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For: Yachdav G, Wilzbach S, Rauscher B, Sheridan R, Sillitoe I, Procter J, Lewis SE, Rost B, Goldberg T. MSAViewer: interactive JavaScript visualization of multiple sequence alignments. Bioinformatics 2016;32:3501-3503. [PMID: 27412096 PMCID: PMC5181560 DOI: 10.1093/bioinformatics/btw474] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 06/03/2016] [Accepted: 06/29/2016] [Indexed: 11/29/2022]  Open
Number Cited by Other Article(s)
1
Dommer J, Van Doorslaer K, Afrasiabi C, Browne K, Ezeji S, Kim L, Dolan M, McBride AA. PaVE 2.0: Behind the Scenes of the Papillomavirus Episteme. J Mol Biol 2025;437:168925. [PMID: 39732323 PMCID: PMC12145264 DOI: 10.1016/j.jmb.2024.168925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Revised: 12/20/2024] [Accepted: 12/23/2024] [Indexed: 12/30/2024]
2
Liu H, Laiho A, Törönen P, Holm L. 3-D substructure search by transitive closure in AlphaFold database. Protein Sci 2025;34:e70169. [PMID: 40400345 PMCID: PMC12095923 DOI: 10.1002/pro.70169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 05/01/2025] [Accepted: 05/02/2025] [Indexed: 05/23/2025]
3
Dapkūnas J, Margelevičius M. Web-based GTalign: bridging speed and accuracy in protein structure analysis. Nucleic Acids Res 2025:gkaf398. [PMID: 40331429 DOI: 10.1093/nar/gkaf398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2025] [Revised: 04/20/2025] [Accepted: 04/28/2025] [Indexed: 05/08/2025]  Open
4
Pérez-Cruz C, Moraleda-Montoya A, Liébana R, Terrones O, Arrizabalaga U, García-Alija M, Lorizate M, Martínez Gascueña A, García-Álvarez I, Nieto-Garai JA, Olazar-Intxausti J, Rodríguez-Colinas B, Mann E, Chiara JL, Contreras FX, Guerin ME, Trastoy B, Alonso-Sáez L. Mechanisms of recalcitrant fucoidan breakdown in marine Planctomycetota. Nat Commun 2024;15:10906. [PMID: 39738071 PMCID: PMC11685898 DOI: 10.1038/s41467-024-55268-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 12/05/2024] [Indexed: 01/01/2025]  Open
5
Aplakidou E, Vergoulidis N, Chasapi M, Venetsianou NK, Kokoli M, Panagiotopoulou E, Iliopoulos I, Karatzas E, Pafilis E, Georgakopoulos-Soares I, Kyrpides NC, Pavlopoulos GA, Baltoumas FA. Visualizing metagenomic and metatranscriptomic data: A comprehensive review. Comput Struct Biotechnol J 2024;23:2011-2033. [PMID: 38765606 PMCID: PMC11101950 DOI: 10.1016/j.csbj.2024.04.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024]  Open
6
McCann HM, Meade CD, Banerjee B, Penev PI, Dean Williams L, Petrov AS. RiboVision2: A Web Server for Advanced Visualization of Ribosomal RNAs. J Mol Biol 2024;436:168556. [PMID: 39237196 DOI: 10.1016/j.jmb.2024.168556] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 09/07/2024]
7
Schebera J, Zeckzer D, Wiegreffe D. A layout framework for genome-wide multiple sequence alignment graphs. FRONTIERS IN BIOINFORMATICS 2024;4:1358374. [PMID: 39221004 PMCID: PMC11362851 DOI: 10.3389/fbinf.2024.1358374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 07/08/2024] [Indexed: 09/04/2024]  Open
8
Andress Huacachino A, Joo J, Narayanan N, Tehim A, Himes BE, Penning TM. Aldo-keto reductase (AKR) superfamily website and database: An update. Chem Biol Interact 2024;398:111111. [PMID: 38878851 PMCID: PMC11232437 DOI: 10.1016/j.cbi.2024.111111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/09/2024] [Accepted: 06/13/2024] [Indexed: 06/23/2024]
9
Sidharthan VK, Reddy V, Kiran G, Rajeswari V, Baranwal VK, Kumar MK, Kumar KS. Probing of plant transcriptomes reveals the hidden genetic diversity of the family Secoviridae. Arch Virol 2024;169:150. [PMID: 38898334 DOI: 10.1007/s00705-024-06076-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 05/07/2024] [Indexed: 06/21/2024]
10
Wendt G, Collins JJ. Horizontal gene transfer of a functional cki homolog in the human pathogen Schistosoma mansoni. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.27.596073. [PMID: 38853947 PMCID: PMC11160599 DOI: 10.1101/2024.05.27.596073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
