Search Results - "Nucleic acids research"

UniProt: the Universal Protein Knowledgebase in 2023 by Bateman, Alex, Martin, Maria-Jesus, Orchard, Sandra, Magrane, Michele, Ahmad, Shadab, Alpi, Emanuele, Bowler-Barnett, Emily H, Britto, Ramona, Bye-A-Jee, Hema, Cukura, Austra, Denny, Paul, Dogan, Tunca, Ebenezer, ThankGod, Fan, Jun, Garmiri, Penelope, da Costa Gonzales, Leonardo Jose, Hatton-Ellis, Emma, Hussein, Abdulrahman, Ignatchenko, Alexandr, Insana, Giuseppe, Ishtiaq, Rizwan, Joshi, Vishal, Jyothi, Dushyanth, Kandasaamy, Swaathi, Lock, Antonia, Luciani, Aurelien, Lugaric, Marija, Luo, Jie, Lussi, Yvonne, MacDougall, Alistair, Madeira, Fabio, Mahmoudy, Mahdi, Mishra, Alok, Moulang, Katie, Nightingale, Andrew, Pundir, Sangya, Qi, Guoying, Raj, Shriya, Raposo, Pedro, Rice, Daniel L, Saidi, Rabie, Santos, Rafael, Speretta, Elena, Stephenson, James, Totoo, Prabhat, Turner, Edward, Tyagi, Nidhi, Vasudev, Preethi, Warner, Kate, Watkins, Xavier, Zaru, Rossana, Zellner, Hermann, Bridge, Alan J, Aimo, Lucila, Argoud-Puy, Ghislaine, Auchincloss, Andrea H, Axelsen, Kristian B, Bansal, Parit, Baratin, Delphine, Batista Neto, Teresa M, Blatter, Marie-Claude, Bolleman, Jerven T, Boutet, Emmanuel, Breuza, Lionel, Gil, Blanca Cabrera, Casals-Casas, Cristina, Echioukh, Kamal Chikh, Coudert, Elisabeth, Cuche, Beatrice, de Castro, Edouard, Estreicher, Anne, Famiglietti, Maria L, Feuermann, Marc, Gasteiger, Elisabeth, Gaudet, Pascale, Gehant, Sebastien, Gerritsen, Vivienne, Gos, Arnaud, Gruaz, Nadine, Hulo, Chantal, Hyka-Nouspikel, Nevila, Jungo, Florence, Kerhornou, Arnaud, Le Mercier, Philippe, Lieberherr, Damien, Masson, Patrick, Morgat, Anne, Muthukrishnan, Venkatesh, Paesano, Salvo, Pedruzzi, Ivo, Pilbout, Sandrine, Pourcel, Lucille, Poux, Sylvain, Pozzato, Monica, Pruess, Manuela, Redaschi, Nicole, Rivoire, Catherine, Sigrist, Christian J A, Sonesson, Karin, Sundaram, Shyamala

“…The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with…”
Get full text

The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest by Szklarczyk, Damian, Kirsch, Rebecca, Koutrouli, Mikaela, Nastou, Katerina, Mehryary, Farrokh, Hachilif, Radja, Gable, Annika L, Fang, Tao, Doncheva, Nadezhda T, Pyysalo, Sampo, Bork, Peer, Jensen, Lars J, von Mering, Christian

“…Much of the complexity within cells arises from functional and regulatory interactions among proteins. The core of these interactions is increasingly known,…”
Get full text

KEGG for taxonomy-based analysis of pathways and genomes by 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…”
Get full text

DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update) by Sherman, Brad T, Hao, Ming, Qiu, Ju, Jiao, Xiaoli, Baseler, Michael W, Lane, H Clifford, Imamichi, Tomozumi, Chang, Weizhong

“…Abstract DAVID is a popular bioinformatics resource system including a web server and web service for functional annotation and enrichment analyses of gene…”
Get full text

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models by Varadi, Mihaly, Anyango, Stephen, Deshpande, Mandar, Nair, Sreenath, Natassia, Cindy, Yordanova, Galabina, Yuan, David, Stroe, Oana, Wood, Gemma, Laydon, Agata, Žídek, Augustin, Green, Tim, Tunyasuvunakool, Kathryn, Petersen, Stig, Jumper, John, Clancy, Ellen, Green, Richard, Vora, Ankur, Lutfi, Mira, Figurnov, Michael, Cowie, Andrew, Hobbs, Nicole, Kohli, Pushmeet, Kleywegt, Gerard, Birney, Ewan, Hassabis, Demis, Velankar, Sameer

