Accèder directement au contenu

Publications

2022

Recommendations for empowering early career researchers to improve research culture and practice.
Kent BA, Holman C, Amoako E, Antonietti A, Azam JM, Ballhausen H, Bediako Y, Belasen AM, Carneiro CFD, Chen YC, Compeer EB, Connor CAC, Crüwell S, Debat H, Dorris E, Ebrahimi H, Erlich JC, Fernández‑Chiappe F, Fischer F, Gazda MA, Glatz T, Grabitz P, Heise V, Kent DG, Lo H, McDowell G, Mehta D, Neumann WJ, Neves K, Patterson M, Penfold NC, Piper SK, Puebla I, Quashie PK, Quezada CP, Riley JL, Rohmann JL, Saladi S, Schwessinger B, Siegerink B, Stehlik P, Tzilivaki A, Umbers KDL, Varma A, Walavalkar K, de Winde CM, Zaza C, Weissgerber TL
PLoS Biol. 2022 Jul 7. 20(7):e3001680.

Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks.
Voznica J, Zhukova A, Boskova V, Saulnier E, Lemoine F, Moslonka‑Lefebvre M, Gascuel O
Nat Commun. 2022 Jul 6. 13(1):3896.

A self-consistent analytical theory for rotator networks under stochastic forcing : Effects of intrinsic noise and common input.
Ranft J, Lindner B
Chaos. 2022 Jun. 32(6):063131.

Antennal movements can be used as behavioral readout of odor valence in honey bees.
Gascue F, Marachlian E, Azcueta M, Locatelli FF, Klappenbach M
IBRO Neurosci Rep. 2022 Jun. 12:323-332.

Critical slowing down may account for the robustness of development.
Zhang W, Scerbo P, Ducos B, Bensimon D
Proc Natl Acad Sci U S A. 2022 Jun 28. 119(26):e2205630119.

Biosynthetic potential of the global ocean microbiome.
Paoli L, Ruscheweyh HJ, Forneris CC, Hubrich F, Kautsar S, Bhushan A, Lotti A, Clayssen Q, Salazar G, Milanese A, Carlström CI, Papadopoulou C, Gehrig D, Karasikov M, Mustafa H, Larralde M, Carroll LM, Sánchez P, Zayed AA, Cronin DR, Acinas SG, Bork P, Bowler C, Delmont TO, Gasol JM, Gossert AD, Kahles A, Sullivan MB, Wincker P, Zeller G, Robinson SL, Piel J, Sunagawa S
Nature. 2022 Jul. 607(7917):111-118.

GluN3A excitatory glycine receptors control adult cortical and amygdalar circuits.
Bossi S, Dhanasobhon D, Ellis‑Davies GCR, Frontera J, de Brito Van Velze M, Lourenço J, Murillo A, Luján R, Casado M, Perez‑Otaño I, Bacci A, Popa D, Paoletti P, Rebola N
Neuron. 2022 Jun 10.

Functional abnormalities in the cerebello-thalamic pathways in a mouse model of DYT25 dystonia.
Aïssa HB, Sala RW, Georgescu Margarint EL, Frontera JL, Varani AP, Menardy F, Pelosi A, Hervé D, Léna C, Popa D
Elife. 2022 Jun 14. 11.

Cerebellar stimulation prevents Levodopa-induced dyskinesia in mice and normalizes activity in a motor network.
Coutant B, Frontera JL, Perrin E, Combes A, Tarpin T, Menardy F, Mailhes‑Hamon C, Perez S, Degos B, Venance L, Léna C, Popa D
Nat Commun. 2022 Jun 9. 13(1):3211.

Diversity and ecological footprint of Global Ocean RNA viruses.
Dominguez‑Huerta G, Zayed AA, Wainaina JM, Guo J, Tian F, Pratama AA, Bolduc B, Mohssen M, Zablocki O, Pelletier E, Delage E, Alberti A, Aury JM, Carradec Q, da Silva C, Labadie K, Poulain J, Bowler C, Eveillard D, Guidi L, Karsenti E, Kuhn JH, Ogata H, Wincker P, Culley A, Chaffron S, Sullivan MB
Science. 2022 Jun 10. 376(6598):1202-1208.

