Yasin Kaya
@ysnky.bsky.social
Bioinformatician, PhD Candidate | Evolutionary genomics of structural variation and local adaptation in 🌱 Hancock Lab | @mpipz.bsky.social | https://github.com/yykaya
Reposted by Yasin Kaya
🌎👩🔬 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 Yasin Kaya
Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!
July 17, 2025 at 7:53 AM
Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!
Reposted by Yasin Kaya
Two research highlights and three full papers about NLR-mediated resistance in wheat. Plant research is taking over @natgenet.nature.com !
💫The June issue of @natgenet.nature.com is live!
Featuring:
✅APOBEC3 mutagenesis in #breastcancer
✅GWAS of long #COVID
✅snRNA gene mutations in neurodevelopmental disorders
✅NLR genes in wheat resistance to pathogens
And much more!
⬇️
www.nature.com/ng/volumes/5...
Featuring:
✅APOBEC3 mutagenesis in #breastcancer
✅GWAS of long #COVID
✅snRNA gene mutations in neurodevelopmental disorders
✅NLR genes in wheat resistance to pathogens
And much more!
⬇️
www.nature.com/ng/volumes/5...
June 17, 2025 at 5:17 PM
Two research highlights and three full papers about NLR-mediated resistance in wheat. Plant research is taking over @natgenet.nature.com !
Reposted by Yasin Kaya
Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment.
arxiv.org/abs/2506.12986
arxiv.org/abs/2506.12986
June 17, 2025 at 1:49 AM
Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment.
arxiv.org/abs/2506.12986
arxiv.org/abs/2506.12986
Reposted by Yasin Kaya
The TAIR12 genome reannotation has FINALLY been submitted to GenBank. Now we await review and approval. Stay tuned for updates, hopefully within the next month. Thank you to everyone that made this project possible. @labschneeberger.bsky.social @bar-plantbio.bsky.social @sigmafacto.bsky.social
May 6, 2025 at 7:18 PM
The TAIR12 genome reannotation has FINALLY been submitted to GenBank. Now we await review and approval. Stay tuned for updates, hopefully within the next month. Thank you to everyone that made this project possible. @labschneeberger.bsky.social @bar-plantbio.bsky.social @sigmafacto.bsky.social
Reposted by Yasin Kaya
#PacBio expands HiFi methylation detection with new deep learning models from CUHK: 5hmC, hemimethylated 5mC, 6mA - no added cost, no new prep. Hear more at our #AACR25 workshop today.
🔗 bit.ly/4jNCnHT
#HiFisequencing
🔗 bit.ly/4jNCnHT
#HiFisequencing
April 28, 2025 at 2:54 PM
#PacBio expands HiFi methylation detection with new deep learning models from CUHK: 5hmC, hemimethylated 5mC, 6mA - no added cost, no new prep. Hear more at our #AACR25 workshop today.
🔗 bit.ly/4jNCnHT
#HiFisequencing
🔗 bit.ly/4jNCnHT
#HiFisequencing
Reposted by Yasin Kaya
Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...
Efficient near telomere-to-telomere assembly of Nanopore Simplex reads
Telomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms capable of near T2T assembly all require Oxford Nanopore Technologies (ONT) ultra-long reads w...
www.biorxiv.org
April 18, 2025 at 9:54 PM
Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...
Reposted by Yasin Kaya
📣Paper Alert! 📣New publication out @nature.com by @labschneeberger.bsky.social @mpipz.bsky.social and @lmumuenchen.bsky.social on the genome reconstruction of historic potato cultivars. 👏🌿🥔 Congratulations! 🥳👏Learn more 👉 bit.ly/3GeGcGX
www.nature.com/articles/s41...
www.nature.com/articles/s41...
The phased pan-genome of tetraploid European potato - Nature
A haplotype-resolved pan-genome of autotetraploid European potato founder lines shows high nucleotide diversity at remarkably low haplotype diversity, which is probably the result of hybridization eve...
www.nature.com
April 17, 2025 at 1:32 PM
📣Paper Alert! 📣New publication out @nature.com by @labschneeberger.bsky.social @mpipz.bsky.social and @lmumuenchen.bsky.social on the genome reconstruction of historic potato cultivars. 👏🌿🥔 Congratulations! 🥳👏Learn more 👉 bit.ly/3GeGcGX
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Yasin Kaya
📣Paper Alert! New publication @science.org by the group of @tonnigrubeandersen.bsky.social @mpipz.bsky.social, colleagues @ucph.bsky.social & others on the Casparian strip and its role in metabolic trade between plants & bacteria. 👏Learn more 👉https://bit.ly/4bJe4Yd
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Apoplastic barriers are essential for nodule formation and nitrogen fixation in Lotus japonicus
Establishment of the apoplastic root barrier known as the Casparian strip occurs early in root development. In legumes, this area overlaps with nitrogen-fixing nodule formation, which raises the possi...
www.science.org
March 21, 2025 at 9:52 AM
📣Paper Alert! New publication @science.org by the group of @tonnigrubeandersen.bsky.social @mpipz.bsky.social, colleagues @ucph.bsky.social & others on the Casparian strip and its role in metabolic trade between plants & bacteria. 👏Learn more 👉https://bit.ly/4bJe4Yd
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Yasin Kaya
The #CologneSpringMeeting poster session featured over 70 presentations, fostering a vibrant social and networking atmosphere. Great discussions, new connections, and inspiring science all around!
March 19, 2025 at 7:24 PM
The #CologneSpringMeeting poster session featured over 70 presentations, fostering a vibrant social and networking atmosphere. Great discussions, new connections, and inspiring science all around!
