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cpherlihy.bsky.social

@cpherlihy.bsky.social
103 followers 128 following 3 posts

Hematology & Oncology Postdoctoral Fellow in the Department of Genome Sciences at the University Washington

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Sarah McAnulty, Ph.D. @sarahmackattack.bsky.social · 29/08/2026
Alright everybody, time to text the teachers in your life. The fall semester is open at SkypeAScientist and we are ready to match classrooms, scout troops, library groups, and more with scientists! Tell the educators in your life, and send them to SkypeAScientist.com
A frog uses its comically long tongue to catch a fleeing fly and the words say “send this to a teacher” pointing right. Then under the tongue it says “Skype a scientist matches classrooms with scientists for free Q&As” and there’s a little pond scene with lily pads and spatterdock flowers and a rock with a snail on it and a salamander with the words get a match at Skype scientist.com
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Nick Riley @nmriley.bsky.social · 28/08/2026
Glycoproteoforms are the unit of biological information in the glycoproteome, but measuring intact glycoproteins to capture combinatorial modification states remains a huge #glycotime challenge. @timveth.bsky.social tackled this issue head on in the latest preprint from @riley-research.bsky.social
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Phil W @pwilmarth.bsky.social · 19/08/2026
#proteomics Detecting PTMs is one of the great strengths of mass spectrometry based proteomics, right? This guide to detecting deamidation of N or Q residues might suggest otherwise. PTM work is really hard and deamidation is particularly challenging. codeberg.org/pwilmart/Det...
codeberg.org
Detecting_Deamidation_Guide
Detailed guide describing how to accurately detect deamidation in bottom-up proteomics datasets.
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Molecular Cell @cp-molcell.bsky.social · 07/08/2026
Broken chromosomes don’t stay home: Tunneling nanotubes carry damaged DNA between human cells
dlvr.it
Broken chromosomes don’t stay home: Tunneling nanotubes carry damaged DNA between human cells
In a recent Cell paper, Maurais et al. show that genomic instability drives human cells to transfer fragmented chromosomes to neighbors via tunneling nanotubes (TNTs), with heritable functional consequences, raising fundamental questions about intercellular communication, genome surveillance, and cancer evolution.
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Science in Seattle @scienceinseattle.com · 15/07/2026
The Damon Runyon Cancer Research Foundation has awarded two @fredhutch.org postdoctoral fellows grants to support investigations of #leukemia and #LungInfections in cancer patients. Congratulations Drs. Vivian Liu and Sahana Kuthyar! bit.ly/4fyGHuz
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Peter Ly @peterlylab.bsky.social · 19/05/2026
Excited to share our latest paper! We found that large pieces of the human genome can transfer between cells upon direct contact, endowing recipient cells with heritable phenotypic changes. @cp-cell.bsky.social (1/7) www.cell.com/cell/fulltex...
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cpherlihy.bsky.social @cpherlihy.bsky.social · 03/05/2026
Really excited to have lead this work alongside Eli and Lidan! I’d love to chat about applying our platform to your system of interest, the advantages of parallel imaging and proteomics, ability to target DNA, RNA, and protein, or advantages over enzyme-based labeling with anyone who’s interested!
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Devin Schweppe @dschweppe.bsky.social · 28/04/2026
More exciting work from the lab! Along with @maccoss.bsky.social (@uwgenome.bsky.social) and Gary Churchill (@jax.org), Dr. Katarina Vlajic's tour de force multi-omics profiling uncovered molecular signatures of healthy splenic aging! www.biorxiv.org/content/10.6...
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Riddhiman Garge @riddhiman.bsky.social · 25/04/2026
1/ Thrilled to share our latest: an exciting collaboration across the @jshendure.bsky.social, @leastarita.bsky.social, @nobuhamazaki.bsky.social and @dschweppe.bsky.social labs! 🧵 below- #SystemsBiology #SCBEM #MultiOmics #Gastruloids www.nature.com/articles/s41...
nature.com
The proteomic landscape and temporal dynamics of human and mouse gastruloid development - Nature Cell Biology
Garge et al. use experimentally matched mass spectrometry and RNA-sequencing to quantify proteins, phosphosites and transcripts across four key stages of human and mouse gastruloid development.
