A roadmap for the adoption of pangenomics in agronomy - a new recommendation from Lucía Campos Dominguez for PCI Genomics! doi.org/10.24072/pci... A recommendation of this preprint by Stéphanie Bocs and colleagues: hal.inrae.fr/hal-05357866

📑 New @genomics.peercommunityin.org recommendation, by Michael Fontaine genomics.peercommunityin.org/articles/rec... On the work of Nyarko et al. (2026) De novo assembly of complete Plasmodium falciparum isolate genomes using PacBio HiFi sequencing technology #OpenAccess #Bioinformatics

Long-read sequencing brings the hypervariable *Plasmodium falcip...

Plasmodium falciparum possesses a highly structured genome with extensive sequence diversity concentrated in Variant Surface Antigen (VSA) families. These genes—var, rif, and stevor—play key roles in…

genomics.peercommunityin.org

Curious about Peer Community In, but not sure where to start? Check out this new paper describing the our model, written by the PCI core team! doi.org/10.1629/uksg...

Peer Community In and Peer Community Journal: a two-step diamond OA process giving research communities back control of publishing | Insights

The current academic publishing system faces many well-identified issues. Not only is it slow and costly, but it is also an opaque system that produces a substantial amount of non-reproducible…

doi.org

📑 New @genomics.peercommunityin.org recommendation, by @saabalde.bsky.social genomics.peercommunityin.org/articles/rec... On the work of Guilio et al. (2026) Comparing DNA extraction methods for successful PacBio HiFi sequencing: a case study of the freshwater mussel Anodonta anatina (Bivalvia...

High-quality HMW-DNA extractions from molluscs: comparing method...

High-quality reference genomes are increasingly recognized as essential resources in biodiversity genomics and conservation. However, successful DNA extraction and long-read sequencing remain highly…

genomics.peercommunityin.org

📑 New @pcigenomics@fediscience.org recommendation, by Charles Lecellier genomics.peercommunityin.org/articles/rec... On the work of Rusakovich et al. (2026) rnaends: an R package to study exact RNA ends at nucleotide resolution #OpenAccess #Bioinformatics

Bridging the gap in RNA-end sequencing analysis

5' and 3' RNA-end sequencing protocols have unlocked new opportunities to study aspects of RNA metabolism such as synthesis, maturation and degradation, by enabling the quantification of exact ends…

genomics.peercommunityin.org

"High-quality de novo transcriptome assemblies of juvenile Sepia officinalis reveal developmental and environmental response landscapes" a recommendation by Jitendra Narayan of a preprint by Thomas Sol Dourdin and colleagues doi.org/10.24072/pci...

📑 New @PCIgenomics recommendation, by @camillemrcht.bsky.social genomics.peercommunityin.org/articles/rec... On the work of Rusakovich et al. (2026) Benchmarking circRNA Detection Tools from Long-Read Sequencing Using Data-Driven... #OpenAccess #Bioinformatics @jobim2025.bsky.social

Evaluating circular RNA detection in the long-read era

Circular RNAs (circRNAs) are unique non-coding RNAs with covalently closed loop structures formed through backsplicing events. Their stability, tissue-specific expression patterns, and potential as…

genomics.peercommunityin.org

📑 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

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,…

genomics.peercommunityin.org

"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

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…

hal.science

📑 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

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…

genomics.peercommunityin.org

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!

"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...

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…

doi.org

📑 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

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

🌐 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

🧬 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!

Torsten Günther@trstngnthr.bsky.social · last yr.

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)

📑 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

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...

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

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

PsyArXivBot@psyarxivbot.bsky.social · last yr.

Peer Community in Psychology: A platform for peer review of preprints across psychology: https://osf.io/m456e

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

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

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

"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

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