Camille Marchet ⚡
@camillemrcht.bsky.social
Researcher in @BonsaiSeqBioinfo
Lille, France. Bioinformatics, data-structures for DNA/RNA.
Lille, France. Bioinformatics, data-structures for DNA/RNA.
Pinned
‘Google for DNA’ brings order to biology’s big data
MetaGraph compresses vast data archives into a search engine for scientists, opening up new frontiers of biological discovery.
www.nature.com
Ca n'est pas si souvent, un article publié dans Nature met ma communauté à l'honneur (la bioinformatique des séquences). Je vous raconte ?
www.nature.com/articles/d41...
www.nature.com/articles/d41...
Reposted by Camille Marchet ⚡
Honoured and quite blown-over to receive this award. I have been, and continue to be, very lucky - first with great mentors, and then really prodigious students, postdocs and collaborators. Working with them has been a joy.
Congratulations to @zaminiqbal.bsky.social from @milnerevolution.bsky.social on being awarded the 2026 Mary Lyon Medal!
November 14, 2025 at 12:55 PM
Honoured and quite blown-over to receive this award. I have been, and continue to be, very lucky - first with great mentors, and then really prodigious students, postdocs and collaborators. Working with them has been a joy.
Reposted by Camille Marchet ⚡
Another example: Stanford RNA folding competitions (Rhiju Das) - www.kaggle.com/competitions...
AI models still lag far behind the level of protein prediction. The best scores rely on old-school templates. Human intuition still matters. 7/8
AI models still lag far behind the level of protein prediction. The best scores rely on old-school templates. Human intuition still matters. 7/8
Stanford RNA 3D Folding
Solve RNA structure prediction, one of biology's remaining grand challenges
www.kaggle.com
November 15, 2025 at 6:08 AM
Another example: Stanford RNA folding competitions (Rhiju Das) - www.kaggle.com/competitions...
AI models still lag far behind the level of protein prediction. The best scores rely on old-school templates. Human intuition still matters. 7/8
AI models still lag far behind the level of protein prediction. The best scores rely on old-school templates. Human intuition still matters. 7/8
Reposted by Camille Marchet ⚡
I've done a lot of work in Python this fall, and it hasn't endeared me to the language at all. Why does stuff have to be so complicated when you're doing it in Python?
blog.genesmindsmachines.com/p/python-is-...
blog.genesmindsmachines.com/p/python-is-...
Python is not a great language for data science. Part 1: The experience
It may be a good language for data science, but it’s not a great one.
blog.genesmindsmachines.com
November 13, 2025 at 4:16 PM
I've done a lot of work in Python this fall, and it hasn't endeared me to the language at all. Why does stuff have to be so complicated when you're doing it in Python?
blog.genesmindsmachines.com/p/python-is-...
blog.genesmindsmachines.com/p/python-is-...
On est le 12 novembre j'habite à Lille et j'ai mangé dehors sous un grand soleil à midi 😎
November 12, 2025 at 1:41 PM
On est le 12 novembre j'habite à Lille et j'ai mangé dehors sous un grand soleil à midi 😎
Reposted by Camille Marchet ⚡
Avec une com dans Nature des chercheurs ayant identifié les failles www.nature.com/articles/s41...
La question de la sécurité doit être au coeur des developpements, y compris en bioinformatique. Au dela du cas d'ONT, cela pose la question des formations ciblées "devs scientifique"et des moyens.
La question de la sécurité doit être au coeur des developpements, y compris en bioinformatique. Au dela du cas d'ONT, cela pose la question des formations ciblées "devs scientifique"et des moyens.
November 12, 2025 at 12:17 PM
Avec une com dans Nature des chercheurs ayant identifié les failles www.nature.com/articles/s41...
La question de la sécurité doit être au coeur des developpements, y compris en bioinformatique. Au dela du cas d'ONT, cela pose la question des formations ciblées "devs scientifique"et des moyens.
La question de la sécurité doit être au coeur des developpements, y compris en bioinformatique. Au dela du cas d'ONT, cela pose la question des formations ciblées "devs scientifique"et des moyens.
Reposted by Camille Marchet ⚡
Le colloque est maintenu. Il se déplace hors des murs du Collège de France. En outre, le colloque sera diffusé en direct et intégralement enregistré.
Bravo aux organisateurs et intervenants !
carep-paris.org/annonce/comm...
