Adam M Novak
@adamnovak.graphs.vg
Bioinformatics Programmer at @ucscgenomics.bsky.social working on #pangenomics.
http://orcid.org/0000-0001-5828-047X
http://orcid.org/0000-0001-5828-047X
Reposted by Adam M Novak
Julie Ahringer from @gurdoninstitute.bsky.social @geneticscam.bsky.social @cam.ac.uk gives talk on decoding genome regulation during development. Exploring how chromatin accessibility changes throughout development enable single cells to become multicellular organisms.
November 7, 2025 at 1:48 PM
Julie Ahringer from @gurdoninstitute.bsky.social @geneticscam.bsky.social @cam.ac.uk gives talk on decoding genome regulation during development. Exploring how chromatin accessibility changes throughout development enable single cells to become multicellular organisms.
@thinks.lol @khmiga.bsky.social Look you're famous
Arglebargle did no one think to invite Erik Garrison? They’re both awesome fwiw. As is Karen Miga
November 7, 2025 at 4:00 PM
@thinks.lol @khmiga.bsky.social Look you're famous
Reposted by Adam M Novak
I think about this post every day 🧪
November 7, 2025 at 12:15 PM
I think about this post every day 🧪
Reposted by Adam M Novak
Haonan Wu gives a talk on "A k-mer-based estimator of the substitution rate between repetitive sequences"
www.biorxiv.org/content/10.1...
This work tackles the issue of Mash which ignores repeats in the genome, providing better distance estimation #GI2025
www.biorxiv.org/content/10.1...
This work tackles the issue of Mash which ignores repeats in the genome, providing better distance estimation #GI2025
November 6, 2025 at 4:38 PM
Haonan Wu gives a talk on "A k-mer-based estimator of the substitution rate between repetitive sequences"
www.biorxiv.org/content/10.1...
This work tackles the issue of Mash which ignores repeats in the genome, providing better distance estimation #GI2025
www.biorxiv.org/content/10.1...
This work tackles the issue of Mash which ignores repeats in the genome, providing better distance estimation #GI2025
Reposted by Adam M Novak
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 Adam M Novak
If you're looking for a faculty position at the intersection of ecology and computing (both broadly defined), please apply to this joint search between the CEE Department and the College of Computing at MIT: cee.mit.edu/people/share...
Faculty Position in the Department of Civil and Environmental Engineering and the Schwarzman College of Computing - cee.mit.edu
The Department of Civil and Environmental Engineering (CEE), together with the Schwarzman College of Computing (SCC) at the Massachusetts Institute of Technology (MIT) in Cambridge MA, seeks candidate...
cee.mit.edu
November 5, 2025 at 7:27 PM
If you're looking for a faculty position at the intersection of ecology and computing (both broadly defined), please apply to this joint search between the CEE Department and the College of Computing at MIT: cee.mit.edu/people/share...
Reposted by Adam M Novak
Support diversity and excellence in STEM by giving to our Research Mentoring Internship (RMI) this Giving Day 🎁 Federal cuts to DEI grants have made your gifts VITAL to keeping this program alive. Please support student mentorship today: www.givecampus.com/schools/Univ...
November 5, 2025 at 12:30 PM
Support diversity and excellence in STEM by giving to our Research Mentoring Internship (RMI) this Giving Day 🎁 Federal cuts to DEI grants have made your gifts VITAL to keeping this program alive. Please support student mentorship today: www.givecampus.com/schools/Univ...
Reposted by Adam M Novak
It's Giving Day!!! You can help support 🎗pediatric cancer research AND a "degree-defining experience" for undergraduates by:
💸 Donating to Treehouse Childhood Cancer Initiative
🗣 Sharing this post to spread the word!
🔗 🎁 bit.ly/give2treehouse
💸 Donating to Treehouse Childhood Cancer Initiative
🗣 Sharing this post to spread the word!
🔗 🎁 bit.ly/give2treehouse
November 5, 2025 at 12:32 PM
It's Giving Day!!! You can help support 🎗pediatric cancer research AND a "degree-defining experience" for undergraduates by:
💸 Donating to Treehouse Childhood Cancer Initiative
🗣 Sharing this post to spread the word!
🔗 🎁 bit.ly/give2treehouse
💸 Donating to Treehouse Childhood Cancer Initiative
🗣 Sharing this post to spread the word!
