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Akademický článek

Effect of sequence depth and length in long-read assembly of the maize inbred NC358

Publikováno v: Nature Communications, Vol 11, Iss 1, Pp 1-10 (2020)

Sequence depth and read length determine the quality of genome assembly. Here, the authors leverage a set of PacBio reads to develop guidelines for sequencing and assembly of complex plant genomes in order to allocate finite resources using maize as

Externí odkaz: https://doaj.org/article/9bfad55a4173428f8acffe7c51e13452

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Towards complete and error-free genome assemblies of all vertebrate species

Autor: Richard Hall, Tandy Warnow, Tanya M. Lama, Oliver A. Ryder, David Haussler, Matthew T. Biegler, Klaus-Peter Koepfli, Ivo Gut, Paul Flicek, Mark Chaisson, James Torrance, Guojie Zhang, Andrew J. Crawford, Federica Di Palma, Michael Hiller, Jennifer A. Marshall Graves, Sadye Paez, Sarah E. London, Mark Wilkinson, Kateryna D. Makova, Byung June Ko, Jimin George, Farooq O. Al-Ajli, Emma C. Teeling, George F. Turner, Robert H. S. Kraus, Sonja C. Vernes, Zev N. Kronenberg, Michelle Smith, Jonas Korlach, Daryl Eason, Jonathan Wood, Simona Secomandi, Claudio V. Mello, Arkarachai Fungtammasan, Arang Rhie, Tomas Marques-Bonet, Benedict Paten, Ekaterina Osipova, Richard Durbin, M. Thomas P. Gilbert, Beth Shapiro, Ivan Sović, Bruce C. Robertson, Richard E. Green, Eugene W. Myers, Leanne Haggerty, Sergey Koren, Martin Pippel, Bettina Haase, Patrick Masterson, Jay Ghurye, Maria Simbirsky, Samantha R. Friedrich, Chul Hee Lee, Luis R Nassar, Lindsey J. Cantin, Kerstin Howe, Erich D. Jarvis, Marlys L. Houck, Jason T. Howard, Jacquelyn Mountcastle, Mark Mooney, Paolo Franchini, Giulio Formenti, Siddarth Selvaraj, Robel E. Dagnew, Brett T. Hannigan, Brian P. Walenz, Alan Tracey, Heebal Kim, Constantina Theofanopoulou, Nicholas H. Putnam, Karen Clark, Iliana Bista, H. William Detrich, Dengfeng Guan, David Iorns, Andrew Digby, Trevor Pesout, Zemin Ning, Gregory Gedman, Woori Kwak, Maximilian Wagner, Joanna Collins, Harris A. Lewin, Hannes Svardal, Milan Malinsky, Byrappa Venkatesh, Françoise Thibaud-Nissen, Joana Damas, Andreas F. Kautt, Olivier Fedrigo, Christopher Dunn, William Chow, Warren E. Johnson, Yang Zhou, Adam M. Phillippy, Taylor Edwards, Paul Medvedev, Peter V. Lovell, Joyce V. Lee, Sylke Winkler, Stephen J. O'Brien, Wesley C. Warren, Alex Hastie, Marcela Uliano-Silva, Kevin L. Howe, Sarah B. Kingan, Fergal J. Martin, Christopher N. Balakrishnan, David F. Clayton, Ying Sims, Robert W. Murphy, Axel Meyer, Dave W Burt, Shane A. McCarthy, Sarah Pelan, Erik Garrison, Mark Diekhans, Frank Grützner, Gavin J. P. Naylor, Robert S. Harris, Hiram Clawson, Jinna Hoffman, Ann C Misuraca, J. H. Kim