Bravo aux organisateurs et intervenants !
carep-paris.org/annonce/comm...
Communiqué n°2 : Notre colloque se tiendra, comme prévu, les 13 et 14 novembre prochains.
Le colloque « La Palestine et l’Europe » se tiendra les 13 et 14 novembre, réaffirmant la liberté académique et le partage du savoir.
carep-paris.org
November 11, 2025 at 9:44 PM
Le colloque est maintenu. Il se déplace hors des murs du Collège de France. En outre, le colloque sera diffusé en direct et intégralement enregistré.
Bravo aux organisateurs et intervenants !
carep-paris.org/annonce/comm...
Bravo aux organisateurs et intervenants !
carep-paris.org/annonce/comm...
Reposted by Camille Marchet ⚡
Metagenomics colleagues!
I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data.
Please help and share!
I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data.
Please help and share!
November 11, 2025 at 8:21 PM
Metagenomics colleagues!
I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data.
Please help and share!
I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data.
Please help and share!
Bioinformatics x cybersecurity: Christina Boucher and her colleague Sara Rampazzi uncovered a basic yet critical vulnerability in MinIONs through the MinKNOW software bioengineer.org/portable-gen...
Portable Genetic Sequencer Security Vulnerabilities Could Endanger Personal
Portable genetic sequencers, particularly those manufactured by Oxford Nanopore Technologies, have revolutionized the field of genomics, making DNA sequencing more accessible and practical across the
bioengineer.org
November 12, 2025 at 7:44 AM
Bioinformatics x cybersecurity: Christina Boucher and her colleague Sara Rampazzi uncovered a basic yet critical vulnerability in MinIONs through the MinKNOW software bioengineer.org/portable-gen...
Reposted by Camille Marchet ⚡
Je voudrais m'acheter une tablette tactile pour :
1) regarder des flims dans le train
2) lire des PDF
3) prendre des notes manuscrites (typiquement pour le boulot)
1) regarder des flims dans le train
2) lire des PDF
3) prendre des notes manuscrites (typiquement pour le boulot)
November 11, 2025 at 6:28 PM
Je voudrais m'acheter une tablette tactile pour :
1) regarder des flims dans le train
2) lire des PDF
3) prendre des notes manuscrites (typiquement pour le boulot)
1) regarder des flims dans le train
2) lire des PDF
3) prendre des notes manuscrites (typiquement pour le boulot)
Reposted by Camille Marchet ⚡
When I was in graduate school my life and carreer were completely transformed by a seminar I attended at Stanford by Dr. Hamilton Smith. In the talk he discussed how TIGR was sequencing whole genomes of organisms. Here is a scan of P1 of my notes. 1/n
November 11, 2025 at 5:42 AM
When I was in graduate school my life and carreer were completely transformed by a seminar I attended at Stanford by Dr. Hamilton Smith. In the talk he discussed how TIGR was sequencing whole genomes of organisms. Here is a scan of P1 of my notes. 1/n
Reposted by Camille Marchet ⚡
Je suis d'accord avec France Universités : « l’annulation du colloque scientifique porte atteinte à la liberté académique ».
Franchement ça me fait tout bizarre d'être d'accord avec France Universités. C'est dire si les pressions de notre ministre (et la décision du CDF) sont inquiétantes.
Franchement ça me fait tout bizarre d'être d'accord avec France Universités. C'est dire si les pressions de notre ministre (et la décision du CDF) sont inquiétantes.
France Universités exprime sa vive inquiétude après l’annulation d’un colloque scientifique au Collège de France.
franceuniversites.fr/actualite/fr...
#LibertéAcadémique
franceuniversites.fr/actualite/fr...
#LibertéAcadémique
November 10, 2025 at 4:24 PM
Je suis d'accord avec France Universités : « l’annulation du colloque scientifique porte atteinte à la liberté académique ».
Franchement ça me fait tout bizarre d'être d'accord avec France Universités. C'est dire si les pressions de notre ministre (et la décision du CDF) sont inquiétantes.
Franchement ça me fait tout bizarre d'être d'accord avec France Universités. C'est dire si les pressions de notre ministre (et la décision du CDF) sont inquiétantes.
Reposted by Camille Marchet ⚡
[ #VeilleESR #CancelCulture ] Suite à des pressions politiques, dont un message du Ministre sur X (le réseau de désinformation du suprémaciste Elon Musk), le Collège de France a été contraint d'annuler un colloque sur la Palestine.
Le Collège de France annule un colloque sur la Palestine « en réaction à la polémique entourant » l’événement
Le Collège de France « ne prône, ni n’encourage, ni ne soutient aucune forme de militantisme », a affirmé l’établissement qui assure de sa « stricte neutralité (…) au regard des questions de nature po...
www.lemonde.fr
November 10, 2025 at 7:30 AM
[ #VeilleESR #CancelCulture ] Suite à des pressions politiques, dont un message du Ministre sur X (le réseau de désinformation du suprémaciste Elon Musk), le Collège de France a été contraint d'annuler un colloque sur la Palestine.
Reposted by Camille Marchet ⚡
Third day of Genome Informatics #GI2025 began with an exciting session on “AI, ML and Integrative Genomics” chaired by Irene Kaplow & Thomas Pierrot.
The first talk, by Irene Kaplow, focused on Challenges in Predicting Enhancer Activity Differences Between Species
doi.org/10.1186/s12864-022-08450-7
The first talk, by Irene Kaplow, focused on Challenges in Predicting Enhancer Activity Differences Between Species
doi.org/10.1186/s12864-022-08450-7
![OCR Ortholog Open Chromatin Status Prediction Framework Overview. a We trained a convolutional neural network (CNN) for predicting brain open chromatin using sequences underlying brain open chromatin region (OCR) orthologs in a small number of species and used the CNN to predict brain OCR ortholog open chromatin status across the species in the Zoonomia Consortium. Specifically, we used the sequences underlying the orthologs for which we have brain open chromatin data to train a CNN for predicting open chromatin. Then, we used the CNN to predict the probability of brain open chromatin for all brain OCR orthologs; predictions are illustrated on the right. Animals for which we do not have open chromatin data are in dark gray instead of black to indicate that their brain open chromatin is imputed. While we cannot evaluate the accuracy of most of our predictions, obtaining open chromatin data from most tissues in most species is infeasible, so predictions might be the best OCR annotations that we can obtain. b To demonstrate that our models can accurately predict whether sequence differences between species are associated with open chromatin differences, in addition to the evaluations described in previous work [57], we evaluated our performance on species-specific open chromatin for a species not used in model training and clade-specific open and closed chromatin for clades not used in model training. Since such regions often comprise a minority of OCR orthologs, models could obtain good overall performance while obtaining poor performance on such regions. We also evaluated our performance on tissue-specific open and closed chromatin for a tissue not used in model training, where we expect models to predict 0 if model learns sequence signatures related to the tissue used in training. c Full mouse test set and lineage-specific OCR accuracy evaluations for mouse sequence-only brain model, illustrating that, even for the best of these models,](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:jkd2l647lviezhenqed454lh/bafkreicgkhegfuippjqhdt2tkku6dr74stuf5znohmtovfk5zojt5w7xkq@jpeg)
November 7, 2025 at 2:28 PM
Third day of Genome Informatics #GI2025 began with an exciting session on “AI, ML and Integrative Genomics” chaired by Irene Kaplow & Thomas Pierrot.
The first talk, by Irene Kaplow, focused on Challenges in Predicting Enhancer Activity Differences Between Species
doi.org/10.1186/s12864-022-08450-7
The first talk, by Irene Kaplow, focused on Challenges in Predicting Enhancer Activity Differences Between Species
doi.org/10.1186/s12864-022-08450-7
Reposted by Camille Marchet ⚡
I wrote a review of James Watson's obituary by CSHL: liorpachter.wordpress.com/2025/11/08/r...
Review of Cold Spring Harbor Laboratory’s Obituary for Dr. James Watson
James Watson, who described himself as “not a racist in a conventional way”, has died at the age of 97. Below is a review of an obituary for Dr. James Watson published by Cold Spring Ha…
liorpachter.wordpress.com
November 8, 2025 at 9:58 PM
I wrote a review of James Watson's obituary by CSHL: liorpachter.wordpress.com/2025/11/08/r...
Reposted by Camille Marchet ⚡
Watson did untold and irreparable damage to science, to its practice, & to people (including talented and brilliant people) along the way whom he disfavored. He was undeniably racist and sexist. He was vehemently anti-Irish. He hurt many people & science's reputation. Yet, the below is still true 👇
If you believe either that Franklin discovered the double helix, and / or Watson and Crick stole her data, ask yourself how you know this. Then take a read of this article.