Genome-wide mapping of individual replication fork velocities using nanopore sequencing.
Theulot B, Lacroix L, Arbona JM, Millot GA, Jean E, Cruaud C, Pellet J, Proux F, Hennion M, Engelen S, Lemainque A, Audit B, Hyrien O, Le Tallec B
Nat Commun. 2022 Jun 8. 13(1):3295.

Mafa-dependent GABAergic activity promotes mouse neonatal apneas.
Lecoin L, Dempsey B, Garancher A, Bourane S, Ruffault PL, Morin‑Surun MP, Rocques N, Goulding M, Eychène A, Pouponnot C, Fortin G, Champagnat J
Nat Commun. 2022 Jun 7. 13(1):3284.

Macroevolutionary dynamics of climatic niche space.
Quintero I, Suchard MA, Jetz W
Proc Biol Sci. 2022 May 25. 289(1975):20220091.

Erratum : Author Correction : Malaria elimination on Hainan Island despite climate change.
Tian H, Li N, Li Y, Kraemer MUG, Tan H, Liu Y, Li Y, Wang B, Wu P, Cazelles B, Lourenço J, Gao D, Sun D, Song W, Li Y, Pybus OG, Wang G, Dye C
Commun Med (Lond). 2022. 2:22.

Malaria elimination on Hainan Island despite climate change.
Tian H, Li N, Li Y, Kraemer MUG, Tan H, Liu Y, Li Y, Wang B, Wu P, Cazelles B, Lourenço J, Gao D, Sun D, Song W, Li Y, Pybus OG, Wang G, Dye C
Commun Med (Lond). 2022. 2:12.

Modified climbing fiber/Purkinje cell synaptic connectivity in the cerebellum of the neonatal phencyclidine model of schizophrenia.
Veleanu M, Urrieta‑Chávez B, Sigoillot SM, Paul MA, Usardi A, Iyer K, Delagrange M, Doyle JP, Heintz N, Bécamel C, Selimi F
Proc Natl Acad Sci U S A. 2022 May 24. 119(21):e2122544119.

A unique cerebellar pattern of microglia activation in a mouse model of encephalopathy of prematurity.
Klein L, Van Steenwinckel J, Fleiss B, Scheuer T, Bührer C, Faivre V, Lemoine S, Blugeon C, Schwendimann L, Csaba Z, Bokobza C, Vousden DA, Lerch JP, Vernon AC, Gressens P, Schmitz T
Glia. 2022 May 17.

RSAT 2022 : regulatory sequence analysis tools.
Santana‑Garcia W, Castro‑Mondragon JA, Padilla‑Gálvez M, Nguyen NTT, Elizondo‑Salas A, Ksouri N, Gerbes F, Thieffry D, Vincens P, Contreras‑Moreira B, van Helden J, Thomas‑Chollier M, Medina‑Rivera A
Nucleic Acids Res. 2022 May 11.

Environmental cues from neural crest derivatives act as metastatic triggers in an embryonic neuroblastoma model.
Ben Amar D, Thoinet K, Villalard B, Imbaud O, Costechareyre C, Jarrosson L, Reynaud F, Novion Ducassou J, Couté Y, Brunet JF, Combaret V, Corradini N, Delloye‑Bourgeois C, Castellani V
Nat Commun. 2022 May 10. 13(1):2549.

FORK-seq : Single-Molecule Profiling of DNA Replication.
Hennion M, Theulot B, Arbona JM, Audit B, Hyrien O
Methods Mol Biol. 2022. 2477:107-128.

Classification of non-coding variants with high pathogenic impact.
Moyon L, Berthelot C, Louis A, Nguyen NTT, Roest Crollius H
PLoS Genet. 2022 Apr. 18(4):e1010191.

Molecular biology for green recovery-A call for action.
Rodríguez‑Martínez M, Nielsen J, Dupont S, Vamathevan J, Glover BJ, Crosswell LC, Rouse B, Luisi BF, Bowler C, Gasser SM, Arendt D, Erb TJ, de Lorenzo V, Heard E, Patil KR
PLoS Biol. 2022 Apr. 20(4):e3001623.

Analysing diversification dynamics using barcoding data : The case of an obligate mycorrhizal symbiont.
Perez‑Lamarque B, Öpik M, Maliet O, Afonso Silva AC, Selosse MA, Martos F, Morlon H
Mol Ecol. 2022 Jun. 31(12):3496-3512.

