Zobrazeno 1 - 10
of 50
pro vyhledávání: '"Travis J Wheeler"'
Autor:
David Geller-McGrath, Kishori M Konwar, Virginia P Edgcomb, Maria Pachiadaki, Jack W Roddy, Travis J Wheeler, Jason E McDermott
Publikováno v:
eLife, Vol 13 (2024)
The reconstruction of complete microbial metabolic pathways using ‘omics data from environmental samples remains challenging. Computational pipelines for pathway reconstruction that utilize machine learning methods to predict the presence or absenc
Externí odkaz:
https://doaj.org/article/387f1b839f4e4c178ed7843a25e9c26d
Autor:
Alexander J Nord, Travis J Wheeler
Publikováno v:
PLoS ONE, Vol 18, Iss 5, p e0285225 (2023)
The organization of homologous protein sequences into multiple sequence alignments (MSAs) is a cornerstone of modern analysis of proteins. Recent focus on the importance of alternatively-spliced isoforms in disease and cell biology has highlighted th
Externí odkaz:
https://doaj.org/article/f43f638efef14770938c10d20aab76df
Autor:
Tim Anderson, Travis J. Wheeler
Publikováno v:
Algorithms for Molecular Biology, Vol 16, Iss 1, Pp 1-13 (2021)
Abstract Background Pattern matching is a key step in a variety of biological sequence analysis pipelines. The FM-index is a compressed data structure for pattern matching, with search run time that is independent of the length of the database text.
Externí odkaz:
https://doaj.org/article/cce5c4452d344971908b8d72a19c95e1
Autor:
Patrick R. Secor, Elizabeth B. Burgener, M. Kinnersley, Laura K. Jennings, Valery Roman-Cruz, Medeea Popescu, Jonas D. Van Belleghem, Naomi Haddock, Conner Copeland, Lia A. Michaels, Christiaan R. de Vries, Qingquan Chen, Julie Pourtois, Travis J. Wheeler, Carlos E. Milla, Paul L. Bollyky
Publikováno v:
Frontiers in Immunology, Vol 11 (2020)
Pf bacteriophage are temperate phages that infect the bacterium Pseudomonas aeruginosa, a major cause of chronic lung infections in cystic fibrosis (CF) and other settings. Pf and other temperate phages have evolved complex, mutualistic relationships
Externí odkaz:
https://doaj.org/article/0fbbcd58934c4e5bade6db1d83a8f046
Autor:
Johannes Schimunek, Philipp Seidl, Katarina Elez, Tim Hempel, Tuan Le, Frank Noé, Simon Olsson, Lluís Raich, Robin Winter, Hatice Gokcan, Filipp Gusev, Evgeny M. Gutkin, Olexandr Isayev, Maria G. Kurnikova, Chamali H. Narangoda, Roman Zubatyuk, Ivan P. Bosko, Konstantin V. Furs, Anna D. Karpenko, Yury V. Kornoushenko, Mikita Shuldau, Artsemi Yushkevich, Mohammed B. Benabderrahmane, Patrick Bousquet-Melou, Ronan Bureau, Beatrice Charton, Bertrand C. Cirou, Gérard Gil, William J. Allen, Suman Sirimulla, Stanley Watowich, Nick A. Antonopoulos, Nikolaos E. Epitropakis, Agamemnon K. Krasoulis, Vassilis P. Pitsikalis, Stavros T. Theodorakis, Igor Kozlovskii, Anton Maliutin, Alexander Medvedev, Petr Popov, Mark Zaretckii, Hamid Eghbal-zadeh, Christina Halmich, Sepp Hochreiter, Andreas Mayr, Peter Ruch, Michael Widrich, Francois Berenger, Ashutosh Kumar, Yoshihiro Yamanishi, Kam Y.J. Zhang, Emmanuel Bengio, Yoshua Bengio, Moksh J. Jain, Maksym Korablyov, Cheng-Hao Liu, Gilles Marcou, Enrico Glaab, Kelly Barnsley, Suhasini M. Iyengar, Mary Jo Ondrechen, V. Joachim Haupt, Florian Kaiser, Michael Schroeder, Luisa Pugliese, Simone Albani, Christina Athanasiou, Andrea Beccari, Paolo Carloni, Giulia D'Arrigo, Eleonora Gianquinto, Jonas Goßen, Anton Hanke, Benjamin P. Joseph, Daria B. Kokh, Sandra Kovachka, Candida Manelfi, Goutam Mukherjee, Abraham Muñiz-Chicharro, Francesco Musiani, Ariane Nunes-Alves, Giulia Paiardi, Giulia Rossetti, S. Kashif Sadiq, Francesca Spyrakis, Carmine Talarico, Alexandros Tsengenes, Rebecca