Département de biologie computationnelle

Equipe principale
Publications | Mémoires et thèses

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793 publications

En préparation
 
Indigenous peoples in eastern Brazil: insights from 19<sup>th</sup> century genomes and metagenomes
Cruz Dávalos Diana Ivette, Arizmendi Cárdenas Yami Ommar, Bravo-Lopez Miriam Jetzabel, Neuenschwander Samuel, Reis Silvia, Bastos Murilo Q. R., Stenderup Jesper, Yediay Fulya Eylem, Villa-Islas Viridiana, Reyna-Blanco Carlos S. et al..
[DOI][serval:BIB_47F5B2CAEC7C]
 
Imputation of ancient genomes
Sousa da Mota Bárbara, Rubinacci Simone, Cruz Dávalos Diana Ivette, Amorim Carlos Eduardo G., Sikora Martin, Johannsen Niels N., Szmyt Marzena, Włodarczak Piotr, Szczepanek Anita, Przybyła Marcin M. et al..
[DOI][serval:BIB_AC8F25835B20]
Sous presse
 
Bridging Time Scales in Evolutionary Biology
Hartasánchez Diego A., Latrille Thibault, Brasó-Vives Marina, Navarro Arcadi dans Mathematics Online First Collections, Springer International Publishing.
[URN][DOI][serval:BIB_715001A031E0]
 
An RNA-dependent and phase-separated active subnuclear compartment safeguards repressive chromatin domains.
Lerra L., Panatta M., Bär D., Zanini I., Tan J.Y., Pisano A., Mungo C., Baroux C., Panse V.G., Marques A.C. et al. Molecular cell. Peer-reviewed.
[DOI][Pmid][serval:BIB_7E94B9835811]
 
Recurrent gene flow events occurred during the diversification of clownfishes of the skunk complex.
Marcionetti A., Bertrand JAM, Cortesi F., Donati GFA, Heim S., Huyghe F., Kochzius M., Pellissier L., Salamin N. Molecular ecology. Peer-reviewed.
[DOI][Pmid][serval:BIB_6E177F953F6F]
 
Frequent jumps from human hosts.
Moi D., Dessimoz C. Nature ecology & evolution. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_EFCEB8CFF30F]
 
Quality assessment of gene repertoire annotations with OMArk.
Nevers Y., Warwick Vesztrocy A., Rossier V., Train C.M., Altenhoff A., Dessimoz C., Glover N.M. Nature biotechnology. Peer-reviewed.
[DOI][Pmid][serval:BIB_85062152E9B8]
 
The neurobiology of life course socioeconomic conditions and associated cognitive performance in middle to late adulthood.
Schrempft S., Trofimova O., Künzi M., Ramponi C., Lutti A., Kherif F., Latypova A., Vollenweider P., Marques-Vidal P., Preisig M. et al. The Journal of neuroscience. Peer-reviewed.
[DOI][Pmid][serval:BIB_8A36291FEC74]
 
Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers.
Singh A.K., Walavalkar K., Tavernari D., Ciriello G., Notani D., Sabarinathan R. Molecular oncology. Peer-reviewed.
[DOI][Pmid][serval:BIB_C481A745E22C]
2024
E2F transcription factor-1 modulates expression of glutamine metabolic genes in mouse embryonic fibroblasts and uterine sarcoma cells
Huber Katharina, Giralt Albert, Dreos René, Michenthaler Helene, Geller Sarah, Barquissau Valentin, Ziegler Dorian V., Tavernari Daniele, Gallart-Ayala Hector, Krajina Katarina et al., 2024/06. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, 1871 (5) p. 119721. Peer-reviewed.
[DOI][Pmid][serval:BIB_5EAE29F4CAA9]
 
Functional hypoxia reduces mitochondrial calcium uptake.
Donnelly C., Komlódi T., Cecatto C., Cardoso LHD, Compagnion A.C., Matera A., Tavernari D., Campiche O., Paolicelli R.C., Zanou N. et al., 2024/05. Redox biology, 71 p. 103037. Peer-reviewed.
[DOI][Pmid][serval:BIB_2E8283116312]
Synergy and anti-cooperativity in allostery: Molecular dynamics study of WT and oncogenic KRAS-RGL1.
Hacisuleyman A., Erman B., 2024/05. Proteins, 92 (5) pp. 665-678. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_87CA828A4D75]
 
Genetic determinants of plasma protein levels in the Estonian population.
Kalnapenkis A., Jõeloo M., Lepik K., Kukuškina V., Kals M., Alasoo K., Estonian Biobank Research Team, Mägi R., Esko T., Võsa U., 2024/04/02. Scientific reports, 14 (1) p. 7694. Peer-reviewed.
[DOI][Pmid][serval:BIB_2ED69D7E6C4B]
 
Assessing the impact of post-mortem damage and contamination on imputation performance in ancient DNA.
Garrido Marques A., Rubinacci S., Malaspinas A.S., Delaneau O., Sousa da Mota B., 2024/03/14. Scientific reports, 14 (1) p. 6227. Peer-reviewed.
[DOI][Pmid][serval:BIB_6950F9B87B01]
 
AI and the democratization of knowledge.
Dessimoz C., Thomas P.D., 2024/03/05. Scientific data, 11 (1) p. 268. Peer-reviewed.
[DOI][Pmid][serval:BIB_68521EFB4037]
Exploring the conformational changes of theMunc18-1/syntaxin 1a complex.
Stefani Ioanna, Iwaszkiewicz Justyna, Fasshauer Dirk, 2024/03. Protein Science, 33 (3) pp. e4870. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_46EE05B7E159]
 
PheWAS-based clustering of Mendelian Randomisation instruments reveals distinct mechanism-specific causal effects between obesity and educational attainment.
Darrous L., Hemani G., Davey Smith G., Kutalik Z., 2024/02/15. Nature communications, 15 (1) p. 1420. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_606B3CD78234]
 
ANKRD1 is a mesenchymal-specific driver of cancer-associated fibroblast activation bridging androgen receptor loss to AP-1 activation.
Mazzeo L., Ghosh S., Di Cicco E., Isma J., Tavernari D., Samarkina A., Ostano P., Youssef M.K., Simon C., Dotto G.P., 2024/02/03. Nature communications, 15 (1) p. 1038. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_2999AA526D89]
 
Causality-enriched epigenetic age uncouples damage and adaptation.
Ying K., Liu H., Tarkhov A.E., Sadler M.C., Lu A.T., Moqri M., Horvath S., Kutalik Z., Shen X., Gladyshev V.N., 2024/02. Nature aging, 4 (2) pp. 231-246. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_18FB43C5A730]
Publisher Correction: Population genomics of post-glacial western Eurasia.
Allentoft M.E., Sikora M., Refoyo-Martínez A., Irving-Pease E.K., Fischer A., Barrie W., Ingason A., Stenderup J., Sjögren K.G., Pearson A. et al., 2024/02. Nature, 626 (7997) pp. E3. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_DAEDB9D9F04F]
Cancer Evolution: A Multifaceted Affair.
Ciriello G., Magnani L., Aitken S.J., Akkari L., Behjati S., Hanahan D., Landau D.A., Lopez-Bigas N., Lupiáñez D.G., Marine J.C. et al., 2024/01/12. Cancer discovery, 14 (1) pp. 36-48. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_43F23549D204]
 
Rare copy-number variants as modulators of common disease susceptibility.
Auwerx C., Jõeloo M., Sadler M.C., Tesio N., Ojavee S., Clark C.J., Mägi R., Estonian Biobank Research Team, Reymond A., Kutalik Z., 2024/01/08. Genome medicine, 16 (1) p. 5. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_91B2F5588645]
 
ELM-the Eukaryotic Linear Motif resource-2024 update.
Kumar M., Michael S., Alvarado-Valverde J., Zeke A., Lazar T., Glavina J., Nagy-Kanta E., Donagh J.M., Kalman Z.E., Pascarelli S. et al., 2024/01/05. Nucleic acids research, 52 (D1) pp. D442-D455. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_BE2B431F3782]
 
OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem.
Altenhoff A.M., Warwick Vesztrocy A., Bernard C., Train C.M., Nicheperovich A., Prieto Baños S., Julca I., Moi D., Nevers Y., Majidian S. et al., 2024/01/05. Nucleic acids research, 52 (D1) pp. D513-D521. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_B96DA0D62CDE]
100 ancient genomes show repeated population turnovers in Neolithic Denmark.
Allentoft M.E., Sikora M., Fischer A., Sjögren K.G., Ingason A., Macleod R., Rosengren A., Schulz Paulsson B., Jørkov MLS, Novosolov M. et al., 2024/01. Nature, 625 (7994) pp. 329-337. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_BEA13B225A2F]
 
CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity.
Varrone M., Tavernari D., Santamaria-Martínez A., Walsh L.A., Ciriello G., 2024/01. Nature genetics, 56 (1) pp. 74-84. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_27DAAEFFFB59]
 
Design of IIR full-band differentiators with improved nearly linear phase
Stančić Goran, Krstić Ivan, Kostić Ivana, Petrović Miljan, 2024/01. Digital Signal Processing, 144 p. 104276.
[DOI][WoS][serval:BIB_9655C6A3809C]
 
Hyper-Cryptic radiation of a tropical montane plant lineage.
Olivares I., Tusso S., José Sanín M., de La Harpe M., Loiseau O., Rolland J., Salamin N., Kessler M., Shimizu K.K., Paris M., 2024/01. Molecular phylogenetics and evolution, 190 p. 107954. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_33075489A124]
 
Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree.
Dylus D., Altenhoff A., Majidian S., Sedlazeck F.J., Dessimoz C., 2024/01. Nature biotechnology, 42 (1) pp. 139-147. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_AB990544B7BE]
Melanin-based plumage coloration and melanin content in organs in the barn owl.
Roulin A., Dubey S., Ito S., Wakamatsu K., 2024. Journal of ornithology, 165 (2) pp. 429-438. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_5AC90247B016]
Population genomics of post-glacial western Eurasia.
Allentoft M.E., Sikora M., Refoyo-Martínez A., Irving-Pease E.K., Fischer A., Barrie W., Ingason A., Stenderup J., Sjögren K.G., Pearson A. et al., 2024/01. Nature, 625 (7994) pp. 301-311. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_FDD564D26AB5]
2023
 
From microbiome composition to functional engineering, one step at a time.
Burz S.D., Causevic S., Dal Co A., Dmitrijeva M., Engel P., Garrido-Sanz D., Greub G., Hapfelmeier S., Hardt W-D, Hatzimanikatis V. et al., 2023/12/20. Microbiology and molecular biology reviews, 87 (4) pp. e0006323. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_422DE1C48246]
Cannabis use and atherosclerotic cardiovascular disease: a Mendelian randomization study.
de La Harpe R., Schoeler T., Thorball C.W., Thomas A., Kutalik Z., Vaucher J., 2023/12/13. BMC cardiovascular disorders, 23 (1) p. 611. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_2C9E1FFFC502]
 
Polygenic risk scores for cervical HPV infection, neoplasia and cancer show potential for personalised screening: comparison of two methods.
Tisler A., Uusküla A., Ojavee S.E., Läll K., Estonian Biobank research team, Laisk T., 2023/12/07. Infectious agents and cancer, 18 (1) p. 82. Peer-reviewed.
[DOI][Pmid][serval:BIB_2F36ADE09E9C]
 
Remote homolog detection places insect chemoreceptors in a cryptic protein superfamily spanning the tree of life.
Himmel N.J., Moi D., Benton R., 2023/11/20. Current biology, 33 (22) pp. 5023-5033.e4. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_3B786407249F]
 
Incarceration history is associated with HIV infection among community-recruited people who inject drugs in Europe: A propensity-score matched analysis of cross-sectional studies.
Uusküla A., Rannap J., Weijler L., Abagiu A., Arendt V., Barrio G., Barros H., Brummer-Korvenkontio H., Casabona J., Croes E. et al., 2023/11. Addiction, 118 (11) pp. 2177-2192. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_B0167832F12C]
Resistance mechanism to Notch inhibition and combination therapy in human T-cell acute lymphoblastic leukemia.
Cao L., Ruiz Buendía G.A., Fournier N., Liu Y., Armand F., Hamelin R., Pavlou M., Radtke F., 2023/10/24. Blood advances, 7 (20) pp. 6240-6252. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_E01F5C4F58A0]
Genomic variant benchmark: if you cannot measure it, you cannot improve it.
Majidian S., Agustinho D.P., Chin C.S., Sedlazeck F.J., Mahmoud M., 2023/10/05. Genome biology, 24 (1) p. 221. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_BFFAA42506DB]
Fine tuning rigid body docking results using the Dreiding force field: A computational study of 36 known nanobody-protein complexes.
Hacisuleyman A., Erman B., 2023/10. Proteins, 91 (10) pp. 1417-1426. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_AD4A1D2EC8A3]
Expression of cell-wall related genes is highly variable and correlates with sepal morphology
Hartasánchez Diego A., Kiss Annamaria, Battu Virginie, Soraru Charline, Delgado-Vaquera Abigail, Massinon Florian, Brasó-Vives Marina, Mollier Corentin, Martin-Magniette Marie-Laure, Boudaoud Arezki et al., 2023/09/28. Peer Community Journal, 3. Peer-reviewed.
[URN][DOI][serval:BIB_5B2668E2D1B4]
Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma.
Gentien D., Saberi-Ansari E., Servant N., Jolly A., de la Grange P., Némati F., Liot G., Saule S., Teissandier A., Bourc'his D. et al., 2023/09/26. Cell reports, 42 (9) p. 113132. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_16A831564906]
The leaderless communication peptide (LCP) class of quorum-sensing peptides is broadly distributed among Firmicutes.
Aggarwal S., Huang E., Do H., Makthal N., Li Y., Bapteste E., Lopez P., Bernard C., Kumaraswami M., 2023/09/23. Nature communications, 14 (1) p. 5947. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_DC405EC6F879]
Genetic insights into the age-specific biological mechanisms governing human ovarian aging.
Ojavee S.E., Darrous L., Patxot M., Läll K., Fischer K., Mägi R., Kutalik Z., Robinson M.R., 2023/09/07. American journal of human genetics, 110 (9) pp. 1549-1563. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_278672D79D5D]
 
The ancestry and geographical origins of St Helena's liberated Africans.
Sandoval-Velasco M., Jagadeesan A., Ramos-Madrigal J., Ávila-Arcos M.C., Fortes-Lima C.A., Watson J., Johannesdóttir E., Cruz-Dávalos D.I., Gopalakrishnan S., Moreno-Mayar J.V. et al., 2023/09/07. American journal of human genetics, 110 (9) pp. 1590-1599. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_474D89291681]
μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data.
Cozzi D., Rossi M., Rubinacci S., Gagie T., Köppl D., Boucher C., Bonizzoni P., 2023/09/02. Bioinformatics, 39 (9). Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A05A8B57A5AB]
Genome-wide Association Studies of Retinal Vessel Tortuosity Identify Numerous Novel Loci Revealing Genes and Pathways Associated With Ocular and Cardiometabolic Diseases.
Tomasoni M., Beyeler M.J., Vela S.O., Mounier N., Porcu E., Corre T., Krefl D., Button A.L., Abouzeid H., Konstantinidis Lazaros et al., 2023/09. Ophthalmology science, 3 (3) p. 100288. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E95C7A7DDD8F]
 
Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions.
Mészáros B., Hatos A., Palopoli N., Quaglia F., Salladini E., Van Roey K., Arthanari H., Dosztányi Z., Felli I.C., Fischer P.D. et al., 2023/09. Nature methods, 20 (9) pp. 1291-1303. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_ABFD74A3E19E]
 
The SWI/SNF complex member SMARCB1 supports lineage fidelity in kidney cancer.
Wesolowski L., Ge J., Castillon L., Sesia D., Dyas A., Hirosue S., Caraffini V., Warren A.Y., Rodrigues P., Ciriello G. et al., 2023/08/18. iScience, 26 (8) p. 107360. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_4190C534A22E]
Chromosomal deletions on 16p11.2 encompassing SH2B1 are associated with accelerated metabolic disease.
Hanssen R., Auwerx C., Jõeloo M., Sadler M.C., Estonian Biobank Research Team, Henning E., Keogh J., Bounds R., Smith M., Firth H.V. et al., 2023/08/15. Cell reports. Medicine, 4 (8) p. 101155. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_67978CA3D37E]
 
CXCL9:SPP1 macrophage polarity identifies a network of cellular programs that control human cancers.
Bill R., Wirapati P., Messemaker M., Roh W., Zitti B., Duval F., Kiss M., Park J.C., Saal T.M., Hoelzl J. et al., 2023/08/04. Science, 381 (6657) pp. 515-524. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_17A3A9510B2F]
 
