Selected Publications

. Reprogramming of bivalent chromatin states in NRAS mutant melanoma suggests PRC2 inhibition as a therapeutic strategy. In Cell Reports, 2021.

PDF Code

. HieRFIT: A hierarchical cell type classification tool for projections from complex single-cell atlas datasets . In Bioinformatics, 2021.

Preprint Code Paper Link

. CHIPS: A Snakemake pipeline for quality control and reproducible processing of chromatin profiling data. In F1000Research, 2021.

Preprint Code link to F1000

. The histologic phenotype of lung cancers may be driven by transcriptomic features rather than genomic characteristics. Accepted in Nature Communications, In BioRxiv, 2021.

Preprint

. Evaluating single-cell cluster stability using the Jaccard similarity index. In Bioinformatics, 2020.

Preprint Code Dataset Paper Link

. Enhancer Reprogramming Confers Dependence on Glycolysis and IGF Signaling in KMT2D Mutant Melanoma. In Cell Reports, 2020.

PDF Code

. Integrative analyses of single-cell transcriptome and regulome using MAESTRO. In Genome Biology, 2020.

PDF Code

. KMT2D Deficiency Impairs Super-Enhancers to Confer a Glycolytic Vulnerability in Lung Cancer. In Cancer Cell, Highlight in ScienceSignaling: Tumor’s loss is clinician’s gain, 2020.

PDF Code

. Fast analysis of scATAC-seq data using a predefined set of genomic regions. In F1000 Research, 2020.

PDF Code Source Document

. Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma. In Cancer Cell, 2017.

PDF

. ChIP-seq analysis Book chapter for Biostar Handbook. In Biostar Handbook, 2017.

PDF

. Systematic analysis of telomere length and somatic alterations in 31 cancer types. In Nature Genetics, 2017.

PDF

. A Molecular Take on Malignant Rhabdoid Tumors. In Trends in Cancer, 2016.

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Recent Publications

. Enhancer reprogramming in PRC2-deficient malignant peripheral nerve sheath tumors induces a targetable de-differentiated state. In Acta Neuropathol, 2021.

Pubmed link

. Reprogramming of bivalent chromatin states in NRAS mutant melanoma suggests PRC2 inhibition as a therapeutic strategy. In Cell Reports, 2021.

PDF Code

. HieRFIT: A hierarchical cell type classification tool for projections from complex single-cell atlas datasets . In Bioinformatics, 2021.

Preprint Code Paper Link

. CHIPS: A Snakemake pipeline for quality control and reproducible processing of chromatin profiling data. In F1000Research, 2021.

Preprint Code link to F1000

. The histologic phenotype of lung cancers may be driven by transcriptomic features rather than genomic characteristics. Accepted in Nature Communications, In BioRxiv, 2021.

Preprint

. Evaluating single-cell cluster stability using the Jaccard similarity index. In Bioinformatics, 2020.

Preprint Code Dataset Paper Link

. Enhancer Reprogramming Confers Dependence on Glycolysis and IGF Signaling in KMT2D Mutant Melanoma. In Cell Reports, 2020.

PDF Code

. Integrative analyses of single-cell transcriptome and regulome using MAESTRO. In Genome Biology, 2020.

PDF Code

. KMT2D Deficiency Impairs Super-Enhancers to Confer a Glycolytic Vulnerability in Lung Cancer. In Cancer Cell, Highlight in ScienceSignaling: Tumor’s loss is clinician’s gain, 2020.

PDF Code

. Fast analysis of scATAC-seq data using a predefined set of genomic regions. In F1000 Research, 2020.

PDF Code Source Document

. LATS kinase–mediated CTCF phosphorylation and selective loss of genomic binding. In Science Advances, 2020.

PDF

. KRAS-IRF2 Axis Drives Immune Suppression and Immune Therapy Resistance in Colorectal Cancer. In Cancer Cell, 2019.

PDF

. The Tandem Duplicator Phenotype Is a Prevalent Genome-Wide Cancer Configuration Driven by Distinct Gene Mutations. In Cancer Cell, 2018.

PDF

. TumorFusions: an integrative resource for cancer-associated transcript fusions. In Nucleic Acids Research, 2018.

PDF

. Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma. In Cancer Cell, 2017.

PDF

. ChIP-seq analysis Book chapter for Biostar Handbook. In Biostar Handbook, 2017.

PDF

. Systematic analysis of telomere length and somatic alterations in 31 cancer types. In Nature Genetics, 2017.

PDF

. A Molecular Take on Malignant Rhabdoid Tumors. In Trends in Cancer, 2016.

PDF

. TRIM29 Suppresses TWIST1 and Invasive Breast Cancer Behavior. In Cancer Research, 2014.

PDF

Talks & Teachings

More Talks

Reproducible research in genomic data science
Sep 12, 2021 6:00 AM
Fast analysis of scATAC-seq data using a predefined set of genomic regions
Apr 23, 2021 10:00 AM
STAT115 single cell ATACseq lecture
Mar 30, 2021 12:00 PM
reproducible computing for your own benifit
Jun 2, 2020 11:00 AM
Tools and tricks for a data scientist
Mar 9, 2020 11:00 AM
Harvard FAS informatics nanocourse
Aug 19, 2019 10:40 AM
Reproducible research in bioinformatics
Mar 28, 2019 2:30 PM

Recent Posts

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Projects

CANCER IMMUNOLOGIC DATA COMMONS(CIDC)

The Cancer Immunologic Data Commons (CIDC), hosted by Dana-Farber Cancer Institute, will serve the bioinformatics needs of the network, optimization of data collection methodologies suitable for immune-related biomarkers, data integration and building a biomarker database for the secondary use by the large immuno-oncology community.

Snakemake pipeline post-processing scATAC-seq

A snakemake pipeline to split scATACseq bam by cluster, make bigwig tracks, call peaks and recount

Evaluating single cell RNAseq cluster stability

An R package for evaluating and visualizing scRNAseq cluster stability

Snakemake Pipelines

Snakemake pipelines for processing high-throughput sequencing data

CV

Find my CV in PDF here.

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