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cpherlihy.bsky.social @cpherlihy.bsky.social · 08/04/2026
First co-author paper from the first year of my time here at UW is now live! Always happy to chat about it with anyone who is interested ☺️
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Andy Moore @aaandmoore.bsky.social · 07/02/2026
Not something you see in textbooks very often: tripolar mitosis.
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Jeff Vierstra @jeffvierstra.bsky.social · 30/01/2026
Surprised (but also not that surprised) that the AlphaGenome paper didn't officially cite any of the primary data used for training their model (see Fig. 1, thousands of datasets made with tremendous time and effort over >15yrs). What's up with that @nature.com ? www.nature.com/articles/s41...
nature.com
Advancing regulatory variant effect prediction with AlphaGenome - Nature
AlphaGenome, a deep learning model that inputs 1-Mb DNA sequence to predict functional genomic tracks at single-base resolution across diverse modalities, outperforms existing models in variant effect...
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Matthew Berg @matthewberg22.bsky.social · 29/01/2026
Check out our new work now published in G3! We use proteomics and phosphoproteomics to study how cells cope with tRNA variants that mis-insert amino acids.
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Mother Jones @motherjones.com · 24/01/2026
Something is deeply wrong if we, as a society, cannot agree that an administration that snatches up children, uses them as bait to hunt down others, is morally repulsive.
motherjones.com
They want to tell you a kid with a Spider-Man backpack is evil
Liam Ramos' innocence, like the innocence of all kids, is unimpeachable. The visuals of his arrest are excruciating.
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Wajahat Ali @wajali.bsky.social · 23/01/2026
This is a death sentence for America. www.nytimes.com/2026/01/23/h...
nytimes.com
Rejecting Decades of Science, Vaccine Panel Chair Says Polio and Other Shots Should Be Optional
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Job Dekker @jobdekker.bsky.social · 22/12/2025
Exciting new paper out! @allanaschooley.bsky.social and Sergey Venev led this project that let to the discovery of two chromosome folding programs: one inherited via mitotic chromosomes and one mitotic inherited through the cytoplasm! www.nature.com/articles/s41...
nature.com
Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm - Nature Cell Biology
Schooley et al. find that mitotically bookmarked loci drive a transient chromosome folding state during G1 entry that is subsequently modulated by factors inherited through the cytoplasm.
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Michael Hoffman @michaelhoffman.bsky.social · 10/11/2025
The definitive obituary of James Watson, written by the late, great Sharon Begley @statnews.com www.statnews.com/2025/11/07/j...
statnews.com
James Watson, dead at 97, was a scientific legend and a pariah among his peers
James Watson, the co-discoverer of the structure of DNA who died Thursday at 97, was a scientific legend and a pariah among his peers.
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Michael MacCoss @maccoss.bsky.social · 06/11/2025
Fantastic project led by @bo-wen.bsky.social. Excited to see the future uses of AI and transfer learning in proteomics. #massspec #proteomics www.nature.com/articles/s41...
nature.com
Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics - Nature Communications
Accurate spectral libraries are essential for analyzing data-independent acquisition (DIA) proteomics data. Here, the authors present Carafe, which trains on DIA data to build experiment-specific spec...
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Carl Quintanilla @carlquintanilla.bsky.social · 05/11/2025
This really hasn’t gotten enough attention this week. @wired.com #ICE www.wired.com/story/fbi-wa...
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ProPublica @propublica.org · 06/10/2025
NEW: After paying for hotel rooms to shelter homeless people, Seattle deliberately left them vacant. By the end of 2024, taxpayers were spending $4,200 a month per empty room at a time when thousands of residents were without a roof over their heads.
propublica.org
Seattle Spent Millions on Hotel Rooms to Shelter Unhoused People. Then It Stopped Filling Them.
Early last year, the city signed a $2.7 million lease extension to continue using a hotel’s rooms as shelter space. Yet despite committing to pay the rent, the city stopped sending people there.
