collaborative (NMDC) @microbiomedata.org · 17/04/2025Check out the recent publication from NMDC Champion @elmassry.bsky.social! doi.org/10.1016/j.ch... 021
Moamen Elmassry @elmassry.bsky.social · 26/02/2025Briefly, we identified gut microbiome-encoded biosynthetic gene clusters that are enriched in Crohn’s disease patients and the small molecules they produce, which exacerbated disease when introduced to mouse models of colitis. 010
Moamen Elmassry @elmassry.bsky.social · 26/02/2025Excited to share our latest work on the gut microbiome in inflammatory bowel disease patients. This is the result of hard work across generations of trainees in the Donia Lab, in collaboration with amazing scientists (Nobuhiko Kamada and Lea Ann Chen). www.cell.com/cell-host-mi... 292
Moamen Elmassry @elmassry.bsky.social · 02/12/2024www.dailyprincetonian.com/article/2024...dailyprincetonian.comWhy postdocs are demanding open bargaining"Princeton’s resistance to the presence of observers is a break from many academic union negotiations. At Harvard, Weill Cornell, Mt Sinai, Columbia University, and the University of Washington, there... 000
Reposted by Moamen ElmassryJose V. Die @jdieramon.bsky.social · 26/11/2024Come join the workshop this Wednesday, the 27th, where I'll present #refseqR, a new R package for streamlined computational tasks on RefSeq entries (GenBank, NCBI). Don’t miss it! 🚀 #RStats #Bioinformatics Available from CRAN: cran.rstudio.com/web/packages... 043
Reposted by Moamen ElmassryLauren Palmer @laurenpalmer.bsky.social · 15/11/2024SO EXCITED to share our recent work on dietary zinc deficiency worsening Acinetobacter baumannii pneumonia, out today with @natureportfolio.bsky.social!! Surprisingly, this is due at least in part to the allergic-type cytokine IL-13. SharedIt link: rdcu.be/d0h4h Eat your zinc rich foods! 🦪🫘🧀🥩🥜rdcu.beDietary zinc deficiency promotes Acinetobacter baumannii lung infection via IL-13 in miceNature Microbiology - Increased IL-13 drives increased bacterial dissemination and mortality following Acinetobacter baumannii lung infection of zinc-deficient mice and can be countered by... 1416348