Adam Phillippy
@aphillippy.bsky.social
Finished a human genome, working on a few more 👨💻
Lab: https://genomeinformatics.github.io
Posts are my own
Lab: https://genomeinformatics.github.io
Posts are my own
‼️ There are an unprecedented number of Institute Director vacancies at the NIH and many of the application windows close this week or next, including ones that are essential to genomics research in the US including NHGRI, NLM/NCBI, and NIGMS. Please spread the word: hr.nih.gov/careers/open...
hr.nih.gov
November 10, 2025 at 4:08 PM
‼️ There are an unprecedented number of Institute Director vacancies at the NIH and many of the application windows close this week or next, including ones that are essential to genomics research in the US including NHGRI, NLM/NCBI, and NIGMS. Please spread the word: hr.nih.gov/careers/open...
Reposted by Adam Phillippy
I was one of the Editorial Board Members at @gigascience.bsky.social who resigned from the Editorial Board.
🧪 🔓
⬇️
retractionwatch.com/2025/11/03/d...
🧪 🔓
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retractionwatch.com/2025/11/03/d...
Dozens of board members resign from big-data journal after mass staff firings
More than three-fifths of the editorial board of a biomedical sciences journal resigned after the publication’s operations moved from Hong Kong to Shenzhen, China, and the editors and software team…
retractionwatch.com
November 4, 2025 at 3:46 PM
I was one of the Editorial Board Members at @gigascience.bsky.social who resigned from the Editorial Board.
🧪 🔓
⬇️
retractionwatch.com/2025/11/03/d...
🧪 🔓
⬇️
retractionwatch.com/2025/11/03/d...
Reposted by Adam Phillippy
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 Adam Phillippy
About half the GigaScience editorial board (incl me) just resigned (academic.oup.com/gigascience/... is not yet updated). I resigned because it is very unclear what is happening and why - see @scedmunds.bsky.social blog post gigasciencejournal.com/blog/and-its..., for eg
Editorial_Board
Editorial Team
Editor-in-Chief
Xun Xu, PhD; BGI Research, Shenzhen, China
Executive Editor
Hongling Zhou; GigaScience Press, BGI Shenzhen, China
Edito
academic.oup.com
October 29, 2025 at 4:03 PM
About half the GigaScience editorial board (incl me) just resigned (academic.oup.com/gigascience/... is not yet updated). I resigned because it is very unclear what is happening and why - see @scedmunds.bsky.social blog post gigasciencejournal.com/blog/and-its..., for eg
Reposted by Adam Phillippy
1/
WashU research news; excited to share our new paper on Chromosome 9p Syndromes 🧬 Hope you take the time to read it. Here is the link:
link.springer.com/article/10.1...
@washugenetics.bsky.social
WashU research news; excited to share our new paper on Chromosome 9p Syndromes 🧬 Hope you take the time to read it. Here is the link:
link.springer.com/article/10.1...
@washugenetics.bsky.social
Whole-genome sequencing reveals individual and cohort level insights into chromosome 9p syndromes - Genome Medicine
Background Previous genomic efforts on chromosome 9p deletion and duplication syndromes have utilized low-resolution strategies (i.e., karyotypes, chromosome microarrays). These studies have provided ...
link.springer.com
October 28, 2025 at 11:27 PM
1/
WashU research news; excited to share our new paper on Chromosome 9p Syndromes 🧬 Hope you take the time to read it. Here is the link:
link.springer.com/article/10.1...
@washugenetics.bsky.social
WashU research news; excited to share our new paper on Chromosome 9p Syndromes 🧬 Hope you take the time to read it. Here is the link:
link.springer.com/article/10.1...
@washugenetics.bsky.social
Reposted by Adam Phillippy
I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Staff Scientist
About EMBL-EBI EMBL’s European Bioinformatics Institute is a data powerhouse, utilised on a global scale to advance scientific discovery through bioinformatics and solutions to some of the world’s mos...
embl.wd103.myworkdayjobs.com
October 10, 2025 at 7:30 AM
I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Reposted by Adam Phillippy
We investigated Constellation from Illumina @bcmhgsc.bsky.social for rare disease cases @gregor-research.bsky.social from @bcmhouston.bsky.social.
