RICHARD ROSARIO RODRIGUES

****, ********** **** ****., ***. 125, Blacksburg, VA-24060.

508-***-****, acs4gm@r.postjobfree.com

Meticulous, self-motivated, creative, and versatile bioinformatician with interdisciplinary research experience. Ability to learn quickly and collaborate with proven management, communications, and leadership expertise. EDUCATION

Ph.D., Genetics, Bioinformatics, & Computational Biology (GBCB) Virginia Tech, Blacksburg, VA. expected Spring 2016 M.S., Bioinformatics, Rochester Institute of Technology, Rochester, NY. Fall 2011 B.E., Biotechnology, Kolhapur Institute of Technology, India. Spring 2008 SPECIAL SKILLS

Business Skills

Problem-solving ingenuity, interpersonal & leadership skills, grant writing, accounting, project management & organizational abilities, multilingual written & oral communication proficiency. Laboratory Techniques

DNA/RNA extraction, PCR, heteroduplex analysis, gel electrophoresis, silver staining, media preparation, cell culture techniques, microbial growth and maintenance, gas chromatography. Bioinformatics Analyses Tools

Metagenomics: UPARSE, QIIME, Mothur, PICRUSt, MEGAN, MG-RAST, MENAP, ISA.

Transcriptomics: BLAST, Bowtie, TopHat, BEDTools, SAMtools, Cufflinks, Trinity, MapSplice, SpliceMap, RNASEQR, CASAVA, cutadapt, FASTQC, FASTX-toolkit, DESeq.

Microarray: Partek Genomic Suite, Gene Set Enrichment Analysis, Ingenuity Pathway Analysis.

Proficient in databases (GenBank, ENSEMBL, UCSC genome browser) and network analyses. Programming Languages

Python, Perl, Java, C, R, SQL, Shell scripting, Parallel programming, Matlab, HTML, PHP, LATEX. EMPLOYMENT

Graduate Research Assistant, Virginia Tech. Jan. 2012 - May 2016

Trained students and collaborated with plant, soil-microbial, computer, and chemical scientists.

Implemented pipelines for high-throughput genomics and transcriptomics data analysis.

Contributed in experiment design, analyses, result interpretation, and manuscript writing.

Authored four journal articles, five manuscripts in prep., and 12 conference presentations. Treasurer/Director of Finance, Graduate Student Assembly, Virginia Tech. Jan. 2014 - Jul. 2016

Drafted annual budget for Graduate Student Assembly (GSA) and increased funding by 35%.

Maintained accounts of GSA’s financial transactions and presented monthly reports.

Represented 6000 graduate students in University Council Commissions & Committees.

Obtained funds and assisted to organize various research and social programs for the GSA.

Initiated two free rental programs for current and graduating Masters and Ph.D. students. Grader, GCCIS IST, Rochester Institute of Technology (RIT). Aug. 2011 - Nov. 2011

Assisted instructors by grading homework assignments and projects as per their guidelines.

Graded and uploaded scores online in a timely manner.

Raised concerns to the instructors about certain students’ submissions. Bioinformatics Intern, University of Rochester Medical Center. June 2010 - Feb. 2011

Collaborated with liver transplant surgeon and cancer researchers.

Implemented pipelines to analyze and summarize data.

Contributed in transcriptomics data analyses, result interpretation, and manuscript writing.

Resulted in one journal article and two conference presentations. Richard Rodrigues

Computer Lab Assistant, Information and Technology Services, RIT. Nov. 2009 - Nov. 2011

Assisted students, staff, and faculty with computers, softwares, and printers.

Trouble shot problems, recorded equipment usage and status, and maintained computer lab.

Promoted to a Supervisory position and submitted employee evaluations. June - Nov. 2010. Bioinformatics Lecturer, Kolhapur Institute of Technology, India. Jan. 2009 - April 2009

Developed teaching materials and delivered lectures to juniors and seniors.

Set, proctored, and evaluated student examinations.