11
Cannon EK, Portwood JL, Hayford RK, Haley OC, Gardiner JM, Andorf CM, Woodhouse MR. Enhanced pan-genomic resources at the maize genetics and genomics database. Genetics 2024;227:iyae036. [PMID: 38577974 DOI: 10.1093/genetics/iyae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/13/2024] [Indexed: 04/06/2024]  Open
12
Baltoumas FA, Karatzas E, Liu S, Ovchinnikov S, Sofianatos Y, Chen IM, Kyrpides N, Pavlopoulos G. NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes. Nucleic Acids Res 2024;52:D502-D512. [PMID: 37811892 PMCID: PMC10767849 DOI: 10.1093/nar/gkad800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/19/2023] [Indexed: 10/10/2023]  Open
13
Zhao P, Zhou S, Xu P, Su H, Han Y, Dong J, Sui H, Li X, Hu Y, Wu Z, Liu B, Zhang T, Yang F. RVdb: a comprehensive resource and analysis platform for rhinovirus research. Nucleic Acids Res 2024;52:D770-D776. [PMID: 37930838 PMCID: PMC10768139 DOI: 10.1093/nar/gkad937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 11/08/2023]  Open
14
Budiš J, Krampl W, Kucharík M, Hekel R, Goga A, Sitarčík J, Lichvár M, Smol’ak D, Böhmer M, Baláž A, Ďuriš F, Gazdarica J, Šoltys K, Turňa J, Radvánszky J, Szemes T. SnakeLines: integrated set of computational pipelines for sequencing reads. J Integr Bioinform 2023;20:jib-2022-0059. [PMID: 37602733 PMCID: PMC10757078 DOI: 10.1515/jib-2022-0059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 03/21/2023] [Indexed: 08/22/2023]  Open
15
Ouyang Y, Nauwynck HJ. PCV2 Uptake by Porcine Monocytes Is Strain-Dependent and Is Associated with Amino Acid Characteristics on the Capsid Surface. Microbiol Spectr 2023;11:e0380522. [PMID: 36719220 PMCID: PMC10100887 DOI: 10.1128/spectrum.03805-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/13/2023] [Indexed: 02/01/2023]  Open
16
Wafula EK, Zhang H, Von Kuster G, Leebens-Mack JH, Honaas LA, dePamphilis CW. PlantTribes2: Tools for comparative gene family analysis in plant genomics. FRONTIERS IN PLANT SCIENCE 2023;13:1011199. [PMID: 36798801 PMCID: PMC9928214 DOI: 10.3389/fpls.2022.1011199] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/02/2022] [Indexed: 05/12/2023]
17
Kjær KH, Winther Pedersen M, De Sanctis B, De Cahsan B, Korneliussen TS, Michelsen CS, Sand KK, Jelavić S, Ruter AH, Schmidt AMA, Kjeldsen KK, Tesakov AS, Snowball I, Gosse JC, Alsos IG, Wang Y, Dockter C, Rasmussen M, Jørgensen ME, Skadhauge B, Prohaska A, Kristensen JÅ, Bjerager M, Allentoft ME, Coissac E, Rouillard A, Simakova A, Fernandez-Guerra A, Bowler C, Macias-Fauria M, Vinner L, Welch JJ, Hidy AJ, Sikora M, Collins MJ, Durbin R, Larsen NK, Willerslev E. A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA. Nature 2022;612:283-291. [PMID: 36477129 PMCID: PMC9729109 DOI: 10.1038/s41586-022-05453-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/18/2022] [Indexed: 12/12/2022]
18
Brenes Guallar MA, Fokkens L, Rep M, Berke L, van Dam P. Fusarium oxysporum effector clustering version 2: An updated pipeline to infer host range. FRONTIERS IN PLANT SCIENCE 2022;13:1012688. [PMID: 36340405 PMCID: PMC9627151 DOI: 10.3389/fpls.2022.1012688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
19
Droc G, Martin G, Guignon V, Summo M, Sempéré G, Durant E, Soriano A, Baurens FC, Cenci A, Breton C, Shah T, Aury JM, Ge XJ, Harrison PH, Yahiaoui N, D’Hont A, Rouard M. The banana genome hub: a community database for genomics in the Musaceae. HORTICULTURE RESEARCH 2022;9:uhac221. [PMID: 36479579 PMCID: PMC9720444 DOI: 10.1093/hr/uhac221] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/22/2022] [Indexed: 06/17/2023]
20
Yang Q, Liu T, Wu T, Lei T, Li Y, Wang X. GGDB: A Grameneae genome alignment database of homologous genes hierarchically related to evolutionary events. PLANT PHYSIOLOGY 2022;190:340-351. [PMID: 35789395 PMCID: PMC9434254 DOI: 10.1093/plphys/kiac297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
