@plantgenomics.bsky.social
Reposted
It's been awhile, but I found myself recommending to someone today our groundbreaking code, lead by the inimitable Andy Kern, that magically converts pdfs to... pdfs. This solves the conversion issue so many journals pose to the intrepid scientist. github.com/andrewkern/p...
GitHub - andrewkern/pdf2pdf: does the magical pdf-to-pdf conversion popular in academic journal submission sites and does it faster than they do
does the magical pdf-to-pdf conversion popular in academic journal submission sites and does it faster than they do - andrewkern/pdf2pdf
github.com
November 26, 2025 at 12:29 AM
It's been awhile, but I found myself recommending to someone today our groundbreaking code, lead by the inimitable Andy Kern, that magically converts pdfs to... pdfs. This solves the conversion issue so many journals pose to the intrepid scientist. github.com/andrewkern/p...
Reposted
Acer glabrum, our Rocky Mountain Maple, blooming on the Mesa Trail #nativeplants
#FallBackFlowers #FallBack to May 25 🌿
Nobody notices maple flowers, now you have 😎
#FallBackFlowers #FallBack to May 25 🌿
Nobody notices maple flowers, now you have 😎
November 26, 2025 at 1:05 AM
Acer glabrum, our Rocky Mountain Maple, blooming on the Mesa Trail #nativeplants
#FallBackFlowers #FallBack to May 25 🌿
Nobody notices maple flowers, now you have 😎
#FallBackFlowers #FallBack to May 25 🌿
Nobody notices maple flowers, now you have 😎
Reposted
corn. paint and crayon by my daughter several years ago. love this, hanging in my office
November 26, 2025 at 1:13 AM
corn. paint and crayon by my daughter several years ago. love this, hanging in my office
CLCNet: a contrastive learning and chromosome-aware network for genomic prediction in plants
doi.org/10.1101/2024...
Genomic characterization of a nematode tolerance locus in sugar beet
doi.org/10.1101/2023...
doi.org/10.1101/2024...
Genomic characterization of a nematode tolerance locus in sugar beet
doi.org/10.1101/2023...
CLCNet: a contrastive learning and chromosome-aware network for genomic prediction in plants
Genomic selection (GS), which integrates genomic markers with phenotypic data, has emerged as a powerful breeding strategy for predicting phenotypes and estimating breeding values in candidate populat...
doi.org
November 26, 2025 at 5:31 AM
CLCNet: a contrastive learning and chromosome-aware network for genomic prediction in plants
doi.org/10.1101/2024...
Genomic characterization of a nematode tolerance locus in sugar beet
doi.org/10.1101/2023...
doi.org/10.1101/2024...
Genomic characterization of a nematode tolerance locus in sugar beet
doi.org/10.1101/2023...
Genome sequence of the ornamental plant Digitalis purpurea reveals the molecular basis of flower color and morphology variation
doi.org/10.1101/2024...
doi.org/10.1101/2024...
Genome sequence of the ornamental plant Digitalis purpurea reveals the molecular basis of flower color and morphology variation
Digitalis purpurea (foxglove) is a widely distributed ornamental plant and the producer of the biomedical compound digoxin. Here, we present a long read sequencing-based genome sequence of a magenta f...
doi.org
November 26, 2025 at 5:30 AM
Genome sequence of the ornamental plant Digitalis purpurea reveals the molecular basis of flower color and morphology variation
doi.org/10.1101/2024...
doi.org/10.1101/2024...
Reposted
"If the data is accurate...it would call into question the business model of OpenAI and nearly every other general-purpose LLM vendor" www.ft.com/content/fce7...
How high are OpenAI’s compute costs? Possibly a lot higher than we thought
Inference inferred, revenue reconstructed, cash burn quantified
www.ft.com
November 22, 2025 at 2:13 PM
"If the data is accurate...it would call into question the business model of OpenAI and nearly every other general-purpose LLM vendor" www.ft.com/content/fce7...
Genome and transcriptome of haustorial development in Pedicularis groenlandica reveal diverse trajectories of haustoria-associated gene evolution in parasitic plants
doi.org/10.1101/2025...
Cookbook for Plant Genome Sequences
www.preprints.org/manuscript/2...
#Genomics #PlantSci
doi.org/10.1101/2025...
Cookbook for Plant Genome Sequences
www.preprints.org/manuscript/2...
