For a list of papers in Medline, click here

Directory of (p)reprints

Google scholar profile

2025

"Topology-based metrics for finding the optimal sparsity in gene regulatory network inference" Nils Lundqvist, Mateusz Garbulowski, Thomas Hillerton, and Erik Sonnhammer* Bioinformatics, in press [PDF]

"FunCoup 6: advancing functional association networks across species with directed links and improved user experience" Davide Buzzao, Emma Persson, Dimitri Guala and Erik L.L. Sonnhammer* Nucleic Acids Res. 53:D658-D671 (2025) [PDF]

"The Pfam protein families database: embracing AI/ML" Paysan-Lafosse T, Andreeva A, Blum M, Chuguransky SR, Grego T, Pinto BL, Salazar GA, Bileschi ML, Llinares-Lopez F, Meng-Papaxanthos L, Colwell LJ, Grishin NV, Schaeffer RD, Clementel D, Tosatto SCE, Sonnhammer E, Wood V, Bateman A. Nucleic Acids Res., 53:D523-D534 (2025) [PDF]

2024

"The FunCoup Cytoscape App: multi-species network analysis and visualization" Davide Buzzao, Lukas Steininger, Dimitri Guala and Erik L.L. Sonnhammer* Bioinformatics, 41:btae739 (2024) [PDF]

"New developments for the Quest for Orthologs Benchmark Service" Adrian Altenhoff, Yannis Nevers, Vinh Tran, Dushyanth Jyothi, Maria Martin, Salvatore Cosentino, Sina Majidian, Marina Marcet-Houben, Diego Fuentes-Palacios, Emma Persson, Quest for Orthologs Consortium, Thomas Walsh, Odile Lecompte. Toni Gabaldon, Steven Kelly, Yanhui Hu, Salvador, Capella-Gutierrez, Christophe Dessimoz, Paul D. Thomas, Ingo Ebersberger, Erik Sonnhammer* NAR Genomics and Bioinformatics, 6:lqae167 (2024) [PDF]

"Quest for Orthologs in the Era of Biodiversity Genomics" Langschied F, Bordin N, Cosentino S, Fuentes-Palacios D, Glover N, Hiller M, Hu Y, Huerta-Cepas J, Coelho LP, Iwasaki W, Majidian S, Manzano-Morales S, Persson E, Richards TA, Gabaldon T, Sonnhammer E, Thomas PD, Dessimoz C, Ebersberger I. Genome Biol Evol. 16:evae224 (2024) [PDF]

"GeneSPIDER2: large scale GRN simulation and benchmarking with perturbed single-cell data" Mateusz Garbulowski, Thomas Hillerton, Daniel Morgan, Deniz Secilmis, Lisbet Sonnhammer, Andreas Tjaernberg, Torbjoern E M Nordling, Erik L L Sonnhammer* NAR Genomics and Bioinformatics, 6:lqae121 (2024) [PDF] [Supplementary]

"Benchmarking enrichment analysis methods with the disease pathway network" Davide Buzzao, Miguel Castresana-Aguirre, Dimitri Guala, Erik L L Sonnhammer* Briefings in Bioinformatics, 25:bbae069 (2024) [PDF]

PhD Thesis: From multi-omics data to global association networks: Application to disease module finding and pathway analysis, by Davide Buzzao

2023

"InParanoiDB 9: Ortholog Groups for Protein Domains and Full-Length Proteins" Emma Persson and Erik L L Sonnhammer* J. Mol. Biol. 435:168001 (2023) [PDF]

PhD Thesis: In silico modelling for refining gene regulatory network inference, by Thomas Hillerton PhD Thesis: Big data networks and orthology analysis, by Emma Persson

2022

"TOPAS, a network-based approach to detect disease modules in a top-down fashion" Davide Buzzao, Miguel Castresana-Aguirre, Dimitri Guala, Erik L L Sonnhammer* NAR Genomics and Bioinformatics 4:lqac093 (2022) [PDF]

"Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones" Maja Marklund, Niklas Schultz, Stefanie Friedrich, Emelie Berglund, Firas Tarish, Anna Tanoglidi, Yao Liu, Ludvig Bergenstråhle, Andrew Erickson, Thomas Helleday, Alastair D. Lamb, Erik Sonnhammer* & Joakim Lundeberg* Nature Commun. 13:5475 (2022) [PDF]

"Knowledge of the perturbation design is essential for accurate gene regulatory network inference" Deniz Secilmis, Thomas Hillerton, Andreas Tjärnberg, Sven Nelander, Torbjörn E. M. Nordling, Erik L. L. Sonnhammer* Scientific Reports 12:16531 (2022) [PDF]

"Optimal Sparsity Selection Based on an Information Criterion for Accurate Gene Regulatory Network Inference" Deniz Secilmis, Sven Nelander, Erik L. L. Sonnhammer* Front Genet. 13:855770 (2022) [PDF]

"GRNbenchmark - a web server for benchmarking directed gene regulatory network inference methods" Deniz Secilmis, Thomas Hillerton, Erik L. L. Sonnhammer* Nucleic Acids Res., 50:W398-W404 (2022) [PDF]

"The Quest for Orthologs orthology benchmark service in 2022" Nevers Y, Jones TEM, Jyothi D, Yates B, Ferret M, Portell-Silva L, Codo L, Cosentino S, Marcet-Houben M, Vlasova A, Poidevin L, Kress A, Hickman M, Persson E, Pilizota I, Guijarro-Clarke C; OpenEBench team the Quest for Orthologs Consortium, Iwasaki W, Lecompte O, Sonnhammer E, Roos DS, Gabaldon T, Thybert D, Thomas PD, Hu Y, Emms DM, Bruford E, Capella-Gutierrez S, Martin MJ, Dessimoz C, Altenhoff A. Nucleic Acids Res.,50:W398-W404 (2022) [PDF]

