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E

Erik L. L. Sonnhammer

stockholm university

63H-index
223Paper Count
6.5WCitation Count
Published Papers 74
Publication Date
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GeneSNAKE: a Python package for simulation of gene regulatory networks and perturbation-induced expression data
errBioinformatics Advances
IF2.8
err2026-01-01
err0
PREAI
errHillerton, Thomas; Bjork, Anton; Lundqvist, Nils; Zhivkoplias, Erik K.; Garbulowski, Mateusz; Sonnhammer, Erik L. L.
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New developments for the Quest for Orthologs benchmark service
errgenomics proteomics bioinformatics
IF2.8
err2024-12-11
err0
errOAAI
errAltenhoff, Adrian; Nevers, Yannis; Tran, Vinh; Jyothi, Dushyanth; Martin, Maria; Cosentino, Salvatore; Majidian, Sina; Marcet-Houben, Marina; Fuentes-Palacios, Diego; Persson, Emma; Walsh, Thomas; Lecompte, Odile; Gabaldon, Toni; Kelly, Steven; Hu, Yanhui; Iwasaki, Wataru; Capella-Gutierrez, Salvador; Dessimoz, Christophe; Thomas, Paul D.; Ebersberger, Ingo; Sonnhammer, Erik
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FunCoup 6: advancing functional association networks across species with directed links and improved user experience
errNUCLEIC ACIDS RESEARCH
IF13.1
err2024-11-12
err0
errOAAI
errBuzzao, Davide; Persson, Emma; Guala, Dimitri; Sonnhammer, Erik L. L.
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errSave
Quest for Orthologs in the Era of Biodiversity Genomics
errGENOME BIOLOGY AND EVOLUTION
IF2.8
err2024-10-15
err0
errOAAI
errLangschied, Felix; Bordin, Nicola; Cosentino, Salvatore; Fuentes-Palacios, Diego; Glover, Natasha; Hiller, Michael; Hu, Yanhui; Huerta-Cepas, Jaime; Coelho, Luis Pedro; Iwasaki, Wataru; Majidian, Sina; Manzano-Morales, Saioa; Persson, Emma; Richards, Thomas A.; Gabaldon, Toni; Sonnhammer, Erik; Thomas, Paul D.; Dessimoz, Christophe; Ebersberger, Ingo
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GeneSPIDER2: large scale GRN simulation and benchmarking with perturbed single-cell data
errgenomics proteomics bioinformatics
IF2.8
err2024-09-18
err0
errOAAI
errGarbulowski, Mateusz; Hillerton, Thomas; Morgan, Daniel; Secilmis, Deniz; Sonnhammer, Lisbet; Tjarnberg, Andreas; Nordling, Torbjorn E. M.; Sonnhammer, Erik L. L.
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errSave
Benchmarking enrichment analysis methods with the disease pathway network
errBRIEFINGS IN BIOINFORMATICS
IF7.7
err2024-03-02
err2
errOAAI
errBuzzao, Davide; Castresana-Aguirre, Miguel; Guala, Dimitri; Sonnhammer, Erik L. L.
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errSave
TOPAS, a network-based approach to detect disease modules in a top-down fashion
errgenomics proteomics bioinformatics
IF2.8
err2022-11-29
err6
errOAAI
errBuzzao, Davide; Castresana-Aguirre, Miguel; Guala, Dimitri; Sonnhammer, Erik L. L.
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errSave
Knowledge of the perturbation design is essential for accurate gene regulatory network inference
errSCIENTIFIC REPORTS
IF3.9
err2022-10-03
err5
errOAAI
errSecilmis, Deniz; Hillerton, Thomas; Tjarnberg, Andreas; Nelander, Sven; Nordling, Torbjorn E. M.; Sonnhammer, Erik L. L.
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errSave
Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones
errNATURE COMMUNICATIONS
IF15.7
err2022-09-17
err7
errOAAI
errMarklund, Maja; Schultz, Niklas; Friedrich, Stefanie; Berglund, Emelie; Tarish, Firas; Tanoglidi, Anna; Liu, Yao; Bergenstrahle, Ludvig; Erickson, Andrew; Helleday, Thomas; Lamb, Alastair D.; Sonnhammer, Erik; Lundeberg, Joakim
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errSave
GRNbenchmark - a web server for benchmarking directed gene regulatory network inference methods
errNUCLEIC ACIDS RESEARCH
IF13.1
err2022-05-24
err9
errOAAI
errSecilmis, Deniz; Hillerton, Thomas; Sonnhammer, Erik L. L.
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errSave
The Quest for Orthologs orthology benchmark service in 2022
errNUCLEIC ACIDS RESEARCH
IF13.1
err2022-05-12
err30
errOAAI
errNevers, Yannis; Jones, Tamsin E. M.; Jyothi, Dushyanth; Yates, Bethan; Ferret, Meritxell; Portell-Silva, Laura; Codo, Laia; Cosentino, Salvatore; Marcet-Houben, Marina; Vlasova, Anna; Poidevin, Laetitia; Kress, Arnaud; Hickman, Mark; Persson, Emma; Pilizota, Ivana; Guijarro-Clarke, Cristina; Iwasaki, Wataru; Lecompte, Odile; Sonnhammer, Erik; Roos, David S.; Gabaldon, Toni; Thybert, David; Thomas, Paul D.; Hu, Yanhui; Emms, David M.; Bruford, Elspeth; Capella-Gutierrez, Salvador; Martin, Maria J.; Dessimoz, Christophe; Altenhoff, Adrian