Astroblastomas exhibit radial glia stem cell lineages and differential expression of imprinted and X-inactivation escape genes.
Lehman NL, Spassky N, Sak M, Webb A, Zumbar CT, Usubalieva A, Alkhateeb KJ, McElroy JP, Maclean KH, Fadda P, Liu T, Gangalapudi V, Carver J, Abdullaev Z, Timmers C, Parker JR, Pierson CR, Mobley BC, Gokden M, Hattab EM, Parrett T, Cooke RX, Lehman TD, Costinean S, Parwani A, Williams BJ, Jensen RL, Aldape K, Mistry AM
Nat Commun. 2022 Apr 19. 13(1):2083.

Step by step : cells with multiple functions in cortical circuit assembly.
Cossart R, Garel S
Nat Rev Neurosci. 2022 Jul. 23(7):395-410.

Dynamic interplay between thalamic activity and Cajal-Retzius cells regulates the wiring of cortical layer 1.
Genescu I, Aníbal‑Martínez M, Kouskoff V, Chenouard N, Mailhes‑Hamon C, Cartonnet H, Lokmane L, Rijli FM, López‑Bendito G, Gambino F, Garel S
Cell Rep. 2022 Apr 12. 39(2):110667.

The relationship between rising temperatures and malaria incidence in Hainan, China, from 1984 to 2010 : a longitudinal cohort study.
Wang Z, Liu Y, Li Y, Wang G, Lourenço J, Kraemer M, He Q, Cazelles B, Li Y, Wang R, Gao D, Li Y, Song W, Sun D, Dong L, Pybus OG, Stenseth NC, Tian H
Lancet Planet Health. 2022 Apr. 6(4):e350-e358.

Best practices in metabarcoding of fungi : From experimental design to results.
Tedersoo L, Bahram M, Zinger L, Nilsson RH, Kennedy PG, Yang T, Anslan S, Mikryukov V
Mol Ecol. 2022 May. 31(10):2769-2795.

CRISPR/Cas9 gene editing uncovers the roles of CONSTITUTIVE TRIPLE RESPONSE 1 and REPRESSOR OF SILENCING 1 in melon fruit ripening and epigenetic regulation.
Giordano A, Santo Domingo M, Quadrana L, Pujol M, Martín‑Hernández AM, Garcia‑Mas J
J Exp Bot. 2022 Jun 24. 73(12):4022-4033.

Contribution of genome-scale metabolic modelling to niche theory.
Régimbeau A, Budinich M, Larhlimi A, Pierella Karlusich JJ, Aumont O, Memery L, Bowler C, Eveillard D
Ecol Lett. 2022 Jun. 25(6):1352-1364.

Sleep deficiency as a driver of cellular stress and damage in neurological disorders.
Coulson RL, Mourrain P, Wang GX
Sleep Med Rev. 2022 Jun. 63:101616.

Nest architecture is linked with ecological success in songbirds.
Medina I, M Perez D, Silva ACA, Cally J, León C, Maliet O, Quintero I
Ecol Lett. 2022 Jun. 25(6):1365-1375.

Prospectively defined patterns of APOBEC3A mutagenesis are prevalent in human cancers.
DeWeerd RA, Németh E, Póti Á, Petryk N, Chen CL, Hyrien O, Szüts D, Green AM
Cell Rep. 2022 Mar 22. 38(12):110555.

Eukaryotic cellular intricacies shape mitochondrial proteomic complexity.
Hammond M, Dorrell RG, Speijer D, Lukeš J
Bioessays. 2022 May. 44(5):e2100258.

UPMaBoSS : A Novel Framework for Dynamic Cell Population Modeling.
Stoll G, Naldi A, Noël V, Viara E, Barillot E, Kroemer G, Thieffry D, Calzone L
Front Mol Biosci. 2022. 9:800152.