"Benefits and Challenges of Pre-clustered Network-Based Pathway Analysis" Miguel Castresana-Aguirre, Dimitri Guala and Erik L. L. Sonnhammer* Front. Genet. 13:855766 (2022) [PDF]

"InParanoid-DIAMOND: Faster orthology analysis with the InParanoid algorithm" Emma Persson and Erik Sonnhammer* Bioinformatics, 38:2918-2919 (2022) [PDF]

"PathwAX II: Network-based pathway analysis with interactive visualization of network crosstalk" Christoph Ogris, Miguel Castresana-Aguirre, and Erik L.L. Sonnhammer* Bioinformatics, 38:2659-2660 (2022) [PDF]

"Network crosstalk as a basis for drug repurposing" Dimitri Guala and Erik L L Sonnhammer* Front. Genet. 13:792090 (2022) [PDF] Corrigendum

"Fast and accurate gene regulatory network inference by normalized least squares regression" Thomas Hillerton, Deniz Secilmis, Sven Nelander, Erik L L Sonnhammer* Bioinformatics, 38:2263-2268 (2022) [PDF] [Supplement PDF]

"Generation of Realistic Gene Regulatory Networks by Enriching for Feed-Forward Loops" Erik K. Zhivkoplias, Oleg Vavulov. Thomas Hillerton, Erik L. L. Sonnhammer* Front. Genet. 13:815692 (2022) [PDF]

2021

"Drug repurposing improves disease targeting 11-fold and can be augmented by network module targeting, applied to COVID-19" Rivero-Garcia I, Castresana-Aguirre M, Guglielmo L, Guala D, Sonnhammer ELL* Scientific Reports, 11:20687 (2021) [PDF]

"PathBIX - a web server for network-based pathway annotation with adaptive null models" Miguel Castresana-Aguirre, Emma Persson, Erik LL Sonnhammer* Bioinformatics Advances, 1:vbab010 (2021) [PDF]

"Inferring the experimental design for accurate gene regulatory network inference" Deniz Secilmis, Thomas Hillerton, Sven Nelander, Erik L L Sonnhammer* Bioinformatics, 37:3553 (2021) [PDF] Supplement [PDF]

"Ten years of collaborative progress in the Quest for Orthologs" Linard B, Ebersberger I, McGlynn SE, Glover N, Mochizuki T, Patricio M, Lecompte O, Nevers Y; QFO Consortium, Thomas PD, Gabaldon T, Sonnhammer E, Dessimoz C, Uchiyama I. Mol Biol Evol., 38:3033-3045 (2021) [PDF]

"Funcoup 5: Functional association networks in all domains of life, supporting directed links and tissue-specificity" Emma Persson, Miguel Castresana-Aguirre, Davide Buzzao, Dimitri Guala, Erik L.L. Sonnhammer* J. Mol. Biol., 433:166835 (2021) [PDF]

"DNA Methylation Levels in Mononuclear Leukocytes from the Mother and Her Child Are Associated with IgE Sensitization to Allergens in Early Life" Acevedo N, Scala G, Merid SK, Frumento P, Bruhn S, Andersson A, Ogris C, Bottai M, Pershagen G, Koppelman GH, Melen E, Sonnhammer E, Alm J, Soderhall C, Kere J, Greco D, Scheynius A Int. J. Mol. Sci., 22:E801 (2021)

"Pfam: The protein families database in 2021" Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, Sonnhammer ELL, Tosatto SCE, Paladin L, Raj S, Richardson LJ, Finn RD, Bateman A Nucleic Acids Res., 49:D412-D419 (2021) [PDF]

PhD Thesis: From networks to pathway analysis, by Miguel Castresana Aguirre

PhD Thesis: Improving the accuracy of gene regulatory network inference from noisy data, by Deniz Secilmis

2020

"Uncovering cancer gene regulation by accurate regulatory network inference from uninformative data" Deniz Secilmis, Thomas Hillerton, Daniel Morgan, Andreas Tjärnberg, Sven Nelander, Torbjörn E. M. Nordling, Erik L. L. Sonnhammer* NPJ Systems Biology & Applications, 6:37 (2020) [PDF]

"Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms" Daniel Morgan, Matthew Studham, Andreas Tjärnberg, Holger Weishaupt, Fredrik J. Swartling, Torbjörn E. M. Nordling, Erik LL Sonnhammer* Scientific Reports, 10:14149 (2020) [PDF]

"Pathway-specific model estimation for improved pathway annotation by network crosstalk" Miguel Castresana-Aguirre and Erik LL Sonnhammer* Scientific Reports, 10:13585 (2020) [PDF]

"Fusion transcript detection using spatial transcriptomics" Stefanie Friedrich and Erik LL Sonnhammer* BMC Med Genomics. 13:110 (2020) [PDF]

"MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data" Friedrich S, Barbulescu R, Helleday T, Sonnhammer ELL* BMC Med Genomics. 13:76 (2020) [PDF]

"The Quest for Orthologs benchmark service and consensus calls in 2020" Altenhoff AM, Garrayo-Ventas J, Cosentino S, Emms D, Glover NM, Hernandez-Plaza A, Nevers Y, Sundesha V, Szklarczyk D, Fernandez JM, Codo L; Quest for Orthologs Consortium, Gelpi JL, Huerta-Cepas J, Iwasaki W, Kelly S, Lecompte O, Muffato M, Martin MJ, Capella-Gutierrez S, Thomas PD, Sonnhammer E*, Dessimoz C. Nucleic Acids Res. 48:W538-W545 (2020) [PDF]

