Special Bioinformatics Projects----------• WGS, WES, RNA-seq, TSO500 validation• Small variant, CNV, SV calling• TMB, MSI• Variant annotation• CAP germline challenge• PacBio analysis, Iso-Seq, SQANTi3• Differential expression analysis, DESeq2, edgeR

Applications for Novel Sequencing Platform----------• Developed algorithms for somatic variant calling optimized around new sequencing platform• Analyzed data to optimize panel design for improved performanceDevelopment of Novel Sequencing Platform----------• Continued development work initiated as part of Lasergen• Acted as bioinformatics Technical Lead

Development of Novel Sequencing Platform----------• Provided bioinformatics leadership and support for all aspects of a new sequencing platform• Analyzed data from multiple stages of the process, including raw intensity and location information, through fastq/sam files and variant calls• Developed custom analysis pipelines and deployed custom tools to internal users• Used bioinformatics analysis to drive experimental design and inform decisions on instrument hardware*LaserGen was successfully acquired by Agilent in May 2018*

Algorithm and Pipeline Development for Non-Invasive Prenatal Testing----------• Developed novel algorithms for NIPT analysis based on paired-end next-generation sequencing data.• Integrated the DRAGEN hardware-based sequence alignment platform from Edico Genome into an existing NIPT pipeline.• Supported R&D efforts for improvements to NIPT LDTs including report generation, custom analysis and pipeline modifications. Algorithm and Pipeline Development for Liquid Biopsy----------• Worked as part of a team of bioinformatics scientists to develop a novel pipeline for analysis of next-generation sequencing data obtained from a targeted cancer panel. This included molecular barcoding analysis, consensus sequence generation, variant calling and annotation.• Performed detailed analysis on NGS data including base calling errors, singleton reads that did not PCR amplify for error correction, data bleed between different indexes, and the impact of the physical location of clusters on the flowcell.• Developed a novel algorithm for detection of genetic rearrangements such as gene fusions.

Development of Algorithms and Software in Support of Sequenom Panels----------• Developed algorithms to perform genotyping of samples analyzed with Hemo ID, a blood antigen genotyping panel.• Developed algorithms to perform matching and tracking of samples analyzed with Sample ID, a sample identification and quantitation panel.• Adapted and extended an existing clustering algorithm to be suitable for the analysis of polyploid data generated with the MassARRAY system.• Developed software that in each case implemented the algorithms and generated reports. Reports were created in both CSV format for machine readability and HTML format for rich graphical display of results.• Software included GUI elements to define user settings and both reading from and writing to databases.MassARRAY 510(k) Submission----------• Contributed as one of a team of software developers in charge of creating TyperDX, the software component of the MassARRAY 510(k) submission.• Designed and implemented features under design controls including requirements and documentation.• Analyzed mass spectrometry data to ensure that the system was operating according to specifications including statistical analysis of peak intensity and resolution, call rate and accuracy.• Simulated mass spectrometry data to test specifications that could not be probed with real data.• Wrote analysis scripts to perform operational qualification of new system installations.• Worked in an ISO 13845 design control environment.

Development of a Quantitative MS Data Analysis Pipeline----------• Designed and implemented a rapid quantitative data analysis pipeline for MS experiments. The pipeline was instrumental in the publication of 7 papers.• Interfaced the pipeline with a computing cluster at TSRI.• Established best practices in quantitative MS data analysis.• Implemented a MySQL database for archival and rapid retrieval of data.Structural Genomics of T-Cell Activation----------• Screened targets for structural genomics efforts using secondary structure prediction and domain annotation. This work contributed to the award of a $5 million grant to study gene expression changes in T-cell activation.Analysis of Ribosomal Assembly Intermediates Induced by DbpA R331A----------• Determined the protein inventory and quantified the stoichiometry of proteins in 45S intermediates present during overexpression of the DbpA R331A assembly factor mutant. This was a collaboration with Olke Uhlenbeck’s group at Northwestern.Analysis of Ribosomal Assembly Intermediates Induced by Neomycin----------• Identified a continuum of intermediates in E. coli cells treated with neomycin.• Determined the protein inventory and quantified the stoichiometry of proteins in 30S and 50S precursors throughout the continuum.• Pulse-labeled neomycin-treated E. coli to timestamp ribosomal proteins.Elucidation of the Ribosomal Protein Autoregulatory Network----------• Quantified total cellular levels of ribosomal proteins when individually overexpressing ribosomal proteins.• Identified direct and indirect interactions affecting the regulation of ribosomal protein translation.Gene Expression Profiling of E. coli Treated with Antibiotics----------• Clustered expression profiles of E. coli treated with individual antibiotics and combinations of antibiotics. Profiles were grouped based on mechanism and revealed some genes were only regulated by combinations of antibiotics.