Advised three students in their undergraduate thesis. HONORS AND AWARDS

College of Agriculture & Life Science conference travel Award. Fall 2015 Translational Plant Science conference travel Award. Fall 2015 Student budget board funds for GSA to purchase: 2015

- wireless presenters, poster tubes, graduation cap & gowns, laptop, and printer. Who’s Who in American Colleges and Universities. Spring 2015 GSA’s Travel Fund Program Award. Fall 2014 and Fall 2015 GSA’s Graduate Research Development Program Award. Fall 2014 Interdisciplinary Graduate Education Program fellowship, Virginia Tech. Aug. 2012 - Aug. 2013 Tuition scholarship, Rochester Institute of Technology. Aug. 2009 - Nov. 2011

“Best outgoing student”, Kolhapur Institute of Technology, India. 2008 SERVICE AND LEADERSHIP AT VIRGINIA TECH

Treasurer/Director of Finance for Graduate Student Assembly (GSA). Jan. 2014 - Aug. 2016 Member of Student Budget Board, University Advisory Council on Strategic Budgeting & Planning, and Campus Development Committee. Jan. 2014 - Jul. 2016 Volunteer at GSA’s Socials and Professional School Fairs. Jan. 2014 - Jul. 2016 Reviewer for GSA’s Travel Fund Program Awards. Spring 2014 GBCB Delegate for GSA. Aug. 2013 - May 2014

Reviewer for GSA’s Graduate Research Symposium. Spring 2013 and Spring 2015 PROFESSIONAL AFFILIATIONS

American Society of Agronomy (ASA) Biomedical Engineering Society (BMES) Crop Science Society of America (CSSA) Ecological Society of America (ESA) International Society for Computational Biology (ISCB) Soil Science Society of America (SSSA) MENTORING EXPERIENCE

Taught lab safety protocols, designing and performing experiments, lab maintenance, data analyses, and writing and presentation skills to six undergraduate students from Virginia Tech; two summer Multicultural Academic Opportunities Program (MAOP) students; three undergraduate students from Kolhapur Institute of Technology, India.

PUBLICATIONS

Rodrigues RR, Pineda RP, Barney JN, Nilsen ET, Barrett JE, Williams MA. Plant Invasions Asso- ciated with Change in Root-Zone Microbial Community Structure and Diversity, PLoS ONE, 2015, 10(10): e0141424.

Larkin AL, Rodrigues RR, Murali TM, Rajagopalan P. Designing a Multi-cellular Organotypic 3D Liver Model with a Detachable, Nanoscale Polymeric Space of Disse, Tissue Eng Part C Methods, 2013, 19(11): 875-884.

Tarca AL, et al. Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge, Bioinformatics, 2013, 29(22): 2892-9.

Poirel CL, Rahman A, Rodrigues RR, Krishnan A, Addesa JR, Murali TM. Reconciling Differential Gene Expression Data with Molecular Interaction Networks, Bioinformatics, 2013, 29(5): 622-629.

Poirel CL, Rodrigues RR, Chen KC, Tyson JJ, Murali TM. Top-Down Network Analysis to Drive Bottom-Up Modeling of Physiological Processes, J Comput Biol., 2013, 20(5): 409-418. Page 2 of 3

Richard Rodrigues

Rodrigues RR, Barry CT. Gene Pathway Analysis of Hepatocellular Carcinoma Genomic Expression Datasets, J Surg Res., 2011, 170(1): e85-92.

MANUSCRIPTS IN PREPARATION

Rodrigues RR, Zhao B, Williams MA. Structure and Function of Rhizosphere Bacterial Communities Associated with Contrasting Ecotypes of Switchgrass.

Rodrigues RR, Williams MA. Shifts in Interactions of Bacterial and Fungal Communities in Root- Zones of Invasive Plants.

Pineda RP, Rodrigues RR, Williams MA. Soil Fungal Community Dynamics along the Ecosystem Development in two Geographically Distant Chronosequences.