If I see one more stupid Rosalind Franklin take I'm going to lose my mind. Thank god for @matthewcobb.bsky.social and @nccomfort.bsky.social. www.nature.com/articles/d41...
November 8, 2025 at 2:53 PM
Watson did untold and irreparable damage to science, to its practice, & to people (including talented and brilliant people) along the way whom he disfavored. He was undeniably racist and sexist. He was vehemently anti-Irish. He hurt many people & science's reputation. Yet, the below is still true 👇
Reposted by Camille Marchet ⚡
Yes, some people's legacies are complicated. For example, Watson. After all, though he was racist, don't forget his other traits. For example, he was also sexist. And also anti-semitic. And a data / idea thief. So let's not forget all the different facets.
November 8, 2025 at 12:52 AM
Yes, some people's legacies are complicated. For example, Watson. After all, though he was racist, don't forget his other traits. For example, he was also sexist. And also anti-semitic. And a data / idea thief. So let's not forget all the different facets.
Reposted by Camille Marchet ⚡
When people celebrate the individual genius of folks in science, they should also
mourn the collective loss of genius of folks who were actively discouraged or disadvantaged from a career in science because of the same person(s)
mourn the collective loss of genius of folks who were actively discouraged or disadvantaged from a career in science because of the same person(s)
November 7, 2025 at 11:43 PM
When people celebrate the individual genius of folks in science, they should also
mourn the collective loss of genius of folks who were actively discouraged or disadvantaged from a career in science because of the same person(s)
mourn the collective loss of genius of folks who were actively discouraged or disadvantaged from a career in science because of the same person(s)
Reposted by Camille Marchet ⚡
C'est une mise au grand jour éclatante de l'idéologie insensée de nos dirigeants, choisissant entre :
- mettre une taxe-plancher indolore de 2% sur la fortune de 1 800 ultra-riches, et
- détruire le pouvoir d'achat et la confiance de 5,7 millions d'agents publics qui rendent des services vitaux.
- mettre une taxe-plancher indolore de 2% sur la fortune de 1 800 ultra-riches, et
- détruire le pouvoir d'achat et la confiance de 5,7 millions d'agents publics qui rendent des services vitaux.
a woman is making a funny face with the words crystal clear above her
ALT: a woman is making a funny face with the words crystal clear above her
media.tenor.com
November 8, 2025 at 9:16 AM
C'est une mise au grand jour éclatante de l'idéologie insensée de nos dirigeants, choisissant entre :
- mettre une taxe-plancher indolore de 2% sur la fortune de 1 800 ultra-riches, et
- détruire le pouvoir d'achat et la confiance de 5,7 millions d'agents publics qui rendent des services vitaux.
- mettre une taxe-plancher indolore de 2% sur la fortune de 1 800 ultra-riches, et
- détruire le pouvoir d'achat et la confiance de 5,7 millions d'agents publics qui rendent des services vitaux.
Les collègues avaient trouvé une super idée pour un prix à une conférence : avoir son travail illustré par quelqu'un dont c'est le métier. Je mets ça là au cas où :D
Academia.edu propose de faire générer des BD par IA à partir des papiers (ou de leurs abstracts).
Je ne sais pas si ce sera pire que ce que produisent les services com’
Je ne sais pas si ce sera pire que ce que produisent les services com’
Academia.edu - Find Research Papers, Topics, Researchers
Academia.edu is the platform to share, find, and explore 50 Million research papers. Join us to accelerate your research needs & academic interests.
Academia.edu
November 8, 2025 at 11:15 AM
Les collègues avaient trouvé une super idée pour un prix à une conférence : avoir son travail illustré par quelqu'un dont c'est le métier. Je mets ça là au cas où :D
Reposted by Camille Marchet ⚡
Yana Safonova (Penn State) delivered the keynote "Enabling biomedical discoveries through immunogenomics
approaches"
Mammalian Immune Luci: doi.org/10.1093/molbev/msaf152
PatchWorkPlot: doi.org/10.1093/bioinformatics/btaf504
approaches"
Mammalian Immune Luci: doi.org/10.1093/molbev/msaf152
PatchWorkPlot: doi.org/10.1093/bioinformatics/btaf504
November 7, 2025 at 10:34 PM
Yana Safonova (Penn State) delivered the keynote "Enabling biomedical discoveries through immunogenomics
approaches"
Mammalian Immune Luci: doi.org/10.1093/molbev/msaf152
PatchWorkPlot: doi.org/10.1093/bioinformatics/btaf504
approaches"
Mammalian Immune Luci: doi.org/10.1093/molbev/msaf152
PatchWorkPlot: doi.org/10.1093/bioinformatics/btaf504
Reposted by Camille Marchet ⚡
Really excited to see our new work in scaling Mumemto to any size pangenome published in Genome Research this morning. And right on cue with the great opportunity to present this work at #GI2025 this week.
