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Casey Bergman

@caseybergman.bsky.social
655 followers 428 following 79 posts

Dad, bioinformatician, ex-expat. Currently working on transposon bioinformatics & infectious disease genomics.

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Reposted by Casey Bergman
Giorgio Gilestro @giorgio.gilest.ro · 20/09/2026
Academia has seen inflation in the past 30 years but it is now entering Republic of Weimar territory, with value of knowledge moving from "paper to land". In all this, Open hardware is an act of armed resistance to Technofeudalism. giorgio.gilest.ro/the-weimar-o...
giorgio.gilest.ro
The Weimar of knowledge – la bottega
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László Tora @tlaszlo.bsky.social · 17/09/2026
Pierre Chambon was one of the driving architects of modern molecular biology, whose scientific vision transformed the understanding of gene regulation in eukaryotic cells. His passing in May 2026 represents the loss of an extraordinary scientist. www.nature.com/articles/s41...
nature.com
Pierre Chambon (1931–2026) - Nature Genetics
Nature Genetics - Pierre Chambon (1931–2026)
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Rockefeller Institute of Government @rockefellerinst.bsky.social · 10/09/2026
We're thrilled to announce our third cohort of NYS Science Policy Fellows! These PhD scientists are working with the NYS executive and legislature to bring additional scientific expertise to bear on important policy problems. 👇 Meet the fellows! 🧵 rockinst.org/news/article...
rockinst.org
Rockefeller Institute of Government Welcomes Third Cohort of New York State Science Policy Fellows | Rockefeller Institute of Government
Six doctoral-level scientists will serve two-year appointments across New York State government to support evidence-based policymaking.
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Daniel Croll @danielcroll.bsky.social · 04/09/2026
Our lab is looking for PhD students to join us in 2027 🎓🎉 The projects can be structured around our research directions: - Transposable element dynamics - Fungal pangenomics - ML/language model genomics applications - Pathogen adaptation More here pathogen-genomics.org ("Jobs") and please share! 🙏
pathogen-genomics.org
Evolutionary genomics of pathogens
Croll lab at University of Neuchatel. The lab of Daniel Croll wants to understand how pathogens evolve to cause disease. For this, we mainly focus on major crop pathogens to unravel mechanisms of rapi...
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Sternberg Lab @sternberglab.bsky.social · 01/09/2026
Just published! IStrons are a unique class of transposable elements that pack three distinct functions in one nucleotide sequence. In this work, we used pooled library mutagenesis and high-throughput sequencing to systematically map the sequence and structural features that govern these functions.
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Joshua Shapiro @josh.shapiro.foo · 11/08/2026
We're hiring! The @cancerdatalab.bsky.social at @alexslemonade.bsky.social is looking for a Data Scientist to add to our team. We do a lot of things on our small Data Lab team, and we're looking for someone great to help up further our mission. www.ccdatalab.org/open-positio...
ccdatalab.org
Open Position - Data Scientist
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Adam Phillippy @aphillippy.bsky.social · 06/08/2026
🎯 Goodhart’s law: if you make a list of variants the target, people will get really good at calling those variants. But those variants are not a genome! As a result, we’ve been stuck trying to read genomes under the lamppost of short reads [4/15]
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Pleuni Pennings @pleunipennings.bsky.social · 17/07/2026
peppered moth question! Is this graph based on data? And if so, does anyone know the reference? Or another reference with such a figure including the increase and decrease of dark morphs? www.coursehero.com/tutors-probl... @wtf-r-species.bsky.social
graph that shows frequency of light morphs going down and then up while dark morphs go up and then down. x axis goes from 1800 - 2000.
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Mike Schatz @mikeschatz.bsky.social · 08/07/2026
Registration is open for the CSHL Biological Data Science conference on Nov 4-7, 2026. Check out this awesome list of keynote speakers and session chairs. Learn more here: bit.ly/cshl-biodata26
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Bergman Lab @ UGA @bergmanlab.bsky.social · 30/06/2026
New preprint describing collaborative work with Rozario and Ye Labs to assemble and annotate the genome of the rat tapeworm: www.biorxiv.org/content/10.6...
biorxiv.org
Assembly of a high-quality reference genome for the rat tapeworm Hymenolepis diminuta
The rat tapeworm, Hymenolepis diminuta , is an important laboratory model for uncovering molecular processes that underly the success of tapeworms as parasites. Despite its importance, a high-quality ...