We tested HG002-4 & sequenced 21 families. We could detangle complex SV & other interesting findings described here: www.medrxiv.org/content/10.1...
We tested HG002-4 & sequenced 21 families. We could detangle complex SV & other interesting findings described here: www.medrxiv.org/content/10.1...
Constellation illuminates rare disease genetics
Despite significant advances in genomic sequencing, the resolution of many rare disease cases is still hindered by variant detection limitations. Short reads struggle in homologous regions, and long r...
www.medrxiv.org
October 20, 2025 at 1:40 PM
We investigated Constellation from Illumina @bcmhgsc.bsky.social for rare disease cases @gregor-research.bsky.social from @bcmhouston.bsky.social.
We tested HG002-4 & sequenced 21 families. We could detangle complex SV & other interesting findings described here: www.medrxiv.org/content/10.1...
We tested HG002-4 & sequenced 21 families. We could detangle complex SV & other interesting findings described here: www.medrxiv.org/content/10.1...
Reposted by Adam Phillippy
Read the preprint here with all the details, plus lots of other long-read powered analysis! www.medrxiv.org/content/10.1...
Population-scale Long-read Sequencing in the All of Us Research Program
The All of Us Research Program (AoU) is a national biobank seeking to enroll one million individuals in the United States to link genomic and biomedical data, including short- and long-read whole-geno...
www.medrxiv.org
October 14, 2025 at 5:40 PM
Read the preprint here with all the details, plus lots of other long-read powered analysis! www.medrxiv.org/content/10.1...
The T2T zebra finch genome has hatched! 🐣 🧬 @vertebrategenomes.bsky.social
The complete genome of a songbird https://www.biorxiv.org/content/10.1101/2025.10.14.682431v1
October 15, 2025 at 1:08 PM
The T2T zebra finch genome has hatched! 🐣 🧬 @vertebrategenomes.bsky.social
Reposted by Adam Phillippy
For those interested in #Indigenous #Genomics and #ASHG25 in Boston, here are some interested posters/talks/events coming out of the Tsosie Lab, @nativebio.bsky.social, and @d4itdr.bsky.social. For those looking for Friday plans, attend our Ancillary Event, debuting a #Tribal #data repository!
October 14, 2025 at 2:29 PM
For those interested in #Indigenous #Genomics and #ASHG25 in Boston, here are some interested posters/talks/events coming out of the Tsosie Lab, @nativebio.bsky.social, and @d4itdr.bsky.social. For those looking for Friday plans, attend our Ancillary Event, debuting a #Tribal #data repository!
Reposted by Adam Phillippy
Out today via @natgenet.nature.com, the first federally funded #Tribal #data repository, a revolutionary approach to data management and applied/operationalization of IDSov @d4itdr.bsky.social. Also, if you are at #ASHG25, come see us this morning in 205ABC
www.nature.com/articles/s41...
www.nature.com/articles/s41...
October 15, 2025 at 12:43 PM
Out today via @natgenet.nature.com, the first federally funded #Tribal #data repository, a revolutionary approach to data management and applied/operationalization of IDSov @d4itdr.bsky.social. Also, if you are at #ASHG25, come see us this morning in 205ABC
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Adam Phillippy
actually it reminds me more of finding 1000s of human contaminants annotated as proteins within draft bacterial genomes in GenBank, which we published in 2018 (and @aphillippy.bsky.social knows this work): pubmed.ncbi.nlm.nih.gov/31064768/
Human contamination in bacterial genomes has created thousands of spurious proteins - PubMed
Contaminant sequences that appear in published genomes can cause numerous problems for downstream analyses, particularly for evolutionary studies and metagenomics projects. Our large-scale scan of com...
