PCI Genomics
@genomics.peercommunityin.org
Peer Community In Genomics https://genomics.peercommunityin.org
Evaluations and recommendations of preprints in genomics; free for authors and readers.
Evaluations and recommendations of preprints in genomics; free for authors and readers.
📑 New @PCIgenomics recommendation, by @helenechiapello.bsky.social
genomics.peercommunityin.org/articles/rec...
On the work of Noé Robert et al. (2025) Evidencing strain-dependency of metabolic pathways within 1,494 lactic bacteria genomes with the in silico screening Prolipipe pipeline
#OA
genomics.peercommunityin.org/articles/rec...
On the work of Noé Robert et al. (2025) Evidencing strain-dependency of metabolic pathways within 1,494 lactic bacteria genomes with the in silico screening Prolipipe pipeline
#OA
Towards an exploration of metabolic pathways at the strain level...
Genomes from bacteria of interest to the food industry exhibit significant functional variability, yet evaluating this characteristic remains challenging. As public repositories continue to…
genomics.peercommunityin.org
November 18, 2025 at 9:01 AM
📑 New @PCIgenomics recommendation, by @helenechiapello.bsky.social
genomics.peercommunityin.org/articles/rec...
On the work of Noé Robert et al. (2025) Evidencing strain-dependency of metabolic pathways within 1,494 lactic bacteria genomes with the in silico screening Prolipipe pipeline
#OA
genomics.peercommunityin.org/articles/rec...
On the work of Noé Robert et al. (2025) Evidencing strain-dependency of metabolic pathways within 1,494 lactic bacteria genomes with the in silico screening Prolipipe pipeline
#OA
🌐 New PCI Genomics recommendation: GrAnnoT enhances annotation transfer via pangenome graphs, connecting linear and graph-based genomes. 🔬 “a valuable pangenome toolkit addition — fast, conservative, reproducible.” ➡️ genomics.peercommunityin.org/articles/rec... #Pangenome #OpenScience
GrAnnoT: Efficient annotation transfer through pangenome graphs
The increasing availability of genome sequences has highlighted the limitations of using a single reference genome to represent the diversity within a species. Pangenomes, encompassing the genomic…
genomics.peercommunityin.org
November 10, 2025 at 7:00 AM
🌐 New PCI Genomics recommendation: GrAnnoT enhances annotation transfer via pangenome graphs, connecting linear and graph-based genomes. 🔬 “a valuable pangenome toolkit addition — fast, conservative, reproducible.” ➡️ genomics.peercommunityin.org/articles/rec... #Pangenome #OpenScience
🧬 New PCI Genomics recommendation! HaploCharmer: a Snakemake workflow for read-scale haplotype calling adapted to polyploids, by Simon Rio and colleagues.
✨ Recommended by Lucia Campos Dominguez who praised its scalability for highly complex polyploids
🔗 Recommendation: doi.org/10.24072/pci...
✨ Recommended by Lucia Campos Dominguez who praised its scalability for highly complex polyploids
🔗 Recommendation: doi.org/10.24072/pci...
September 23, 2025 at 6:30 AM
🧬 New PCI Genomics recommendation! HaploCharmer: a Snakemake workflow for read-scale haplotype calling adapted to polyploids, by Simon Rio and colleagues.
✨ Recommended by Lucia Campos Dominguez who praised its scalability for highly complex polyploids
🔗 Recommendation: doi.org/10.24072/pci...
✨ Recommended by Lucia Campos Dominguez who praised its scalability for highly complex polyploids
🔗 Recommendation: doi.org/10.24072/pci...
