New genome assembly of the barn owl (Tyto alba alba)

Autor: Anne‐Lyse Ducrest, Samuel Neuenschwander, Emanuel Schmid‐Siegert, Marco Pagni, Clément Train, David Dylus, Yannis Nevers, Alex Warwick Vesztrocy, Luis M. San‐Jose, Mélanie Dupasquier, Christophe Dessimoz, Ioannis Xenarios, Alexandre Roulin, Jérôme Goudet

Publikováno v: Ecology and Evolution, Vol 10, Iss 5, Pp 2284-2298 (2020)

Abstract New genomic tools open doors to study ecology, evolution, and population genomics of wild animals. For the Barn owl species complex, a cosmopolitan nocturnal raptor, a very fragmented draft genome was assembled for the American species (Tyto

Externí odkaz: https://doaj.org/article/16afd23122944a6486294a8fdff6eee1

OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem.

Autor: Altenhoff, Adrian M, Warwick Vesztrocy, Alex, Bernard, Charles, Train, Clement-Marie, Nicheperovich, Alina, Prieto Baños, Silvia, Julca, Irene, Moi, David, Nevers, Yannis, Majidian, Sina, Dessimoz, Christophe, Glover, Natasha M

Publikováno v: Nucleic Acids Research; 1/5/2024, Vol. 52 Issue D1, pD513-D521, 9p

OMA standalone: orthology inference among public and custom genomes and transcriptomes

Autor: Adrian M. Altenhoff, Maximilian J. Telford, Bartlomiej Tomiczek, David Dylus, Natasha Glover, Steven Müller, Christophe Dessimoz, Daniel A. Dalquen, Magdalena Zarowiecki, Jeremy Levy, Alex Warwick Vesztrocy

Publikováno v: Genome research, vol. 29, no. 7, pp. 1152-1163
Genome Research, 29 (7)

Genomes and transcriptomes are now typically sequenced by individual laboratories but analyzing them often remains challenging. One essential step in many analyses lies in identifying orthologs—corresponding genes across multiple species—but this

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4442f9b3c272fc14662bff06e39acaeb
https://doi.org/10.1101/gr.243212.118

The Cafa Challenge Reports Improved Protein Function Prediction And New Functional Annotations For Hundreds Of Genes Through Experimental Screens

Autor: Heiko Schoof, Ahmet Sureyya Rifaioglu, Ian Sillitoe, Shanfeng Zhu, Marco Carraro, Naihui Zhou, Asa Ben-Hur, Rui Fa, Alice C. McHardy, David W. Ritchie, George Georghiou, Filip Ginter, Haixuan Yang, Alex A. Freitas, Constance J. Jeffery, Tapio Salakoski, Radoslav Davidovic, Huy N Nguyen, Devon Johnson, Yotam Frank, Alexandra J. Lee, Sean D. Mooney, Marco Falda, Marie-Dominique Devignes, Gianfranco Politano, David T. Jones, Silvio C. E. Tosatto, Renzhi Cao, Zihan Zhang, Sabeur Aridhi, Stefano Pascarelli, Vedrana Vidulin, Qizhong Mao, Balint Z. Kacsoh, Patricia C. Babbitt, Giovanni Bosco, Farrokh Mehryary, Florian Boecker, Alfonso E. Romero, Angela D. Wilkins, Saso Dzeroski, Richard Bonneau, Hans Moen, Chengxin Zhang, Prajwal Bhat, Giuliano Grossi, Martti Tolvanen, Matteo Re, Meet Barot, Mohammad R. K. Mofrad, Predrag Radivojac, Stefano Di Carlo, Tatyana Goldberg, Branislava Gemovic, Suyang Dai, Pier Luigi Martelli, Giorgio Valentini, Maxat Kulmanov, Maria Jesus Martin, Claire O'Donovan, Dallas J. Larsen, Alexandre Renaux, Alan Medlar, Jeffrey M. Yunes, Erica Suh, Volkan Atalay, Vladimir Gligorijević, Fran Supek, Elaine Zosa, Wei-Cheng Tseng, Nafiz Hamid, Marco Mesiti, Tunca Doğan, Petri Törönen, Hafeez Ur Rehman, Jose Manuel Rodriguez, Alessandro Petrini, Sayoni Das, Burkhard Rost, Miguel Amezola, Mateo Torres, Jianlin Cheng, Daisuke Kihara, Liisa Holm, Marco Frasca, Steven E. Brenner, Stefano Toppo, Adrian M. Altenhoff, Chenguang Zhao, Daniel B. Roche, Alperen Dalkiran, Alex W. Crocker, Marco Notaro, Iddo Friedberg, Michal Linial, Julian Gough, Damiano Piovesan, Slobodan Vucetic, Natalie Thurlby, Olivier Lichtarge, Jari Björne, Jonas Reeb, Rabie Saidi, Yuxiang Jiang, Christophe Dessimoz, Jie Hou, Ronghui You, Tomislav Šmuc, Paolo Fontana, Michele Berselli, Jia-Ming Chang, Deborah A. Hogan, Larry Davis, Ehsaneddin Asgari, Shuwei Yao, Zheng Wang, Fabio Fabris, Michael L. Tress, Caleb Chandler, Christine A. Orengo, Rengul Cetin Atalay, Castrense Savojardo, Danielle A Brackenridge, Peter W. Rose, Yang Zhang, Dane Jo, Gage S. Black, Shanshan Zhang, Aashish Jain, Liam J. McGuffin, Timothy Bergquist, Peter L. Freddolino, Robert Hoehndorf, Rita Casadio, Da Chen Emily Koo, Mark N. Wass, Hai Fang, Casey S. Greene, Suwisa Kaewphan, Magdalena Antczak, Wen-Hung Liao, Enrico Lavezzo, Neven Sumonja, Ashton Omdahl, José M. Fernández, Ilya Novikov, Jonathan B. Dayton, Feng Zhang, Vladimir Perovic, Cen Wan, Jonathan G. Lees, Kai Hakala, Weidong Tian, Alex Warwick Vesztrocy, Domenico Cozzetto, Nevena Veljkovic, Yi-Wei Liu, Imane Boudellioua, Po-Han Chi, Kimberley A. Lewis, Seyed Ziaeddin Alborzi, Giuseppe Profiti, Alberto Paccanaro, Itamar Borukhov, Alfredo Benso, Indika Kahanda, Rebecca L. Hurto

