Ilia Minkin
@minkinpark.bsky.social
A bioinformatics postdoc at Victoria Popic's lab at Broad Institute.
Pinned
Ilia Minkin
@minkinpark.bsky.social
· Mar 23
Check out our new paper in @narjournal.bsky.social on discovering extensive conservation of human introns across hundreds of other mammals, with Ilia Minkin academic.oup.com/nar/article/...
Conservation assessment of human splice site annotation based on a 470-genome alignment
Abstract. Despite many improvements over the years, the annotation of the human genome remains imperfect. The use of evolutionarily conserved sequences pro
academic.oup.com
Our splice site conservation paper is online!
Reposted by Ilia Minkin
If you talk about philosophy of science in interpretability papers you get to learn some incredible facts about what can go wrong with simple causal ablation studies
November 18, 2025 at 11:54 PM
If you talk about philosophy of science in interpretability papers you get to learn some incredible facts about what can go wrong with simple causal ablation studies
Reposted by Ilia Minkin
Reposted by Ilia Minkin
Our department (Comp Sci) at UMD is hiring this cycle. We have an open-rank search (umd.wd1.myworkdayjobs.com/en-US/UMCP/j...). Consider applying to join our department; we’re a pretty cool group if I say so myself ☺️!
Assistant Professor, Associate Professor, Professor
Job Description Summary Organization's Summary Statement: The Department of Computer Science is top-ranked for research and teaching, with its undergraduate computer science program ranked 9th among p...
umd.wd1.myworkdayjobs.com
October 31, 2025 at 3:14 AM
Our department (Comp Sci) at UMD is hiring this cycle. We have an open-rank search (umd.wd1.myworkdayjobs.com/en-US/UMCP/j...). Consider applying to join our department; we’re a pretty cool group if I say so myself ☺️!
Reposted by Ilia Minkin
So, our definitive paper on the human reference gene set is out this week in Database (Oxford).
We merged and compared @ensembl.org / @gencodegenes.bsky.social , RefSeq and UniProtKB coding genes and investigated the agreements and discrepancies.
Details of what we found in the thread ...
We merged and compared @ensembl.org / @gencodegenes.bsky.social , RefSeq and UniProtKB coding genes and investigated the agreements and discrepancies.
Details of what we found in the thread ...
September 30, 2025 at 2:25 PM
So, our definitive paper on the human reference gene set is out this week in Database (Oxford).
We merged and compared @ensembl.org / @gencodegenes.bsky.social , RefSeq and UniProtKB coding genes and investigated the agreements and discrepancies.
Details of what we found in the thread ...
We merged and compared @ensembl.org / @gencodegenes.bsky.social , RefSeq and UniProtKB coding genes and investigated the agreements and discrepancies.
Details of what we found in the thread ...
Reposted by Ilia Minkin
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 Ilia Minkin
I've added 7 videos to my Burrows-Wheeler indexing playlist (www.youtube.com/playlist?lis...), rounding out the r-index series and adding a 5-part series on the move structure. Now 27 videos in that playlist. I aim to add videos on prefix-free parsing, PBWT, Wheeler languages/automata in the future.
Burrows-Wheeler Indexing - YouTube
Videos on : (a) the Burrows-Wheeler Transform (BWT), (b) the FM Index, which uses the BWT to construct a full-text index, (c) Wheeler graphs, (d) r-index, an...
www.youtube.com
October 7, 2025 at 2:17 PM
I've added 7 videos to my Burrows-Wheeler indexing playlist (www.youtube.com/playlist?lis...), rounding out the r-index series and adding a 5-part series on the move structure. Now 27 videos in that playlist. I aim to add videos on prefix-free parsing, PBWT, Wheeler languages/automata in the future.
Reposted by Ilia Minkin
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 Ilia Minkin
Now hiring a computational postdoc (evolutionary genomics, molecular evolution) in my lab at Emory University.
If you’re interested in population genetics, fitness landscapes, and viral evolution — get in touch.
faculty-emory.icims.com/jobs/151181/...
If you’re interested in population genetics, fitness landscapes, and viral evolution — get in touch.
faculty-emory.icims.com/jobs/151181/...
