RobusTAD: reference panel based annotation of nested topologically associating domains
Yanlin Zhang
Rola Dali
Mathieu Blanchette
Topologically associating domains (TADs) are fundamental units of 3D genomes and play essential roles in gene regulation. Hi-C data suggests… (see more) a hierarchical organization of TADs. Accurately annotating nested TADs from Hi-C data remains challenging, both in terms of the precise identification of boundaries and the correct inference of hierarchies. While domain boundary is relatively well conserved across cells, few approaches have taken advantage of this fact. Here, we present RobusTAD to annotate TAD hierarchies. It incorporates additional Hi-C data to refine boundaries annotated from the study sample. RobusTAD outperforms existing tools at boundary and domain annotation across several benchmarking tasks. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-025-03568-9.
2025-05-19
Genome Biology (published)
doi.org
Beyond Scalar Rewards: An Axiomatic Framework for Lexicographic MDPs
Mehran Shakerinava
Siamak Ravanbakhsh
Adam M. Oberman
2025-05-17
ArXiv (preprint)
arxiv.org
arxiv.org
FedWeight: mitigating covariate shift of federated learning on electronic health records data through patients re-weighting
Mike He Zhu
Jun Bai
Na Li
Xiaoxiao Li
Dianbo Liu
David Buckeridge
Yue Li
2025-05-17
NPJ Digital Medicine (published)
doi.org
Search-Based Correction of Reasoning Chains for Language Models
Minsu Kim
Jean-Pierre R. Falet
Oliver E. Richardson
Xiaoyin Chen
Moksh J. Jain
Sungjin Ahn
Sungsoo Ahn
Yoshua Bengio
2025-05-17
ArXiv (preprint)
arxiv.org
arxiv.org
A multi-ancestry genetic reference for the Quebec population
Peyton McClelland
Georgette Femerling
R. Laflamme
Alejandro Mejia-Garcia
Mohadese Sayahian Dehkordi
Hongyu Xiao
Alex Diaz-Papkovich
Justin Pelletier
Jean-Christophe Grenier
Ken Sin Lo
Luke Anderson-Trocmé
Justin Bellavance
Vincent Chapdelaine
Geneviève Gagnon
Annelie De Mori
Gerardo Martinez
Kristen Mohler
Thibault de Malliard
Catherine Labbé
Marjorie Labrecque … (see 14 more)
Alexandre Montpetit
D. Spiegelman
Guy A. Rouleau
Jean-francois Théroux
Hufeng Zhou
Simon L. Girard
Julie Hussin
Anne-Marie Laberge
C. Bhérer
Martine Tétreault
Sarah A. Gagliano Taliun
Daniel Taliun
Simon Gravel
Guillaume Lettre
While international efforts have characterized genetic variation in millions of individuals, the interplay of environmental, social, cultura… (see more)l, and genetic factors is poorly understood for most worldwide populations. The province of Quebec in Canada has been the site of numerous genetic studies, often focusing on individual Mendelian diseases in founder sub-populations. Here, we profiled and analyzed genome-wide genotyped variation in 29,337 Quebec residents from the large population-based cohort CARTaGENE (CaG), including rich phenotype and environmental data. We also sequenced the whole-genome of 2,173 CaG participants, including 163 and 132 individuals with grandparents born in Haiti and Morocco, respectively. We use this genetic information to gain insight into Quebec's demography and to help interpret the potential significance of variants identified in clinically important genes. We built an imputation panel by phasing the CaG whole-genome sequence data and showed, using genome-wide association studies (GWAS), how it improves the discovery of phenotype-genotype associations in this population. We provide allele frequency information and GWAS results through dedicated and publicly available websites. The genetic data, paired with phenotypic and environmental information, is also available for research use upon scientific and ethical review.
2025-05-16
medRxiv (preprint)
doi.org
A Modular Approach for Clinical SLMs Driven by Synthetic Data with Pre-Instruction Tuning, Model Merging, and Clinical-Tasks Alignment
Jean-Philippe Corbeil
Amin Dada
Jean-Michel Attendu
Asma Ben Abacha
Alessandro Sordoni
Lucas Caccia
Franccois Beaulieu
Thomas Lin
Jens Kleesiek
Paul Vozila
2025-05-15
ArXiv (preprint)
arxiv.org
arxiv.org
Persistent signs of poisoning after massive drug ingestion: move the ultrasound probe to the stomach.
