Directory of (p)reprints
For a list of papers in Medline, click here
Google scholar profile
 2019
"Domainoid: domain-oriented orthology inference"
Persson E, Kaduk M, Forslund SK, Sonnhammer ELL.
BMC Bioinformatics 20:523 (2019) [PDF]
"Genome-wide functional association networks: background, data & state-of-the-art resources"
Guala D, Ogris C, Mueller N, Sonnhammer ELL.
Brief Bioinform. In press (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]
 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]
 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]
 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 Theses: Exploring the Boundaries of Gene Regulatory Network Inference, by Andreas Tjärnberg

 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: