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Chris Whelan

Role
Senior Computational Biologist at Broad Institute of MIT and Harvard
Location
Boston, MA, US
LinkedIn followers
500 followers
ScienceView LinkedIn profile

About Chris Whelan

Computational Biologist at the Broad Institute. I work on analyzing genomics data…

Experience

  1. Senior Computational Biologist

    Broad Institute of MIT and Harvard

    Feb 2014 — Present

    Senior Computational Biologist, Talkowski Lab, Broad/MGH Computational methods and analysis lead for cell-free DNA sequencing. I am responsible for the design, development, benchmarking and analysis of computational methods for processing data from sequencing of maternal cell free DNA for use in prenatal clinical genetics. I apply machine learning techniques to produce accurate genetic variant calls that can be interpreted for clinical diagnostics. In addition to working with cell free DNA sequencing data, I also develop variant calling and analysis methods for genomic structural variation in both large scale population studies and clinical contexts. Tech Lead, Structural Variation Team, Data Sciences Platform Methods Group I design, develop, and evaluate computational methods for processing NGS data within the Genome Analysis Toolkit (GATK). Focusing on methods for structural variation detection, I develop algorithms and pipelines for accurately calling variants from sequencing data. As tech lead, I provide guidance, advice, and technical leadership to a team of computational biologists and engineers working on implementing state of the art structural variation detection methods meant for the Broad Institute\'s research and clinical pipelines. Computation Biologist, McCarroll Lab, Stanley Center for Psychiatric Research I design methods and conduct analyses to better understand copy number and structural variation. My focus is on detecting and analyzing copy number variation in regions of the genome that are difficult to access with standard algorithms for processing short read data. I contribute to research projects that aim to understand complex forms of structural variation and their association with disease risk and other phenotypes.

Skills

  • Algorithms
  • Hadoop
  • Machine Learning
  • Agile Methodologies
  • Computational Biology
  • Genomics
  • Oracle
  • Python
  • Scalability
  • Unix
  • Scala
  • Agile Project Management
  • Bioinformatics
  • Web Applications
  • Perl
  • Systems Biology
  • R
  • Computer Science
  • Java
  • Natural Language Processing
  • Web Services
  • Linux
  • Git
  • Data Mining
  • Dna Sequencing
  • Distributed Systems
  • Relational Databases
  • Automated Software Testing

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Chris Whelan — Senior Computational Biologist at Broad Institute of MIT and Harvard in Boston, MA, US | Unifers