Francois Sabot
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Francois Sabot
@francois-sabot.genomic.social.ap.brid.gy
Scientist, biologist, #evolution of #genomes and #pangenomics, #bioinformatics - Joint Director of the #OpenScience Dept @ird_fr - Senior Editor at BMC […]

[bridged from https://genomic.social/@francois_sabot on the fediverse by https://fed.brid.gy/ ]
GrAnnoT, a tool for effecient and reliable annotation transfer through pangenome graph | bioRxiv

https://www.biorxiv.org/content/10.1101/2025.02.26.640337v1
March 3, 2025 at 1:53 PM
Reposted by Francois Sabot
Déclaration visant à défendre la recherche contre la censure du gouvernement américain | Rédaction Médicale et Scientifique https://www.redactionmedicale.fr/2025/02/declaration-visant-a-defendre-la-recherche-contre-la-censure-du-gouvernement-americain
www.redactionmedicale.fr
February 27, 2025 at 7:41 PM
Reposted by Francois Sabot
Données scientifiques effacées : résister à la censure de Trump

https://youtube.com/watch?v=N7dBpdmVWHk&feature=shared

Avec Michel Dubois, de Sorbonne Université.

#SorbonneUniversite
#micheldubois
February 27, 2025 at 5:41 PM
Onagre, monster, invasion and genetics

https://genomics.peercommunityin.org/articles/rec?id=334
February 26, 2025 at 3:55 PM
We have a new preprint! Something different, on archeological remnants!

DateBack, a digital open access repository of archaeobotanical data for reconstructing date palm history | bioRxiv

https://www.biorxiv.org/content/10.1101/2025.02.21.639487v1
DateBack, a digital open access repository of archaeobotanical data for reconstructing date palm history
act The date palm (Phoenix dactylifera L.) has been a cornerstone of oasis agrosystems in West Asia and North Africa for millenia, yet the timeline and processes of its domestication and spread remain poorly documented. Archaeobotanical remains provide critical insights into its cultivation history, but no comprehensive review or dedicated platform currently exists to synthesize and analyze these data. To address this gap, we conducted an extensive literature review and developed DateBack (https://cloudapps.france-bioinformatique.fr/dateback), a digital open access repository of archaeobotanical remains of Phoenix spp. In its first version, DateBack records macroremains (e.g., seeds, fruits, stems, petioles) from prehistoric to Late Antiquity contexts in Southwest and South Asia. We assembled 140 entries from 99 archaeological sites across 110 references, along with a separate table of 55 radiocarbon-dated entries from 17 sites, refining chronological assessments. Most entries comprise charred seeds (55.7%), with a smaller proportion of charred vegetative parts or desiccated remains. Our findings highlight regional disparities in remain distribution, concentrated in the Levant and Gulf, while Saudi Arabia and southern Iran are underrepresented, and in data reliability, particularly dating resolution, complicating the reconstruction of date cultivation history. Our evidence shows that the earliest securely dated remains, indicating date consumption, appear in the Gulf around 5000 BCE, while cultivation emerges later, first in southern Mesopotamia and the northern Gulf in the 4th millennium BCE, then in eastern Arabia and the Indus Valley in the 3rd millennium BCE. The Levant presents challenges, with numerous presumed early finds but significant uncertainties, with secure evidence of cultivation only appearing by the late 2nd millennium BCE, as in northwestern Arabia, while in the southern Arabian Peninsula, it is not attested until the 1st millennium BCE. By compiling and standardizing archaeobotanical data, DateBack facilitates advanced spatiotemporal analyses and supports additional archaeobotany-based research including ancient DNA studies. Moreover, the platform is dynamic, scalable, and collaborative, enhancing data integration and refinement, with future expansions planned to include additional periods (Islamic era and beyond), geographic regions (North Africa), and new types of evidence, such as plant microremains and iconography. ### Competing Interest Statement The authors have declared no competing interest.
www.biorxiv.org
February 24, 2025 at 10:33 AM
Reposted by Francois Sabot
Nouveauté dans #hal, une fenêtre facilite l'ajout d'un lien entre la publication et les ressources adjacentes : données entreposées dans #Nakala ou #RechercheDataGouv, code source archivé dans #softwareheritage ou ressources provenant d'autres entrepôts qui […]

[Original post on mastodon.social]
February 12, 2025 at 7:55 AM
Comment rendre visible la recherche africaine ? - Autour de la question, le magazine de toutes les sciences

Retour sur la Conférence #scienceouverte au Sud @IRD […]
Original post on genomic.social
genomic.social
February 5, 2025 at 9:51 AM