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Bloomington Drosophila Stock Center @bdsc.bsky.social · 23/06/2026
We are pleased to announce a major donation to support the work of the Bloomington Drosophila Stock Center. Lawerence Washington, husband of former BDSC director Kathy Matthews, has established an endowment in her honor. bdsc.indiana.edu/news-events/...
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Tom Sasani @tomsasani.bsky.social · 20/05/2026
Excited to announce that I'll be joining the Department of Genetics at UGA (@universityofga.bsky.social) in January! My lab will use model systems, DNA sequencing, and new computational tools to study mutation rate evolution across the tree of life.
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Mark A. Hanson @hansonmark.bsky.social · 25/05/2026
Official petition for the UK to rejoin the EU, open to UK citizens and residents: petition.parliament.uk/petitions/74... Takes literally 1 minute, very quick. With changing political climate, worth making your UK voice heard if this is your view. Petition closes June 8th 2026.
petition.parliament.uk
Petition: Apply to Rejoin the EU as soon as possible to increase growth in the UK
We believe Brexit's not working. The OBR judges that the UK economy is smaller and trade is weaker because of Brexit, and it will just get worse. 10 years after the Brexit vote, let's apply to rejoin ...
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Casey Bergman @caseybergman.bsky.social · 13/05/2026
MemPang26 conference (today) Schedule: pangenome.github.io/MemPanG26/#_... Free Livestream: tennesseehipaa.zoom.us/j/86514448732
pangenome.github.io
MemPanG26 - Memphis Pangenomics 2026
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Cedric Feschotte @cedricfeschotte.bsky.social · 07/05/2026
👋 Transposon lovers: registration is now open for the CSHL TE meeting! We have a 🔥 lineup of invited speakers and many slots for short talks selected upon abstract across all areas of TE biology. 🧬➰🧬 #TEsky Abstract deadline: July 10 meetings.cshl.edu/meetings.asp...
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The EMBO Journal @embojournal.org · 04/05/2026
Retrovirus insertions in host transcripts trigger de novo piRNA immunity: Kirsten-André Senti, @juliusbrennecke.bsky.social et al investigate the 20th-century invasion of D. melanogaster by iERV Tirant to reveal piRNA-pathway evolution in response to new threats link.springer.com/article/10.1...
link.springer.com
Retrovirus insertions in host transcripts trigger de novo piRNA immunity - The EMBO Journal
How host organisms adapt their defense systems to newly invading transposable elements remains poorly understood. Here, we show how Drosophila melanogaster acquired PIWI-interacting RNA (piRNA)-mediat...
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Chris Jiggins @chrisjiggins.bsky.social · 30/04/2026
No surprise - its Optix and Ivory again - amazing predictability of gene re-use in convergent mimicry phenotypes across amazonian mimicry rings @joanameier.bsky.social @wtf-r-species.bsky.social journals.plos.org/plosbiology/...
journals.plos.org
Genetic parallelism underpins convergent mimicry coloration in Lepidoptera across 120 million years of evolution
The repeated evolution of similar phenotypes, or convergent evolution, is widespread in nature, but there are few studies investigating the genetic mechanisms across wide evolutionary timescales. This...
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Russ Corbett-Detig @russcd.bsky.social · 31/03/2026
Alex Kramer, Alan Zhang and friends posted our preprint today. In it, we introduce Panmap, a tool for phylogenetic placement, assembly, lineage abundance estimation, and eDNA assignment using phylogenetic pangenomes. www.biorxiv.org/content/10.6...
biorxiv.org
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Katharina Hoff @katharinahoff.bsky.social · 11/04/2026
1/ BRAKER4 hatched! The Earth BioGenome Project is on track to sequence ~1.5M eukaryotic species. Every one needs a structural annotation. No Perl monolith was going to survive that. So we rewrote BRAKER from the ground up. github.com/Gaius-August...
