Casey Bergman
@caseybergman.bsky.social
Dad, bioinformatician, ex-expat. Currently working on transposon bioinformatics & infectious disease genomics.
Reposted by Casey Bergman
💡 Novel work supported by HPRC members highlights Locityper, a tool bringing accurate genotyping to some of the most challenging regions of the human genome.
Fast and precise, it outperforms current pipelines and scales to biobank-sized cohorts.
More at:
www.nature.com/articles/s41...
Fast and precise, it outperforms current pipelines and scales to biobank-sized cohorts.
More at:
www.nature.com/articles/s41...
Locityper enables targeted genotyping of complex polymorphic genes - Nature Genetics
Locityper is a general-purpose genotyper that can efficiently genotype and analyze a diverse set of genes, such as hyperpolymorphic HLA genes, using both short-read and long-read whole-genome sequenci...
www.nature.com
November 19, 2025 at 9:36 PM
💡 Novel work supported by HPRC members highlights Locityper, a tool bringing accurate genotyping to some of the most challenging regions of the human genome.
Fast and precise, it outperforms current pipelines and scales to biobank-sized cohorts.
More at:
www.nature.com/articles/s41...
Fast and precise, it outperforms current pipelines and scales to biobank-sized cohorts.
More at:
www.nature.com/articles/s41...
Reposted by Casey Bergman
Thrilled to share our latest review! T2T assemblies are reshaping how we study genomic diversity. Pangenomes unlock structural variants, gene presence-absence, and genotype-phenotype relationship, across humans, plants, animals, and fungi.
www.cell.com/cell-genomic...
www.cell.com/cell-genomic...
Dynamics of genome evolution in the era of pangenome analysis
Long-read sequencing and telomere-to-telomere (T2T) assemblies have enabled the generation
of pangenomes that capture genetic diversity beyond single reference genomes. This
review highlights how T2T ...
www.cell.com
November 19, 2025 at 4:49 AM
Thrilled to share our latest review! T2T assemblies are reshaping how we study genomic diversity. Pangenomes unlock structural variants, gene presence-absence, and genotype-phenotype relationship, across humans, plants, animals, and fungi.
www.cell.com/cell-genomic...
www.cell.com/cell-genomic...
Reposted by Casey Bergman
#Wolbachia has puzzled scientists with its power to rewire insect reproduction. What if I tell you that we found one of the keys Wolbachia use to rewire its host AND a small molecule inhibitor uses this key to mimic what this microbe has mastered for millions of years.
www.cell.com/cell-reports...
www.cell.com/cell-reports...
Beyond Wolbachia—Can a small molecule control insect reproduction?
Kaur et al. demonstrate reduced histone acetylation as a key mechanism underpinning
Wolbachia’s paternal-effect embryonic lethality trait in Drosophila melanogaster.
Recapitulation of this trait by in...
www.cell.com
October 3, 2025 at 12:58 PM
#Wolbachia has puzzled scientists with its power to rewire insect reproduction. What if I tell you that we found one of the keys Wolbachia use to rewire its host AND a small molecule inhibitor uses this key to mimic what this microbe has mastered for millions of years.
www.cell.com/cell-reports...
www.cell.com/cell-reports...
Reposted by Casey Bergman
If you're interested in using pangenome graphs for comparative genomics, check out my webinar, part of EMBL-EBI's "Concepts, methods, and resources in pangenomics" series, available on-demand: www.ebi.ac.uk/training/eve...
Pangenome graphs as a new paradigm in comparative genomics -
Pangenome graphs as a new paradigm in comparative genomics -
www.ebi.ac.uk
November 6, 2025 at 11:40 AM
If you're interested in using pangenome graphs for comparative genomics, check out my webinar, part of EMBL-EBI's "Concepts, methods, and resources in pangenomics" series, available on-demand: www.ebi.ac.uk/training/eve...
Reposted by Casey Bergman
Reposted by Casey Bergman
Yesterday, Nina Marthe, our wonderful PhD student with Matthias Zytnicky, resubmit our tool GrAnnoT, for pangenome variation graph annotation!
@ird-fr.bsky.social @inrae-france.bsky.social @peercommunityin.bsky.social #pangenomics 💻
www.biorxiv.org/content/10.1...
@ird-fr.bsky.social @inrae-france.bsky.social @peercommunityin.bsky.social #pangenomics 💻
www.biorxiv.org/content/10.1...
GrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph
The increasing availability of genome sequences has highlighted the limitations of using a single reference genome to represent the diversity within a species. Pangenomes, encompassing the genomic inf...
www.biorxiv.org
October 30, 2025 at 3:46 PM
Yesterday, Nina Marthe, our wonderful PhD student with Matthias Zytnicky, resubmit our tool GrAnnoT, for pangenome variation graph annotation!
@ird-fr.bsky.social @inrae-france.bsky.social @peercommunityin.bsky.social #pangenomics 💻
www.biorxiv.org/content/10.1...
@ird-fr.bsky.social @inrae-france.bsky.social @peercommunityin.bsky.social #pangenomics 💻
www.biorxiv.org/content/10.1...
Reposted by Casey Bergman
My former mentor, colleague, and friend Hamilton Smith passed away this week. He was a giant in science, a Nobel Laureate, but also one of the nicest people you could ever meet. He will be missed by many. www.jcvi.org/media-center...
Remembering Hamilton O. Smith
Hamilton O. Smith
August 31, 1931 – October 25, 2025
It is with profound sorrow that we announce the loss of Hamilton O. Smith, M.D., a...
www.jcvi.org
October 29, 2025 at 11:26 PM
My former mentor, colleague, and friend Hamilton Smith passed away this week. He was a giant in science, a Nobel Laureate, but also one of the nicest people you could ever meet. He will be missed by many. www.jcvi.org/media-center...
Reposted by Casey Bergman
We @uga_genetics are hiring a TT assistant professor in Human Genetics to investigate how genetic makeup influences an individual’s risks for diseases or responses to drugs and therapies. All research
approaches will be considered. Please RT. ugajobsearch.com/postings/456597
approaches will be considered. Please RT. ugajobsearch.com/postings/456597
October 21, 2025 at 8:19 PM
We @uga_genetics are hiring a TT assistant professor in Human Genetics to investigate how genetic makeup influences an individual’s risks for diseases or responses to drugs and therapies. All research
approaches will be considered. Please RT. ugajobsearch.com/postings/456597
approaches will be considered. Please RT. ugajobsearch.com/postings/456597
Reposted by Casey Bergman
When transposons jump, genomes diverge - even in cultured cells.
I am happy to share our new preprint: a chromosome-scale genome assembly for Drosophila OSC cells, one of the key model systems in the piRNA field, especially for nuclear piRNA biology. 🧬🧵 (1/12)
I am happy to share our new preprint: a chromosome-scale genome assembly for Drosophila OSC cells, one of the key model systems in the piRNA field, especially for nuclear piRNA biology. 🧬🧵 (1/12)
October 14, 2025 at 8:34 PM
When transposons jump, genomes diverge - even in cultured cells.
I am happy to share our new preprint: a chromosome-scale genome assembly for Drosophila OSC cells, one of the key model systems in the piRNA field, especially for nuclear piRNA biology. 🧬🧵 (1/12)
I am happy to share our new preprint: a chromosome-scale genome assembly for Drosophila OSC cells, one of the key model systems in the piRNA field, especially for nuclear piRNA biology. 🧬🧵 (1/12)
Reposted by Casey Bergman
C. elegans is a real animal and we set out to understand how it comes to have its distinctive biogeography. Its ancestral center of diversity is in the higher elevation forests of Hawaii. Its closest relatives are spread across east Asia. Did they travel from Asia? [Preprint 🧵]
September 24, 2025 at 8:33 PM
C. elegans is a real animal and we set out to understand how it comes to have its distinctive biogeography. Its ancestral center of diversity is in the higher elevation forests of Hawaii. Its closest relatives are spread across east Asia. Did they travel from Asia? [Preprint 🧵]
Reposted by Casey Bergman
Come be our head of bioinformatics at @mrc-lms.bsky.social !
Our bioinformatics team are closely involved with lots of interesting science and we love working with them. Topics inc. development, cancer, metabolism, aging, TEs (my favourite of course 😜) #TEsky lms.mrc.ac.uk/work/vacanci...
Our bioinformatics team are closely involved with lots of interesting science and we love working with them. Topics inc. development, cancer, metabolism, aging, TEs (my favourite of course 😜) #TEsky lms.mrc.ac.uk/work/vacanci...
Head of Bioinformatics - MRC Laboratory of Medical Sciences
We are recruiting for a Head of Bioinformatics to lead our Bioinformatics facility
lms.mrc.ac.uk
September 19, 2025 at 8:25 AM
Come be our head of bioinformatics at @mrc-lms.bsky.social !