#GI2025 Vikram Shivakumar from Ben Langmead's lab (@benlangmead.bsky.social) presents "MumemtoM - partitioned Multi-MUM finding for scalable pangenomics ". Now published in Genome Research @genomeresearch.bsky.social. Read full text here ➡️ tinyurl.com/Genome-Res-2...
November 7, 2025 at 9:29 PM
Really excited to see our new work in scaling Mumemto to any size pangenome published in Genome Research this morning. And right on cue with the great opportunity to present this work at #GI2025 this week.
Reposted by Camille Marchet ⚡
Hey folks, as news of Watson's demise spreads, please don't set aside his weighty legacy of misogyny and racism. He was truly among the worst of us. www.vox.com/2019/1/15/18...
DNA scientist James Watson has a remarkably long history of sexist, racist public comments
“People say it would be terrible if we made all girls pretty,” he said in 2003. “I think it would be great.”
www.vox.com
November 7, 2025 at 7:45 PM
Hey folks, as news of Watson's demise spreads, please don't set aside his weighty legacy of misogyny and racism. He was truly among the worst of us. www.vox.com/2019/1/15/18...
Third day covered! Thank you Sina #GI2025
Third day of Genome Informatics #GI2025 began with an exciting session on “AI, ML and Integrative Genomics” chaired by Irene Kaplow & Thomas Pierrot.
The first talk, by Irene Kaplow, focused on Challenges in Predicting Enhancer Activity Differences Between Species
doi.org/10.1186/s12864-022-08450-7
The first talk, by Irene Kaplow, focused on Challenges in Predicting Enhancer Activity Differences Between Species
doi.org/10.1186/s12864-022-08450-7
November 7, 2025 at 6:51 PM
Third day covered! Thank you Sina #GI2025
Reposted by Camille Marchet ⚡
On commence à voir apparaitre des motions en lien avec la disparition de postes décidée unilatéralement par la Direction Général après les jurys d'admission
Plusieurs postes CR Inria (au moins 3 sur 18) n'ont pas été pourvus alors qu'il restait des personnes sur liste complémentaire. Ceci se rajoute à un poste DR externe (sur 2).
Plus de budget ? Plafond d'emploi dépassé ? Ou "stratégie" scientifique ? Pour l'instant nous n'avons pas d'information.
Plus de budget ? Plafond d'emploi dépassé ? Ou "stratégie" scientifique ? Pour l'instant nous n'avons pas d'information.
November 6, 2025 at 2:23 PM
On commence à voir apparaitre des motions en lien avec la disparition de postes décidée unilatéralement par la Direction Général après les jurys d'admission
Reposted by Camille Marchet ⚡
Mme la Présidente,il est regrettable qu’une réaction «à chaud» amène à une mauvaise interprétation de la #laïcité.
Les personnes du public sont des usagers donc pas soumis à la neutralité ni à la loi de 2004 qui ne concerne que les élèves du public (sauf si c’est 1 sortie scolaire).
MÊME SI…
THREAD
Les personnes du public sont des usagers donc pas soumis à la neutralité ni à la loi de 2004 qui ne concerne que les élèves du public (sauf si c’est 1 sortie scolaire).
MÊME SI…
THREAD
November 6, 2025 at 9:10 AM
Mme la Présidente,il est regrettable qu’une réaction «à chaud» amène à une mauvaise interprétation de la #laïcité.
Les personnes du public sont des usagers donc pas soumis à la neutralité ni à la loi de 2004 qui ne concerne que les élèves du public (sauf si c’est 1 sortie scolaire).
MÊME SI…
THREAD
Les personnes du public sont des usagers donc pas soumis à la neutralité ni à la loi de 2004 qui ne concerne que les élèves du public (sauf si c’est 1 sortie scolaire).
MÊME SI…
THREAD