Bioinformatics Scientist application

Neil Kindlon

*** ***** **** #**, ********, CT ***05

********@*****.*** 203-***-****

Bioinformatics Software Developer with M.S. in Bioinformatics, 10 years in industry, 9 years of C++

EDUCATION

M.S. Applied Science, Bioinformatics. August 2004, Rensselaer Polytechnic Institute, Troy, NY

B.S. Computer Science. December 1996, Rensselaer Polytechnic Institute, Troy, NY

KEY SKILLS

Programming: C++, STL, Matlab 6.5, Perl, Java, Visual Basic, FORTRAN

Bioinformatics: Genomic and cDNA Mapping and Assembly, Dynamic Programming, BLAST, BLAT

Operating Systems and Databases: Linux, Unix, Oracle, MySQL, Windows, VMS

EXPERIENCE

Bioinformatics Developer III, 454 Life Sciences, a member of the Roche Group, Branford, CT (12/06 - present)

• Engineered C++ software in Linux environment for genomic and cDNA reference-guided assembly

• Awarded permanent position in March 2007 after 3 month contract spent augmenting pairwise aligner for chimeras

• Promoted from Bioinformatics Developer II in March 2009 for outstanding performance

• Outperformed primary competitor’s software with structural variation detection application. Locates otherwise nearly undetectable gene fusions, critical to oncological research. Incorporates signal processing for consistent deviations in paired-end data mapping and customized clustering strategies for partially and chimerically aligned shotgun reads

• Advanced structural variation detection effectiveness with subsequent categorization application

• Specialized in handling chimeric segments of next-gen sequencing reads for reference-guided assembly

• Aided in converting non-threaded legacy code to efficient lockless multi-threading model

• Upgraded code base with extensive core algorithm changes, functionality enhancements and performance improvements

• Vastly enhanced speed, scope, and accuracy of testing by unprompted development of automated output testing tools

• Contributed to documentation efforts with release notes, user manual, and internal customer support FAQs

Document Analyst, Amici LLC, Albany, NY (9/04 – 12/05)

• Spearheaded successful massive team effort to process high throughput workload for major client

• Revised critical update system for multi-terabyte document storage utilizing MySQL, Oracle, Linux scripts, and Perl scripts

Graduate Student, Rensselaer Polytechnic Institute, Troy, NY (8/03-7/04)

• Successfully completed aggressively paced 30 credit Master of Science program in a single year

• Master’s project - Created a suite of C++ programs in Linux for modified BLAST search of genomic databases that accounts for adjacent nucleotide stacking energies, temperatures, and salt concentrations

• Independent study, Sequence mining - Developed a C++ application in Linux to search genomic databases for closed frequent sequences that implemented the newly published algorithm “BIDE”

• Soft computing - Programmed a genetic algorithm in Matlab 6.5 for multiple protein sequence alignment, and other scripts for fuzzy clustering, neural nets, and cased-based reasoning

• Additional coursework in sequence analysis, molecular biology, molecular modeling, probability theory, and data mining

Software Engineer, Flow Management Technologies, Saratago Springs, NY (8/99 – 4/00)

• Developed medical office administrative applications in Visual Basic

• Programmed SQL server connections between GUIs and databases

Systems Programmer, Cendant Internet Engineering, Cambridge, MA (6/98 – 10/98)

• Wrote C++ programs with Oracle APIs for data mining of customer transaction logs

• Educated the engineering staff in awareness and usage of the Standard Template Library

Software Engineer, FactSet Research Systems, Greenwich, CT (7/96 – 6/98)

• Wrote C++ programs for database management and updates of in-house database system

• Designed and implemented GUI applications as the front-end for financial databases

• Programmed batch job submission, control, and execution of nightly file transfers and database updates scripts in VMS for a DEC Alpha mainframe

• Created software to track, organize, and display update records of financial databases

• Worked with marketing and client support to develop application specifications and address enhancement requests

• Trained new engineers in in-house development environment and procedures

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