Arpit M. Email & Phone Number

Miami, Fl, Us

New York, United States

Miami, Florida, United States

Miami/Fort Lauderdale Area

Miami-Fort Lauderdale Area

Director of Bioinformatics, CardioPath Lab -Larkin Uni COVID grant. July 2020-Present Design of COVID-19 Sequencing panels capturing different strains using Thermofisher and SeeGene technologies, setting up bioinformatics pipeline to identify the variants and produce clinical report. Setting up Covid-19 testing panels using HOLOGIC panther fusion and TMA assay, Building result interface with State of… Show more Director of Bioinformatics, CardioPath Lab -Larkin Uni COVID grant. July 2020-Present Design of COVID-19 Sequencing panels capturing different strains using Thermofisher and SeeGene technologies, setting up bioinformatics pipeline to identify the variants and produce clinical report. Setting up Covid-19 testing panels using HOLOGIC panther fusion and TMA assay, Building result interface with State of Florida.Discovery of SARS-Cov-2 in cardiomyocytes via sequencing, project in collaboration with Mayo clinic.Designed and Implemented bioinformatics pipelines for Molecular diagnostic lab for Cardiac Next generation sequencing panels. Conducted Analytical and Bioinformatics validation of theses panels for genetic testing of Cardiac patients. Established limit of detection and sensitivity/specificity threshold for these panels.• Establishing LIMS system for the lab. Show less

Miami/Fort Lauderdale Area

Leading interdisciplinary teams to set up Bioinformatics and Data management processes at Center for genomic medicine, Molecular diagnostic lab and office of clinical research at MCI• Designed and Implemented bioinformatics pipelines for Molecular diagnostic lab for Oncology Next generation sequencing panels. Conducted Analytical and Bioinformatics validation of theses panels for genetic testing of cancer patients. Established limit of detection and sensitivity/specificity threshold for… Show more Leading interdisciplinary teams to set up Bioinformatics and Data management processes at Center for genomic medicine, Molecular diagnostic lab and office of clinical research at MCI• Designed and Implemented bioinformatics pipelines for Molecular diagnostic lab for Oncology Next generation sequencing panels. Conducted Analytical and Bioinformatics validation of theses panels for genetic testing of cancer patients. Established limit of detection and sensitivity/specificity threshold for these panels.• Established web Interface for the lab to visualize, annotate and interpret results from various clinical databases and generate patient reports with recommended therapies• Led the CAP/CLEA accreditation process for the bioinformatics and LIMS (laboratory information management system). Established HIPPA compliant protocols for data generation, transfer, analysis, interpretation, storage and maintenance according to the CAP standards. Received the CAP accreditation for the lab in 2019 with zero remarks.• Established High performance compute core for the genomic big data analysis. Designed the system architecture and budget for the core. Supervised the bioinformatics and Map-reduce based software for faster processing of data. Created In house genomics variation database for storing the variants and other genetic information coming from the analysis. Wrote protocols for generation of fastq, bam, vcfs and other genomics files along with the storage archival and maintenance process in line with NIH-DBGAP guidelines. • Consulted and supported Principal Investigators and Physicians for designing retrospective research studies, Investigator initiated trials for Office of clinical research. • Represented MCI at various scientific conferences by presenting posters/research articles. Show less

Miami, Florida

• Developed and implemented pipelines for the analysis of large genomic data sets - including whole genome/exome sequencing (DNA-seq), Transcriptome analysis (RNA-seq), DNA Methylation, Microbiome studies, Omics data Analyses and cancer biology. Analyzed and evaluated new methods for QC, alignment, assembly, annotation and differential expression of genomic data. Analyzed more than 2000 exomes and over 500 rna-seq samples every year. • Implemented GATK, Bow-Tie, BWA, MAQ, Galaxy, TopHat… Show more • Developed and implemented pipelines for the analysis of large genomic data sets - including whole genome/exome sequencing (DNA-seq), Transcriptome analysis (RNA-seq), DNA Methylation, Microbiome studies, Omics data Analyses and cancer biology. Analyzed and evaluated new methods for QC, alignment, assembly, annotation and differential expression of genomic data. Analyzed more than 2000 exomes and over 500 rna-seq samples every year. • Implemented GATK, Bow-Tie, BWA, MAQ, Galaxy, TopHat, Cufflinks, STAR, Samtools, CLC-bio, bedtools, Annotation tools, NCBI-all tools, IGV, edgeR, DEseq, Mac-Vector, GeneSpring,GeneGo metacore, life-scope etc.• Developed Front end applications for the end user for querying the databases, designing forms for data entry and update using PhP, AJAX and Jquery. Perl, Unix, python, R and C++ were used for the development of pipelines for analysis of Data• Machine Learning Approaches like Random Forest and Support Vector machines to predict the data and corresponding attributes. • High Performance cluster management using lsf scheduler, resource allocation and node distribution were prime task. Error and failure management using lsf flags. • Database and Software development and management for the Variation (SNP) datasets. 5+ years of experience in the analysis, design, development, implementation, testing, maintenance, and documentation of Database and Client Server applications for Research Data.• Lead Bioinformatics consultant 3+ years’ experience in Leading the consulting core projects (40% of job duty), Rendering research analysis services to all the other departments and institutes in University of Miami • Interacting with Principal Investigators (PIs) and Doctors on daily basis for variety of Projects, grants and result discussions. • Training other analyst on the Bioinformatics technology and Generating Publication ready material for PIs and labs 7+ publications and 20+ posters in leading journals and conferences Show less

DNA sequencing facility and Microbiology lab of Dr. Fredrick BushmanManagement of data coming out of Roche 454 sequencer, building Web Based tools for data access, processing and display. Providing support for various project involving statisticalanalysis of data in Microbiology lab, developing web interfaces and automatizing the data analysis process using R, Perl, PHP and python as major programming languages.

Encoded Library Technology (ELT) Discovery TeamCreated a multi-user MS Access database accessed either via a web interface or access forms to help the discovery community. Data source included 2 illumina GA2, 2 Roche FLX genome sequencers, qPCR, BioAnalyzer, and various robotic platforms.

Working On Next Generation Sequencing projects.Design and implementation of system architecture for data processing

Dot Net specialist, working on MS share point server 2007

Doctor Of Philosophy - Phd, Computer Science And Bioinformtics

phd with work

Graduate Buisness Diploma, Business Administration And Management, General

Ms, Bioinformatics

Activities and Societies: Hindu Student Council

Bachelor Of Engineering, Biotechnology