#Genomics #PlantSci
A reference genome and transcriptome of haustorial development in Pedicularis groenlandica reveal diverse trajectories of haustoria-associated gene evolution in parasitic plants
Novel traits frequently evolve by co-opting existing genetic pathways through direct repurposing of existing genes or neofunctionalization of duplicated genes. Parasitism represents a major innovation...
doi.org
November 23, 2025 at 8:41 AM
Genome and transcriptome of haustorial development in Pedicularis groenlandica reveal diverse trajectories of haustoria-associated gene evolution in parasitic plants
doi.org/10.1101/2025...
Cookbook for Plant Genome Sequences
www.preprints.org/manuscript/2...
#Genomics #PlantSci
doi.org/10.1101/2025...
Cookbook for Plant Genome Sequences
www.preprints.org/manuscript/2...
#Genomics #PlantSci
AlterNet: Alternative splicing-aware gene regulatory network inference
doi.org/10.1101/2025...
Animal, fungi, and plant genome sequences harbour different non-canonical splice sites
doi.org/10.1101/616565
doi.org/10.1101/2025...
Animal, fungi, and plant genome sequences harbour different non-canonical splice sites
doi.org/10.1101/616565
AlterNet: Alternative splicing-aware gene regulatory network inference
Abstract. Gene regulatory networks (GRNs) help decode biological systems by identifying how genes interact and regulate cellular processes. However, conventional GRN inference methods operate at the g...
doi.org
November 23, 2025 at 8:37 AM
AlterNet: Alternative splicing-aware gene regulatory network inference
doi.org/10.1101/2025...
Animal, fungi, and plant genome sequences harbour different non-canonical splice sites
doi.org/10.1101/616565
doi.org/10.1101/2025...
Animal, fungi, and plant genome sequences harbour different non-canonical splice sites
doi.org/10.1101/616565
Reposted
Updated our P2 output summary! 📊
Even with strong variation between flow cells, we are seeing an average yield of ~80 Gbp.
Huge thanks to Julie for the sequencing work.
More details: www.izmb.uni-bonn.de/en/pbb/news#...
#Genomics #LongReads #OpenScience
Even with strong variation between flow cells, we are seeing an average yield of ~80 Gbp.
Huge thanks to Julie for the sequencing work.
More details: www.izmb.uni-bonn.de/en/pbb/news#...
#Genomics #LongReads #OpenScience
November 22, 2025 at 9:52 AM
Updated our P2 output summary! 📊
Even with strong variation between flow cells, we are seeing an average yield of ~80 Gbp.
Huge thanks to Julie for the sequencing work.
More details: www.izmb.uni-bonn.de/en/pbb/news#...
#Genomics #LongReads #OpenScience
Even with strong variation between flow cells, we are seeing an average yield of ~80 Gbp.
Huge thanks to Julie for the sequencing work.
More details: www.izmb.uni-bonn.de/en/pbb/news#...
#Genomics #LongReads #OpenScience
Reposted
Yesterday, Nancy shared her Cucurbitaceae anthocyanin loss story with colleagues at our institute. Comprehensive talk highlighting the most striking discoveries. Please find the full story here:
doi.org/10.1101/2025...
#PlantSci #Evolution
doi.org/10.1101/2025...
#PlantSci #Evolution
November 5, 2025 at 6:05 AM
Yesterday, Nancy shared her Cucurbitaceae anthocyanin loss story with colleagues at our institute. Comprehensive talk highlighting the most striking discoveries. Please find the full story here:
doi.org/10.1101/2025...
#PlantSci #Evolution
doi.org/10.1101/2025...
#PlantSci #Evolution
Reposted
After 10 Fridays, 10 flowers, and 100+ drawings, the Florédex is complete! ✨
Come take a tour of the design and science behind 10 iconic flowers 🌺🧵
Come take a tour of the design and science behind 10 iconic flowers 🌺🧵
November 21, 2025 at 9:59 AM
After 10 Fridays, 10 flowers, and 100+ drawings, the Florédex is complete! ✨
Come take a tour of the design and science behind 10 iconic flowers 🌺🧵
Come take a tour of the design and science behind 10 iconic flowers 🌺🧵
Reposted
Read the article here: https://learndirt.com/learn/dwarf-blue-curled-kale/
November 21, 2025 at 9:00 PM
Read the article here: https://learndirt.com/learn/dwarf-blue-curled-kale/
Reposted
Pediocactus simpsonii, our Mountain Ball Cactus, blooming above the infamous failed Chimney Rock Dam #nativeplants
#FallbackFlowers #Fallback to May 21 🌿
#FallbackFlowers #Fallback to May 21 🌿
November 21, 2025 at 7:07 PM
Pediocactus simpsonii, our Mountain Ball Cactus, blooming above the infamous failed Chimney Rock Dam #nativeplants
#FallbackFlowers #Fallback to May 21 🌿
#FallbackFlowers #Fallback to May 21 🌿
Reposted
Had a great day visiting Michigan State and looking forward to another tomorrow at Kellogg Biological Station! Thanks Morgan Clark for the seminar art! 👌🏻
November 21, 2025 at 2:22 AM
Had a great day visiting Michigan State and looking forward to another tomorrow at Kellogg Biological Station! Thanks Morgan Clark for the seminar art! 👌🏻
Reposted
Anyone have a csv of the Kew C-Value database? I want to remake this figure but looks like website won't let me just download all values anymore. cvalues.science.kew.org/search/angio...
