Directory of (p)reprints
For a list of papers in Medline, click here
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"Gearing up to handle the mosaic nature of life in the quest for orthologs"
in press (2018) [PDF]
"FunCoup 4: new species, data, and visualization"
Ogris C, Guala D, Kaduk M, Sonnhammer ELL.
46:D601-D607 (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]
"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]
"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]
"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

"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)
"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)
"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)
"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)
"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]
"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]
"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]
"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]
"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]
"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]
"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]
"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]
"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]
"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]
"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]
"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]
"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]

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