Alexey Sergushichev
@asergushichev.bsky.social
Assistant professor, WashU Pathology & Immunology
Author of FGSEA and other packages for omics data analysis
https://scholar.google.com/citations?user=fcH0gPgAAAAJ
https://github.com/assaron
Author of FGSEA and other packages for omics data analysis
https://scholar.google.com/citations?user=fcH0gPgAAAAJ
https://github.com/assaron
Reposted by Alexey Sergushichev
📢 We are announcing the Adaptive Immune Profiling Challenge 2025!
Can you predict immune state labels from adaptive immune receptor repertoires?
💰 $10,000 prize pool!
🗓️ Launches Nov 5 on @kaggle.com
More Info: uio-bmi.github.io/adaptive_imm...
Can you predict immune state labels from adaptive immune receptor repertoires?
💰 $10,000 prize pool!
🗓️ Launches Nov 5 on @kaggle.com
More Info: uio-bmi.github.io/adaptive_imm...
October 22, 2025 at 7:09 PM
📢 We are announcing the Adaptive Immune Profiling Challenge 2025!
Can you predict immune state labels from adaptive immune receptor repertoires?
💰 $10,000 prize pool!
🗓️ Launches Nov 5 on @kaggle.com
More Info: uio-bmi.github.io/adaptive_imm...
Can you predict immune state labels from adaptive immune receptor repertoires?
💰 $10,000 prize pool!
🗓️ Launches Nov 5 on @kaggle.com
More Info: uio-bmi.github.io/adaptive_imm...
Does anyone have a high-res version of NCBI GEO logo (www.ncbi.nlm.nih.gov/geo/img/geo_...)? I hate putting their low-res version in the slides/figures. I've tried to use AI tools for upscaling, but the results aren't perfect (colors are off). Anyone want to take a shot at it? Here is my best take:
October 18, 2025 at 11:15 PM
Does anyone have a high-res version of NCBI GEO logo (www.ncbi.nlm.nih.gov/geo/img/geo_...)? I hate putting their low-res version in the slides/figures. I've tried to use AI tools for upscaling, but the results aren't perfect (colors are off). Anyone want to take a shot at it? Here is my best take:
Reposted by Alexey Sergushichev
ohhhhhhhh wow
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Somatic mutation and selection at population scale - Nature
A new version of nanorate DNA sequencing, with an error rate lower than five errors per billion base pairs and compatible with whole-exome and targeted capture, enables epidemiological-scale studies of somatic mutation and selection and the generation of high-resolution selection maps across coding and non-coding sites for many genes.
www.nature.com
October 8, 2025 at 4:00 PM
ohhhhhhhh wow
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Alexey Sergushichev
Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...
docs.google.com/document/d/1...
Postdoc Description.docx
Title: Postdoctoral Associate Summary statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks, as well ...
docs.google.com
October 8, 2025 at 4:03 PM
Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...
docs.google.com/document/d/1...
Reposted by Alexey Sergushichev
Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution @cellcellpress.bsky.social @sstevenwang.bsky.social @yalepress.bsky.social
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
October 2, 2025 at 2:55 AM
Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution @cellcellpress.bsky.social @sstevenwang.bsky.social @yalepress.bsky.social
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Reposted by Alexey Sergushichev
Redid this thanks to @james-gagnon.bsky.social reminding me about NIH Databook. R01 applications numbers are dropping greatly at NIGMS but success rates (after being flat) dropped greatly last year. Suspect this will be even more drastic in 2025
September 30, 2025 at 7:43 PM
Redid this thanks to @james-gagnon.bsky.social reminding me about NIH Databook. R01 applications numbers are dropping greatly at NIGMS but success rates (after being flat) dropped greatly last year. Suspect this will be even more drastic in 2025
Reposted by Alexey Sergushichev
A nice shift in perceived colour between central and peripheral vision. The fixated disc looks purple while the others look blue.
The effect presumably comes from the absence of S-cones in the fovea.
From Hinnerk Schulz-Hildebrandt:
arxiv.org/pdf/2509.115...
The effect presumably comes from the absence of S-cones in the fovea.
From Hinnerk Schulz-Hildebrandt:
arxiv.org/pdf/2509.115...
September 24, 2025 at 12:04 PM
A nice shift in perceived colour between central and peripheral vision. The fixated disc looks purple while the others look blue.
The effect presumably comes from the absence of S-cones in the fovea.
From Hinnerk Schulz-Hildebrandt:
arxiv.org/pdf/2509.115...
The effect presumably comes from the absence of S-cones in the fovea.
From Hinnerk Schulz-Hildebrandt:
arxiv.org/pdf/2509.115...
Reposted by Alexey Sergushichev
Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]
A complete diploid human genome benchmark for personalized genomics
Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...
www.biorxiv.org
September 22, 2025 at 5:01 PM
Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]
Reposted by Alexey Sergushichev
hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!
