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Author Details

Erik L L Sonnhammer
Stockholm University
1992
167
58
Emma Lundberg (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
35266519PathwAX II: network-based pathway analysis with interactive visualization of network crosstalk.Bioinformatics2022
35350247Network Crosstalk as a Basis for Drug Repurposing.Front Genet2022
35609981GRNbenchmark - a web server for benchmarking directed gene regulatory network inference methods.Nucleic Acids Res2022
35561192InParanoid-DIAMOND: faster orthology analysis with the InParanoid algorithm.Bioinformatics2022
35656321Corrigendum: Network Crosstalk as a Basis for Drug Repurposing.Front Genet2022
35620466Benefits and Challenges of Pre-clustered Network-Based Pathway Analysis.Front Genet2022
35552456The Quest for Orthologs orthology benchmark service in 2022.Nucleic Acids Res2022
36458021TOPAS, a network-based approach to detect disease modules in a top-down fashion.NAR Genom Bioinform2022
35923701Optimal Sparsity Selection Based on an Information Criterion for Accurate Gene Regulatory Network Inference.Front Genet2022
36192495Knowledge of the perturbation design is essential for accurate gene regulatory network inference.Sci Rep2022
36115838Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones.Nat Commun2022
35222536Generation of Realistic Gene Regulatory Networks by Enriching for Feed-Forward Loops.Front Genet2022
33466918DNA Methylation Levels in Mononuclear Leukocytes from the Mother and Her Child Are Associated with IgE Sensitization to Allergens in Early Life.Int J Mol Sci2021
36700096PathBIX-a web server for network-based pathway annotation with adaptive null models.Bioinform Adv2021
33539890FunCoup 5: Functional Association Networks in All Domains of Life, Supporting Directed Links and Tissue-Specificity.J Mol Biol2021
34667255Drug repurposing improves disease targeting 11-fold and can be augmented by network module targeting, applied to COVID-19.Sci Rep2021
33978748Inferring the experimental design for accurate gene regulatory network inference.Bioinformatics2021
33125078Pfam: The protein families database in 2021.Nucleic Acids Res2021
31281921Genome-wide functional association networks: background, data & state-of-the-art resources.Brief Bioinform2020
33168813Uncovering cancer gene regulation by accurate regulatory network inference from uninformative data.NPJ Syst Biol Appl2020
32788619Pathway-specific model estimation for improved pathway annotation by network crosstalk.Sci Rep2020
32843692Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms.Sci Rep2020
32753032Fusion transcript detection using spatial transcriptomics.BMC Med Genomics2020
32374845The Quest for Orthologs benchmark service and consensus calls in 2020.Nucleic Acids Res2020
32487140MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data.BMC Med Genomics2020
30357350The Pfam protein families database in 2019.Nucleic Acids Res2019
31660857Domainoid: domain-oriented orthology inference.BMC Bioinformatics2019
30169550A generalized framework for controlling FDR in gene regulatory network inference.Bioinformatics2019
31241141Advances and Applications in the Quest for Orthologs.Mol Biol Evol2019
31278674Evolution of Protein Domain Architectures.Methods Mol Biol2019
30850359A Novel ACKR2-Dependent Role of Fibroblast-Derived CXCL14 in Epithelial-to-Mesenchymal Transition and Metastasis of Breast Cancer.Clin Cancer Res2019
29311716Discovering viral genomes in human metagenomic data by predicting unknown protein families.Sci Rep2018
29925878Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity.Nat Commun2018
29570091Experimental validation of predicted cancer genes using FRET.Methods Appl Fluoresc2018
28968857Gearing up to handle the mosaic nature of life in the quest for orthologs.Bioinformatics2018
27742821HieranoiDB: a database of orthologs inferred by Hieranoid.Nucleic Acids Res2017
28485748GeneSPIDER - gene regulatory network inference benchmarking with controlled network and data properties.Mol Biosyst2017
28429739A large-scale benchmark of gene prioritization methods.Sci Rep2017
28096085Improved orthology inference with Hieranoid 2.Bioinformatics2017
29142246A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family.Nat Commun2017
27664219A novel method for crosstalk analysis of biological networks: improving accuracy of pathway annotation.Nucleic Acids Res2017
27043882Standardized benchmarking in the quest for orthologs.Nat Methods2016
27151197PathwAX: a web server for network crosstalk based pathway annotation.Nucleic Acids Res2016
27256311Benchmarking the next generation of homology inference tools.Bioinformatics2016
27153675TreeDom: a graphical web tool for analysing domain architecture evolution.Bioinformatics2016
25377664Avoiding pitfalls in L1-regularised inference of gene networks.Mol Biosyst2015
27462432A genome-wide IR-induced RAD51 foci RNAi screen identifies CDC73 involved in chromatin remodeling for DNA repair.Cell Discov2015
25429972InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic.Nucleic Acids Res2015
24184361Avoiding pitfalls in gene (co)expression meta-analysis.Genomics2014
25261295The Chironomus tentans genome sequence and the organization of the Balbiani ring genes.BMC Genomics2014
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Collaborators

Kristoffer Forslund
Max Delbruck Center for Molecular Medicine (MDC)
Co-authored papers 17
Richard Durbin
University of Cambridge
Co-authored papers 12
Dimitri Guala
Stockholm University
Co-authored papers 12
Alex Bateman
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 12
Andrey Alexeyenko
Karolinska Institutet
Co-authored papers 10
Robert D Finn
European Bioinformatics Institute
Co-authored papers 9
Christophe Dessimoz
University of Lausanne
Co-authored papers 8
Thomas Helleday
The University of Sheffield
Co-authored papers 7
Jaina Mistry
Co-authored papers 7
Toni Gabald??n
Catalan Institution for Research and Advanced Studies
Co-authored papers 7
Alistair M Chalk
Co-authored papers 7
Timo Lassmann
Telethon Kids Institute, University of Western Australia
Co-authored papers 7
Matthew Studham
Stockholm University
Co-authored papers 6
Maria J Martin
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 5
Paul D Thomas
University of Southern California
Co-authored papers 5
Claes Wahlestedt
Co-authored papers 4
Ewan Birney
European Bioinformatics Institute
Co-authored papers 4
Penny Coggill
Co-authored papers 4
Adrian M Altenhoff
ETH Zurich, Universitatstr. 6
Co-authored papers 4
John Tate
Co-authored papers 4
Salvador Capella-Gutierrez
Spanish National Bioinformatics Institute (INB/ELIXIR-ES)
Co-authored papers 4
Joakim Lundeberg
KTH Royal Institute of Technology
Co-authored papers 3
Gunnar von Heijne
Stockholm University
Co-authored papers 3
Liisa Holm
Institute of Biotechnology, University of Helsinki
Co-authored papers 3
Brigitte Boeckmann
Co-authored papers 3
Suzanna E Lewis
Lawrence Berkeley National Laboratory
Co-authored papers 3
Peer Bork
University of Wurzburg
Co-authored papers 3
Marco Punta
Co-authored papers 2
Lorna Richardson
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 2
Carsten O Daub
International Institute of Molecular and Cell Biology in Warsaw
Co-authored papers 2
Release 1.2