Works matching AU Sonnhammer, Erik L. L.

Results: 93

A comparison of sequence and structure protein domain families as a basis for structural genomics.

Published in:

Bioinformatics, 1999, v. 15, n. 6, p. 480, doi. 10.1093/bioinformatics/15.6.480

By:

Elofsson, Arne;
Sonnhammer, Erik L. L.

Publication type:

Article

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.

Published in:

Nucleic Acids Research, 2010, v. 38, p. D196, doi. 10.1093/nar/gkp931

By:

Östlund, Gabriel;
Schmitt, Thomas;
Forslund, Kristoffer;
Köstler, Tina;
Messina, David N.;
Roopra, Sanjit;
Frings, Oliver;
Sonnhammer, Erik L. L.

Publication type:

Article

Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features.

Published in:

Nucleic Acids Research, 2009, v. 37, n. 3, p. 858, doi. 10.1093/nar/gkn1006

By:

Lassmann, Timo;
Frings, Oliver;
Sonnhammer, Erik L. L.

Publication type:

Article

The Pfam protein families database.

Published in:

Nucleic Acids Research, 2008, v. 36, p. D281

By:

Finn, Robert D.;
Tate, John;
Mistry, Jaina;
Coggill, Penny C.;
Sammut, Stephen John;
Hotz, Hans-Rudolf;
Ceric, Goran;
Forslund, Kristoffer;
Eddy, Sean R.;
Sonnhammer, Erik L. L.;
Bateman, Alex

Publication type:

Article

InParanoid 6: eukaryotic ortholog clusters with inparalogs.

Published in:

Nucleic Acids Research, 2008, v. 36, p. D263

By:

Berglund, Ann-Charlotte;
Sjölund, Erik;
Östlund, Gabriel;
Sonnhammer, Erik L. L.

Publication type:

Article

Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment.

Published in:

Nucleic Acids Research, 2006, v. 34, n. 11, p. w596, doi. 10.1093/nar/gkl191

By:

Lassmann, Timo;
Sonnhammer, Erik L. L.

Publication type:

Article

Pfam: clans, web tools and services.

Published in:

Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d247, doi. 10.1093/nar/gkj149

By:

Finn, Robert D.;
Mistry, Jaina;
Schuster-Böckler, Benjamin;
Griffiths-Jones, Sam;
Hollich, Volker;
Lassmann, Timo;
Moxon, Simon;
Marshall, Mhairi;
Khanna, Ajay;
Durbin, Richard;
Eddy, Sean R.;
Sonnhammer, Erik L. L.;
Bateman, Alex

Publication type:

Article

Automatic assessment of alignment quality.

Published in:

Nucleic Acids Research, 2005, v. 33, n. 22, p. 7120, doi. 10.1093/nar/gki1020

By:

Lassmann, Timo;
Sonnhammer, Erik L. L.

Publication type:

Article

siRNAdb: a database of siRNA sequences.

Published in:

Nucleic Acids Research, 2005, v. 33, n. 5, p. 1737, doi. 10.1093/nar/gki294

By:

Chalk, Alistair M.;
Warfinge, Richard E.;
Georgii-Hemming, Patrick;
Sonnhammer, Erik L. L.

Publication type:

Article

siRNAdb: a database of siRNA sequences.

Published in:

Nucleic Acids Research, 2005, v. 33, n. suppl 1, p. d131

By:

Chalk, Alistair M.;
Warfinge, Richard E.;
Georgii-Hemming, Patrick;
Sonnhammer, Erik L. L.

Publication type:

Article

Inparanoid: a comprehensive database of eukaryotic orthologs.

Published in:

Nucleic Acids Research, 2005, v. 33, n. suppl 1, p. d476

By:

O'Brien, Kevin P.;
Remm, Maido;
Sonnhammer, Erik L. L.

Publication type:

Article

FunShift: a database of function shift analysis on protein subfamilies.

Published in:

Nucleic Acids Research, 2005, v. 33, n. suppl 1, p. d197

By:

Abhiman, Saraswathi;
Sonnhammer, Erik L. L.

Publication type:

Article

The Pfam protein families database.