N. Lautrou-cabasson
H. Pirollet
C. Lombois
Guillaume Dumas
2025-05-15
Intensive Care Medicine (published)
doi.org
Plasticity as the Mirror of Empowerment
David Abel
Michael Bowling
Andre Barreto
Will Dabney
Shi Dong
Steven Hansen
Anna Harutyunyan
Khimya Khetarpal
Clare Lyle
Razvan Pascanu
Georgios Piliouras
Doina Precup
Jonathan Richens
Mark Rowland
Tom Schaul
Satinder Singh
2025-05-15
ArXiv (preprint)
arxiv.org
arxiv.org
Language Agents Mirror Human Causal Reasoning Biases. How Can We Help Them Think Like Scientists?
Anthony GX-Chen
Dongyan Lin
Mandana Samiei
Doina Precup
Blake Richards
Rob Fergus
Kenneth Marino
2025-05-14
ArXiv (preprint)
arxiv.org
arxiv.org
The CASTOR mission
Patrick Côté
T. Woods
John Hutchings
J. Rhodes
R. Sánchez-Janssen
Alan D. Scott
J. Pazder
Melissa Amenouche
Michael Balogh
Simon Blouin
Alain Cournoyer
M. Drout
Nick Kuzmin
Katherine J. Mack
Laura Ferrarese
Wesley C. Fraser
Sarah C. Gallagher
Frederic J. Grandmont
Daryl Haggard
Paul Harrison … (see 160 more)
Vincent Hénault-Brunet
J. Kavelaars
V. Khatu
J. Roediger
J. Rowe
Marcin Sawicki
Jesper Skottfelt
Matt Taylor
Ludo van Waerbeke
Laurie Amen
Dhananjhay Bansal
Martin Bergeron
Toby Brown
Greg Burley
Hum Chand
Isaac Cheng
Ryan Cloutier
N. Dickson
Oleg Djazovski
Ivana Damjanov
James Doherty
K. Finner
Macarena García Del Valle Espinosa
Jennifer Glover
A. I. Gómez de Castro
Or Graur
Tim Hardy
Michelle Kao
D A Leahy
Deborah Lokhorst
A. I. Malz
Allison Man
Madeline A. Marshall
Sean McGee
Ryan McKenzie
Kai Michaud
Surhud S. More
David Morris
Patrick W. Morris
T. Moutard
Wasi Naqvi
Matthew Nicholl
G. Noirot
M. S. Oey
C. Opitom
Samir Salim
Bryan R. Scott
Charles Shapiro
Daniel Stern
A. Subramaniam
David Thilke
I. Wevers
Dmitri Vorobiev
L. Y. Aaron Yung
Frédéric Zamkotsian
S. Aigrain
A. Alavi
Martin Barstow
Peter Bartosik
Hadleigh Bluhm
J. Bovy
Peter Cameron
R. Carlberg
Jessie L. Christiansen
Yuyang Chen
Paul Crowther
Kristen Dage
Aaron Dotter
Patrick Dufour
Jean Dupuis
B. Dryer
A. Duara
Gwendolyn M. Eadie
Marielle R. Eduardo
V. Estrada-Carpenter
Sebastien Fabbro
A. Faisst
N. M. Ford
Morgan Fraser
Boris T. Gaensicke
Shashkiran Ganesh
Poshak Gandhi
Melissa L. Graham
Rebecca Hamel
Martin Hellmich
John J. Hennessy
Kaitlyn Hessel
J. Heyl
Catherine Heymans
Yashar Hezaveh
Renée Hložek
Michael Hoenk
Andrew Holland
Eric Huff
Ian Hutchinson
Ikuru Iwata
April D. Jewell
Doug Johnstone
Maia Jones
Todd J. Jones
D. Lang
J. Lapington
Justin Larivière
C. Lawlor-Forsyth
Denis Laurin
Charles Lee
Ronan Legin
Ting S. Li
Sungsoon Lim
B. Ludwig
Matt Kozun
V. M
Robert Mann
Alan McConnachie
Evan McDonough
S. Metchev
David R. Miller
Takashi Moriya
Cameron Morgan
Julio F. Navarro
Y. Nazé
Shouleh Nikzad
Vivek Oad
N. N.-Q. Ouellette
E. Pass
Will J. Percival
Laurence Perreault-Levasseur
Joe Postma
Nayyer Raza
G. T. Richards
Harvey Richer
Carmelle Robert
Erik Rosolowsky
J. Ruan
Sarah Rugheimer
S. Safi-Harb
Kanak Saha
Vicky Scowcroft
