Výsledky vyhledávání - "Genomics methods"

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets Autor Szklarczyk, Damian, Gable, Annika L, Lyon, David, Junge, Alexander, Wyder, Stefan, Huerta-Cepas, Jaime, Simonovic, Milan, Doncheva, Nadezhda T, Morris, John H, Bork, Peer, Jensen, Lars J, Mering, Christian von

“…Abstract Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full…”
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KEGG for taxonomy-based analysis of pathways and genomes Autor Kanehisa, Minoru, Furumichi, Miho, Sato, Yoko, Kawashima, Masayuki, Ishiguro-Watanabe, Mari

“…KEGG (https://www.kegg.jp) is a manually curated database resource integrating various biological objects categorized into systems, genomic, chemical and…”
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Genomics has more to reveal Autor Fenwarth, Laurène, Duployez, Nicolas

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MGnify: the microbiome sequence data analysis resource in 2023 Autor Richardson, Lorna, Allen, Ben, Baldi, Germana, Beracochea, Martin, Bileschi, Maxwell L, Burdett, Tony, Burgin, Josephine, Caballero-Pérez, Juan, Cochrane, Guy, Colwell, Lucy J, Curtis, Tom, Escobar-Zepeda, Alejandra, Gurbich, Tatiana A, Kale, Varsha, Korobeynikov, Anton, Raj, Shriya, Rogers, Alexander B, Sakharova, Ekaterina, Sanchez, Santiago, Wilkinson, Darren J, Finn, Robert D

“…The MGnify platform (https://www.ebi.ac.uk/metagenomics) facilitates the assembly, analysis and archiving of microbiome-derived nucleic acid sequences. The…”
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Acquired Resistance to BET-PROTACs (Proteolysis-Targeting Chimeras) Caused by Genomic Alterations in Core Components of E3 Ligase Complexes Autor Zhang, Lu, Riley-Gillis, Bridget, Vijay, Priyanka, Shen, Yu

“…Proteolysis-targeting chimeras (PROTAC) are bifunctional molecules that hijack endogenous E3 ubiquitin ligases to induce ubiquitination and subsequent…”
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GenBank Autor 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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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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Next-Generation Lineage Tracing and Fate Mapping to Interrogate Development Autor VanHorn, Sadie, Morris, Samantha A

“…Lineage tracing and fate mapping, overlapping yet distinct disciplines to follow cells and their progeny, have evolved rapidly over the last century. Lineage…”
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The UCSC Genome Browser database: 2023 update Autor Nassar, Luis R, Barber, Galt P, Benet-Pagès, Anna, Casper, Jonathan, Clawson, Hiram, Diekhans, Mark, Fischer, Clay, Gonzalez, Jairo Navarro, Hinrichs, Angie S, Lee, Brian T, Lee, Christopher M, Muthuraman, Pranav, Nguy, Beagan, Pereira, Tiana, Nejad, Parisa, Perez, Gerardo, Raney, Brian J, Schmelter, Daniel, Speir, Matthew L, Wick, Brittney D, Zweig, Ann S, Haussler, David, Kuhn, Robert M, Haeussler, Maximilian, Kent, W James

“…The UCSC Genome Browser (https://genome.ucsc.edu) is an omics data consolidator, graphical viewer, and general bioinformatics resource that continues to serve…”
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miRBase: from microRNA sequences to function Autor 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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DRAM for distilling microbial metabolism to automate the curation of microbiome function Autor Shaffer, Michael, Borton, Mikayla A, McGivern, Bridget B, Zayed, Ahmed A, La Rosa, Sabina Leanti, Solden, Lindsey M, Liu, Pengfei, Narrowe, Adrienne B, Rodríguez-Ramos, Josué, Bolduc, Benjamin, Gazitúa, M Consuelo, Daly, Rebecca A, Smith, Garrett J, Vik, Dean R, Pope, Phil B, Sullivan, Matthew B, Roux, Simon, Wrighton, Kelly C

