Zobrazeno 1 - 10
of 83
pro vyhledávání: '"Daniel Doerr"'
Publikováno v:
Algorithms for Molecular Biology, Vol 18, Iss 1, Pp 1-15 (2023)
Abstract Homologous recombination between the maternal and paternal copies of a chromosome is a key mechanism for human inheritance and shapes population genetic properties of our species. However, a similar mechanism can also act between different c
Externí odkaz:
https://doaj.org/article/246274888f224a80a2409ba975e0fbdc
Publikováno v:
Algorithms for Molecular Biology, Vol 18, Iss 1, Pp 1-1 (2023)
Externí odkaz:
https://doaj.org/article/796e492df6ac414bac4d37e4b2d3faa7
Publikováno v:
BMC Genomics, Vol 21, Iss S2, Pp 1-11 (2020)
Abstract Background Computationally inferred ancestral genomes play an important role in many areas of genome research. We present an improved workflow for the reconstruction from highly diverged genomes such as those of plants. Results Our work reli
Externí odkaz:
https://doaj.org/article/dd5ae9b9c0b3433ba95766c24c1d6aa6
Autor:
Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian K. Lucas, Jean Monlong, Haley J. Abel, Silvia Buonaiuto, Xian H. Chang, Haoyu Cheng, Justin Chu, Vincenza Colonna, Jordan M. Eizenga, Xiaowen Feng, Christian Fischer, Robert S. Fulton, Shilpa Garg, Cristian Groza, Andrea Guarracino, William T. Harvey, Simon Heumos, Kerstin Howe, Miten Jain, Tsung-Yu Lu, Charles Markello, Fergal J. Martin, Matthew W. Mitchell, Katherine M. Munson, Moses Njagi Mwaniki, Adam M. Novak, Hugh E. Olsen, Trevor Pesout, David Porubsky, Pjotr Prins, Jonas A. Sibbesen, Jouni Sirén, Chad Tomlinson, Flavia Villani, Mitchell R. Vollger, Lucinda L. Antonacci-Fulton, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Andrew Carroll, Pi-Chuan Chang, Sarah Cody, Daniel E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Peter Ebert, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Giulio Formenti, Adam Frankish, Yan Gao, Nanibaa’ A. Garrison, Carlos Garcia Giron, Richard E. Green, Leanne Haggerty, Kendra Hoekzema, Thibaut Hourlier, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P. Lewis, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Ann McCartney, Jennifer McDaniel, Jacquelyn Mountcastle, Maria Nattestad, Sergey Nurk, Nathan D. Olson, Alice B. Popejoy, Daniela Puiu, Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valerie A. Schneider, Baergen I. Schultz, Kishwar Shafin, Michael W. Smith, Heidi J. Sofia, Ahmad N. Abou Tayoun, Françoise Thibaud-Nissen, Francesca Floriana Tricomi, Justin Wagner, Brian Walenz, Jonathan M. D. Wood, Aleksey V. Zimin, Guillaume Bourque, Mark J. P. Chaisson, Paul Flicek, Adam M. Phillippy, Justin M. Zook, Evan E. Eichler, David Haussler, Ting Wang, Erich D. Jarvis, Karen H. Miga, Erik Garrison, Tobias Marschall, Ira M. Hall, Heng Li, Benedict Paten
Publikováno v:
Nature. 617:312-324
Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ce56c54eebc15371aabecb5595f996d0
https://doi.org/10.1038/s41586-023-05896-x
https://doi.org/10.1038/s41586-023-05896-x
Autor:
Helmuth O.M. Silva, Diego P. Rubert, Eloi Araujo, Eckhard Steffen, Daniel Doerr, Fábio V. Martinez
Publikováno v:
RAIRO - Operations Research. 57:1045-1058
Ancestral reconstruction is a classic task in comparative genomics. Here, we study the genome median problem, a related computational problem which, given a set of three or more genomes, asks to find a new genome that minimizes the sum of pairwise di
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::987abfef651b0a561fd2057b99482cc5
https://doi.org/10.1051/ro/2023052
https://doi.org/10.1051/ro/2023052
Publikováno v:
BMC Genomics, Vol 19, Iss S5, Pp 59-70 (2018)
Abstract Background Hi-C sequencing offers novel, cost-effective means to study the spatial conformation of chromosomes. We use data obtained from Hi-C experiments to provide new evidence for the existence of spatial gene clusters. These are sets of
Externí odkaz:
https://doaj.org/article/9d2a6511f48a4542b790b23a94d7c4ab
Publikováno v:
Algorithms for Molecular Biology, Vol 12, Iss 1, Pp 1-14 (2017)
Abstract Background The gene family-free framework for comparative genomics aims at providing methods for gene order analysis that do not require prior gene family assignment, but work directly on a sequence similarity graph. We study two problems re
Externí odkaz:
https://doaj.org/article/701fbc85be564a298e8c09687275af1f
Publikováno v:
Molecular Biology and Evolution. 37:1470-1479
The dramatic decrease in time and cost for generating genetic sequence data has opened up vast opportunities in molecular systematics, one of which is the ability to decipher the evolutionary history of strains of a species. Under this fine systemati
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d63fe2ac70f9a87a6e7ec272c468cbf5
https://doi.org/10.1093/molbev/msz302
https://doi.org/10.1093/molbev/msz302
Autor:
Cedric Chauve, Daniel Doerr
Publikováno v:
Journal of Bioinformatics and Computational Biology. 19
Reconstructing ancestral gene orders is an important step towards understanding genome evolution. The Small Parsimony Problem (SPP) has been extensively studied in this regard. The problem aims at finding the gene orders at internal nodes of a given
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1c6fd3c1b3b9a36f271beaa633394170
https://doi.org/10.1142/s0219720021400096
https://doi.org/10.1142/s0219720021400096
Publikováno v:
Journal of bioinformatics and computational biology. 19(6)
Recently, we proposed an efficient ILP formulation [Rubert DP, Martinez FV, Braga MDV, Natural family-free genomic distance, Algorithms Mol Biol 16:4, 2021] for exactly computing the rearrangement distance of two genomes in a family-free setting. In
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8b0caac56c675cea508df29687e1066d
https://pubmed.ncbi.nlm.nih.gov/34775922
https://pubmed.ncbi.nlm.nih.gov/34775922