PCI Genomics

Decoding the genome of a novel *Trichoderma gamsii* strain with ... Trichoderma gamsii is a filamentous fungus widely recognized for its beneficial roles in agriculture, particularly for its ability to suppress plant pathogens and enhance crop health. However,…

📑 New @genomics.peercommunityin.org recommendation, by Fabienne Malagnac
genomics.peercommunityin.org/articles/rec...

On the work of Justine Colou et al. (2025) Genome of Trichoderma gamsii strain T035 a promising beneficial fungus in agriculture

#OpenAccess #Bioinformatics

Explainable AI for Marine Ecological Quality Prediction: Integrating Microbiome Data, Metadata, and Diversity <div><p>Assessing ecological quality (EQ) is crucial for marine biodiversity monitoring. With the advent of High-Throughput Sequencing technologies, metabarcoding has enabled large-scale microbial…

"Using explainable machine learning for monitoring marine biodiversity" - the latest PCI Genomics recommendation from @raphaelmourad.bsky.social doi.org/10.24072/pci...

Based on preprint by Houria Braikia, Sana Ben Hamida, and Marta Rukoz: hal.science/hal-05046103v1

Recovered helicase loader *dciA* reshapes replication-initiation... At the onset of bacterial chromosome replication initiation, replicative helicases are loaded onto DNA, a process requiring helicase loaders. While organisms documented as lacking a helicase loader…

📑 New @genomics.peercommunityin.org recommendation, by @gecko1990.bsky.social
genomics.peercommunityin.org/articles/rec...

On the work of Pierre Brézellec (2025) The identification of the replicative helicase loader gene dciA within the Helicobacter pylori genome...

#OpenAccess #Bioinformatics

A recommendation of this preprint from Pierre Brézellec: doi.org/10.1101/2025...

New PCI Genomics recommendation from Patrick Forterre: "Interactome study reveals extensive interaction of the SARS-CoV-2 virus spike protein with coiled-coil proteins mostly involved in cytoskeletal functions" - doi.org/10.24072/pci...

All Recommenders are invited to the PCI Genomics Recommenders’ Meeting! We will present our goals and discuss possible ways to improve user experience and engagement. Two online meetings: Feb 9th, 18h CET OR Feb 11th, 15h CET. If not a Recommender yet, send us an email!

Thank you to the recommender and two reviewers for evaluating this manuscript! 🙌

Bulk-based hypothesis weighing increases power in single-cell differential expression analysis Due to the costs of single-cell sequencing, sample sizes are often relatively limited, sometimes leading to poorly reproducible results. In many contexts, however, larger bulk RNAseq data is…

📝 A recommendation of this preprint from Pierre-Luc Germain, Jiayi Wang, and @markrobinsonca.bsky.social: doi.org/10.1101/2025...

Bulk RNA-seq to the rescue of differential expression analysis i... Due to the costs of single-cell sequencing, sample sizes are often relatively limited, sometimes leading to poorly reproducible results. In many contexts, however, larger bulk RNAseq data is…

"Bulk RNA-seq to the rescue of differential expression analysis in single-cell transcriptomics" 🧫 📑 A new PCI Genomics recommendation by @mireyaplass.bsky.social: doi.org/10.24072/pci...

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…

📑 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

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…

🌐 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

HaploCharmer: a Snakemake workflow for read-scale haplotype calling adapted to polyploids The advent of next-generation sequencing (NGS) has revolutionized the study of single nucleotide polymorphisms (SNPs), making it increasingly cost-effective. Haplotypes, which combine alleles from…

📄 Preprint: doi.org/10.1101/2025...

Big thank you to the recommender and two reviewers!

#Genomics #Polyploids #Bioinformatics #PlantGenomics

🧬 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...

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.✍️ 🔬

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

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

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…

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...

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

If you are interested in applying to be a recommender but Genomics doesn't fit your expertise, then be sure to check out the other communities under the PCI umbrella: peercommunityin.org/current-pcis/

cc' @peercommunityin.bsky.social‬

Peer Community In represents an innovative alternative to the publishing norms in most fields. As we are entirely grant-funded, our model is free for authors and readers: the focus is on the research.

We appreciate that all researchers have limited time for volunteer service work, but strongly believe that volunteering with Peer Community In is impactful if you want to help improve scholarly publishing.

PCI Genomics Peer Community in Genomics

If interested, please reach out to the board with a link to your website or CV (see our email here: genomics.peercommunityin.org/about/contact).

You can read more about the Peer Community In model and the recommender role here: genomics.peercommunityin.org/about/about

PCI Genomics Peer Community in Genomics

They only handle manuscripts they specifically find interesting (and have time to handle). They are also expected to write a short recommendation text (~400 words) if the article passes evaluation.

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

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…

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!

❗❗❗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....

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