Genetic insights into resting heart rate and its role in cardiovascular disease.
van de Vegte Y.J., Eppinga R.N., van der Ende M.Y., Hagemeijer Y.P., Mahendran Y., Salfati E., Smith A.V., Tan V.Y., Arking D.E., Ntalla I. et al., 2023/08/02. Nature communications, 14 (1) p. 4646. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_3D61EEADF3D4]
 
Conceptual and empirical bridges between micro- and macroevolution.
Rolland J., Henao-Diaz L.F., Doebeli M., Germain R., Harmon L.J., Knowles L.L., Liow L.H., Mank J.E., Machac A., Otto S.P. et al., 2023/08. Nature ecology & evolution, 7 (8) pp. 1181-1193. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_8AB15E512733]
Multi-layered genetic approaches to identify approved drug targets.
Sadler M.C., Auwerx C., Deelen P., Kutalik Z., 2023/07/12. Cell genomics, 3 (7) p. 100341. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_08B78C732656]
 
Response to Bassett et al.
Zamariolli M., Auwerx C., Sadler M.C., van der Graaf A., Lepik K., Schoeler T., Moysés-Oliveira M., Dantas A.G., Melaragno M.I., Kutalik Z., 2023/07/06. American journal of human genetics, 110 (7) pp. 1219-1220. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_01B60F44C10B]
 
FuzPred: a web server for the sequence-based prediction of the context-dependent binding modes of proteins.
Hatos A., Teixeira JMC, Barrera-Vilarmau S., Horvath A., Tosatto SCE, Vendruscolo M., Fuxreiter M., 2023/07/05. Nucleic acids research, 51 (W1) pp. W198-W206. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_6EA32D9B8875]
 
Insights into the Genomics of Clownfish Adaptive Radiation: The Genomic Substrate of the Diversification.
Marcionetti A., Salamin N., 2023/07/03. Genome biology and evolution, 15 (7). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_35025EC7D7BF]
 
Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank.
Hofmeister R.J., Ribeiro D.M., Rubinacci S., Delaneau O., 2023/07. Nature genetics, 55 (7) pp. 1243-1249. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_EA0C8B7D22EF]
 
Imputation of low-coverage sequencing data from 150,119 UK Biobank genomes.
Rubinacci S., Hofmeister R.J., Sousa da Mota B., Delaneau O., 2023/07. Nature genetics, 55 (7) pp. 1088-1090. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_11B2963EE6A6]
 
Ontogeny and phylogeny of mating behaviour: social heteroch rony in primates.
Génin F., Rambeloarivony H., Silvestro D., Masters J.C., 2023/07/01. Theoretical biology forum, 116 (1-2) pp. 15-50. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_FF98699BCB91]
 
Understanding the relationship between loneliness, substance use traits and psychiatric disorders: A genetically informed approach.
Martin E., Schoeler T., Pingault J.B., Barkhuizen W., 2023/07. Psychiatry research, 325 p. 115218. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_EEBC0DB12EEB]
 
Protein S-acylation controls the subcellular localization and biological activity of PHYTOCHROME KINASE SUBSTRATE.
Lopez Vazquez A., Allenbach Petrolati L., Legris M., Dessimoz C., Lampugnani E.R., Glover N., Fankhauser C., 2023/06/26. The Plant cell, 35 (7) pp. 2635-2653. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_58EBDD8BFA7C]
 
Resting heart rate and antisocial behaviour: a Mendelian randomisation study.
Karwatowska L., Frach L., Schoeler T., Tielbeek J.J., Murray J., de Geus E., Viding E., Pingault J.B., 2023/06/23. Scientific reports, 13 (1) p. 10212. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_9C5288D07FAA]
Data in use for Alzheimer disease study: combining gene expression, orthology, bioresource and disease datasets
Mendes de Farias Tarcisio, Kushida Tatsuya, Sima Ana-Claudia, Dessimoz Christophe, Chiba Hirokazu, Bastian Frédéric, Masuya Hiroshi, 2023/06/22. dans SWAT4HCLS 2023: The 14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences.
[URN][serval:BIB_818CA7FA57C2]
 
Towards predicting essential proteins via federated SPARQL queries
Liakopoulos Petros, Banfalvi Borbala, Wang Xinyi, Majidian Sina, Mendes de Farias Tarcisio, Dessimoz Christophe, Sima Ana Claudia, 2023/06/22. dans SWAT4HCLS 2023: The 14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences.
[serval:BIB_5DBECBB5FD4F]
 
Imputation of ancient human genomes.
Sousa da Mota B., Rubinacci S., Cruz Dávalos D.I., G Amorim C.E., Sikora M., Johannsen N.N., Szmyt M.H., Włodarczak P., Szczepanek A., Przybyła M.M. et al., 2023/06/20. Nature communications, 14 (1) p. 3660. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_6B67ECE9FE90]
 
Protein length distribution is remarkably uniform across the tree of life.
Nevers Y., Glover N.M., Dessimoz C., Lecompte O., 2023/06/08. Genome biology, 24 (1) p. 135. Peer-reviewed.
[DOI][Pmid][serval:BIB_2F921C9DBF4A]
Stressful life events and relapse of psychosis: analysis of causal association in a 2-year prospective observational cohort of individuals with first-episode psychosis in the UK.
Bhattacharyya S., Schoeler T., Di Forti M., Murray R., Cullen A.E., Colizzi M., 2023/06. The lancet. Psychiatry, 10 (6) pp. 414-425. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_AC76544A4F9E]
 
Multimodal single cell analysis infers widespread enhancer co-activity in a lymphoblastoid cell line.
Ziyani C., Delaneau O., Ribeiro D.M., 2023/05/26. Communications biology, 6 (1) p. 563. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_2BC7F8C69310]
 
Author Correction: Possible association of 16p11.2 copy number variation with altered lymphocyte and neutrophil counts.
Giannuzzi G., Chatron N., Mannik K., Auwerx C., Pradervand S., Willemin G., Hoekzema K., Nuttle X., Chrast J., Sadler M.C. et al., 2023/05/24. NPJ genomic medicine, 8 (1) p. 9. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_BB9CACD534D5]
 
Phylogenetic profiling in eukaryotes comes of age.
Moi D., Dessimoz C., 2023/05/09. Proceedings of the National Academy of Sciences of the United States of America, 120 (19) pp. e2305013120. Peer-reviewed.
[DOI][Pmid][serval:BIB_81FD40AAF6F4]
PascalX: a Python library for GWAS gene and pathway enrichment tests.
Krefl D., Brandulas Cammarata A., Bergmann S., 2023/05/04. Bioinformatics, 39 (5) pp. btad296. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_D8824EBDC2F5]
 
Genome-wide analysis identifies genetic effects on reproductive success and ongoing natural selection at the FADS locus.
Mathieson I., Day F.R., Barban N., Tropf F.C., Brazel D.M., eQTLGen Consortium, BIOS Consortium, Vaez A., van Zuydam N., Bitarello B.D. et al., 2023/05. Nature human behaviour, 7 (5) pp. 790-801. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F6DE9D216FAD]
 
Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition.
Hansen S.B., Bozzi D., Mak SST, Clausen C.G., Nielsen T.K., Kodama M., Hansen L.H., Gilbert MTP, Limborg M.T., 2023/05. Genomics, 115 (3) p. 110629. Peer-reviewed.
[DOI][Pmid][serval:BIB_5BEFC9E5466B]
Partner choice, confounding and trait convergence all contribute to phenotypic partner similarity.
Sjaarda J., Kutalik Z., 2023/05. Nature human behaviour, 7 (5) pp. 776-789. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_2DBEF2BE43D3]
Topography of associations between cardiovascular risk factors and myelin loss in the ageing human brain.
Trofimova O., Latypova A., DiDomenicantonio G., Lutti A., de Lange A.G., Kliegel M., Stringhini S., Marques-Vidal P., Vaucher J., Vollenweider P. et al., 2023/04/10. Communications biology, 6 (1) p. 392. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_611EAA504585]
 
Large-Scale Identification of Known and Novel RRNPP Quorum-Sensing Systems by RRNPP_Detector Captures Novel Features of Bacterial, Plasmidic, and Viral Coevolution.
Bernard C., Li Y., Lopez P., Bapteste E., 2023/04/04. Molecular biology and evolution, 40 (4) pp. msad062. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_AAB7BEC3DAE2]
A combined experimental-computational approach uncovers a role for the Golgi matrix protein Giantin in breast cancer progression.
Ghannoum S., Fantini D., Zahoor M., Reiterer V., Phuyal S., Leoncio Netto W., Sørensen Ø., Iyer A., Sengupta D., Prasmickaite L. et al., 2023/04. PLoS computational biology, 19 (4) pp. e1010995. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_3C3B7E71A649]
 