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Nichole Broderick, PhD @nabroderick.bsky.social · 30/03/2026
Dear letter writers, study sections, grant panels, etc…..(though expecting little will resonate)….
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Caiti Smukowski Heil @caitismuheil.bsky.social · 26/03/2026
Congrats Maitreya!!!! 🎉🥳 A wonderful scientist, mentor, teacher, and leader @maitreya.bsky.social
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VivienM @vivienm.bsky.social · 19/03/2026
From my pangenomics story in @natmethods.nature.com, It's a colorful pangenome world, which is here www.nature.com/articles/s41... and here: rdcu.be/e8ZYC A comment from @camillemrcht.bsky.social
A comment from the story:It's a colorful pangenome world . From: It’s a colorful pangenome world... When digging into pangenomics methods to avoid reference bias, a hurdle is that “when you represent a lot of variations, it becomes, paradoxically, harder to correctly place the ‘nonaligners,’”
says Camille
Marchet. Aligning sequence
to graphs offers “no trivial
answer.” She and her team use
the De Bruijn graph and her
lab’s latest method is Vizitig.
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Andrea Guarracino @andreaguarracino.bsky.social · 17/03/2026
Level up your #pangenomics game! Workshop, conference & biohackathon in #Memphis, May 11-15, 2026. Join us and get your hands dirty with sequence alignment, explicit and implicit graphs, cutting-edge methods, and AI. Register now! pangenome.github.io/MemPanG26/ #Bioinformatics #MemPanG26
Trippy Memphis bridge https://pangenome.github.io/MemPanG26/
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Toby Baril @tobybarilbio.bsky.social · 05/03/2026
Need to annotate transposons in fungal genomes? 🧬 Good news #MycoMobilome is now live! Check it out here: doi.org/10.1093/narg... Access the sequences through our Zenodo community (you can also contribute seqs with credit), and synchronisation with @dfam.bsky.social! w/ @danielcroll.bsky.social
doi.org
MycoMobilome: a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom
Abstract. Transposable elements (TEs) are found in nearly all eukaryotic genomes. Despite significant advances in the sequencing of genomes, TE resources r
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flyroom.net @flyroom.net · 10/03/2026
We just launched flyRoom — modern web-based stock management for Drosophila labs. No more spreadsheets, no more messy labels, no more lost stocks. Free to start, built by researchers for researchers. www.flyroom.net
flyroom.net
flyRoom - Drosophila Stock Management for Research Labs
Modern stock management for Drosophila research labs. Track stocks, plan crosses, import from FlyBase, print labels, and collaborate across institutions.
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Stephen Turner @stephenturner.us · 09/03/2026
Remembering Phil Bourne. Personal reflections on a legendary scientist, leader, builder, and mentor. blog.stephenturner.us/p/rememberin...
blog.stephenturner.us
Remembering Phil Bourne
Personal reflections on a legendary scientist, leader, builder, and mentor
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Joseph Schacherer @schacherer.bsky.social · 03/03/2026
Thrilled and honored to be part of the 2026 GSA Award recipient! This honor reflects years of teamwork - huge thanks to everyone who has been part of the #haploteam. Proud to share this with you all! @genetics-gsa.bsky.social genestogenomes.org/the-2026-gsa...
genestogenomes.org
The 2026 GSA Awards: The brightest geneticists combine intellect with excellence in education, research, and mentorship
This year’s award recipients bring to the table expertise and leadership that have shaped, and will shape, science for years to come.