Publisher Correction : Discovery of a genetic module essential for assigning left-right asymmetry in humans and ancestral vertebrates.
Szenker‑Ravi E, Ott T, Khatoo M, de Bellaing AM, Goh WX, Chong YL, Beckers A, Kannesan D, Louvel G, Anujan P, Ravi V, Bonnard C, Moutton S, Schoen P, Fradin M, Colin E, Megarbane A, Daou L, Chehab G, Di Filippo S, Rooryck C, Deleuze JF, Boland A, Arribard N, Eker R, Tohari S, Ng AY, Rio M, Lim CT, Eisenhaber B, Eisenhaber F, Venkatesh B, Amiel J, Crollius HR, Gordon CT, Gossler A, Roy S, Attie‑Bitach T, Blum M, Bouvagnet P, Reversade B
Nat Genet. 2022 Jun. 54(6):906.

Extra kinetic dimensions for label discrimination.
Chouket R, Pellissier‑Tanon A, Lahlou A, Zhang R, Kim D, Plamont MA, Zhang M, Zhang X, Xu P, Desprat N, Bourgeois D, Espagne A, Lemarchand A, Saux TL, Jullien L
Nat Commun. 2022 Mar 18. 13(1):1482.

Fast co-evolution of anti-silencing systems shapes the invasiveness of Mu-like DNA transposons in eudicots.
Sasaki T, Ro K, Caillieux E, Manabe R, Bohl‑Viallefond G, Baduel P, Colot V, Kakutani T, Quadrana L
EMBO J. 2022 Apr 19. 41(8):e110070.

Amber Suppression Technology for Mapping Site-specific Viral-host Protein Interactions in Mammalian Cells.
Isa NF, Bensaude O, Murphy S
Bio Protoc. 2022 Feb 5. 12(3):e4315.

Measuring the effects of COVID-19-related disruption on dengue transmission in southeast Asia and Latin America : a statistical modelling study.
Chen Y, Li N, Lourenço J, Wang L, Cazelles B, Dong L, Li B, Liu Y, Jit M, Bosse NI, Abbott S, Velayudhan R, Wilder‑Smith A, Tian H, Brady OJ
Lancet Infect Dis. 2022 May. 22(5):657-667.

Studying speciation and extinction dynamics from phylogenies : addressing identifiability issues.
Morlon H, Robin S, Hartig F
Trends Ecol Evol. 2022 Jun. 37(6):497-506.

Author Correction : HR-Bac, a toolbox based on homologous recombination for expression, screening and production of multiprotein complexes using the baculovirus expression system.
Kolesnikova O, Zachayus A, Pichard S, Osz J, Rochel N, Rossolillo P, Kolb‑Cheynel I, Troffer‑Charlier N, Compe E, Bensaude O, Berger I, Poterszman A
Sci Rep. 2022 Feb 24. 12(1):3443.

Hyperexcitable arousal circuits drive sleep instability during aging.
Li SB, Damonte VM, Chen C, Wang GX, Kebschull JM, Yamaguchi H, Bian WJ, Purmann C, Pattni R, Urban AE, Mourrain P, Kauer JA, Scherrer G, de Lecea L
Science. 2022 Feb 25. 375(6583):eabh3021.

Activity-dependent modulation of NMDA receptors by endogenous zinc shapes dendritic function in cortical neurons.
Morabito A, Zerlaut Y, Serraz B, Sala R, Paoletti P, Rebola N
Cell Rep. 2022 Feb 22. 38(8):110415.

Reply to Piochon et al. : NMDARs in Purkinje cells are not involved in parallel fiber-Purkinje cell synaptic plasticity or motor learning.
Schonewille M, Girasole AE, De Zeeuw CI, Bouvier G
Proc Natl Acad Sci U S A. 2022 Feb 22. 119(8).

Nucleosome Positioning on Large Tandem DNA Repeats of the ’601’ Sequence Engineered in Saccharomyces cerevisiae.
Lancrey A, Joubert A, Duvernois‑Berthet E, Routhier E, Raj S, Thierry A, Sigarteu M, Ponger L, Croquette V, Mozziconacci J, Boulé JB
J Mol Biol. 2022 Apr 15. 434(7):167497.

Intracellular reactive oxygen species trafficking participates in seed dormancy alleviation in Arabidopsis seeds.
Jurdak R, Rodrigues GAG, Chaumont N, Schivre G, Bourbousse C, Barneche F, Bou Dagher Kharrat M, Bailly C
New Phytol. 2022 May. 234(3):850-866.