Genetic variation in cis-regulatory domains suggests cell type-specific regulatory mechanisms in immunity.
Avalos D., Rey G., Ribeiro D.M., Ramisch A., Dermitzakis E.T., Delaneau O., 2023/03/28. Communications biology, 6 (1) p. 335. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_1A474A50E8FF]
Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale.
Latrille T., Rodrigue N., Lartillot N., 2023/03/14. Proceedings of the National Academy of Sciences of the United States of America, 120 (11) pp. e2214977120. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_98262F56D636]
Exploiting the mediating role of the metabolome to unravel transcript-to-phenotype associations.
Auwerx C., Sadler M.C., Woh T., Reymond A., Kutalik Z., Porcu E., 2023/03/09. eLife, 12 pp. e81097. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_33296666D7F5]
Exploiting parallelization in positional Burrows-Wheeler transform (PBWT) algorithms for efficient haplotype matching and compression.
Wertenbroek R., Xenarios I., Thoma Y., Delaneau O., 2023/03. Bioinformatics advances, 3 (1) pp. vbad021. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_9B3CD4626BAA]
 
Novel Biological Insights Into the Common Heritable Liability to Substance Involvement: A Multivariate Genome-wide Association Study
Schoeler Tabea, Baldwin Jessie, Allegrini Andrea, Barkhuizen Wikus, McQuillin Andrew, Pirastu Nicola, Kutalik Zoltán, Pingault Jean-Baptiste, 2023/03. Biological Psychiatry, 93 (6) pp. 524-535. Peer-reviewed.
[DOI][WoS][serval:BIB_CB17FE6B148D]
The first genetic landscape of inherited retinal dystrophies in Portuguese patients identifies recurrent homozygous mutations as a frequent cause of pathogenesis.
Peter V.G., Kaminska K., Santos C., Quinodoz M., Cancellieri F., Cisarova K., Pescini Gobert R., Rodrigues R., Custódio S., Paris L.P. et al., 2023/03. PNAS nexus, 2 (3) pp. pgad043. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_5376D39C0896]
Whole-genome doubling drives oncogenic loss of chromatin segregation.
Lambuta R.A., Nanni L., Liu Y., Diaz-Miyar J., Iyer A., Tavernari D., Katanayeva N., Ciriello G., Oricchio E., 2023/03. Nature, 615 (7954) pp. 925-933. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_4691B7A968A0]
Spatial self-organization of metabolism in microbial systems: A matter of enzymes and chemicals.
Dal Co A., Ackermann M., van Vliet S., 2023/02/15. Cell systems, 14 (2) pp. 98-108. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_1FC650CE1CAA]
Divergence in metabolomic profile in clownfish and damselfish skin mucus
Heim S., Teav T., Gallart-Ayala H., Ivanisevic J., Salamin N., 2023/02/07. Frontiers in Ecology and Evolution, 11.
[URN][DOI][WoS][serval:BIB_6E38BFCA1196]
 
Mapache: a flexible pipeline to map ancient DNA.
Neuenschwander S., Cruz Dávalos D.I., Anchieri L., Sousa da Mota B., Bozzi D., Rubinacci S., Delaneau O., Rasmussen S., Malaspinas A.S., 2023/02/03. Bioinformatics, 39 (2) pp. btad028. Peer-reviewed.
[DOI][Pmid][serval:BIB_B6D821D0E6BE]
 
The impact of 22q11.2 copy-number variants on human traits in the general population.
Zamariolli M., Auwerx C., Sadler M.C., van der Graaf A., Lepik K., Schoeler T., Moysés-Oliveira M., Dantas A.G., Melaragno M.I., Kutalik Z., 2023/02/02. American journal of human genetics, 110 (2) pp. 300-313. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_CD61220861A1]
 
Association between stressful life events and psychosis relapse: a 2-year prospective study in first-episode psychosis.
Colizzi M., Cullen A.E., Martland N., Di Forti M., Murray R., Schoeler T., Bhattacharyya S., 2023/02. World psychiatry, 22 (1) pp. 159-160. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_8EA786527534]
Childhood Maltreatment and Mental Health Problems: A Systematic Review and Meta-Analysis of Quasi-Experimental Studies.
Baldwin J.R., Wang B., Karwatowska L., Schoeler T., Tsaligopoulou A., Munafò M.R., Pingault J.B., 2023/02/01. The American journal of psychiatry, 180 (2) pp. 117-126. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_B150C143EA1D]
Dendritic cells direct circadian anti-tumour immune responses.
Wang C., Barnoud C., Cenerenti M., Sun M., Caffa I., Kizil B., Bill R., Liu Y., Pick R., Garnier L. et al., 2023/02. Nature, 614 (7946) pp. 136-143. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_33489F389D05]
Accuracy of haplotype estimation and whole genome imputation affects complex trait analyses in complex biobanks.
Appadurai V., Bybjerg-Grauholm J., Krebs M.D., Rosengren A., Buil A., Ingason A., Mors O., Børglum A.D., Hougaard D.M., Nordentoft M. et al., 2023/01/26. Communications biology, 6 (1) p. 101. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_1803C776AAF4]
 
Bringing science to the public in the light of evolution.
Blatter M.C., Zahn-Zabal M., Moix S., Pichon B., Dessimoz C., Glover N., 2023. Biology methods & protocols, 8 (1) pp. bpad040. Peer-reviewed.
[DOI][Pmid][serval:BIB_C552E0B3489B]
 
DrosOMA: the Drosophila Orthologous Matrix browser.
Thiébaut A., Altenhoff A.M., Campli G., Glover N., Dessimoz C., Waterhouse R.M., 2023. F1000Research, 12 p. 936. Peer-reviewed.
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The HLA-B*57:01 allele corresponds to a very large MHC haploblock likely explaining its massive effect for HIV-1 elite control.
Rahmouni M., De Marco L., Spadoni J.L., Tison M., Medina-Santos R., Labib T., Noirel J., Tamouza R., Limou S., Delaneau O. et al., 2023. Frontiers in immunology, 14 p. 1305856. Peer-reviewed.
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2022
 
Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression.
Sciacovelli M., Dugourd A., Jimenez L.V., Yang M., Nikitopoulou E., Costa ASH, Tronci L., Caraffini V., Rodrigues P., Schmidt C. et al., 2022/12/20. Nature communications, 13 (1) p. 7830. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F0C978935693]
Epistasis and evolutionary dependencies in human cancers.
Mina M., Iyer A., Ciriello G., 2022/12. Current opinion in genetics & development, 77 p. 101989. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_87AEECFCDB0B]
Gene set enrichment analysis of pathophysiological pathways highlights oxidative stress in psychosis.
Pistis G., Vázquez-Bourgon J., Fournier M., Jenni R., Cleusix M., Papiol S., Smart S.E., Pardiñas A.F., Walters JTR, MacCabe J.H. et al., 2022/12. Molecular psychiatry, 27 (12) pp. 5135-5143. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_42876FD4E721]
 
Publisher Correction: Stroke genetics informs drug discovery and risk prediction across ancestries.
Mishra A., Malik R., Hachiya T., Jürgenson T., Namba S., Posner D.C., Kamanu F.K., Koido M., Le Grand Q., Shi M. et al., 2022/12. Nature, 612 (7938) pp. E7. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_BB7A1C34FEAF]
3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources.
Varadi M., Nair S., Sillitoe I., Tauriello G., Anyango S., Bienert S., Borges C., Deshpande M., Green T., Hassabis D. et al., 2022/11/30. GigaScience, 11 pp. giac118. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_8AF1FE2C8116]
 