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 1, p. d138

By:

Bateman, Alex;
Coin, Lachlan;
Durbin, Richard;
Finn, Robert D.;
Hollich, Volker;
Griffiths‐Jones, Sam;
Khanna, Ajay;
Marshall, Mhairi;
Moxon, Simon;
Sonnhammer, Erik L. L.;
Studholme, David J.;
Yeats, Corin;
Eddy, Sean R.

Publication type:

Article

The Pfam Protein Families Database.

Published in:

Nucleic Acids Research, 2002, v. 30, n. 1, p. 276, doi. 10.1093/nar/30.1.276

By:

Bateman, Alex;
Birney, Ewan;
Cerruti, Lorenzo;
Durbin, Richard;
Etwiller, Laurence;
Eddy, Sean R.;
Griffiths-Jones, Sam;
Howe, Kevin L.;
Marshall, Mhairi;
Sonnhammer, Erik L. L.

Publication type:

Article

The Pfam Protein Families Database.

Published in:

Nucleic Acids Research, 2000, v. 28, n. 1, p. 263, doi. 10.1093/nar/28.1.263

By:

Bateman, Alex;
Birney, Ewan;
Durbin, Richard;
Eddy, Sean R.;
Howe, Kevin L.;
Sonnhammer, Erik L. L.

Publication type:

Article

Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.

Published in:

Nucleic Acids Research, 1999, v. 27, n. 1, p. 260, doi. 10.1093/nar/27.1.260

By:

Bateman, Alex;
Birney, Ewan;
Durbin, Richard;
Eddy, Sean R.;
Finn, Robert D.;
Sonnhammer, Erik L. L.

Publication type:

Article

Domainoid: domain-oriented orthology inference.

Published in:

BMC Bioinformatics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12859-019-3137-2

By:

Persson, Emma;
Kaduk, Mateusz;
Forslund, Sofia K.;
Sonnhammer, Erik L. L.

Publication type:

Article

GeneSPIDER2: large scale GRN simulation and benchmarking with perturbed single-cell data.

Published in:

NAR Genomics & Bioinformatics, 2024, v. 6, n. 3, p. 1, doi. 10.1093/nargab/lqae121

By:

Garbulowski, Mateusz;
Hillerton, Thomas;
Morgan, Daniel;
Seçilmiş, Deniz;
Sonnhammer, Lisbet;
Tjärnberg, Andreas;
Nordling, Torbjörn E M;
Sonnhammer, Erik L L

Publication type:

Article

TOPAS, a network-based approach to detect disease modules in a top-down fashion.

Published in:

NAR Genomics & Bioinformatics, 2022, v. 4, n. 4, p. 1, doi. 10.1093/nargab/lqac093

By:

Buzzao, Davide;
Castresana-Aguirre, Miguel;
Guala, Dimitri;
Sonnhammer, Erik L L

Publication type:

Article

Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41598-020-70941-y

By:

Morgan, Daniel;
Studham, Matthew;
Tjärnberg, Andreas;
Weishaupt, Holger;
Swartling, Fredrik J.;
Nordling, Torbjörn E. M.;
Sonnhammer, Erik L. L.

Publication type:

Article

Pathway-specific model estimation for improved pathway annotation by network crosstalk.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-70239-z

By:

Castresana-Aguirre, Miguel;
Sonnhammer, Erik L. L.

Publication type:

Article

Employing conservation of co-expression to improve functional inference.

Published in:

BMC Systems Biology, 2008, v. 2, p. 1, doi. 10.1186/1752-0509-2-81

By:

Daub, Carsten O.;
Sonnhammer, Erik L. L.

Publication type:

Article

Uncovering cancer gene regulation by accurate regulatory network inference from uninformative data.

Published in:

NPJ Systems Biology & Applications, 2020, v. 6, n. 1, p. N.PAG, doi. 10.1038/s41540-020-00154-6

By:

Seçilmiş, Deniz;
Hillerton, Thomas;
Morgan, Daniel;
Tjärnberg, Andreas;
Nelander, Sven;
Nordling, Torbjörn E. M.;
Sonnhammer, Erik L. L.