November 21, 2025 at 4:29 AM
Anyone have a csv of the Kew C-Value database? I want to remake this figure but looks like website won't let me just download all values anymore. cvalues.science.kew.org/search/angio...
IRCAS: a novel end-to-end approach to identify, rectify and classify comprehensive alternative splicing events in a transcriptome without genome reference
doi.org/10.1101/2025...
Animal, fungi, and plant genome sequences harbour different non-canonical splice sites
doi.org/10.1101/616565
doi.org/10.1101/2025...
Animal, fungi, and plant genome sequences harbour different non-canonical splice sites
doi.org/10.1101/616565
IRCAS: a novel end-to-end approach to identify, rectify and classify comprehensive alternative splicing events in a transcriptome without genome reference
Alternative splicing (AS) is a fundamental post-transcriptional mechanism that amplifies proteomic diversity and enables adaptive responses across eukaryotes. Current AS detection methods rely heavily...
doi.org
November 21, 2025 at 5:12 AM
IRCAS: a novel end-to-end approach to identify, rectify and classify comprehensive alternative splicing events in a transcriptome without genome reference
doi.org/10.1101/2025...
Animal, fungi, and plant genome sequences harbour different non-canonical splice sites
doi.org/10.1101/616565
doi.org/10.1101/2025...
Animal, fungi, and plant genome sequences harbour different non-canonical splice sites
doi.org/10.1101/616565
A deep learning model captures position-specific effects of plant regulatory sequences and suggests genes under complex regulation
doi.org/10.1101/2025...
NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction
doi.org/10.1101/596718
doi.org/10.1101/2025...
NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction
doi.org/10.1101/596718
A deep learning model captures position-specific effects of plant regulatory sequences and suggests genes under complex regulation
Deep neural networks can be trained to predict gene expression directly from genomic sequence, thereby implicitly learning regulatory sequence patterns from scratch, minimizing the bias imposed by pri...
doi.org
November 20, 2025 at 5:39 AM
A deep learning model captures position-specific effects of plant regulatory sequences and suggests genes under complex regulation
doi.org/10.1101/2025...
NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction
doi.org/10.1101/596718
doi.org/10.1101/2025...
NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction
doi.org/10.1101/596718
PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms
doi.org/10.1101/2025...
KIPEs3: Automatic annotation of biosynthesis pathways
doi.org/10.1101/2022...
#Bioinformatics #Genomics #FunctionalAnnotation
doi.org/10.1101/2025...
KIPEs3: Automatic annotation of biosynthesis pathways
doi.org/10.1101/2022...
#Bioinformatics #Genomics #FunctionalAnnotation
PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms
Understanding how DNA sequence encodes biological function remains a fundamental challenge in biology. Flowering plants (angiosperms), the dominant terrestrial clade, exhibit maximal biochemical compl...
doi.org
November 20, 2025 at 5:38 AM
PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms
doi.org/10.1101/2025...
KIPEs3: Automatic annotation of biosynthesis pathways
doi.org/10.1101/2022...
#Bioinformatics #Genomics #FunctionalAnnotation
doi.org/10.1101/2025...
KIPEs3: Automatic annotation of biosynthesis pathways
doi.org/10.1101/2022...
#Bioinformatics #Genomics #FunctionalAnnotation
Reposted
Getting ready for our #PlantGenomics courses! 🌱🔬
The course is almost full, so check out the details soon if you want to join and learn about the power of long-read sequencing and cloud-based data analysis.
Feel free to spread the word!
👉 www.izmb.uni-bonn.de/en/pbb/news#...
@puckerlab.bsky.social
The course is almost full, so check out the details soon if you want to join and learn about the power of long-read sequencing and cloud-based data analysis.
Feel free to spread the word!
👉 www.izmb.uni-bonn.de/en/pbb/news#...