🔗 🎁 bit.ly/give2treehouse
Reposted by Adam M Novak
The year is 2025. C++ modules still don't just work.
November 5, 2025 at 12:58 PM
The year is 2025. C++ modules still don't just work.
Reposted by Adam M Novak
Going through @samuelhorsfield.bsky.social presentation on pangenome graphs in comparative genomics, courtesy of @training.ebi.embl.org.
Fascinating tidbit on history of alignment based sequence graph - it goes all the way back to 1989 (Hein), era of Apple IIs and IBM PS/2s. Great talk!
💻🧬🦠🧫
Fascinating tidbit on history of alignment based sequence graph - it goes all the way back to 1989 (Hein), era of Apple IIs and IBM PS/2s. Great talk!
💻🧬🦠🧫
November 5, 2025 at 3:19 PM
Going through @samuelhorsfield.bsky.social presentation on pangenome graphs in comparative genomics, courtesy of @training.ebi.embl.org.
Fascinating tidbit on history of alignment based sequence graph - it goes all the way back to 1989 (Hein), era of Apple IIs and IBM PS/2s. Great talk!
💻🧬🦠🧫
Fascinating tidbit on history of alignment based sequence graph - it goes all the way back to 1989 (Hein), era of Apple IIs and IBM PS/2s. Great talk!
💻🧬🦠🧫
Reposted by Adam M Novak
“Bonferonni correction”, an invaluable method in #statistics, refers to the act of repeatedly correcting misspellings of the word Bonferroni at multiple places in a draft manuscript.
#science #academia
#science #academia
November 11, 2024 at 2:52 PM
“Bonferonni correction”, an invaluable method in #statistics, refers to the act of repeatedly correcting misspellings of the word Bonferroni at multiple places in a draft manuscript.
#science #academia
#science #academia
Reposted by Adam M Novak
🪰 folks! I spoke to the Transmitter about FlyBase. As noted at flybase.org, bridge $ ran out and many staff were laid off.
Good news is stopgap contributions will keep core FlyBase operations active. But community support remains essential. Please donate @FlyBase and share! 1/2
tinyurl.com/FlyBase
Good news is stopgap contributions will keep core FlyBase operations active. But community support remains essential. Please donate @FlyBase and share! 1/2
tinyurl.com/FlyBase
FlyBase secures funding for year, but future still uncertain
The FlyBase team’s fundraising efforts have proven successful in the short term, but restoration of its federal grant remains uncertain.
tinyurl.com
October 29, 2025 at 12:31 PM
🪰 folks! I spoke to the Transmitter about FlyBase. As noted at flybase.org, bridge $ ran out and many staff were laid off.
Good news is stopgap contributions will keep core FlyBase operations active. But community support remains essential. Please donate @FlyBase and share! 1/2
tinyurl.com/FlyBase
Good news is stopgap contributions will keep core FlyBase operations active. But community support remains essential. Please donate @FlyBase and share! 1/2
tinyurl.com/FlyBase
Reposted by Adam M Novak
UCSC's Brooks Lab tool FLAIR is helping to rewrite the story of cancer research—pushing precision medicine closer to truly individualized care. Learn how: santacruzworks.org/n...
Genomics Rooftop Mixer: Mapping Gene Isoforms to Improve Treatment — Santa Cruz Works
Angela Brooks and her team are rewriting cancer research with FLAIR, a tool
that reveals hidden RNA isoforms driving tumor growth and drug
resistance—insights that could revolutionize precision medicine.
www.santacruzworks.org
October 25, 2025 at 12:01 AM
UCSC's Brooks Lab tool FLAIR is helping to rewrite the story of cancer research—pushing precision medicine closer to truly individualized care. Learn how: santacruzworks.org/n...
Reposted by Adam M Novak
Going through #pangenome lecture from @camillemrcht.bsky.social I missed yesterday. It looks like I get a shoutout on a slide! 🥳 Fantastic presentation, love the conceptual connection between traditional natural history collections and the modern bioinfo repos 🧬💻
www.ebi.ac.uk/training/eve...
www.ebi.ac.uk/training/eve...
October 23, 2025 at 5:36 PM
Going through #pangenome lecture from @camillemrcht.bsky.social I missed yesterday. It looks like I get a shoutout on a slide! 🥳 Fantastic presentation, love the conceptual connection between traditional natural history collections and the modern bioinfo repos 🧬💻
www.ebi.ac.uk/training/eve...
www.ebi.ac.uk/training/eve...