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Joseph Schacherer @schacherer.bsky.social · 02/03/2026
Sad to learn that David Botstein has passed away. Few people truly shape how you think and do science, and David was definitely one of them. I had a fun and influential time at Princeton with the Botstein, Kruglyak and co gangs. It shaped the way I do science. www.online-tribute.com/DavidBotstein
online-tribute.com
David Botstein | 1942 - 2026 | Online-Tribute.com
David was a beloved husband, father, brother, scientist, teacher, mentor, musician, friend, who touched the lives of thousands. David’s wide-ranging scientific career spanned decades with a legacy o…
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 28/02/2026
So I pleased to announce the conceptual spawn of FigTree: PearTree (acronym still to be finalised). If you want to dive right in it is hosted as a web app here: artic-network.github.io/peartree (click the “Example...” button for immediate candy and then click every button you can find).
artic-network.github.io
PearTree — Phylogenetic Tree Viewer
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Samuli Reijula @samulireijula.net · 01/03/2026
how LLMs change incentives for research - a great talk by @carlbergstrom.com , had to watch in parts, a lot to digest. #institutional_epistemology at its best! www.youtube.com/watch?v=9Mj3... #philsci
youtube.com
AI and the Nature of Science: Keynote presentation by Carl Bergstrom
YouTube video by MN Center for Philosophy of Science
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Wei Shen 沈 伟 @shenwei356.bsky.social · 27/02/2026
Can't wait to release a 10-year-old birthday version for SeqKit! - 10 years - 2 papers, 3500 citations - 20 contributors - 40 subcommands - 880 commits - 500 issues - 685.5K Bioconda total downloads Thank you all, dear contributors and users! I'll keep maintaining it. github.com/shenwei356/s...
github.com
Release SeqKit v2.13.0 (10-year-old birthday version) · shenwei356/seqkit
Changelog SeqKit is 10 years old! SeqKit v2.13.0 - 2026-02-28 seqkit: add support for reading and writing LZ4 compression format. new command: seqkit sample2: improved seqkit sample by @stahiga....
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Shen Tian 田申 @tianshenbio.bsky.social · 27/02/2026
Amazing peppered moth story from Saccheri lab - same locus, but different structural variants, underly parallel evolution of industrial melanism in the UK and across continental Europe.
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Russ Corbett-Detig @russcd.bsky.social · 24/02/2026
@pratikkatte.bsky.social and I just released Lorax 🌲, a tool for interactive exploration of biobank-scale ancestral recombination graphs (ARGs). If you’ve ever wanted to scroll across the ancestries of thousands of genomes… this is for you.
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Isheng Jason Tsai @ishengtsai.bsky.social · 16/02/2026
With @litinice.bsky.social, we built a haploid resource from 33 wild Taiwanese Saccharomyces cerevisiae strains — including some of the most genetically divergent Asian lineages — to bring natural yeast diversity into a genetically tractable framework. www.biorxiv.org/content/10.6...
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PLOS Biology @plosbiology.org · 19/02/2026
The #fly community aims to achieve a comprehensive genomic study of the Drosophilidae family. @pankajd.bsky.social @bernardkim.bsky.social @petrovadmitri.bsky.social @darrenobbard.bsky.social present a comparative gene annotation for 301 #Drosophilidae species @plosbiology.org 🧪 plos.io/4c3pyrI
Time-calibrated phylogeny of the family Drosophilidae showing major species groups, surrounded by representative adult flies that highlight the remarkable morphological diversity of this model insect group. The composite image was created using Microsoft PowerPoint. Fly photographs were taken by Darren J. Obbard and are published under the Creative Commons Attribution License with permission.
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Max Haase @maxhaase.bsky.social · 18/02/2026
Our paper is now out in Nature: “Ancient co-option of LTR retrotransposons as yeast centromeres” www.nature.com/articles/s41... A short thread on how retrotransposons helped give rise to yeast point centromeres. 1/14
nature.com
Ancient co-option of LTR retrotransposons as yeast centromeres - Nature
Evolutionarily related ‘proto-point’ centromeres providing resolution to the evolutionary origins of point centromeres are identified in yeast, and comparison shows they evolved in an ancestor with re...
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Johann Confais @johannconfais.bsky.social · 16/02/2026
🚨📢📄 Article in press in Genome Biology doi.org/10.1186/s130... We introduce panREPET, a reference-free pipeline to detect shared transposable element (TE) insertions across pangenomes and retrace their evolutionary dynamics #TEsky 🧵👇
doi.org
A reference-free pipeline for detecting shared transposable elements from pan-genomes to retrace their dynamics in a species - Genome Biology
Background The role of transposable elements (TEs) in host adaptation has gained interest in recent years. Individuals of the same species undergo independent TE insertions, providing genetic variabil...