"Genome-wide functional association networks: background, data & state-of-the-art resources" Guala D, Ogris C, Mueller N, Sonnhammer ELL* Brief Bioinformatics 21:1224-1237 (2020) [PDF]

PhD Thesis: Computational Analysis of Tumour Heterogeneity, by Stefanie Friedrich

2019

"Domainoid: domain-oriented orthology inference" Persson E, Kaduk M, Forslund SK, Sonnhammer ELL* BMC Bioinformatics 20:523 (2019) [PDF]

"Advances and Applications in the Quest for Orthologs" Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldon T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, Sousa da Silva A, Wang Y, Sonnhammer E, Thomas PD; Quest for Orthologs Consortium. Mol Biol Evol. 36:2157-2164 (2019) [PDF]

"Evolution of Protein Domain Architectures" Forslund SK, Kaduk M, Sonnhammer ELL Methods Mol Biol. 1910:469-504 (2019) [PDF]

"A novel ACKR2-dependent role of fibroblast-derived CXCL14 in epithelial-to-mesenchymal transition and metastasis of breast cancer" Elin Sjöberg, Max Meyrath, Laura Milde, Mercedes Herrera, John Lovrot, Daniel Hagerstrand, Oliver Frings, Margarita Bartish, Charlotte Rolny, Erik Sonnhammer, Andy Chevigne, Martin Augsten, and Arne Östman Clinical Cancer Research, 25:3702-3717 (2019) [PDF]

"The Pfam protein families database in 2019" 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, Finn RD Nucleic Acids Res. 2019 47:D427-D432 (2019) [PDF]

"A Generalized Framework for Controlling FDR in Gene Regulatory Network Inference" Morgan D, Tjärnberg A, Nordling TEM, Sonnhammer ELL. Bioinformatics 35:1026-1032 (2019) [PDF]

PhD Thesis: Towards Reliable Gene Regulatory Network Inference, by Daniel Morgan

2018

"Spatial Maps of Prostate Cancer Transcriptomes Reveal an Unexplored Landscape of Heterogeneity" Berglund E, Maaskola J, Schultz N, Friedrich S, Marklund M, Bergenstråhle J, Tarish F, Tanoglidi A, Vickovic S, Larsson L, Salmen F, Ogris C, Wallenborg K, Lagergren J, Ståhl P, Sonnhammer E, Helleday T, Lundeberg J Nature Communications 9:2419 (2018) [PDF]

"Experimental validation of predicted cancer genes using FRET" Guala D, Bernhem K, Ait Blal H, Jans D, Lundberg E, Brismar H, Sonnhammer ELL Methods Appl Fluoresc. 6:035007 (2018) [PDF]

"Gearing up to handle the mosaic nature of life in the quest for orthologs" 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, Fernandez Breis JT, Quest for Orthologs Consortium, Boeckmann B, Gabaldon T, Sonnhammer E, Dessimoz C, Lewis S Bioinformatics, 34:323-329 (2018) [PDF]

"Discovering viral genomes in human metagenomic data by predicting unknown protein families" Mauricio Barrientos-Somarribas, David Messina, Christian Pou, Fredrik Lysholm, Annelie Bjerkner, Tobias Allander, Björn Andersson, and Erik Sonnhammer Scientific Reports, 8:28 (2018) [PDF]

"FunCoup 4: new species, data, and visualization" Ogris C, Guala D, Kaduk M, Sonnhammer ELL. NAR 46:D601-D607 (2018) [PDF]

PhD Thesis: Functional Inference from Orthology and Domain Architecture, by Mateusz Kaduk

2017

"A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family" Carreras-Puigvert J, Zitnik M, Jemth AS, Carter M, Unterlass JE, Hallstrom B, Loseva O, Karem Z, Calder-Montano JM, Lindskog C, Edqvist PH, Matuszewski DJ, Ait Blal H, Berntsson RPA, Haggblad M, Martens U, Studham M, Lundgren B, Wahlby C, Sonnhammer ELL, Lundberg E, Stenmark P, Zupan B, Helleday T Nat Communications, 8:1541 (2017) [PDF]

"GeneSPIDER - Gene regulatory network inference benchmarking with controlled network and data properties" Andreas Tjärnberg, Daniel C Morgan, Torbjörn EM Nordling, Erik LL Sonnhammer Mol. Biosystems, 13:1304-1312 (2017) [PDF] [Suppl 1] [Suppl 2]

"A large-scale benchmark of gene prioritization methods" Guala D, Sonnhammer ELL Scientific Reports, 7:46598 (2017) [PDF]

"Improved orthology inference with Hieranoid 2" Kaduk M, Sonnhammer ELL Bioinformatics 33:1154-1159 (2017) [PDF]

"HieranoiDB: a database of orthologs inferred by Hieranoid" Kaduk M, Riegler C, Lemp O, Sonnhammer ELL Nucleic Acids Res., 45:D687-D690 (2017) [PDF]

"A Novel Method for Crosstalk Analysis of Biological Networks: Improving accuracy of Pathway Annotation" Ogris C, Guala D, Helleday T, Sonnhammer ELL. Nucleic Acids Res., 45:e8 (2017) [PDF]

PhD Thesis: Functional association networks for disease gene prediction, by Dimitri Guala

PhD Thesis: Global functional association network inference and crosstalk analysis for pathway annotation, by Christoph Ogris

2016

"Benchmarking the next generation of homology inference tools" Ganapathi Varma Saripella, Erik L.L. Sonnhammer, and Kristoffer Forslund Bioinformatics, 32:2636-2641 (2016) [PDF]

"Standardized benchmarking in the quest for orthologs" 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, Lecompte O, von Mering C, Xenarios I, Sjolander K, Jensen LJ, Martin MJ, Muffato M; Quest for Orthologs consortium, Gabaldon T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C. Nature Methods, 13:425-430 (2016) [PDF]