Our bioinformatics team are closely involved with lots of interesting science and we love working with them. Topics inc. development, cancer, metabolism, aging, TEs (my favourite of course 😜) #TEsky lms.mrc.ac.uk/work/vacanci...
Our bioinformatics team are closely involved with lots of interesting science and we love working with them. Topics inc. development, cancer, metabolism, aging, TEs (my favourite of course 😜) #TEsky lms.mrc.ac.uk/work/vacanci...
Reposted by Casey Bergman
Kicked off a series on #Drosophila TE discovery and naming. The first post covers elements that predate the term "mobile element", and more. artemilin.dev/posts/te_nam...
Drosophila TE name origins, Part 1 – Postdoc Postpunk
artemilin.dev
September 21, 2025 at 7:49 PM
Kicked off a series on #Drosophila TE discovery and naming. The first post covers elements that predate the term "mobile element", and more. artemilin.dev/posts/te_nam...
Reposted by Casey Bergman
I share this picture of a printed out genome every once in while.
It just occurred to me: it's got to be cheaper to acquire a finished copy of your genome (high accuracy, phased, SV-resolved) than to print it as a collection of bound books.
(back-of-envelope checks out - anyone done the math?)
It just occurred to me: it's got to be cheaper to acquire a finished copy of your genome (high accuracy, phased, SV-resolved) than to print it as a collection of bound books.
(back-of-envelope checks out - anyone done the math?)
September 12, 2025 at 8:36 PM
I share this picture of a printed out genome every once in while.
It just occurred to me: it's got to be cheaper to acquire a finished copy of your genome (high accuracy, phased, SV-resolved) than to print it as a collection of bound books.
(back-of-envelope checks out - anyone done the math?)
It just occurred to me: it's got to be cheaper to acquire a finished copy of your genome (high accuracy, phased, SV-resolved) than to print it as a collection of bound books.
(back-of-envelope checks out - anyone done the math?)
Reposted by Casey Bergman
We are all super happy and proud to see our work on the function and evolution of the #cephalic #furrow published in @nature.com. Let me say a few things about the background and history of this work on the #Evolution_of_Morphogenesis (1/12)
September 4, 2025 at 8:22 AM
We are all super happy and proud to see our work on the function and evolution of the #cephalic #furrow published in @nature.com. Let me say a few things about the background and history of this work on the #Evolution_of_Morphogenesis (1/12)
Reposted by Casey Bergman
Pangene, an innovative computational tool, maps gene orientation, order & copy-number changes across genomes. Applied to the human pangenome, it reveals both known variation & complex haplotypes.
Read more:
academic.oup.com/bioinformati...
Read more:
academic.oup.com/bioinformati...
Exploring gene content with pangene graphs
AbstractMotivation. The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although
academic.oup.com
August 29, 2025 at 4:48 PM
Pangene, an innovative computational tool, maps gene orientation, order & copy-number changes across genomes. Applied to the human pangenome, it reveals both known variation & complex haplotypes.
Read more:
academic.oup.com/bioinformati...
Read more:
academic.oup.com/bioinformati...
Reposted by Casey Bergman
An interesting editorial by @judithmank.bsky.social, with thoughts on the use and misuse of AI in academic publishing at @evolletters.bsky.social (and elsewhere).
Many of us are using LLMs in coding and scientific writing. They are very helpful tools, but we need to be thoughtful as we integrate them into our work flows to preserve accountability, voice and trust. academic.oup.com/evlett/advan.... An editorial at @evolletters.bsky.social for discussion:
Editorial: Accountability, voice, and trust - responsible use of GenAI in scientific publishing
Over the last few years, the development and rapid advancement of Generative Artificial Intelligence (GenAI) and Large Language Models (LLMs) such as ChatG
academic.oup.com
August 22, 2025 at 3:11 PM
An interesting editorial by @judithmank.bsky.social, with thoughts on the use and misuse of AI in academic publishing at @evolletters.bsky.social (and elsewhere).
Reposted by Casey Bergman
~ 5 and 1/2 years ago, my then postdoc advisor @plantevolution.bsky.social gave me complete freedom to assemble a team and interrogate NLR diversity in pangenomic context. We used @pacbio.bsky.social CCS and Iso-Seq, to annotate genomes with pathogen-challenged transcriptome. We then manually.....
August 14, 2025 at 9:13 PM
~ 5 and 1/2 years ago, my then postdoc advisor @plantevolution.bsky.social gave me complete freedom to assemble a team and interrogate NLR diversity in pangenomic context. We used @pacbio.bsky.social CCS and Iso-Seq, to annotate genomes with pathogen-challenged transcriptome. We then manually.....
