GitHub - NikolayOskolkov/MCWorkflow
Contribute to NikolayOskolkov/MCWorkflow development by creating an account on GitHub.
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...
04.10.2025 09:21 — 👍 1 🔁 0 💬 1 📌 0
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=...
04.10.2025 09:20 — 👍 11 🔁 3 💬 2 📌 0
Only 1 seat left @oskolkov.bsky.social
22.09.2025 12:26 — 👍 2 🔁 2 💬 0 📌 0
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
11.09.2025 12:49 — 👍 5 🔁 1 💬 0 📌 0
🚀 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!
09.09.2025 12:35 — 👍 1 🔁 1 💬 0 📌 0
Nature discusses our article on mammoth microbiome www.nature.com/articles/d41...
04.09.2025 05:12 — 👍 3 🔁 0 💬 0 📌 0
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...
03.09.2025 03:49 — 👍 16 🔁 3 💬 1 📌 0
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!
27.05.2025 08:48 — 👍 79 🔁 49 💬 0 📌 4
AI for Genomics: From CNNs and LSTMs to Transformers
9-11 September 2025 To foster international participation, this course will be held online
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...
31.07.2025 15:23 — 👍 2 🔁 2 💬 0 📌 0
Definitely recommend working with Nikolay, great opportunity in Riga.
24.07.2025 21:25 — 👍 1 🔁 1 💬 0 📌 0
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 ⬇️
24.07.2025 09:02 — 👍 3 🔁 1 💬 0 📌 0
Consider joining Nikolay's lab! 🎉 He's a brilliant researcher and bioinformatician!
23.07.2025 19:11 — 👍 2 🔁 1 💬 0 📌 0
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.
23.07.2025 18:53 — 👍 6 🔁 2 💬 0 📌 0
Go check out @oskolkov.bsky.social project and research if you are interested in working with a great scientist (and in a beautiful city 🇱🇻) ⬇️⬇️
23.07.2025 17:14 — 👍 2 🔁 1 💬 0 📌 0
I strongly recommend considering this opportunity to work with a great scientist and friend in an exceptional place.
23.07.2025 17:01 — 👍 1 🔁 1 💬 0 📌 0
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.
18.07.2025 09:03 — 👍 35 🔁 30 💬 0 📌 7
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
15.07.2025 05:01 — 👍 3 🔁 1 💬 0 📌 0
Our paper on ancient infectious diseases in Eurasia is out in Nature. Congratulations Martin Sikora, Eske Willerslev and all the co-authors!
10.07.2025 04:49 — 👍 2 🔁 0 💬 0 📌 0
Everyone is very welcome to join, looking forward!
08.07.2025 14:00 — 👍 2 🔁 0 💬 0 📌 0
🚨 Join us for the Environmental Metagenomics course (Oct 13–17, online) with @oskolkov.bsky.social & @aroneys.bsky.social !
🔬 Hands-on training on read-based & assembly-based methods, MAGs, and integrating short & long-read @nanoporetech.com data.
shorturl.at/HOm6X
30.06.2025 13:21 — 👍 10 🔁 6 💬 0 📌 1
Teaching stats and machine learning at #RaukR is always fun, thanks everyone for the great discussion!
19.06.2025 13:30 — 👍 3 🔁 0 💬 1 📌 0
The #OpenScience journal from BGI & OUP publishing articles using/generating large datasets. And linked to GigaDB #opendata hosting/analysis repository.
Website: http://gigasciencejournal.com
Conservation genetics & population genomics of tropical island populations, occasionally ancient DNA, phylogenetics, biogeography, & biodiversity informatics, mostly mammals 🐗🐂. She/her. 🇲🇨. X/Twitter previously sagitaninta.
geoarchaeolgist interested in human evolution, fire, ancient dna and most of all dirt
Scientific Officer (Biodiversity Genomics) @ Research Centre for Ecosystem Resilience, Botanic Gardens of Sydney 🌱.
Palaeogenomics | Population Genomics
Currently in 🇦🇺, previously in 🇳🇿🇸🇪
Scientist living in Germany. Two^H^H^H Three loud kids, population genetics, sediment DNA, Neandertals, beer, whiskey, non-German food. Group leader @ MPI EVA
My lab studies wild animal microbiomes at Uppsala University, Sweden. Previously been at Brown University & Smithsonian. Molecular Ecology, Evolutionary Biology, Genomics, Hologenomics, Conservation Biology. she/her. https://www.videvall.com/
Population Genetics and aDNA of domestic and wild animals at LMU. Studying domestication processes and ancient sheep. I also love swords.
Spanish and English
ESPRIT FWF Project Leader/Senior Postdoctoral Researcher University of Vienna - Ancient DNA - Microbial Genomics, Metagenomics & Pathogen Evolution 💀🧬🦠
Asst. Prof. and DDLS fellow
Dept. Zoology, Stockholm University and SciLifeLab
🇦🇷 -> 🇫🇮 -> 🇸🇪
Evo-devo and dynamical systems
https://lisandromilocco.github.io/
Passionate about human diversity, travelling and colours.
GenEpi Senior Research Fellow at the University of Leicester
Writing modeling packages at @posit.co (née RStudio). Opinions are my own. https://max-kuhn.org/
Associate Professor in Cancer Data Science at iCAN, University of Helsinki, Group leader in Computational Biology and Systems Medicine at NCMBM, University of Oslo. Research focus on precision network medicine in cancer.
Postdoc at Globe, UCPH - all things bioinformatics for ancient environmental DNA 🦴👩🏼💻 🏳️🌈🦭
PhD student
University of Lausanne (UNIL)
Swiss Institute of Bioinformatics (SIB)
Research focus: ancient DNA🧬, metagenomics and pathogens evolution🦠
MVIF President @microbiomevif.bsky.social
Sr. PM at PreBiomics on oral microbiome
Scientific Advisor
previously @cibiocm.bsky.social
Asking bioarchaeological Qs using skeletal remains 🦴 and the genomes 🧬 they harbor 🦠 Formerly @StoneLab_ASU | Currently @WhatIsInAHouse postdoc | she/her
UTA > UNTHSC (MSc) > Max Planck SHH (PhD) > Institut Pasteur Postdoc > SMU Assistant Prof and director of the Modern and Ancient Microbial Genomics labs.
PhD student
@edinburgh-uni.bsky.social
(via 🇬🇷 🇸🇪 🇵🇹 🇹🇹 🇪🇸) studying oral microbiome evolution using museum specimens 💀
#evolution #museomics #microbiome #genomics
