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Erik Sonnhammer - Publications

Affiliations: 
Stockholm University, Stockholm, Stockholms län, Sweden 
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53 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Persson E, Sonnhammer ELL. InParanoiDB 9: Ortholog Groups for Protein Domains and Full-Length Proteins. Journal of Molecular Biology. 168001. PMID 36764355 DOI: 10.1016/j.jmb.2023.168001  0.422
2021 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. Molecular Biology and Evolution. PMID 33822172 DOI: 10.1093/molbev/msab098  0.348
2020 Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, Sonnhammer ELL, Tosatto SCE, Paladin L, Raj S, Richardson LJ, Finn RD, Bateman A. Pfam: The protein families database in 2021. Nucleic Acids Research. PMID 33125078 DOI: 10.1093/nar/gkaa913  0.376
2020 Altenhoff AM, Garrayo-Ventas J, Cosentino S, Emms D, Glover NM, Hernández-Plaza A, Nevers Y, Sundesha V, Szklarczyk D, Fernández JM, Codó L, Gelpi JL, Huerta-Cepas J, Iwasaki W, ... ... Sonnhammer E, et al. The Quest for Orthologs benchmark service and consensus calls in 2020. Nucleic Acids Research. PMID 32374845 DOI: 10.1093/Nar/Gkaa308  0.411
2019 Persson E, Kaduk M, Forslund SK, Sonnhammer ELL. Domainoid: domain-oriented orthology inference. Bmc Bioinformatics. 20: 523. PMID 31660857 DOI: 10.1186/S12859-019-3137-2  0.655
2019 Forslund SK, Kaduk M, Sonnhammer ELL. Evolution of Protein Domain Architectures. Methods in Molecular Biology (Clifton, N.J.). 1910: 469-504. PMID 31278674 DOI: 10.1007/978-1-4939-9074-0_15  0.645
2019 Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldón T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, Sousa da Silva A, Wang Y, Sonnhammer E, Thomas PD. Advances and Applications in the Quest for Orthologs. Molecular Biology and Evolution. PMID 31241141 DOI: 10.1093/Molbev/Msz150  0.639
2018 El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A, Sonnhammer ELL, Hirsh L, Paladin L, Piovesan D, Tosatto SCE, et al. The Pfam protein families database in 2019. Nucleic Acids Research. PMID 30357350 DOI: 10.1093/Nar/Gky995  0.388
2018 Barrientos-Somarribas M, Messina DN, Pou C, Lysholm F, Bjerkner A, Allander T, Andersson B, Sonnhammer ELL. Discovering viral genomes in human metagenomic data by predicting unknown protein families. Scientific Reports. 8: 28. PMID 29311716 DOI: 10.1038/s41598-017-18341-7  0.374
2017 Forslund K, Pereira C, Capella-Gutierrez S, Sousa da Silva A, Altenhoff A, Huerta-Cepas J, Muffato M, Patricio M, Vandepoele K, Ebersberger I, Blake J, Fernández Breis JT, Boeckmann B, Gabaldón T, ... Sonnhammer E, et al. Gearing up to handle the mosaic nature of life in the quest for orthologs. Bioinformatics (Oxford, England). PMID 28968857 DOI: 10.1093/Bioinformatics/Btx542  0.42
2016 Haider C, Kavic M, Sonnhammer EL. TreeDom: a graphical web tool for analysing domain architecture evolution. Bioinformatics (Oxford, England). PMID 27153675 DOI: 10.1093/bioinformatics/btw140  0.459
2016 Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, ... ... Sonnhammer E, et al. Standardized benchmarking in the quest for orthologs. Nature Methods. PMID 27043882 DOI: 10.1038/Nmeth.3830  0.499
2014 Kutsenko A, Svensson T, Nystedt B, Lundeberg J, Björk P, Sonnhammer E, Giacomello S, Visa N, Wieslander L. The Chironomus tentans genome sequence and the organization of the Balbiani ring genes. Bmc Genomics. 15: 819. PMID 25261295 DOI: 10.1186/1471-2164-15-819  0.348
2014 Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M. Pfam: the protein families database. Nucleic Acids Research. 42: D222-30. PMID 24288371 DOI: 10.1093/Nar/Gkt1223  0.377
2012 Forslund K, Sonnhammer EL. Evolution of protein domain architectures. Methods in Molecular Biology (Clifton, N.J.). 856: 187-216. PMID 22399460 DOI: 10.1007/978-1-61779-585-5_8  0.384