Reposted by Casey Bergman
Very impressive demonstration of the rise of China as a scientific superpower in crop research!
All papers on #crop genetics and genomics in the latest issue of Nature Genetics were produced by scientists working at Chinese research institutes.
TOC: www.nature.com/ng/volumes/5...
All papers on #crop genetics and genomics in the latest issue of Nature Genetics were produced by scientists working at Chinese research institutes.
TOC: www.nature.com/ng/volumes/5...
August 12, 2025 at 7:50 AM
Very impressive demonstration of the rise of China as a scientific superpower in crop research!
All papers on #crop genetics and genomics in the latest issue of Nature Genetics were produced by scientists working at Chinese research institutes.
TOC: www.nature.com/ng/volumes/5...
All papers on #crop genetics and genomics in the latest issue of Nature Genetics were produced by scientists working at Chinese research institutes.
TOC: www.nature.com/ng/volumes/5...
Reposted by Casey Bergman
New Paper! In 2019, my first dissertation chapter revealed complicated polyploidies in the cotton family (Malvaceae) but we lacked the tools and genomes to truly understand it. Now with better genomes and improved methods, it's much more complicated than we thought. www.nature.com/articles/s41...
August 13, 2025 at 8:31 PM
New Paper! In 2019, my first dissertation chapter revealed complicated polyploidies in the cotton family (Malvaceae) but we lacked the tools and genomes to truly understand it. Now with better genomes and improved methods, it's much more complicated than we thought. www.nature.com/articles/s41...
Reposted by Casey Bergman
“In the heart of Illinois, while researching wildlife disease, I made a discovery that stunned me: More than half of the raccoons I sampled were infected with Trypanosoma cruzi, the parasite that causes Chagas’ disease… It’s here, in the United States, spreading silently in wildlife.”
A ‘tropical’ disease is spreading in American wildlife
This neglected tropical disease is no longer confined to the tropics. It’s here, in the United States, spreading silently in wildlife.
www.statnews.com
August 8, 2025 at 11:44 AM
“In the heart of Illinois, while researching wildlife disease, I made a discovery that stunned me: More than half of the raccoons I sampled were infected with Trypanosoma cruzi, the parasite that causes Chagas’ disease… It’s here, in the United States, spreading silently in wildlife.”
Reposted by Casey Bergman
Looking forward to this new installment of the Woods Hole Mobile DNA Meeting! Fantastic program, laid-back atmosphere, and gorgeous setting at the Marine Biological Laboratory ⛵️🪼🐋
Abstract submission closes Aug 7 but registration after that date is possible. www.eventsquid.com/event.cfm?ev...
Abstract submission closes Aug 7 but registration after that date is possible. www.eventsquid.com/event.cfm?ev...
August 5, 2025 at 8:47 PM
Looking forward to this new installment of the Woods Hole Mobile DNA Meeting! Fantastic program, laid-back atmosphere, and gorgeous setting at the Marine Biological Laboratory ⛵️🪼🐋
Abstract submission closes Aug 7 but registration after that date is possible. www.eventsquid.com/event.cfm?ev...
Abstract submission closes Aug 7 but registration after that date is possible. www.eventsquid.com/event.cfm?ev...
Reposted by Casey Bergman
Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!
July 17, 2025 at 7:53 AM
Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!
Reposted by Casey Bergman
My colleague David Garfinkel is looking for a postdoc to join our NIH-funded project on the “Evolution of Retrotransposon Control Mechanisms”
More info here: reporter.nih.gov/search/u7dKr....
The official job listing can be found here: www.ugajobsearch.com/postings/437...
Please repost! #TEsky
More info here: reporter.nih.gov/search/u7dKr....
The official job listing can be found here: www.ugajobsearch.com/postings/437...
Please repost! #TEsky
RePORT ⟩ RePORTER
reporter.nih.gov
July 16, 2025 at 6:25 PM
My colleague David Garfinkel is looking for a postdoc to join our NIH-funded project on the “Evolution of Retrotransposon Control Mechanisms”
More info here: reporter.nih.gov/search/u7dKr....
The official job listing can be found here: www.ugajobsearch.com/postings/437...
Please repost! #TEsky
More info here: reporter.nih.gov/search/u7dKr....
The official job listing can be found here: www.ugajobsearch.com/postings/437...
Please repost! #TEsky