Reposted by PCI Genomics
ICYM ASAPbio seeks new board members to support our mission of driving positive change in science communication!🚀
🤝 Board members are involved in strategic planning, participate in decision-making, and engage the community to help connect ASAPbio to contacts who can help us achieve our mission.✍️ 🔬
🤝 Board members are involved in strategic planning, participate in decision-making, and engage the community to help connect ASAPbio to contacts who can help us achieve our mission.✍️ 🔬
August 26, 2025 at 10:29 AM
ICYM ASAPbio seeks new board members to support our mission of driving positive change in science communication!🚀
🤝 Board members are involved in strategic planning, participate in decision-making, and engage the community to help connect ASAPbio to contacts who can help us achieve our mission.✍️ 🔬
🤝 Board members are involved in strategic planning, participate in decision-making, and engage the community to help connect ASAPbio to contacts who can help us achieve our mission.✍️ 🔬
Great to see this article recommended in PCI Genomics out in G3!
Results of our (extremely long-term) side project with @amygoldberg.bsky.social and @jgschraiber.bsky.social out now in G3: doi.org/10.1093/g3jo...
We benchmarked methods for estimating ancestry proportions under mapping bias and present an adjusted GenotypeLikelihood to mitigate its impact (1/2)
We benchmarked methods for estimating ancestry proportions under mapping bias and present an adjusted GenotypeLikelihood to mitigate its impact (1/2)
Estimating allele frequencies, ancestry proportions and genotype likelihoods in the presence of mapping bias
Abstract. Population genomic analyses rely on an accurate and unbiased characterization of the genetic composition of the studied population. For short-rea
doi.org
August 4, 2025 at 9:34 PM
Great to see this article recommended in PCI Genomics out in G3!
📑 New @genomics.peercommunityin.org recommendation, by @sishuowang.bsky.social
genomics.peercommunityin.org/articles/rec...
On the work of David Robelin et al. (2025) localScore: an R package to highlight optimal and suboptimal segment in a sequence with associated p-values computation
#OpenAccess
genomics.peercommunityin.org/articles/rec...
On the work of David Robelin et al. (2025) localScore: an R package to highlight optimal and suboptimal segment in a sequence with associated p-values computation
#OpenAccess
July 19, 2025 at 8:00 AM
📑 New @genomics.peercommunityin.org recommendation, by @sishuowang.bsky.social
genomics.peercommunityin.org/articles/rec...
On the work of David Robelin et al. (2025) localScore: an R package to highlight optimal and suboptimal segment in a sequence with associated p-values computation
#OpenAccess
genomics.peercommunityin.org/articles/rec...
On the work of David Robelin et al. (2025) localScore: an R package to highlight optimal and suboptimal segment in a sequence with associated p-values computation
#OpenAccess
Reposted by PCI Genomics
Our description of the transcriptomic changes during sexual development in #Podospora anserina is out in @genomics.peercommunityin.org ! peercommunityjournal.org/articles/10....
@i2bcparissaclay.bsky.social @univparissaclay.bsky.social
@i2bcparissaclay.bsky.social @univparissaclay.bsky.social
Sexual reproduction is controlled by successive transcriptomic waves in Podospora anserina
peercommunityjournal.org
July 7, 2025 at 5:40 AM
Our description of the transcriptomic changes during sexual development in #Podospora anserina is out in @genomics.peercommunityin.org ! peercommunityjournal.org/articles/10....
@i2bcparissaclay.bsky.social @univparissaclay.bsky.social
@i2bcparissaclay.bsky.social @univparissaclay.bsky.social
New PCI Genomics recommendation! Of this preprint: "Sexual reproduction is controlled by successive transcriptomic waves in Podospora anserina"
Recommendation by Sébastien Bloyer: doi.org/10.24072/pci...
Preprint from Bidard and colleagues: doi.org/10.1101/2024...
Recommendation by Sébastien Bloyer: doi.org/10.24072/pci...
Preprint from Bidard and colleagues: doi.org/10.1101/2024...
Transcriptomic reprogramming during fungal sexual reproduction
Despite the inherent challenge of finding suitable mating partners, most eukaryotes use sexual reproduction to produce offspring endowed with increase genetic diversity and fitness. The persistence…
doi.org
June 18, 2025 at 6:45 AM
New PCI Genomics recommendation! Of this preprint: "Sexual reproduction is controlled by successive transcriptomic waves in Podospora anserina"
Recommendation by Sébastien Bloyer: doi.org/10.24072/pci...