pubmed.ncbi.nlm.nih.gov
October 14, 2025 at 3:05 PM
actually it reminds me more of finding 1000s of human contaminants annotated as proteins within draft bacterial genomes in GenBank, which we published in 2018 (and @aphillippy.bsky.social knows this work): pubmed.ncbi.nlm.nih.gov/31064768/
Reposted by Adam Phillippy
A telomere-to-telomere map of somatic mutation burden and functional impact in cancer https://www.biorxiv.org/content/10.1101/2025.10.10.681725v1
October 13, 2025 at 11:33 PM
A telomere-to-telomere map of somatic mutation burden and functional impact in cancer https://www.biorxiv.org/content/10.1101/2025.10.10.681725v1
Reposted by Adam Phillippy
Excited to share our new paper on predicting gene expression in yeast! We introduce "Shorkie," a supervised ML model that builds off a self-supervised foundation to interpret regulatory DNA.
Preprint: www.biorxiv.org/content/10.1...
Preprint: www.biorxiv.org/content/10.1...
Predicting dynamic expression patterns in budding yeast with a fungal DNA language model
Predicting gene expression from DNA sequence remains challenging due to complex regulatory codes. We introduce a masked DNA language model pretrained on 165 fungal genomes closely related to budding y...
www.biorxiv.org
October 13, 2025 at 11:06 PM
Excited to share our new paper on predicting gene expression in yeast! We introduce "Shorkie," a supervised ML model that builds off a self-supervised foundation to interpret regulatory DNA.
Preprint: www.biorxiv.org/content/10.1...
Preprint: www.biorxiv.org/content/10.1...
In honor of ASHG week (since I won’t be there), see "Choose your human genome reference wisely", in which Vivien Marx interviewed me @fergalmartin.bsky.social @lh3lh3.bsky.social @danrdanny.bsky.social @heidirehm.bsky.social and others on the state of the human reference rdcu.be/eJejg 🧵[1/10]
October 13, 2025 at 8:14 PM
In honor of ASHG week (since I won’t be there), see "Choose your human genome reference wisely", in which Vivien Marx interviewed me @fergalmartin.bsky.social @lh3lh3.bsky.social @danrdanny.bsky.social @heidirehm.bsky.social and others on the state of the human reference rdcu.be/eJejg 🧵[1/10]
Reposted by Adam Phillippy
Now Hiring! Whitney Laboratory Assistant/Associate Professor in Marine Bioscience
Apply & More Info - explore.jobs.ufl.edu/en-us/job/53...
We seek a creative, collaborative scientist whose research harnesses or advances cutting-edge tools. Please help spread the word & reach out with any questions!
Apply & More Info - explore.jobs.ufl.edu/en-us/job/53...
We seek a creative, collaborative scientist whose research harnesses or advances cutting-edge tools. Please help spread the word & reach out with any questions!
September 29, 2025 at 3:53 PM
Now Hiring! Whitney Laboratory Assistant/Associate Professor in Marine Bioscience
Apply & More Info - explore.jobs.ufl.edu/en-us/job/53...
We seek a creative, collaborative scientist whose research harnesses or advances cutting-edge tools. Please help spread the word & reach out with any questions!
Apply & More Info - explore.jobs.ufl.edu/en-us/job/53...
We seek a creative, collaborative scientist whose research harnesses or advances cutting-edge tools. Please help spread the word & reach out with any questions!
Reposted by Adam Phillippy
Big news! We're hiring lots of new faculty here at the University of Virginia School of Data Science @uvadatascience.bsky.social! You can find all our postings here: datascience.virginia.edu/faculty-jobs
October 13, 2025 at 3:28 PM
Big news! We're hiring lots of new faculty here at the University of Virginia School of Data Science @uvadatascience.bsky.social! You can find all our postings here: datascience.virginia.edu/faculty-jobs
Reposted by Adam Phillippy
🚨 New paper alert on telomeres! 🚨
Something different from the group! Thanks to Yuxin, a talented student in the lab, we used long-reads in 75 human trios to study telomeres and their inheritance.
