Learn how to tame big data:
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    Selected Publications

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

    Preprint Paper 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

    . 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.

    PDF

    Recent Publications

    . Comprehensive Characterizations of Immune Receptor Repertoire in Tumors and Cancer Immunotherapy Studies. In Cancer Immunology Research, 2022.

    Paper Link

    . Immunogenomic intertumor heterogeneity across primary and metastatic sites in a patient with lung adenocarcinoma. In Journal of Experimental & Clinical Cancer Research, 2022.

    Paper Link

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

    Preprint Paper link

    . Fast alignment and preprocessing of chromatin profiles with Chromap. In Nature Communications, 2021.

    Paper Link

    . 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

    . 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.

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    . 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 genomic data science
    Jul 9, 2022 2:30 PM
    Single-Cell Analysis 101: Current Approaches and Open Questions
    Mar 29, 2022 12:30 PM
    Annual postdoc Alternative careers event King's College London
    Mar 9, 2022 6:00 AM
    Career mentoring for Department of Genomic Medicine, MD Anderson Cancer Center
    Jan 3, 2022 11:00 AM
    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

    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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