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For: Tran NV, Greshake Tzovaras B, Ebersberger I. PhyloProfile: dynamic visualization and exploration of multi-layered phylogenetic profiles. Bioinformatics 2019;34:3041-3043. [PMID: 29659708 DOI: 10.1093/bioinformatics/bty225] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 04/05/2018] [Indexed: 01/16/2023]  Open
Number Cited by Other Article(s)
1
Hsieh YC, Bockwoldt M, Heiland I. ProTaxoVis-protein taxonomic visualisation of presence. BMC Bioinformatics 2025;26:128. [PMID: 40389829 PMCID: PMC12087122 DOI: 10.1186/s12859-025-06146-9] [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: 10/14/2023] [Accepted: 04/23/2025] [Indexed: 05/21/2025]  Open
2
Tran JS, Ward RD, Iruegas-López R, Ebersberger I, Peters JM. Chemical genomics informs antibiotic and essential gene function in Acinetobacter baumannii. PLoS Genet 2025;21:e1011642. [PMID: 40153700 PMCID: PMC11975115 DOI: 10.1371/journal.pgen.1011642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2024] [Revised: 04/07/2025] [Accepted: 03/03/2025] [Indexed: 03/30/2025]  Open
3
Tran JS, Ward RD, Iruegas-López R, Ebersberger I, Peters JM. Chemical genomics informs antibiotic and essential gene function in Acinetobacter baumannii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.05.627103. [PMID: 39677645 PMCID: PMC11643038 DOI: 10.1101/2024.12.05.627103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
4
Xu Y, Gehlot R, Capon SJ, Albu M, Gretz J, Bloomekatz J, Mattonet K, Vucicevic D, Talyan S, Kikhi K, Günther S, Looso M, Firulli BA, Sanda M, Firulli AB, Lacadie SA, Yelon D, Stainier DYR. PDGFRA is a conserved HAND2 effector during early cardiac development. NATURE CARDIOVASCULAR RESEARCH 2024;3:1531-1548. [PMID: 39658721 PMCID: PMC11634778 DOI: 10.1038/s44161-024-00574-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 10/29/2024] [Indexed: 12/12/2024]
5
Muelbaier H, Arthen F, Collins G, Hickler T, Hohberg K, Lehmitz R, Pauchet Y, Pfenninger M, Potapov A, Romahn J, Schaefer I, Scheu S, Schneider C, Ebersberger I, Bálint M. Genomic evidence for the widespread presence of GH45 cellulases among soil invertebrates. Mol Ecol 2024;33:e17351. [PMID: 38712904 DOI: 10.1111/mec.17351] [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: 09/05/2023] [Revised: 12/06/2023] [Accepted: 02/26/2024] [Indexed: 05/08/2024]
6
Rossier V, Train C, Nevers Y, Robinson-Rechavi M, Dessimoz C. Matreex: Compact and Interactive Visualization for Scalable Studies of Large Gene Families. Genome Biol Evol 2024;16:evae100. [PMID: 38742690 PMCID: PMC11149776 DOI: 10.1093/gbe/evae100] [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: 11/15/2023] [Revised: 04/17/2024] [Accepted: 05/03/2024] [Indexed: 05/16/2024]  Open
7
Langschied F, Leisegang MS, Brandes RP, Ebersberger I. ncOrtho: efficient and reliable identification of miRNA orthologs. Nucleic Acids Res 2023;51:e71. [PMID: 37260093 PMCID: PMC10359484 DOI: 10.1093/nar/gkad467] [Citation(s) in RCA: 6] [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: 12/06/2022] [Revised: 05/04/2023] [Accepted: 05/30/2023] [Indexed: 06/02/2023]  Open
8
Iruegas R, Pfefferle K, Göttig S, Averhoff B, Ebersberger I. Feature architecture aware phylogenetic profiling indicates a functional diversification of type IVa pili in the nosocomial pathogen Acinetobacter baumannii. PLoS Genet 2023;19:e1010646. [PMID: 37498819 PMCID: PMC10374093 DOI: 10.1371/journal.pgen.1010646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/06/2023] [Indexed: 07/29/2023]  Open