Publication type:

Article

Network Analysis of Functional Genomics Data: Application to Avian Sex-Biased Gene Expression.

Published in:

Scientific World Journal, 2012, p. 1, doi. 10.1100/2012/130491

By:

Frings, Oliver;
Mank, Judith E.;
Alexeyenko, Andrey;
Sonnhammer, Erik L. L.

Publication type:

Article

Functional association networks as priors for gene regulatory network inference.

Published in:

2014

By:

Studham, Matthew E.;
Tjärnberg, Andreas;
Nordling, Torbjörn E.M.;
Nelander, Sven;
Sonnhammer, Erik L. L.

Publication type:

Product Review

Toward community standards in the quest for orthologs.

Published in:

Bioinformatics, 2012, v. 28, n. 6, p. 900

By:

Dessimoz, Christophe;
Gabaldón, Toni;
Roos, David S.;
Sonnhammer, Erik L. L.;
Herrero, Javier

Publication type:

Article

Comparative analysis and unification of domain–domain interaction networks.

Published in:

Bioinformatics, 2009, v. 25, n. 22, p. 3020, doi. 10.1093/bioinformatics/btp522

By:

Björkholm, Patrik;
Sonnhammer, Erik L. L.

Publication type:

Article

Benchmarking homology detection procedures with low complexity filters.

Published in:

Bioinformatics, 2009, v. 25, n. 19, p. 2500, doi. 10.1093/bioinformatics/btp446

By:

Forslund, Kristoffer;
Sonnhammer, Erik L. L.

Publication type:

Article

DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System.

Published in:

Bioinformatics, 2009, v. 25, n. 10, p. 1333, doi. 10.1093/bioinformatics/btp153

By:

David N. Messina;
Erik L. L. Sonnhammer

Publication type:

Article

Predicting protein function from domain content.

Published in:

Bioinformatics, 2009, v. 25, n. 9, p. 1214, doi. 10.1093/bioinformatics/btp186

By:

Kristoffer Forslund;
Erik L. L. Sonnhammer

Publication type:

Article

Predicting protein function from domain content.

Published in:

Bioinformatics, 2008, v. 24, n. 19, p. 2275, doi. 10.1093/bioinformatics/btn447

By:

Kristoffer Forslund;
Erik L. L. Sonnhammer

Publication type:

Article

Predicting protein function from domain content.

Published in:

Bioinformatics, 2008, v. 24, n. 15, p. 1681, doi. 10.1093/bioinformatics/btn312

By:

Kristoffer Forslund;
Erik L. L. Sonnhammer

Publication type:

Article

jSquid: a Java applet for graphical on-line network exploration.

Published in:

Bioinformatics, 2008, v. 24, n. 12, p. 1467, doi. 10.1093/bioinformatics/btn213

By:

Martin Klammer;
Sanjit Roopra;
Erik L. L. Sonnhammer

Publication type:

Article

siRNA specificity searching incorporating mismatch tolerance data.

Published in:

Bioinformatics, 2008, v. 24, n. 10, p. 1316, doi. 10.1093/bioinformatics/btn121

By:

Alistair M. Chalk;
Erik L. L. Sonnhammer

Publication type:

Article

An HMM posterior decoder for sequence feature prediction that includes homology information.

Published in:

Bioinformatics, 2005, v. 21, p. i251, doi. 10.1093/bioinformatics/bti1014

By:

Käll, Lukas;
Krogh, Anders;
Sonnhammer, Erik L. L.

Publication type:

Article

An HMM posterior decoder for sequence feature prediction that includes homology information.

Published in:

Bioinformatics, 2005, v. 21, n. 1, p. i251, doi. 10.1093/bioinformatics/bti1014

By:

Lukas Käll;
Anders Krogh;
Erik L. L. Sonnhammer

Publication type:

Article

Sfixem—graphical sequence feature display in Java.

Published in:

Bioinformatics, 2004, v. 20, n. 15, p. 2488, doi. 10.1093/bioinformatics/bth265

By:

Alistair M. Chalk;
Martin Wennerberg;
Erik L. L. Sonnhammer

Publication type:

Article

ChromoWheel: a new spin on eukaryotic chromosome visualization.