Aberrant hyperexpression of the RNA binding protein FMRP in tumors mediates immune evasion.
Zeng Q., Saghafinia S., Chryplewicz A., Fournier N., Christe L., Xie Y.Q., Guillot J., Yucel S., Li P., Galván J.A. et al., 2022/11/18. Science, 378 (6621) pp. eabl7207. Peer-reviewed.
[DOI][Pmid][serval:BIB_324086550512]
Parallel evolution of amphioxus and vertebrate small-scale gene duplications.
Brasó-Vives M., Marlétaz F., Echchiki A., Mantica F., Acemel R.D., Gómez-Skarmeta J.L., Hartasánchez D.A., Le Targa L., Pontarotti P., Tena J.J. et al., 2022/11/18. Genome biology, 23 (1) p. 243. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_B6794F5FB6F2]
Parent-of-Origin inference for biobanks.
Hofmeister R.J., Rubinacci S., Ribeiro D.M., Buil A., Kutalik Z., Delaneau O., 2022/11/05. Nature communications, 13 (1) p. 6668. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_3678C632F528]
Liability-scale heritability estimation for biobank studies of low-prevalence disease.
Ojavee S.E., Kutalik Z., Robinson M.R., 2022/11/03. American journal of human genetics, 109 (11) pp. 2009-2017. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_9B059FA24681]
Stroke genetics informs drug discovery and risk prediction across ancestries.
Mishra A., Malik R., Hachiya T., Jürgenson T., Namba S., Posner D.C., Kamanu F.K., Koido M., Le Grand Q., Shi M. et al., 2022/11. Nature, 611 (7934) pp. 115-123. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_AC35CD14FB1F]
Omics-informed CNV calls reduce false-positive rates and improve power for CNV-trait associations.
Lepamets M., Auwerx C., Nõukas M., Claringbould A., Porcu E., Kals M., Jürgenson T., Estonian Biobank Research Team, Morris A.P., Võsa U. et al., 2022/10/13. HGG advances, 3 (4) p. 100133. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_ACC82F5026CE]
A Linear Time Solution to the Labeled Robinson-Foulds Distance Problem.
Briand S., Dessimoz C., El-Mabrouk N., Nevers Y., 2022/10/12. Systematic biology, 71 (6) pp. 1391-1403. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_04DEB6D05802]
 
Sex- and age-dependent genetics of longevity in a heterogeneous mouse population.
Bou Sleiman M., Roy S., Gao A.W., Sadler M.C., von Alvensleben GVG, Li H., Sen S., Harrison D.E., Nelson J.F., Strong R. et al., 2022/09/30. Science, 377 (6614) pp. eabo3191. Peer-reviewed.
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Rates and correlates of cannabis-associated psychotic symptoms in over 230,000 people who use cannabis.
Schoeler T., Ferris J., Winstock A.R., 2022/09/06. Translational psychiatry, 12 (1) p. 369. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_31C935CF358D]
Estimating roe deer density using motion‐sensitive cameras in Switzerland
Hinojo Amael, Christe Philippe, Moreno Inès, Hofmeister Robin J., Dandliker Gottlieb, Zimmermann Fridolin, 2022/09/02. The Journal of Wildlife Management. Peer-reviewed.
[URN][DOI][WoS][serval:BIB_9841656E1979]
Cross-GWAS coherence test at the gene and pathway level.
Krefl D., Bergmann S., 2022/09. PLoS computational biology, 18 (9) pp. e1010517. Peer-reviewed.
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Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention.
Wang Z., Emmerich A., Pillon N.J., Moore T., Hemerich D., Cornelis M.C., Mazzaferro E., Broos S., Ahluwalia T.S., Bartz T.M. et al., 2022/09. Nature genetics, 54 (9) pp. 1332-1344. Peer-reviewed.
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Geogenomics of montane palms points to Miocene-Pliocene Andean segmentation related to strike-slip tectonics.
Sanín María José, Mejía-Franco Fabián Gregorio, Paris Margot, Valencia-Montoya Wendy A., Salamin Nicolas, Kessler Michael, Olivares Ingrid, Jaramillo Juan Sebastián, Cardona Agustín, 2022/09. Journal of Biogeography, 49 (9) pp. 1711-1725.
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Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy.
Parikh V.N., Ioannidis A.G., Jimenez-Morales D., Gorzynski J.E., De Jong H.N., Liu X., Roque J., Cepeda-Espinoza V.P., Osoegawa K., Hughes C. et al., 2022/08/30. Nature communications, 13 (1) p. 5107. Peer-reviewed.
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Shared regulation and functional relevance of local gene co-expression revealed by single cell analysis.
M Ribeiro D., Ziyani C., Delaneau O., 2022/08/26. Communications biology, 5 (1) p. 876. Peer-reviewed.
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Limited evidence for blood eQTLs in human sexual dimorphism.
Porcu E., Claringbould A., Weihs A., Lepik K., BIOS Consortium, Richardson T.G., Völker U., Santoni F.A., Teumer A., Franke L. et al., 2022/08/11. Genome medicine, 14 (1) p. 89. Peer-reviewed.
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CYP2C19 expression modulates affective functioning and hippocampal subiculum volume-a large single-center community-dwelling cohort study.
Grosu C., Trofimova O., Gholam-Rezaee M., Strippoli M.F., Kherif F., Lutti A., Preisig M., Draganski B., Eap C.B., 2022/08/05. Translational psychiatry, 12 (1) p. 316. Peer-reviewed.
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Federating and querying heterogeneous and distributed Web APIs and triple stores
Mendes de Farias Tarcisio, Dessimoz Christophe, Ayllon Benitez Aaron, Yang Chen, Long Jiao, Sima Ana-Claudia, 2022/08/02. dans 2022 ISMB Bio-Ontologies Community of Special Interest. Peer-reviewed.
[URN][DOI][serval:BIB_6A2C0BEAD983]
Improving GWAS discovery and genomic prediction accuracy in biobank data.
Orliac E.J., Trejo Banos D., Ojavee S.E., Läll K., Mägi R., Visscher P.M., Robinson M.R., 2022/08/02. Proceedings of the National Academy of Sciences of the United States of America, 119 (31) pp. e2121279119. Peer-reviewed.
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XSI-a genotype compression tool for compressive genomics in large biobanks.
Wertenbroek R., Rubinacci S., Xenarios I., Thoma Y., Delaneau O., 2022/08/02. Bioinformatics, 38 (15) pp. 3778-3784. Peer-reviewed.
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Haematological changes from conception to childbirth: An indicator of major pregnancy complications.
Patxot M., Stojanov M., Ojavee S.E., Pescini Gobert R., Kutalik Z., Gavillet M., Baud D., Robinson M.R., 2022/08. European journal of haematology, 109 (5) pp. 566-575. Peer-reviewed.
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Megaviruses contain various genes encoding for eukaryotic vesicle trafficking factors.
Khalifeh D., Neveu E., Fasshauer D., 2022/08. Traffic, 23 (8) pp. 414-425. Peer-reviewed.
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The role of wingbeat frequency and amplitude in flight power.
Krishnan K., Garde B., Bennison A., Cole N.C., Cole E.L., Darby J., Elliott K.H., Fell A., Gómez-Laich A., de Grissac S. et al., 2022/08. Journal of the Royal Society, Interface, 19 (193) p. 20220168. Peer-reviewed.
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Improving polygenic prediction with genetically inferred ancestry.
Naret O., Kutalik Z., Hodel F., Xu Z.M., Marques-Vidal P., Fellay J., 2022/07/14. HGG advances, 3 (3) p. 100109. Peer-reviewed.
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Polynomial Mendelian randomization reveals non-linear causal effects for obesity-related traits.
Sulc J., Sjaarda J., Kutalik Z., 2022/07/14. HGG advances, 3 (3) p. 100124. Peer-reviewed.
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Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins.
Moi D., Nishio S., Li X., Valansi C., Langleib M., Brukman N.G., Flyak K., Dessimoz C., de Sanctis D., Tunyasuvunakool K. et al., 2022/07/06. Nature communications, 13 (1) p. 3880. Peer-reviewed.
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The Quest for Orthologs orthology benchmark service in 2022.
Nevers Y., Jones TEM, Jyothi D., Yates B., Ferret M., Portell-Silva L., Codo L., Cosentino S., Marcet-Houben M., Vlasova A. et al., 2022/07/05. Nucleic acids research, 50 (W1) pp. W623-W632. Peer-reviewed.
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ISMB 2022 proceedings.
Dessimoz C., Roy S., 2022/06/24. Bioinformatics, 38 (Supplement_1) pp. i8-i9. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_3B1BABE512BE]
The 3D architecture of the pepper genome and its relationship to function and evolution.
Liao Y., Wang J., Zhu Z., Liu Y., Chen J., Zhou Y., Liu F., Lei J., Gaut B.S., Cao B. et al., 2022/06/16. Nature communications, 13 (1) p. 3479. Peer-reviewed.
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Differential and shared genetic effects on kidney function between diabetic and non-diabetic individuals.
Winkler T.W., Rasheed H., Teumer A., Gorski M., Rowan B.X., Stanzick K.J., Thomas L.F., Tin A., Hoppmann A., Chu A.Y. et al., 2022/06/13. Communications biology, 5 (1) p. 580. Peer-reviewed.
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SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata.
Agostinetto G., Bozzi D., Porro D., Casiraghi M., Labra M., Bruno A., 2022/05/16. Database, 2022 pp. baac033. Peer-reviewed.
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Frequent 4EBP1 Amplification Induces Synthetic Dependence on FGFR Signaling in Cancer.
Mohan P., Pasion J., Ciriello G., Lailler N., de Stanchina E., Viale A., van den Berg A., Diepstra A., Wendel H.G., Sanghvi V.R. et al., 2022/05/13. Cancers, 14 (10) p. 2397. Peer-reviewed.
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OMAMO: orthology-based alternative model organism selection.
Nicheperovich A., Altenhoff A.M., Dessimoz C., Majidian S., 2022/05/13. Bioinformatics, 38 (10) pp. 2965-2966. Peer-reviewed.
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Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic labeling experiment.
Hersch M., Biasini A., Marques A.C., Bergmann S., 2022/04/22. BMC bioinformatics, 23 (1) p. 147. Peer-reviewed.
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Tcf1 is essential for initiation of oncogenic Notch1-driven chromatin topology in T-ALL.
Antoszewski M., Fournier N., Ruiz Buendía G.A., Lourenco J., Liu Y., Sugrue T., Dubey C., Nkosi M., Pritchard CEJ, Huijbers I.J. et al., 2022/04/21. Blood, 139 (16) pp. 2483-2498. Peer-reviewed.
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From pharmacogenetics to pharmaco-omics: Milestones and future directions.
Auwerx C., Sadler M.C., Reymond A., Kutalik Z., 2022/04/14. HGG advances, 3 (2) p. 100100. Peer-reviewed.
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GCAT|Panel, a comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing.
Valls-Margarit J., Galván-Femenía I., Matías-Sánchez D., Blay N., Puiggròs M., Carreras A., Salvoro C., Cortés B., Amela R., Farre X. et al., 2022/03/21. Nucleic acids research, 50 (5) pp. 2464-2479. Peer-reviewed.
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Genomic consequences of colonisation, migration and genetic drift in barn owl insular populations of the eastern Mediterranean.
Machado A.P., Topaloudis A., Cumer T., Lavanchy E., Bontzorlos V., Ceccherelli R., Charter M., Kassinis N., Lymberakis P., Manzia F. et al., 2022/03. Molecular ecology, 31 (5) pp. 1375-1388. Peer-reviewed.
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Global dynamics of microbial communities emerge from local interaction rules.
van Vliet S., Hauert C., Fridberg K., Ackermann M., Dal Co A., 2022/03. PLoS computational biology, 18 (3) pp. e1009877. Peer-reviewed.
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Meta-GWAS Reveals Novel Genetic Variants Associated with Urinary Excretion of Uromodulin.
Joseph C.B., Mariniello M., Yoshifuji A., Schiano G., Lake J., Marten J., Richmond A., Huffman J.E., Campbell A., Harris S.E. et al., 2022/03. Journal of the American Society of Nephrology, 33 (3) pp. 511-529. Peer-reviewed.
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Analysis of Eukaryotic lincRNA Sequences Indicates Signatures of Hindered Translation Linked to Selection Pressure.
Brümmer A., Dreos R., Marques A.C., Bergmann S., 2022/02/03. Molecular biology and evolution, 39 (2) pp. msab356. Peer-reviewed.
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Citrullination Was Introduced into Animals by Horizontal Gene Transfer from Cyanobacteria.
Cummings TFM, Gori K., Sanchez-Pulido L., Gavriilidis G., Moi D., Wilson A.R., Murchison E., Dessimoz C., Ponting C.P., Christophorou M.A., 2022/02/03. Molecular biology and evolution, 39 (2) pp. msab317. Peer-reviewed.
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Challenges and future directions for studying effects of host genetics on the gut microbiome.
Sanna S., Kurilshikov A., van der Graaf A., Fu J., Zhernakova A., 2022/02. Nature genetics, 54 (2) pp. 100-106. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_EDBDCE1B5921]
A strategic model of a host-microbe-microbe system reveals the importance of a joint host-microbe immune response to combat stress-induced gut dysbiosis.
Scheuring I., Rasmussen J.A., Bozzi D., Limborg M.T., 2022. Frontiers in microbiology, 13 p. 912806. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_1083624C0363]
Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study.
Arizmendi Cárdenas Y.O., Neuenschwander S., Malaspinas A.S., 2022. PeerJ, 10 pp. e12784. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_F63ADE26A585]
Bio-SODA UX: enabling natural language question answering over knowledge graphs with user disambiguation.
Sima A.C., Mendes de Farias T., Anisimova M., Dessimoz C., Robinson-Rechavi M., Zbinden E., Stockinger K., 2022. Distributed and parallel databases, 40 (2-3) pp. 409-440. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_EE90AD3795B0]
From pairwise to multiple spliced alignment.
Jammali S., Djossou A., Ouédraogo WDD, Nevers Y., Chegrane I., Ouangraoua A., 2022. Bioinformatics advances, 2 (1) pp. vbab044. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_F9ACA285ED46]
 