Preprint from Bidard and colleagues: doi.org/10.1101/2024...
Recommendation by Sébastien Bloyer: doi.org/10.24072/pci...
Preprint from Bidard and colleagues: doi.org/10.1101/2024...
Reposted by PCI Genomics
PCI Psychology is here!! 🎉🥳
After over a year of hard work by so many people, we are thrilled to announce that we are open for submissions! Join us in making publishing more efficient, equitable, and open: psych.peercommunityin.org
#PsychSciSky #scipub
After over a year of hard work by so many people, we are thrilled to announce that we are open for submissions! Join us in making publishing more efficient, equitable, and open: psych.peercommunityin.org
#PsychSciSky #scipub
June 11, 2025 at 11:03 PM
PCI Psychology is here!! 🎉🥳
After over a year of hard work by so many people, we are thrilled to announce that we are open for submissions! Join us in making publishing more efficient, equitable, and open: psych.peercommunityin.org
#PsychSciSky #scipub
After over a year of hard work by so many people, we are thrilled to announce that we are open for submissions! Join us in making publishing more efficient, equitable, and open: psych.peercommunityin.org
#PsychSciSky #scipub
We are looking for new recommenders to join Peer Community in Genomics! The position of “recommender” is analogous to an associate editor at a traditional journal. However, recommenders are not obliged to handle any manuscripts.
June 12, 2025 at 6:02 AM
We are looking for new recommenders to join Peer Community in Genomics! The position of “recommender” is analogous to an associate editor at a traditional journal. However, recommenders are not obliged to handle any manuscripts.
At PCI Genomics, we are pleased to have recommended all ERGA manuscripts and publications to date, helping to bring together this vital body of work at the heart of European biodiversity genomics.
🔗 genomics.peercommunityin.org
#ERGA #Genomics #Biodiversity #PCIGenomics #OpenScience
🔗 genomics.peercommunityin.org
#ERGA #Genomics #Biodiversity #PCIGenomics #OpenScience
June 5, 2025 at 8:01 AM
At PCI Genomics, we are pleased to have recommended all ERGA manuscripts and publications to date, helping to bring together this vital body of work at the heart of European biodiversity genomics.
🔗 genomics.peercommunityin.org
#ERGA #Genomics #Biodiversity #PCIGenomics #OpenScience
🔗 genomics.peercommunityin.org
#ERGA #Genomics #Biodiversity #PCIGenomics #OpenScience
Lopezguerra & Douglas recommend the high-quality Xylocopa violacea reference genome by Nash et al., 2024, Heredity, the first annotated pseudo-chromosomal assembly for any Xylocopa bee! 🐝 A crucial step for pollinator research, conservation, and even cancer therapy studies #ERGA tinyurl.com/vwknzu2b
A high-quality genome assembly for carpenter bees
We present a reference genome assembly from an individual male Violet Carpenter Bee (Xylocopa violacea, Linnaeus 1758). The assembly is 1.02 gigabases in span. 48% of the assembly is scaffolded into…
tinyurl.com
June 5, 2025 at 7:01 AM
Lopezguerra & Douglas recommend the high-quality Xylocopa violacea reference genome by Nash et al., 2024, Heredity, the first annotated pseudo-chromosomal assembly for any Xylocopa bee! 🐝 A crucial step for pollinator research, conservation, and even cancer therapy studies #ERGA tinyurl.com/vwknzu2b
Marino, Fiston-Lavier & Mayoud recommend the VGP-Galaxy pipeline (Larivière et al. 2024), a scalable, open, and user-friendly tool for high-quality genome assembly, powering efforts like the Earth BioGenome Project.
📖 A must-read for the future of biodiversity genomics!
📖 A must-read for the future of biodiversity genomics!