“…Abstract The AlphaFold Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) is an openly accessible, extensive database of high-accuracy…”
Get full text

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences by Perez-Riverol, Yasset, Bai, Jingwen, Bandla, Chakradhar, García-Seisdedos, David, Hewapathirana, Suresh, Kamatchinathan, Selvakumar, Kundu, Deepti J, Prakash, Ananth, Frericks-Zipper, Anika, Eisenacher, Martin, Walzer, Mathias, Wang, Shengbo, Brazma, Alvis, Vizcaíno, Juan Antonio

“…Abstract The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based…”
Get full text

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation by Letunic, Ivica, Bork, Peer

“…Abstract The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It…”
Get full text

PubChem 2023 update by Kim, Sunghwan, Chen, Jie, Cheng, Tiejun, Gindulyte, Asta, He, Jia, He, Siqian, Li, Qingliang, Shoemaker, Benjamin A, Thiessen, Paul A, Yu, Bo, Zaslavsky, Leonid, Zhang, Jian, Bolton, Evan E

“…PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves a wide range of use cases. In the past two years, a number of…”
Get full text

Search and sequence analysis tools services from EMBL-EBI in 2022 by Madeira, Fábio, Pearce, Matt, Tivey, Adrian R N, Basutkar, Prasad, Lee, Joon, Edbali, Ossama, Madhusoodanan, Nandana, Kolesnikov, Anton, Lopez, Rodrigo

“…Abstract The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI’s data resources and core bioinformatics analytical…”
Get full text

InterPro in 2022 by Paysan-Lafosse, Typhaine, Blum, Matthias, Chuguransky, Sara, Grego, Tiago, Pinto, Beatriz Lázaro, Salazar, Gustavo A, Bileschi, Maxwell L, Bork, Peer, Bridge, Alan, Colwell, Lucy, Gough, Julian, Haft, Daniel H, Letunić, Ivica, Marchler-Bauer, Aron, Mi, Huaiyu, Natale, Darren A, Orengo, Christine A, Pandurangan, Arun P, Rivoire, Catherine, Sigrist, Christian J A, Sillitoe, Ian, Thanki, Narmada, Thomas, Paul D, Tosatto, Silvio C E, Wu, Cathy H, Bateman, Alex

“…The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally…”
Get full text

MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights by Pang, Zhiqiang, Chong, Jasmine, Zhou, Guangyan, de Lima Morais, David Anderson, Chang, Le, Barrette, Michel, Gauthier, Carol, Jacques, Pierre-Étienne, Li, Shuzhao, Xia, Jianguo

“…Abstract Since its first release over a decade ago, the MetaboAnalyst web-based platform has become widely used for comprehensive metabolomics data analysis…”
Get full text

The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets by Szklarczyk, Damian, Gable, Annika L, Nastou, Katerina C, Lyon, David, Kirsch, Rebecca, Pyysalo, Sampo, Doncheva, Nadezhda T, Legeay, Marc, Fang, Tao, Bork, Peer, Jensen, Lars J, von Mering, Christian

“…Abstract Cellular life depends on a complex web of functional associations between biomolecules. Among these associations, protein–protein interactions are…”
Get full text

UniProt: the universal protein knowledgebase in 2021 by Bateman, Alex, Martin, Maria-Jesus, Orchard, Sandra, Magrane, Michele, Agivetova, Rahat, Ahmad, Shadab, Alpi, Emanuele, Bowler-Barnett, Emily H, Britto, Ramona, Bursteinas, Borisas, Bye-A-Jee, Hema, Coetzee, Ray, Cukura, Austra, Da Silva, Alan, Denny, Paul, Dogan, Tunca, Ebenezer, ThankGod, Fan, Jun, Castro, Leyla Garcia, Garmiri, Penelope, Georghiou, George, Gonzales, Leonardo, Hatton-Ellis, Emma, Hussein, Abdulrahman, Ignatchenko, Alexandr, Insana, Giuseppe, Ishtiaq, Rizwan, Jokinen, Petteri, Joshi, Vishal, Jyothi, Dushyanth, Lock, Antonia, Lopez, Rodrigo, Luciani, Aurelien, Luo, Jie, Lussi, Yvonne, MacDougall, Alistair, Madeira, Fabio, Mahmoudy, Mahdi, Menchi, Manuela, Mishra, Alok, Moulang, Katie, Nightingale, Andrew, Oliveira, Carla Susana, Pundir, Sangya, Qi, Guoying, Raj, Shriya, Rice, Daniel, Lopez, Milagros Rodriguez, Saidi, Rabie, Sampson, Joseph, Sawford, Tony, Speretta, Elena, Turner, Edward, Tyagi, Nidhi, Vasudev, Preethi, Volynkin, Vladimir, Warner, Kate, Watkins, Xavier, Zaru, Rossana, Zellner, Hermann, Bridge, Alan, Poux, Sylvain, Redaschi, Nicole, Aimo, Lucila, Argoud-Puy, Ghislaine, Auchincloss, Andrea, Axelsen, Kristian, Bansal, Parit, Baratin, Delphine, Blatter, Marie-Claude, Bolleman, Jerven, Boutet, Emmanuel, Breuza, Lionel, Casals-Casas, Cristina, de Castro, Edouard, Echioukh, Kamal Chikh, Coudert, Elisabeth, Cuche, Beatrice, Doche, Mikael, Dornevil, Dolnide, Estreicher, Anne, Famiglietti, Maria Livia, Feuermann, Marc, Gasteiger, Elisabeth, Gehant, Sebastien, Gerritsen, Vivienne, Gos, Arnaud, Gruaz-Gumowski, Nadine, Hinz, Ursula, Hulo, Chantal, Hyka-Nouspikel, Nevila, Jungo, Florence, Keller, Guillaume, Kerhornou, Arnaud, Lara, Vicente, Le Mercier, Philippe, Lieberherr, Damien, Lombardot, Thierry, Martin, Xavier, Masson, Patrick