@puckerlab.bsky.social
November 19, 2025 at 6:01 AM
Getting ready for our #PlantGenomics courses! 🌱🔬
The course is almost full, so check out the details soon if you want to join and learn about the power of long-read sequencing and cloud-based data analysis.
Feel free to spread the word!
👉 www.izmb.uni-bonn.de/en/pbb/news#...
@puckerlab.bsky.social
The course is almost full, so check out the details soon if you want to join and learn about the power of long-read sequencing and cloud-based data analysis.
Feel free to spread the word!
👉 www.izmb.uni-bonn.de/en/pbb/news#...
@puckerlab.bsky.social
Benchmarking the impact of reference genome selection on taxonomic profiling accuracy
doi.org/10.1101/2025...
Cookbook for Plant Genome Sequences
www.preprints.org/manuscript/2...
doi.org/10.1101/2025...
Cookbook for Plant Genome Sequences
www.preprints.org/manuscript/2...
doi.org
November 19, 2025 at 5:01 AM
Benchmarking the impact of reference genome selection on taxonomic profiling accuracy
doi.org/10.1101/2025...
Cookbook for Plant Genome Sequences
www.preprints.org/manuscript/2...
doi.org/10.1101/2025...
Cookbook for Plant Genome Sequences
www.preprints.org/manuscript/2...
Reposted
"Postdoctoral Researcher, Plant Genetics and Cell Wall Biology at University of Helsinki, Helsinki, Finland
*Application Deadline: 12/15/2025"
Read more here: https://jobs.helsinki.fi/job/Helsinki-Postdoctoral-Researcher-in-Plant-Genetics-and-Cell-Wall-Biology/1332229757
#PlantSciJobs
*Application Deadline: 12/15/2025"
Read more here: https://jobs.helsinki.fi/job/Helsinki-Postdoctoral-Researcher-in-Plant-Genetics-and-Cell-Wall-Biology/1332229757
#PlantSciJobs
November 19, 2025 at 1:51 AM
"Postdoctoral Researcher, Plant Genetics and Cell Wall Biology at University of Helsinki, Helsinki, Finland
*Application Deadline: 12/15/2025"
Read more here: https://jobs.helsinki.fi/job/Helsinki-Postdoctoral-Researcher-in-Plant-Genetics-and-Cell-Wall-Biology/1332229757
#PlantSciJobs
*Application Deadline: 12/15/2025"
Read more here: https://jobs.helsinki.fi/job/Helsinki-Postdoctoral-Researcher-in-Plant-Genetics-and-Cell-Wall-Biology/1332229757
#PlantSciJobs
Efficient near telomere-to-telomere assembly of Nanopore Simplex reads
doi.org/10.1101/2025...
Cookbook for Plant Genome Sequences
www.preprints.org/manuscript/2...
doi.org/10.1101/2025...
Cookbook for Plant Genome Sequences
www.preprints.org/manuscript/2...
doi.org
November 19, 2025 at 4:52 AM
Efficient near telomere-to-telomere assembly of Nanopore Simplex reads
doi.org/10.1101/2025...
Cookbook for Plant Genome Sequences
www.preprints.org/manuscript/2...
doi.org/10.1101/2025...
Cookbook for Plant Genome Sequences
www.preprints.org/manuscript/2...
Reposted
Delphinium nuttallianum (Nuttall's Larkspur) blooming at Roxborough Park #nativeplants
#FallBackFlowers #FallBack to May 17 🌿
#FallBackFlowers #FallBack to May 17 🌿
November 17, 2025 at 3:05 PM
Delphinium nuttallianum (Nuttall's Larkspur) blooming at Roxborough Park #nativeplants
#FallBackFlowers #FallBack to May 17 🌿
#FallBackFlowers #FallBack to May 17 🌿
Reposted
Ribes americanum (American Black Currant) blooming at Roxborough Park #nativeplants
#FallBackFlowers #FallBack to May 17 🌿
#FallBackFlowers #FallBack to May 17 🌿
November 17, 2025 at 3:04 PM
Ribes americanum (American Black Currant) blooming at Roxborough Park #nativeplants
#FallBackFlowers #FallBack to May 17 🌿
#FallBackFlowers #FallBack to May 17 🌿
Reposted
So grapevine no different than Arabidopsis, where century-scale methylome stability was demonstrated 10 years ago...
journals.plos.org/plosgenetics...
journals.plos.org/plosgenetics...
November 18, 2025 at 9:24 PM
So grapevine no different than Arabidopsis, where century-scale methylome stability was demonstrated 10 years ago...
journals.plos.org/plosgenetics...
journals.plos.org/plosgenetics...