Arjun Krishnan
@compbiologist.bsky.social
ML/AI methods & tools for using massive public data collections to gain insights into complex disease mechanisms.
Associate Professor & Group leader thekrishnanlab.org at the Dept. of Biomedical Informatics at CU Anschutz.
Associate Professor & Group leader thekrishnanlab.org at the Dept. of Biomedical Informatics at CU Anschutz.
Reposted by Arjun Krishnan
This preprint is now out after peer review! Check it out: www.cell.com/cell-genomic.... Huge congrats (and thanks!) to the whole team that contributed!
May 21, 2025 at 6:34 PM
This preprint is now out after peer review! Check it out: www.cell.com/cell-genomic.... Huge congrats (and thanks!) to the whole team that contributed!
Reposted by Arjun Krishnan
Very proud to be a member of this team. A huge group effort to improve the lives of those with Down syndrome. Thank you to everyone that has helped us along the way.
The Linda Crnic Institute for Down Syndrome is proud to announce that we have been awarded the 2025 Research Collaboration Award at the 2025 @cuanschutz.bsky.social Research Awards! This award recognizes a team for outstanding contributions in research collaborations.
February 14, 2025 at 3:42 AM
Very proud to be a member of this team. A huge group effort to improve the lives of those with Down syndrome. Thank you to everyone that has helped us along the way.
Congratulations! Kudos to @richabdill.com & @samanthagraham.bsky.social for leading this huge project!
Thanks for bring us onboard! Mansooreh Ahmadian & Parker Hicks lead the part of the work on inferring study annotations from unstructured metadata and text from the linked publications.
Thanks for bring us onboard! Mansooreh Ahmadian & Parker Hicks lead the part of the work on inferring study annotations from unstructured metadata and text from the linked publications.
Today we report a new compendium of human gut microbiomes with >168,000 samples
By analyzing this massive dataset, we discovered distinct microbiome patterns across the globe, and show we can predict where a person lives just from their gut bacteria
Now out in Cell:
www.cell.com/cell/fulltex...
By analyzing this massive dataset, we discovered distinct microbiome patterns across the globe, and show we can predict where a person lives just from their gut bacteria
Now out in Cell:
www.cell.com/cell/fulltex...
Integration of 168,000 samples reveals global patterns of the human gut microbiome
The Human Microbiome Compendium is a unified database of publicly available human
gut microbiome 16S samples, built with the integrated data from hundreds of independent
projects. The compendium is us...
www.cell.com
January 22, 2025 at 6:08 PM
Congratulations! Kudos to @richabdill.com & @samanthagraham.bsky.social for leading this huge project!
Thanks for bring us onboard! Mansooreh Ahmadian & Parker Hicks lead the part of the work on inferring study annotations from unstructured metadata and text from the linked publications.
Thanks for bring us onboard! Mansooreh Ahmadian & Parker Hicks lead the part of the work on inferring study annotations from unstructured metadata and text from the linked publications.
A favorite!
Interestingly, Goodhart stated (in 1975): “Any observed statistical regularity will tend to collapse once pressure is placed upon it for control purposes.”
Marilyn Strathern generalized it in 1997 to its famous version👇🏽
pmc.ncbi.nlm.nih.gov/articles/PMC...
Interestingly, Goodhart stated (in 1975): “Any observed statistical regularity will tend to collapse once pressure is placed upon it for control purposes.”
Marilyn Strathern generalized it in 1997 to its famous version👇🏽
pmc.ncbi.nlm.nih.gov/articles/PMC...
December 20, 2024 at 3:47 PM
A favorite!
Interestingly, Goodhart stated (in 1975): “Any observed statistical regularity will tend to collapse once pressure is placed upon it for control purposes.”
Marilyn Strathern generalized it in 1997 to its famous version👇🏽
pmc.ncbi.nlm.nih.gov/articles/PMC...
Interestingly, Goodhart stated (in 1975): “Any observed statistical regularity will tend to collapse once pressure is placed upon it for control purposes.”
Marilyn Strathern generalized it in 1997 to its famous version👇🏽
pmc.ncbi.nlm.nih.gov/articles/PMC...
Reposted by Arjun Krishnan
Regularly tempted to write in my NIH grants innovation section: "Funding software that already exists and works well would be highly innovative for the NIH."
(I bet half the panel would break down ROFL, but I'm also highly skeptical that I'd get a good score, or that the PO would be amused.)