Methods for the Analysis of Topologically Associating Domains (TADs).
Zufferey M., Tavernari D., Ciriello G., 2022. pp. 39-59 dans Hi-C Data Analysis, Springer.
[DOI][Pmid][serval:BIB_BD884CBE0DC3]
 
Pretrained Knowledge Base Embeddings for improved Sentential Relation Extraction
Papaluca Andrea, Krefl Daniel, Suominen Hanna, Lenskiy Artem, 2022., 60th Annual Meeting of the Association-for-Computational-Linguistics (ACL) pp. 373-382 dans Proceedings of the 60th Annual Meeting of the Association for Computational Linguistics: Student Research Workshop. Peer-reviewed.
[DOI][WoS][serval:BIB_7CBA92AF9878]
 
The activity of human enhancers is modulated by the splicing of their associated lncRNAs.
Tan J.Y., Marques A.C., 2022/01. PLoS computational biology, 18 (1) pp. e1009722. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_EAB0E8EBFA4A]
The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.
Walker K., Kalra D., Lowdon R., Chen G., Molik D., Soto D.C., Dabbaghie F., Khleifat A.A., Mahmoud M., Paulin L.F. et al., 2022. F1000Research, 11 p. 530. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_96ED1132ABD0]
2021
Genomics Reveal Admixture and Unexpected Patterns of Diversity in a Parapatric Pair of Butterflies.
Tahami M.S., Dincă V., Lee K.M., Vila R., Joshi M., Heikkilä M., Dapporto L., Schmid S., Huemer P., Mutanen M., 2021/12/17. Genes, 12 (12) p. 2009. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_EDF21675F09C]
Fossil-Informed Models Reveal a Boreotropical Origin and Divergent Evolutionary Trajectories in the Walnut Family (Juglandaceae).
Zhang Q., Ree R.H., Salamin N., Xing Y., Silvestro D., 2021/12/16. Systematic biology, 71 (1) pp. 242-258. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_C1BA117F09FD]
Simultaneous estimation of bi-directional causal effects and heritable confounding from GWAS summary statistics.
Darrous L., Mounier N., Kutalik Z., 2021/12/14. Nature communications, 12 (1) p. 7274. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_E3BA5FA37823]
 
BET1 variants establish impaired vesicular transport as a cause for muscular dystrophy with epilepsy.
Donkervoort S., Krause N., Dergai M., Yun P., Koliwer J., Gorokhova S., Geist Hauserman J., Cummings B.B., Hu Y., Smith R. et al., 2021/12/07. EMBO molecular medicine, 13 (12) pp. e13787. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_8EED34C1BBF1]
 
Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits.
Patxot M., Banos D.T., Kousathanas A., Orliac E.J., Ojavee S.E., Moser G., Holloway A., Sidorenko J., Kutalik Z., Mägi R. et al., 2021/11/30. Nature communications, 12 (1) p. 6972. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_9710808BCDCD]
Untargeted Metabolome- and Transcriptome-Wide Association Study Suggests Causal Genes Modulating Metabolite Concentrations in Urine.
Sönmez Flitman R., Khalili B., Kutalik Z., Rueedi R., Brümmer A., Bergmann S., 2021/11/05. Journal of proteome research, 20 (11) pp. 5103-5114. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_83A8DE848FD3]
 