Pineda RP, Rodrigues RR, Williams MA. Soil Fungal Communities along the Michigan Sand-Dune Soil Chronosequence and its Relationship with Potential Ecosystem Drivers. PRESENTATIONS

Poudel D, Rodrigues RR, Zhao B, Williams MA. Associative Nitrogen Fixation Potential in Root Zones of Switchgrass Cultivars. Poster presentation at Annual Biomedical Research Conference for Minority Students, 2015, Seattle, WA.

Rodrigues RR, Zhao B, Williams MA. Investigating the associative nitrogen-fixing bacteria for sus- tainable production of Switchgrass. Oral presentation at Ecological Society of America Meeting, 2015, Baltimore, MD.

Pineda RP, Rodrigues RR, Williams MA. Soil fungal community change associated with ecosystem development. Oral presentation at Ecological Society of America Meeting, 2015, Baltimore, MD.

Muchlinski A, Tholl D, Chen F, Rodrigues RR, Williams MA. Probing the Volatile Terpenome in Switchgrass (Panicum virgatum) Roots in the Interaction with Rhizobacteria. Poster presentation at TERPNET, 2015, Vancouver, Canada.

Rodrigues RR, Zhao B, Williams MA. Nitrogen-fixing bacteria for sustainable production of Switch- grass. Oral presentation at GSA’s Graduate Research Symposium, 2015, Virginia Tech.

Rodrigues RR, Pineda RP, Barrett JE, Barney JN, Nilsen ET, Williams MA. Plant Invasions Are Associated with Changes in Root-zone Bacterial Communities. Poster presentation at ASA, CSSA and SSSA International Annual Meeting, 2014, Long Beach, CA.

Pineda RP, Rodrigues RR, Williams MA. Soil Fungal Community Dynamics Associated with Season- ality Change and 4000Y of Ecosystem Development. Oral presentation at ASA, CSSA and SSSA International Annual Meeting, 2014, Long Beach, CA.

Rodrigues RR, Pineda RP, Barrett JE, Barney JN, Nilsen ET, Williams MA. Plant Invasions Are Associated with Changes in Root-zone Fungal Communities. Poster presentation at Complex Soil Systems Conference, 2014, Berkeley, CA.

Rodrigues RR, Larkin AL, Vu LT, Tegge AN, Murali TN, Rajagopalan P. Transcriptome Analysis of Multi-cellular Signaling in an Organotypic 3D Liver Model. Poster presentation at Biomedical Engi- neering Society (BMES), 2013, Seattle, WA.

Poirel CL, Rodrigues RR, Chen KC, Tyson JJ, Murali TM. Top-Down Network Analysis to Drive Bottom-Up Modeling of Physiological Processes. Highlights talk at ACM International Conference on Bioinformatics, Computational Biol., and Biomed. Informatics (ACM BCB), 2013, Washington DC.

Poirel CL, Rodrigues RR, Chen KC, Tyson JJ, Murali TM. Top-Down Network Analysis to Drive Bottom-Up Modeling of Physiological Processes. Oral presentation at the Annual RECOMB Confer- ence on Regulatory and Systems Genomics 2012, Redwood City, CA.

Larkin AL, Jain E, Rodrigues RR, Murali TM, Rajagopalan P. 3D Liver Models to Investigate Hepato- toxicity. Invited talk in Nanotoxicity, BMES Annual Meeting, 2012, Atlanta, GA.

Rodrigues RR, Barry CT. Gene Pathway Meta-Analysis Describes Two Clinically Distinct Hepatocel- lular Carcinoma Subtypes. Poster presentation at American Transplant Congress, 2011, Philadelphia, PA. Am J Transplant 2011; suppl 2(11):273.

Rodrigues RR, Barry CT. Gene Pathway Analysis of Hepatocellular Carcinoma Genomic Expression Datasets. Oral presentation at Academic Surgical Congress, 2011, Huntington Beach, CA. Page 3 of 3

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