Something different from the group! Thanks to Yuxin, a talented student in the lab, we used long-reads in 75 human trios to study telomeres and their inheritance.
October 9, 2025 at 5:33 AM
🚨 New paper alert on telomeres! 🚨
Something different from the group! Thanks to Yuxin, a talented student in the lab, we used long-reads in 75 human trios to study telomeres and their inheritance.
Something different from the group! Thanks to Yuxin, a talented student in the lab, we used long-reads in 75 human trios to study telomeres and their inheritance.
Last week we were in the Washington Post for our characterization of Robertsonian chromosomes. This week we are entering our 10th day of being shut down and all of our research is on hold. To help me feel not-so-bad, here is a thread of some studies we released right before the shutdown 🧵 [1/n]...
October 10, 2025 at 3:24 PM
Last week we were in the Washington Post for our characterization of Robertsonian chromosomes. This week we are entering our 10th day of being shut down and all of our research is on hold. To help me feel not-so-bad, here is a thread of some studies we released right before the shutdown 🧵 [1/n]...
Reposted by Adam Phillippy
Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians!
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
October 7, 2025 at 3:24 PM
Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians!
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
Reposted by Adam Phillippy
And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
October 8, 2025 at 4:53 PM
And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
Reposted by Adam Phillippy
Read ‘Sperm sequencing reveals extensive positive selection in the male germline’ from @sangerinstitute.bsky.social and collaborators in @nature.com below:
nature.com/articles/s41...
nature.com/articles/s41...
Sperm sequencing reveals extensive positive selection in the male germline - Nature
A combination of whole-genome NanoSeq with deep whole-exome and targeted NanoSeq is used to accurately characterize mutation rates and genes under positive selection in sperm cells.
nature.com
October 8, 2025 at 3:36 PM
Read ‘Sperm sequencing reveals extensive positive selection in the male germline’ from @sangerinstitute.bsky.social and collaborators in @nature.com below:
nature.com/articles/s41...
nature.com/articles/s41...
Reposted by Adam Phillippy
I’m pleased as punch to share our hot off the presses article in @ajhgnews.bsky.social : A scalable approach for genomic-first rare disorder detection in a healthcare-based population
Also presenting next week at #ashg25 #ashg2025
www.cell.com/ajhg/abstrac...
Also presenting next week at #ashg25 #ashg2025
www.cell.com/ajhg/abstrac...
A scalable approach for genomic-first rare disorder detection in a healthcare-based population
Beyond commonly screened disorders, genomic-first ascertainment of genetic disorders
remains underexplored. We developed a scalable framework for 2,701 additional rare
genetic disorders, identifying p...
www.cell.com
October 6, 2025 at 2:47 PM
I’m pleased as punch to share our hot off the presses article in @ajhgnews.bsky.social : A scalable approach for genomic-first rare disorder detection in a healthcare-based population
Also presenting next week at #ashg25 #ashg2025
www.cell.com/ajhg/abstrac...
Also presenting next week at #ashg25 #ashg2025
www.cell.com/ajhg/abstrac...
How Robertsonian chromosomes can lead to miscarriage or trisomy explained in one great figure from Human Molecular Genetics (Strachan and Read) that I have referred to many times
September 24, 2025 at 8:27 PM
How Robertsonian chromosomes can lead to miscarriage or trisomy explained in one great figure from Human Molecular Genetics (Strachan and Read) that I have referred to many times
🚂 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/JmlY5omxQVc
📄 www.nature.com/articles/s41...
How Stowers Scientists Found the DNA Site Where Robertsonian Chromosomes Fuse
YouTube video by Stowers Institute for Medical Research
youtu.be
September 24, 2025 at 6:48 PM
🚂 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/JmlY5omxQVc
📄 www.nature.com/articles/s41...