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errSave
Drug repurposing improves disease targeting 11-fold and can be augmented by network module targeting, applied to COVID-19
errSCIENTIFIC REPORTS
IF3.9
err2021-10-19
err4
errOAAI
errRivero-Garcia, Ines; Castresana-Aguirre, Miguel; Guglielmo, Luca; Guala, Dimitri; Sonnhammer, Erik L. L.
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errSave
Ten Years of Collaborative Progress in the Quest for Orthologs
errMOLECULAR BIOLOGY AND EVOLUTION
IF5.3
err2021-04-02
err21
errOAAI
errLinard, Benjamin; Ebersberger, Ingo; McGlynn, Shawn E.; Glover, Natasha; Mochizuki, Tomohiro; Patricio, Mateus; Lecompte, Odile; Nevers, Yannis; Thomas, Paul D.; Gabaldon, Toni; Sonnhammer, Erik; Dessimoz, Christophe; Uchiyama, Ikuo
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errSave
Uncovering cancer gene regulation by accurate regulatory network inference from uninformative data
errNPJ SYSTEMS BIOLOGY AND APPLICATIONS
IF3.5
err2020-11-09
err15
errOAAI
errSecilmis, Deniz; Hillerton, Thomas; Morgan, Daniel; Tjarnberg, Andreas; Nelander, Sven; Nordling, Torbjorn E. M.; Sonnhammer, Erik L. L.
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errSave
Pfam: The protein families database in 2021
errNUCLEIC ACIDS RESEARCH
IF13.1
err2020-10-30
err3.3K
errOAAI
errMistry, 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
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errSave
Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms
errSCIENTIFIC REPORTS
IF3.9
err2020-08-25
err7
errOAAI
errMorgan, Daniel; Studham, Matthew; Tjarnberg, Andreas; Weishaupt, Holger; Swartling, Fredrik J.; Nordling, Torbjorn E. M.; Sonnhammer, Erik L. L.
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errSave
Pathway-specific model estimation for improved pathway annotation by network crosstalk
errSCIENTIFIC REPORTS
IF3.9
err2020-08-12
err13
errOAAI
errCastresana-Aguirre, Miguel; Sonnhammer, Erik L. L.
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errSave
The Quest for Orthologs benchmark service and consensus calls in 2020
errNUCLEIC ACIDS RESEARCH
IF13.1
err2020-05-06
err21
errOAAI
errAltenhoff, Adrian M.; Garrayo-Ventas, Javier; Cosentino, Salvatore; Emms, David; Glover, Natasha M.; Hernandez-Plaza, Ana; Nevers, Yannis; Sundesha, Vicky; Szklarczyk, Damian; Fernandez, Jose M.; Codo, Laia; Li Gelpi, Josep; Huerta-Cepas, Jaime; Iwasaki, Wataru; Kelly, Steven; Lecompte, Odile; Muffato, Matthieu; Martin, Maria J.; Capella-Gutierrez, Salvador; Thomas, Paul D.; Sonnhammer, Erik; Dessimoz, Christophe
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errSave
Genome-wide functional association networks: background, data & state-of-the-art resources
errBRIEFINGS IN BIOINFORMATICS
IF7.7
err2019-07-05
err19
errOAAI
errGuala, Dimitri; Ogris, Christoph; Muller, Nikola; Sonnhammer, Erik L. L.
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Advances and Applications in the Quest for Orthologs
errMOLECULAR BIOLOGY AND EVOLUTION
IF5.3
err2019-06-27
err58
errOAAI
errGlover, Natasha; Dessimoz, Christophe; Ebersberger, Ingo; Forslund, Sofia K.; Gabaldon, Toni; Huerta-Cepas, Jaime; Martin, Maria-Jesus; Muffato, Matthieu; Patricio, Mateus; Pereira, Cecile; da Silva, Alan Sousa; Wang, Yan; Sonnhammer, Erik; Thomas, Paul D.; Altenhoff, Adrian; Blake, Judith A.; Capella-Gutierrez, Salvador; Chiba, Hirokazu; Dessimoz, Christophe; Durand, Dannie; Ebersberger, Ingo; Fernandez-Breis, Jesualdo Tomas; Forslund, Sofia; Gabaldon, Toni; Glover, Natasha; Huerta-Cepas, Jaime; Lecompte, Odile; Lewis, Suzanna; Linard, Benjamin; Houben, Marina Marcet; Marcotte, Edward M.; Martin, Maria-Jesus; McWhite, Claire; de Farias, Tarcisio Mendes; Muffato, Matthieu; Nevers, Yannis; Patricio, Mateus; Pereira, Cecile; Pryszcz, Leszek; Saha, Surya; Schiffer, Philipp; Sonnhammer, Erik; da Silva, Alan Sousa; Tang, Haiming; Thomas, Paul D.; Uchiyama, Ikuo; Wang, Yan
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Research Directions

No research directions
Co-authors
Cooperation Journals
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Peer Bork
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Gunnar von Heijne
H-index: 119 · Papers: 502
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JamesMichaelWhelan (James Whelan)
H-index: 109 · Papers: 768
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