Quality Control Project

RAKESH PONNALA

***** ******** ****, ************, ** 46077

650-***-**** ( ******.*********@*****.***

Summary

Integrative Scientist with more than 5 years of successful experience in

Genomics

. Project leader for design & implementation of Next Gen sequencing LIMS

systems

. Project management experience with design & Implementation of several

Next Gen projects in collaboration with various R&D partners

. Experience with Next Generation sequencing technologies - ion torrent-

PGM, illumina (Hiseq2500, Miseq) & Roche 454

. Experience with Linux, high performance computing (HPC) environments,

and queuing systems

. Co-authored Next Gen papers in peer journals such as Nature Biotech &

Cancer Research

. Programming experience in UNIX Shell, REST-API, C, HPC, PERL, Python

. Experience building analysis pipelines for Mapping & genome assembly

using Next Gen data

TECHNICAL SKILLS

Computer Skills: UNIX, REST-API, HPC, C, Python, Pipeline pilot, JAVA, and

Microsoft Office Suite

Laboratory Skills: Illumina Next Gen library preparations-- m-RNA, small

RNA, bisulfite, Mate-pair, Whole genome, Sequence capture, Genotyping by

sequencing (GBS)

PROFESSIONAL EXPERIENCE

DOW Chemicals

Indianapolis, IN

Lead Scientist, Next Generation Sequencing Center of expertise

10/2011-Till Date

. Designed & Implemented Next Gen projects by collaborating with

different R& D Partners

. Project leader for LIMS-Successfully designed, tested & implemented

Next Gen LIMS in core lab

. Bioinformatics focal point for Next Generation sequencing core

facility

RAKESH PONNALA

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. Manage daily activities of technicians and contractors in core lab

. Develop lab automation & LIMS Integration for Next Gen core lab using

REST-API scripting

. Experience with UNIX Shell, high performance computing (HPC)

environments, and queuing systems

. Developed analysis and quality control pipelines for a variety of Next

Gen Sequencing (NGS) applications such as m-RNA, SNP calling,

transcript detection, small RNA, bisulfate & mate pair

. Extensive Analysis experience with variety of Next Gen projects like

Bacterial genome Assembly, cry genes discovery, transgenes

Identifications

. Experience with development of robot automation work flows like High

Throughput (HTP)/Robots such as Biomek FXP Laboratory Automation

Workstation, Apollo 324, Caliper- Lab chip EZ & Fragment Analyzer Next

Gen instruments

SMITH HANLEY CONSULTING GROUP

Lake MARY, FL

Client: HOFFMANN-LA ROCHE

Research Scientist, Translational Research Sciences- pRED

10/2010 - 10/2011

. Identified Biomarkers in solid tumors using Next generation sequencing

platforms-NGS (mate pair, paired end, transcriptome sequencing, Roche-

454-GS-FLX, Amplicon-sequencing)

. Sequenced breast cancer cell lines and prostate tumors using illumina

paired end methodology

. Performed whole genome sequencing on pancreatic tumors using illumina

mate pair platforms from library preparation, sequencing-c-bot

amplification (GA-IIx) sequencing & data analysis

ADECCO INC

Nutley, NJ

Client: HOFFMANN-LA ROCHE

Research Scientist, Translational Research Sciences- pRED

01/2010 - 10/2010

. Evaluated Alignment algorithms like BWA, MAQ, Novo align & GSNAP for

structural variations

. Developed Secondary Analysis pipelines using Break dancer & SVdetect

algorithms, and discovered structural variations in solid tumors using

whole genome sequencing data

. Validated Structural Variations such as Deletions, indels, inversions

& gene fusions using q-PCR

. Analysis experience with NGS Algorithms like fastqc, Bowtie, SOAP,

samtools, Picard tools-java, CASAVA & IGV

RAKESH PONNALA Page 3

Michigan Center for Translational Pathology

Ann Arbor, MI

Research Intern, Advisor- Dr. Arul Chinnaiyan

01/09 -01/10

. Contributed towards the development of Next Gen sequencing Algorithm

"Consig"

. Applied "Consig" on lung cancer RNAseq data & nominated lung cancer

gene fusions

. Identified a recurrent gene fusion R3HDM2-NFE2 in lung cancer by q-PCR

methods

. Characterized the biology of R3HDM2-NFE2 by various Molecular

biology methods

GVK Biosciences

Hyderabad, India

Research Associate, Pharmacogenomics

01/07 - 12/07

. Learned basics of library preparation for Next Gen sequencing

platforms -Solexa & 454

. Exposure to Next Generation sequencing Analysis such as 454 & Solexa

. Hands on experience with Next Gen sequencing instrumentation

. Experience with Linux, high performance computing (HPC) environments,

and queuing systems.

EDUCATION

UNIVERSITY OF SOUTH CAROLINA

Columbia, SC

Master of Science, Biology (GPA: 3.27/4.0)

May 2010

Jawaharlal Nehru Technological University

Hyderabad, India

Bachelor of Technology, Biotechnology (GPA: 3.8/4.0)

May 2007

PUBLICATIONS

. Qing-Wen Xu, Wei Zhao, Dong-Mei Han, Maureen A. Sartor, Rakesh

Ponnala, Yong Chen, Hong-Mei Zhao, Jiang-Ying Yang, Qing-Yun Zhang,

Fag-Fang Liu, Feng Lan, Yan-Hui, Yu Zhang, Xiao-song Wang, Wei-Feng

Chen." An integrated genome-wide approach to discover tumor specific

genes as potential immunological and clinical targets in cancer"

Cancer Research .2012

. Xiao-Song Wang, John Prensner, Guoan Chen, Qi Cao, Bo Han, Saravana M

Dhanasekaran, Rakesh Ponnala, Xuhong Cao, Sooryanarayana Varambally,

Dafydd G.Thomas, Thomas J. Giordano, David G. Beer, Nallasivam

Palanisamy, Maureen A. Sartor, Gilbert S. Omenn, Arul M. Chinnaiyan.

"An Integrative Approach to Reveal Driver gene fusions from paired-end

sequencing data in Cancer" Nature Biotechnology.2009 November;

1(37):D767-72

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