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ORCIDErik L. L. Sonnhammer
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2020 – today
- 2022
[j73]Thomas Hillerton
, Deniz Seçilmis, Sven Nelander, Erik L. L. Sonnhammer:
Fast and accurate gene regulatory network inference by normalized least squares regression. Bioinform. 38(8): 2263-2268 (2022)- [j72]Emma Persson, Erik L. L. Sonnhammer:
InParanoid-DIAMOND: faster orthology analysis with the InParanoid algorithm. Bioinform. 38(10): 2918-2919 (2022) - [j71]Deniz Seçilmis, Thomas Hillerton, Erik L. L. Sonnhammer:
GRNbenchmark - a web server for benchmarking directed gene regulatory network inference methods. Nucleic Acids Res. 50(W1): 398-404 (2022) - [j70]Yannis Nevers, Tamsin E. M. Jones, Dushyanth Jyothi, Bethan Yates, Meritxell Ferret, Laura Portell-Silva, Laia Codó, Salvatore Cosentino, Marina Marcet-Houben, Anna Vlasova, Laetitia Poidevin, Arnaud Kress, Mark Hickman, Emma Persson, Ivana Pilizota, Cristina Guijarro-Clarke, Adrian M. Altenhoff, Elspeth A. Bruford, Christophe Dessimoz, Ingo Ebersberger, David M. Emms, Toni Gabaldón, Natasha M. Glover, Yanhui Hu, Wataru Iwasaki, Odile Lecompte, Benjamin Linard, María J. Martín, David S. Roos, Erik Sonhammer, Paul D. Thomas, David Thybert, Klaas Vandepoele, Salvador Capella-Gutiérrez, Asier Gonzalez-Uriarte, Javier Garrayo-Ventas, Dmitry Repchevsky, Vicky Sundesha, Erik L. L. Sonnhammer:
The Quest for Orthologs orthology benchmark service in 2022. Nucleic Acids Res. 50(W1): 623-632 (2022) - 2021
- [j69]Deniz Seçilmis, Thomas Hillerton, Sven Nelander, Erik L. L. Sonnhammer:
Inferring the experimental design for accurate gene regulatory network inference. Bioinform. 37(20): 3553-3559 (2021) - [j68]Jaina Mistry, Sara Chuguransky, Lowri Williams, Matloob Qureshi, Gustavo A. Salazar, Erik L. L. Sonnhammer, Silvio C. E. Tosatto, Lisanna Paladin, Shriya Raj, Lorna J. Richardson, Robert D. Finn, Alex Bateman:
Pfam: The protein families database in 2021. Nucleic Acids Res. 49(Database-Issue): D412-D419 (2021) - 2020
- [j67]Dimitri Guala, Christoph Ogris, Nikola Müller, Erik L. L. Sonnhammer:
Genome-wide functional association networks: background, data & state-of-the-art resources. Briefings Bioinform. 21(4): 1224-1237 (2020) - [j66]Adrian M. Altenhoff, Javier Garrayo-Ventas, Salvatore Cosentino, David Emms, Natasha M. Glover, Ana Hernández-Plaza, Yannis Nevers, Vicky Sundesha, Damian Szklarczyk, José María Fernández, Laia Codó, The Quest for Orthologs Consortium, Josep Lluis Gelpí, Jaime Huerta-Cepas, Wataru Iwasaki, Steven Kelly, Odile Lecompte, Matthieu Muffato, Maria Jesus Martin, Salvador Capella-Gutiérrez, Paul D. Thomas, Erik L. L. Sonnhammer, Christophe Dessimoz:
The Quest for Orthologs benchmark service and consensus calls in 2020. Nucleic Acids Res. 48(Webserver-Issue): W538-W545 (2020)
2010 – 2019
- 2019
- [j65]Daniel Morgan, Andreas Tjärnberg, Torbjörn E. M. Nordling, Erik L. L. Sonnhammer:
A generalized framework for controlling FDR in gene regulatory network inference. Bioinform. 35(6): 1026-1032 (2019) - [j64]Emma Persson, Mateusz Kaduk, Sofia K. Forslund, Erik L. L. Sonnhammer:
Domainoid: domain-oriented orthology inference. BMC Bioinform. 20(1): 523:1-523:12 (2019) - [j63]Sara El-Gebali, Jaina Mistry, Alex Bateman, Sean R. Eddy, Aurelien Luciani, Simon C. Potter, Matloob Qureshi, Lorna J. Richardson, Gustavo A. Salazar, Alfredo Smart, Erik L. L. Sonnhammer, Layla Hirsh, Lisanna Paladin, Damiano Piovesan, Silvio C. E. Tosatto, Robert D. Finn:
The Pfam protein families database in 2019. Nucleic Acids Res. 47(Database-Issue): D427-D432 (2019) - 2018
- [j62]Kristoffer Forslund, Cécile Pereira, Salvador Capella-Gutiérrez, Alan W. Sousa da Silva, Adrian M. Altenhoff, Jaime Huerta-Cepas, Matthieu Muffato, Mateus Patricio, Klaas Vandepoele, Ingo Ebersberger, Judith A. Blake, Jesualdo Tomás Fernández-Breis, The Quest for Orthologs Consortium, Brigitte Boeckmann, Toni Gabaldón, Erik L. L. Sonnhammer, Christophe Dessimoz, Suzanna Lewis:
Gearing up to handle the mosaic nature of life in the quest for orthologs. Bioinform. 34(2): 323-329 (2018) - [j61]Christoph Ogris, Dimitri Guala, Mateusz Kaduk, Erik L. L. Sonnhammer:
FunCoup 4: new species, data, and visualization. Nucleic Acids Res. 46(Database-Issue): D601-D607 (2018) - 2017
- [j60]Mateusz Kaduk, Erik L. L. Sonnhammer:
Improved orthology inference with Hieranoid 2. Bioinform. 33(8): 1154-1159 (2017) - [j59]Mateusz Kaduk, Christian Riegler, Oliver Lemp, Erik L. L. Sonnhammer:
HieranoiDB: a database of orthologs inferred by Hieranoid. Nucleic Acids Res. 45(Database-Issue): D687-D690 (2017) - 2016
- [j58]Christian Haider, Marina Kavic, Erik L. L. Sonnhammer:
TreeDom: a graphical web tool for analysing domain architecture evolution. Bioinform. 32(15): 2384-2385 (2016) - [j57]Ganapathi Varma Saripella, Erik L. L. Sonnhammer, Kristoffer Forslund:
Benchmarking the next generation of homology inference tools. Bioinform. 32(17): 2636-2641 (2016) - [j56]Christoph Ogris, Thomas Helleday, Erik L. L. Sonnhammer:
PathwAX: a web server for network crosstalk based pathway annotation. Nucleic Acids Res. 44(Webserver-Issue): W105-W109 (2016) - 2015
- [j55]Erik L. L. Sonnhammer, Gabriel Östlund:
InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic. Nucleic Acids Res. 43(Database-Issue): 234-239 (2015) - 2014
- [j54]Matthew Studham, Andreas Tjärnberg, Torbjörn E. M. Nordling, Sven Nelander, Erik L. L. Sonnhammer:
Functional association networks as priors for gene regulatory network inference. Bioinform. 30(12): 130-138 (2014) - [j53]Dimitri Guala, Erik Sjölund, Erik L. L. Sonnhammer:
MaxLink: network-based prioritization of genes tightly linked to a disease seed set. Bioinform. 30(18): 2689-2690 (2014) - [j52]Erik L. L. Sonnhammer, Toni Gabaldón, Alan W. Sousa da Silva, Maria Jesus Martin, Marc Robinson-Rechavi, Brigitte Boeckmann, Paul D. Thomas, Christophe Dessimoz, The Quest for Orthologs Consortium:
Big data and other challenges in the quest for orthologs. Bioinform. 30(21): 2993-2998 (2014) - [j51]Robert D. Finn, Alex Bateman, Jody Clements, Penelope Coggill, Ruth Y. Eberhardt, Sean R. Eddy, Andreas Heger, Kirstie Hetherington, Liisa Holm, Jaina Mistry, Erik L. L. Sonnhammer, John G. Tate, Marco Punta:
Pfam: the protein families database. Nucleic Acids Res. 42(Database-Issue): 222-230 (2014) - [j50]Thomas Schmitt, Christoph Ogris, Erik L. L. Sonnhammer:
FunCoup 3.0: database of genome-wide functional coupling networks. Nucleic Acids Res. 42(Database-Issue): 380-388 (2014) - 2013