“…Abstract The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated…”
Get full text

Ensembl 2022 by Cunningham, Fiona, Allen, James E, Allen, Jamie, Alvarez-Jarreta, Jorge, Amode, M Ridwan, Armean, Irina M, Austine-Orimoloye, Olanrewaju, Azov, Andrey G, Barnes, If, Bennett, Ruth, Berry, Andrew, Bhai, Jyothish, Bignell, Alexandra, Billis, Konstantinos, Boddu, Sanjay, Brooks, Lucy, Charkhchi, Mehrnaz, Cummins, Carla, Da Rin Fioretto, Luca, Davidson, Claire, Dodiya, Kamalkumar, Donaldson, Sarah, El Houdaigui, Bilal, El Naboulsi, Tamara, Fatima, Reham, Giron, Carlos Garcia, Genez, Thiago, Martinez, Jose Gonzalez, Guijarro-Clarke, Cristina, Gymer, Arthur, Hardy, Matthew, Hollis, Zoe, Hourlier, Thibaut, Hunt, Toby, Juettemann, Thomas, Kaikala, Vinay, Kay, Mike, Lavidas, Ilias, Le, Tuan, Lemos, Diana, Marugán, José Carlos, Mohanan, Shamika, Mushtaq, Aleena, Naven, Marc, Ogeh, Denye N, Parker, Anne, Parton, Andrew, Perry, Malcolm, Piližota, Ivana, Prosovetskaia, Irina, Sakthivel, Manoj Pandian, Salam, Ahamed Imran Abdul, Schmitt, Bianca M, Schuilenburg, Helen, Sheppard, Dan, Pérez-Silva, José G, Stark, William, Steed, Emily, Sutinen, Kyösti, Sukumaran, Ranjit, Sumathipala, Dulika, Suner, Marie-Marthe, Szpak, Michal, Thormann, Anja, Tricomi, Francesca Floriana, Urbina-Gómez, David, Veidenberg, Andres, Walsh, Thomas A, Walts, Brandon, Willhoft, Natalie, Winterbottom, Andrea, Wass, Elizabeth, Chakiachvili, Marc, Flint, Bethany, Frankish, Adam, Giorgetti, Stefano, Haggerty, Leanne, Hunt, Sarah E, IIsley, Garth R, Loveland, Jane E, Martin, Fergal J, Moore, Benjamin, Mudge, Jonathan M, Muffato, Matthieu, Perry, Emily, Ruffier, Magali, Tate, John, Thybert, David, Trevanion, Stephen J, Dyer, Sarah, Harrison, Peter W, Howe, Kevin L, Yates, Andrew D, Zerbino, Daniel R, Flicek, Paul

“…Abstract Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation. It has been designed to…”
Get full text

Pfam: The protein families database in 2021 by Mistry, Jaina, Chuguransky, Sara, Williams, Lowri, Qureshi, Matloob, Salazar, Gustavo A, Sonnhammer, Erik L L, Tosatto, Silvio C E, Paladin, Lisanna, Raj, Shriya, Richardson, Lorna J, Finn, Robert D, Bateman, Alex