Adaptations of intracellular bacteria to vacuolar or cytosolic niches.
Petit TJP, Lebreton A
Trends Microbiol. 2022 Feb 12.

Optimal Transport improves cell-cell similarity inference in single-cell omics data.
Huizing GJ, Peyré G, Cantini L
Bioinformatics. 2022 Feb 14.

Fgf8 dynamics and critical slowing down may account for the temperature independence of somitogenesis.
Zhang W, Scerbo P, Delagrange M, Candat V, Mayr V, Vriz S, Distel M, Ducos B, Bensimon D
Commun Biol. 2022 Feb 7. 5(1):113.

HR-Bac, a toolbox based on homologous recombination for expression, screening and production of multiprotein complexes using the baculovirus expression system.
Kolesnikova O, Zachayus A, Pichard S, Osz J, Rochel N, Rossolillo P, Kolb‑Cheynel I, Troffer‑Charlier N, Compe E, Bensaude O, Berger I, Poterszman A
Sci Rep. 2022 Feb 7. 12(1):2030.

A robust approach to estimate relative phytoplankton cell abundances from metagenomes.
Pierella Karlusich JJ, Pelletier E, Zinger L, Lombard F, Zingone A, Colin S, Gasol JM, Dorrell RG, Henry N, Scalco E, Acinas SG, Wincker P, de Vargas C, Bowler C
Mol Ecol Resour. 2022 Feb 2.

Publisher Correction : Fast optical recording of neuronal activity by three-dimensional custom-access serial holography.
Akemann W, Wolf S, Villette V, Mathieu B, Tangara A, Fodor J, Ventalon C, Léger JF, Dieudonné S, Bourdieu L
Nat Methods. 2022 Feb. 19(2):257.

Limited Evidence for Microbial Transmission in the Phylosymbiosis between Hawaiian Spiders and Their Microbiota.
Perez‑Lamarque B, Krehenwinkel H, Gillespie RG, Morlon H
mSystems. 2022 Feb 22. 7(1):e0110421.

Correction to : Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean.
Delmont TO, Pierella Karlusich JJ, Veseli I, Fuessel J, Eren AM, Foster RA, Bowler C, Wincker P, Pelletier E
ISME J. 2022 Apr. 16(4):1203.

Complex genetic patterns and distribution limits mediated by native congeners of the worldwide invasive red-eared slider turtle.
Espindola S, Vázquez‑Domínguez E, Nakamura M, Osorio‑Olvera L, Martínez‑Meyer E, Myers EA, Overcast I, Reid BN, Burbrink FT
Mol Ecol. 2022 Mar. 31(6):1766-1782.

The chloroplast redox-responsive transcriptome of solanaceous plants reveals significant nuclear gene regulatory motifs associated to stress acclimation.
Arce RC, Carrillo N, Pierella Karlusich JJ
Plant Mol Biol. 2022 Apr. 108(6):513-530.

The CLASSY family controls tissue-specific DNA methylation patterns in Arabidopsis.
Zhou M, Coruh C, Xu G, Martins LM, Bourbousse C, Lambolez A, Law JA
Nat Commun. 2022 Jan 11. 13(1):244.

Comparative transcriptome analysis of goat (Capra hircus) adipose tissue reveals physiological regulation of body reserve recovery after the peak of lactation.
Faulconnier Y, Boby C, Coulpier F, Lemoine S, Martin P, Leroux C
Comp Biochem Physiol Part D Genomics Proteomics. 2022 Mar. 41:100956.

A novel reticular node in the brainstem synchronizes neonatal mouse crying with breathing.
Wei XP, Collie M, Dempsey B, Fortin G, Yackle K
Neuron. 2022 Feb 16. 110(4):644-657.e6.

The possible fates of Fragilariopsis cylindrus (polar diatom) cells exposed to prolonged darkness.
Sciandra T, Forget MH, Bruyant F, Béguin M, Lacour T, Bowler C, Babin M
J Phycol. 2022 Apr. 58(2):281-296.

Fast optical recording of neuronal activity by three-dimensional custom-access serial holography.
Akemann W, Wolf S, Villette V, Mathieu B, Tangara A, Fodor J, Ventalon C, Léger JF, Dieudonné S, Bourdieu L
Nat Methods. 2022 Jan. 19(1):100-110.

