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Professional in bioinformatics software and pipeline developments, large-scale data system analysis and manuscript grant writing. Gain a wide experience in the majority analyses of genomic (WGS, WES, PacBio-seq), epigenetic (CHIP-seq, MNase-seq, ATAC-seq), transcriptome (Spatial, Single Cell, and Bulk), proteomic sequences under different Platforms. And strong background in DNA damage repair, cancer genome instability, comparative and evolutionary genomics.

General Information

Full Name Xin Wang
Languages English, Chinese

Education

  • 01/15 -- 10/18
    PhD
    King Abdullah University of Science and Technology (KAUST)
    • Created two automatic pipelines to assemble 8 whole genomes and annotate them.
    • Investigated the evolution of coral calcification and thermal resilience specification in corals, and understood the evolutionary processes that allowed the soft ancestor to become the ecosystem builder they are today.
    • Understood the role of genetics/epigenetics in response to stress, and explore new strategies to increase the thermal resilience of corals in tropical areas
  • 09/11 – 07/14
    Master
    Beijing Institute of genomics, Chinese Academy of Science

Experience

  • 11/23- now
    Bioinformatic Director, Kidney and Urinary Tract Center
    Nationwide children’s hospital
    • Leading bioinformatic team at KUTC and extensively working with all our Center principal investigators.
    • Consulting pre- or post experiment to determine proper sequencing approaches, design, and integration.
    • Customizing advanced analysis of in-depth investigations and developing new methods or pipelines.
    • Contributing to grants and manuscripts, including developing the bioinformatic components, generating high quality figures, finding potential storyboards, and drafting manuscripts
    • Managing data storage and providing data analysis suggestions for the integration of large multi-omics data sets.
    • Supervising and training postdocs or students for basic bioinformatic approaches.
    • Performing bioinformatics analysis to interpret high throughput genomic data, including spatial transcriptome, scRNAseq, ChIP-seq, ATAC-seq, RNA-seq, whole genome and exome sequencing in the Kidney and Urinary Tract center
  • 11/22- now
    Senior Bioinformatic Scientist, Kidney and Urinary Tract Center
    Nationwide children’s hospital
  • 11/20- 11/22
    Postdoctoral fellow
    Boston Children’s Hospital, Harvard Medical School
    • Developed DSBins software toolkits to identify and functionally profile large insertion events and other repair products at DNA double stand break.
    • Understood the mechanisms of large insertions at DSB sites in various DNA damage repair gene deficiency, mitochondrion gene defects and aging, illustrating the genomic features, i.e., R-loops, G-quadruplex, Rad52 break site, ARS, TSS.
    • Developed MutaGene to systematically decoded mutation driver of cancer genomic instability to elucidate potential biomarkers for immunotherapy outcomes by integrating loads of cancer resources.
    • Developed novel pipelines, including detecting nucleosome distribution in forward and reverse strand at DSBs and tracing the nascent RNA changes after irradiation using ERCC normalization.
  • 12/18 – 10/20
    Postdoctoral fellow
    Houston Methodist Hospital, Weill Cornell Medical College

Open Source Projects

  • 2015-now
    gucascau
    • A series of software developments to screen DNA damage products and their features, including iDSBins, iDSBindel, iDSBInvert, LargeInsertionFeature, iMMBIR

Highlighted Publication

  • Yu Y^, Wang X^, Fox J^, Yu R, Thakre P, McCauley B, Nicoloutsos N, Li Q, Hastings PJ, Dang W, Chen KF* and Ira G*. Yeast EndoG prevents genome instability by degrading cytoplasmic DNA, Nature Communication (2024, in press)
  • Yu Y^, Wang X^, Fox J, Hastings PJ, Chen KF, Ira G. RPA and Rad27 limit templated and inverted insertions at DNA breaks (Under review in Nucleic Acids Research)
  • Chen Z^, Wang X^, Gao X, Arslanovic N, Chen KF* and Tyler J*. Bulk transcriptional inhibition after irradiation is mainly due to loss of nascent transcripts from the rDNA and histone genes. Elife (2024).
  • Jun C^, Wang X^, Advani V, Lu YW, Malizia A, Singh GB, Huang ZP, Liu J, Wang C, Oliveria E, Mably J,Chen KF, and Wang D. Mitochondrial Tyrosine 5 tiRNAs are important regulators for mitochondrial and cell health in skeletal muscle myoblast, Cell Proliferation (2023)
  • Wang X, Zoccola D, Liew YJ, Tambutte E, Cui G, Allemand D, Tambutte S, Aranda M, The evolution of calcification in reef-building corals, Molecular Biology and Evolution (2021).
  • Wang X, Liew YJ, Li Y, Zoccola D, Tambutte S, Aranda M. Draft genomes of the corallimorpharians Amplexidiscus fenestrafer and Discosoma sp. Molecular Ecology Resources (2017).
  • Wang X, Drillon G, Ryu T, Voolstra CR, Aranda M. Genome based analyses of six hexacorallian species reject the Naked coral Hypothesis. Genome Biology and Evolution (2017).
  • Liew YJ, Howells EJ, Wang X, Michell C, Burt JA, Idaghdour Y & Aranda M. Intergenerational epigenetic inheritance in reef-building corals, Nature Climate Change (2020)

Other Interests

  • Hobbies: Hiking, Snowing, Swimming, Diving (Certified Rescue Diver), Running, Gym etc.