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Lessons offered by Radu
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The lessons will be held
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Taught subjects
  • Mathematics
  • Physics
  • Algebra
  • Trigonometry
  • Geometry
  • Physics - Chemistry
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  • All Levels

Radu Cojocaru - BS, MS, PhD Physics, BS Mathematics and Computer Science

Methodology

BS, MS, PhD in Physics
BS Mathematics and Computer Science
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Background

Teaching Physics and Math Classes for high school and college students - undergraduate and graduate classes.
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Rates

Rate for online lessons : $25/h
Lessons offered by Radu
Individual
In group
The lessons will be held
at his home
at your home
webcam
Taught subjects
  • Mathematics
  • Physics
  • Algebra
  • Trigonometry
  • Geometry
  • Physics - Chemistry
Levels
  • All Levels

Radu's resume

Radu I. Cojocaru, Ph.D. 6594 Daylily Drive | Carlsbad, CA 92011
(concealed information) | (concealed information)


Radu Ionut Cojocaru - 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, Thermo Fisher Scientific, Annai Systems); 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 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

Computational Skills (Bioinformatics)

• Big Data Analysis: Association Studies, Population Stratification, Cohort Analyses; GWAS and Meta-Analyses, Natural Language Processing, Data Mining, Information Extraction, Ontology, Semantic Technology
• Machine Learning and Deep Learning: Probabilistic Graphical Models, Clustering and Classification, Neural Networks, Hidden Markov Models; Message Passing Algorithms, Belief Propagation
• 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, MutSigCV, Phred, Picard, Pindel, SAMtools, TopHat, VarScan, VarSifter, VCFTools
• Databases: gatekeeper for 9 datasets hosted by NCBI linked to publications; 1000 Genomes, COSMIC, UCSC, Oncomine, TCGA, ICGC, CaSNP, dbSNP, dbVar, ClinVar, dbGaP, ExAC…
• Sequence Analysis: Annovar, Blast, ClustalW, Emboss, Fasta, PolyPhen-2, Sift, Torrent Variant Caller…
• Linkage and Phylogenetic Analysis: Madeline, BEAST, Merlin, LAMP, MACH, Plink, Metal…
• Microarray Analysis: Affymetrix Power Tools, Matlab, BRB – Array Tools, Bioconductor and R
• Systems Biology: Ingenuity Pathways Analysis, Pathway Studio, GeneGO, Cytoscape and its plugins, Spotfire, Gorilla, DAVID, Reactome, KEGG…
• Agile Methodology to configure and develop processes, standards and procedures using JIRA and software development methodologies including Agile and Scrum
• Off-the-shelf software: IPA, GeneGO, Pathway Studio, Partek, Genespring, Genomatix, CLCBio…
• Bioinformatics cores: Helix Systems and Biowulf from National Institutes of Health and The Orchestra High Performance Computing Cluster from Harvard Medical School

Professional Profile
Director of Bioinformatics - Annai Systems, Carlsbad, CA October 2015 – Present
Leadership Role
• 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
• Report on delivery status and progress to the CEO, the VP and key stakeholders throughout the course of the projects; define the overall Bioinformatics and NGS strategic vision including products, services and business development; guide Annai’s expansion to new genomic markets  
Scientific Role/Hands On
• Develop tools for analysis of sequencing and variant quality metrics, annotation and interpretation; Integrate commonly used open source bioinformatics software applications like PCA, K-means or MutSigCV into company’s platform
• Build and maintain knowledgebase for the discovery of novel variation and association with disease with main focus on cancer genomics
• 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
Senior Manager R&D Bioinformatics - Thermo Fisher Scientific, Carlsbad, CA July 2014 – February 2015
Leadership Role
• Developed and implemented vision for bioinformatics scientists to support R&D and clinical data analysis; worked with key stakeholders to prioritize bioinformatics services to best meet customer needs; ensured robust and scalable end-to-end bioinformatics pipelines and provide custom solutions
• Developed staffing plans and oversee recruitments as needed; mentored and managed a talented group that worked 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
• Worked 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; built strong relationships with departmental leaders throughout the company, and contribute to leadership decisions
Scientific Role/Hands On
• 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
• Oversaw parts of 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
• Implement and support for gene-panel, exome, and whole genome re-sequencing pipelines; supported bioinformatics analysis of mapping, detection, annotation and interpretation of variants
• Implemented parts of the execution of population-scale genomic medicine projects performing large-scale association studies to identify disease-causing genes and genetic risk factors; worked with clinicians and software developers in designing, analyzing and preparing customized clinical reports
Senior Bioinformatics Scientist - Elsevier, Rockville, MD October 2012 – May 2014
Leadership Role
• Provided scientific and technical leadership to an offshore development team and biologists using Scrum/Agile software methodology
• Maintained 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/Hands On
• 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)
• Developed 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)
Senior Bioinformatics Fellow - National Institutes of Health (NIH), Bethesda, MD January 2008 – October 2012
Leadership Role
• Served as a liaison member between NEI labs and Information Technology division to provide IT solutions in accordance to NIH regulations; designated as essential personnel during potential furloughs
• Participated in recruiting students and post-docs; mentor post baccalaureate students; trained and taught graduate students and postdoc in analyzing and interpreting various genomic data
• Coordinated teams of postdoc, bench scientists and post-baccalaureate students to ensure solid bioinformatics results delivered in a timely matter
Scientific Role/Hands On
• Reorganized data handling and acquisition for a lab of +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
• Initiated collaborations with investigators across NIH campus and universities resulting in more than 30 projects that led to 10 publications in top peer-review journals
• Set up pipelines and performed statistical analysis for microarray and Next Generation Sequence data from various platforms including Illumina, 454, Ion Torrent, Affymetryx and Agilent
• Data Analysis: RNA-seq, ChIP-seq, DNA-seq, Exome-seq, miRNA-seq, using open source (Perl, Python, R and Bioconductor, Helix/Biowulf cluster) and of-the shelf tools (Partek, Genespring, CLCBio, Genomatix)
• Active hands-on member of High Performance Computing (Helix Systems) and the NIH Biowulf cluster; the first bioinformatics fellow at National Eye Institute that had: administrative privileges on NEI computers, Linux installed on NEI computers and a Biowulf/Helix account
Postdoc Bioinformatics - University Of Michigan, Kellogg Eye Center, Ann Arbor, MI January 2007 – January 2008
• 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 to explore the systems-level functionality of genes; key disease genes were identified and validated (Matlab, Bioconductor, R)
Research Assistant - Michigan State University, Department of Physics, East Lansing, MI Sept 2000 – December 2006
• Machine learning: (i) developed a message passing algorithms to approximate inference problem based on passing local messages; (ii) worked on probabilistic graphical models of SAT on a tree (C++, Perl and Python)
• Deep Learning: theoretical calculations for Standard Belief Propagation for graphical models with loops; an application for Pairwise Random Markov Fields with N hidden nodes
• Worked on combinatorial optimization algorithms and their applications to disordered systems; developed novel algorithms for solving approximately NP-C hard problems like Satisfiability (SAT) and Coloring
• Numerical simulations on statistical models with and without quenched disorder using the mean field approximation (C++, Fortran); Molecular Dynamics, Monte Carlo, Simulated Annealing (Fortran)
• Systems approach for genomic data: worked on weighted gene networks and pathways reconstruction using minimum spanning tree and network flow methods like MinCut - MaxFlow algorithms (Matlab, Python)
Staff Scientist - 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)

Recent Honors and Awards
Annual PBT Meeting 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
DREAM Challenge, Genome in a Bottle Organization for Rare Disease India

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)
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

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