(I bet half the panel would break down ROFL, but I'm also highly skeptical that I'd get a good score, or that the PO would be amused.)
December 16, 2024 at 8:13 PM
Regularly tempted to write in my NIH grants innovation section: "Funding software that already exists and works well would be highly innovative for the NIH."
(I bet half the panel would break down ROFL, but I'm also highly skeptical that I'd get a good score, or that the PO would be amused.)
(I bet half the panel would break down ROFL, but I'm also highly skeptical that I'd get a good score, or that the PO would be amused.)
Reposted by Arjun Krishnan
Last update of our databases for the year.
Download them here:
493 early-career funding opportunities: research.jhu.edu/rdt/funding-...
313 postdoc fellowships: research.jhu.edu/rdt/funding-...
189 PhD fellowships: research.jhu.edu/rdt/funding-...
Download them here:
493 early-career funding opportunities: research.jhu.edu/rdt/funding-...
313 postdoc fellowships: research.jhu.edu/rdt/funding-...
189 PhD fellowships: research.jhu.edu/rdt/funding-...
December 14, 2024 at 6:28 PM
Last update of our databases for the year.
Download them here:
493 early-career funding opportunities: research.jhu.edu/rdt/funding-...
313 postdoc fellowships: research.jhu.edu/rdt/funding-...
189 PhD fellowships: research.jhu.edu/rdt/funding-...
Download them here:
493 early-career funding opportunities: research.jhu.edu/rdt/funding-...
313 postdoc fellowships: research.jhu.edu/rdt/funding-...
189 PhD fellowships: research.jhu.edu/rdt/funding-...
Reposted by Arjun Krishnan
The views from the office are another real perk of working here at @cubiomedinfo.bsky.social.
December 10, 2024 at 4:57 PM
The views from the office are another real perk of working here at @cubiomedinfo.bsky.social.
Monday motivation from the wonderful @pracheeac.bsky.social:
“[I hate the term] incentive structure… if you ask people to do a thing that they perceive to be against those processes and principles, well, you can't ask that — that it's somehow unacceptable…
“[I hate the term] incentive structure… if you ask people to do a thing that they perceive to be against those processes and principles, well, you can't ask that — that it's somehow unacceptable…
December 9, 2024 at 3:26 PM
Monday motivation from the wonderful @pracheeac.bsky.social:
“[I hate the term] incentive structure… if you ask people to do a thing that they perceive to be against those processes and principles, well, you can't ask that — that it's somehow unacceptable…
“[I hate the term] incentive structure… if you ask people to do a thing that they perceive to be against those processes and principles, well, you can't ask that — that it's somehow unacceptable…
Reposted by Arjun Krishnan
I participated in a faculty panel a few weeks ago in which senior (ahem) faculty gave advice on careers in academia by pretending luck had very little to do with our success. One piece of advice riled me up, in which it was argued that a reason for their success was their ability to say no. 1/
December 9, 2024 at 3:16 AM
I participated in a faculty panel a few weeks ago in which senior (ahem) faculty gave advice on careers in academia by pretending luck had very little to do with our success. One piece of advice riled me up, in which it was argued that a reason for their success was their ability to say no. 1/
Reposted by Arjun Krishnan
I’ve seen some posts recently, about the value of basic research, in light of funding cuts and demands that research have immediate economic justification.
Let me collect some info here, in a thread, about why it’s a bad idea to attach those sorts of demands to funding. 🧵 🧪 ⚛️
Let me collect some info here, in a thread, about why it’s a bad idea to attach those sorts of demands to funding. 🧵 🧪 ⚛️
December 4, 2024 at 4:13 AM
I’ve seen some posts recently, about the value of basic research, in light of funding cuts and demands that research have immediate economic justification.
Let me collect some info here, in a thread, about why it’s a bad idea to attach those sorts of demands to funding. 🧵 🧪 ⚛️
Let me collect some info here, in a thread, about why it’s a bad idea to attach those sorts of demands to funding. 🧵 🧪 ⚛️
Reposted by Arjun Krishnan
Same reason that nanopore work with direct clinical application gets published in Annals of Obscurities while the tumor poopome and AlphaFold3 (which wasn’t even competitive in CASP16!) get published in Nature over the objections of highly qualified reviewers
December 3, 2024 at 2:42 PM
Same reason that nanopore work with direct clinical application gets published in Annals of Obscurities while the tumor poopome and AlphaFold3 (which wasn’t even competitive in CASP16!) get published in Nature over the objections of highly qualified reviewers
Reposted by Arjun Krishnan
Because it makes for a better $$$ barrier to entry.