2012 Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, et al. The Pfam protein families database. Nucleic Acids Research. 40: D290-301. PMID 22127870 DOI: 10.1093/Nar/Gkr1065  0.324
2011 Forslund K, Pekkari I, Sonnhammer EL. Domain architecture conservation in orthologs. Bmc Bioinformatics. 12: 326. PMID 21819573 DOI: 10.7490/F1000Research.2071.1  0.482
2010 Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A. The Pfam protein families database. Nucleic Acids Research. 38: D211-22. PMID 19920124 DOI: 10.1093/nar/gkp985  0.377
2010 Ostlund G, Schmitt T, Forslund K, Köstler T, Messina DN, Roopra S, Frings O, Sonnhammer EL. InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Research. 38: D196-203. PMID 19892828 DOI: 10.1093/nar/gkp931  0.3
2009 Messina DN, Sonnhammer EL. DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System. Bioinformatics (Oxford, England). 25: 1333-4. PMID 19297349 DOI: 10.1093/bioinformatics/btp153  0.314
2009 Lassmann T, Frings O, Sonnhammer EL. Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features. Nucleic Acids Research. 37: 858-65. PMID 19103665 DOI: 10.1093/nar/gkn1006  0.311
2008 Forslund K, Sonnhammer EL. Predicting protein function from domain content. Bioinformatics (Oxford, England). 24: 1681-7. PMID 18591194 DOI: 10.1093/bioinformatics/btn312  0.388
2008 Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A. The Pfam protein families database. Nucleic Acids Research. 36: D281-8. PMID 18039703 DOI: 10.1093/nar/gkm960  0.45
2008 Forslund K, Henricson A, Hollich V, Sonnhammer EL. Domain tree-based analysis of protein architecture evolution. Molecular Biology and Evolution. 25: 254-64. PMID 18025066 DOI: 10.1093/molbev/msm254  0.38
2007 Hollich V, Sonnhammer EL. PfamAlyzer: domain-centric homology search. Bioinformatics (Oxford, England). 23: 3382-3. PMID 17977882 DOI: 10.1093/bioinformatics/btm521  0.351
2006 Kemmer D, Podowski RM, Arenillas D, Lim J, Hodges E, Roth P, Sonnhammer EL, Höög C, Wasserman WW. NovelFam3000--uncharacterized human protein domains conserved across model organisms. Bmc Genomics. 7: 48. PMID 16533400 DOI: 10.1186/1471-2164-7-48  0.389
2006 Wistrand M, Käll L, Sonnhammer EL. A general model of G protein-coupled receptor sequences and its application to detect remote homologs. Protein Science : a Publication of the Protein Society. 15: 509-21. PMID 16452613 DOI: 10.1110/ps.051745906  0.314
2006 Finn RD, Mistry J, Schuster-Böckler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A. Pfam: clans, web tools and services. Nucleic Acids Research. 34: D247-51. PMID 16381856 DOI: 10.1093/Nar/Gkj149  0.519
2005 Lassmann T, Sonnhammer EL. Kalign--an accurate and fast multiple sequence alignment algorithm. Bmc Bioinformatics. 6: 298. PMID 16343337 DOI: 10.1186/1471-2105-6-298  0.39
2005 Abhiman S, Sonnhammer EL. Large-scale prediction of function shift in protein families with a focus on enzymatic function. Proteins. 60: 758-68. PMID 16001403 DOI: 10.1002/prot.20550  0.318
2005 Henricson A, Käll L, Sonnhammer EL. A novel transmembrane topology of presenilin based on reconciling experimental and computational evidence. The Febs Journal. 272: 2727-33. PMID 15943807 DOI: 10.1111/j.1742-4658.2005.04691.x  0.323
2005 Abhiman S, Sonnhammer EL. FunShift: a database of function shift analysis on protein subfamilies. Nucleic Acids Research. 33: D197-200. PMID 15608176 DOI: 10.1093/nar/gki067  0.33
2004 Sun X, Zhao J, Kylberg K, Soop T, Palka K, Sonnhammer E, Visa N, Alzhanova-Ericsson AT, Daneholt B. Conspicuous accumulation of transcription elongation repressor hrp130/CA150 on the intron-rich Balbiani ring 3 gene. Chromosoma. 113: 244-57. PMID 15480727 DOI: 10.1007/S00412-004-0314-4  0.364
2004 Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR. The Pfam protein families database. Nucleic Acids Research. 32: D138-41. PMID 14681378 DOI: 10.1093/nar/gkh121  0.614
