PCI Genomics

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.

117 followers56 following51 posts

PCI Genomics
@genomics.peercommunityin.org

"Identifying proteins with similar genomic context across diverse prokaryotes using NetSyn", a new PCI Genomics recommendation from Makena Tremblay and @gmdouglas.bsky.social: doi.org/10.24072/pci... Based on this preprint from Mark Stam and colleagues: doi.org/10.1101/2023...

doi.orgIdentifying proteins with similar genomic context across diverse...Background : The growing availability of large prokaryotic genomic datasets presents an opportunity to discover new metabolic pathways and enzymatic reactions useful for industrial or synthetic…
PCI Genomics
@genomics.peercommunityin.org

📑 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

genomics.peercommunityin.orgLong-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…
PCI Genomics
@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...

doi.orgPeer Community In and Peer Community Journal: a two-step diamond OA process giving research communities back control of publishing | InsightsThe 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…
PCI Genomics
@genomics.peercommunityin.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...

genomics.peercommunityin.orgHigh-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…
PCI Genomics
@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

genomics.peercommunityin.orgBridging the gap in RNA-end sequencing analysis5' 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…
PCI Genomics
@genomics.peercommunityin.org

📑 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

genomics.peercommunityin.orgEvaluating circular RNA detection in the long-read eraCircular 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…
PCI Genomics
@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

genomics.peercommunityin.orgDecoding 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,…
PCI Genomics
@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

hal.scienceExplainable 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…
PCI Genomics
@genomics.peercommunityin.org

📑 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

genomics.peercommunityin.orgRecovered 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…
PCI Genomics
@genomics.peercommunityin.org

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!

PCI Genomics
@genomics.peercommunityin.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

genomics.peercommunityin.orgTowards 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…
PCI Genomics
@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

genomics.peercommunityin.orgGrAnnoT: Efficient annotation transfer through pangenome graphsThe 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…

PCI Genomics reposted

ASAPbio
@asapbio.bsky.social

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.✍️ 🔬

PCI Genomics
@genomics.peercommunityin.org

Great to see this article recommended in PCI Genomics out in G3!

Torsten Günther@trstngnthr.bsky.social

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)

doi.orgEstimating allele frequencies, ancestry proportions and genotype likelihoods in the presence of mapping biasAbstract. Population genomic analyses rely on an accurate and unbiased characterization of the genetic composition of the studied population. For short-rea
PCI Genomics
@genomics.peercommunityin.org

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...

doi.orgTranscriptomic reprogramming during fungal sexual reproductionDespite 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…

PCI Genomics reposted

PCI Psychology
@psych.peercommunityin.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

psych.peercommunityin.orgPCI PsychologyPeer Community in Psychology
PsyArXivBot@psyarxivbot.bsky.social

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

PCI Genomics
@genomics.peercommunityin.org

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.

View full thread
PCI Genomics
@genomics.peercommunityin.org

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

peercommunityin.orgCurrent PCIs - Peer Community InHere is the list of the different Peer Communities In already created, hosting recommendations and peer-reviews of preprints and ready to receive your submissions
PCI Genomics
@genomics.peercommunityin.org

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.

View full thread
PCI Genomics
@genomics.peercommunityin.org

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.

PCI Genomics
@genomics.peercommunityin.org

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

tinyurl.comA high-quality genome assembly for carpenter beesWe 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…
PCI Genomics
@genomics.peercommunityin.org

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!

PCI Genomics reposted

Peer Community In
@peercommunityin.bsky.social

❗❗❗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....

jscaux.orgJean-Sébastien Caux: blogpost on SciPost at a crossroadsFor 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…
PCI Genomics
@genomics.peercommunityin.org

The full pre-print author list: Eric Lombaert, ‪@cklopp66.bsky.social‬, Aurélie Blin, Gwenolah Annonay, Carole Iampietro, Jérôme Lluch, Marine Sallaberry, Sophie Valière, Riccardo Poloni, Mathieu Joron, Emeline Deleury

PCI Genomics
@genomics.peercommunityin.org

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

doi.orgThree more reference genomes of invasive insect speciesCydalima 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…
PCI Genomics
@genomics.peercommunityin.org

A recommendation of the preprint "Genomic changes are varied across congeneric species pairs of animals" by Warren Francis, Sergio Vargas, and Gert Wörheide: tinyurl.com/y82japny

tinyurl.comGenomic changes are varied across congeneric species pairs of animalsSynteny, the shared arrangement of genes on chromosomes between related species, is a marker of shared ancestry, and synteny-breaking events can result in genomic incompatibilities between…
PCI Genomics
@genomics.peercommunityin.org

📑 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...

biorxiv.orgComparison 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…