MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

Autor: Marcela Uliano-Silva, João Gabriel R. N. Ferreira, Ksenia Krasheninnikova, Darwin Tree of Life Consortium, Giulio Formenti, Linelle Abueg, James Torrance, Eugene W. Myers, Richard Durbin, Mark Blaxter, Shane A. McCarthy

Publikováno v: BMC Bioinformatics, Vol 24, Iss 1, Pp 1-13 (2023)

Abstract Background PacBio high fidelity (HiFi) sequencing reads are both long (15–20 kb) and highly accurate (> Q20). Because of these properties, they have revolutionised genome assembly leading to more accurate and contiguous genomes. In eukaryo

Externí odkaz: https://doaj.org/article/83a929ea54734f328969ac7528d3ad5f

A novel nematode species from the Siberian permafrost shares adaptive mechanisms for cryptobiotic survival with C. elegans dauer larva.

Autor: Anastasia Shatilovich, Vamshidhar R Gade, Martin Pippel, Tarja T Hoffmeyer, Alexei V Tchesunov, Lewis Stevens, Sylke Winkler, Graham M Hughes, Sofia Traikov, Michael Hiller, Elizaveta Rivkina, Philipp H Schiffer, Eugene W Myers, Teymuras V Kurzchalia

Publikováno v: PLoS Genetics, Vol 19, Iss 7, p e1010798 (2023)

Some organisms in nature have developed the ability to enter a state of suspended metabolism called cryptobiosis when environmental conditions are unfavorable. This state-transition requires execution of a combination of genetic and biochemical pathw

Externí odkaz: https://doaj.org/article/e261884506e04248b7ae74c36830e69d

Rod nuclear architecture determines contrast transmission of the retina and behavioral sensitivity in mice

Autor: Kaushikaram Subramanian, Martin Weigert, Oliver Borsch, Heike Petzold, Alfonso Garcia-Ulloa, Eugene W Myers, Marius Ader, Irina Solovei, Moritz Kreysing

Publikováno v: eLife, Vol 8 (2019)

Rod photoreceptors of nocturnal mammals display a striking inversion of nuclear architecture, which has been proposed as an evolutionary adaptation to dark environments. However, the nature of visual benefits and the underlying mechanisms remains unc

Externí odkaz: https://doaj.org/article/2a383c82c94d471fad04fe39824eaaf6

The complete sequence of a human genome

Autor: Sergey Nurk, Sergey Koren, Arang Rhie, Mikko Rautiainen, Andrey V. Bzikadze, Alla Mikheenko, Mitchell R. Vollger, Nicolas Altemose, Lev Uralsky, Ariel Gershman, Sergey Aganezov, Savannah J. Hoyt, Mark Diekhans, Glennis A. Logsdon, Michael Alonge, Stylianos E. Antonarakis, Matthew Borchers, Gerard G. Bouffard, Shelise Y. Brooks, Gina V. Caldas, Nae-Chyun Chen, Haoyu Cheng, Chen-Shan Chin, William Chow, Leonardo G. de Lima, Philip C. Dishuck, Richard Durbin, Tatiana Dvorkina, Ian T. Fiddes, Giulio Formenti, Robert S. Fulton, Arkarachai Fungtammasan, Erik Garrison, Patrick G. S. Grady, Tina A. Graves-Lindsay, Ira M. Hall, Nancy F. Hansen, Gabrielle A. Hartley, Marina Haukness, Kerstin Howe, Michael W. Hunkapiller, Chirag Jain, Miten Jain, Erich D. Jarvis, Peter Kerpedjiev, Melanie Kirsche, Mikhail Kolmogorov, Jonas Korlach, Milinn Kremitzki, Heng Li, Valerie V. Maduro, Tobias Marschall, Ann M. McCartney, Jennifer McDaniel, Danny E. Miller, James C. Mullikin, Eugene W. Myers, Nathan D. Olson, Benedict Paten, Paul Peluso, Pavel A. Pevzner, David Porubsky, Tamara Potapova, Evgeny I. Rogaev, Jeffrey A. Rosenfeld, Steven L. Salzberg, Valerie A. Schneider, Fritz J. Sedlazeck, Kishwar Shafin, Colin J. Shew, Alaina Shumate, Ying Sims, Arian F. A. Smit, Daniela C. Soto, Ivan Sović, Jessica M. Storer, Aaron Streets, Beth A. Sullivan, Françoise Thibaud-Nissen, James Torrance, Justin Wagner, Brian P. Walenz, Aaron Wenger, Jonathan M. D. Wood, Chunlin Xiao, Stephanie M. Yan, Alice C. Young, Samantha Zarate, Urvashi Surti, Rajiv C. McCoy, Megan Y. Dennis, Ivan A. Alexandrov, Jennifer L. Gerton, Rachel J. O’Neill, Winston Timp, Justin M. Zook, Michael C. Schatz, Evan E. Eichler, Karen H. Miga, Adam M. Phillippy

Publikováno v: Science (New York, N.Y.), vol 376, iss 6588

Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Con

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::57a90349d97678f40cdb370a46304d2d
https://doi.org/10.1126/science.abj6987

Biobeam-Multiplexed wave-optical simulations of light-sheet microscopy.

Autor: Martin Weigert, Kaushikaram Subramanian, Sebastian T Bundschuh, Eugene W Myers, Moritz Kreysing

Publikováno v: PLoS Computational Biology, Vol 14, Iss 4, p e1006079 (2018)

Sample-induced image-degradation remains an intricate wave-optical problem in light-sheet microscopy. Here we present biobeam, an open-source software package that enables simulation of operational light-sheet microscopes by combining data from 105-1

Externí odkaz: https://doaj.org/article/f537b1a4003b4813bf23f4d0220904cb