2003 Storm CE, Sonnhammer EL. Comprehensive analysis of orthologous protein domains using the HOPS database. Genome Research. 13: 2353-62. PMID 14525933 DOI: 10.1101/gr1305203  0.502
2002 Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL. The Pfam protein families database. Nucleic Acids Research. 30: 276-80. PMID 11752314  0.699
2001 Sonnhammer EL, Wolfsberg TG. Identification of motifs in protein sequences Current Protocols in Cell Biology / Editorial Board, Juan S. Bonifacino ... [Et Al.]. PMID 18228275  0.34
2001 Remm M, Storm CE, Sonnhammer EL. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. Journal of Molecular Biology. 314: 1041-52. PMID 11743721 DOI: 10.1006/jmbi.2000.5197  0.321
2001 Sonnhammer ELL, Wootton JC. Integrated graphical analysis of protein sequence features predicted from sequence composition Proteins: Structure, Function and Genetics. 45: 262-273. PMID 11599029 DOI: 10.1002/prot.1146  0.333
2001 Storm CE, Sonnhammer EL. NIFAS: visual analysis of domain evolution in proteins. Bioinformatics (Oxford, England). 17: 343-8. PMID 11301303  0.416
2000 Remm M, Sonnhammer E. Classification of transmembrane protein families in the Caenorhabditis elegans genome and identification of human orthologs Genome Research. 10: 1679-1689. PMID 11076853 DOI: 10.1101/Gr.Gr-1491R  0.492
2000 Andersson B, Tomko R, Edwards K, Mirza M, Darban H, Öncü D, Sonnhammer E, Sollerbrant K, Philipson L. Putative regulatory domains in the human and mouse CVADR genes Gene Function & Disease. 1: 82-86. DOI: 10.1002/1438-826X(200009)1:2<82::Aid-Gnfd82>3.0.Co;2-Y  0.389
1999 Elofsson A, Sonnhammer EL. A comparison of sequence and structure protein domain families as a basis for structural genomics. Bioinformatics (Oxford, England). 15: 480-500. PMID 10383473 DOI: 10.1093/Bioinformatics/15.6.480  0.408
1999 Bateman A, Birney E, Durbin R, Eddy SR, Finn RD, Sonnhammer ELL. Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins Nucleic Acids Research. 27: 260-262. PMID 9847196 DOI: 10.1093/Nar/27.1.260  0.658
1998 Sonnhammer ELL, Eddy SR, Birney E, Bateman A, Durbin R. Pfam: Multiple sequence alignments and HMM-profiles of protein domains Nucleic Acids Research. 26: 320-322. PMID 9399864 DOI: 10.1093/Nar/26.1.320  0.71
1997 Sonnhammer ELL, Durbin R. Analysis of protein domain families in Caenorhabditis elegans Genomics. 46: 200-216. PMID 9417907 DOI: 10.1006/Geno.1997.4989  0.639
1997 Sonnhammer ELL, Eddy SR, Durbin R. Pfam: A comprehensive database of protein domain families based on seed alignments Proteins: Structure, Function and Genetics. 28: 405-420. PMID 9223186 DOI: 10.1002/(Sici)1097-0134(199707)28:3<405::Aid-Prot10>3.0.Co;2-L  0.649
1996 Hope IA, Albertson DG, Martinelli SD, Lynch AS, Sonnhammer E, Durbin R. The C. elegans expression pattern database: a beginning Trends in Genetics. 12: 370-371. DOI: 10.1016/S0168-9525(96)80021-7  0.464
1995 Sonnhammer ELL, Durbin R. A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis Gene. 167. PMID 8566757 DOI: 10.1016/0378-1119(95)00714-8  0.517
1994 Sonnhammer ELL, Kahn D. Modular arrangement of proteins as inferred from analysis of homology Protein Science. 3: 482-492. PMID 8019419  0.475
1994 Sonnhammer ELL, Durbin R. A workbench for large-scale sequence homology analysis Bioinformatics. 10: 301-307. PMID 7922687 DOI: 10.1093/Bioinformatics/10.3.301  0.53
1992 Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E. What's in a genome? Nature. 358: 287. PMID 1641000 DOI: 10.1038/358287A0  0.452
1992 Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E. Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III. Protein Science : a Publication of the Protein Society. 1: 1677-90. PMID 1304897 DOI: 10.1002/Pro.5560011216  0.591
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