Environmental control of marine phytoplankton stoichiometry in the North Atlantic Ocean.
Sauterey B, Ward BA
Proc Natl Acad Sci U S A. 2022 Jan 4. 119(1).

Discovery of a genetic module essential for assigning left-right asymmetry in humans and ancestral vertebrates.
Szenker‑Ravi E, Ott T, Khatoo M, de Bellaing AM, Goh WX, Chong YL, Beckers A, Kannesan D, Louvel G, Anujan P, Ravi V, Bonnard C, Moutton S, Schoen P, Fradin M, Colin E, Megarbane A, Daou L, Chehab G, Di Filippo S, Rooryck C, Deleuze JF, Boland A, Arribard N, Eker R, Tohari S, Ng AY, Rio M, Lim CT, Eisenhaber B, Eisenhaber F, Venkatesh B, Amiel J, Crollius HR, Gordon CT, Gossler A, Roy S, Attie‑Bitach T, Blum M, Bouvagnet P, Reversade B
Nat Genet. 2022 Jan. 54(1):62-72.

Eco-evolutionary responses of the microbial loop to surface ocean warming and consequences for primary production.
Cherabier P, Ferrière R
ISME J. 2022 Apr. 16(4):1130-1139.

A holobiont view of island biogeography : Unravelling patterns driving the nascent diversification of a Hawaiian spider and its microbial associates.
Armstrong EE, Perez‑Lamarque B, Bi K, Chen C, Becking LE, Lim JY, Linderoth T, Krehenwinkel H, Gillespie RG
Mol Ecol. 2022 Feb. 31(4):1299-1316.

Decay of similarity across tropical forest communities : integrating spatial distance with soil nutrients.
Peguero G, Ferrín M, Sardans J, Verbruggen E, Ramírez‑Rojas I, Van Langenhove L, Verryckt LT, Murienne J, Iribar A, Zinger L, Grau O, Orivel J, Stahl C, Courtois EA, Asensio D, Gargallo‑Garriga A, Llusià J, Margalef O, Ogaya R, Richter A, Janssens IA, Peñuelas J
Ecology. 2022 Feb. 103(2):e03599.

Genomicus in 2022 : comparative tools for thousands of genomes and reconstructed ancestors.
Nguyen NTT, Vincens P, Dufayard JF, Roest Crollius H, Louis A
Nucleic Acids Res. 2022 Jan 7. 50(D1):D1025-D1031.

Hepatitis C virus core protein uses triacylglycerols to fold onto the endoplasmic reticulum membrane.
Ajjaji D, Ben M’barek K, Boson B, Omrane M, Gassama‑Diagne A, Blaud M, Penin F, Diaz E, Ducos B, Cosset FL, Thiam AR
Traffic. 2022 Jan. 23(1):63-80.

The Waiting Room Hypothesis revisited by orchids : were orchid mycorrhizal fungi recruited among root endophytes ?
Selosse MA, Petrolli R, Mujica MI, Laurent L, Perez‑Lamarque B, Figura T, Bourceret A, Jacquemyn H, Li T, Gao J, Minasiewicz J, Martos F
Ann Bot. 2022 Feb 11. 129(3):259-270.

Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean.
Delmont TO, Pierella Karlusich JJ, Veseli I, Fuessel J, Eren AM, Foster RA, Bowler C, Wincker P, Pelletier E
ISME J. 2022 Apr. 16(4):927-936.

Coming of age for COI metabarcoding of whole organism community DNA : Towards bioinformatic harmonisation.
Creedy TJ, Andújar C, Meramveliotakis E, Noguerales V, Overcast I, Papadopoulou A, Morlon H, Vogler AP, Emerson BC, Arribas P
Mol Ecol Resour. 2022 Apr. 22(3):847-861.

Positive allosteric modulation of NMDA receptors : mechanisms, physiological impact and therapeutic potential.
Geoffroy C, Paoletti P, Mony L
J Physiol. 2022 Jan. 600(2):233-259.

Fast and Accurate Estimation of Species-Specific Diversification Rates Using Data Augmentation.
Maliet O, Morlon H
Syst Biol. 2022 Feb 10. 71(2):353-366.