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Karl Jacoby @karl-jacoby.bsky.social · 02/10/2025
Note that the Trump Administration is already going back to schools with whom it earlier reached "deals" (such as UPenn and Brown) for further concessions. Conceding to a bully has only emboldened them to make new demands.
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The Associated Press @apnews.com · 03/10/2025
The New York Yankees beat the Boston Red Sox in Wild Card Series to advance to the AL Division Series against the Toronto Blue Jays.
bit.ly
Schlittler strikes out 12 in postseason debut as Yankees beat Red Sox 4-0 to win Wild Card Series
Rookie right-hander Cam Schlittler struck out 12 as he shut down Boston with 100 mph heat, and the New York Yankees took advantage of a pair misplays in a four-run fourth inning to beat the Red Sox 4-0 for a 2-1 AL Wild Card Series win and a Division Series matchup against Toronto.
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Nobu Hamazaki @nobuhamazaki.bsky.social · 26/09/2025
New paper from my lab and @jshendure.bsky.social lab! Led by the brilliant @zukailiu.bsky.social and @cxqiu.bsky.social. We tackled how anterior and posterior progenitor cells cooperate to self-organize into an embryonic structure (termed AP-gastruloid). (1/n) www.biorxiv.org/content/10.1...
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Adam Phillippy @aphillippy.bsky.social · 24/09/2025
🚂 The T2T train keeps rolling: "The formation and propagation of human Robertsonian chromosomes" with Gerton and Garrison labs is out! What's a Robertsonian chromosome? Let Jen tell you herself in this great video, or read our paper: [1/3] 📺 youtu.be/JmlY5omxQVc 📄 www.nature.com/articles/s41...
youtu.be
How Stowers Scientists Found the DNA Site Where Robertsonian Chromosomes Fuse
YouTube video by Stowers Institute for Medical Research
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Mother Jones @motherjones.com · 24/09/2025
Elite colleges are infamous for funneling students into the Big Three—consulting, tech, and finance—high-paying fields that perpetuate status and wealth. To some young people, it feels like entrapment: “They get you before you could be exposed to other jobs.”
motherjones.com
America’s elite colleges are perpetual inequality machines. It doesn't have to be this way.
Rather than steer the nation's top students toward the most lucrative careers, schools could help them build meaningful lives.
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Vijay Ramani @vram142.bsky.social · 20/09/2025
Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up! www.biorxiv.org/content/10.1... A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
biorxiv.org
The eukaryotic replisome intrinsically generates asymmetric daughter chromatin fibers
DNA replication is molecularly asymmetric, due to distinct mechanisms for lagging and leading strand DNA synthesis. Whether chromatin assembly on newly replicated strands is also asymmetric remains un...
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Science Friday @scifri.bsky.social · 19/09/2025
Today, scientists know that genetics plays a role in many conditions and diseases. But back in the ’90s, geneticist Mary-Claire King was the first to link a gene to an inherited form of a common cancer.
buff.ly
A Trailblazing Geneticist Reflects On Her Life And Work
Dr. Mary-Claire King was the first to link a gene to hereditary cancer risk with the identification of BRCA1. She was just getting started.
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Devin Schweppe @dschweppe.bsky.social · 09/09/2025
Real-time API control of mass specs has been hard to get started (C#, VS, etc). Mike Hoopmann's recent work makes dev easier & more open!: Nova - lightweight dev library schweppelab.github.io/Nova/ pubs.acs.org/doi/full/10.... Helios - a unified instrument API now @ JPR github.com/SchweppeLab/...
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Shan-Lu Liu @shanluliu.bsky.social · 08/09/2025
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Johannes Stein @jmstein.bsky.social · 13/08/2025
(1/n) DNA-PAINT imaging inside the nucleus at single antibody resolution using TIRF? Ultrathin sectioning makes it happen! Grateful to share my postdoctoral work introducing “tomographic & kinetically-enhanced DNA-PAINT” or in brief: tkPAINT. Out in @pnas.org! doi.org/10.1073/pnas... 👇🧵
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