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Online Resources:

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Genoppi: an open-source software for robust and standardized integration of proteomic and genetic data

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GeNets: Broad Institute Web Platform for Genome Networks

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NetSig: Network-based discovery from cancer genomes

Heiko Horn*, Michael S. Lawrence*, Candace R. Chouinard, Yashaswi Shrestha, Jessica Xin Hu, Elizabeth Worstell, Emily Shea, Nina Ilic, Eejung Kim, Atanas Kamburov, Alireza Kashani, William C. Hahn, Joshua D. Campbell, Jesse S. Boehm+, Gad Getz+, and Kasper Lage+

Fig1

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Bash script application of the expectation maximization algorithm

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Published papers:

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A scored human protein-protein interaction network to catalyze genomic interpretation  

Taibo Li*, Rasmus Wernersson*, Rasmus B. Hansen*, Heiko Horn, Johnathan M. Mercer, Greg Slodkowicz, Christopher T. Workman, Olga Rigina, Kristoffer Rapacki, Hans-Henrik Staerfeldt, Soren Brunak, Thomas S. Jensen#, Kasper Lage# 

Nat Methods. 2016 Nov 28 | Full text

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A global reference for human genetic variation   

1000 Genomes Project Consortium 

Nature 526(7571):68-74 2015 | Full text

nihms753481f1

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Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics  

Alicia Lundby*Elizabeth J Rossin*Annette B SteffensenMoshe Rav AchaChristopher Newton-ChehArne PfeuferStacey N LynchThe QT Interval International GWAS Consortium (QT-IGC)Søren-Peter OlesenSøren BrunakPatrick T EllinorJ Wouter JukemaStella TrompetIan FordPeter W MacfarlaneBouwe P KrijtheAlbert HofmanAndré G UitterlindenBruno H StrickerHendrik M NathoeWilko SpieringMark J DalyFolkert W AsselbergsPim van der HarstDavid J MilanPaul I W de Bakker#, #Kasper Lage & #Jesper V Olsen

Nature Methods 11, 868-874 2014 | Full text

LundbyRossin

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Protein-protein interactions and genetic diseases: The interactome

Kasper Lage  

Biochem Biophys Acta 1842(10):1971-1980 | Full text

LageK2014

  • This article is part of a special issue ‘From Genome to Function’ – see all articles here: From genome to function

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Genetic and environmental risk factors in congenital heart disease functionally converge in protein networks driving heart development

Kasper Lage, Steven C. Greenway, Jill A. Rosenfeld, Hiroko Wakimoto, Joshua M. Gorham, Ayellet V. Segrè, Amy E. Roberts, Leslie B. Smoot, William T. Pu, Alexandre C. Pereira, Sonia M. Mesquita, Niels Tommerup, Søren Brunak, Blake C. Ballif, Lisa G. Shaffer, Patricia K. Donahoe, Mark J. Daly, Jonathan G. Seidman, Christine E. Seidman#, Lars A. Larsen#
PNAS, Early Edition August 16,2012 | Full text

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Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology 

Elizabeth J Rossin, Kasper Lage, Soumya Raychaudhuri, Ramnik Xavier, Diana Tatar, Yair Benita, International Inflammatory Bowel Disease Genetics Consortium, Chris Cotsapas#, Mark Daly# 
PLoS Genetics  Jan; 7(1): e1001273 (2011) | Full text

  • Access DAPPLE here (developed by Elizabeth Rossin in the lab of Mark Daly): DAPPLE

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Dissecting spatio-temporal protein networks driving human heart development and related disorders

Kasper Lage, Kjeld Møllgård, Steven Greenway, Hiroko Wakimoto, Joshua M Gorham, Christopher T Workman, Eske Bendsen, Niclas T Hansen, Olga Rigina, Francisco S Roque, Cornelia Wiese, Vincent M Christoffels, Amy E Roberts, Leslie B Smoot, William T Pu, Patricia K Donahoe, Niels Tommerup, Søren Brunak, Christine E Seidman, Jonathan G Seidman and Lars A Larsen
Molecular Systems Biology 6:381 (2010) | Full text

LageEtAl2010

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A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes 

Kasper Lage*, Niclas Tue Hansen*, E. Olof Karlberg, Aron C. Eklund, Francisco S. Roque, Patricia K. Donahoe, Zoltan Szallasi, Thomas Skøt Jensen, Søren Brunak
PNAS, 52, 20870-20875 (2008) | Full text

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A human phenome-interactome network of protein complexes in genetic disorders

Kasper Lage*, E. Olof Karlberg*, Zenia M. Størling, Páll Ísólfur Ólason, Anders Gorm Pedersen, Olga Rigina, Anders M Hinsby, Zeynep Tümer, Flemming Pociot, Niels Tommerup, Yves Moreau and Søren Brunak
Nature Biotechnology, 25, 309 – 316 (2007) | Abstract

LageEtAl2007