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Nikolay Oskolkov @oskolkov.bsky.social · 9h

Come and learn environmental metagenomics together with us www.physalia-courses.org/courses-work...

Dates 13-17 October 2025 To foster international participation, this course will be held online

Nikolay Oskolkov @oskolkov.bsky.social · 4d

We screened ~3000 eukaryotic NCBI RefSeq and 1323 PhyloNorway genomes for microbial-like regions and compiled a resource with genomic coordinates doi.org/10.17044/sci..., enabling masking before population genomics or taxonomic inference aeDNA analyses

Coordinates of microbial contamination in eukaryotic reference genomes

This dataset contains coordinates of microbial contamination in eukaryotic chromosome-level reference genomes of 96 plant, 114 invertebrate and 162 non-mammalian vertebrate species, 566 chromosome- an...

doi.org

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Nikolay Oskolkov @oskolkov.bsky.social · 4d

Our method can be used for masking potential exogenous (microbial or human) regions in eukaryotic references for better taxonomic inference from ancient environmental metagenomics data. The method is implemented in Nextflow and available here github.com/NikolayOskol...

GitHub - NikolayOskolkov/MCWorkflow

Contribute to NikolayOskolkov/MCWorkflow development by creating an account on GitHub.

github.com

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Nikolay Oskolkov @oskolkov.bsky.social · 4d

Our method, GENome EXogenous (GENEX) sequence detection, for identifying microbial-like regions in eukaryotic reference genomes is online in GigaScience track.smtpsendmail.com/9032119/c?p=...

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Reposted by Nikolay Oskolkov

Physalia-courses@Online @physaliacourses.bsky.social · 16d

Only 1 seat left @oskolkov.bsky.social

Physalia-courses@Online @physaliacourses.bsky.social · Sep 2

We would like to inform you that only four seats are left for the in-person course, “Machine Learning for Multi-Omics Integration,” with @oskolkov.bsky.social taking place on 15–17 December at the University of Barcelona @irbio-ub.bsky.social

www.physalia-courses.org/courses-work...

Machine Learning for Multi-Omics Integration

15-17 December 2025 Dept. Evolutionary Biology, Ecology & Environmental Sciences Faculty of Biology, University of Barcelona Institut de Recerca de la Biodiversitat (IRBio) Av. Diagonal, 643, Les ...

www.physalia-courses.org

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Nikolay Oskolkov @oskolkov.bsky.social · 17d

I am running Deep Learning for Complex Datasets instats.org/seminar/deep... seminar on the 26th of September, everyone is welcome to attend!

Deep Learning for Complex Datasets with ChatGPT - Live-streaming:

This Instats seminar on Deep Learning for Complex Datasets with ChatGPT taught by Nikolay Oskolkov will help you take your research to the next level. Sign up today!

instats.org

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Reposted by Nikolay Oskolkov

Physalia-courses@Online @physaliacourses.bsky.social · 27d

We are wrapping up the first edition of our AI for Genomics course! 🚀 Huge thanks to @oskolkov.bsky.social and all participants who joined us this week 🙏🧬
#AI #Genomics #DeepLearning

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Reposted by Nikolay Oskolkov

Physalia-courses@Online @physaliacourses.bsky.social · 29d

🚀 We’ve just kicked off the first edition of our 3-day course “AI for Genomics: From CNNs and LSTMs to Transformers” with @oskolkov.bsky.social

Participants will dive into cutting-edge AI methods applied to genomics & metagenomics, with hands-on labs & real-world case studies. Exciting days ahead!

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Nikolay Oskolkov @oskolkov.bsky.social · Sep 6

Press release on our paper in Cell about mammoth microbiome:
1) www.forskning.se/2025/09/03/v...
2) www.su.se/english/news...

Mammutens tand avslöjar uråldriga bakterier - forskning.se

Ett internationellt forskarteam har analyserat dna från 483 mammutprover. Med avancerade metoder har forskarna lyckats skilja ut mikrober, alltså små organismer som bakterier och virus, som levde med ...

www.forskning.se

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Nikolay Oskolkov @oskolkov.bsky.social · Sep 4

Nature discusses our article on mammoth microbiome www.nature.com/articles/d41...