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Arnaud Le Rouzic @arnaudlerouzic.bsky.social · 13/02/2026
We were all very sad to learn the death of Pierre Capy. Pierre was a professor at University Paris Saclay, in the 1990s, he started a group working on the evolutionary genomics of transposable elements; this group is still very active today. He was a great teacher, mentor, and colleague.
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Dominik Handler @86dominik.bsky.social · 13/02/2026
How does the piRNA pathway solve the self vs. non-self problem? 🧬 Since piRNAs come from single-stranded RNA, how does the cell choose the right ones? For years, "piRNA clusters" were seen as THE privileged source. But are they really special and earmarked for biogenesis? (1/19)
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Andrea Guarracino @andreaguarracino.bsky.social · 06/02/2026
Looking for a postdoc to build my new lab at TGen (Phoenix, AZ) focused on pangenome methods for cancer and complex disease. Full stack — from pangenome assembly and compression to association studies and somatic variant discovery. Reach out if interested! guarracinolab.github.io#join
guarracinolab.github.io
Guarracino Lab | Pangenome Research
We develop methods to build and analyze pangenomes, with applications in cancer and complex disease. Translational Genomics Research Institute, Phoenix, AZ.
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Cedric Feschotte @cedricfeschotte.bsky.social · 22/01/2026
Crushed to hear of Mark Batzer’s passing. He was the Boyd Professor at Louisiana State University. His influential research revealed how mobile elements shape the genomes of humans & other mammals. Mark’s personality, generosity & positivity were larger than life. He lifted everyone up. HUGE loss 💔
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Toby Baril @tobybarilbio.bsky.social · 19/01/2026
🍄Transposon traffic in the mycocosmos🍄 Fascinating work reveals extensive horizontal TE transfer across fungi (@jromeijn.bsky.social, Iñigo Bañales & @mfseidl.bsky.social; doi.org/10.1016/j.cu...). I wrote a Dispatch to prime non-specialists,check it out here: doi.org/10.1016/j.cu.... #TEworldwide
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Nathaniel Comfort @nccomfort.bsky.social · 17/01/2026
Hey, good folks of #TEsky— Looking for good recent review, suitable for undergrads, of the fnxns of transposable elements in the genome, for class session on the nonlinear, highly regulated, 4D nucleome. Suggestions welcome! (I'm the author of the "other book" on Barbara McClintock) TIA!
amazon.com
The Tangled Field: Barbara McClintock's Search for the Patterns of Genetic Control
Buy The Tangled Field: Barbara McClintock's Search for the Patterns of Genetic Control on Amazon.com ✓ FREE SHIPPING on qualified orders
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Steven Salzberg @stevensalzberg.bsky.social · 16/01/2026
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
embl.org
In remembrance of Peer Bork  | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
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EEID 2026 at Virginia Tech @eeid2026.bsky.social · 15/12/2025
We are excited to invite abstract submissions for talks and posters for the 2026 Ecology and Evolution of Infectious Diseases meeting at Virginia Tech (June 2-4). Abstract submissions should be made by February 3, 2026 for consideration, using the google form here: cpe.vt.edu/eeid2026/abs...
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Casey Bergman @caseybergman.bsky.social · 05/01/2026
Hivemind: has anyone had a response from #NCBI about submissions started prior to the government shutdown?
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Casey Bergman @caseybergman.bsky.social · 05/01/2026
Hivemind: has anyone had a response from #NCBI about submissions started prior to the government shutdown?
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Takumi Kamiyama @tkmkmym.bsky.social · 14/02/2025
I have created a bot account. This bot will receive information about newly uploaded #Drosophila papers from pubmed and will automatically post every hour. If you find any bugs, please let me know! @fly-broadcast.bsky.social
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Genetics Society UK @gensocuk.bsky.social · 14/11/2025
Congratulations to Richard Durbin on being awarded our Genetics Society Medal!
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