Erik Sonnhammer - Publications

Affiliations: 
Stockholm University, Stockholm, Stockholms län, Sweden 

131 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
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  0.32
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  0.44
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  0.32
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  0.6
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  0.6
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  0.32
2019 Sjöberg E, Meyrath M, Milde L, Herrera M, Lövrot J, Hägerstrand D, Frings O, Bartish M, Rolny C, Sonnhammer E, Chevigné A, Augsten M, Ostman A. A novel ACKR2-dependent role of fibroblast-derived CXCL14 in epithelial-to-mesenchymal transition and metastasis of breast cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 30850359 DOI: 10.1158/1078-0432.Ccr-18-1294  0.4
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  0.44
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  0.4
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  0.6
2016 Saripella GV, Sonnhammer EL, Forslund K. Benchmarking the next generation of homology inference tools. Bioinformatics (Oxford, England). PMID 27256311 DOI: 10.1093/bioinformatics/btw305  0.6
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  0.6
2015 Herr P, Lundin C, Evers B, Ebner D, Bauerschmidt C, Kingham G, Palmai-Pallag T, Mortusewicz O, Frings O, Sonnhammer E, Helleday T. A genome-wide IR-induced RAD51 foci RNAi screen identifies CDC73 involved in chromatin remodeling for DNA repair. Cell Discovery. 1: 15034. PMID 27462432 DOI: 10.1038/Celldisc.2015.34  0.4
2015 Sonnhammer EL, Östlund G. InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic. Nucleic Acids Research. 43: D234-9. PMID 25429972 DOI: 10.1093/nar/gku1203  0.6
2015 Tjärnberg A, Nordling TE, Studham M, Nelander S, Sonnhammer EL. Avoiding pitfalls in L1-regularised inference of gene networks. Molecular Biosystems. 11: 287-96. PMID 25377664 DOI: 10.1039/C4Mb00419A  0.6
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  0.6
2014 Sonnhammer EL, Gabaldón T, Sousa da Silva AW, Martin M, Robinson-Rechavi M, Boeckmann B, Thomas PD, Dessimoz C. Big data and other challenges in the quest for orthologs. Bioinformatics (Oxford, England). 30: 2993-8. PMID 25064571 DOI: 10.1093/Bioinformatics/Btu492  0.6
2014 Studham ME, Tjärnberg A, Nordling TE, Nelander S, Sonnhammer EL. Functional association networks as priors for gene regulatory network inference. Bioinformatics (Oxford, England). 30: i130-8. PMID 24931976 DOI: 10.1093/Bioinformatics/Btu285  0.6
2014 Guala D, Sjölund E, Sonnhammer EL. MaxLink: network-based prioritization of genes tightly linked to a disease seed set. Bioinformatics (Oxford, England). 30: 2689-90. PMID 24849579 DOI: 10.1093/bioinformatics/btu344  0.6
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  0.6
2014 Schmitt T, Ogris C, Sonnhammer EL. FunCoup 3.0: database of genome-wide functional coupling networks. Nucleic Acids Research. 42: D380-8. PMID 24185702 DOI: 10.1093/nar/gkt984  0.6
2014 Ostlund G, Sonnhammer EL. Avoiding pitfalls in gene (co)expression meta-analysis. Genomics. 103: 21-30. PMID 24184361 DOI: 10.1016/j.ygeno.2013.10.006  0.6
2013 Tjärnberg A, Nordling TE, Studham M, Sonnhammer EL. Optimal sparsity criteria for network inference. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 398-408. PMID 23641867 DOI: 10.1089/cmb.2012.0268  0.6
2013 Frings O, Augsten M, Tobin NP, Carlson J, Paulsson J, Pena C, Olsson E, Veerla S, Bergh J, Ostman A, Sonnhammer EL. Prognostic significance in breast cancer of a gene signature capturing stromal PDGF signaling. The American Journal of Pathology. 182: 2037-47. PMID 23583284 DOI: 10.1016/J.Ajpath.2013.02.018  0.6
2013 Schreiber F, Sonnhammer EL. Hieranoid: hierarchical orthology inference. Journal of Molecular Biology. 425: 2072-81. PMID 23485417 DOI: 10.1016/J.Jmb.2013.02.018  0.6
2013 Frings O, Alexeyenko A, Sonnhammer EL. MGclus: network clustering employing shared neighbors. Molecular Biosystems. 9: 1670-5. PMID 23396516 DOI: 10.1039/c3mb25473a  0.6