Careers | Emory University | Atlanta GA
faculty-emory.icims.com
September 18, 2025 at 3:38 PM
Now hiring a computational postdoc (evolutionary genomics, molecular evolution) in my lab at Emory University.
If you’re interested in population genetics, fitness landscapes, and viral evolution — get in touch.
faculty-emory.icims.com/jobs/151181/...
If you’re interested in population genetics, fitness landscapes, and viral evolution — get in touch.
faculty-emory.icims.com/jobs/151181/...
Reposted by Ilia Minkin
Yes, I am on the academic job market looking to start my own lab at the intersection of molecular, computational, and systems neuroscience! If you think my work may be interest to your department, please don't hesitate to reach out.
Thank you, Keri!
Thank you, Keri!
Congrats Michael! Really appreciate the brilliance & creativity you brought to the analyses and as always, sincere dedication to open science 🧪 🧠
@mictott.bsky.social is on the job market!! Amazing skillset spanning wet lab/computational at molecular, cellular + systems level - and across species!
@mictott.bsky.social is on the job market!! Amazing skillset spanning wet lab/computational at molecular, cellular + systems level - and across species!
Very excited to share my second postdoc, now out in Science Advances! We used targeted snRNA-seq to profile four major subnuclei of the primate across three species (including humans). 1/13 www.science.org/doi/10.1126/...
September 18, 2025 at 1:31 AM
Yes, I am on the academic job market looking to start my own lab at the intersection of molecular, computational, and systems neuroscience! If you think my work may be interest to your department, please don't hesitate to reach out.
Thank you, Keri!
Thank you, Keri!
Reposted by Ilia Minkin
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 Ilia Minkin
Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology
LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.
www.nature.com
September 10, 2025 at 9:12 AM
Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
Reposted by Ilia Minkin
We're still not finding any good evidence for a microbiome in any cancer type: see our new paper in @ScienceTM led by PhD student Yuchen (Peter) Ge www.science.org/doi/10.1126/... and the accompanying news piece, www.science.org/content/arti...
Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project
An analysis of TCGA whole-genome sequencing samples yields a comprehensive resource for investigating the role of microbes in cancer.
www.science.org
September 3, 2025 at 8:45 PM
We're still not finding any good evidence for a microbiome in any cancer type: see our new paper in @ScienceTM led by PhD student Yuchen (Peter) Ge www.science.org/doi/10.1126/... and the accompanying news piece, www.science.org/content/arti...
Reposted by Ilia Minkin
🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
September 3, 2025 at 8:39 AM
🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Reposted by Ilia Minkin
Feeling mitochondrially challenged lately?
Here are two classic reviews on #mitochondria that should help.
www.cell.com/current-biol...
www.cell.com/current-biol...
Here are two classic reviews on #mitochondria that should help.
www.cell.com/current-biol...
www.cell.com/current-biol...
The Origin and Diversification of Mitochondria
Moving beyond the simplistic view of mitochondria as the power house of the cell,
Roger et al. present the immense diversity of mitochondria and mitochondrial functions
across eukaryotes, and bring th...
www.cell.com
August 28, 2025 at 10:28 PM
Feeling mitochondrially challenged lately?
Here are two classic reviews on #mitochondria that should help.
www.cell.com/current-biol...
www.cell.com/current-biol...
Here are two classic reviews on #mitochondria that should help.
www.cell.com/current-biol...
www.cell.com/current-biol...
Reposted by Ilia Minkin
This is how the AI apocalypse will arrive - not as malicious super intelligent AGI, but by well practiced malicious hackers taking advantage of the myth of “coding is easy, so let an LLM do it”
Excellent piece by @garymarcus.bsky.social and Nathan Hamiel:
garymarcus.substack.com/p/llms-codin...
Excellent piece by @garymarcus.bsky.social and Nathan Hamiel:
garymarcus.substack.com/p/llms-codin...
LLMs + Coding Agents = Security Nightmare
Things are about to get wild
garymarcus.substack.com
August 17, 2025 at 5:59 PM
This is how the AI apocalypse will arrive - not as malicious super intelligent AGI, but by well practiced malicious hackers taking advantage of the myth of “coding is easy, so let an LLM do it”
Excellent piece by @garymarcus.bsky.social and Nathan Hamiel:
garymarcus.substack.com/p/llms-codin...
Excellent piece by @garymarcus.bsky.social and Nathan Hamiel:
garymarcus.substack.com/p/llms-codin...
Reposted by Ilia Minkin
Cool new paper out by @mfeltes.bsky.social and @stefarber.bsky.social, collaborating with my colleague Aleksey Zimin (and me). We used WGS to discover and map genes causing dark yolk mutations in zebrafish. Great combo of computational + wet bench science!
journals.plos.org/plosgenetics...
journals.plos.org/plosgenetics...
Phenotype to genotype: A new and rapid approach using whole-genome sequencing
Author summary Forward genetic mutagenesis screening is an unbiased approach for the identification of mutations linked to a phenotype of interest. While this approach can be a powerful tool for uncov...
journals.plos.org
July 18, 2025 at 5:29 PM
Cool new paper out by @mfeltes.bsky.social and @stefarber.bsky.social, collaborating with my colleague Aleksey Zimin (and me). We used WGS to discover and map genes causing dark yolk mutations in zebrafish. Great combo of computational + wet bench science!
journals.plos.org/plosgenetics...
journals.plos.org/plosgenetics...
Reposted by Ilia Minkin
🧵1/n
Estimating mutation rates using k-mers is fast—but what happens when repeats dominate the genome?
In a new preprint, Haonan Wu, Antonio Blanca, and myself propose a *repeat-aware* estimator that's accurate even in centromeres.
Estimating mutation rates using k-mers is fast—but what happens when repeats dominate the genome?
In a new preprint, Haonan Wu, Antonio Blanca, and myself propose a *repeat-aware* estimator that's accurate even in centromeres.
A k-mer-based estimator of the substitution rate between repetitive sequences https://www.biorxiv.org/content/10.1101/2025.06.19.660607v1
June 25, 2025 at 1:19 PM
🧵1/n
Estimating mutation rates using k-mers is fast—but what happens when repeats dominate the genome?
In a new preprint, Haonan Wu, Antonio Blanca, and myself propose a *repeat-aware* estimator that's accurate even in centromeres.
Estimating mutation rates using k-mers is fast—but what happens when repeats dominate the genome?
In a new preprint, Haonan Wu, Antonio Blanca, and myself propose a *repeat-aware* estimator that's accurate even in centromeres.
Reposted by Ilia Minkin
1/4 Hash functions in genomic sequence analysis (tinyurl.com/4kk9ccmt) : a new survey written together with Ke Chen, Xiang Li, Qian Shi, and Mingfu Shao. Before submitting it, we are posting it online to get feedback from the community.
Dropbox
tinyurl.com
June 12, 2025 at 11:26 AM
1/4 Hash functions in genomic sequence analysis (tinyurl.com/4kk9ccmt) : a new survey written together with Ke Chen, Xiang Li, Qian Shi, and Mingfu Shao. Before submitting it, we are posting it online to get feedback from the community.
Reposted by Ilia Minkin
This is what happens when you go over your time at Woodstock Night Science #TCTEAC @barakrotblat.bsky.social
June 11, 2025 at 1:15 PM
This is what happens when you go over your time at Woodstock Night Science #TCTEAC @barakrotblat.bsky.social
Reposted by Ilia Minkin
Introns have to come from somewhere, right? @celineh2ooo.bsky.social and I looked at multiple genome alignments with 1000s of genomes and found 342 cases where humans (and our relatives) had gained a new intron. Still not sure where these come from, but it's a fascinating question
@celineh2ooo.bsky.social and @stevensalzberg.bsky.social compared 3,493 vertebrate genomes to identify 342 gains of introns in human genes, tracing their origins and identifying cases of intronization as a mechanism of intron emergence.
🔗 doi.org/10.1093/gbe/evaf091
#genome #evolution #introns
🔗 doi.org/10.1093/gbe/evaf091
#genome #evolution #introns
June 4, 2025 at 8:13 PM
Introns have to come from somewhere, right? @celineh2ooo.bsky.social and I looked at multiple genome alignments with 1000s of genomes and found 342 cases where humans (and our relatives) had gained a new intron. Still not sure where these come from, but it's a fascinating question
Reposted by Ilia Minkin
Slides from my talk (with @kamilsjaron.bsky.social) on an history of k-mers in bioinformatics: rayan.chikhi.name/pdf/2025-kme...
June 3, 2025 at 9:25 AM
Slides from my talk (with @kamilsjaron.bsky.social) on an history of k-mers in bioinformatics: rayan.chikhi.name/pdf/2025-kme...
Reposted by Ilia Minkin
Bioinformatics folks: check out our @biorxivpreprint on a new, very efficient and accurate system for automated genome annotation, EviAnn, led by my colleague Aleksey Zimin: www.biorxiv.org/content/10.1...
Efficient evidence-based genome annotation with EviAnn
For many years, machine learning-based ab initio gene finding approaches have been the central components of eukaryotic genome annotation pipelines, and they remain so today. The reliance on these app...
www.biorxiv.org
May 13, 2025 at 5:52 PM
Bioinformatics folks: check out our @biorxivpreprint on a new, very efficient and accurate system for automated genome annotation, EviAnn, led by my colleague Aleksey Zimin: www.biorxiv.org/content/10.1...
Reposted by Ilia Minkin
Hello Bluesky 👋🏾
I’m going to be defending my thesis on Wednesday, so I thought this was as good a time as any to introduce myself and my work.
I’m Arun Das, I’m a PhD student in Schatz Lab @ JHU, and my work broadly focuses on algorithms to improve accessibility and representation in genomics.
I’m going to be defending my thesis on Wednesday, so I thought this was as good a time as any to introduce myself and my work.
I’m Arun Das, I’m a PhD student in Schatz Lab @ JHU, and my work broadly focuses on algorithms to improve accessibility and representation in genomics.
April 21, 2025 at 9:24 PM
Hello Bluesky 👋🏾
I’m going to be defending my thesis on Wednesday, so I thought this was as good a time as any to introduce myself and my work.
I’m Arun Das, I’m a PhD student in Schatz Lab @ JHU, and my work broadly focuses on algorithms to improve accessibility and representation in genomics.
I’m going to be defending my thesis on Wednesday, so I thought this was as good a time as any to introduce myself and my work.
I’m Arun Das, I’m a PhD student in Schatz Lab @ JHU, and my work broadly focuses on algorithms to improve accessibility and representation in genomics.
Reposted by Ilia Minkin
In today's episode of the Night Science Podcast we talk with Martin Schwartz from Yale about the importance of stupidity in science: while learning science makes you feel smart, true scientific discovery often involves feeling stupid, because it means venturing into the unknown.
April 21, 2025 at 11:31 AM
In today's episode of the Night Science Podcast we talk with Martin Schwartz from Yale about the importance of stupidity in science: while learning science makes you feel smart, true scientific discovery often involves feeling stupid, because it means venturing into the unknown.
Reposted by Ilia Minkin
Join us at Genome Institute of Singapore! Great environment, stable funding!!
Apply now and be part of a team that values innovation, collaboration, and excellence!
Check out www.linkedin.com/jobs/view/42... for more details.
Find out more about the exciting work we do by our team – @jonathangoeke.bsky.social, @msikic.bsky.social
Check out www.linkedin.com/jobs/view/42... for more details.
Find out more about the exciting work we do by our team – @jonathangoeke.bsky.social, @msikic.bsky.social
A*STAR - Agency for Science, Technology and Research hiring Principal Investigators (GIS) in Singapore, Singapore | LinkedIn
Posted 11:59:37 AM. The Genome Institute of Singapore (GIS) is Singapore"s flagship institute for the genomic sciences.…See this and similar jobs on LinkedIn.
www.linkedin.com
April 14, 2025 at 5:26 AM
Join us at Genome Institute of Singapore! Great environment, stable funding!!