Works matching AU Sonnhammer, Erik L. L.

Results: 93

Benchmarking the next generation of homology inference tools.

Published in:

Bioinformatics, 2016, v. 32, n. 17, p. 2636, doi. 10.1093/bioinformatics/btw305

By:

Saripella, Ganapathi Varma;
Sonnhammer, Erik L. L.;
Forslund, Kristoffer

Publication type:

Article

MaxLink: network-based prioritization of genes tightly linked to a disease seed set.

Published in:

Bioinformatics, 2014, v. 30, n. 18, p. 2689, doi. 10.1093/bioinformatics/btu344

By:

Guala, Dimitri;
Sjölund, Erik;
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

Discovering viral genomes in human metagenomic data by predicting unknown protein families.

Published in:

Scientific Reports, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41598-017-18341-7

By:

Barrientos-Somarribas, Mauricio;
Messina, David N.;
Pou, Christian;
Lysholm, Fredrik;
Bjerkner, Annelie;
Allander, Tobias;
Andersson, Björn;
Sonnhammer, Erik L. L.

Publication type:

Article

Orthology confers intron position conservation.

Published in:

BMC Genomics, 2010, v. 11, p. 412, doi. 10.1186/1471-2164-11-412

By:

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

Publication type:

Article

Sub-grouping and sub-functionalization of the RIFIN multi-copy protein family.

Published in:

BMC Genomics, 2008, v. 9, p. 1, doi. 10.1186/1471-2164-9-19

By:

Joannin, Nicolas;
Abhiman, Saraswathi;
Sonnhammer, Erik L.;
Wahlgren, Mats

Publication type:

Article

Functional characterization in Caenorhabditis elegans of transmembrane worm-human orthologs.

Published in:

BMC Genomics, 2004, v. 5, p. 1, doi. 10.1186/1471-2164-5-85

By:

Henricson, Anna;
Sonnhammer, Erik L. L.;
Baillie, David L.;
Gomes, Ana Vaz

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

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

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

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

Statistical Assessment of Crosstalk Enrichment between Gene Groups in Biological Networks.

Published in:

PLoS ONE, 2013, v. 8, n. 1, p. 1, doi. 10.1371/journal.pone.0054945

By:

McCormack, Theodore;
Frings, Oliver;
Alexeyenko, Andrey;
Sonnhammer, Erik L. L.

Publication type:

Article

Dynamic Zebrafish Interactome Reveals Transcriptional Mechanisms of Dioxin Toxicity.

Published in:

PLoS ONE, 2010, v. 5, n. 5, p. 1, doi. 10.1371/journal.pone.0010465

By:

Alexeyenko, Andrey;
Wassenberg, Deena M.;
Lobenhofer, Edward K.;
Yen, Jerry;
Linney, Elwood;
Sonnhammer, Erik L. L.;
Meyer, Joel N.

Publication type:

Article

Fusion transcript detection using spatial transcriptomics.

Published in:

BMC Medical Genomics, 2020, v. 13, p. 1, doi. 10.1186/s12920-020-00738-5

By:

Friedrich, Stefanie;
Sonnhammer, Erik L. L.

Publication type:

Article

MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data.

Published in:

BMC Medical Genomics, 2020, v. 13, n. 1, p. 1, doi. 10.1186/s12920-020-00731-y

By:

Friedrich, Stefanie;
Barbulescu, Remus;
Helleday, Thomas;
Sonnhammer, Erik L. L.

Publication type:

Article

A large-scale benchmark of gene prioritization methods.

Published in:

Scientific Reports, 2017, p. 46598, doi. 10.1038/srep46598

By:

Guala, Dimitri;
Sonnhammer, Erik L. L.

Publication type:

Article

Optimal Sparsity Selection Based on an Information Criterion for Accurate Gene Regulatory Network Inference.

Published in:

Frontiers in Genetics, 2022, v. 13, p. 1, doi. 10.3389/fgene.2022.855770

By:

Seçilmiş, Deniz;
Nelander, Sven;
Sonnhammer, Erik L. L.

Publication type:

Article

Corrigendum: Network Crosstalk as a Basis for Drug Repurposing.

Published in:

2022

By:

Guala, Dimitri;
Sonnhammer, Erik L. L.