2013 McCormack T, Frings O, Alexeyenko A, Sonnhammer EL. Statistical assessment of crosstalk enrichment between gene groups in biological networks. Plos One. 8: e54945. PMID 23372799 DOI: 10.1371/journal.pone.0054945  0.6
2012 Frings O, Mank JE, Alexeyenko A, Sonnhammer EL. Network analysis of functional genomics data: application to avian sex-biased gene expression. Thescientificworldjournal. 2012: 130491. PMID 23319882 DOI: 10.1100/2012/130491  0.6
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  0.6
2012 Dessimoz C, Gabaldón T, Roos DS, Sonnhammer EL, Herrero J. Toward community standards in the quest for orthologs. Bioinformatics (Oxford, England). 28: 900-4. PMID 22332236 DOI: 10.1093/Bioinformatics/Bts050  0.6
2012 Ostlund G, Sonnhammer EL. Quality criteria for finding genes with high mRNA-protein expression correlation and coexpression correlation. Gene. 497: 228-36. PMID 22326533 DOI: 10.1016/j.gene.2012.01.029  0.6
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  0.6
2012 Alexeyenko A, Schmitt T, Tjärnberg A, Guala D, Frings O, Sonnhammer EL. Comparative interactomics with Funcoup 2.0. Nucleic Acids Research. 40: D821-8. PMID 22110034 DOI: 10.1093/nar/gkr1062  0.6
2011 Forslund K, Pekkari I, Sonnhammer EL. Domain architecture conservation in orthologs. Bmc Bioinformatics. 12: 326. PMID 21819573 DOI: 10.7490/F1000Research.2071.1  0.6
2011 Schmitt T, Messina DN, Schreiber F, Sonnhammer EL. Letter to the editor: SeqXML and OrthoXML: standards for sequence and orthology information. Briefings in Bioinformatics. 12: 485-8. PMID 21666252 DOI: 10.1093/Bib/Bbr025  0.6
2011 Forslund K, Schreiber F, Thanintorn N, Sonnhammer EL. OrthoDisease: tracking disease gene orthologs across 100 species. Briefings in Bioinformatics. 12: 463-73. PMID 21565935 DOI: 10.1093/Bib/Bbr024  0.6
2010 Henricson A, Forslund K, Sonnhammer EL. Orthology confers intron position conservation. Bmc Genomics. 11: 412. PMID 20598118 DOI: 10.1186/1471-2164-11-412  0.6
2010 Alexeyenko A, Wassenberg DM, Lobenhofer EK, Yen J, Linney E, Sonnhammer EL, Meyer JN. Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicity. Plos One. 5: e10465. PMID 20463971 DOI: 10.1371/Journal.Pone.0010465  0.6
2010 Ostlund G, Lindskog M, Sonnhammer EL. Network-based Identification of novel cancer genes. Molecular & Cellular Proteomics : McP. 9: 648-55. PMID 19959820 DOI: 10.1074/mcp.M900227-MCP200  0.6
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  0.6
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  0.6
2009 Klammer M, Messina DN, Schmitt T, Sonnhammer EL. MetaTM - a consensus method for transmembrane protein topology prediction. Bmc Bioinformatics. 10: 314. PMID 19785723 DOI: 10.1186/1471-2105-10-314  0.6
2009 Gabaldón T, Dessimoz C, Huxley-Jones J, Vilella AJ, Sonnhammer EL, Lewis S. Joining forces in the quest for orthologs. Genome Biology. 10: 403. PMID 19785718 DOI: 10.1186/Gb-2009-10-9-403  0.6
2009 Björkholm P, Sonnhammer EL. Comparative analysis and unification of domain-domain interaction networks. Bioinformatics (Oxford, England). 25: 3020-5. PMID 19720675 DOI: 10.1093/bioinformatics/btp522  0.6
2009 Forslund K, Sonnhammer EL. Benchmarking homology detection procedures with low complexity filters. Bioinformatics (Oxford, England). 25: 2500-5. PMID 19620098 DOI: 10.1093/bioinformatics/btp446  0.6
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  0.6
2009 Alexeyenko A, Sonnhammer EL. Global networks of functional coupling in eukaryotes from comprehensive data integration. Genome Research. 19: 1107-16. PMID 19246318 DOI: 10.1101/gr.087528.108  0.6
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  0.6
2008 Daub CO, Sonnhammer EL. Employing conservation of co-expression to improve functional inference. Bmc Systems Biology. 2: 81. PMID 18808668 DOI: 10.1186/1752-0509-2-81  0.6
2008 Forslund K, Sonnhammer EL. Predicting protein function from domain content. Bioinformatics (Oxford, England). 24: 1681-7. PMID 18591194 DOI: 10.1093/bioinformatics/btn312  0.6
2008 Klammer M, Roopra S, Sonnhammer EL. jSquid: a Java applet for graphical on-line network exploration. Bioinformatics (Oxford, England). 24: 1467-8. PMID 18445606 DOI: 10.1093/bioinformatics/btn213  0.6
2008 Chalk AM, Sonnhammer EL. siRNA specificity searching incorporating mismatch tolerance data. Bioinformatics (Oxford, England). 24: 1316-7. PMID 18397893 DOI: 10.1093/bioinformatics/btn121  0.6
2008 Hong J, Wei N, Chalk A, Wang J, Song Y, Yi F, Qiao RP, Sonnhammer EL, Wahlestedt C, Liang Z, Du Q. Focusing on RISC assembly in mammalian cells. Biochemical and Biophysical Research Communications. 368: 703-8. PMID 18252196 DOI: 10.1016/J.Bbrc.2008.01.116  0.6
2008 Joannin N, Abhiman S, Sonnhammer EL, Wahlgren M. Sub-grouping and sub-functionalization of the RIFIN multi-copy protein family. Bmc Genomics. 9: 19. PMID 18197962 DOI: 10.1186/1471-2164-9-19  0.6
2008 Berglund AC, Sjölund E, Ostlund G, Sonnhammer EL. InParanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Research. 36: D263-6. PMID 18055500 DOI: 10.1093/nar/gkm1020  0.6
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  0.6
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  0.6
2007 Lundin C, Käll L, Kreher SA, Kapp K, Sonnhammer EL, Carlson JR, Heijne Gv, Nilsson I. Membrane topology of the Drosophila OR83b odorant receptor. Febs Letters. 581: 5601-4. PMID 18005664 DOI: 10.1016/J.Febslet.2007.11.007  0.6
2007 Hollich V, Sonnhammer EL. PfamAlyzer: domain-centric homology search. Bioinformatics (Oxford, England). 23: 3382-3. PMID 17977882 DOI: 10.1093/bioinformatics/btm521  0.6
2007 Lassmann T, Sonnhammer EL. Automatic extraction of reliable regions from multiple sequence alignments. Bmc Bioinformatics. 8: S9. PMID 17570868 DOI: 10.1186/1471-2105-8-S5-S9  0.6
2007 Käll L, Krogh A, Sonnhammer EL. Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server. Nucleic Acids Research. 35: W429-32. PMID 17483518 DOI: 10.1093/Nar/Gkm256  0.6
2006 Alexeyenko A, Lindberg J, Pérez-Bercoff A, Sonnhammer EL. Overview and comparison of ortholog databases. Drug Discovery Today. Technologies. 3: 137-43. PMID 24980400 DOI: 10.1016/j.ddtec.2006.06.002  0.6
2006 Alexeyenko A, Millar AH, Whelan J, Sonnhammer EL. Chromosomal clustering of nuclear genes encoding mitochondrial and chloroplast proteins in Arabidopsis. Trends in Genetics : Tig. 22: 589-93. PMID 16979780 DOI: 10.1016/j.tig.2006.09.002  0.6
2006 Alexeyenko A, Tamas I, Liu G, Sonnhammer EL. Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics (Oxford, England). 22: e9-15. PMID 16873526 DOI: 10.1093/bioinformatics/btl213  0.6
2006 Lassmann T, Sonnhammer EL. Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment. Nucleic Acids Research. 34: W596-9. PMID 16845078 DOI: 10.1093/nar/gkl191  0.6
2006 Abhiman S, Daub CO, Sonnhammer EL. Prediction of function divergence in protein families using the substitution rate variation parameter alpha. Molecular Biology and Evolution. 23: 1406-13. PMID 16672285 DOI: 10.1093/molbev/msl002  0.6
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  0.6
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  0.6
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  0.6
2005 Lassmann T, Sonnhammer EL. Automatic assessment of alignment quality. Nucleic Acids Research. 33: 7120-8. PMID 16361270 DOI: 10.1093/nar/gki1020  0.6
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  0.6
2005 Hollich V, Milchert L, Arvestad L, Sonnhammer EL. Assessment of protein distance measures and tree-building methods for phylogenetic tree reconstruction. Molecular Biology and Evolution. 22: 2257-64. PMID 16049194 DOI: 10.1093/Molbev/Msi224  0.6
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  0.6
2005 Käll L, Krogh A, Sonnhammer EL. An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics (Oxford, England). 21: i251-7. PMID 15961464 DOI: 10.1093/Bioinformatics/Bti1014  0.6
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  0.6
2005 Sonnhammer EL, Hollich V. Scoredist: a simple and robust protein sequence distance estimator. Bmc Bioinformatics. 6: 108. PMID 15857510 DOI: 10.1186/1471-2105-6-108  0.6
2005 Wistrand M, Sonnhammer EL. Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER. Bmc Bioinformatics. 6: 99. PMID 15831105 DOI: 10.1186/1471-2105-6-99  0.6
2005 Sonnhammer EL. Genome informatics: taming the avalanche of genomic data. Genome Biology. 6: 301. PMID 15642109 DOI: 10.1186/gb-2004-6-1-301  0.6
2005 O'Brien KP, Remm M, Sonnhammer EL. Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Research. 33: D476-80. PMID 15608241 DOI: 10.1093/nar/gki107  0.6
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  0.6
2005 Chalk AM, Warfinge RE, Georgii-Hemming P, Sonnhammer EL. siRNAdb: a database of siRNA sequences. Nucleic Acids Research. 33: D131-4. PMID 15608162 DOI: 10.1093/nar/gki136  0.6
2004 Kemmer D, Faxén M, Hodges E, Lim J, Herzog E, Ljungström E, Lundmark A, Olsen MK, Podowski R, Sonnhammer EL, Nilsson P, Reimers M, Lenhard B, Roberds SL, Wahlestedt C, et al. Exploring the foundation of genomics: a northern blot reference set for the comparative analysis of transcript profiling technologies. Comparative and Functional Genomics. 5: 584-95. PMID 18629180 DOI: 10.1002/Cfg.443  0.6
2004 Henricson A, Sonnhammer EL, Baillie DL, Gomes AV. Functional characterization in Caenorhabditis elegans of transmembrane worm-human orthologs. Bmc Genomics. 5: 85. PMID 15533247 DOI: 10.1186/1471-2164-5-85  0.6
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  0.6
2004 Camps-Valls G, Chalk AM, Serrano-López AJ, Martín-Guerrero JD, Sonnhammer EL. Profiled support vector machines for antisense oligonucleotide efficacy prediction. Bmc Bioinformatics. 5: 135. PMID 15383156 DOI: 10.1186/1471-2105-5-135  0.6
2004 O'Brien KP, Westerlund I, Sonnhammer EL. OrthoDisease: a database of human disease orthologs. Human Mutation. 24: 112-9. PMID 15241792 DOI: 10.1002/humu.20068  0.6
2004 Chalk AM, Wahlestedt C, Sonnhammer EL. Improved and automated prediction of effective siRNA. Biochemical and Biophysical Research Communications. 319: 264-74. PMID 15158471 DOI: 10.1016/J.Bbrc.2004.04.181  0.6
2004 Käll L, Krogh A, Sonnhammer EL. A combined transmembrane topology and signal peptide prediction method. Journal of Molecular Biology. 338: 1027-36. PMID 15111065 DOI: 10.1016/J.Jmb.2004.03.016  0.6
2004 Wistrand M, Sonnhammer EL. Improving profile HMM discrimination by adapting transition probabilities. Journal of Molecular Biology. 338: 847-54. PMID 15099750 DOI: 10.1016/j.jmb.2004.03.023  0.6
2004 Chalk AM, Wennerberg M, Sonnhammer EL. Sfixem--graphical sequence feature display in Java. Bioinformatics (Oxford, England). 20: 2488-90. PMID 15087316 DOI: 10.1093/bioinformatics/bth265  0.6
2004 Wistrand M, Sonnhammer EL. transition priors for protein hidden Markov models: an empirical study towards maximum discrimination. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 181-93. PMID 15072695 DOI: 10.1089/106652704773416957  0.6
2004 Ekdahl S, Sonnhammer EL. ChromoWheel: a new spin on eukaryotic chromosome visualization. Bioinformatics (Oxford, England). 20: 576-7. PMID 14990454 DOI: 10.1093/bioinformatics/btg448  0.6
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  0.6
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  0.6
2003 Lee JM, Sonnhammer EL. Genomic gene clustering analysis of pathways in eukaryotes. Genome Research. 13: 875-82. PMID 12695325 DOI: 10.1101/gr.737703  0.6
2002 Chalk AM, Sonnhammer EL. Computational antisense oligo prediction with a neural network model. Bioinformatics (Oxford, England). 18: 1567-75. PMID 12490440 DOI: 10.1093/bioinformatics/18.12.1567  0.6
2002 Käll L, Sonnhammer EL. Reliability of transmembrane predictions in whole-genome data. Febs Letters. 532: 415-8. PMID 12482603 DOI: 10.1016/S0014-5793(02)03730-4  0.6
2002 Sonnhammer EL, Koonin EV. Orthology, paralogy and proposed classification for paralog subtypes. Trends in Genetics : Tig. 18: 619-20. PMID 12446146 DOI: 10.1016/S0168-9525(02)02793-2  0.6
2002 Lassmann T, Sonnhammer EL. Quality assessment of multiple alignment programs. Febs Letters. 529: 126-30. PMID 12354624 DOI: 10.1016/S0014-5793(02)03189-7  0.6
2002 Hollich V, Storm CE, Sonnhammer EL. OrthoGUI: graphical presentation of Orthostrapper results. Bioinformatics (Oxford, England). 18: 1272-3. PMID 12217923  0.6
2002 Storm CE, Sonnhammer EL. Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics (Oxford, England). 18: 92-9. PMID 11836216  0.6
