RADU I. COJOCARU, PH.D. **** Daylily Drive Carlsbad, CA 92011

202-***-**** acrlnc@r.postjobfree.com

SENIOR MANAGER R&D BIOINFORMATICS

Key Highlights

Over 15 years of software development coupled with 10 years of hands on experience and leadership in genomics, big data management, analysis pipelines, interpretation and application development in academic

(University of Michigan, Ann Arbor), government (National Institutes of Health, Bethesda, MD) and commercial settings (Elsevier and Thermo Fisher); recent NGS publications in top tier journals including Nature Genetics, American J of Human Genetics, J Neuroscience, Neurobiology of Aging

Adaptable personality in a hybrid environment; able to focus, set priorities, yet maintain flexibly in changing environments; proficient in implementing appropriate project management methodologies; dynamic very detailed oriented team player with strong interpersonal, communications, planning and execution skills Education

Ph.D. Computational Physics – Complex Systems 2006 MICHIGAN STATE UNIVERSITY, EAST LANSING, MI

Bachelor of Science, Mathematics and Computer Science 1999 UNIVERSITY OF TIMISOARA, TIMISOARA, ROMANIA

Master of Science, Theoretical Physics 1995

UNIVERSITY OF TIMISOARA, TIMISOARA, ROMANIA

Bachelor of Science, Physics 1994

UNIVERSITY OF TIMISOARA, TIMISOARA, ROMANIA

Professional Profile

THERMO FISHER SCIENTIFIC, CARLSBAD, CA July 2014 – February 2015 Senior Manager/Associate Director R&D Bioinformatics Leadership Role

Lead locally and remotely a team of software developers, bioinformatics scientists and project managers in assessing and transforming the team into an agile, collaborative, continuous delivery one;

Team performance management and code/project review using Github and JIRA; generate documentations and participate in requirements, design and traceability review; code inspection and walk through as well as verification and validation efforts

Develop and implement vision for bioinformatics scientists to support R&D and clinical data analysis; work with research key stakeholders to prioritize bioinformatics services to best meet customer needs; ensure robust and scalable end-to-end bioinformatics pipelines and provide custom solutions

Develop staffing plans and oversee recruitments as needed; mentor and manage a talented group that works together with other R&D teams to build leading edge genomics diagnostic products and web-based software to support internal process automation and laboratory information systems RADU I COJOCARU, PHD

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Work closely with Corporate Development and Patent teams to implement the company’s intellectual property decision in written agreements (CDA, NDA, PIA and other confidentially agreements); familiar working in a GCP, GMP and FDA environment; build strong relationships with departmental leaders throughout the company, and contribute to leadership decisions Scientific Role

Oversee execution of Bioinformatics and IT infrastructure for national-scale level projects including Saudi Genome Project, Kuwaiti Genome Project, Stratified Medicine Scotland and Million Veterans Program

Bioinformatics design, implement and support for gene-panel, exome, and whole genome re-sequencing pipelines; support bioinformatics analysis of mapping, detection, annotation and interpretation of variants

Identify the costs and benefits of third party software tools versus de novo or in-house implementations; experienced with off-the-shelf tools and proprietary algorithms for variant annotation and interpretation

Work with clinicians and software developers in designing, analyzing and preparing customized clinical reports;

Develop new tools for analysis of sequencing and variant quality metrics, annotation and interpretation; integrate commonly used open source bioinformatics software applications into existing suite (Ion Torrent); build and maintain knowledgebase for the discovery of novel variation and association with disease

Provide rapid bioinformatics support to population study projects for gene panels and genome re- sequencing; implement the execution of population-scale genomic medicine projects, and on designing and performing large-scale studies to identify disease-causing genes and genetic risk factors ELSEVIER, ROCKVILLE, MD October 2012 – May 2014

Senior Bioinformatics Scientist

Leadership Role

Manage multiple projects to ensure successful delivery in accordance to scope, time and resources using Agile methodology; provided scientific and technical leadership to an offshore development team and biologists using Scrum software methodology

Reported on delivery status and progress to key stakeholders and the VP throughout the course of the projects; defined the overall Bioinformatics and NGS strategic vision including products, services and business development

Maintain awareness of existing and emerging infrastructure technologies, regulatory issues, and market factors and assist in the development of the IT strategy and plan; addressed key informatics challenges in NGS big data management, analysis and interpretation for agricultural and molecular biology applications Scientific Role

Initiated and organized weekly bioinformatics seminars by inviting customers, colleagues and collaborators to present their work and to establish new collaborations

De novo analysis for Jute genome, developed new database of predict orthologs and metabolic pathways (R)

Proposed, developed and delivered from scratch a standalone module for Variant Calling analysis including easy-to-use customizable workflows for identifying variants from various public databases

Implemented a novel network algorithm for identifying upstream regulators that can explain the observed expression patterns in a user’s dataset; then examine the biological processes, pathways and diseases the regulators and their targets may control (R/Bioconductor, C++, Java)

Developed a Genomic Data Repository automatic pipeline to provide Pathway Studio users access to freely available microarray data for clinical and pathway information for disease studies (R/Bioconductor) RADU I COJOCARU, PHD

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NATIONAL INSTITUTES OF HEALTH (NIH) / NATIONAL EYE INSTITUTE (NEI), BETHESDA, MD January 2008 – October 2012 Senior Bioinformatics Fellow

Leadership Role

Active hands-on member of High Performance Computing (Helix Systems) and the NIH Biowulf cluster

Served as a liaison member between NEI labs and Information Technology division within NEI to provide IT solutions in accordance to NIH regulations; served as a liaison between NEI IT members and other Institutes within NIH; Designated as essential personnel during potential furloughs

Advised in recruiting students, post-docs and principal investigators; mentor post baccalaureate students; trained and taught graduate students and postdoc in analyzing and interpreting various genomic data Scientific Role

The first bioinformatics fellow in National Eye Institute history that had: (i) administrative privileges on his NEI computers, (ii) Linux on one of his NEI computers and (iii) a Biowulf/Helix account

Set up pipelines and performed statistical analysis for microarray and Next Generation Sequence data from various platforms (Illumina, 454, Ion Torrent): ChIP-seq, DNA-seq, Exome-seq, miRNA-seq, RNA-seq using open source (Perl, Python, R and Bioconductor, Helix/Biowulf cluster) and also of-the shelf tools

Compiled and integrated bioinformatics, genomics and proteomics public efforts to analyze and interpret various omics data

Initiated collaborations with investigators across NIH campus and universities that led to 10 publications in peer-review journals and about 20 posters; coordinated teams composed of postdoc and bench scientists to ensure solid bioinformatics results delivered in a timely matter

Reorganized data handling and acquisition for a lab with +50 people that made possible sharing the entire collection of genomics data (including terabyte scale data generators like Illumina GA IIx sequencer) within the lab and also with other members of the scientific community; administrator for in-house databases UNIVERSITY OF MICHIGAN, KELLOGG EYE CENTER, ANN ARBOR, MI January 2007 – January 2008 Postdoctoral Bioinformatics

Determined patterns between genes using flow sorted microarray data from retina by reducing the complex network of gene interactions to a topological model using network flows algorithms (Python, Matlab, C++)

Worked on gene co-expression network methods used to explore the systems-level functionality of genes; key disease genes were identified and validated by bench scientists (Matlab, Bioconductor, R) MICHIGAN STATE UNIVERSITY, DEPARTMENT OF PHYSICS, EAST LANSING, MI September 2000 – December 2006 Research Assistant

Combinatorial optimization algorithms and their applications to disordered systems; developed novel algorithms for studying NP-C hard problems like Satisfiability and Coloring using message passing algorithms and probabilistic graphical models (C++, Perl and Python).

Weighted network reconstruction using gene expression data; implemented polynomial algorithms - minimum spanning tree, and network flow algorithms - MinCut-MaxFlow (Matlab, Python)

Numerical simulations on statistical models with and without quenched disorder using the mean field approximation (C++, Fortran); Molecular Dynamics, Monte Carlo, Simulated Annealing (Fortran)

Taught graduate (Quantum Mechanics and Statistics) and undergraduate classes (Mathematica and Matlab) NATIONAL INSTITUTE FOR CONDENSED MATTER RESEARCH, TIMISOARA, ROMANIA July 1996 – July 1999

Developed a database for the Institute’s library (FoxPro) and performed numerical calculations (Fortran77) RADU I COJOCARU, PHD

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Skills (Bioinformatics)

Sequence Analysis: Annovar, Blast, ClustalW, Emboss, Fasta, PolyPhen-2, Sift, Torrent Variant Caller

Next-Generation Sequencing: BamTools, bamUtil, BCFTools, BedTools, BFast, Bowtie, BWA, Casava, CGATools, CoNIFER, Cufflinks, DeFuse, FastQC, FusionSeq, FusiopnMap, Galaxy, GATK, IGV, MACS, Megan, miRanda, MuTect, MutSig, Phred, Picard, Pindel, SAMtools, TopHat, VarScan, VarSifter, VCFTools

Microarray Analysis: Affymetrix Power Tools, Matlab, Bioconductor and R

Phylogenetic and Analysis: Madeline, BEAST, Merlin, Plink, Metal

Systems Biology: PhD dissertation, Ingenuity Pathways Analysis, Pathway Studio, GeneGO, Cytoscape and its plugins, Spotfire, Gorilla, DAVID, Reactome, KEGG…

Databases: gatekeeper for 9 datasets linked to publications; COSMIC, UCSC, Oncomine, TCGA, CaSNP, dbSNP, dbVar, ClinVar, dbGaP, GTR…

Agile Methodology to configure and develop process, standards and procedures using JIRA; various software development methodologies like Agile and Scrum

