Author

Jonathan Barenboim

Ontario Institute for Cancer Research

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genomics· 3 Bioinformatics· 1 Cancer Biology· 1

Signature Assays, Organisms & Methods

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Organism:human· 5 Approach:statistical model· 5 Assay:whole-genome sequencing· 4 Research Focus:database / resource· 2 Research Focus:differential expression· 2 Research Focus:gene regulatory network inference· 2 Approach:benchmark study· 1 Research Focus:benchmarking· 1

Frequent Co-Authors

Federico AbascaliD· 4 shared Gary D. BaderiD· 4 shared Rameen BeroukhimiD· 4 shared Samirkumar B. AminiD· 4 shared Abdullah KahramaniD· 3 shared Benjamin J. RaphaeliD· 3 shared David HaaniD· 3 shared Ekta KhuranaiD· 3 shared

Activity by Year

2018-2020 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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4 shared papersGenomics

Federico AbascalORCID

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Author profile →

5 papers

Recent·Most cited

Unique genomic features and deeply-conserved functions of long non-coding RNAs in the Cancer LncRNA Census (CLC)

Joana Carlevaro-Fita, Andrés Lanzós, Lars Feuerbach, Chen Hong, David Mas-Ponte, Jakob Skou Pedersen, PCAWG Drivers and Functional Interpretation Group, Federico Abascal, Samirkumar B. Amin, Gary D. Bader, Jonathan Barenboim, Rameen Beroukhim, Johanna Bertl, Keith A. Boroevich, Søren Brunak, , S. Cenk Şahinalp

The paper introduces the Cancer LncRNA Census (CLC), a curated resource of lncRNAs with causative roles in cancer, and shows their genomic and evolutionary features.

Communications Biology · Feb 5, 2020Peer-reviewedGenomics

Germline determinants of the somatic mutation landscape in 2,642 cancer genomes

Lauri A. Aaltonen, Federico Abascal, Adam A. Abeshouse, Hiroyuki Aburatani, David J. Adams, Nishant Agrawal, Keun Soo Ahn, Sung-Min Ahn, Hiroshi Aikata, Rehan Akbani, Kadir Caner Akdemir, Hikmat A Al‐Ahmadie, Sultan T. Al‐Sedairy, Fátima Al‐Shahrour, Malik Alawi, , Johann Sebastian De Bono

This study identifies germline genetic variants influencing somatic mutation patterns in 2,642 cancer genomes across 39 cancer types.

Nature · Feb 5, 2020Peer-reviewedGenomics

Comprehensive Molecular Characterization of Mitochondrial Genomes in Human Cancers

Yuan Yuan, Young Seok Ju, Young-Wook Kim, Jun Li, Yumeng Wang, Sung-Soo Yoon, Yang Yang, Iñigo Martincorena, Chad J. Creighton, John N. Weinstein, Yanxun Xu, Leng Han, Hyung‐Lae Kim, Hidewaki Nakagawa, Keunchil Park, , Mario Berríos

This study characterizes mitochondrial genomes in 2,700 cancer patients across 37 types using whole-genome sequencing and RNA-seq, revealing mutational patterns, truncating mutations, and nuclear transfer of mitochondrial DNA.

Nature Genetics · Feb 5, 2020Peer-reviewedGenomics

Integrative pathway enrichment analysis of multivariate omics data

Marta Paczkowska, Jonathan Barenboim, Nardnisa Sintupisut, Natalie S. Fox, Helen Zhu, Diala Abd-Rabbo, Miles W. Mee, Paul Christopher Boutros, PCAWG Drivers and Functional Interpretation Working Group, Federico Abascal, Samirkumar B. Amin, Gary D. Bader, Rameen Beroukhim, Johanna Bertl, Keith A. Boroevich, , Leonidas Salichos

ActivePathways integrates multivariate omics data to identify enriched pathways, revealing cancer driver genes and prognostic pathways in breast cancer.

Nature Communications · Feb 5, 2020Peer-reviewedBioinformatics

Pathway and network analysis of more than 2,500 whole cancer genomes

Matthew A. Reyna, David Haan, Marta Paczkowska, Lieven P.C. Verbeke, Miguel Vazquez, Abdullah Kahraman, Sergio Pulido-Tamayo, Jonathan Barenboim, Lina Wadi, Priyanka Dhingra, Raunak Shrestha, Gad Getz, Michael S. Lawrence, Jakob Skou Pedersen, Mark A. Rubin, , on behalf of the PCAWG Drivers and Functional Interpretation Group and the ICGC/TCGA Pan-Cancer Analysis of Whole Genome Network

The paper analyzes non-coding mutations across 2,583 cancer genomes to identify genes and pathways affected, finding clusters of interacting proteins and insights into cancer mechanisms.

bioRxiv · Aug 7, 2018 · PreprintCancer Biology