21
Ruggiero E, Lavezzo E, Grazioli M, Zanin I, Marušič M, Plavec J, Richter SN, Toppo S. Human Virus Genomes Are Enriched in Conserved Adenine/Thymine/Uracil Multiple Tracts That Pause Polymerase Progression. Front Microbiol 2022;13:915069. [PMID: 35722311 PMCID: PMC9198555 DOI: 10.3389/fmicb.2022.915069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022]  Open
22
Samanta MK, Gayen S, Harris C, Maclary E, Murata-Nakamura Y, Malcore RM, Porter RS, Garay PM, Vallianatos CN, Samollow PB, Iwase S, Kalantry S. Activation of Xist by an evolutionarily conserved function of KDM5C demethylase. Nat Commun 2022;13:2602. [PMID: 35545632 PMCID: PMC9095838 DOI: 10.1038/s41467-022-30352-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 04/26/2022] [Indexed: 12/03/2022]  Open
23
Lukačišin M, Espinosa-Cantú A, Bollenbach T. Intron-mediated induction of phenotypic heterogeneity. Nature 2022;605:113-118. [PMID: 35444278 PMCID: PMC9068511 DOI: 10.1038/s41586-022-04633-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 03/11/2022] [Indexed: 11/12/2022]
24
Isolation and Characterization of a Novel Autographiviridae Phage and Its Combined Effect with Tigecycline in Controlling Multidrug-Resistant Acinetobacter baumannii-Associated Skin and Soft Tissue Infections. Viruses 2022;14:v14020194. [PMID: 35215788 PMCID: PMC8878389 DOI: 10.3390/v14020194] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/24/2022]  Open
25
Tourasse NJ, Darfeuille F. T1TAdb: the database of type I toxin-antitoxin systems. RNA (NEW YORK, N.Y.) 2021;27:1471-1481. [PMID: 34531327 PMCID: PMC8594479 DOI: 10.1261/rna.078802.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/03/2021] [Indexed: 05/11/2023]
26
Martin EJ, Meagher TR, Barker D. Using sound to understand protein sequence data: new sonification algorithms for protein sequences and multiple sequence alignments. BMC Bioinformatics 2021;22:456. [PMID: 34556048 PMCID: PMC8459479 DOI: 10.1186/s12859-021-04362-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 08/23/2021] [Indexed: 11/10/2022]  Open
27
Torun FM, Bilgin HI, Kaplan OI. MSABrowser: dynamic and fast visualization of sequence alignments, variations and annotations. BIOINFORMATICS ADVANCES 2021;1:vbab009. [PMID: 36700112 PMCID: PMC9710668 DOI: 10.1093/bioadv/vbab009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/25/2021] [Indexed: 01/28/2023]
28
Keseler IM, Gama-Castro S, Mackie A, Billington R, Bonavides-Martínez C, Caspi R, Kothari A, Krummenacker M, Midford PE, Muñiz-Rascado L, Ong WK, Paley S, Santos-Zavaleta A, Subhraveti P, Tierrafría VH, Wolfe AJ, Collado-Vides J, Paulsen IT, Karp PD. The EcoCyc Database in 2021. Front Microbiol 2021;12:711077. [PMID: 34394059 PMCID: PMC8357350 DOI: 10.3389/fmicb.2021.711077] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/02/2021] [Indexed: 11/13/2022]  Open
29
Lemoine F, Blassel L, Voznica J, Gascuel O. COVID-Align: accurate online alignment of hCoV-19 genomes using a profile HMM. Bioinformatics 2021;37:1761-1762. [PMID: 33045068 PMCID: PMC7745650 DOI: 10.1093/bioinformatics/btaa871] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 05/23/2020] [Accepted: 09/24/2020] [Indexed: 11/12/2022]  Open
30
Penev PI, McCann HM, Meade CD, Alvarez-Carreño C, Maddala A, Bernier CR, Chivukula VL, Ahmad M, Gulen B, Sharma A, Williams LD, Petrov AS. ProteoVision: web server for advanced visualization of ribosomal proteins. Nucleic Acids Res 2021;49:W578-W588. [PMID: 33999189 PMCID: PMC8265156 DOI: 10.1093/nar/gkab351] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/11/2021] [Accepted: 04/21/2021] [Indexed: 11/26/2022]  Open
31
Tohma K, Lepore CJ, Martinez M, Degiuseppe JI, Khamrin P, Saito M, Mayta H, Nwaba AUA, Ford-Siltz LA, Green KY, Galeano ME, Zimic M, Stupka JA, Gilman RH, Maneekarn N, Ushijima H, Parra GI. Genome-wide analyses of human noroviruses provide insights on evolutionary dynamics and evidence of coexisting viral populations evolving under recombination constraints. PLoS Pathog 2021;17:e1009744. [PMID: 34255807 PMCID: PMC8318288 DOI: 10.1371/journal.ppat.1009744] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 07/28/2021] [Accepted: 06/23/2021] [Indexed: 12/14/2022]  Open