Broke: we fit a linear model and predicted results of a CRISPR screen
Woke: we burned down the Amazon to train a 96-head transformer on 500 million cells and did ALMOST AS WELL as the linear model that runs on my phone
Broke: we fit a linear model and predicted results of a CRISPR screen
Woke: we burned down the Amazon to train a 96-head transformer on 500 million cells and did ALMOST AS WELL as the linear model that runs on my phone
December 3, 2024 at 2:40 PM
Because it makes for a better $$$ barrier to entry.
Broke: we fit a linear model and predicted results of a CRISPR screen
Woke: we burned down the Amazon to train a 96-head transformer on 500 million cells and did ALMOST AS WELL as the linear model that runs on my phone
Broke: we fit a linear model and predicted results of a CRISPR screen
Woke: we burned down the Amazon to train a 96-head transformer on 500 million cells and did ALMOST AS WELL as the linear model that runs on my phone
Reposted by Arjun Krishnan
Sharing a Shiny app I've been working on at
@leviwaldron1.bsky.social 's lab: BugSigDBEnrich. The app lets you compare a list of bacteria with published microbial signatures curated in bugsigdb.org.
shiny.sph.cuny.edu/BugSigDBEnri...
#rstats #microbiome #microbiomeresearch
@leviwaldron1.bsky.social 's lab: BugSigDBEnrich. The app lets you compare a list of bacteria with published microbial signatures curated in bugsigdb.org.
shiny.sph.cuny.edu/BugSigDBEnri...
#rstats #microbiome #microbiomeresearch
November 28, 2024 at 2:05 AM
Sharing a Shiny app I've been working on at
@leviwaldron1.bsky.social 's lab: BugSigDBEnrich. The app lets you compare a list of bacteria with published microbial signatures curated in bugsigdb.org.
shiny.sph.cuny.edu/BugSigDBEnri...
#rstats #microbiome #microbiomeresearch
@leviwaldron1.bsky.social 's lab: BugSigDBEnrich. The app lets you compare a list of bacteria with published microbial signatures curated in bugsigdb.org.
shiny.sph.cuny.edu/BugSigDBEnri...
#rstats #microbiome #microbiomeresearch
As a fan of the super @nightsciencepod.bsky.social (highly recommend it!), I enjoyed listening to the latest episode of another favorite — Work Life — where @adamgrant.bsky.social talks to Nathan Myhrvold about invention and creativity!
podcasts.apple.com/us/podcast/w...
podcasts.apple.com/us/podcast/w...
The art of invention with Nathan Myhrvold
Podcast Episode · WorkLife with Adam Grant · 11/26/2024 · 27m
podcasts.apple.com
November 27, 2024 at 4:28 PM
As a fan of the super @nightsciencepod.bsky.social (highly recommend it!), I enjoyed listening to the latest episode of another favorite — Work Life — where @adamgrant.bsky.social talks to Nathan Myhrvold about invention and creativity!
podcasts.apple.com/us/podcast/w...
podcasts.apple.com/us/podcast/w...
Reposted by Arjun Krishnan
Abstract submissions are still open for the CSHL Network Biology meeting in March 11 - 15 2025 (abstract deadline: Jan 10). A large fraction of talks will be selected from the abstracts. On behalf of the organizers, we look forward to welcoming you there.
meetings.cshl.edu/meetings.asp...
meetings.cshl.edu/meetings.asp...
November 26, 2024 at 1:17 PM
Abstract submissions are still open for the CSHL Network Biology meeting in March 11 - 15 2025 (abstract deadline: Jan 10). A large fraction of talks will be selected from the abstracts. On behalf of the organizers, we look forward to welcoming you there.
meetings.cshl.edu/meetings.asp...
meetings.cshl.edu/meetings.asp...
Reposted by Arjun Krishnan
We present NetworkCommons, a unified platform 🪐 for network biology, providing access to omics data, knowledge, and contextualization methods, all with a consistent API 👇🧵
Paper: doi.org/10.1101/2024...
Docs: networkcommons.readthedocs.io
Paper: doi.org/10.1101/2024...