Reposted by Yasin Kaya
Cologne Spring Meeting starts with “Plant Ecological Genetics: From Lab to Nature and Back” talk by @meauxjuliette.bsky.social Exploring the bridge between laboratory insights and real-world plant ecology. #EcologicalGenetics #PlantScience
March 18, 2025 at 9:23 AM
Cologne Spring Meeting starts with “Plant Ecological Genetics: From Lab to Nature and Back” talk by @meauxjuliette.bsky.social Exploring the bridge between laboratory insights and real-world plant ecology. #EcologicalGenetics #PlantScience
Reposted by Yasin Kaya
Join the “PhD Career Perspectives Event” at the Cologne Spring Meeting 2025, March 17th at 17:00!
Speakers:
👩🔬 Dr. Dorit Grundewald, Scientific Coordinator, Food Security Network
💡 Christina Kothes M.Sc., Innovation Manager, Institute for Plant Sciences
📍 MTI-Building (44b), Joseph-Stelzmann-Str. 9
Speakers:
👩🔬 Dr. Dorit Grundewald, Scientific Coordinator, Food Security Network
💡 Christina Kothes M.Sc., Innovation Manager, Institute for Plant Sciences
📍 MTI-Building (44b), Joseph-Stelzmann-Str. 9
March 16, 2025 at 12:01 PM
Join the “PhD Career Perspectives Event” at the Cologne Spring Meeting 2025, March 17th at 17:00!
Speakers:
👩🔬 Dr. Dorit Grundewald, Scientific Coordinator, Food Security Network
💡 Christina Kothes M.Sc., Innovation Manager, Institute for Plant Sciences
📍 MTI-Building (44b), Joseph-Stelzmann-Str. 9
Speakers:
👩🔬 Dr. Dorit Grundewald, Scientific Coordinator, Food Security Network
💡 Christina Kothes M.Sc., Innovation Manager, Institute for Plant Sciences
📍 MTI-Building (44b), Joseph-Stelzmann-Str. 9
Reposted by Yasin Kaya
March 5, 2025 at 5:43 PM
Reposted by Yasin Kaya
Today we celebrate a wide diversity in plant sciences at the Symposium of our institute at @unicologne.bsky.social with support from @ceplas.bsky.social & @trr341.bsky.social #PlantScience
February 20, 2025 at 8:18 AM
Today we celebrate a wide diversity in plant sciences at the Symposium of our institute at @unicologne.bsky.social with support from @ceplas.bsky.social & @trr341.bsky.social #PlantScience
Reposted by Yasin Kaya
Centrophilic Retrotransposons of Plant Genomes
www.annualreviews.org/content/jour...
new review @annualreviews.bsky.social from @abousios.bsky.social, Tetsuji Kakutani, and myself on my favourite type of mobile genetic element
www.annualreviews.org/content/jour...
new review @annualreviews.bsky.social from @abousios.bsky.social, Tetsuji Kakutani, and myself on my favourite type of mobile genetic element
Centrophilic Retrotransposons of Plant Genomes | Annual Reviews
The centromeres of eukaryotic chromosomes are required to load CENH3/CENP-A variant nucleosomes and the kinetochore complex, which connects to spindle microtubules during cell division. Despite their ...
www.annualreviews.org
February 18, 2025 at 11:20 AM
Centrophilic Retrotransposons of Plant Genomes
www.annualreviews.org/content/jour...
new review @annualreviews.bsky.social from @abousios.bsky.social, Tetsuji Kakutani, and myself on my favourite type of mobile genetic element
www.annualreviews.org/content/jour...
new review @annualreviews.bsky.social from @abousios.bsky.social, Tetsuji Kakutani, and myself on my favourite type of mobile genetic element
Reposted by Yasin Kaya
No job ad yet, but I'll be hiring a postdoc at Purdue in population genetics/quantitative genetics/genomics in plants. DM if you have relevant experience and are potentially interested.
February 15, 2025 at 4:07 PM
No job ad yet, but I'll be hiring a postdoc at Purdue in population genetics/quantitative genetics/genomics in plants. DM if you have relevant experience and are potentially interested.
Reposted by Yasin Kaya
We made it 😀 - excited to share our latest research and engage with this vibrant community here at Bluesky 🌿🪴
February 10, 2025 at 3:02 PM
We made it 😀 - excited to share our latest research and engage with this vibrant community here at Bluesky 🌿🪴
Reposted by Yasin Kaya
New Resource: "Transposon proliferation drives genome architecture and regulatory evolution in wild and domesticated peppers" rdcu.be/d7YSt
11 genomes of wild and domesticated pepper: transposable elements have shaped the evolution of genome structure.
11 genomes of wild and domesticated pepper: transposable elements have shaped the evolution of genome structure.
January 29, 2025 at 11:34 PM
New Resource: "Transposon proliferation drives genome architecture and regulatory evolution in wild and domesticated peppers" rdcu.be/d7YSt
11 genomes of wild and domesticated pepper: transposable elements have shaped the evolution of genome structure.
11 genomes of wild and domesticated pepper: transposable elements have shaped the evolution of genome structure.
Reposted by Yasin Kaya
New Article: "Convergent reduction of immune receptor repertoires during plant adaptation to diverse special lifestyles and habitats" rdcu.be/d6uFq
A survey of plant immune receptor repertoires in 808 angiosperm genomes. #PlantScience
A survey of plant immune receptor repertoires in 808 angiosperm genomes. #PlantScience
January 16, 2025 at 5:57 PM
New Article: "Convergent reduction of immune receptor repertoires during plant adaptation to diverse special lifestyles and habitats" rdcu.be/d6uFq
A survey of plant immune receptor repertoires in 808 angiosperm genomes. #PlantScience
A survey of plant immune receptor repertoires in 808 angiosperm genomes. #PlantScience