Suchergebnisse - "Computational Biology/methods"

Omic technologies: Current situation and future challenges von Quiroga, Cecilia

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Computational model reproduces electrochemical properties of the mammalian cochlea von Nin, Fumiaki, Hibino, Hiroshi, Kurachi, Yoshihisa

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Escalating model sizes and complexities call for standardized forms of representation von Hucka, Michael, Finney, Andrew

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M 3 HOGAT: A Multi-View Multi-Modal Multi-Scale High-Order Graph Attention Network for Microbe-Disease Association Prediction von Wang, Shuang, Liu, Jin-Xing, Li, Feng, Wang, Juan, Gao, Ying-Lian

“… Numerous scientific studies have found a link between diverse microorganisms in the human body and complex human diseases. Because traditional experimental …”
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The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024 von Madeira, Fábio, Madhusoodanan, Nandana, Lee, Joonheung, Eusebi, Alberto, Niewielska, Ania, Tivey, Adrian R N, Lopez, Rodrigo, Butcher, Sarah

“… The EMBL-EBI Job Dispatcher sequence analysis tools framework (https://www.ebi.ac.uk/jdispatcher) enables the scientific community to perform a diverse range …”
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Computational Resources for Molecular Biology 2024 von Casadio, Rita, Mathews, David H., Sternberg, Michael J.E.

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TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes von Meier-Kolthoff, Jan P, Carbasse, Joaquim Sardà, Peinado-Olarte, Rosa L, Göker, Markus

“… Abstract Microbial systematics is heavily influenced by genome-based methods and challenged by an ever increasing number of taxon names and associated …”
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GenBank von Sayers, Eric W, Cavanaugh, Mark, Clark, Karen, Ostell, James, Pruitt, Kim D, Karsch-Mizrachi, Ilene

“… Abstract GenBank® (www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains over 6.25 trillion base pairs from over 1.6 billion …”
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Fiji: an open-source platform for biological-image analysis von Schindelin, Johannes, Arganda-Carreras, Ignacio, Frise, Erwin, Kaynig, Verena, Longair, Mark, Pietzsch, Tobias, Preibisch, Stephan, Rueden, Curtis, Saalfeld, Stephan, Schmid, Benjamin, Tinevez, Jean-Yves, White, Daniel James, Hartenstein, Volker, Eliceiri, Kevin, Tomancak, Pavel, Cardona, Albert

“… Presented is an overview of the image-analysis software platform Fiji, a distribution of ImageJ that updates the underlying ImageJ architecture and adds modern …”
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The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update von Abueg, Linelle Ann L, Afgan, Enis, Allart, Olivier, Awan, Ahmed H, Bacon, Wendi A, Baker, Dannon, Bassetti, Madeline, Batut, Bérénice, Bernt, Matthias, Blankenberg, Daniel, Bombarely, Aureliano, Bretaudeau, Anthony, Bromhead, Catherine J, Burke, Melissa L, Capon, Patrick K, Čech, Martin, Chavero-Díez, María, Chilton, John M, Collins, Tyler J, Coppens, Frederik, Coraor, Nate, Cuccuru, Gianmauro, Cumbo, Fabio, Davis, John, De Geest, Paul F, de Koning, Willem, Demko, Martin, DeSanto, Assunta, Begines, José Manuel Domínguez, Doyle, Maria A, Droesbeke, Bert, Erxleben-Eggenhofer, Anika, Föll, Melanie C, Formenti, Giulio, Fouilloux, Anne, Gangazhe, Rendani, Genthon, Tanguy, Goecks, Jeremy, Beltran, Alejandra N Gonzalez, Goonasekera, Nuwan A, Goué, Nadia, Griffin, Timothy J, Grüning, Björn A, Guerler, Aysam, Gundersen, Sveinung, Gustafsson, Ove Johan Ragnar, Hall, Christina, Harrop, Thomas W, Hecht, Helge, Heidari, Alireza, Heisner, Tillman, Heyl, Florian, Hiltemann, Saskia, Hotz, Hans-Rudolf, Hyde, Cameron J, Jagtap, Pratik D, Jakiela, Julia, Johnson, James E, Joshi, Jayadev, Jossé, Marie, Jum’ah, Khaled, Kalaš, Matúš, Kamieniecka, Katarzyna, Kayikcioglu, Tunc, Konkol, Markus, Kostrykin, Leonid, Kucher, Natalie, Kumar, Anup, Kuntz, Mira, Lariviere, Delphine, Lazarus, Ross, Bras, Yvan Le, Corguillé, Gildas Le, Lee, Justin, Leo, Simone, Liborio, Leandro, Libouban, Romane, Tabernero, David López, Lopez-Delisle, Lucille, Los, Laila S, Mahmoud, Alexandru, Makunin, Igor, Marin, Pierre, Mehta, Subina, Mok, Winnie, Moreno, Pablo A, Morier-Genoud, François, Mosher, Stephen, Müller, Teresa, Nasr, Engy, Nekrutenko, Anton, Nelson, Tiffanie M, Oba, Asime J, Ostrovsky, Alexander, Polunina, Polina V, Poterlowicz, Krzysztof, Price, Elliott J, Price, Gareth R, Rasche, Helena, Raubenolt, Bryan

“… Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope …”
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UniProt: the universal protein knowledgebase

“… The UniProt knowledgebase is a large resource of protein sequences and associated detailed annotation. The database contains over 60 million sequences, of …”
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Microbe-disease associations prediction by graph regularized non-negative matrix factorization with L 2 , 1 $$ {L}_{2,1} $$ norm regularization terms von Chen, Ziwei, Zhang, Liangzhe, Li, Jingyi, Chen, Hang

“… Microbes are involved in a wide range of biological processes and are closely associated with disease. Inferring potential disease-associated microbes as the …”
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The ProteomeXchange consortium at 10 years: 2023 update von Deutsch, Eric W, Bandeira, Nuno, Perez-Riverol, Yasset, Sharma, Vagisha, Carver, Jeremy J, Mendoza, Luis, Kundu, Deepti J, Wang, Shengbo, Bandla, Chakradhar, Kamatchinathan, Selvakumar, Hewapathirana, Suresh, Pullman, Benjamin S, Wertz, Julie, Sun, Zhi, Kawano, Shin, Okuda, Shujiro, Watanabe, Yu, MacLean, Brendan, MacCoss, Michael J, Zhu, Yunping, Ishihama, Yasushi, Vizcaíno, Juan Antonio

“… Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources …”
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Variant Interpretation: Functional Assays to the Rescue von Starita, Lea M, Ahituv, Nadav, Dunham, Maitreya J, Kitzman, Jacob O, Roth, Frederick P, Seelig, Georg, Shendure, Jay, Fowler, Douglas M

“… Classical genetic approaches for interpreting variants, such as case-control or co-segregation studies, require finding many individuals with each variant …”
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PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API von Mi, Huaiyu, Ebert, Dustin, Muruganujan, Anushya, Mills, Caitlin, Albou, Laurent-Philippe, Mushayamaha, Tremayne, Thomas, Paul D

“… Abstract PANTHER (Protein Analysis Through Evolutionary Relationships, http://www.pantherdb.org) is a resource for the evolutionary and functional …”
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miRDB: an online database for prediction of functional microRNA targets von Chen, Yuhao, Wang, Xiaowei

“… Abstract MicroRNAs (miRNAs) are small noncoding RNAs that act as master regulators in many biological processes. miRNAs function mainly by downregulating the …”
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IPD-IMGT/HLA Database von Robinson, James, Barker, Dominic J, Georgiou, Xenia, Cooper, Michael A, Flicek, Paul, Marsh, Steven G E

“… Abstract The IPD-IMGT/HLA Database, http://www.ebi.ac.uk/ipd/imgt/hla/, currently contains over 25 000 allele sequence for 45 genes, which are located within …”
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The Cellosaurus, a Cell-Line Knowledge Resource von Bairoch, Amos

“… The Cellosaurus is a knowledge resource on cell lines. It aims to describe all cell lines used in biomedical research. Its scope encompasses both vertebrates …”
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miRBase: from microRNA sequences to function von Kozomara, Ana, Birgaoanu, Maria, Griffiths-Jones, Sam

“… Abstract miRBase catalogs, names and distributes microRNA gene sequences. The latest release of miRBase (v22) contains microRNA sequences from 271 organisms: …”
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NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis von Zhou, Guangyan, Soufan, Othman, Ewald, Jessica, Hancock, Robert E W, Basu, Niladri, Xia, Jianguo

“… The growing application of gene expression profiling demands powerful yet user-friendly bioinformatics tools to support systems-level data understanding …”
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