Emma Sheriff, PhD

Imagine my surprise seeing my own picture in the FEMS newsletter this week 😅

Had a great time chatting about my paper and discussing some of the excitement (and challenges) surrounding phage research. Check it out!

Great start to November with an inspiring panel sharing their career journeys with our PhD and postdoc community 😄

Big thanks to Prof. Alan Schulman, Dr. Jana Buzkova, Prof. Anne Spang and Prof. Karla Neugebauer, and to the Institute of Biotechnology (BI) for sponsoring and celebrating 35 years! 🥳

Interested in doing a PhD in phage biology? See below a super cool project on megaphage ecology and evolution available at the University of Jyväskylä (FIN) in Elina Laanto's lab (Project no. 4). Co-supervision provided by yours truly.

Day 24, Magic. Finding something new in science feels like magic at times. #Drawtober #SciArt #PhageSky

Help shape the future of microbiology in Europe. FEMS is conducting a survey to better understand the needs of microbiologists.

Your input will help identify key challenges & ensure the community’s voice is heard across Europe.

Complete it today and share with your network: 🔗 buff.ly/5eCowPX

Awesome #phage #bioinformatics preprint from @shelbyeandersen.bsky.social, who is also very close to finishing her PhD and on the lookout for her next position 👀

Fun fact: In reference 28 here, I used the word strain to mean something similar to the lineage level because a reviewer refused to let me use the word lineage.

There is still a lot of confusion in this space, and I strongly recommend defining whatever terminology you use.

Our latest efforts to understand Enterococcal wound infection. In long-term collaboration with @gthibault.bsky.social, we discovered how E. faecalis makes extracellular ROS - via EET!⚡️Which in turn dysregulates host UPR to delay wound healing. Led by @aarontan.bsky.social - his videos below are 🤩!

Congratulations Haider! Well-deserved 🎉

Preview of the dashboard

Recently collaborator Tessa Pierce Ward helped mentor M.S. student Vienna Elmgreen to make a dashboard to visualize our meta-analysis of almost 10,000 Ralstonia isolations.

ralstoniadashboard.shinyapps.io/RalstoniaWil...

'This work illustrates that shallow metagenomics provides the necessary sensitivity and taxonomic resolution to characterize species and strain-level diversity in extremely low biomass samples, opening possibilities for microbiome discovery in previously unexplored niches'

F mechanisms are student and postdoc fellowships.

This is the US choking off funding for training the next generation of talent.

Where is the university leadership response?

Congratulations to our winners of the 2024 #FEMSMicrobes Article Award!

Congratulations also to @duerkoplab.bsky.social, @shelbyeandersen.bsky.social, Fernanda Salvato, @manuelkleiner.bsky.social, and Anushila Chatterjee -- thank you all for your hard work and collaboration!

Enterococcal quorum-controlled protease alters phage infection A protease from Enterococcus faecalis alters phage infection.

Just received the exciting news that the paper representing the bulk of my thesis work was selected as the best FEMS Microbes paper of 2024! Huge thanks to the editors-in-chief at FEMS Microbes (@femsjournals.bsky.social) for selecting me for this honor.
academic.oup.com/femsmicrobes...

Agreed -- have you tried spinning down and filtering your enrichment before spotting?

The President & the richest man in the world are recklessly attacking medical research—with researchers being laid off, studies being canceled, & kids now unable to get the lifesaving treatment they need. It’s absolutely heartless & will have devastating consequences for us all.

👋 Hi antiphage defense community, we are soon releasing an update of DefenseFinder.

We are doing our best to include all the great discoveries from the community, but with so much going on we might miss things.

Please answer wt preprints/papers with new systems or mail/git them to us. 🙏

Based on GitHub comments, I'm not the only one having these issues, and there's a broken link preventing me from downloading all the files I need to get it up and running locally.

Does anyone have other suggestions of tools to predict phage structural proteins (specifically tail proteins)?

Ever want to see what the inside of a refrigerated centrifuge looks like? Now you know! 🦠🧫🧪🧬

I've had good luck with PhANNs in the past and need to annotate only structural proteins from a large dataset of phage genomes, so it seemed like the most straightforward option. Willing to try out other tools though if anyone has suggestions!
#bioinformatics #proteinprediction

Any fellow #phage researchers having trouble running PhANNs through the web tool? I'm able to upload and submit the fasta file, but the predictions never finish running...

Congrats to Lucy Chou-Zheng from the Hatoum-Aslan lab (my former research home) for her recent publication in Nucleic Acids Research! I worked on this project during my undergraduate research, and it's so exciting to see it finally out -- check it out here: academic.oup.com/nar/advance-...