Docs: networkcommons.readthedocs.io
November 26, 2024 at 9:44 AM
We present NetworkCommons, a unified platform 🪐 for network biology, providing access to omics data, knowledge, and contextualization methods, all with a consistent API 👇🧵
Paper: doi.org/10.1101/2024...
Docs: networkcommons.readthedocs.io
Paper: doi.org/10.1101/2024...
Docs: networkcommons.readthedocs.io
Reposted by Arjun Krishnan
I feel this in my bones. In early career, I had access to more support and flexible funding. As I transitioned to mid-career, not only did a lot of those buffers go away, I was taking on more institutional responsibility, including to fix systemic issues and protect more people.
I wish there was an easier way to communicate to early career people what being at the next stage is actually like.
You can describe it, but it’s like an embodied experience that’s very hard to help people really understand. There’s no analog.
You can describe it, but it’s like an embodied experience that’s very hard to help people really understand. There’s no analog.
November 23, 2024 at 9:49 PM
I feel this in my bones. In early career, I had access to more support and flexible funding. As I transitioned to mid-career, not only did a lot of those buffers go away, I was taking on more institutional responsibility, including to fix systemic issues and protect more people.
Reposted by Arjun Krishnan
A bluetorial about some challenges for our two-career family and some flaws in the culture of biomedical research.
homer simpson from the simpsons is holding a cup in front of a picture
ALT: homer simpson from the simpsons is holding a cup in front of a picture
media.tenor.com
November 24, 2024 at 11:31 AM
A bluetorial about some challenges for our two-career family and some flaws in the culture of biomedical research.
Reposted by Arjun Krishnan
Only five days left to apply for our Functional Genomics in animal model systems faculty position at Michigan State University!
🦋🐍🐸🐟🐢🐞🐓🦀🐙🐛🦎🐜🦇🐀🦗🦜🦞🐊🪱🪸🪰🕷️🐚🐖🐝🦄
We love research connecting genomes to biodiversity and are highly supportive of developing non-traditional model systems. Come join us in MI!
🦋🐍🐸🐟🐢🐞🐓🦀🐙🐛🦎🐜🦇🐀🦗🦜🦞🐊🪱🪸🪰🕷️🐚🐖🐝🦄
We love research connecting genomes to biodiversity and are highly supportive of developing non-traditional model systems. Come join us in MI!
Faculty Job Alert! #ScienceJobs
Michigan State University Integrative Biology is looking for a TT Assist Prof in Functional #Genomics. Join a vibrant research community for non-traditional #EvoDevo animal models! tinyurl.com/4hya8vet Deadline: 11/27/24 integrativebiology.natsci.msu.edu
Pls repost!
Michigan State University Integrative Biology is looking for a TT Assist Prof in Functional #Genomics. Join a vibrant research community for non-traditional #EvoDevo animal models! tinyurl.com/4hya8vet Deadline: 11/27/24 integrativebiology.natsci.msu.edu
Pls repost!
MSU Careers Details - Assistant Professor-Tenure System - Functional Genomics
tinyurl.com
November 22, 2024 at 11:21 AM
Only five days left to apply for our Functional Genomics in animal model systems faculty position at Michigan State University!
🦋🐍🐸🐟🐢🐞🐓🦀🐙🐛🦎🐜🦇🐀🦗🦜🦞🐊🪱🪸🪰🕷️🐚🐖🐝🦄
We love research connecting genomes to biodiversity and are highly supportive of developing non-traditional model systems. Come join us in MI!
🦋🐍🐸🐟🐢🐞🐓🦀🐙🐛🦎🐜🦇🐀🦗🦜🦞🐊🪱🪸🪰🕷️🐚🐖🐝🦄
We love research connecting genomes to biodiversity and are highly supportive of developing non-traditional model systems. Come join us in MI!
Reposted by Arjun Krishnan
Check out our updated database of 189 PhD fellowships and funding opportunities.
For each fellowship, we provide a description, $ amount, deadline, link to funder and eligibility criteria (such as citizenship).
Good luck!
Download freely here: research.jhu.edu/rdt/funding-...
For each fellowship, we provide a description, $ amount, deadline, link to funder and eligibility criteria (such as citizenship).
Good luck!
Download freely here: research.jhu.edu/rdt/funding-...
November 19, 2024 at 1:13 PM
Check out our updated database of 189 PhD fellowships and funding opportunities.