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  0.6
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  0.6
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  0.6
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  0.6
2001 Podowski RM, Sonnhammer ELL. MEDUSA: Large scale automatic selection and visual assessment of PCR primer pairs Bioinformatics. 17: 656-657. PMID 11448885  0.6
2001 Storm CE, Sonnhammer EL. NIFAS: visual analysis of domain evolution in proteins. Bioinformatics (Oxford, England). 17: 343-8. PMID 11301303  0.6
2001 Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Journal of Molecular Biology. 305: 567-80. PMID 11152613 DOI: 10.1006/Jmbi.2000.4315  0.6
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  0.6
2000 Protopopov A, Kashuba V, Podowski R, Gizatullin R, Sonnhammer E, Wahlestedt C, Zabarovsky ER. Assignment of the GPR14 gene coding for the G-protein-coupled receptor 14 to human chromosome 17q25.3 by fluorescent in situ hybridization. Cytogenetics and Cell Genetics. 88: 312-3. PMID 10828617 DOI: 10.1159/000015516  0.6
2000 Bosotti R, Isacchi A, Sonnhammer ELL. FAT: A novel domain in PIK-related kinases Trends in Biochemical Sciences. 25: 225-227. PMID 10782091 DOI: 10.1016/S0968-0004(00)01563-2  0.6
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  0.6
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  0.6
1998 Sonnhammer ELL, Wootton JC. Dynamic contact maps of protein structures Journal of Molecular Graphics and Modelling. 16: 1-5. PMID 9783253 DOI: 10.1016/S1093-3263(98)00009-6  0.6
1998 Sonnhammer EL, von Heijne G, Krogh A. A hidden Markov model for predicting transmembrane helices in protein sequences. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 6: 175-82. PMID 9783223  0.6
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  0.6
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  0.6
1997 Sonnhammer EL, Wootton JC. Widespread eukaryotic sequences, highly similar to bacterial DNA polymerase I, looking for functions Current Biology : Cb. 7. PMID 9259570  0.6
1997 Corbett SJ, Tomlinson IM, Sonnhammer EL, Buck D, Winter G. Sequence of the human immunoglobulin diversity (D) segment locus: a systematic analysis provides no evidence for the use of DIR segments, inverted D segments, "minor" D segments or D-D recombination. Journal of Molecular Biology. 270: 587-97. PMID 9245589 DOI: 10.1006/jmbi.1997.1141  0.6
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  0.6
1996 Hope IA, Albertson DG, Martinelli SD, Lynch AS, Sonnhammer E, Durban R. The C. elegans expression pattern database: A beginning Trends in Genetics. 12: 370-371. PMID 8855668 DOI: 10.1016/0168-9525(96)60033-X  0.6
1996 Tomlinson IM, Walter G, Jones PT, Dear PH, Sonnhammer ELL, Winter G. The imprint of somatic hypermutation on the repertoire of human germline V genes Journal of Molecular Biology. 256: 813-817. PMID 8601832 DOI: 10.1006/jmbi.1996.0127  0.6
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  0.44
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  0.6
1995 Walter G, Tomlinson IM, Dear PH, Sonnhammer ELL, Cook GP, Winter G. Comparison of the human germline and rearranged V(H) repertoire reveals complementarity between germline variability and somatic mutation Annals of the New York Academy of Sciences. 764: 180-182. PMID 7486518  0.6
1994 Gerstein M, Sonnhammer ELL, Chothia C. Volume changes in protein evolution Journal of Molecular Biology. 236: 1067-1078. PMID 8120887 DOI: 10.1016/0022-2836(94)90012-4  0.6
1994 Sonnhammer ELL, Kahn D. Modular arrangement of proteins as inferred from analysis of homology Protein Science. 3: 482-492. PMID 8019419  0.6
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  0.6
1994 Sonnhammer EL, Durbin R. An expert system for processing sequence homology data Proceedings / . International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 2: 363-368. PMID 7584413  0.6
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  0.6
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  0.6
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