"PathwAX: a web server for network crosstalk based pathway annotation" Christoph Ogris, Thomas Helleday, Erik L.L. Sonnhammer Nucleic Acids Res., 44:W105-109 (2016) [PDF]

"TreeDom: a graphical web tool for analysing domain architecture evolution" Haider C, Kavic M, Sonnhammer ELL Bioinformatics, 32:2384-2385 (2016) [PDF]

2015

"A genome-wide IR-induced RAD51 foci RNAi screen identifies CDC73 involved in chromatin remodeling for DNA repair" Patrick Herr, Cecilia Lundin, Bastiaan Evers, Daniel Ebner, Christina Bauerschmidt, Guy Kingham, Timea Palmai-Pallag, Oliver Mortusewicz, Oliver Frings, Erik Sonnhammer & Thomas Helleday Cell Discovery 1:15034 (2015)

"InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic" Erik L.L.Sonnhammer and Gabriel Östlund Nucleic Acids Res. 43:D234-D239 (2015)

"Avoiding pitfalls in L1-regularised inference of gene networks" Andreas Tjärnberg, Torbjörn E.M. Nordling, Matthew Studham, Sven Nelander and Erik L. L. Sonnhammer Mol. BioSyst. 11:287-296 (2015) [PDF] [Supplemental material]

PhD Thesis: Exploring the Boundaries of Gene Regulatory Network Inference, by Andreas Tjärnberg. See also Torbjörn Nordling's PhD thesis.

2014

"The Chironomus tentans genome sequence and the organization of the Balbiani ring genes" Alexey Kutsenko, Thomas Svensson, Björn Nystedt, Petra Bjök, Erik Sonnhammer, Stefania Giacomello, Neus Visa, Lars Wieslander BMC Genomics 15:819 (2014)

"Big Data and Other Challenges in the Quest for Orthologs" Erik L.L. Sonnhammer, Gabaldon T, Wilter Sousa da Silva A, Martin M, Robinson-Rechavi M, Boeckmann B, Thomas P, Dessimoz C; the Quest for Orthologs consortium Bioinformatics 30:2993-2998 (2014)

"MaxLink: network-based prioritization of genes tightly linked to a disease seed set" Dimitri Guala, Erik Sjölund and Erik L.L. Sonnhammer Bioinformatics 30:2689-2690 (2014)

"Functional Association Networks as Priors for Gene Regulatory Network Inference" Matthew E. Studham, Andreas Tjärnberg, Torbjörn E.M. Nordling, Sven Nelander, and Erik L.L. Sonnhammer Bioinformatics 30:i130-i138 (2014)

"Avoiding pitfalls in gene (co)expression meta-analysis" Gabriel Östlund and Erik L.L.Sonnhammer Genomics. 103:21-30 (2014) [PDF]

"FunCoup 3.0: database of genome-wide functional coupling networks" Thomas Schmitt, Christoph Ogris, Erik L.L.Sonnhammer Nucleic Acids Res. 42:D380-8 (2014)

"Pfam: the protein families database" 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 Nucleic Acids Res. 42:D222-30 (2014)

2013

"Prognostic significance in breast cancer of a gene signature capturing stromal PDGF signaling" Oliver Frings, Martin Augsten, Nicholas P. Tobin, Joseph Carlson, Janna Paulsson, Cristina Pena, Eleonor Olsson, Sunny Veerla, Jonas Bergh, Arne Östman, Erik Sonnhammer American Journal of Pathology 182:2037-2047 (2013)

"MGclus: network clustering employing shared neighbors" Oliver Frings, Andrey Alexeyenko, Erik L.L. Sonnhammer Molecular BioSystems 9:1670-1675 (2013)

"Optimal sparsity criteria for network inference" Andreas Tjärnberg, Torbjörn E. M. Nordling, Matthew Studham, Erik L.L. Sonnhammer J. Computational Biology 20:398-408 (2013)

"Statistical Assessment of Crosstalk Enrichment between Gene Groups in Biological Networks" McCormack T, Frings O, Alexeyenko A, Sonnhammer ELL PLoS ONE, 8:e54945 (2013)

"Hieranoid: hierarchical orthology inference" Fabian Schreiber, Erik LL Sonnhammer J. Mol. Biol. 425:2072-81 (2013)

PhD Thesis: Data integration for robust network-based disease gene prediction, by Gabriel Östlund

2012

"Network analysis of functional genomics data: application to avian sex-biased gene expression" Frings O, Mank JE, Alexeyenko A, Sonnhammer EL. The Scientific World Journal (Special Issue on Computational Systems Biology), 2012:130491 (2012)

"Evolution of protein domain architectures" Kristoffer Forslund and Erik LL Sonnhammer Methods in Molecular Biology, 856:187-216 (2012)

"Toward Community Standards in the Quest for Orthologs" Dessimoz C, Gabaldon T, Roos DS, Sonnhammer E, Herrero J; the Quest for Orthologs Consortium Bioinformatics, 28:900-904 (2012)

"Quality criteria for finding genes with high mRNA-protein expression correlation and coexpression correlation" Gabriel Östlund and Erik LL Sonnhammer Gene, 497:228-236 (2012)

"The Pfam protein families database" Punta, M., Coggill, P.C., Eberhardt, R.Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J., Heger, A., Holm, L., Sonnhammer, E.L., Eddy, S.R., Bateman, A. and Finn, R.D. Nucleic Acids Research, 40:D290-D301 (2012)

"Comparative interactomics with Funcoup 2.0" Andrey Alexeyenko, Thomas Schmitt, Andreas Tjärnberg, Dmitri Guala, Oliver Frings, Erik L.L. Sonnhammer Nucleic Acids Research, 40:D821-D828 (2012)

