‘A scored human protein–protein interaction network to catalyze genomic interpretation’ published in Nature Methods

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Today the Lage Lab published an article describing a quality controlled and scored human protein-protein interaction network to help functionally interpreting genomic data. Congratulations to Taibo Li, Heiko Horn and Kasper Lage.


Link to Nature Methods webpage: article.

Link to Broad Institute Snapshot on the article: Broad Institute Snapshot.

Link to press release from MGH: MGH press release.

For more information see here: InWeb_IM.



Kasper Lage to chair and present at this year’s meeting of the American Society of Human Genetics in Vancouver

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For more information click here.

Time: Wednesday, October 19, 11:00 AM–1:00 PM
Title: Augmenting and Interpreting Genomic Data Using Tissue- and Cell-type-specific Networks
Loctaion: Room 221, West Building, Convention Centre


Kasper Lage, MGH  / Broad Inst / Harvard University
Olga Troyanskaya, Princeton University



11:00 AM   Cell-type-specific protein interaction networks perturbed by genetics in psychiatric diseases. K. Lage. Broad Institute / Harvard U.
11:30 AM   Transcriptome-wide networks for understanding diverse categories of genetic variation. A. Battle. Johns Hopkins University.
12:00 PM   Tissue-specific networks for integrative disease gene identification. O. Troyanskaya. Princeton University.
12:30 PM   Building multi-omic networks for type 2 diabetes and related phenotypes. M. McCarthy. Oxford University.



Anna Sappington and Justin Lim join the lab.

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We are happy to welcome Anna Sappington (MIT undergraduate studying Computer Science and Molecular Biology) and Justin Lim (MIT undergraduate studying Mathematics and Computer Science) to the lab.

Anna and Justin will be working on Broadnex10 projects to map cellular network perturbed by genetics in early onset myocardial infraction and the Cancer Complex Compendium. For more information about these projects click here.

Jakob Jespersen presented his work at the Center for Mendelian Genetics at the Broad Institute

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Jakob's Presentation


Jakob Jespersen, member of Lage Lab at MGH and the Broad Institute, presented at the Center for Mendelian Genetics Analysis meeting the Interpretation of missense variants using protein structures and features. Jakob explained that with a vast amount of exome sequencing data, it is difficult to identify the missense variants that may be implicated in diseases. While it is possible to crudely classify variants as “loss of function” based on observations such as the mutation being in a splice site, creating a stop codon or frameshift, it is much more difficult to determine whether missense mutations are deleterious or benign.


Since the Protein Data Bank (PDB) hosts information on more than 6,000 different human proteins, it is possible to add structural information to help the classification of missense mutations. Some methods are already utilizing features from 3D protein structures, so the presentation was focused on features that we can extract and calculate which are not in use yet as well as a computational tool set Jakob has developed for this purpose.


Enjoy the recording of the Jakob’s presentation in the video below (Sep 20th, 2016)

Kasper Lage gave Keynote Talk at the annual meeting of the iPSYCH consortium

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Edyta Malolepsza, April Kim and Kasper Lage attended the annual meeting of the “The Lundbeck Foundation Initiative for Integrative Psychiatric Research” – iPSYCH – consortium June 1st to 4th  where Kasper was invited to give a Keynote Address titled ‘Human Brain Networks Perturbed by Genetics and Targeted by Therapeutics in Psychiatric Disorders.


For more information about the iPSYCH meeting click here.


From the iPSYCH website (http://ipsych.au.dk/):  “The Lundbeck Foundation Initiative for Integrative Psychiatric Research” – iPSYCH project will study five specific mental disorders; autism, Attention Deficit Hyperactive Disorder (ADHD), schizophrenia, bipolar disorder and depression. All disorders are associated with major human and societal costs all over the world. The project will study these disorders from many different angles, ranging from genes and cells to population studies, from fetus to adult, from cause to symptoms of the disorder, and this knowledge will be combined in new ways across scientific fields.

The main goals are to identify the causes of these disorders by studying the genetic and environmental factors. The perspective is to offer better and more personalized treatment, providing a better life for each individual patient – and perhaps even ways to prevent the development of the disorder in some cases.