F. Sestito
Himanshu Sharma
James Sikora
G. Sivakoff
T. S. Sivarani
Patrick Smith
Warren Soh
R. Sorba
S. Subramanian
Hossen Teimoorinia
H. Teplitz
Shaylin Thadani
Shavon Thadani
Aaron Tohuvavohu
K. Venn
Nicholas Vieira
Jeremy J. Webb
P. Wiegert
Ryan Wierckx
Yanqin Wu
Jade Yeung
S. K. Yi
2025-05-14
Journal of Astronomical Telescopes Instruments and Systems (published)
doi.org
The CASTOR mission
Patrick Côté
T. Woods
John Hutchings
J. Rhodes
R. Sánchez-Janssen
Alan D. Scott
J. Pazder
Melissa Amenouche
Michael Balogh
Simon Blouin
Alain Cournoyer
M. Drout
Nick Kuzmin
Katherine J. Mack
Laura Ferrarese
Wesley C. Fraser
Sarah C. Gallagher
Frederic J. Grandmont
Daryl Haggard
Paul Harrison … (see 160 more)
Vincent Hénault-Brunet
J. Kavelaars
V. Khatu
J. Roediger
J. Rowe
Marcin Sawicki
Jesper Skottfelt
Matt Taylor
Ludo van Waerbeke
Laurie Amen
Dhananjhay Bansal
Martin Bergeron
Toby Brown
Greg Burley
Hum Chand
Isaac Cheng
Ryan Cloutier
N. Dickson
Oleg Djazovski
Ivana Damjanov
James Doherty
K. Finner
Macarena García Del Valle Espinosa
Jennifer Glover
A. I. Gómez de Castro
Or Graur
Tim Hardy
Michelle Kao
D A Leahy
Deborah Lokhorst
A. I. Malz
Allison Man
Madeline A. Marshall
Sean McGee
Ryan McKenzie
Kai Michaud
Surhud S. More
David Morris
Patrick W. Morris
T. Moutard
Wasi Naqvi
Matthew Nicholl
G. Noirot
M. S. Oey
C. Opitom
Samir Salim
Bryan R. Scott
Charles Shapiro
Daniel Stern
A. Subramaniam
David Thilke
I. Wevers
Dmitri Vorobiev
L. Y. Aaron Yung
Frédéric Zamkotsian
S. Aigrain
A. Alavi
Martin Barstow
Peter Bartosik
Hadleigh Bluhm
J. Bovy
Peter Cameron
R. Carlberg
J. Christiansen
Yuyang Chen
P. Crowther
Kristen Dage
Aaron Dotter
Patrick Dufour
Jean Dupuis
B. Dryer
A. Duara
Gwendolyn M. Eadie
Marielle R. Eduardo
V. Estrada-Carpenter
Sebastien Fabbro
A. Faisst
N. M. Ford
Morgan Fraser
Boris T. Gaensicke
Shashkiran Ganesh
Poshak Gandhi
Melissa L. Graham
Rebecca Hamel
Martin Hellmich
John J. Hennessy
Kaitlyn Hessel
J. Heyl
Catherine Heymans
Yashar Hezaveh
Renée Hložek
Michael Hoenk
Andrew Holland
Eric Huff
Ian Hutchinson
Ikuru Iwata
April D. Jewell
Doug Johnstone
Maia Jones
Todd J. Jones
D. Lang
J. Lapington
Justin Larivière
C. Lawlor-Forsyth
Denis Laurin
Charles Lee
Ronan Legin
Ting S. Li
Sungsoon Lim
B. Ludwig
Matt Kozun
V. M
Robert Mann
Alan McConnachie
Evan McDonough
S. Metchev
David R. Miller
Takashi Moriya
Cameron Morgan
Julio F. Navarro
Y. Nazé
Shouleh Nikzad
Vivek Oad
N. N.-Q. Ouellette
E. Pass
Will J. Percival
Laurence Perreault-Levasseur
Joe Postma
Nayyer Raza
G. T. Richards
Harvey Richer
Carmelle Robert
Erik Rosolowsky
J. Ruan
Sarah Rugheimer
S. Safi-Harb
Kanak Saha
Vicky Scowcroft
F. Sestito
Himanshu Sharma
James Sikora
G. Sivakoff
T. S. Sivarani
Patrick Smith
Warren Soh
R. Sorba
S. Subramanian
Hossen Teimoorinia
H. Teplitz
Shaylin Thadani
Shavon Thadani
Aaron Tohuvavohu
K. Venn
Nicholas Vieira
Jeremy J. Webb
P. Wiegert
Ryan Wierckx
Yanqin Wu
Jade Yeung
S. K. Yi
2025-05-14
