Chantal Roth Email & Phone Number

Bern, Bern, Switzerland

South San Francisco, California, United States

• Development of various algorithms for DNA mixture deconvolution for forensics• Design of reusable system and application architecture of modular client/server platform• Development of a fully continuous Probabilistic Genotyping model for forensics (including LR calculation, deconvolution, robustness analysis etc); with a complex JavaFX user interface• Development of algorithm to identify which primers might contribute to contaminating PCR signals due to the presence of microbial… Show more • Development of various algorithms for DNA mixture deconvolution for forensics• Design of reusable system and application architecture of modular client/server platform• Development of a fully continuous Probabilistic Genotyping model for forensics (including LR calculation, deconvolution, robustness analysis etc); with a complex JavaFX user interface• Development of algorithm to identify which primers might contribute to contaminating PCR signals due to the presence of microbial, fungal or other organisms, by computing its entropy, enthalpy and melting temperature and suffix tree based search algorithm; with JavaFX user interface• Design and development of forensics DNA profile search algorithm (supporting both STR and NGS) and design of an extensible framework• Design and development of mtDNA variant caller, custom mtDNA specific Smith-Waterman algorithm and mito IGV plugin to view and edit mtDNA variants (forensics)• Design and development of components for Broad’s Open Source Integrative Genomics Viewer (IGV), including flow space data visualization, an interactive karyogram (chromosome) viewer, ionogram alignments and custom tracks in particular for aneuploidy/copy number variation (CNV) data (Java, Java WebStart)• Development of the Open Source IGV.JS project via Inside-Out grant in collaboration with the Broad Institute (JavaScript, jQuery, Java)• Development of multi sample data visualization heat map plugins for Ion Reporter (Python, MongoDB)• Development of Torrent Scout and Torrent Scout Light, Open Source applications to visualize raw data generated by the Ion Torrent Personal Genome Machine (PGM). (Vaadin, Java, Google GWT, NetBeans)• Development of Shakespeare, a tool for whole genome indexing and mapping specific for the StarLight single molecule DNA sequencing platform, including error modelling and simulations of reads using probabilistic models (Java, probabilistic modeling, algorithms) Show less

San Diego, California, United States

• Management of software engineering group of 8-10 people• Design and development of IRobot, a robot schedule optimization application (Java, algorithms)• Design and development of Symphony, a general workflow application framework that is able to support any kind of workflow and process based on ontologies (DAG) (Java)• Continued and lead development of bioinformatics platform BioSphere for Syngenta, including viewers and editors for metabolic pathways, expression data and search… Show more • Management of software engineering group of 8-10 people• Design and development of IRobot, a robot schedule optimization application (Java, algorithms)• Design and development of Symphony, a general workflow application framework that is able to support any kind of workflow and process based on ontologies (DAG) (Java)• Continued and lead development of bioinformatics platform BioSphere for Syngenta, including viewers and editors for metabolic pathways, expression data and search tools (Java) Show less

San Diego, California, United States

• Project lead, design and implementation of BioSphere, a globally deployed bioinformatics platform to visualize and integrate sequence data, alignments, annotations, chromosome and other types of data (software architecture, software design, Java)• Designed and developed Saphire, a general reusable multi tier architecture including request/response framework, persistence framework, graphics framework and application framework (similar to Spring framework) • Development of TRex, a… Show more • Project lead, design and implementation of BioSphere, a globally deployed bioinformatics platform to visualize and integrate sequence data, alignments, annotations, chromosome and other types of data (software architecture, software design, Java)• Designed and developed Saphire, a general reusable multi tier architecture including request/response framework, persistence framework, graphics framework and application framework (similar to Spring framework) • Development of TRex, a generic data/XML loader that can automatically resolve foreign key relationships, identify existing rows and generate primary keys for various db systems (SqlServer, Oracle, MySql, Postgres).• Designed and implemented Raptor, a template based code generator (and O/R mapping tool) to create Java Beans, DAO objects and other for any language that is related to a data model. Show less

Phd, Computer Science (Computational Biology)

Masters, Biochemistry