Publikováno v: Repisalud
Instituto de Salud Carlos III (ISCIII)
Genome Biology
Genome Biology, BioMed Central, 2019, 20 (1), ⟨10.1186/s13059-019-1835-8⟩
Zhou, N, Jiang, Y, Bergquist, T R, Lee, A J, Kacsoh, B Z, Crocker, A W, Lewis, K A, Georghiou, G, Nguyen, H N, Hamid, M N, Davis, L, Dogan, T, Atalay, V, Rifaioglu, A S, Dalklran, A, Cetin Atalay, R, Zhang, C, Hurto, R L, Freddolino, P L, Zhang, Y, Bhat, P, Supek, F, Fernández, J M, Gemovic, B, Perovic, V R, Davidović, R S, Sumonja, N, Veljkovic, N, Asgari, E, Mofrad, M R K, Profiti, G, Savojardo, C, Martelli, P L, Casadio, R, Boecker, F, Schoof, H, Kahanda, I, Thurlby, N, McHardy, A C, Renaux, A, Saidi, R, Gough, J, Freitas, A A, Antczak, M, Fabris, F, Wass, M N, Hou, J, Cheng, J, Wang, Z, Romero, A E, Paccanaro, A, Yang, H, Goldberg, T, Zhao, C, Holm, L, Törönen, P, Medlar, A J, Zosa, E, Borukhov, I, Novikov, I, Wilkins, A, Lichtarge, O, Chi, P H, Tseng, W C, Linial, M, Rose, P W, Dessimoz, C, Vidulin, V, Dzeroski, S, Sillitoe, I, Das, S, Lees, J G, Jones, D T, Wan, C, Cozzetto, D, Fa, R, Torres, M, Warwick Vesztrocy, A, Rodriguez, J M, Tress, M L, Frasca, M, Notaro, M, Grossi, G, Petrini, A, Re, M, Valentini, G, Mesiti, M, Roche, D B, Reeb, J, Ritchie, D W, Aridhi, S, Alborzi, S Z, Devignes, M D, Koo, D C E, Bonneau, R, Gligorijević, V, Barot, M, Fang, H, Toppo, S, Lavezzo, E, Falda, M, Berselli, M, Tosatto, S C E, Carraro, M, Piovesan, D, Ur Rehman, H, Mao, Q, Zhang, S, Vucetic, S, Black, G S, Jo, D, Suh, E, Dayton, J B, Larsen, D J, Omdahl, A R, McGuffin, L J, Brackenridge, D A, Babbitt, P C, Yunes, J M, Fontana, P, Zhang, F, Zhu, S, You, R, Zhang, Z, Dai, S, Yao, S, Tian, W, Cao, R, Chandler, C, Amezola, M, Johnson, D, Chang, J M, Liao, W H, Liu, Y W, Pascarelli, S, Frank, Y, Hoehndorf, R, Kulmanov, M, Boudellioua, I, Politano, G, Di Carlo, S, Benso, A, Hakala, K, Ginter, F, Mehryary, F, Kaewphan, S, Björne, J, Moen, H, Tolvanen, M E E, Salakoski, T, Kihara, D, Jain, A, Šmuc, T, Altenhoff, A, Ben-Hur, A, Rost, B, Brenner, S E, Orengo, C A, Jeffery, C J, Bosco, G, Hogan, D A, Martin, M J, O'Donovan, C, Mooney, S D, Greene, C S, Radivojac, P & Friedberg, I 2019, ' The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens ', Genome Biology, vol. 20, no. 1, 244 (2019) . https://doi.org/10.1186/s13059-019-1835-8
Genome biology
Genome Biology, Vol 20, Iss 1, Pp 1-23 (2019)
Genome Biology, 2019, 20 (1), ⟨10.1186/s13059-019-1835-8⟩

Tosatto, Silvio/0000-0003-4525-7793; Zhang, Feng/0000-0003-3447-897X; Gonzalez, Jose Maria Fernandez/0000-0002-4806-5140; Devignes, Marie-Dominique/0000-0002-0399-8713; Wass, Mark/0000-0001-5428-6479; Falda, Marco/0000-0003-2642-519X; Thurlby, Natali

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::99caa2a2ab2b36bdcf4f44143c8015a5
http://hdl.handle.net/11655/24591

OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches

Autor: Victor Rossier, Christophe Dessimoz, Marc Robinson-Rechavi, Alex Warwick Vesztrocy

Publikováno v: Bioinformatics
Bioinformatics, vol. 37, no. 18, pp. 2866-2873

Motivation Assigning new sequences to known protein families and subfamilies is a prerequisite for many functional, comparative and evolutionary genomics analyses. Such assignment is commonly achieved by looking for the closest sequence in a referenc

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c87d4ab175f1cab38b9c91a88ecdbc4a
https://pubmed.ncbi.nlm.nih.gov/33787851