9
Dosch J, Bergmann H, Tran V, Ebersberger I. FAS: assessing the similarity between proteins using multi-layered feature architectures. Bioinformatics 2023;39:btad226. [PMID: 37084276 PMCID: PMC10185405 DOI: 10.1093/bioinformatics/btad226] [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: 11/15/2022] [Revised: 02/23/2023] [Accepted: 04/13/2023] [Indexed: 04/23/2023]  Open
10
Elhabashy H, Merino F, Alva V, Kohlbacher O, Lupas AN. Exploring protein-protein interactions at the proteome level. Structure 2022;30:462-475. [DOI: 10.1016/j.str.2022.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/26/2021] [Accepted: 02/02/2022] [Indexed: 02/08/2023]
11
Ilnitskiy IS, Zharikova AA, Mironov AA. OUP accepted manuscript. Nucleic Acids Res 2022;50:W534-W540. [PMID: 35610035 PMCID: PMC9252792 DOI: 10.1093/nar/gkac385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/19/2022] [Accepted: 04/29/2022] [Indexed: 11/27/2022]  Open
12
Birikmen M, Bohnsack KE, Tran V, Somayaji S, Bohnsack MT, Ebersberger I. Tracing Eukaryotic Ribosome Biogenesis Factors Into the Archaeal Domain Sheds Light on the Evolution of Functional Complexity. Front Microbiol 2021;12:739000. [PMID: 34603269 PMCID: PMC8481954 DOI: 10.3389/fmicb.2021.739000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/17/2021] [Indexed: 01/23/2023]  Open
13
Linard B, Ebersberger I, McGlynn SE, Glover N, Mochizuki T, Patricio M, Lecompte O, Nevers Y, Thomas PD, Gabaldón T, Sonnhammer E, Dessimoz C, Uchiyama I. Ten Years of Collaborative Progress in the Quest for Orthologs. Mol Biol Evol 2021;38:3033-3045. [PMID: 33822172 PMCID: PMC8321534 DOI: 10.1093/molbev/msab098] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/07/2021] [Accepted: 04/01/2021] [Indexed: 12/19/2022]  Open
14
Harris LA, Saint-Vincent PMB, Guo X, Hudson GA, DiCaprio AJ, Zhu L, Mitchell DA. Reactivity-Based Screening for Citrulline-Containing Natural Products Reveals a Family of Bacterial Peptidyl Arginine Deiminases. ACS Chem Biol 2020;15:3167-3175. [PMID: 33249828 DOI: 10.1021/acschembio.0c00685] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
15
Jiang Z, Carlantoni C, Allanki S, Ebersberger I, Stainier DYR. Tek (Tie2) is not required for cardiovascular development in zebrafish. Development 2020;147:dev.193029. [PMID: 32928907 DOI: 10.1242/dev.193029] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 09/03/2020] [Indexed: 12/13/2022]
16
Weidensdorfer M, Ishikawa M, Hori K, Linke D, Djahanschiri B, Iruegas R, Ebersberger I, Riedel-Christ S, Enders G, Leukert L, Kraiczy P, Rothweiler F, Cinatl J, Berger J, Hipp K, Kempf VAJ, Göttig S. The Acinetobacter trimeric autotransporter adhesin Ata controls key virulence traits of Acinetobacter baumannii. Virulence 2020;10:68-81. [PMID: 31874074 PMCID: PMC6363060 DOI: 10.1080/21505594.2018.1558693] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
17
Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldón T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, da Silva AS, Wang Y, Sonnhammer E, Thomas PD. Advances and Applications in the Quest for Orthologs. Mol Biol Evol 2020;36:2157-2164. [PMID: 31241141 PMCID: PMC6759064 DOI: 10.1093/molbev/msz150] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]  Open
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