June 5, 2025 at 6:01 AM
Marino, Fiston-Lavier & Mayoud recommend the VGP-Galaxy pipeline (Larivière et al. 2024), a scalable, open, and user-friendly tool for high-quality genome assembly, powering efforts like the Earth BioGenome Project.
📖 A must-read for the future of biodiversity genomics!
📖 A must-read for the future of biodiversity genomics!
Reposted by PCI Genomics
❗❗❗If SciPost has benefited you or your institution, now is the time to show support! Read the SciPost team's open letter here: jscaux.org/blog/post/20... and their previous one here: scipost.org/blog/post/20....
Jean-Sébastien Caux: blogpost on SciPost at a crossroads
For 9 years now, thanks to your involvement, SciPost has grown into being recognized as an essential open science infrastructure. We are often touted as a template for journals of the future and case…
jscaux.org
May 27, 2025 at 9:17 AM
❗❗❗If SciPost has benefited you or your institution, now is the time to show support! Read the SciPost team's open letter here: jscaux.org/blog/post/20... and their previous one here: scipost.org/blog/post/20....
Reposted by PCI Genomics
We just published our first paper in the Peer Community Journal - diamond open access, no APCs!
Awesome experience, with less than a week from submission after receommendation by #pcigenomics.
Highly recommended!
#molpalmuc
@lmumuenchen.bsky.social
@peercommunityin.bsky.social
Awesome experience, with less than a week from submission after receommendation by #pcigenomics.
Highly recommended!
#molpalmuc
@lmumuenchen.bsky.social
@peercommunityin.bsky.social
Genomic changes are varied across congeneric species pairs of animals
peercommunityjournal.org
May 22, 2025 at 11:00 AM
We just published our first paper in the Peer Community Journal - diamond open access, no APCs!
Awesome experience, with less than a week from submission after receommendation by #pcigenomics.
Highly recommended!
#molpalmuc
@lmumuenchen.bsky.social
@peercommunityin.bsky.social
Awesome experience, with less than a week from submission after receommendation by #pcigenomics.
Highly recommended!
#molpalmuc
@lmumuenchen.bsky.social
@peercommunityin.bsky.social
"A new simulation pipeline enhances benchmarking of transposon polymorphism detection tools" - a new PCI Genomics recommendation from Raúl Castanera: tinyurl.com/mr2ac84m
A new simulation pipeline enhances benchmarking of transposon po...
Transposable elements (TEs) have an important role in genome evolution but are challenging for bioinformatics detection due to their repetitive nature and ability to move and replicate within…
tinyurl.com
May 22, 2025 at 6:00 AM
"A new simulation pipeline enhances benchmarking of transposon polymorphism detection tools" - a new PCI Genomics recommendation from Raúl Castanera: tinyurl.com/mr2ac84m
Invasive insects are a major issue, but few relevant genomic resources are available. This topic is addressed in the latest PCI Genomics recommendation: "Three more reference genomes of invasive insect species" by Vincent Lacroix tinyurl.com/uvfef7wb
Three more reference genomes of invasive insect species
Cydalima perspectalis (the box tree moth), Leptoglossus occidentalis (the western conifer seed bug), and Tecia solanivora (the Guatemalan tuber moth) are three economically harmful invasive insect…
doi.org
May 20, 2025 at 10:36 PM
Invasive insects are a major issue, but few relevant genomic resources are available. This topic is addressed in the latest PCI Genomics recommendation: "Three more reference genomes of invasive insect species" by Vincent Lacroix tinyurl.com/uvfef7wb
"Exploring the correlation between speciation and genome rearrangements", a new PCI Genomics recommendation from Javier del Campo! tinyurl.com/24b5jdsn
Exploring the correlation between speciation and genome rearrang...
Francis et al. (2025) investigate the relationship between genomic rearrangement, specifically macro- and micro-synteny, and speciation across a broad range of animal phyla. Using chromosome-level…
tinyurl.com
May 15, 2025 at 6:00 AM
"Exploring the correlation between speciation and genome rearrangements", a new PCI Genomics recommendation from Javier del Campo! tinyurl.com/24b5jdsn
📑 New PCI Genomics recommendation, by @saabalde.bsky.social
genomics.peercommunityin.org/articles/rec...