32
Staton M, Cannon E, Sanderson LA, Wegrzyn J, Anderson T, Buehler S, Cobo-Simón I, Faaberg K, Grau E, Guignon V, Gunoskey J, Inderski B, Jung S, Lager K, Main D, Poelchau M, Ramnath R, Richter P, West J, Ficklin S. Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases. Brief Bioinform 2021;22:6318561. [PMID: 34251419 PMCID: PMC8574961 DOI: 10.1093/bib/bbab238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 12/01/2022]  Open
33
Erdős G, Pajkos M, Dosztányi Z. IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation. Nucleic Acids Res 2021;49:W297-W303. [PMID: 34048569 PMCID: PMC8262696 DOI: 10.1093/nar/gkab408] [Citation(s) in RCA: 317] [Impact Index Per Article: 79.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/21/2021] [Accepted: 05/14/2021] [Indexed: 12/22/2022]  Open
34
Anantharajah A, Helaers R, Defour JP, Olive N, Kabera F, Croonen L, Deldime F, Vaerman JL, Barbée C, Bodéus M, Scohy A, Verroken A, Rodriguez-Villalobos H, Kabamba-Mukadi B. How to choose the right real-time RT-PCR primer sets for the SARS-CoV-2 genome detection? J Virol Methods 2021;295:114197. [PMID: 34033854 PMCID: PMC8141720 DOI: 10.1016/j.jviromet.2021.114197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 05/12/2021] [Accepted: 05/21/2021] [Indexed: 01/10/2023]
35
Theofanopoulou C, Gedman G, Cahill JA, Boeckx C, Jarvis ED. Universal nomenclature for oxytocin-vasotocin ligand and receptor families. Nature 2021;592:747-755. [PMID: 33911268 PMCID: PMC8081664 DOI: 10.1038/s41586-020-03040-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 05/29/2020] [Indexed: 02/02/2023]
36
Vornhagen J, Bassis CM, Ramakrishnan S, Hein R, Mason S, Bergman Y, Sunshine N, Fan Y, Holmes CL, Timp W, Schatz MC, Young VB, Simner PJ, Bachman MA. A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor. PLoS Pathog 2021;17:e1009537. [PMID: 33930099 PMCID: PMC8115787 DOI: 10.1371/journal.ppat.1009537] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/12/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023]  Open
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Krebs FS, Zoete V, Trottet M, Pouchon T, Bovigny C, Michielin O. Swiss-PO: a new tool to analyze the impact of mutations on protein three-dimensional structures for precision oncology. NPJ Precis Oncol 2021;5:19. [PMID: 33737716 PMCID: PMC7973488 DOI: 10.1038/s41698-021-00156-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 02/04/2021] [Indexed: 12/12/2022]  Open
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Torres MDT, Cao J, Franco OL, Lu TK, de la Fuente-Nunez C. Synthetic Biology and Computer-Based Frameworks for Antimicrobial Peptide Discovery. ACS NANO 2021;15:2143-2164. [PMID: 33538585 PMCID: PMC8734659 DOI: 10.1021/acsnano.0c09509] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
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Blum M, Chang HY, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, Richardson L, Salazar GA, Williams L, Bork P, Bridge A, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Necci M, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A, Finn RD. The InterPro protein families and domains database: 20 years on. Nucleic Acids Res 2021;49:D344-D354. [PMID: 33156333 PMCID: PMC7778928 DOI: 10.1093/nar/gkaa977] [Citation(s) in RCA: 1351] [Impact Index Per Article: 337.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/08/2020] [Accepted: 10/23/2020] [Indexed: 01/22/2023]  Open
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Valentin G, Abdel T, Gaëtan D, Jean-François D, Matthieu C, Mathieu R. GreenPhylDB v5: a comparative pangenomic database for plant genomes. Nucleic Acids Res 2021;49:D1464-D1471. [PMID: 33237299 PMCID: PMC7779052 DOI: 10.1093/nar/gkaa1068] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 12/28/2022]  Open