2011

"SeqXML and OrthoXML: standards for sequence and orthology information" Thomas Schmitt, David N. Messina, Fabian Schreiber and Erik L.L. Sonnhammer Briefings in Bioinformatics, 12:485-488 (2011) [PDF]

"OrthoDisease: tracking disease gene orthologs across 100 species" Kristoffer Forslund, Fabian Schreiber, Nattaphon Thanintorn and Erik L.L. Sonnhammer Briefings in Bioinformatics, 12:463-473 (2011) [PDF]

"Domain architecture conservation in orthologs" Kristoffer Forslund, Isabella Pekkari and Erik LL Sonnhammer BMC Genomics, 11:412 (2011)

PhD Thesis: The relationship between orthology, protein domain architecture and protein function, by Kristoffer Forslund

2010

"Orthology confers intron position conservation" Henricson A, Forslund K, Sonnhammer ELL BMC Genomics, 11:412 (2010)

"Dynamic Zebrafish Interactome Reveals Transcriptional Mechanisms of Dioxin Toxicity" Andrey Alexeyenko, Deena M Wassenberg, Edward K Lobenhofer, Jerry Yen, Elwood Linney, Erik LL Sonnhammer, Joel N Meyer PloS ONE, 5:e10465 (2010)

"Network-based identification of novel cancer genes" Gabriel Östlund, Mats Lindskog, and Erik L.L. Sonnhammer Molecular and Cellular Proteomics, 9:648-655 (2010) [PDF] [Supplemental figure] [Supplemental tables]

"The Pfam protein families database" Finn Rob, Mistry Jaina, Tate John, Coggill Penny, Heger Andreas, Pollington Joanne, Gavin O. Luke, Ceric Goran, Forslund Kristoffer, Holm Liisa, Sonnhammer Erik L.L., Eddy Sean, Bateman Alex Nucleic Acids Research, 38:D211-D222 (2010) [PDF]

"InParanoid 7:New algorithms and tools for eukaryotic orthology analysis" Gabriel Östlund, Thomas Schmitt, Kristoffer Forslund, Tina Köstler, David N Messina, Sanjit Roopra, Oliver Frings, Erik L.L. Sonnhammer Nucleic Acids Research, 38:D196-D203 (2010) [PDF]

2009

"Comparative analysis and unification and of domain-domain interactions " Patrik Björkholm and Erik LL Sonnhammer Bioinformatics, 25:3020-3025 (2009) [PDF]

"MetaTM - A Consensus Method for Transmembrane Topology Prediction" Martin Klammer, David N Messina, Thomas Schmitt and Erik LL Sonnhammer BMC Bioinformatics, 10:314 (2009) [PDF]

"Joining forces in the quest for orthologs" Gabaldon T, Dessimoz C, Huxley-Jones J, Vilella AJ, Sonnhammer ELL and Lewis S Genome Biology, 10:403 (2009) [PDF]

"Benchmarking homology detection procedures with low complexity filters" Forslund K and Erik L.L. Sonnhammer Bioinformatics, 25:2500-2505 (2009) [PDF]

"Global networks of functional coupling in eukaryotes from comprehensive data integration" Andrey Alexeyenko and Erik L.L. Sonnhammer Genome Research, 19:1107-1116 (2009) [PDF] [Supplemental material]

"DASher: a stand alone protein sequence client for DAS, the Distributed Annotation System" David N Messina and Erik L.L. Sonnhammer Bioinformatics, 25:1333-1334 (2009) [PDF]

"Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features" Timo Lassmann, Oliver Frings, and Erik L.L. Sonnhammer NAR 37:858-865 (2009) [PDF]

2008

"Employing conservation of co-expression to improve functional inference" Carsten O. Daub and Erik L.L. Sonnhammer" BMC Systems Biology, 2:81 (2008) [PDF]

"Predicting protein function from domain content" Forslund K, Sonnhammer ELL" Bioinformatics, 24:1681-1687 (2008) [PDF]

"jSquid: a Java applet for graphical on-line network exploration" Klammer M, Roopra S, Sonnhammer ELL" Bioinformatics, 24:1467-1468 (2008) [PDF]

"siRNA specificity searching incorporating mismatch tolerance data" Alistair M. Chalk and Erik L.L. Sonnhammer Bioinformatics, 24:1316-1317 (2008) [PDF] [Supplement 1 PDF] [Supplement 2 PDF]

"Domain Tree Based Analysis of Protein Architecture Evolution" Kristoffer Forslund, Volker Hollich, Anna Henricson, and Erik L.L. Sonnhammer MBE 25:254-264 (2008) [PDF]

"InParanoid 6: eukaryotic ortholog clusters with inparalogs" Berglund AC, Sjölund E, Ostlund G, Sonnhammer ELL Nucleic Acids Res. 36:D263-266 (2008) [PDF]

"The Pfam protein families database" Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer ELL, Bateman A Nucleic Acids Res. 36:D281-288 (2008) [PDF]

"Sub-grouping and sub-functionalization of the RIFIN multi-copy protein family" Joannin N, Abhiman S, Sonnhammer EL, Wahlgren M BMC Genomics 9:19 (2008) [PDF]

2007

"PfamAlyzer: Domain-Centric Homology Search" Hollich V, Sonnhammer EL. Bioinformatics, 23:3382-3383 (2007) [PDF]

"Membrane topology of the Drosophila OR83b odorant receptor" Lundin C, Kall L, Kreher SA, Kapp K, Sonnhammer EL, Carlson JR, Heijne GV, Nilsson I. FEBS Lett. 581:5601-5604 (2007) [PDF]