On Ole K. Tørresen et al. (2025) Comparison of whole-genome assemblies of European river lamprey (Lampetra fluviatilis) and brook lamprey (Lampetra planeri) www.biorxiv.org/content/10.1...
genomics.peercommunityin.org/articles/rec...
On Ole K. Tørresen et al. (2025) Comparison of whole-genome assemblies of European river lamprey (Lampetra fluviatilis) and brook lamprey (Lampetra planeri) www.biorxiv.org/content/10.1...
Comparison of whole-genome assemblies of European river lamprey (Lampetra fluviatilis) and brook lamprey (Lampetra planeri)
We present haplotype-resolved whole-genome assemblies from one individual European river lamprey ( Lampetra fluviatilis ) and one individual brook lamprey ( Lampetra planeri ), usually regarded as…
www.biorxiv.org
May 7, 2025 at 7:01 AM
📑 New PCI Genomics recommendation, by @saabalde.bsky.social
genomics.peercommunityin.org/articles/rec...
On Ole K. Tørresen et al. (2025) Comparison of whole-genome assemblies of European river lamprey (Lampetra fluviatilis) and brook lamprey (Lampetra planeri) www.biorxiv.org/content/10.1...
genomics.peercommunityin.org/articles/rec...
On Ole K. Tørresen et al. (2025) Comparison of whole-genome assemblies of European river lamprey (Lampetra fluviatilis) and brook lamprey (Lampetra planeri) www.biorxiv.org/content/10.1...
🌳 New recommendation at PCI Genomics!
Duruflé et al. (2025) combine GWAS, transcriptomics & population genetics to link chalcone isomerase to radial stem growth in black poplar — advancing sustainable biomass breeding. genomics.peercommunityin.org/articles/rec...
Duruflé et al. (2025) combine GWAS, transcriptomics & population genetics to link chalcone isomerase to radial stem growth in black poplar — advancing sustainable biomass breeding. genomics.peercommunityin.org/articles/rec...
May 1, 2025 at 6:00 AM
🌳 New recommendation at PCI Genomics!
Duruflé et al. (2025) combine GWAS, transcriptomics & population genetics to link chalcone isomerase to radial stem growth in black poplar — advancing sustainable biomass breeding. genomics.peercommunityin.org/articles/rec...
Duruflé et al. (2025) combine GWAS, transcriptomics & population genetics to link chalcone isomerase to radial stem growth in black poplar — advancing sustainable biomass breeding. genomics.peercommunityin.org/articles/rec...
Reposted by PCI Genomics
How do portable peer review (PPR), Review Commons and Peer Community In make peer review more sustainable? Check out this editorial in PLOS Biology!
journals.plos.org/plosbiology/...
journals.plos.org/plosbiology/...
April 1, 2025 at 2:00 PM
How do portable peer review (PPR), Review Commons and Peer Community In make peer review more sustainable? Check out this editorial in PLOS Biology!
journals.plos.org/plosbiology/...
journals.plos.org/plosbiology/...
📑 New PCI Genomics recommendation, by S. E. Ramos-Onsins: genomics.peercommunityin.org/articles/rec...
On the work of Günther et al. (2025) Estimating allele frequencies, ancestry proportions and genotype likelihoods in the presence of mapping bias www.biorxiv.org/lookup/doi/1...
On the work of Günther et al. (2025) Estimating allele frequencies, ancestry proportions and genotype likelihoods in the presence of mapping bias www.biorxiv.org/lookup/doi/1...
A novel genotype likelihood-based method to reduce mapping bias ...
The study of genomic variability within and between populations, as well as among species, relies on comparative analyses of homologous positions—sites that share a common evolutionary origin.…
genomics.peercommunityin.org
March 18, 2025 at 8:00 AM
📑 New PCI Genomics recommendation, by S. E. Ramos-Onsins: genomics.peercommunityin.org/articles/rec...