- [j49]Andreas Tjärnberg, Torbjörn E. M. Nordling, Matthew Studham, Erik L. L. Sonnhammer:
Optimal Sparsity Criteria for Network Inference. J. Comput. Biol. 20(5): 398-408 (2013) - 2012
- [j48]Christophe Dessimoz, Toni Gabaldón, David S. Roos, Erik L. L. Sonnhammer, Javier Herrero:
Toward community standards in the quest for orthologs. Bioinform. 28(6): 900-904 (2012) - [j47]Marco Punta, Penny C. Coggill, Ruth Y. Eberhardt, Jaina Mistry, John G. Tate, Chris Boursnell, Ningze Pang, Kristoffer Forslund, Goran Ceric, Jody Clements, Andreas Heger, Liisa Holm, Erik L. L. Sonnhammer, Sean R. Eddy, Alex Bateman, Robert D. Finn:
The Pfam protein families database. Nucleic Acids Res. 40(Database-Issue): 290-301 (2012) - [j46]Andrey Alexeyenko, Thomas Schmitt, Andreas Tjärnberg, Dimitri Guala, Oliver Frings, Erik L. L. Sonnhammer:
Comparative interactomics with Funcoup 2.0. Nucleic Acids Res. 40(Database-Issue): 821-828 (2012) - 2011
- [j45]Kristoffer Forslund, Fabian Schreiber, Nattaphon Thanintorn, Erik L. L. Sonnhammer:
OrthoDisease: tracking disease gene orthologs across 100 species. Briefings Bioinform. 12(5): 463-473 (2011) - [j44]Thomas Schmitt, David N. Messina, Fabian Schreiber, Erik L. L. Sonnhammer:
Letter to the Editor: SeqXML and OrthoXML: standards for sequence and orthology information. Briefings Bioinform. 12(5): 485-488 (2011) - [j43]Kristoffer Forslund, Isabella Pekkari, Erik L. L. Sonnhammer:
Domain architecture conservation in orthologs. BMC Bioinform. 12: 326 (2011) - 2010
- [j42]Gabriel Östlund, Thomas Schmitt, Kristoffer Forslund, Tina Köstler, David N. Messina, Sanjit Roopra, Oliver Frings, Erik L. L. Sonnhammer:
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res. 38(Database-Issue): 196-203 (2010) - [j41]Robert D. Finn, Jaina Mistry, John G. Tate, Penny C. Coggill, Andreas Heger, Joanne E. Pollington, O. Luke Gavin, Prasad Gunasekaran, Goran Ceric, Kristoffer Forslund, Liisa Holm, Erik L. L. Sonnhammer, Sean R. Eddy, Alex Bateman:
The Pfam protein families database. Nucleic Acids Res. 38(Database-Issue): 211-222 (2010)
2000 – 2009
- 2009
- [j40]Kristoffer Forslund, Erik L. L. Sonnhammer:
Predicting protein function from domain content. Bioinform. 25(9): 1214 (2009) - [j39]David N. Messina, Erik L. L. Sonnhammer:
DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System. Bioinform. 25(10): 1333-1334 (2009) - [j38]Kristoffer Forslund, Erik L. L. Sonnhammer:
Benchmarking homology detection procedures with low complexity filters. Bioinform. 25(19): 2500-2505 (2009) - [j37]Patrik Björkholm, Erik L. L. Sonnhammer:
Comparative analysis and unification of domain-domain interaction networks. Bioinform. 25(22): 3020-3025 (2009) - [j36]Martin Klammer, David N. Messina, Thomas Schmitt, Erik L. L. Sonnhammer:
MetaTM - a consensus method for transmembrane protein topology prediction. BMC Bioinform. 10: 314 (2009) - 2008
- [j35]Alistair M. Chalk, Erik L. L. Sonnhammer:
siRNA specificity searching incorporating mismatch tolerance data. Bioinform. 24(10): 1316-1317 (2008) - [j34]Martin Klammer, Sanjit Roopra, Erik L. L. Sonnhammer:
jSquid: a Java applet for graphical on-line network exploration. Bioinform. 24(12): 1467-1468 (2008) - [j33]Kristoffer Forslund, Erik L. L. Sonnhammer:
Predicting protein function from domain content. Bioinform. 24(15): 1681-1687 (2008) - [j32]Kristoffer Forslund, Erik L. L. Sonnhammer:
Predicting protein function from domain content. Bioinform. 24(19): 2275 (2008) - [j31]Carsten O. Daub, Erik L. L. Sonnhammer:
Employing conservation of co-expression to improve functional inference. BMC Syst. Biol. 2: 81 (2008) - [j30]Ann-Charlotte Berglund, Erik Sjölund, Gabriel Östlund, Erik L. L. Sonnhammer:
InParanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res. 36(Database-Issue): 263-266 (2008) - [j29]Robert D. Finn, John G. Tate, Jaina Mistry, Penny C. Coggill, Stephen John Sammut, Hans-Rudolf Hotz, Goran Ceric, Kristoffer Forslund, Sean R. Eddy, Erik L. L. Sonnhammer, Alex Bateman:
The Pfam protein families database. Nucleic Acids Res. 36(Database-Issue): 281-288 (2008) - 2007
- [j28]Volker Hollich, Erik L. L. Sonnhammer:
PfamAlyzer: domain-centric homology search. Bioinform. 23(24): 3382-3383 (2007) - [j27]Timo Lassmann, Erik L. L. Sonnhammer:
Automatic extraction of reliable regions from multiple sequence alignments. BMC Bioinform. 8(S-5) (2007) - [j26]Lukas Käll, Anders Krogh, Erik L. L. Sonnhammer:
Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server. Nucleic Acids Res. 35(Web-Server-Issue): 429-432 (2007) - 2006
- [j25]Robert D. Finn, Jaina Mistry, Benjamin Schuster-Böckler, Sam Griffiths-Jones, Volker Hollich, Timo Lassmann, Simon Moxon, Mhairi Marshall, Ajay Khanna, Richard Durbin, Sean R. Eddy, Erik L. L. Sonnhammer, Alex Bateman:
Pfam: clans, web tools and services. Nucleic Acids Res. 34(Database-Issue): 247-251 (2006) - [j24]Timo Lassmann, Erik L. L. Sonnhammer:
Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment. Nucleic Acids Res. 34(Web-Server-Issue): 596-599 (2006) - [c4]Andrey Alexeyenko, Ivica Tamas, Gang Liu, Erik L. L. Sonnhammer:
Automatic clustering of orthologs and inparalogs shared by multiple proteomes. ISMB (Supplement of Bioinformatics) 2006: 9-15 - 2005
- [j23]Markus Wistrand, Erik L. L. Sonnhammer:
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER. BMC Bioinform. 6: 99 (2005) - [j22]Erik L. L. Sonnhammer, Volker Hollich:
Scoredist: A simple and robust protein sequence distance estimator. BMC Bioinform. 6: 108 (2005) - [j21]Timo Lassmann, Erik L. L. Sonnhammer:
Kalign - an accurate and fast multiple sequence alignment algorithm. BMC Bioinform. 6: 298 (2005) - [j20]Alistair M. Chalk, Richard E. Warfinge, Patrick Georgii-Hemming, Erik L. L. Sonnhammer:
siRNAdb: a database of siRNA sequences. Nucleic Acids Res. 33(Database-Issue): 131-134 (2005) - [j19]Saraswathi Abhiman, Erik L. L. Sonnhammer:
FunShift: a database of function shift analysis on protein subfamilies. Nucleic Acids Res. 33(Database-Issue): 197-200 (2005) - [j18]Kevin P. O'Brien, Maido Remm, Erik L. L. Sonnhammer:
Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res. 33(Database-Issue): 476-480 (2005) - [c3]Lukas Käll, Anders Krogh, Erik L. L. Sonnhammer:
An HMM posterior decoder for sequence feature prediction that includes homology information. ISMB (Supplement of Bioinformatics) 2005: 251-257 - 2004
- [j17]Sven Ekdahl, Erik L. L. Sonnhammer:
ChromoWheel: a new spin on eukaryotic chromosome visualization. Bioinform. 20(4): 576-577 (2004) - [j16]Alistair M. Chalk, Martin Wennerberg, Erik L. L. Sonnhammer:
Sfixem - graphical sequence feature display in Java. Bioinform. 20(15): 2488-2490 (2004) - [j15]Gustavo Camps-Valls, Alistair M. Chalk, Antonio J. Serrano-López, José David Martín-Guerrero, Erik L. L. Sonnhammer:
Profiled support vector machines for antisense oligonucleotide efficacy prediction. BMC Bioinform. 5: 135 (2004) - [j14]Markus Wistrand, Erik L. L. Sonnhammer:
Transition Priors for Protein Hidden Markov Models: An Empirical Study towards Maximum Discrimination. J. Comput. Biol. 11(1): 181-193 (2004) - [j13]Alex Bateman, Lachlan James M. Coin, Richard Durbin, Robert D. Finn, Volker Hollich, Sam Griffiths-Jones, Ajay Khanna, Mhairi Marshall, Simon Moxon, Erik L. L. Sonnhammer, David J. Studholme, Corin Yeats, Sean R. Eddy:
The Pfam protein families database. Nucleic Acids Res. 32(Database-Issue): 138-141 (2004) - 2002
- [j12]Christian E. V. Storm, Erik L. L. Sonnhammer:
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinform. 18(1): 92-99 (2002) - [j11]Volker Hollich, Christian E. V. Storm, Erik L. L. Sonnhammer:
OrthoGUI: graphical presentation of Orthostrapper results. Bioinform. 18(9): 1272-1273 (2002) - [j10]Alistair M. Chalk, Erik L. L. Sonnhammer:
Computational antisense oligo prediction with a neural network model. Bioinform. 18(12): 1567-1575 (2002) - [j9]Alex Bateman, Ewan Birney, Lorenzo Cerutti, Richard Durbin, Laurence Ettwiller, Sean R. Eddy, Sam Griffiths-Jones, Kevin L. Howe, Mhairi Marshall, Erik L. L. Sonnhammer:
The Pfam Protein Families Database. Nucleic Acids Res. 30(1): 276-280 (2002) - 2001
- [j8]Christian E. V. Storm, Erik L. L. Sonnhammer:
NIFAS: visual analysis of domain evolution in proteins. Bioinform. 17(4): 343-348 (2001) - [j7]Raf M. Podowski, Erik L. L. Sonnhammer:
MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs. Bioinform. 17(7): 656-657 (2001) - 2000
- [j6]Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Kevin L. Howe, Erik L. L. Sonnhammer:
The Pfam Protein Families Database. Nucleic Acids Res. 28(1): 263-266 (2000)
1990 – 1999
- 1999
- [j5]Arne Elofsson, Erik L. L. Sonnhammer:
A comparison of sequence and structure protein domain families as a basis for structural genomics. Bioinform. 15(6): 480-500 (1999) - [j4]Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Robert D. Finn, Erik L. L. Sonnhammer:
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res. 27(1): 260-262 (1999) - 1998
- [j3]Erik L. L. Sonnhammer, Sean R. Eddy, Ewan Birney, Alex Bateman, Richard Durbin:
Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res. 26(1): 320-322 (1998) - [c2]Erik L. L. Sonnhammer, Gunnar von Heijne, Anders Krogh:
A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences. ISMB 1998: 175-182 - 1994
- [j2]Erik L. L. Sonnhammer, Richard Durbin:
A workbench for large-scale sequence homology analysis. Comput. Appl. Biosci. 10(3): 301-307 (1994) - [c1]Erik L. L. Sonnhammer, Richard Durbin:
An Expert System for Processing Sequence Homology Data. ISMB 1994: 363-368 - 1992
- [j1]H. J. Stoffers, Erik L. L. Sonnhammer, G. J. Blommestijn, N. J. Raat, Hans V. Westerhoff:
METASIM: object-oriented modelling of cell regulation. Comput. Appl. Biosci. 8(5): 443-449 (1992)
Coauthor Index
Sofia K. Forslund
aka: Kristoffer Forslund
aka: Kristoffer Forslund
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