"High-throughput in vivo analysis of gene expression in Caenorhabditis elegans" Hunt-Newbury R, Viveiros R, Johnsen R, Mah A, Anastas D, Fang L, Halfnight E, Lee D, Lin J, Lorch A, McKay S, Okada HM, Pan J, Schulz AK, Tu D, Wong K, Zhao Z, Alexeyenko A, Burglin T, Sonnhammer E, Schnabel R, Jones SJ, Marra MA, Baillie DL, Moerman DG. PLoS Biol. 5:e237 (2007) [PDF]

"Automatic extraction of reliable regions from multiple sequence alignments" Timo Lassmann and Erik L.L. Sonnhammer BMC Bioinformatics, 8:Suppl 5:S9 (2007) [PDF]

"Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server" Lukas Kall, Anders Krogh, and Erik L.L. Sonnhammer Nucleic Acids Res., 5:W429-32 (2007) [PDF]

2006

"Chromosomal clustering of nuclear genes encoding mitochondrial and chloroplast proteins in Arabidopsis" Andrey Alexeyenko, A. Harvey Millar, James Whelan and Erik L.L. Sonnhammer TIG 22:589-593 (2006). [PDF]

"Overview and comparison of ortholog databases" Andrey Alexeyenko, Julia Lindberg, Asa Perez-Bercoff, Erik L.L. Sonnhammer Drug Discovery Today: Technologies; 3:137-143 (2006). [PDF]

"Automatic clustering of orthologs and inparalogs shared by multiple proteomes." Alexeyenko A, Tamas I, Liu G, Sonnhammer EL. Bioinformatics; 22(14):e9-e15 (2006). [PDF]

"Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment." Lassmann T, Sonnhammer EL. Nucleic Acids Res.; 34 (Web Server issue):W596-9 (2006). [PDF]

"Prediction of function divergence in protein families using the substitution rate variation parameter alpha." Abhiman S, Daub CO, Sonnhammer EL. Mol Biol Evol.; 23(7):1406-13 (2006). [PDF]

"NovelFam3000 - Uncharacterized human protein domains conserved across model organisms." Kemmer D, Podowski RM, Arenillas D, Lim J, Hodges E, Roth P, Sonnhammer EL, Hoog C, Wasserman WW. BMC Genomics.; 7(1):48 (2006). [PDF]

"A general model of G protein-coupled receptor sequences and its application to detect remote homologs." Wistrand M, Kall L, Sonnhammer EL. Protein Sci.; 15(3):509-521 (2006). [PDF]

"Pfam: clans, web tools and services." Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A. Nucleic Acids Res;34(Database issue):D247-51.(2006) [PDF]

2005

"Automatic assessment of alignment quality." Timo Lassmann, Erik L.L. Sonnhammer Nucleic Acids Res;33(22):7120-7128.(2005) [PDF]

"Kalign--an accurate and fast multiple sequence alignment algorithm." Timo Lassmann, Erik L.L. Sonnhammer BMC Bioinformatics;6:298 (2005) [PDF]

"Assessment of Protein Distance Measures and Tree-Building Methods for Phylogenetic Tree Reconstruction." Hollich Volker, Milchert Lena, Arvestad Lars, Erik L.L. Sonnhammer Mol Biol Evol 22:2257-2264 (2005) [PDF]

"Large-scale prediction of function shift in protein families with a focus on enzymatic function." Abhiman S, Erik L.L. Sonnhammer Proteins 60:758-768 (2005) [PDF]

"An HMM posterior decoder for sequence feature prediction that includes homology information." Lukas Käll, Anders Krogh, and Erik L.L. Sonnhammer Bioinformatics 21 Suppl 1:i251-i257 (2005) [PDF]

"A novel transmembrane topology of presenilin based on reconciling experimental and computational evidence" Anna Henricson, Lukas Käll, and Erik L.L. Sonnhammer FEBS J. 272:2727-2733 (2005) [PDF]

"Scoredist: A simple and robust protein sequence distance estimator" Erik LL Sonnhammer and Volker Hollich BMC Bioinformatics 6:108 (2005) [PDF]

"Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER" Wistrand M and Sonnhammer ELL BMC Bioinformatics 6:99 (2005) [PDF]

"Inparanoid: A Comprehensive Database of Eukaryotic Orthologs" O'Brien Kevin P, Remm Maido and Sonnhammer Erik L.L NAR 33:D476-D480 (2005) [PDF]

"FunShift: A Database of Function Shift Analysis on Protein Subfamilies" S. Abhiman and Erik L.L. Sonnhammer NAR 33:D197-D200 (2005) [PDF]

"siRNAdb: A Database of siRNA Sequences" Chalk Alistair M, Warfvinge Richard E, Georgii-Hemming Patrick, Sonnhammer Erik LL NAR 33:D131-D134 (2005) [PDF]

"Transmembrane topology prediction" Lukas Kall and Erik Sonnhammer In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, edited by Jorde, Little, Dunn and Subramaniam, Wiley & Sons, Ltd. (2005)

2004

"Exploring the Foundation of Genomics: A Northern Blot Reference Set for the Comparative Analysis of Transcript Profiling Technologies" D. Kemmer, M Faxen, E Hodges, J Lim, E Herzog, E Ljungström, A Lundmark, M K Olsen, R Podowski, E.L.L. Sonnhammer, P Nilsson, M Reimers, B Lenhard, S L. Roberds, C Wahlestedt, C Höög, P Agarwal, and W.W. Wasserman Comparative and Functional Genomics, 5:584-595 (2004) [PDF]

"Genome Informatics: taming the avalanche of genomic data" Erik L.L. Sonnhammer Genome Biology 6:301 (2005) [PDF]

"Functional characterization in Caenorhabditis elegans of transmembrane worm-human orthologs" Henricson A, Sonnhammer EL, Baillie DL, Vaz Gomes A. BMC Genomics 5:85 (2004) [PDF]

