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PCI Genomics @genomics.peercommunityin.org · 15d

📄 Preprint: doi.org/10.1101/2025...

Big thank you to the recommender and two reviewers!

#Genomics #Polyploids #Bioinformatics #PlantGenomics

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…

doi.org

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PCI Genomics @genomics.peercommunityin.org · 15d

🧬 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...

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Reposted by PCI Genomics

ASAPbio @asapbio.bsky.social · Aug 26

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.✍️ 🔬

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PCI Genomics @genomics.peercommunityin.org · Aug 4

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

Torsten Günther @trstngnthr.bsky.social · Aug 4

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)

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

PCI Genomics @genomics.peercommunityin.org · Jul 19

📑 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

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Reposted by PCI Genomics

Pierre Grognet @pierregrognet.bsky.social · Jul 7

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

Sexual reproduction is controlled by successive transcriptomic waves in Podospora anserina

peercommunityjournal.org

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PCI Genomics @genomics.peercommunityin.org · Jun 18

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

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Reposted by PCI Genomics

PCI Psychology @psych.peercommunityin.org · Jun 11

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

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PCI Genomics @genomics.peercommunityin.org · Jun 12

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

Current PCIs - Peer Community In

Here is the list of the different Peer Communities In already created, hosting recommendations and peer-reviews of preprints and ready to receive your submissions

peercommunityin.org

PCI Genomics @genomics.peercommunityin.org · Jun 12

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.

Current PCIs - Peer Community In

Here is the list of the different Peer Communities In already created, hosting recommendations and peer-reviews of preprints and ready to receive your submissions

peercommunityin.org

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PCI Genomics @genomics.peercommunityin.org · Jun 12

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.

Current PCIs - Peer Community In

Here is the list of the different Peer Communities In already created, hosting recommendations and peer-reviews of preprints and ready to receive your submissions

peercommunityin.org

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PCI Genomics @genomics.peercommunityin.org · Jun 12

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

genomics.peercommunityin.org

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PCI Genomics @genomics.peercommunityin.org · Jun 12

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.

PCI Genomics

Peer Community in Genomics

genomics.peercommunityin.org

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PCI Genomics @genomics.peercommunityin.org · Jun 12

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.

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PCI Genomics @genomics.peercommunityin.org · Jun 5

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

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PCI Genomics @genomics.peercommunityin.org · Jun 5

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

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PCI Genomics @genomics.peercommunityin.org · Jun 5

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!

Reposted by PCI Genomics

Peer Community In @peercommunityin.bsky.social · May 27

❗❗❗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

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Reposted by PCI Genomics

Gert Wörheide @gwoerhe.bsky.social · May 22

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

Genomic changes are varied across congeneric species pairs of animals

peercommunityjournal.org

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PCI Genomics @genomics.peercommunityin.org · May 22

Thanks to Tianxiong Yu and one anonymous reviewer for reviewing the manuscript!

PCI Genomics @genomics.peercommunityin.org · May 22

Based on the preprint from Marie Verneret, Van Anthony Le, Thomas Faraut, Jocelyn Turpin, and Emmanuelle Lerat: tinyurl.com/5djbmbr7

Particular sequence characteristics induce bias in the detection of polymorphic transposable element insertions

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

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PCI Genomics @genomics.peercommunityin.org · May 22

"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

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PCI Genomics @genomics.peercommunityin.org · May 20

Big thanks to the recommender and to @jm-aury.bsky.social‬ and ‪@nicolasparisot.bsky.social‬ for reviewing this manuscript!

PCI Genomics @genomics.peercommunityin.org · May 20

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

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PCI Genomics @genomics.peercommunityin.org · May 20

A recommendation of the preprint "Draft genome and transcriptomic sequence data of three invasive insect species" by Eric Lombaert et al. tinyurl.com/3k4st24a

Draft genome and transcriptomic sequence data of three 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…

tinyurl.com

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