Published in:

Bioinformatics, 2004, v. 20, n. 4, p. 576, doi. 10.1093/bioinformatics/btg448

By:

Sven Ekdahl;
Erik L. L. Sonnhammer

Publication type:

Article

Computational antisense oligo prediction with a neural network model.

Published in:

Bioinformatics, 2002, v. 18, n. 12, p. 1567, doi. 10.1093/bioinformatics/18.12.1567

By:

Chalk, Alistair M.;
Sonnhammer, Erik L. L.

Publication type:

Article

OrthoGUI: graphical presentation of Orthostrapper results.

Published in:

Bioinformatics, 2002, v. 18, n. 9, p. 1272, doi. 10.1093/bioinformatics/18.9.1272

By:

Hollich, Volker;
Storm, Christian E. V.;
Sonnhammer, Erik L. L

Publication type:

Article

Automated ortholog inference from phylogenetic trees and calculation of orthology reliability.

Published in:

Bioinformatics, 2002, v. 18, n. 1, p. 92, doi. 10.1093/bioinformatics/18.1.92

By:

Storm, Christian E. V.;
Sonnhammer, Erik L. L.

Publication type:

Article

MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs.

Published in:

Bioinformatics, 2001, v. 17, n. 7, p. 656, doi. 10.1093/bioinformatics/17.7.656

By:

Podowski, Raf M.;
Sonnhammer, Erik L. L.

Publication type:

Article

NIFAS: visual analysis of domain evolution in proteins.

Published in:

Bioinformatics, 2001, v. 17, n. 4, p. 343, doi. 10.1093/bioinformatics/17.4.343

By:

Storm, Christian E. V.;
Sonnhammer, Erik L. L.

Publication type:

Article

Drug repurposing improves disease targeting 11-fold and can be augmented by network module targeting, applied to COVID-19.

Published in:

Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-99721-y

By:

Rivero-García, Inés;
Castresana-Aguirre, Miguel;
Guglielmo, Luca;
Guala, Dimitri;
Sonnhammer, Erik L. L.

Publication type:

Article

Pfam: multiple sequence alignments and HMM‐profiles of protein domains.

Published in:

Nucleic Acids Research, 1998, v. 26, n. 1, p. 322

By:

Sonnhammer, Erik L. L.;
Eddy, Sean R.;
Birney, Ewan;
Bateman, Alex;
Durbin, Richard

Publication type:

Article

Automatic extraction of reliable regions from multiple sequence alignments.

Published in:

BMC Bioinformatics, 2007, v. 8, p. S9, doi. 10.1186/1471-2105-8-S5-S9

By:

Lassmann, Timo;
Sonnhammer, Erik L. L.

Publication type:

Article

Domain Tree-Based Analysis of Protein Architecture Evolution.

Published in:

Molecular Biology & Evolution, 2008, v. 25, n. 2, p. 254, doi. 10.1093/molbev/msm254

By:

Forslund, Kristoffer;
Henricson, Anna;
Hollich, Volker;
Sonnhammer, Erik L. L.

Publication type:

Article

Prediction of Function Divergence in Protein Families Using the Substitution Rate Variation Parameter Alpha.

Published in:

Molecular Biology & Evolution, 2006, v. 23, n. 7, p. 1406, doi. 10.1093/molbev/msl002

By:

Abhiman, Saraswathi;
Daub, Carsten O.;
Sonnhammer, Erik L. L.

Publication type:

Article

Assessment of Protein Distance Measures and Tree-Building Methods for Phylogenetic Tree Reconstruction.

Published in:

Molecular Biology & Evolution, 2005, v. 22, n. 11, p. 2257, doi. 10.1093/molbev/msi224

By:

Hollich, Volker;
Milchert, Lena;
Arvestad, Lars;
Sonnhammer, Erik L. L.

Publication type:

Article

The FunCoup Cytoscape App: multi-species network analysis and visualization.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae739

By:

Buzzao, Davide;
Steininger, Lukas;
Guala, Dimitri;
Sonnhammer, Erik L L

Publication type:

Article