"Conspicuous accumulation of transcription elongation repressor hrp130/CA150 on the intron-rich Balbiani ring 3 gene." Sun X, Zhao J, Kylberg K, Soop T, Palka K, Sonnhammer E, Visa N, Alzhanova-Ericsson AT, Daneholt B. Chromosoma 113:244-257 (2004) [PDF]

"Profiled support vector machines for antisense oligonucleotide efficacy prediction." Camps-Valls G, Chalk AM, Serrano-Lopez AJ, Martin-Guerrero JD, Sonnhammer EL. BMC Bioinformatics 5:135 (2004) [PDF]

"Sfixem--graphical sequence feature display in Java" Chalk AM, Wennerberg M, Sonnhammer ELL. Bioinformatics 20:2488-2490 (2004) [PDF]

"OrthoDisease: a database of human disease orthologs" O'Brien KP, Westerlund I, Sonnhammer ELL Human Mutation 24:112-119 (2004) [PDF]

"Improved and automated prediction of effective siRNA" Alistair M. Chalk, Claes Wahlestedt and Erik L.L. Sonnhammer BBRC 319:264-274 (2004) [PDF]

"A combined transmembrane topology and signal peptide prediction method" Lukas Käll, Anders Krogh and Erik L.L. Sonnhammer J. Mol. Biol. 338:1027-1036 (2004) [PDF]

"Improving Profile HMM Discrimination by Adapting Transition Probabilities" Markus Wistrand and Erik L.L. Sonnhammer J. Mol. Biol. 338:847-854 (2004) [PDF]

"Transition priors for protein hidden Markov models: An empirical study towards maximum discrimination" Markus Wistrand and Erik L.L. Sonnhammer J. Computational Biology 11:181-194 (2004) [PDF]

"ChromoWheel: a new spin on eukaryotic chromosome visualization" Sven Ekdahl and Erik L.L. Sonnhammer Bioinformatics 20:576-577 (2004) [PDF]

"The Pfam protein families database" 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. Nucleic Acids Res. 32:D138-D141 (2004) [PDF]

2003

"Gene expression profiling of cells, tissues, and developmental stages of the nematode C. elegans" McKay SJ, et al. Cold Spring Harb Symp Quant Biol. 68:159-169. (2003) [PDF]

"Comprehensive analysis of orthologous protein domains using the HOPS database" Christian E.V. Storm and Erik L.L. Sonnhammer Genome Research 13:2353-2362 (2003) [PDF]

"Genomic Gene Clustering Analysis of Pathways in Eukaryotes" Lee JM, Erik L.L. Sonnhammer Genome Research 13:875-882 (2003) [PDF] Erratum for Genome Research 13:875-882 (2003) [PDF]

2002

"Reliability of transmembrane predictions in whole-genome data" Lukas Käll and Erik L.L. Sonnhammer FEBS Letters 532:415-418 (2002) [PDF]

"Orthology, paralogy and proposed classification for paralog subtypes" Sonnhammer EL, Koonin EV. Trends Genet. 18(12):619-20 (2002) [PDF]

"Computational Antisense Oligo Prediction with a Neural Network Model" Alistair Chalk and Erik L.L. Sonnhammer Bioinformatics 18:1567-1575 (2002) [PDF]

"Quality assessment of multiple alignment programs" Lassmann T, Sonnhammer EL. FEBS Lett. 529(1):126-30 (2002) [PDF]

"OrthoGUI: graphical presentation of Orthostrapper results" Hollich V, Storm CE, Sonnhammer EL. Bioinformatics. 18(9):1272-3 (2002) [PDF]

"Automated ortholog inference from phylogenetic trees and calculation of orthology reliability" Christian Storm and Erik Sonnhammer Bioinformatics 18:92-99 (2002) [PDF]

"The Pfam protein families database" Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL. Nucleic Acids Res. 30:276-280 (2002) [PDF]

2001

"Automatic clustering of orthologs and in-paralogs from pairwise species comparisons" Maido Remm, Christian E. V. Storm, and Erik L. L. Sonnhammer J. Mol. Biol. 314:1041-1052 (2001) [PDF]

"Integrated graphical analysis of protein sequence features predicted from sequence composition" Erik L.L. Sonnhammer and John C. Wootton Proteins 45:262-273 (2001) [PDF]

Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes. Anders Krogh, Björn Larsson, Gunnar von Heijne, and Erik L.L. Sonnhammer J. Mol. Biol. 305:567-580 (2001) [PDF]

"NIFAS:Visual analysis of domain structure evolution" Christian Storm and Erik L.L. Sonnhammer Bioinformatics 17:343-348 (2001) [PDF]

"MEDUSA: Large scale automatic selection and visual assessment of PCR primer pairs." Raf Podowski and Erik L.L. Sonnhammer Bioinformatics 17:656-657 (2001) [PDF]

2000

"Classification of Transmembrane Protein Families in the Caenorhabditis elegans Genome and Identification of Human Orthologs" Maido Remm and Erik Sonnhammer Genome Research 10:1679-1689 (2000) [PDF]

"Assignment of the GPR14 gene coding for the G-protein-coupled receptor 14 to human chromosome 17q25.3 by fluorescent in situ hybridization" Protopopov A, Kashuba V, Podowski R, Gizatullin R, Sonnhammer E, Wahlestedt C, Zabarovsky ER Cytogenet Cell Genet 88:312-313 (2000)

"FAT: a novel domain in PIK-related kinases." Bosotti R, Isacchi A, Sonnhammer EL. Trends Biochem Sci. 25:225-227 (2000) [PDF]

"The Pfam protein families database." Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, Sonnhammer EL. Nucleic Acids Res. 28:263-266 (2000) [PDF]

