Libusha Kelly

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Libusha Kelly

Libusha Kelly

@microbegrrl

Microbial ecologist, computational and systems biologist, genomics freak

Bx, NYC Bergabung Ocak 2014
882 Mengikuti1.2K Pengikut
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Mikala Egeblad
Mikala Egeblad@megeblad·
Two weeks left to apply! We seek candidates who are addressing fundamental problems of relevance to cancer cell biology for a tenure-track Assistant or Associate Professor position. Join our collaborative department: jobs.sciencecareers.org/job/660742/ass…
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Sorek Lab
Sorek Lab@SorekLab·
Our paper out today @nature: phages reconstitute NAD+ to counter bacterial immunity Phaged invented a new biochemical pathway for NAD+ synthesis - including previously unknown enzymatic reactions - to evade bacterial defenses Congrats @IlyaOsterman! nature.com/articles/s4158…
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Zachary Flamholz
Zachary Flamholz@zflam94·
Our AI for viral annotation review is out! I spent much of my dissertation discussing the opportunities and challenges that new AI methods pose for viral annotation. It is an exciting time!! @microbegrrl @mbiojournal @ASMicrobiology
Biology+AI Daily@BiologyAIDaily

Improving viral annotation with artificial intelligence 1/ This review highlights the potential of using artificial intelligence, specifically protein language models (pLMs), to tackle one of virology's toughest challenges: the annotation of viral sequences that lack homology with known proteins. 2/ The key innovation is leveraging pLMs to bridge the gap left by traditional sequence-based annotation tools, which struggle with the diversity and rapid evolution of viral proteins, especially those from uncultivated viral genomes. 3/ A central breakthrough is the use of self-supervised learning to train models on massive datasets of amino acid sequences. These models capture structural and functional properties of viral proteins, even when sequence homology is too distant to detect. 4/ The paper emphasizes how protein embeddings generated by pLMs can predict functions for unknown viral proteins, significantly improving annotation for metagenomic data, especially for ocean viromes. 5/ One notable success is the expansion of annotated viral protein families using pretrained pLMs, discovering novel viral capsid proteins and mobile genetic elements previously hidden in environmental samples. 6/ The review outlines key limitations of current pLMs, including their bias toward well-represented protein families and the computational resources required for training. However, it proposes future directions, such as fine-tuning pLMs for specific viral contexts. 7/ The authors propose a roadmap for developing virus-specific language models, potentially incorporating genomic context and neighborhood information to enhance annotations for understudied viral protein families. @microbegrrl @zflam94 @ASMicrobiology 📜Paper: doi.org/10.1128/mbio.0…

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Joe Bondy-Denomy
Joe Bondy-Denomy@joeBondyDenomy·
Search: Tenure track Faculty Position @UCSF in the Dept. of Micro and Immuno, with lab space at the Mission Bay campus! We seek a creative investigator with a strong independent research plan who will be a great mentor, colleague, and peer. Job ad soon. Assistant Prof level.
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Iain Cheeseman
Iain Cheeseman@iaincheeseman·
Come be my colleague! Two faculty searches @WhiteheadInst. One is focused on mammalian biology. The other on "emerging" biology including innovative new ideas or technologies, as well as artificial intelligence/machine learning. Apply today. wi.mit.edu/news/whitehead…
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Joanna Kelley
Joanna Kelley@joannalkelley·
Come join us at UCSC in Ecology and Evolutionary Biology! We're hiring an Assistant Professor of Coastal or Marine Ecology! @UCSCscience @ucsc
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Andy Goodman
Andy Goodman@Goodman_lab·
Faculty search! @YaleMicroPath is looking to hire assistant professor(s) focused on the pathogenesis of viral, bacterial, parasitic, or fungal infections. Info: apply.interfolio.com/151755. Q&A webinar in Sept. Please RT!
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JSeeliger Lab
JSeeliger Lab@jcslab·
When it rains, it pours! 🌧️We're hiring not only 2x Asst Prof (see below), but also 1x✨Asst/Associate Prof✨. Open search (all bio-related fields, all types of experience) in @SBUPharm @stonybrooku. Please spread the word! New! Asst/Assoc Prof: apply.interfolio.com/150233
JSeeliger Lab@jcslab

Open search for 2x Asst Prof in my department @SBUPharm @StonyBrookMed @stonybrooku! Please spread the word. Apply here: apply.interfolio.com/150220

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Michael Meers
Michael Meers@mpmeers·
After a successful faculty recruitment that brought in two stellar new Assistant Profs, we're not resting on our laurels: @WashUGenetics is hiring again. I'm on the search committee this year, and we're prepared to make a bunch of offers. Let me tell you why you should apply 1/6
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Phage Directory
Phage Directory@phagedirectory·
ePhective (San Francisco) is a newly founded #phagetherapy company started by @joeBondyDenomy (@UCSF) & Zemer Gitai (@Princeton). They are currently looking for: 2 #Phage Scientists to lead projects in phage discovery, characterization, & engineering
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