Amrita Pati Email & Phone Number

Belmont, Ca, Us

Thousand Oaks, Ca, Us

• Support Amgen clinical trials in Oncology, Inflammation, Cardiometabolic disorders and Rare disease through Precision Medicine Bioinformatics and Computational Biology• Support the definition of the Precision Medicine departmental form and function and the formulation of strategic objectives, data governance and a cross-functional data ecosystem• Lead the definition of a framework to enable reverse translation at Amgen• Leadership of multiple workstreams on Amgen’s AI/ML initiative• All other responsibilities captured below under “Director, Computational Biology”

Thousand Oaks, Ca, Us

- Support Amgen clinical trials in Oncology, Inflammation and Cardiovascular disease through Precision Medicine Bioinformatics and Computational Biology- Lead functional team and support cross-functional product development through collaboration, communication, technology development and provision of clinical and translational data insights- Support the formulation and execution of biomarker and diagnostic development through fit-for-purpose computational and statistical analyses- Development and custodianship of the precision-medicine data platform, serving as the central data system for biomarker and omics data across all Amgen clinical trials- Development and application of novel and fit-for-purpose AI/ML methods and predictive analytics in the context of generation of clinical and translational data insights supporting Amgen clinical trials and internal translational analyses- Collaborative formulation of standards for biomarker and omics data, cross-functional governance models for accessing data associated with Amgen clinical trials- Working cross-functionally with clinical teams, data management, biostatistics, medical and therapeutic area functions - Contributing to external publications, abstracts, communications and discussions with KOLs- Leadership, team-building and cultivation of positive work culture

Switzerland 🇨🇭 , Ch

- Bioinformatics algorithm development for Roche AVENIO Oncology Assays, Roche Sample Prep Solutions, Harmony NIPT test. - Leadership, team-building, cross-functional development- Customer-facing technical exchanges and business development

Switzerland 🇨🇭 , Ch

- Technology and people management for the Development Bioinformatics organization within a fast moving and developing landscape.- Strategic decision making and product roadmap definition within a multidisciplinary environment in the Oncology disease area for NGS assays and related applications. Service as the representative for the software and bioinformatics function within the disease area product life cycle teams.- Definition of best practices for software development, processes, test frameworks and documentation for compliance with IEC 62304 and cultivation of a culture of compliance within a heterogeneous team of high-performing scientists and software engineers.- Driving innovation through the development of novel algorithms and product designs for therapy selection using guideline-based biomarkers (TMB, MSI, gene fusions, indels, etc.) and emerging biomarkers as well as for surveillance using ctDNA.- Working with other functions within a multidisciplinary setting in order to deliver end-to-end distributed NGS assay and software products.- Architecture of extensible, flexible, modular, and testable bioinformatics analysis workflows for both in-house and distributed NGS applications. Development of continuous delivery systems that offer end to end automation and tracking of metrics for bioinformatics analysis workflows. Development of systems that continuously monitor the performance of aberration callers within a multi-dimensional setting of panels, applications, samples and code versions to deliver KPIs in a temporal fashion.- Coaching of staff within a matrix setting in order to meet individual and organizational needs and cultivate talent.

Switzerland 🇨🇭 , Ch

In this position, I led and heavily contributed to the development of NGS analysis workflows for Oncology (therapy selection & surveillance) applications for both solid tumors and circulating cell free DNA extracted from plasma within the Development organization. Said workflows became a part of distributed end-to-end assay+software solutions launched in 2017 and 2018. I built a high-performing team that laid down the foundation for HPC Bfx workflows for a new sequencing organization and developed algorithms for several classes of aberrations. Other major responsibilities included the building of metadata and analysis tracking systems, support for assay development and support for Pharma collaborations.

http://jgi.doe.gov/our-science/scientists-jgi/omics-analysis/Development of production computational pipelines for mining genomes and metagenomes for gene clusters involved in secondary metabolite biosynthesis: https://img.jgi.doe.gov/abcDevelopment of production bioinformatics pipelines for detecting and reporting DNA methylation in PacBio sequenced genomes and evaluating them within genome context. https://img.jgi.doe.gov/cgi-bin/er/main.cgi?section=Methylomics&page=methylomicsDevelopment of production pipelines for the automation, integration and comparative analysis of RNAseq data in metagenomes. https://img.jgi.doe.gov/cgi-bin/mer/main.cgi?section=RNAStudies&page=rnastudiesIdentification of species-delineating Average Nucleotide Identity (ANI) thresholds for bacterial genomes: http://ani.jgi-psf.orgStructural and functional annotation of genes in genomes and metagenomes leveraging HPC architectures comprised of thousands of cores and utilizing the Hadoop framework.Development of custom bioinformatics pipelines for the detection of recoded bacterial contigs.GEBA-KMG: The GEBA one thousand microbial genomes project.

Automation of gene model quality control (http://geneprimp.jgi-psf.org/)Binning metagenomic datasets based on sequence composition and underlying Markovian and de Bruijn graph properties (http://clams.jgi-psf.org/)Statistical models for analysis of metagenomes (http://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=AbundanceProfiles)Deployment of pipelines for functional annotation of large metagenomes at the NERSC (http://www.nersc.gov/) supercomputing facility. Experience with genepool, hopper, carver.Latest:- Development of computational models to enable comparison between large metagenomes (hundreds of millions of genes) in IMG with respect to functional and phylogenetic profiles within a Hadoop framework.- Development of automatic gene model curation methods for the automatic reannotation of all existing isolate genomes. (http://genome.jgi.doe.gov/programs/bacteria-archaea/reannotation.jsf)

Blacksburg, Va, Us

Blacksburg, Va, Us

Brentford, Middlesex, Gb

Blacksburg, Va, Us

San Jose, California, Us

Ph.D., Computer Science, Bioinformatics And Computational Biology

B.E. (Hons), Computer Science