Expert with off-the-shelf software: IPA, GeneGO, Pathway Studio, Partek, Genespring, Genomatix, CLCBio…

Teaching and training scientists various bioinformatics concepts and pipelines tailored to their needs

Bioinformatics cores: Helix Systems and Biowulf from NIH and The Orchestra high performance computing cluster from Harvard Medical School

Recent Honors and Awards

Annual PBT Meeting Poster Presentation Award – Elsevier Pharma and Biotech Division 2013 Special Act Award, National Eye Institute, National Institutes of Health 2012 Scientific Director Award, National Eye Institute, National Institutes of Health 2010 Professional Affiliations (since 2004)

American Physics Society International Society for Computational Biology

American Statistical Association Complex Biological Systems Alliance

The Science Advisory Board The Association for Research in Vision and Ophthalmology Publications (Bioinformatics)

Myung Kuk, Heung Sun Kwon, Cojocaru R.I., Stanislav Tomarev Myocilin regulates cell proliferation and survival by activating the ERK pathway. J. Biol Chem 2014 Apr 4; 289(14):10155-67 Wenxin Ma*, Cojocaru R.I.*, Linn Gieser, Norimoto Gotoh, Tiziana Cogliati, Anand Swaroop, Wai Wong Age-related changes in the gene expression patterns in mouse retinal microglia. Neurobiology of Aging 2013 Oct 34(10):2310-21 The AMD Gene Consortium - Cojocaru R.I Seven New Loci Associated with Age-Related Macular Degeneration, Nature Genetics. 2013 Apr: 45(4:433-9)

Yagya V. Sharma, Cojocaru R.I., Linda M. Ritter, Nidhi Khattree, Brooks M, Scott A, Swaroop A. Protective gene expression changes elicited by an inherited defect in photoreceptor structure. PLoS One 2012; 7(2) RADU I COJOCARU, PHD

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Roger JE, Ranganath K, Zhao L, Cojocaru R.I., Brooks M, Gotoh N, Veleri S, Hiriyanna A, Rachel RA, Campos MM, Fariss RN, Wong WT, Swaroop A. Preservation of cone photoreceptors after a rapid yet transient degeneration and remodeling in cone-only Nrl-/- mouse retina. J. Neurosci. 2012, Jan 11; 32(2):528-41 Saravanamuthu SS, Le TT, Gao CY, Cojocaru R.I., Pandiyan P, Liu C, Zhang J, Zelenka PS, Brown NL. Conditional ablation of the Notch2 receptor in the ocular lens. Dev Biol. 2012 Feb 15; 362(2):219-29 Fanchiang SS, Cojocaru R.I., Othman M, Khanna R, Brooks MJ, Smith T, Tang X, Maricic IL, Swaroop A, Kumar V. Global expression profiling of peripheral Qa-1-restricted CD8αα+TCRαβ+ regulatory T cells reveals innate-like features: Implications for immune-regulatory repertoire. Hum Immunology. 2012 Mar; 73(3); 214-22 Xue W*, Cojocaru R.I.*, Dudley VJ, Brooks M, Swaroop A, Sarthy V.P. Ciliary neurotrophic factor induces genes associated with inflammation and gliosis in the retina: a gene profiling study of flow-sorted cells. PLoS One. 2011; 6(5):e20326. Epub 2011 May 26.

Parapuram SK*, Cojocaru R.I.*, Chang JR, Khana R, Brooks M, Othman M, Zareparsi S, Khan NW, Gotoh N, Cogliati T, Swaroop A. Distinct signature of altered homeostasis in aging rod photoreceptors: implications for retinal disease. PloS One. 2010 Nov 8; 5(11)

Friedman JS, Ray JW, Waseem N … Cojocaru R.I. … Swaroop A. Mutations in a BTB-Kelch protein, KLHL7, cause autosomal-dominant retinitis pigmentosa. Am J Hum Genet. 2009 Jun; 84(6):792-800

* contributed equally

REFERENCES

Anand Swaroop, Ph.D. Phil Duxbury, Ph.D.

Lab Chief, National Institutes of Health Professor and Chair, Department of Physics National Eye Institute Michigan State University

Building 6, Room 338 BPS Building, Room 4260

Bethesda, MD 20892-0610 East Lansing, MI

Phone: 301-***-**** Phone: 517-***-****

Email: acrlnc@r.postjobfree.com Email: acrlnc@r.postjobfree.com Travis Vaught, Ph.D. Lawrence Lucia

Senior Scientific Product Solution Specialist Admin Lab Manager, National Eye Institute Elsevier National Institutes of Health

5635 Fisher Lane, Room 123 Building 6, Room 341

Rockville, MD 20852 Bethesda, MD 20892-0610

Email: acrlnc@r.postjobfree.com Email: acrlnc@r.postjobfree.com Phone: 240-***-**** Phone: 301-***-****

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