September 15, 2025 at 5:26 PM
hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!
Reposted by Alexey Sergushichev
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
September 15, 2025 at 8:40 AM
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
Reposted by Alexey Sergushichev
Oh, fun: Someone did some personal science to evaluate if _they personally_ benefit from "AI", and this is what they found:
«Yes, it’s a limited sample and could be chance, but also so far AI appears to slow me down by a median of 21%, exactly in line with the METR study. I can say definitively […]
«Yes, it’s a limited sample and could be chance, but also so far AI appears to slow me down by a median of 21%, exactly in line with the METR study. I can say definitively […]
Original post on scholar.social
scholar.social
September 5, 2025 at 1:57 AM
Oh, fun: Someone did some personal science to evaluate if _they personally_ benefit from "AI", and this is what they found:
«Yes, it’s a limited sample and could be chance, but also so far AI appears to slow me down by a median of 21%, exactly in line with the METR study. I can say definitively […]
«Yes, it’s a limited sample and could be chance, but also so far AI appears to slow me down by a median of 21%, exactly in line with the METR study. I can say definitively […]
Reposted by Alexey Sergushichev
Job Alert: A stealth startup focused on non-cancer diagnostics is keen to hire a deep learning for genomics/bio engineer. I am an advisor for the startup & closely involved. Please see the job description below and get in touch if interested. Plz forward.
August 12, 2025 at 12:35 AM
Job Alert: A stealth startup focused on non-cancer diagnostics is keen to hire a deep learning for genomics/bio engineer. I am an advisor for the startup & closely involved. Please see the job description below and get in touch if interested. Plz forward.
An important milestone for me and my lab: fgsea has passed DESeq2 on the list of most downloaded Bioconductor packages. It started as a side project during my PhD, back when DESeq2 was already a staple of RNA-seq analysis. I never even thought it could go this far — but here we are!
August 14, 2025 at 3:48 PM
An important milestone for me and my lab: fgsea has passed DESeq2 on the list of most downloaded Bioconductor packages. It started as a side project during my PhD, back when DESeq2 was already a staple of RNA-seq analysis. I never even thought it could go this far — but here we are!
Reposted by Alexey Sergushichev
1. Make an Excel file with your author information
2. Drag and drop
3. Copy a nicely formatted author list into Word
🐶 slowkow.com/authorbud
2. Drag and drop
3. Copy a nicely formatted author list into Word
🐶 slowkow.com/authorbud
August 8, 2025 at 6:56 PM
1. Make an Excel file with your author information
2. Drag and drop
3. Copy a nicely formatted author list into Word
🐶 slowkow.com/authorbud
2. Drag and drop
3. Copy a nicely formatted author list into Word
🐶 slowkow.com/authorbud
Reposted by Alexey Sergushichev
Does water always recede prior to the arrival of a tsunami?
I was asked this yesterday after posting a graph of observed water levels at a station in Hawaii, which shows water levels first *increasing,* contrary to what many have heard about tsunamis.
The answer: no, not always! A thread... 🧵 1/9
I was asked this yesterday after posting a graph of observed water levels at a station in Hawaii, which shows water levels first *increasing,* contrary to what many have heard about tsunamis.
The answer: no, not always! A thread... 🧵 1/9
July 30, 2025 at 7:43 PM
Does water always recede prior to the arrival of a tsunami?
I was asked this yesterday after posting a graph of observed water levels at a station in Hawaii, which shows water levels first *increasing,* contrary to what many have heard about tsunamis.
The answer: no, not always! A thread... 🧵 1/9
I was asked this yesterday after posting a graph of observed water levels at a station in Hawaii, which shows water levels first *increasing,* contrary to what many have heard about tsunamis.
The answer: no, not always! A thread... 🧵 1/9
Reposted by Alexey Sergushichev
Fabulous post by @randomwalker.bsky.social & Sayash raising the same concern many of us have about whether we're on the right track with how we're using AI for science. Everyone should read it, take a deep breath & think through the implications.
www.aisnakeoil.com/p/could-ai-s...
www.aisnakeoil.com/p/could-ai-s...
Could AI slow science?
Confronting the production-progress paradox
www.aisnakeoil.com
July 17, 2025 at 4:05 PM
Fabulous post by @randomwalker.bsky.social & Sayash raising the same concern many of us have about whether we're on the right track with how we're using AI for science. Everyone should read it, take a deep breath & think through the implications.
www.aisnakeoil.com/p/could-ai-s...
www.aisnakeoil.com/p/could-ai-s...
Getting tired of 2FA everywhere, I've recently discovered that my password manager supports generating one-time passcodes. My life got a bit less miserable, but then—what's the point of 2FA?
July 16, 2025 at 9:55 PM
Getting tired of 2FA everywhere, I've recently discovered that my password manager supports generating one-time passcodes. My life got a bit less miserable, but then—what's the point of 2FA?