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Nikolay Oskolkov @oskolkov.bsky.social · Sep 3

Our paper on ancient mammoth microbiome analysis is out in Cell. Congratulations Ben Guinet, Tom van der Valk and all the co-authors! authors.elsevier.com/c/1liYML7PXu...

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Reposted by Nikolay Oskolkov

Physalia-courses@Online @physaliacourses.bsky.social · Sep 2

We would like to inform you that only four seats are left for the in-person course, “Machine Learning for Multi-Omics Integration,” with @oskolkov.bsky.social taking place on 15–17 December at the University of Barcelona @irbio-ub.bsky.social

www.physalia-courses.org/courses-work...

Machine Learning for Multi-Omics Integration

15-17 December 2025 Dept. Evolutionary Biology, Ecology & Environmental Sciences Faculty of Biology, University of Barcelona Institut de Recerca de la Biodiversitat (IRBio) Av. Diagonal, 643, Les ...

www.physalia-courses.org

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Reposted by Nikolay Oskolkov

Department of Biology, Lund University @biologylu.bsky.social · Aug 27

A big study of ancient human DNA confirms what researchers had previously suspected but were unable to fully confirm. Humans were affected by a large number of new diseases when our ancestors began domesticating animals.
@oskolkov.bsky.social @natcomms.nature.com

www.nature.com/articles/s41...

The spatiotemporal distribution of human pathogens in ancient Eurasia - Nature

Screening shotgun-sequencing data from ancient humans covering 37,000 years of Eurasian history uncovers the widespread presence of ancient bacterial, viral and parasite DNA and zoonotic pathogens coi...

www.nature.com

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Reposted by Nikolay Oskolkov

ICP2026 Stockholm @palaeogenomics.bsky.social · May 27

The FIRST International Conference on Palaeogenomics will happen in Stockholm, Sweden, June 23-26, 2026!

Topics will encompass all corners of ancient DNA research, from humans to wildlife and sediments🧬🦣💀🦠

Save the dates ✅

Check the website icp2026.palaeogenomics.org and follow us for updates!

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Nikolay Oskolkov @oskolkov.bsky.social · Aug 8

Last day to apply for a postdoc position in my metabolic research group:

euraxess.ec.europa.eu/jobs/358375
euraxess.ec.europa.eu/jobs/358370

Postdoctoral Researcher of Metabolic Research Group

Latvian Institute of Organic Synthesis (LIOS) - the leading drug discovery centre in the Baltic countries is offering One permanent position of principal investigator /PostDoc of Metabolic Research Gr...

euraxess.ec.europa.eu

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Nikolay Oskolkov @oskolkov.bsky.social · Aug 5

Please RT, two open postdoc positions in my metabolic research group:

euraxess.ec.europa.eu/jobs/358375
euraxess.ec.europa.eu/jobs/358370

Postdoctoral Researcher of Metabolic Research Group

Latvian Institute of Organic Synthesis (LIOS) - the leading drug discovery centre in the Baltic countries is offering One permanent position of principal investigator /PostDoc of Metabolic Research Gr...

euraxess.ec.europa.eu

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Reposted by Nikolay Oskolkov

Physalia-courses@Online @physaliacourses.bsky.social · Jul 31

We want to inform you that the Physalia online course with @oskolkov.bsky.social "AI for Genomics: From CNNs and LSTMs to Transformers" (9–11 September) is almost full.

If interested, we recommend registering as soon as possible to secure your spot.
www.physalia-courses.org/courses-work...

AI for Genomics: From CNNs and LSTMs to Transformers

9-11 September 2025 To foster international participation, this course will be held online

www.physalia-courses.org

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Reposted by Nikolay Oskolkov

J. Camilo Chacón-Duque @jcchacond.bsky.social · Jul 24

Definitely recommend working with Nikolay, great opportunity in Riga.

