Zobrazeno 1 - 10
of 60
pro vyhledávání: '"David Koslicki"'
Autor:
E. C. Wood, Amy K. Glen, Lindsey G. Kvarfordt, Finn Womack, Liliana Acevedo, Timothy S. Yoon, Chunyu Ma, Veronica Flores, Meghamala Sinha, Yodsawalai Chodpathumwan, Arash Termehchy, Jared C. Roach, Luis Mendoza, Andrew S. Hoffman, Eric W. Deutsch, David Koslicki, Stephen A. Ramsey
Publikováno v:
BMC Bioinformatics, Vol 23, Iss 1, Pp 1-33 (2022)
Abstract Background Biomedical translational science is increasingly using computational reasoning on repositories of structured knowledge (such as UMLS, SemMedDB, ChEMBL, Reactome, DrugBank, and SMPDB in order to facilitate discovery of new therapeu
Externí odkaz:
https://doaj.org/article/676d08bd8b4148498728c8e5fe06aba5
Autor:
Karamarie Fecho, Chris Bizon, Tursynay Issabekova, Sierra Moxon, Anne E. Thessen, Shervin Abdollahi, Sergio E. Baranzini, Basazin Belhu, William E. Byrd, Lawrence Chung, Andrew Crouse, Marc P. Duby, Stephen Ferguson, Aleksandra Foksinska, Laura Forero, Jennifer Friedman, Vicki Gardner, Gwênlyn Glusman, Jennifer Hadlock, Kristina Hanspers, Eugene Hinderer, Charlotte Hobbs, Gregory Hyde, Sui Huang, David Koslicki, Philip Mease, Sandrine Muller, Christopher J. Mungall, Stephen A. Ramsey, Jared Roach, Irit Rubin, Shepherd H. Schurman, Anath Shalev, Brett Smith, Karthik Soman, Sarah Stemann, Andrew I. Su, Casey Ta, Paul B. Watkins, Mark D. Williams, Chunlei Wu, Colleen H. Xu, The Biomedical Data Translator Consortium
Publikováno v:
Journal of Clinical and Translational Science, Vol 7 (2023)
Knowledge graphs have become a common approach for knowledge representation. Yet, the application of graph methodology is elusive due to the sheer number and complexity of knowledge sources. In addition, semantic incompatibilities hinder efforts to h
Externí odkaz:
https://doaj.org/article/8d108ce3ebbb408b85a7a73670319e07
Autor:
Karamarie Fecho, James Balhoff, Chris Bizon, William E. Byrd, Sui Hang, David Koslicki, Stefano E. Rensi, Patrick L. Schmitt, Mathias J. Wawer, Mark Williams, Stanley C. Ahalt
Publikováno v:
Clinical and Translational Science, Vol 14, Iss 5, Pp 1719-1724 (2021)
Abstract “Knowledge graphs” (KGs) have become a common approach for representing biomedical knowledge. In a KG, multiple biomedical data sets can be linked together as a graph representation, with nodes representing entities, such as “chemical
Externí odkaz:
https://doaj.org/article/c34bcbf95d5c4da1880ae6f9228aa90c
Autor:
Mohammed Alser, Jeremy Rotman, Dhrithi Deshpande, Kodi Taraszka, Huwenbo Shi, Pelin Icer Baykal, Harry Taegyun Yang, Victor Xue, Sergey Knyazev, Benjamin D. Singer, Brunilda Balliu, David Koslicki, Pavel Skums, Alex Zelikovsky, Can Alkan, Onur Mutlu, Serghei Mangul
Publikováno v:
Genome Biology, Vol 22, Iss 1, Pp 1-34 (2021)
Abstract Aligning sequencing reads onto a reference is an essential step of the majority of genomic analysis pipelines. Computational algorithms for read alignment have evolved in accordance with technological advances, leading to today’s diverse a
Externí odkaz:
https://doaj.org/article/9840492eb89d411dbaa3bbe06431087f
Publikováno v:
Genome Biology, Vol 21, Iss 1, Pp 1-15 (2020)
Abstract Metagenomic profiling, predicting the presence and relative abundances of microbes in a sample, is a critical first step in microbiome analysis. Alignment-based approaches are often considered accurate yet computationally infeasible. Here, w
Externí odkaz:
https://doaj.org/article/b5473715bc964e9596bffb9322df1136
Autor:
Caitlin Loeffler, Aaron Karlsberg, Lana S. Martin, Eleazar Eskin, David Koslicki, Serghei Mangul
Publikováno v:
BMC Biology, Vol 18, Iss 1, Pp 1-6 (2020)
Abstract Metagenomics studies leverage genomic reference databases to generate discoveries in basic science and translational research. However, current microbial studies use disparate reference databases that lack consistent standards of specimen in
Externí odkaz:
https://doaj.org/article/d7833fd3c7fc43cda5bcbe1bcda19637
Autor:
Nathan LaPierre, Serghei Mangul, Mohammed Alser, Igor Mandric, Nicholas C. Wu, David Koslicki, Eleazar Eskin
Publikováno v:
BMC Genomics, Vol 20, Iss S5, Pp 1-10 (2019)
Abstract Background High throughput sequencing has spurred the development of metagenomics, which involves the direct analysis of microbial communities in various environments such as soil, ocean water, and the human body. Many existing methods based
Externí odkaz:
https://doaj.org/article/1ac96691a26446e68af7be3c02970b83
Autor:
Fernando Meyer, Andreas Bremges, Peter Belmann, Stefan Janssen, Alice C. McHardy, David Koslicki
Publikováno v:
Genome Biology, Vol 20, Iss 1, Pp 1-10 (2019)
Abstract The explosive growth in taxonomic metagenome profiling methods over the past years has created a need for systematic comparisons using relevant performance criteria. The Open-community Profiling Assessment tooL (OPAL) implements commonly use
Externí odkaz:
https://doaj.org/article/251e449427f24036819570cca9065667
Autor:
Loes M. Olde Loohuis, Serghei Mangul, Anil P. S. Ori, Guillaume Jospin, David Koslicki, Harry Taegyun Yang, Timothy Wu, Marco P. Boks, Catherine Lomen-Hoerth, Martina Wiedau-Pazos, Rita M. Cantor, Willem M. de Vos, René S. Kahn, Eleazar Eskin, Roel A. Ophoff
Publikováno v:
Translational Psychiatry, Vol 8, Iss 1, Pp 1-9 (2018)
Abstract The role of the human microbiome in health and disease is increasingly appreciated. We studied the composition of microbial communities present in blood across 192 individuals, including healthy controls and patients with three disorders aff
Externí odkaz:
https://doaj.org/article/17562bdf44234e028412afcbfe62fa09
Autor:
Caitlin Loeffler, Aaron Karlsberg, Lana S. Martin, Eleazar Eskin, David Koslicki, Serghei Mangul
Publikováno v:
BMC Biology, Vol 18, Iss 1, Pp 1-1 (2020)
An amendment to this paper has been published and can be accessed via the original article.
Externí odkaz:
https://doaj.org/article/2a76d9f86ff24b63b61c79c708d6fce3