Publikováno v: Nature, 592, 737-746
Nature
Rhie, A, McCarthy, S A, Fedrigo, O, Damas, J, Formenti, G, Koren, S, Uliano-Silva, M, Chow, W, Fungtammasan, A, Kim, J, Lee, C, Ko, B J, Chaisson, M, Gedman, G L, Cantin, L J, Thibaud-Nissen, F, Haggerty, L, Bista, I, Smith, M, Haase, B, Mountcastle, J, Winkler, S, Paez, S, Howard, J, Vernes, S C, Lama, T M, Grutzner, F, Warren, W C, Balakrishnan, C N, Burt, D, George, J M, Biegler, M T, Iorns, D, Digby, A, Eason, D, Robertson, B, Edwards, T, Wilkinson, M, Turner, G, Meyer, A, Kautt, A F, Franchini, P, Detrich, H W, Svardal, H, Wagner, M, Naylor, G J P, Pippel, M, Malinsky, M, Mooney, M, Simbirsky, M, Hannigan, B T, Pesout, T, Houck, M, Misuraca, A, Kingan, S B, Hall, R, Kronenberg, Z, Sović, I, Dunn, C, Ning, Z, Hastie, A, Lee, J, Selvaraj, S, Green, R E, Putnam, N H, Gut, I, Ghurye, J, Garrison, E, Sims, Y, Collins, J, Pelan, S, Torrance, J, Tracey, A, Wood, J, Dagnew, R E, Guan, D, London, S E, Clayton, D F, Mello, C V, Friedrich, S R, Lovell, P V, Osipova, E, Al-Ajli, F O, Secomandi, S, Kim, H, Theofanopoulou, C, Hiller, M, Zhou, Y, Harris, R S, Makova, K D, Medvedev, P, Hoffman, J, Masterson, P, Clark, K, Martin, F, Howe, K, Flicek, P, Walenz, B P, Kwak, W, Clawson, H, Diekhans, M, Nassar, L, Paten, B, Kraus, R H S, Crawford, A J, Gilbert, M T P, Zhang, G, Venkatesh, B, Murphy, R W, Koepfli, K-P, Shapiro, B, Johnson, W E, Di Palma, F, Marques-Bonet, T, Teeling, E C, Warnow, T, Graves, J M, Ryder, O A, Haussler, D, O’Brien, S J, Korlach, J, Lewin, H A, Howe, K, Myers, E W, Durbin, R, Phillippy, A M & Jarvis, E D 2021, ' Towards complete and error-free genome assemblies of all vertebrate species ', Nature, vol. 592, no. 7856, pp. 737-746 . https://doi.org/10.1038/s41586-021-03451-0
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Nature, 592, 7856, pp. 737-746

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1,2,3,4. To address t

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d50f2a74ee7e66ef185d231bcebbd6ea
https://doi.org/10.1038/s41586-021-03451-0

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Effect of sequence depth and length in long-read assembly of the maize inbred NC358

Publikováno v: Nature Communications, Vol 11, Iss 1, Pp 1-10 (2020)
Nature Communications

Improvements in long-read data and scaffolding technologies have enabled rapid generation of reference-quality assemblies for complex genomes. Still, an assessment of critical sequence depth and read length is important for allocating limited resourc

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e80e0dbb5b920674479f8508b45c205a
https://doaj.org/article/9bfad55a4173428f8acffe7c51e13452

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Akademický článek

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How well can we create phased, diploid, human genomes?: An assessment of FALCON-Unzip phasing using a human trio

Autor: Arkarachai Fungtammasan, Brett T. Hannigan

Long read sequencing technology has allowed researchers to create de novo assemblies with impressive continuity[1,2]. This advancement has dramatically increased the number of reference genomes available and hints at the possibility of a future where

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f11cda4087cbe88a012918b9432f8e0e
https://doi.org/10.1101/262196

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Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL)

Autor: Gevorg Grigoryan, Alessandro Senes, Jason E. Donald, Daniel W. Kulp, Sabareesh Subramaniam, Benjamin K. Mueller, Brett T. Hannigan

Publikováno v: Journal of Computational Chemistry. 33:1645-1661

We present the Molecular Software Library (MSL), a Cþþ library for molecular modeling. MSL is a set of tools that supports a large variety of algorithms for the design, modeling, and analysis of macromolecules. Among the main features supported by

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9ef9a9003d27b0adf4e17e6c9c450a04
https://doi.org/10.1002/jcc.22968

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Knowledge-Based Potential for Positioning Membrane-Associated Structures and Assessing Residue-Specific Energetic Contributions

Autor: Jason E. Donald, Chaim A. Schramm, Jeffery G. Saven, Chen Keasar, William F. DeGrado, Brett T. Hannigan, Ilan Samish

Publikováno v: Structure. 20(5):924-935

Summary The complex hydrophobic and hydrophilic milieus of membrane-associated proteins pose experimental and theoretical challenges to their understanding. Here, we produce a nonredundant database to compute knowledge-based asymmetric cross-membrane

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c9adee363cabf8eafea30b168d431c98

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