"Putative regulatory domains in the human and mouse CVADR genes" Bjorn Andersson, Richard Tomko, Kimberly Andersson, Momina Mizra, Hamid Darban, Delal Oncu, Erik Sonnhammer, Kerstin Sollerbrant, Lennart Philipson. Gene Function and Disease 2:82-86 (2000)

1999

"A comparison of sequence and structure protein domain families as a basis for structural genomics" Arne Elofsson and Erik L. L. Sonnhammer Bioinformatics 15:480-500 (1999) [PDF]

"Identification of Motifs in Protein Sequences" Erik L.L. Sonnhammer and Tyra G. Wolfsberg In Current Protocols in Cell Biology, ed. J. Bonifacino (1999)

"Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins" Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Robert D. Finn, and Erik L.L. Sonnhammer Nucleic Acids Res. 27:260-262 (1999) [PDF]

1998

"Protein family databases for automated protein domain identification" Erik L.L. Sonnhammer Mathematical Modelling and Scientific Computing, 9:68-78 (1998) [PDF]

"A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences" Erik L.L. Sonnhammer, Gunnar von Heijne, and Anders Krogh. ISMB 6:175-182 (1998) [PDF]

"Dynamic contact maps of protein structures" Erik L.L. Sonnhammer and John C. Wootton J. Mol. Graphics and Modelling, 16:1-5, 33 (1998)

"Pfam: Multiple Sequence Alignments and HMM-Profiles of Protein Domains" Sonnhammer, E.L.L., Eddy, S.R., Birney, E., Bateman, A., Durbin, R. Nucleic Acids Research, 26:322-325 (1998) [PDF]

1997

"Analysis of protein domain families in Caenorhabditis elegans" Sonnhammer, E.L.L. and Durbin, R. Genomics, 46:200-216 (1997)

"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" Corbett, S.J., Tomlinson, I.M., Sonnhammer, E.L.L., Buck, D., Winter, G. J. Mol. Biol. 270:587-597 (1997)

"Widespread eukaryotic sequences, highly similar to bacterial DNA polymerase I, looking for functions" Sonnhammer, E.L.L. and Wootton, J.C. Current Biology, 7:R463-R465 (1997)

"Pfam: a Comprehensive Database of Protein Domain Families Based on Seed Alignments" Sonnhammer, E.L.L., Eddy, S.R. and Durbin, R. Proteins, 28:405-420 (1997) [PDF]

1996

"The imprint of Somatic Hypermutation on the Repertoire of Human Germline V Genes" Tomlinson I.M., Walter G., Jones, P.T., Dear P.H., Sonnhammer E.L.L. and Winter G. J. Mol. Biol. 256:813-817 (1996)

"The C. elegans expression pattern database: a beginning" Hope I.A., Albertson, D.G., Martinelli, S.D., Lynch, A.S., Sonnhammer, E., Durbin, R. Trends in Genetics, 12:370-371 (1996)

1995

"A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis" Sonnhammer, E.L.L. and Durbin, R. Gene 167: GC1-10 (1995) [PDF]

"Comparison of the human germline and rearranged V-H repertoire reveals complementarity between germline variability and somatic mutation" Walter, G., Tomlinson, I.M., Dear, P.H., Sonnhammer, E.L.L., Cook, G.P. and Winter, G. Annals of the New York Academy of Sciences, 764:180-182 (1995)

1994

"A workbench for large-scale sequence homology analysis" Sonnhammer, E.L.L. and Durbin, R. Comput. Appl. Biosci. 10:301-307 (1994) [PDF]

"Modular arrangement of proteinvs as inferred from analysis of homology" Sonnhammer, E.L.L. and Kahn, D. Protein Science 3:482-492 (1994) [PDF]

"An expert system for processing sequence homology data" Sonnhammer, E.L.L. and Durbin, R. ISMB 2:363-368 (1994)

"Volume changes in Protein evolution. Appendix: A Method to Weight Protein Sequences to Correct for Unequal Representation" Gerstein, M., Sonnhammer, E.L.L. and Chothia, C. J. Mol. Biol. 236:1067-1078 (1994) [PDF]

"2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans" R. Wilson, R. Ainscough, K. Anderson, C. Baynes, M. Berks, J. Bonfield, J. Burton, M. Connell, T. Copsey, J. Cooper, A. Coulson, M. Craxton, S. Dear, Z. Du, R. Durbin, A. Favello, A. Fraser, L. Fulton, A. Gardner, P. Green, T. Hawkins, L. Hillier, M. Jier, L. Johnston, M. Jones, J. Kershaw, J. Kirsten, N. Laisster, P. Latreille, J. Lightning, C. Lloyd, B. Mortimore, M. O'Callaghan, J. Parsons, C. Percy, L. Rifken, A. Roopra, D. Saunders, R. Shownkeen, M. Sims, N. Smaldon, A. Smith, M. Smith, E. Sonnhammer, R. Staden, J. Sulston, J. Thierry-Mieg, K. Thomas, M. Vaudin, K. Vaughan, R. Waterston, A. Watson, L. Weinstock, J. Wilkinson-Sproat & P. Wohldman Nature 368:32-38 (1994)

1992

"Comprehensive analysis of the 182 predicted open reading frames of yeast chromosome III" Bork P., Ouzounis C., Sander C., Sonnhammer E.L.L., Scharf M. and Schneider R. Protein Science 1:1677-1690 (1992)

"What's in a genome?" Bork P., Ouzounis C., Sander C., Scharf M., Schneider R. and Sonnhammer E.L.L. Nature 358:287-287 (1992)

"METASIM: Object Oriented Modelling of Cell Regulation" Stoffers H.J., Sonnhammer E.L.L., Blommestijn G.J.F., Raat H.N.J. and Westerhoff H.V. Comput. Appl. Biosci. 8:443-449 (1992)