Prathik Kumar Email & Phone Number

Hyderabad, Telangana, India

- Currently serving as Program Manager, leading a team of 10 bioinformatics developers in the Computational Oncology department.- Spearheading the successful launch of various NGS pipelines for clients, including BulkRNA seq, lncRNAseq, and WGS (germline and somatic), on clients' clusters.- Implementing Agile program management methods across the Computational Oncology department to enhance project efficiency and collaboration.- Designing and building customized Jira boards for each of the 4 pillars within the department, optimizing project tracking and transparency.- Collecting and analyzing data to create robust Jira architectures for each team, facilitating seamless workflow management.- Creating comprehensive Jira overviews and user guides to empower teams in navigating and leveraging the platform's capabilities effectively.- Actively networking and seeking opportunities to collaborate with professionals in the bioinformatics and computational oncology fields.

Bengaluru, Karnataka, India

- New initiatives to increase the productivity of team by 50% by developing a product for automated daily news collections- Timely delivery of Market research and CI landscape and summary quarterly reports for fertility and maternal health indication for US and EU markets - Responsible for delivering monthly, quarterly and yearly news letters for reproductive and maternal health indication for US and EU clients Playing a key role in training and mentoring team members- Convert complex data and findings into understandable figures, tables, graphs, and written reports, measuring the effectiveness of marketing programs and strategies

Chennai, Tamil Nadu, India

- Analyse client’s Bulk-RNA seq data as per the requirements- Onboard and train associates with bioinformatics concepts - support metagenomics/microbiome projects- Develop data visualisation application for bioinformatics data through Rshiny

Greater Boston Area

In addition to Associate Bioinformatician I duties, - Driving effort to replace in-house Whole Genome Sequence analysis on HPC with cloud computing - Lead for developing cloud-based computing pipeline for Clinical Whole Genome Sequence Analysis. Pipeline development including scripting in WDL, running it on firecloud (google cloud). Optimize thresholds for true-positive, false-positive, false-negative WGS variant calls. Validating the clinical pipeline against 1000 genomes project data and writing validation reports- Liaison between in-house Bioinformatics team and Bioinformaticians and cloud IT services team at Broad Institute to manage data releases and data tracking - Coordinate between in-house Research core, Assay development team, and Bioinformatics teams to build automation tools to reduce manual work prone to errors- Rebuild old RNA-sequence QC and Differential Expression Analysis pipeline (scripting, testing, and validation) with the current newer in bioinformatics tools in the industry - Multitask between 5-6 projects by offering as support in troubleshooting production pipeline along with multiple one-off research projects- Organize team meetings and team outingshttps://onlinelibrary.wiley.com/doi/10.1111/vox.12963

Greater Boston Area

- RNA-seq pipeline maintenance, deployment and regularly version control for the tools used in the pipeline- Work on various moving parts of bioinformatics analysis for BabySeq, MilSeq and Know your genome projects- Operational and maintenance of Differential Expression analysis pipeline for RNAseq analysis- Support collaborators and researchers with bioinformatics requests for their research (Realigning hg38 to hg19 genomic data, create graphs, tables specific for research)- Create Region of Interest (ROI) files, bating and othe files required for WES, targeted panels and optimizing thresholds for TP, FP, FN variant calls in the pipeline- Update in house autoclassification tool with new HGMD and Alamut data- Involved in bioinformatics end of processing partners biobank data (genotype, imputed and withdrawals)- Support various research projects along with daily operational work and developmental work

Greater San Diego Area

Thesis: Metagenomic analysis uncovers strong relationship between periodontal pathogens and vascular dysfunction in American Indian population- write statistical programs to analyze human metagenomic sequence data and find any co-relation between PD and CVD- Act as liaison between members of the Institute of public health (SDSU) and bioinformatics team and keep them updated about the project progress

Greater San Diego Area

- Teaching Assistant for Principles in Cell and Molecular Biology (200 level) lab program- Conducted interactive discussions on a weekly basis with 60 students and assisting them through question clarification- Set up the lab for new experiments and teach the basics of how to use lab equipment and teach various lab calculation concepts to help students through Cell and Molecular Biology theory class - Wrote weekly quizzes, graded quizzes and lab reports, track the student records using blackboard

Greater San Diego Area

- Upload paired end and long read files (fastq) to 1000 genome project webserver- Determine the moleculo structural variant (SV) calls quality using the False Discovery Rate (FDR). Filter these SV calls based on various criteria to achieve lower FDR- Validate moleculo SV calls with 1000 genome project sequenced SV calls

Greater San Diego Area

- Desk Assistant at TEC desk- As a DA at the desk, was responsible for maintaining package logs- Attending calls, mails and respond to students living at the resident hall

- As a Market research analyst for the pharma team, have maintained clinical trial database for various indication (Diabetes, Head and neck cancer) and analyzed the clinical trial data- Created and maintained a database for KOL profiles- Involved in Market research, Market intelligence and Indication landscape projects- Worked on competitive intelligence projects on various therapeutic areas (Metabolic, Oncology and Respiratory)- Timed delivery of reports (monthly and quarterly reports)

Bengaluru Area, India

- Process development for quantification of residual kanamycin using HPLC- Hands on experience working with High Pressure Liquid Chromatography

Master’S Degree, Bioinformatics, 3.65

Python programming, Methods in bioinformatics, Biochemistry, Statistics, Data analysis using R

Bachelor Of Engineering (B.E.), Biotechnology, 3.7

- Extraction of polysaccharides from vegetable waste and their Eco-Friendly reuse

High School

Education record