Journal of Astronomical Telescopes Instruments and Systems (published)
doi.org
The CASTOR mission
Patrick Côté
Tyrone E. Woods
John B. Hutchings
Jason D. Rhodes
Rubén Sánchez-Janssen
Alan D. Scott
John Pazder
Melissa Amenouche
Michael Balogh
Simon Blouin
Alain Cournoyer
Maria R. Drout
Nick Kuzmin
Katherine J. Mack
Laura Ferrarese
Wesley C. Fraser
Sarah C. Gallagher
Frédéric Grandmont
Daryl Haggard
Paul Harrison … (see 160 more)
Vincent Hénault-Brunet
J. J. Kavelaars
Viraja Khatu
Joel C. Roediger
Jason Rowe
Marcin Sawicki
Jesper Skottfelt
Matt Taylor
Ludo van Waerbeke
Laurie Amen
Dhananjhay Bansal
Martin Bergeron
Toby Brown
Greg Burley
Hum Chand
Isaac Cheng
Ryan Cloutier
Nolan Dickson
Oleg Djazovski
Ivana Damjanov
James Doherty
Kyle Finner
Macarena García Del Valle Espinosa
Jennifer Glover
Ana I. Gómez de Castro
Or Graur
Tim Hardy
Michelle Kao
Denis Leahy
Deborah Lokhorst
Alex I. Malz
Allison Man
Madeline A. Marshall
Sean McGee
Ryan McKenzie
Kai Michaud
Surhud S. More
David Morris
Patrick W. Morris
Thibaud Moutard
Wasi Naqvi
Matt Nicholl
Gaël Noirot
M. S. Oey
Cyrielle Opitom
Samir Salim
Bryan R. Scott
Charles A. Shapiro
Daniel Stern
Annapurni Subramaniam
David Thilke
Ivan Wevers
Dmitri Vorobiev
L. Y. Aaron Yung
Frédéric Zamkotsian
Suzanne Aigrain
Anahita Alavi
Martin Barstow
Peter Bartosik
Hadleigh Bluhm
Jo Bovy
Peter Cameron
Raymond G. Carlberg
Jessie L. Christiansen
Yuyang Chen
Paul Crowther
Kristen Dage
Aaron L. Dotter
Patrick Dufour
Jean Dupuis
Ben Dryer
Angaraj Duara
Gwendolyn M. Eadie
Marielle R. Eduardo
Vincente Estrada-Carpenter
Sebastien Fabbro
Andreas Faisst
Nicole M. Ford
Morgan Fraser
Boris T. Gaensicke
Shashkiran Ganesh
Poshak Gandhi
Melissa L. Graham
Rebecca Hamel
Martin Hellmich
John Hennessy
Kaitlyn Hessel
Jeremy Heyl
Catherine Heymans
Yashar Hezaveh
Renée Hložek
Michael E. Hoenk
Andrew Holland
Eric Huff
Ian Hutchinson
Ikuru Iwata
April D. Jewell
Doug Johnstone
Maia Jones
Todd Jones
Dustin Lang
Jon Lapington
Justin Larivière
Cameron Lawlor-Forsyth
Denis Laurin
Charles Lee
Ronan Legin
Ting S. Li
Sungsoon Lim
Bethany Ludwig
Matt Kozun
Vivek M.
Robert Mann
Alan W. McConnachie
Evan McDonough
Stanimir Metchev
David R. Miller
Takashi Moriya
Cameron Morgan
Julio Navarro
Yaël Nazé
Shouleh Nikzad
Vivek Oad
Nathalie Ouellette
Emily K. Pass
Will J. Percival
Laurence Perreault Levasseur
Joe Postma
Nayyer Raza
Gordon T. Richards
Harvey Richer
Carmelle Robert
Erik Rosolowsky
John J. Ruan
Sarah Rugheimer
Samar Safi-Harb
Kanak Saha
Vicky Scowcroft
Federico Sestito
Himanshu Sharma
James Sikora
Gregory R. Sivakoff
Thirupathi Sivarani
Patrick Smith
Warren Soh
Robert Sorba
Smitha Subramanian
Hossen Teimoorinia
Harry I. Teplitz
Shaylin Thadani
Shavon Thadani
Aaron Tohuvavohu
Kim A. Venn
Nicholas Vieira
Jeremy J. Webb
Paul Wiegert
Ryan Wierckx
Yanqin Wu
Jade Yeung
Sukyoung K. Yi
2025-05-14
Journal of Astronomical Telescopes, Instruments, and Systems (published)
doi.org