A New Tool for Mutational Signature Analysis
Hu and Doga describe MuSiCal (Mutational Signature Calculator) for analysis of somatic mutations (Nat Genetics 2024)
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Tissue-specific proliferative effects underlie tumor CNA patterns
Chromosome evolution screens using single cell genome sequencing (Emma/Jake, Nat Genetics, 2024)
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Chromoscope for SV analysis
Interactive multiscale visualization for structural variation by Sehi and Dominik (Nat Methods, 2023)
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Widespread emergence of mosaic CNVs in normal human tissues
A pan-tissue survey of mosaic chromosomal alterations in 948 individuals (Teng/Kharchenko Lab, Nat Genetics, 2023)
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A new mechanism for breast cancers
Jake discovers Translocation-Bridge Amplification that generates focal amplifications (Nature, 2023)
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Single-cell genome sequencing of human neurons
Joe finds enrichment of somatic SNVs and indels in regulatory elements (Nat Genetics, 2022)
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Computational analysis of Cancer Genome Sequencing Data
Isidro et al discuss recent advances in cancer genome analysis (Nature Reviews Genetics, 2022)
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Landmarks of embryonic development inscribed in somatic mutations
Mosaic variants in multiple organs resolve post-zygotic lineages (Science, 2021)
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Origins/genetic interactions of KRAS mutations are allele- and tissue-specific
Analysis of KRAS mutations at the allele level using >13K samples (Nat Comm, 2021)
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Comprehensive analysis of chromothripsis using whole-genome data
Analysis of >2500 cancer genomes shows that chromothripsis events are prevalent across multiple tumor types (Nat Genetics, 2020)
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Detecting mosaic mutations using a ML algorithm (MosaicForecast)
Yanmei et al develop MosaicForecast, a machine learning-based variant caller for mosaic mutations (Nat Biotech, 2020)
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Detecting the mutational signature of homologous recombination deficiency
Doga et al develop SigMA to identify patients who may benefit from PARP inhibitor treatment (Nat Genetics, 2019)
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LiRA identifies mutations in scDNA-seq data
Craig develops a method for detection of somatic variants in single cells (Nat Genetics, 2019)
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Review: Detecting somatic mutations in normal cells
Yanmei, Heather, Joe, and Peter discuss issues in detection of somatic variants (Trends in Genetics, 2018)
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Aging & neurodegeneration assoc. with increased mutations in neurons
Analysis of the largest single cell WGS dataset to date (Science, 2018)
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PaSD-qc: quality control for single cell whole-genome sequencing data
Sherman et al. (Nucleic Acids Research, 2017) develop a QC method based on power density estimation
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Analysis of microsatellite instability identifies patients that may benefit from immunotherapy
Cortes-Ciriano et al,Nat Comm, June, 2017
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Impact of mutation in a chromatin remodeling protein complex
Three papers from a collaboration with the Roberts lab inNature GeneticsandNature Communications
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Detecting structural variants from exome data
Yang et al (AJHG, 2016) analyze nearly 5000 cancer exomes and identify thousands of rearrangements.
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Sequencing single neurons
Lineage tracing of neurons using mutational analysis of single cell whole-genome sequencing data (Science, 2015; cover)
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4D Nucleome project to understand higher-order nuclear organization
The Park lab, along with the Kharchenko and Gehlenborg labs at DBMI, are leading the Data Coordination and Integration Center
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Cell lineage analysis in human brain using endogenous retroelements
Gilad Evrony, Alice Lee, et al. inNeuron, 2015 (Collaboration with the Chris Walsh lab)
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Comparative analysis of metazoan chromatin organization
A cross-species analysis from the ENCODE and modENCODE consortia, led by Park lab members,Nature, 2014
Introduction
We are a bioinformatics research group in the Department of Biomedical Informatics at Harvard Medical School. We are part of the Ludwig Center at Harvard, Division of Genetics at Brigham and Women’s Hospital and Harvard-MIT Division of Health, Science, & Technology.
Our main aim is to understand the genetic and epigenetic mechanisms that underlie disease processes through computational and statistical analysis of genomic data. We are particularly interested in mutational processes in normal and cancer cells and their impact in gene regulation.
Collaborative science
We have the privilege of collaborating with a number of superb experimental laboratories at Harvard Medical School and its affiliated hospitals, as well as around the world. Our recent and current collaborators include Connie Cepko, George Daley, Steve Elledge, Konrad Hochedlinger, Mark Johnson, Mitzi Kuroda, Jordan Kreidberg, Bob Kingston, William Pu, Charlie Roberts, Chris Walsh, and Fred Winston.
Here are some consortium projects in which we are involved:
- SMaHT (Somatic Mosaicism across Human Tissues), starting in 2023 - Do mutations accumulate in non-cancer cells? Where and how? Can those mutations lead to cancer or other diseases?
- 4D Nucleome - What are the principles underlying three-dimensional organization of the human genome? What is the role of the nuclear architecture in gene regulation? As the Data Coordination and Analysis Center for this major NIH initiative, we will collect, process, and display all data generated in the consortium and to perform integrative analysis. Main collaborators: Peter Kharchenko (HMS), Leonid Mirny (MIT), Nils Gehlenborg (HMS), Hanspeter Pfister (Harvard) and Ting Wang (WashU).
- Brain Somatic Mosaicism Network - The aim of this network is to characterize the spectrum of somatic variation in human brain samples and its role in psychiatric disorders. We are studying somatic mosaicism in autism with Chris Walsh (Boston Children’s) and schizophrenia with Andy Chess (Mt. Sinai).
- Ludwig Center - This center brings together investigators from across Harvard to develop strategies to overcome the problem of therapy resistence in cancer.
- International Cancer Genome Consortium - This is an effort by the international cancer genomics community to jointly analyze ~2,500 cancer genomes.
Latest News
Jul 2026: Park Lab takes on a 5k
The runners of Park Lab took on a 5k together (on quite a hot day)! New lab outing tradition?
With sadness but excitement for their futures, we said farewell to Dominik as he begins his own lab and a faculty position at Beth Israel Deaconess, and to Dominika, Joseph, and Michail who are starting their PhDs at Boston University, Tri-I, and Harvard (BIG) respectively. They will all be greatly missed in Park Lab!
Apr 2026: Farewell Jan!
We said farewell to Jan as he wraps up his work in Park Lab and will soon be graduating from university. Park Lab is excited to send Jan off to Cambridge next year to get his Master’s Degree.
Apr 2026: Welcome Cait!
Cait Harrigan joined Park Lab in April as our newest postdoc. She received her PhD in Computer Science from the University of Toronto with thesis work on modelling DNA repair deficiencies in cancer with mutational signatures and scaling probabilistic methods to large cohorts. Welcome Cait!
Apr 2026: Farewell Michele!
Park Lab said goodbye to Michele on his last day with the team. He was a Bioinformatics Scientist in the lab for more than seven years! We all wish him the best of luck back at home in Italy.