On the work of Günther et al. (2025) Estimating allele frequencies, ancestry proportions and genotype likelihoods in the presence of mapping bias www.biorxiv.org/lookup/doi/1...
On the work of Günther et al. (2025) Estimating allele frequencies, ancestry proportions and genotype likelihoods in the presence of mapping bias www.biorxiv.org/lookup/doi/1...
Reposted by PCI Genomics
If for you also, Onagre were monsters imagined by Pierre Bordage, you have to read my edito and the paper from Barloy-Hubler et al on #invasive #plants from this family 🧬🖥️ 🧪
@genomics.peercommunityin.org @peercommunityin.bsky.social
doi.org/10.24072/pci...
@genomics.peercommunityin.org @peercommunityin.bsky.social
doi.org/10.24072/pci...
doi.org
February 26, 2025 at 3:51 PM
If for you also, Onagre were monsters imagined by Pierre Bordage, you have to read my edito and the paper from Barloy-Hubler et al on #invasive #plants from this family 🧬🖥️ 🧪
@genomics.peercommunityin.org @peercommunityin.bsky.social
doi.org/10.24072/pci...
@genomics.peercommunityin.org @peercommunityin.bsky.social
doi.org/10.24072/pci...
🎉 Pittion and colleagues’ preprint on #HDMAX2 has been recommended in PCI Genomics! This R package enhances mediation analysis, supporting multiple exposures & non-continuous variables in high-dimensional data. Explore its impact on epidemiology!
🔗 buff.ly/zXXnlcT
#Genomics #DataScience #RStats
🔗 buff.ly/zXXnlcT
#Genomics #DataScience #RStats
hdmax2, an R package to perform high dimension mediation analysis
Mediation analysis plays a crucial role in epidemiology, unraveling the intricate path- ways through which exposures exert influence on health outcomes. Recent advances in high-throughput sequencing…
buff.ly
March 11, 2025 at 7:00 AM
🎉 Pittion and colleagues’ preprint on #HDMAX2 has been recommended in PCI Genomics! This R package enhances mediation analysis, supporting multiple exposures & non-continuous variables in high-dimensional data. Explore its impact on epidemiology!
🔗 buff.ly/zXXnlcT
#Genomics #DataScience #RStats
🔗 buff.ly/zXXnlcT
#Genomics #DataScience #RStats
🚨 New in PCI Genomics! 🚨
Barloy-Hubler et al. assemble plastomes for Ludwigia grandiflora & Ludwigia peploides using hybrid sequencing, revealing haplotypes & positive selection in key genes. A leap forward for Onagraceae genomics! 🌱🔬
🔗 Read more: https://buff.ly/3ETgEi9
#Phylogenetics #PCIGenomics
Barloy-Hubler et al. assemble plastomes for Ludwigia grandiflora & Ludwigia peploides using hybrid sequencing, revealing haplotypes & positive selection in key genes. A leap forward for Onagraceae genomics! 🌱🔬
🔗 Read more: https://buff.ly/3ETgEi9
#Phylogenetics #PCIGenomics
Onagre, monster, invasion and genetics
Reviews
buff.ly
February 27, 2025 at 7:00 AM
🚨 New in PCI Genomics! 🚨
Barloy-Hubler et al. assemble plastomes for Ludwigia grandiflora & Ludwigia peploides using hybrid sequencing, revealing haplotypes & positive selection in key genes. A leap forward for Onagraceae genomics! 🌱🔬
🔗 Read more: https://buff.ly/3ETgEi9
#Phylogenetics #PCIGenomics
Barloy-Hubler et al. assemble plastomes for Ludwigia grandiflora & Ludwigia peploides using hybrid sequencing, revealing haplotypes & positive selection in key genes. A leap forward for Onagraceae genomics! 🌱🔬
🔗 Read more: https://buff.ly/3ETgEi9
#Phylogenetics #PCIGenomics