“…Abstract The Pfam database is a widely used resource for classifying protein sequences into families and domains. Since Pfam was last described in this…”
Get full text

antiSMASH 6.0: improving cluster detection and comparison capabilities by Blin, Kai, Shaw, Simon, Kloosterman, Alexander M, Charlop-Powers, Zach, van Wezel, Gilles P, Medema, Marnix H, Weber, Tilmann

“…Abstract Many microorganisms produce natural products that form the basis of antimicrobials, antivirals, and other drugs. Genome mining is routinely used to…”
Get full text

antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation by Blin, Kai, Shaw, Simon, Augustijn, Hannah E, Reitz, Zachary L, Biermann, Friederike, Alanjary, Mohammad, Fetter, Artem, Terlouw, Barbara R, Metcalf, William W, Helfrich, Eric J N, van Wezel, Gilles P, Medema, Marnix H, Weber, Tilmann

“…Abstract Microorganisms produce small bioactive compounds as part of their secondary or specialised metabolism. Often, such metabolites have antimicrobial,…”
Get full text

KEGG: integrating viruses and cellular organisms by Kanehisa, Minoru, Furumichi, Miho, Sato, Yoko, Ishiguro-Watanabe, Mari, Tanabe, Mao

“…Abstract KEGG (https://www.kegg.jp/) is a manually curated resource integrating eighteen databases categorized into systems, genomic, chemical and health…”
Get full text

The Gene Ontology resource: enriching a GOld mine by Carbon, Seth, Douglass, Eric, Good, Benjamin M, Unni, Deepak R, Harris, Nomi L, Mungall, Christopher J, Basu, Siddartha, Chisholm, Rex L, Dodson, Robert J, Hartline, Eric, Fey, Petra, Thomas, Paul D, Albou, Laurent-Philippe, Ebert, Dustin, Kesling, Michael J, Mi, Huaiyu, Muruganujan, Anushya, Huang, Xiaosong, Mushayahama, Tremayne, LaBonte, Sandra A, Siegele, Deborah A, Antonazzo, Giulia, Attrill, Helen, Brown, Nick H, Garapati, Phani, Marygold, Steven J, Trovisco, Vitor, dos Santos, Gil, Falls, Kathleen, Tabone, Christopher, Zhou, Pinglei, Goodman, Joshua L, Strelets, Victor B, Thurmond, Jim, Garmiri, Penelope, Ishtiaq, Rizwan, Rodríguez-López, Milagros, Acencio, Marcio L, Kuiper, Martin, Lægreid, Astrid, Logie, Colin, Lovering, Ruth C, Kramarz, Barbara, Saverimuttu, Shirin C C, Pinheiro, Sandra M, Gunn, Heather, Su, Renzhi, Thurlow, Katherine E, Chibucos, Marcus, Giglio, Michelle, Nadendla, Suvarna, Munro, James, Jackson, Rebecca, Duesbury, Margaret J, Del-Toro, Noemi, Meldal, Birgit H M, Paneerselvam, Kalpana, Perfetto, Livia, Porras, Pablo, Orchard, Sandra, Shrivastava, Anjali, Chang, Hsin-Yu, Finn, Robert Daniel, Mitchell, Alexander Lawson, Rawlings, Neil David, Richardson, Lorna, Sangrador-Vegas, Amaia, Blake, Judith A, Christie, Karen R, Dolan, Mary E, Drabkin, Harold J, Hill, David P, Ni, Li, Sitnikov, Dmitry M, Harris, Midori A, Oliver, Stephen G, Rutherford, Kim, Wood, Valerie, Hayles, Jaqueline, Bähler, Jürg, Bolton, Elizabeth R, De Pons, Jeffery L, Dwinell, Melinda R, Hayman, G Thomas, Kaldunski, Mary L, Kwitek, Anne E, Laulederkind, Stanley J F, Plasterer, Cody, Tutaj, Marek A, Vedi, Mahima, Wang, Shur-Jen, D’Eustachio, Peter, Matthews, Lisa, Balhoff, James P, Aleksander, Suzi A, Alexander, Michael J, Cherry, J Michael, Engel, Stacia R, Gondwe, Felix, Karra, Kalpana

“…Abstract The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of…”
Get full text

PubChem in 2021: new data content and improved web interfaces by Kim, Sunghwan, Chen, Jie, Cheng, Tiejun, Gindulyte, Asta, He, Jia, He, Siqian, Li, Qingliang, Shoemaker, Benjamin A, Thiessen, Paul A, Yu, Bo, Zaslavsky, Leonid, Zhang, Jian, Bolton, Evan E

“…Abstract PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves the scientific community as well as the general…”
Get full text