41
Procter JB, Carstairs GM, Soares B, Mourão K, Ofoegbu TC, Barton D, Lui L, Menard A, Sherstnev N, Roldan-Martinez D, Duce S, Martin DMA, Barton GJ. Alignment of Biological Sequences with Jalview. Methods Mol Biol 2021;2231:203-224. [PMID: 33289895 PMCID: PMC7116599 DOI: 10.1007/978-1-0716-1036-7_13] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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On the Identity of Species of Oreobates (Anura: Craugastoridae) from Central South America, with the Description of a New Species from Bolivia. J HERPETOL 2020. [DOI: 10.1670/20-001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
43
Iqbal S, Hoksza D, Pérez-Palma E, May P, Jespersen JB, Ahmed SS, Rifat ZT, Heyne HO, Rahman MS, Cottrell JR, Wagner FF, Daly MJ, Campbell AJ, Lal D. MISCAST: MIssense variant to protein StruCture Analysis web SuiTe. Nucleic Acids Res 2020;48:W132-W139. [PMID: 32402084 PMCID: PMC7319582 DOI: 10.1093/nar/gkaa361] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/17/2020] [Accepted: 05/11/2020] [Indexed: 12/19/2022]  Open
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Coulton A, Edwards KJ. AutoCloner: automatic homologue-specific primer design for full-gene cloning in polyploids. BMC Bioinformatics 2020;21:311. [PMID: 32677889 PMCID: PMC7364506 DOI: 10.1186/s12859-020-03601-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 06/11/2020] [Indexed: 12/02/2022]  Open
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Bouyssié D, Lesne J, Locard-Paulet M, Albigot R, Burlet-Schiltz O, Marcoux J. HDX-Viewer: interactive 3D visualization of hydrogen-deuterium exchange data. Bioinformatics 2020;35:5331-5333. [PMID: 31287496 PMCID: PMC6954641 DOI: 10.1093/bioinformatics/btz550] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 07/04/2019] [Accepted: 07/08/2019] [Indexed: 11/26/2022]  Open
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Palaniappan K, Chen IMA, Chu K, Ratner A, Seshadri R, Kyrpides NC, Ivanova NN, Mouncey NJ. IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase. Nucleic Acids Res 2020;48:D422-D430. [PMID: 31665416 DOI: 10.1093/nar/gkz932] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/02/2019] [Accepted: 10/09/2019] [Indexed: 01/14/2023]  Open
47
Lemoine F, Correia D, Lefort V, Doppelt-Azeroual O, Mareuil F, Cohen-Boulakia S, Gascuel O. NGPhylogeny.fr: new generation phylogenetic services for non-specialists. Nucleic Acids Res 2020;47:W260-W265. [PMID: 31028399 PMCID: PMC6602494 DOI: 10.1093/nar/gkz303] [Citation(s) in RCA: 465] [Impact Index Per Article: 93.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/05/2019] [Accepted: 04/17/2019] [Indexed: 11/14/2022]  Open
48
Kunzmann P, Mayer BE, Hamacher K. Substitution matrix based color schemes for sequence alignment visualization. BMC Bioinformatics 2020;21:209. [PMID: 32448181 PMCID: PMC7245768 DOI: 10.1186/s12859-020-3526-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/30/2020] [Indexed: 11/20/2022]  Open
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Zhu Z, Guan Z, Liu G, Wang Y, Zhang Z. SGID: a comprehensive and interactive database of the silkworm. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020;2019:5677404. [PMID: 31836898 PMCID: PMC6911161 DOI: 10.1093/database/baz134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/27/2019] [Accepted: 11/01/2019] [Indexed: 11/12/2022]
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Dagan-Wiener A, Di Pizio A, Nissim I, Bahia MS, Dubovski N, Margulis E, Niv MY. BitterDB: taste ligands and receptors database in 2019. Nucleic Acids Res 2020;47:D1179-D1185. [PMID: 30357384 PMCID: PMC6323989 DOI: 10.1093/nar/gky974] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 10/09/2018] [Indexed: 01/22/2023]  Open
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