For each fellowship, we provide a description, $ amount, deadline, link to funder and eligibility criteria (such as citizenship).
Good luck!
Download freely here: research.jhu.edu/rdt/funding-...
For each fellowship, we provide a description, $ amount, deadline, link to funder and eligibility criteria (such as citizenship).
Good luck!
Download freely here: research.jhu.edu/rdt/funding-...
Reposted by Arjun Krishnan
Thank you to everyone who joined our Town Hall on Opportunities for Allyship in Computational Biology last week, our largest event yet!
We are grateful to have partnered with Chrissie Bonner of Illustrating Progress, who provided a live graphic recording of our event.
1/2
We are grateful to have partnered with Chrissie Bonner of Illustrating Progress, who provided a live graphic recording of our event.
1/2
March 4, 2024 at 5:47 PM
Thank you to everyone who joined our Town Hall on Opportunities for Allyship in Computational Biology last week, our largest event yet!
We are grateful to have partnered with Chrissie Bonner of Illustrating Progress, who provided a live graphic recording of our event.
1/2
We are grateful to have partnered with Chrissie Bonner of Illustrating Progress, who provided a live graphic recording of our event.
1/2
The world doesn’t need one more blog, and yet I started one and plan to write semi-regularly!
compbiologist.substack.com/p/computing-...
compbiologist.substack.com/p/computing-...
Computing for life
A new space for reflections at the interface of data, ML/AI, and biomedical research
compbiologist.substack.com
December 8, 2023 at 8:03 PM
The world doesn’t need one more blog, and yet I started one and plan to write semi-regularly!
compbiologist.substack.com/p/computing-...
compbiologist.substack.com/p/computing-...
Very much looking forward to #MLCB2023, meeting folks & learning a lot!
Do checkout our PMLR poster, led by Renming Liu:
Open Biomedical Network Benchmark: A Python Toolkit for Benchmarking Datasets with Biomedical Networks
Preprint: doi.org/10.1101/2023...
Code: github.com/krishnanlab/...
Do checkout our PMLR poster, led by Renming Liu:
Open Biomedical Network Benchmark: A Python Toolkit for Benchmarking Datasets with Biomedical Networks
Preprint: doi.org/10.1101/2023...
Code: github.com/krishnanlab/...
November 29, 2023 at 5:30 PM
Very much looking forward to #MLCB2023, meeting folks & learning a lot!
Do checkout our PMLR poster, led by Renming Liu:
Open Biomedical Network Benchmark: A Python Toolkit for Benchmarking Datasets with Biomedical Networks
Preprint: doi.org/10.1101/2023...
Code: github.com/krishnanlab/...
Do checkout our PMLR poster, led by Renming Liu:
Open Biomedical Network Benchmark: A Python Toolkit for Benchmarking Datasets with Biomedical Networks
Preprint: doi.org/10.1101/2023...
Code: github.com/krishnanlab/...
Reposted by Arjun Krishnan
Excited to announce the 10th release & 20th-anniversary update of JASPAR, a leading resource in computational regulatory genomics!
Important to note that JASPAR has a new URL: jaspar.elixir.no
The manuscript can be found at academic.oup.com/nar/advance-...
Important to note that JASPAR has a new URL: jaspar.elixir.no
The manuscript can be found at academic.oup.com/nar/advance-...
JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles
Abstract. JASPAR (https://jaspar.elixir.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profil
academic.oup.com
November 14, 2023 at 10:41 AM
Excited to announce the 10th release & 20th-anniversary update of JASPAR, a leading resource in computational regulatory genomics!
Important to note that JASPAR has a new URL: jaspar.elixir.no
The manuscript can be found at academic.oup.com/nar/advance-...
Important to note that JASPAR has a new URL: jaspar.elixir.no
The manuscript can be found at academic.oup.com/nar/advance-...
Reposted by Arjun Krishnan
As jobs are coming out and folks are applying, here's your regular reminder of lots of examples of successful job apps (mostly research academia but also industry, PUI, gov). And if you've gotten a job recently, please consider contributing! github.com/RILAB/statem...
November 14, 2023 at 5:01 PM
As jobs are coming out and folks are applying, here's your regular reminder of lots of examples of successful job apps (mostly research academia but also industry, PUI, gov). And if you've gotten a job recently, please consider contributing! github.com/RILAB/statem...