Parimala Devi

Kuninkaankatu ** **B, ***** Tampere, Finland • +358********** • adgnuv@r.postjobfree.com EDUCATION

Georgia Institute of Technology Atlanta, GA

Master of Science - Bioinformatics, GPA: 3.35/4.00 August 2013 – December 2014 Rashtriya Vidyalaya College of Engineering Bangalore, India Bachelor of Engineering - Biotechnology, GPA: 3.97/4.00 September 2009 – June 2013 WORK EXPERIENCE

Genevia Technologies Oy Tampere, Finland

Bioinformatician, Research and Development March 2020 – present

• Developed ATAC-seq analysis pipeline to assess genome-wide chromatin accessibility using Snakemake workflow management system and Singularity container Jubilant Biosys Limited Bangalore, India

Bioinformatics Consultant, Department of Informatics January 2019 – December 2019

• Designed RNA-Seq differential expression pipeline for Breast cancer data

• Calculation of Pathway Activation Score for biomarker identification Project Intern, Department of Informatics January 2018 – January 2019

• Implemented graph theory algorithms to find largest connected component (LCC) of weighted human pro- tein-protein interaction

• Calculated topological features of proteins in the LCC to compute features to be used for classification via Machine Learning algorithms like mRMR, SVM to find potential drug targets University of Washington School of Medicine Seattle, WA Software Engineer 2, Department of Biomedical & Health Informatics February 2016 – March 2017 Electronic Medical Records and Genomics (eMERGE) Network

• Streamlined variant call pipeline to generate multisample VCF file of ~9000 PGRNseq data (targeted se- quencing in 84 pharmacogenomics genes). Tools used: GATK, Picard, BWA, SAMTools

• Compiling exome chip data from various sites using PLINK

• Worked as the point of contact for the eMERGE Network and University of Washington-IT department

• Managed release of variant data to the eMERGE Network and public database (dbGaP) Georgia Institute of Technology Atlanta, GA

Research Assistant, School of Biology February 2015 – February 2016

• Identified candidate multicellularity loci and determined genetic basis of increased cluster size in snowflake yeast

• Determined genetic basis of increased cell size and programmed cell death in snowflake yeast Graduate Research Assistant, School of Biology May 2014 – December 2014

• Determined molecular basis of multicellularity in experimentally evolved S.cerevisiae and C.reinhardtii

• Developed a pipeline for the whole genome SNP discovery and analysis of variants in the yeast S. cerevisiae

• Analyzed RNA-Seq data from a time-course experiment to examine regulatory basis of a novel multicellular life cycle in Chlamydomonas reinhardtii

RESEARCH PROJECTS

Georgia Institute of Technology Atlanta, GA

Applied Human Computational Genomics: Clinical Metagenomics August 2014 – December 2014 Developed Clinical Metagenomics services app for cystic fibrosis lung microbiota

• Designed a metagenomics pipeline and curated microbial database using Python, Kraken and Krona

• Curated clinically relevant fungal database along with bacterial and virus databases Georgia Institute of Technology Atlanta, GA

Computational Genomics: Gene Prediction and Comparative Genomics January 2014 – April 2014 Five Stage Computational Genomics pipeline to characterize strains of N. meningitidis obtained from Sub-Saharan Africa and determine their infectiousness, in collaboration with Centers for Disease Control and Prevention (CDC)

• Gene Prediction: Performed ab-initio and homology based gene prediction to find significant homology between novel sequences and known gene sequences. Tools used: Blast, Blat

• Comparative Genomics: Performed alignment of FATSQ files. Tools used: Bowtie2, BLAT, MOSAIK, soap2, variant detection using Samtools, Freebayes, bcftools, vcftools, and analysis of the VCF files using SnpEff and annovar

Georgia Institute of Technology

Atlanta, GA

Exome Variation Analysis August 2013 – December 2013 Determined genes and variants which could potentially be pathogenic. GBR HG00146 exome dataset from 1000 Genomes study was chosen for this project

• Variants were called, viewed in Genome browser and annotated

• Rare genes were selected based on a criteria and researched to analyze potential problematic mutations

• The criteria included quality, read depth, rare variant based on the 1000 Genomes frequency, protein coding region and related to or causes a known disease Tools used: Samtools, IGV Genome browser, SnpEff, MS Excel

Georgia Institute of Technology Atlanta, GA

Comparison of differentially expressed gene detection techniques August 2013 – December 2013

• Performed analysis of differentially expressed genes in the RNA-seq pipeline

• Compared different techniques of detection of differentially expressed (DE) genes, using DEGSeq, edgeR, baySeq, and DESeq R packages

COURSES

• Computational Genomics • Bayesian Biostatistics

• Programming for Bioinformatics • Data Visuals and Analytics

• Applied Human Computational Genomics • CS for Bioinformatics

• Genomics for Applied Bioinformatics • Cancer Biology and Biotechnology

• Probability and Statistics

SKILLS

Software Skills: Python, Shell scripting, Perl, Snakemake workflow management system, Singularity container, Slurm Workload Manager, MySQL, Git version control Platforms: Windows- 7, 8.1; Linux- Ubuntu

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