Publication type:

Correction Notice

Benefits and Challenges of Pre-clustered Network-Based Pathway Analysis.

Published in:

Frontiers in Genetics, 2022, v. 13, p. 1, doi. 10.3389/fgene.2022.855766

By:

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

Publication type:

Article

Network Crosstalk as a Basis for Drug Repurposing.

Published in:

Frontiers in Genetics, 2022, v. 13, p. 1, doi. 10.3389/fgene.2022.792090

By:

Guala, Dimitri;
Sonnhammer, Erik L. L.

Publication type:

Article

Generation of Realistic Gene Regulatory Networks by Enriching for Feed-Forward Loops.

Published in:

Frontiers in Genetics, 2022, v. 13, p. 1, doi. 10.3389/fgene.2022.815692

By:

Zhivkoplias, Erik K.;
Vavulov, Oleg;
Hillerton, Thomas;
Sonnhammer, Erik L. L.

Publication type:

Article

Membrane topology of the Drosophila OR83b odorant receptor

Published in:

FEBS Letters, 2007, v. 581, n. 29, p. 5601, doi. 10.1016/j.febslet.2007.11.007

By:

Lundin, Carolina;
Käll, Lukas;
Kreher, Scott A.;
Kapp, Katja;
Sonnhammer, Erik L.;
Carlson, John R.;
Heijne, Gunnar von;
Nilsson, IngMarie

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

PathBIX—a web server for network-based pathway annotation with adaptive null models.

Published in:

Bioinformatics Advances, 2021, v. 1, n. 1, p. 1, doi. 10.1093/bioadv/vbab010

By:

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

Publication type:

Article

Benchmarking enrichment analysis methods with the disease pathway network.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae069

By:

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

Publication type:

Article

Genome-wide functional association networks: background, data & state-of-the-art resources.

Published in:

Briefings in Bioinformatics, 2020, v. 21, n. 4, p. 1224, doi. 10.1093/bib/bbz064

By:

Guala, Dimitri;
Ogris, Christoph;
Müller, Nikola;
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

FunCoup 6: advancing functional association networks across species with directed links and improved user experience.

Published in:

Nucleic Acids Research, 2025, v. 53, n. D1, p. D658, doi. 10.1093/nar/gkae1021

By:

Buzzao, Davide;
Persson, Emma;
Guala, Dimitri;
Sonnhammer, Erik L L

Publication type:

Article

GRNbenchmark - a web server for benchmarking directed gene regulatory network inference methods.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W398, doi. 10.1093/nar/gkac377

By:

Seçilmiş, Deniz;
Hillerton, Thomas;
Sonnhammer, Erik L L

Publication type:

Article

Pfam: The protein families database in 2021.

Published in:

Nucleic Acids Research, 2021, v. 49, n. D1, p. D412, doi. 10.1093/nar/gkaa913

By:

Mistry, Jaina;
Chuguransky, Sara;
Williams, Lowri;
Qureshi, Matloob;
Salazar, Gustavo A;
Sonnhammer, Erik L L;
Tosatto, Silvio C E;
Paladin, Lisanna;
Raj, Shriya;
Richardson, Lorna J;
Finn, Robert D;
Bateman, Alex

Publication type:

Article

The Pfam protein families database in 2019.

Published in:

Nucleic Acids Research, 2019, v. 47, n. D1, p. D427, doi. 10.1093/nar/gky995

By:

El-Gebali, Sara;
Mistry, Jaina;
Bateman, Alex;
Eddy, Sean R;
Luciani, Aurélien;
Potter, Simon C;
Qureshi, Matloob;
Richardson, Lorna J;
Salazar, Gustavo A;
Smart, Alfredo;
Sonnhammer, Erik L L;
Hirsh, Layla;
Paladin, Lisanna;
Piovesan, Damiano;
Tosatto, Silvio C E;
Finn, Robert D

Publication type:

Article

FunCoup 4: new species, data, and visualization.

Published in:

Nucleic Acids Research, 2018, v. 46, n. D1, p. D601, doi. 10.1093/nar/gkx1138

By:

Ogris, Christoph;
Guala, Dimitri;
Kaduk, Mateusz;
Sonnhammer, Erik L L

Publication type:

Article