RAFI SHAIK

Mobile: +01-906*******; E-Mail I.D: ab0izt@r.postjobfree.com

Address: **** ******* *****, ********, ** – 49931

Summary

A bioinformatics scientist with seven years of research experience aspiring for a R&D position to

contribute to the advancement of genomics and its applications.

Work experience

• Pursuing Ph.D in Bioinformatics with focus on grass stress genomics

• Graduate Teaching Assistant - Michigan Technological University, Sep 2009 – Present

• Scientist A - Philips Research Asia, Nov 06 – Nov 08

Education

• Sep, 2009- Present: Ph.D in Bioinformatics and Molecular Biology, Michigan Technological University,

USA

• Oct, 2005- Apr, 2007: Post Graduate Diploma in Bioinformatics (PGDB), Institute of

Bioinformatics and Applied Biotechnology (IBAB), India

• Jun,2003-Apr,2005: M.Sc, Human Genetics, Andhra University, India

• Jun,2000-Apr,2003: B.Sc, Microbiology, Biochemistry and Chemistry, Sri

Venkateshwara University, India

Publications

• Shaik R and Ramakrishna W (2012) Bioinformatic Analysis of Epigenetic and

MicroRNA Mediated Regulation of Drought Responsive Genes in Rice. Plos One 7,

e49331.

• Xu Z, Shaik R, and Ramakrishna W (2011) Polymorphisms and evolutionary history of

retrotransposon insertions in rice promoters. Genome / National Research Council Canada Genome / Conseil

national de recherches Canada 54, 629-38.

• Lalit Gupta, Sunil Kumar, Randeep Singh, Shaik Rafi, Nevenka Dimitrova:

Classification Method for Microarray Probe Selection using Sequence, Thermodynamic

and Secondary Structure Parameters. International Conference on Pattern Recognition

(ICPR), December 8-11 2008, Tampa, Florida, USA

Under Review/Preparation

• Shaik R and Ramakrishna W: Genes and Co-expression Modules Common to

Drought and Bacterial Stress Responses in Arabidopsis and Rice (Under review with

Molecular Plant, April 2013)

• Shaik R, Aparna D, Srinivas S, Dhadi S.R, Wan Jin Jahng and Ramakrishna W:

Metabolomic and proteomic analysis identifies candidates for anticancer activity of rice

callus suspension culture. (Under review with Nutrition and Cancer, Jan 2013)

• Shaik R and Ramakrishna W: Identification and evaluation of stress responsive

genes to distinguish multiple stress conditions in rice using machine learning approaches

(Manuscript under preparation)

Patent

• Shaik Rafi, Nevenka Dimitrova Information systems for pedigree analysis Pub.

No.: US 2011/0093448

Book chapter

• Shaik R and Ramakrishna W (2013) Comparative Genomics of Maize: A

Goldmine of Molecular Evolution, Book name: Genetics, Genomics and Breeding of

Maize, Publisher: SCIENCE PUBLISHERS

Research Skills

Computational skills:

• microarray data using R (Bioconductor), PERL and shell scripting

• Genome sequence analysis using Biomart, GALAXY tools and original code

• Database management and web interfacing using MySQL and PHP

• co-expression network analysis using custom R scripts and packages like WGCNA

• classification analysis using machine learning techniques using SVM, RF in WEKA

• Functional analysis using AgriGO, PlantCyc, Metaboanalysist

• De novo motif discovery using MEME suite and motif analysis using PLANT care and Transfac

• Visualization using Cytoscape and Gephi

Wet lab skills:

• Plant Molecular biology and genomics techniques:

o Gateway cloning to transform agrobacterium and rice callus/seedlings

o Probe/primer design and restriction mapping

o Stable and transient expression line generation

o Expression analysis using SEM/Confocal/Flourscence microscopy and, GUS, GFP and RFP

assays and qPCR

• Proteomic and metabolomic techniques:

o Protein isolation and quantification

o Two-D gel electrophoresis and western blotting

o In-gel digestion and protein identification

o Bacterial and plant proteome/metabolites isolation and fractionation.

• Analytical techniques:

o ABI310 Genome Analyzer

o GC-MS, HPLC-MS/MS

o MALDI-TOF

Research Experience

Michigan Technological University, Houghton, MI, USA

• Comparative transcriptomics of multiple stress response in rice

• Epigenetic and microRNA mediated regulation of drought responsive genes in Rice

• Anticancer agent discovery using rice callus

• Proteomic and metabolomic analysis of maize in response copper stress and plant growth promoting bacteria

Philips Research Asia – Bangalore, India

• Clinical bioinformatics: analysis of polymorphism data for identification of disease

association

• Methylation prediction of CpG islands in different tissues for bio-marker discovery

Institute of Bioinformatics and Applied Biotechnology, Bangalore, India

● Analysis of co-regulated and co-expressed genes in mouse

Integration of developmental pathways in mouse and their role in cancer

●

Teaching experience

• Graduate teaching assistant (GTA) for “Molecular biology Techniques Lab Course” – fall

2010-12.

• GTA for “Biochemistry Lab Course” – spring 2010, 2013.

• GTA for “Principles of Biology Lab Course” – fall 2009, spring 2012.

• Instructor for “Summer Youth Programs-MTU”-2010

• Guided several undergraduates for research.

Presentations and Posters

• Shaik R, Mychal W Ivancich and Ramakrishna W Meta analysis of microarray studies

identifies distinct molecular profiles of abiotic and biotic stress responses in Rice. PAG

XXI 2013, San Diego, CA (Poster)

• Shaik R and Ramakrishna W Epigenetic and microRNA mediated regulation of drought

responsive genes in rice. Genomics Research 2012, Boston, MA (Poster)

• Shaik R and Ramakrishna W Anticancer Activity of Rice Callus Suspension Culture.

Graduate Research Colloquium 2012, Michigan Tech, Houghton MI. (Presenter)

Awards and Honors

• Critic’s choice award for best poster BRC colloquium 2012

• Exceptional Graduate Student Teaching Award, Michigan Technological University,

2011.

• Qualified in CSIR UGC NET – LS (Council of Scientific and Industrial Research,

University Grants Commission, National Eligibility Test - Lectureship) - Dec, 2004.

Contact Information of References

Dr. Ramakrishna Wusirika (Ph. D advisor)

Associate Professor

Research Areas: Plant Molecular Biology and Comparative Genomics; Bioinformatics; Evolutionary and Functional

Analysis of Plant Genes, Promoters, and Transposable Elements.

Department of Biological Science, MTU, Houghton, MI, 49931, USA

E-mail: ab0izt@r.postjobfree.com Tel: 906-***-****

Dr. Hairong Wei (Committee member)

Associate Professor

Research Areas: Biological Regulatory Network Analysis, Systems Biology, Bioinformatics Algorthims and Tool

Development

School of Forest Resources and Environmental Science, MTU, MI, 49931, USA

Email: ab0izt@r.postjobfree.com Tel: 906-***-****

Dr. Chandrashekhar P. Joshi

Interim Chair and Professor of Plant Molecular Genetics

Research Areas: Unraveling the mechanism of cellulose biosynthesis in trees

Department of Biological Science, MTU, Houghton, MI, 49931, USA

Email: ab0izt@r.postjobfree.com Tel: 906-***-****

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