Reposted by Alexey Sergushichev
Automated metadata curation with human-level accuracy, dataset-wide scale, and traceable quality.
Our Agentic AI system extracted 23+ metadata fields with 93% recall from GEO, papers, and supplementary files across 211 studies.
Our Agentic AI system extracted 23+ metadata fields with 93% recall from GEO, papers, and supplementary files across 211 studies.
June 19, 2025 at 7:07 PM
Automated metadata curation with human-level accuracy, dataset-wide scale, and traceable quality.
Our Agentic AI system extracted 23+ metadata fields with 93% recall from GEO, papers, and supplementary files across 211 studies.
Our Agentic AI system extracted 23+ metadata fields with 93% recall from GEO, papers, and supplementary files across 211 studies.
Reposted by Alexey Sergushichev
Are you looking for a faculty job? We are hiring in my department at Roswell Park NOW. Contact me for details as I await the formal ad. (Please RT.)
June 4, 2025 at 6:34 PM
Are you looking for a faculty job? We are hiring in my department at Roswell Park NOW. Contact me for details as I await the formal ad. (Please RT.)
Reposted by Alexey Sergushichev
Mechanisms and timing of programmed DNA elimination in songbirds www.biorxiv.org/content/10.1...
Mechanisms and timing of programmed DNA elimination in songbirds
It is commonly assumed that multicellular organisms contain the same genetic information in all the cells of an individual. However, there is a growing list of species in which parts of the genome are...
www.biorxiv.org
June 1, 2025 at 9:24 PM
Mechanisms and timing of programmed DNA elimination in songbirds www.biorxiv.org/content/10.1...
Reposted by Alexey Sergushichev
Terminal Genome Viewer (tgv), written in Rust github.com/zeqianli/tgv
May 27, 2025 at 5:37 PM
Terminal Genome Viewer (tgv), written in Rust github.com/zeqianli/tgv
Reposted by Alexey Sergushichev
Cool videos from our new paper applying Diversity Search to Flow-Lenia to explore a vast space of eco-evolutionary dynamics. Preprint paper, dataset and online visualization tool soon available, stay tuned!
I'll present this and other Lenia experiments on May 27 at www.dem.eco
#ALife #Open-endedness
I'll present this and other Lenia experiments on May 27 at www.dem.eco
#ALife #Open-endedness
May 14, 2025 at 12:50 PM
Cool videos from our new paper applying Diversity Search to Flow-Lenia to explore a vast space of eco-evolutionary dynamics. Preprint paper, dataset and online visualization tool soon available, stay tuned!
I'll present this and other Lenia experiments on May 27 at www.dem.eco
#ALife #Open-endedness
I'll present this and other Lenia experiments on May 27 at www.dem.eco
#ALife #Open-endedness
Reposted by Alexey Sergushichev
The deadline for WABI 2025 has been extended (but is still rapidly approaching) wabiconf.github.io/2025/
* abstract deadline: May 12 (AoE)
* paper deadline: May 15 (AoE)
Consider submitting your exciting algorithmic bioinformatics work to the WABI conference!
* abstract deadline: May 12 (AoE)
* paper deadline: May 15 (AoE)
Consider submitting your exciting algorithmic bioinformatics work to the WABI conference!
WABI 2025
WABI Conference on Algorithms in Bioinformatics
wabiconf.github.io
May 7, 2025 at 7:14 PM
The deadline for WABI 2025 has been extended (but is still rapidly approaching) wabiconf.github.io/2025/
* abstract deadline: May 12 (AoE)
* paper deadline: May 15 (AoE)
Consider submitting your exciting algorithmic bioinformatics work to the WABI conference!
* abstract deadline: May 12 (AoE)
* paper deadline: May 15 (AoE)
Consider submitting your exciting algorithmic bioinformatics work to the WABI conference!
I'm happy to present our new web-tool CORESH alserglab.wustl.edu/coresh/ for searching public gene expression datasets using gene signature as a query, which was just published in @narjournal.bsky.social doi.org/10.1093/nar/... 1/n 🧬 🖥️
May 7, 2025 at 2:03 PM
I'm happy to present our new web-tool CORESH alserglab.wustl.edu/coresh/ for searching public gene expression datasets using gene signature as a query, which was just published in @narjournal.bsky.social doi.org/10.1093/nar/... 1/n 🧬 🖥️
Grant deadlines are approaching, which means I need to stop procrastinating by working on the mascarade package. The new 0.2 version features a better algorithm that should work automatically on most of UMAP/tSNE plots. github.com/alserglab/ma... rpubs.com/asergushiche... 1/4
April 21, 2025 at 2:18 PM
Grant deadlines are approaching, which means I need to stop procrastinating by working on the mascarade package. The new 0.2 version features a better algorithm that should work automatically on most of UMAP/tSNE plots. github.com/alserglab/ma... rpubs.com/asergushiche... 1/4