“…Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to…”
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Classification and Personalized Prognostic Assessment on the Basis of Clinical and Genomic Features in Myelodysplastic Syndromes Autor Bersanelli, Matteo, Travaglino, Erica, Meggendorfer, Manja, Matteuzzi, Tommaso, Sala, Claudia, Mosca, Ettore, Chiereghin, Chiara, Di Nanni, Noemi, Gnocchi, Matteo, Zampini, Matteo, Rossi, Marianna, Maggioni, Giulia, Termanini, Alberto, Angelucci, Emanuele, Bernardi, Massimo, Borin, Lorenza, Bruno, Benedetto, Bonifazi, Francesca, Santini, Valeria, Bacigalupo, Andrea, Voso, Maria Teresa, Oliva, Esther, Riva, Marta, Ubezio, Marta, Morabito, Lucio, Campagna, Alessia, Saitta, Claudia, Savevski, Victor, Giampieri, Enrico, Remondini, Daniel, Passamonti, Francesco, Ciceri, Fabio, Bolli, Niccolò, Rambaldi, Alessandro, Kern, Wolfgang, Kordasti, Shahram, Sole, Francesc, Palomo, Laura, Sanz, Guillermo, Santoro, Armando, Platzbecker, Uwe, Fenaux, Pierre, Milanesi, Luciano, Haferlach, Torsten, Castellani, Gastone, Della Porta, Matteo G

“…Recurrently mutated genes and chromosomal abnormalities have been identified in myelodysplastic syndromes (MDS). We aim to integrate these genomic features…”
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The MetaCyc database of metabolic pathways and enzymes - a 2019 update Autor Caspi, Ron, Billington, Richard, Keseler, Ingrid M, Kothari, Anamika, Krummenacker, Markus, Midford, Peter E, Ong, Wai Kit, Paley, Suzanne, Subhraveti, Pallavi, Karp, Peter D

“…Abstract MetaCyc (MetaCyc.org) is a comprehensive reference database of metabolic pathways and enzymes from all domains of life. It contains 2749 pathways…”
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New approach for understanding genome variations in KEGG Autor Kanehisa, Minoru, Sato, Yoko, Furumichi, Miho, Morishima, Kanae, Tanabe, Mao

“…Abstract KEGG (Kyoto Encyclopedia of Genes and Genomes; https://www.kegg.jp/ or https://www.genome.jp/kegg/) is a reference knowledge base for biological…”
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VFDB 2019: a comparative pathogenomic platform with an interactive web interface Autor Liu, Bo, Zheng, Dandan, Jin, Qi, Chen, Lihong, Yang, Jian

“…Abstract The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) is devoted to providing the scientific community with a comprehensive warehouse and…”
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More than 18,000 effectors in the Legionella genus genome provide multiple, independent combinations for replication in human cells Autor Gomez-Valero, Laura, Rusniok, Christophe, Carson, Danielle, Mondino, Sonia, Pérez-Cobas, Ana Elena, Rolando, Monica, Pasricha, Shivani, Reuter, Sandra, Demirtas, Jasmin, Crumbach, Johannes, Descorps-Declere, Stephane, Hartland, Elizabeth L, Jarraud, Sophie, Dougan, Gordon, Schroeder, Gunnar N, Frankel, Gad, Buchrieser, Carmen

“…The genus comprises 65 species, among which is a human pathogen causing severe pneumonia. To understand the evolution of an environmental to an accidental…”
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edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets Autor Chen, Yunshun, Chen, Lizhong, Lun, Aaron T L, Baldoni, Pedro L, Smyth, Gordon K

“…Abstract edgeR is an R/Bioconductor software package for differential analyses of sequencing data in the form of read counts for genes or genomic features…”
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OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species Autor Xu, Ling, Dong, Zhaobin, Fang, Lu, Luo, Yongjiang, Wei, Zhaoyuan, Guo, Hailong, Zhang, Guoqing, Gu, Yong Q, Coleman-Derr, Devin, Xia, Qingyou, Wang, Yi

“…OrthoVenn is a powerful web platform for the comparison and analysis of whole-genome orthologous clusters. Here we present an updated version, OrthoVenn2,…”
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KEGG: new perspectives on genomes, pathways, diseases and drugs Autor Kanehisa, Minoru, Furumichi, Miho, Tanabe, Mao, Sato, Yoko, Morishima, Kanae

“…KEGG (http://www.kegg.jp/ or http://www.genome.jp/kegg/) is an encyclopedia of genes and genomes. Assigning functional meanings to genes and genomes both at…”
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metaSPAdes: a new versatile metagenomic assembler Autor Nurk, Sergey, Meleshko, Dmitry, Korobeynikov, Anton, Pevzner, Pavel A

“…While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus…”
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