Nikolay Oskolkov @oskolkov.bsky.social · Jul 18

I am starting a computational lab at LIOS, Riga, Latvia, and going to recruit a few people. Please DM if you are interested in a postdoc or PhD position in my Metabolic Research Group within the TARGETWISE project. I can highly recommend Riga, it is a beautiful city with very good living conditions.

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Reposted by Nikolay Oskolkov

Torsten Günther @trstngnthr.bsky.social · Jul 24

Nikolay is starting his own lab. Sad to see him leave Sweden but looking forward to the innovative stuff that will come out of his new group. He has several positions available ⬇️

Nikolay Oskolkov @oskolkov.bsky.social · Jul 18

I am starting a computational lab at LIOS, Riga, Latvia, and going to recruit a few people. Please DM if you are interested in a postdoc or PhD position in my Metabolic Research Group within the TARGETWISE project. I can highly recommend Riga, it is a beautiful city with very good living conditions.

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Reposted by Nikolay Oskolkov

Elin Videvall @elinvidevall.bsky.social · Jul 23

Consider joining Nikolay's lab! 🎉 He's a brilliant researcher and bioinformatician!

Nikolay Oskolkov @oskolkov.bsky.social · Jul 18

I am starting a computational lab at LIOS, Riga, Latvia, and going to recruit a few people. Please DM if you are interested in a postdoc or PhD position in my Metabolic Research Group within the TARGETWISE project. I can highly recommend Riga, it is a beautiful city with very good living conditions.

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Reposted by Nikolay Oskolkov

Katerina Guschanski @kguschan.bsky.social · Jul 23

Positions open with one of the best people in the field, who developed tools that are now standard in #aDNA #ancient #metagenomics! Don’t miss this chance.

Nikolay Oskolkov @oskolkov.bsky.social · Jul 18

I am starting a computational lab at LIOS, Riga, Latvia, and going to recruit a few people. Please DM if you are interested in a postdoc or PhD position in my Metabolic Research Group within the TARGETWISE project. I can highly recommend Riga, it is a beautiful city with very good living conditions.

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Reposted by Nikolay Oskolkov

Biancamaria Bonucci @bbonucci.bsky.social · Jul 23

Go check out @oskolkov.bsky.social project and research if you are interested in working with a great scientist (and in a beautiful city 🇱🇻) ⬇️⬇️

Nikolay Oskolkov @oskolkov.bsky.social · Jul 18

I am starting a computational lab at LIOS, Riga, Latvia, and going to recruit a few people. Please DM if you are interested in a postdoc or PhD position in my Metabolic Research Group within the TARGETWISE project. I can highly recommend Riga, it is a beautiful city with very good living conditions.

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Reposted by Nikolay Oskolkov

Andrea Quagliariello @microquaglia.bsky.social · Jul 23

I strongly recommend considering this opportunity to work with a great scientist and friend in an exceptional place.

Nikolay Oskolkov @oskolkov.bsky.social · Jul 18

I am starting a computational lab at LIOS, Riga, Latvia, and going to recruit a few people. Please DM if you are interested in a postdoc or PhD position in my Metabolic Research Group within the TARGETWISE project. I can highly recommend Riga, it is a beautiful city with very good living conditions.

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Nikolay Oskolkov @oskolkov.bsky.social · Jul 18

I am starting a computational lab at LIOS, Riga, Latvia, and going to recruit a few people. Please DM if you are interested in a postdoc or PhD position in my Metabolic Research Group within the TARGETWISE project. I can highly recommend Riga, it is a beautiful city with very good living conditions.

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Reposted by Nikolay Oskolkov

Maria Lopopolo @marialopopolo.bsky.social · Jul 15

Don't miss our #SPAAMTisch seminar given by John Tay on "Bayesian Phylogenetic Methods for Microbial Pathogens" here is the link to follow the talk **TODAY** at **4pm CET**

Join Zoom Meeting
ut-ee.zoom.us/j/94984441034?…

Meeting ID: 949 8444 1034
Passcode: 986313

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