C. Wade, Conner Copeland, Jeremiah Gaiser, Daniel R. Olson, Amitava Roy, Vishwesh Venkatraman, Travis J. Wheeler, Haribabu Arthanari, Klara Blaschitz, Marco Cespugli, Vedat Durmaz, Konstantin Fackeldey, Patrick D. Fischer, Christoph Gorgulla, Christian Gruber, Karl Gruber, Michael Hetmann, Jamie E. Kinney, Krishna M. Padmanabha Das, Shreya Pandita, Amit Singh, Georg Steinkellner, Guilhem Tesseyre, Gerhard Wagner, Zi-Fu Wang, Ryan J. Yust, Dmitry S. Druzhilovskiy, Dmitry A. Filimonov, Pavel V. Pogodin, Vladimir Poroikov, Anastassia V. Rudik, Leonid A. Stolbov, Alexander V. Veselovsky, Maria De Rosa, Giada De Simone, Maria R. Gulotta, Jessica Lombino, Nedra Mekni, Ugo Perricone, Arturo Casini, Amanda Embree, D. Benjamin Gordon, David Lei, Katelin Pratt, Christopher A. Voigt, Kuang-Yu Chen, Yves Jacob, Tim Krischuns, Pierre Lafaye, Agnès Zettor, M. Luis Rodríguez, Kris M. White, Daren Fearon, Frank Von Delft, Martin A. Walsh, Dragos Horvath, Charles L. Brooks III, Babak Falsafi, Bryan Ford, Adolfo García-Sastre, Sang Yup Lee, Nadia Naffakh, Alexandre Varnek, Günter Klambauer, Thomas M. Hermans
The COVID-19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availability of vaccines, searching for efficient small-molecule drugs that are widely available, including in low- and
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::28010b1a0350f378ef0dcc633e87f6e1
https://doi.org/10.26434/chemrxiv-2023-1d5w8
https://doi.org/10.26434/chemrxiv-2023-1d5w8
Publikováno v:
bioRxiv
Recordings of animal sounds enable a wide range of observational inquiries into animal communication, behavior, and diversity. Automated labeling of sound events in such recordings can improve both throughput and reproducibility of analysis. Here, we
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::387415f5eee1efad99d07d401d7a4c39
https://doi.org/10.1101/2023.01.24.525459
https://doi.org/10.1101/2023.01.24.525459
Autor:
Jessica M. Storer, Jerilyn A. Walker, Jasmine N. Baker, Shifat Hossain, Christian Roos, Travis J. Wheeler, Mark A. Batzer
Publikováno v:
Genes
Volume 14
Issue 2
Pages: 249
Volume 14
Issue 2
Pages: 249
The history of Alu retroposons has been choreographed by the systematic accumulation of inherited diagnostic nucleotide substitutions to form discrete subfamilies, each having a distinct nucleotide consensus sequence. The oldest subfamily, AluJ, gave
Autor:
Travis J. Wheeler, Tim Anderson
Publikováno v:
Algorithms for Molecular Biology, Vol 16, Iss 1, Pp 1-13 (2021)
Algorithms for Molecular Biology : AMB
Algorithms for Molecular Biology : AMB
Background Pattern matching is a key step in a variety of biological sequence analysis pipelines. The FM-index is a compressed data structure for pattern matching, with search run time that is independent of the length of the database text. Implement
Computational approaches for small molecule drug discovery now regularly scale to consideration of libraries containing billions of candidate small molecules. One promising path to increased speed in evaluating billion-molecule libraries is to develo
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::61fb8b930ff56b91c73a401132fc38d8
https://doi.org/10.1101/2022.09.20.508800
https://doi.org/10.1101/2022.09.20.508800
We present SODA, a lightweight and open-source visualization library for biological sequence annotations that enables straightforward development of flexible, dynamic and interactive web graphics. SODA is implemented in TypeScript and can be used as
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::547c8ad6d3bf4bcc0fd01e94113e1692
http://arxiv.org/abs/2205.06349
http://arxiv.org/abs/2205.06349