Influence of historical changes in tropical reef habitat on the diversification of coral reef fishes.
Leprieur F., Pellissier L., Mouillot D., Gaboriau T., 2021/10/20. Scientific reports, 11 (1) p. 20731. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_FD80558DF662]
 
Cancer Cells Retrace a Stepwise Differentiation Program during Malignant Progression.
Saghafinia S., Homicsko K., Di Domenico A., Wullschleger S., Perren A., Marinoni I., Ciriello G., Michael I.P., Hanahan D., 2021/10. Cancer discovery, 11 (10) pp. 2638-2657. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_E3BABADE6621]
Comparison of sequence-capture and ddRAD approaches in resolving species and populations in hexacorallian anthozoans.
Glon H., Quattrini A., Rodríguez E., Titus B.M., Daly M., 2021/10. Molecular phylogenetics and evolution, 163 p. 107233. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_271D970E4F44]
 
Enteral nutrition and dynamics of citrulline and intestinal fatty acid-binding protein in adult ICU patients.
Padar M., Starkopf J., Starkopf L., Forbes A., Hiesmayr M., Jakob S.M., Rooijackers O., Wernerman J., Ojavee S.E., Reintam Blaser A., 2021/10. Clinical nutrition ESPEN, 45 pp. 322-332. Peer-reviewed.
[DOI][Pmid][serval:BIB_84240EF05272]
OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches.
Rossier V., Warwick Vesztrocy A., Robinson-Rechavi M., Dessimoz C., 2021/09/29. Bioinformatics, 37 (18) pp. 2866-2873. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E9D32F404F19]
 
Species ecology explains the spatial components of genetic diversity in tropical reef fishes.
Donati GFA, Zemp N., Manel S., Poirier M., Claverie T., Ferraton F., Gaboriau T., Govinden R., Hagen O., Ibrahim S. et al., 2021/09/29. Proceedings. Biological sciences, 288 (1959) p. 20211574. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_6C9EE8F3FD06]
Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy.
Robinson M.R., Patxot M., Stojanov M., Blum S., Baud D., 2021/09/28. Scientific reports, 11 (1) p. 19238. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_BA8FC21210D4]
Differentially expressed genes reflect disease-induced rather than disease-causing changes in the transcriptome.
Porcu E., Sadler M.C., Lepik K., Auwerx C., Wood A.R., Weihs A., Sleiman MSB, Ribeiro D.M., Bandinelli S., Tanaka T. et al., 2021/09/24. Nature communications, 12 (1) p. 5647. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_253FEBED3C3F]
 
Inosine Substitutions in RNA Activate Latent G-Quadruplexes.
Hagen T., Laski A., Brümmer A., Pruška A., Schlösser V., Cléry A., Allain F.H., Zenobi R., Bergmann S., Hall J., 2021/09/22. Journal of the American Chemical Society, 143 (37) pp. 15120-15130. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_419D75E87BF6]
 
Novel Approach Combining Transcriptional and Evolutionary Signatures to Identify New Multiciliation Genes.
Defosset A., Merlat D., Poidevin L., Nevers Y., Kress A., Poch O., Lecompte O., 2021/09/21. Genes, 12 (9) p. 1452. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F7D3952B2536]
 
Heritability and association with distinct genetic loci of erythropoietin levels in the general population.
Corre T., Ponte B., Pivin E., Pruijm M., Ackermann D., Ehret G., Spanaus K., Bochud M., Wenger R.H., 2021/09/01. Haematologica, 106 (9) pp. 2499-2501. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A24F2D13A3DD]
 
Hidden cell diversity in Placozoa: ultrastructural insights from Hoilungia hongkongensis.
Romanova D.Y., Varoqueaux F., Daraspe J., Nikitin M.A., Eitel M., Fasshauer D., Moroz L.L., 2021/09. Cell and tissue research, 385 (3) pp. 623-637. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_C466BC2969FF]
Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression.
Võsa U., Claringbould A., Westra H.J., Bonder M.J., Deelen P., Zeng B., Kirsten H., Saha A., Kreuzhuber R., Yazar S. et al., 2021/09. Nature genetics, 53 (9) pp. 1300-1310. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_9462F2AB5F22]
The molecular basis, genetic control and pleiotropic effects of local gene co-expression.
Ribeiro D.M., Rubinacci S., Ramisch A., Hofmeister R.J., Dermitzakis E.T., Delaneau O., 2021/08/10. Nature communications, 12 (1) p. 4842. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_5AA3BA80411A]
 
Systematic assessment of gene co-regulation within chromatin domains determines differentially active domains across human cancers.
Zufferey M., Liu Y., Tavernari D., Mina M., Ciriello G., 2021/08/03. Genome biology, 22 (1) p. 218. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_0C0A83ACB23F]
 
Genetic insights into biological mechanisms governing human ovarian ageing.
Ruth K.S., Day F.R., Hussain J., Martínez-Marchal A., Aiken C.E., Azad A., Thompson D.J., Knoblochova L., Abe H., Tarry-Adkins J.L. et al., 2021/08. Nature, 596 (7872) pp. 393-397. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_AEC34ED6E894]
Ten Years of Collaborative Progress in the Quest for Orthologs.
Linard B., Ebersberger I., McGlynn S.E., Glover N., Mochizuki T., Patricio M., Lecompte O., Nevers Y., Thomas P.D., Gabaldón T. et al., 2021/07/29. Molecular biology and evolution, 38 (8) pp. 3033-3045. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_69FF3D639B70]
Cell-autonomous inflammation of BRCA1-deficient ovarian cancers drives both tumor-intrinsic immunoreactivity and immune resistance via STING.
Bruand M., Barras D., Mina M., Ghisoni E., Morotti M., Lanitis E., Fahr N., Desbuisson M., Grimm A., Zhang H. et al., 2021/07/20. Cell reports, 36 (3) p. 109412. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_745449157CA6]
 
CEP78 functions downstream of CEP350 to control biogenesis of primary cilia by negatively regulating CP110 levels.
Gonçalves A.B., Hasselbalch S.K., Joensen B.B., Patzke S., Martens P., Ohlsen S.K., Quinodoz M., Nikopoulos K., Suleiman R., Damsø Jeppesen M.P. et al., 2021/07/14. eLife, 10 pp. e63731. Peer-reviewed.
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ISMB/ECCB 2021 proceedings.
Dessimoz C., Przytycka T.M., 2021/07/12. Bioinformatics, 37 (Suppl_1) pp. i7-i8. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_896DE61ACD8B]
Bio-SODA: Enabling Natural Language Question Answering over Knowledge Graphs without Training Data
Sima Ana Claudia, Mendes de Farias Tarcisio, Anisimova Maria, Dessimoz Christophe, Robinson-Rechavi Marc, Zbinden Erich, Stockinger Kurt, 2021/07/06. 33rd International Conference on Scientific and Statistical Database Management. Peer-reviewed.
[URN][DOI][serval:BIB_A6616600154D]
A live single-cell reporter assay links intratumor heterogeneity to metastatic proclivity in Ewing sarcoma.
Keskin T., Rucci B., Cornaz-Buros S., Martin P., Fusco C., Broye L., Cisarova K., Perez E.M., Letovanec I., La Rosa S. et al., 2021/07. Science advances, 7 (27) pp. eabf9394. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_16E18D416FE5]
 
Evolution of life cycles and reproductive traits: Insights from the brown algae.
Heesch S., Serrano-Serrano M., Barrera-Redondo J., Luthringer R., Peters A.F., Destombe C., Cock J.M., Valero M., Roze D., Salamin N. et al., 2021/07. Journal of evolutionary biology, 34 (7) pp. 992-1009. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_9FC279E4C2BC]
Large-scale whole-genome resequencing unravels the domestication history of Cannabis sativa.
Ren G., Zhang X., Li Y., Ridout K., Serrano-Serrano M.L., Yang Y., Liu A., Ravikanth G., Nawaz M.A., Mumtaz A.S. et al., 2021/07. Science Advances, 7 (29) pp. eabg2286. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_961363B69EFE]
A Cautionary Note on the Use of Genotype Callers in Phylogenomics.
Duchen P., Salamin N., 2021/06/16. Systematic biology, 70 (4) pp. 844-854. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_BE78FE659A7E]
Homoeolog Inference Methods Requiring Bidirectional Best Hits or Synteny Miss Many Pairs.
Glover N., Sheppard S., Dessimoz C., 2021/06/08. Genome biology and evolution, 13 (6) pp. evab077. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_9739D4F55417]
 