Reposted by Adam M Novak
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 M Novak
With a major influx of new people on here, guess it's time to re-share and update my starter pack of researchers working on scientific racism. If you know of any scientists, historians, journalists, or anyone else working this beat that aren't already included, please let me know so I can add them!
October 16, 2025 at 2:33 PM
With a major influx of new people on here, guess it's time to re-share and update my starter pack of researchers working on scientific racism. If you know of any scientists, historians, journalists, or anyone else working this beat that aren't already included, please let me know so I can add them!
Reposted by Adam M Novak
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 M Novak
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 M Novak
🦒Long read giraffe is out!🦒
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe https://www.biorxiv.org/content/10.1101/2025.09.29.678807v1
October 2, 2025 at 6:28 AM
🦒Long read giraffe is out!🦒
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Reposted by Adam M Novak
Also note: for comparison speed, 1-bit hashes beat everything else (top-right red line here). Because each bit is an independent sample, the entropy is very high.
(Whereas comparing 8-bit sketches loses some information, because if two 8-bit values differ in the first bit, the other 7 are unused.)
(Whereas comparing 8-bit sketches loses some information, because if two 8-bit values differ in the first bit, the other 7 are unused.)
October 1, 2025 at 3:03 PM
Also note: for comparison speed, 1-bit hashes beat everything else (top-right red line here). Because each bit is an independent sample, the entropy is very high.
(Whereas comparing 8-bit sketches loses some information, because if two 8-bit values differ in the first bit, the other 7 are unused.)
(Whereas comparing 8-bit sketches loses some information, because if two 8-bit values differ in the first bit, the other 7 are unused.)
Reposted by Adam M Novak
Here are the results in terms of the number of projects.
The number of funded projects in FY2025 is 4014 fewer than the number for FY2024.
2/3
The number of funded projects in FY2025 is 4014 fewer than the number for FY2024.
2/3
September 29, 2025 at 5:38 PM
Here are the results in terms of the number of projects.
The number of funded projects in FY2025 is 4014 fewer than the number for FY2024.
2/3
The number of funded projects in FY2025 is 4014 fewer than the number for FY2024.
2/3
I have eaten
the precisionFDATruth Challenge v2 dataset
that was in
the NIST Public Data Repository
and which
you were probably
going to cite
in your paper
Forgive me
it takes 2.85 minutes
to load
vendor.js
the precisionFDATruth Challenge v2 dataset
that was in
the NIST Public Data Repository
and which
you were probably
going to cite
in your paper
Forgive me
it takes 2.85 minutes
to load
vendor.js
Today the system knows the dataset exists, but displays a "Loading..." page forever instead of the data I wanted.
September 17, 2025 at 4:00 PM
I have eaten
the precisionFDATruth Challenge v2 dataset
that was in
the NIST Public Data Repository
and which
you were probably
going to cite
in your paper
Forgive me
it takes 2.85 minutes
to load
vendor.js
the precisionFDATruth Challenge v2 dataset
that was in
the NIST Public Data Repository
and which
you were probably
going to cite
in your paper
Forgive me
it takes 2.85 minutes
to load
vendor.js
Is the #precisionFDA Truth Challenge v2 dataset in NIST's Public Data Repository under doi.org/10.18434/mds... meant to be mysteriously missing?
doi.org
September 16, 2025 at 2:30 PM
Is the #precisionFDA Truth Challenge v2 dataset in NIST's Public Data Repository under doi.org/10.18434/mds... meant to be mysteriously missing?
Reposted by Adam M Novak
"We present exciting and novel new findings on the topic of the gel I'm about to run, with confirmatory experiments I'll run next Tuesday..."
September 12, 2025 at 6:50 PM
"We present exciting and novel new findings on the topic of the gel I'm about to run, with confirmatory experiments I'll run next Tuesday..."
Reposted by Adam M Novak
for some reason i thought being a professor would involve more mentoring and research and less filling out disclosures concerning whether plants and seeds were used in my computational study
September 9, 2025 at 7:24 PM
for some reason i thought being a professor would involve more mentoring and research and less filling out disclosures concerning whether plants and seeds were used in my computational study