Thyroid hormones regulate the formation and environmental plasticity of white bars in clownfishes.
Salis P., Roux N., Huang D., Marcionetti A., Mouginot P., Reynaud M., Salles O., Salamin N., Pujol B., Parichy D.M. et al., 2021/06/08. Proceedings of the National Academy of Sciences of the United States of America, 118 (23). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_3175D86F9AC6]
 
Combining generative artificial intelligence and on-chip synthesis for de novo drug design.
Grisoni F., Huisman BJH, Button A.L., Moret M., Atz K., Merk D., Schneider G., 2021/06. Science advances, 7 (24) pp. eabg3338. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_5661285AE083]
Gene-educational attainment interactions in a multi-ancestry genome-wide meta-analysis identify novel blood pressure loci.
de Las Fuentes L., Sung Y.J., Noordam R., Winkler T., Feitosa M.F., Schwander K., Bentley A.R., Brown M.R., Guo X., Manning A. et al., 2021/06. Molecular psychiatry, 26 (6) pp. 2111-2125. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_7C997FACA438]
Nongenetic Evolution Drives Lung Adenocarcinoma Spatial Heterogeneity and Progression.
Tavernari D., Battistello E., Dheilly E., Petruzzella A.S., Mina M., Sordet-Dessimoz J., Peters S., Krueger T., Gfeller D., Riggi N. et al., 2021/06. Cancer discovery, 11 (6) pp. 1490-1507. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F6D4BAEDCE1E]
The trans-ancestral genomic architecture of glycemic traits.
Chen J., Spracklen C.N., Marenne G., Varshney A., Corbin L.J., Luan J., Willems S.M., Wu Y., Zhang X., Horikoshi M. et al., 2021/06. Nature genetics, 53 (6) pp. 840-860. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_53C688CA509F]
The many faces of cancer evolution.
Ciriello G., Magnani L., 2021/05/21. iScience, 24 (5) p. 102403. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_FC9DC8DD021C]
The genomic history of the Aegean palatial civilizations.
Clemente F., Unterländer M., Dolgova O., Amorim CEG, Coroado-Santos F., Neuenschwander S., Ganiatsou E., Cruz Dávalos D.I., Anchieri L., Michaud F. et al., 2021/05/13. Cell, 184 (10) pp. 2565-2586.e21. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_114B1DCAE1B5]
Systematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes.
Liu Y., Nanni L., Sungalee S., Zufferey M., Tavernari D., Mina M., Ceri S., Oricchio E., Ciriello G., 2021/05/10. Nature communications, 12 (1) p. 2439. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_95E06884F11E]
 
Histone acetylation dynamics modulates chromatin conformation and allele-specific interactions at oncogenic loci.
Sungalee S., Liu Y., Lambuta R.A., Katanayeva N., Donaldson Collier M., Tavernari D., Roulland S., Ciriello G., Oricchio E., 2021/05. Nature genetics, 53 (5) pp. 650-662. Peer-reviewed.
[DOI][Pmid][serval:BIB_D9CCA98B8DC1]
 
How should functional relationships be evaluated using phylogenetic comparative methods? A case study using metabolic rate and body temperature.
Uyeda J.C., Bone N., McHugh S., Rolland J., Pennell M.W., 2021/05. Evolution; international journal of organic evolution, 75 (5) pp. 1097-1105. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_15EE0FF290BB]
Genomic architecture and prediction of censored time-to-event phenotypes with a Bayesian genome-wide analysis.
Ojavee S.E., Kousathanas A., Trejo Banos D., Orliac E.J., Patxot M., Läll K., Mägi R., Fischer K., Kutalik Z., Robinson M.R., 2021/04/20. Nature communications, 12 (1) p. 2337. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_DD352C34FFE4]
Cervical cancer screening patterns among HIV-positive women in Estonia: a population-based retrospective cohort study.
Tisler A., Ojavee S.E., Veerus P., Soodla P., Uusküla A., 2021/04/01. BMC cancer, 21 (1) p. 350. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_045E7F13188C]
 
Fossil data support a pre-Cretaceous origin of flowering plants.
Silvestro D., Bacon C.D., Ding W., Zhang Q., Donoghue PCJ, Antonelli A., Xing Y., 2021/04. Nature ecology & evolution, 5 (4) pp. 449-457. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_1D5BD4D622BA]
 
Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator.
Allou L., Balzano S., Magg A., Quinodoz M., Royer-Bertrand B., Schöpflin R., Chan W.L., Speck-Martins C.E., Carvalho D.R., Farage L. et al., 2021/04. Nature, 592 (7852) pp. 93-98. Peer-reviewed.
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On the Origin of Coexisting Species.
Germain R.M., Hart S.P., Turcotte M.M., Otto S.P., Sakarchi J., Rolland J., Usui T., Angert A.L., Schluter D., Bassar R.D. et al., 2021/04. Trends in ecology & evolution, 36 (4) pp. 284-293. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_247B5F780114]
Phylogenomics of Gesneriaceae using targeted capture of nuclear genes.
Ogutcen Ezgi, Christe Camille, Nishii Kanae, Salamin Nicolas, Möller Michael, Perret Mathieu, 2021/04. Molecular phylogenetics and evolution, 157 p. 107068. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_0102B1359D1E]
 
Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.
Niarakis A., Kuiper M., Ostaszewski M., Malik Sheriff R.S., Casals-Casas C., Thieffry D., Freeman T.C., Thomas P., Touré V., Noël V. et al., 2021/03/22. Briefings in bioinformatics, 22 (2) pp. 1848-1859. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_CFABEDE09323]
Gene Duplication and Gain in the Trematode Atriophallophorus winterbourni Contributes to Adaptation to Parasitism.
Zajac N., Zoller S., Seppälä K., Moi D., Dessimoz C., Jokela J., Hartikainen H., Glover N., 2021/03/01. Genome biology and evolution, 13 (3) pp. evab010. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_37EBF9C1AD84]
 
Publisher Correction: Efficient phasing and imputation of low-coverage sequencing data using large reference panels.
Rubinacci S., Ribeiro D.M., Hofmeister R.J., Delaneau O., 2021/03..
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Want to track pandemic variants faster? Fix the bioinformatics bottleneck.
Hodcroft E.B., De Maio N., Lanfear R., MacCannell D.R., Minh B.Q., Schmidt H.A., Stamatakis A., Goldman N., Dessimoz C., 2021/03. Nature, 591 (7848) pp. 30-33.
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March Mammal Madness and the power of narrative in science outreach.
Hinde K., Amorim CEG, Brokaw A.F., Burt N., Casillas M.C., Chen A., Chestnut T., Connors P.K., Dasari M., Ditelberg C.F. et al., 2021/02/22. eLife, 10 pp. e65066. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_6F054A6CCE5A]
Prediction of neo-epitope immunogenicity reveals TCR recognition determinants and provides insight into immunoediting.
Schmidt J., Smith A.R., Magnin M., Racle J., Devlin J.R., Bobisse S., Cesbron J., Bonnet V., Carmona S.J., Huber F. et al., 2021/02/16. Cell reports. Medicine, 2 (2) p. 100194. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_9AA90BD897A9]
On the Effect of Asymmetrical Trait Inheritance on Models of Trait Evolution.
Duchen P., Alfaro M.L., Rolland J., Salamin N., Silvestro D., 2021/02/10. Systematic biology, 70 (2) pp. 376-388. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_FDE71488549F]
Gene regulation contributes to explain the impact of early life socioeconomic disadvantage on adult inflammatory levels in two cohort studies.
Carmeli C., Kutalik Z., Mishra P.P., Porcu E., Delpierre C., Delaneau O., Kelly-Irving M., Bochud M., Dhayat N.A., Ponte B. et al., 2021/02/04. Scientific reports, 11 (1) p. 3100. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_39953DE1C692]
Sustained androgen receptor signaling is a determinant of melanoma cell growth potential and tumorigenesis.
Ma M., Ghosh S., Tavernari D., Katarkar A., Clocchiatti A., Mazzeo L., Samarkina A., Epiney J., Yu Y.R., Ho P.C. et al., 2021/02/01. The Journal of experimental medicine, 218 (2) pp. e20201137. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_3B2A745CA757]
Translation is required for miRNA-dependent decay of endogenous transcripts.
Biasini A., Abdulkarim B., de Pretis S., Tan J.Y., Arora R., Wischnewski H., Dreos R., Pelizzola M., Ciaudo C., Marques A.C., 2021/02/01. The EMBO journal, 40 (3) pp. e104569. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_1E9949CC6BEE]
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