PhD scientist with expertise in bioinformatics and full stack engineering. Strong background in computational methods and high performance computing, Next Generation Sequencing, web development, databases, ETL and data processing and analysis, Linux environment. Skill set: - Programming: * Languages: Python, C/C++, bash shell * Web development and RESTful services: javascript/backbone.js/node.js, PHP, AJAX/single page applications * DevOps: setup and maintain linux servers * Databases: MySQL, MongoDB, redis * Hadoop - Bioinformatics/scientific computation: * Next generation sequencing (NGS) pipelines: read mapping, variant calling and prioritization. * Molecular dynamics simulations/molecular graphics (namd, autodock); * Crystallography packages (CCP4, HKL2000, COOT, PYMOL, VMD); - Wet lab: * Protein production and purification. * Structure determination and biophysics: Protein crystallization, x-ray data collection and processing; Protein interactions by NMR, ITC, fluorescence polarization. * Biochemistry: enzyme kinetic assays, HPLC instruments * Microscopy: fluorescent, EM. * Mammalian tissue culture. * general molecular biology techniques - Communication: * Grant-writing and manuscript preparation.

Software Developer @ SiteCompli is a powerful technology that helps New York City real estate owners, managers and service companies keep on top of critical compliance issues. SiteCompli automatically and continuously aggregates and analyzes compliance data on violations, complaints, inspections and the like from the various New York City government agencies (i.e. DOB, ECB, DSNY, DOF, HPD, FDNY, etc). For more information, visit http://www.sitecompli.com. From June 2015 to Present (5 months) New York, NYBioinformatician / Data Manager @ Data Manager / software engineer for Mount Sinai's Center for Research on Influenza Pathogenesis (https://cripdb.mssm.edu). I Developed a comprehensive data management and processing platform for the Center for Research in Influenza Pathogenesis (cripdb.mssm.edu), which monitors the evolution of potentially pandemic Influenza virus strains around the world. - Responsible for full stack engineering, including web application development, database schema design, data validation, processing, querying and visualization (JavaScript, PHP slim microframework, Python) - Implemented a background, real-time, asynchronous web application with task queuing, messaging (ZeroMQ), and websockets - Developed software (Python) and pipelines (Bash shell scripts) to process large Next Generation Sequencing datasets on Mount Sinai’s High Performance Computing cluster - Designed and Implemented efficient algorithms for intensive computations, including modules in C. - Responsible for the Linux machines and web servers (Apache and Nginx) - Developed interactive data visualizations with JavaScript’s D3 library From May 2014 to June 2015 (1 year 2 months) Greater New York City AreaBioinformatician @ - Ran Next Generation Sequencing Variant Prioritization pipelines. - Wrote custom scripts (shell, python, C) for interacting with NGS pipeline and downstream analysis. Developed Data visualization Single Page Application (SPA): - https://pintolab.mssm.edu/papers/pinto_ajhg_2014/ - Interactive network graph visualization with JavaScript's D3 library + bootstrap Created Lab database and Single Page web Application interface: - https://pintolab.mssm.edu/samples/ - Private database with password protected access. - frontend: Javascript + backbone.js + marionette.js + AJAX - backend: MySQL database; PHP for serving static code and RESTful services (database access) From November 2013 to May 2014 (7 months) New YorkResearch Fellow @ Conducted translational biomedical research: - Conceived, designed, and analyzed experiments in partnership with physician scientists to identify mutations driving kidney cancer, a disease with a ~$2.7 billion annual oncology market. - Elucidated and characterized clinical biomarkers, including “mTOR hyperactivation” genetic alterations by molecular dynamics simulations and molecular modeling, advancing personalized medicine for a class of drugs worth $1 billion/yr. - Solved how “small molecule” compounds inhibit cancer promoting activity of the taspase-1 enzyme, using X-ray crystallography. - Developed a high-throughput screen to identify biological agents capable inhibiting the cancer molecule Mcl-1. - Developed web apps for data and inventory management used by a 25-member lab group. - Co-wrote a successfully funded grant proposal worth $200,000 and published papers in peer-reviewed journals. - Authored the taspase-1 chapter of the Handbook of Proteolytic Enzymes (Academic Press). From June 2011 to November 2013 (2 years 6 months) Software Developer @ Developed concept, Designed and Implemented a mobile web Single Page Application (SPA) for mapping New York City real-time Bus location and arrival times. - App Submitted to MTA's 2013 APP QUEST: http://2013mtaappquest.challengepost.com/ - Frontend: * JavaScript + JQuery + backbone.js + google maps API, AJAX, JSON - Backend: * Node.js, REDIS, PHP (RESTful services for data access), MySQL From March 2013 to August 2013 (6 months) Greater New York City AreaPostdoctoral Fellow @ Collaboration project between Columbia University and Memorial Sloan Kettering labs: Trained in X-ray crystallography methods in the lab of Dr. Liang Tong. Performed protein crystallization, using commercial and home made kits, using a mosquito robot. Collected x-ray diffraction data at in-house source and at the Brookaven National Laboratories light source. used software, such as HKL2000, Phenix and Coot for 3D structure determination. Developed software to improve efficiency of protein engineering design and data management. From June 2011 to June 2012 (1 year 1 month) New York, NYPostdoctoral Fellow @ Conducted NIH funded structural studies on neuromuscular (NM) junction formation - Used AKTA system to produce and purify specialized NM proteins, including detergent solubilized full-length membrane receptor from a unique insect cell/baculovirus system; Employed biophysical methods such as isothermal titration calorimetry, multi-angle light scattering (MALS) to characterize these proteins; Established optimal crystallization conditions using a mosquito crystallization robot. From March 2009 to March 2011 (2 years 1 month) Postdoctoral Fellow @ Performed primary research for PhD thesis dissertation: - genetic mutation detection and characterization for families with hereditary porphyria cutanea tarda - high level expression and purification of heme biosynthetic proteins. - enzymatic charaterization - stable isotope labeling and NMR experiments to map the active site of uroporphyrinogen synthase - molecular docking and molecular dynamics simulations to characterize the binding mode and reaction mechanism Publications: http://www.ncbi.nlm.nih.gov/pubmed?term=cunha%2C%20desnick Additionally, collaborated with several groups to provide protein modeling and simulation expertise. Publications: http://www.ncbi.nlm.nih.gov/pubmed?term=cunha%20and%20naidu%20or%20cunha%20and%20jabs%20or%20cunha%20and%20porotto From June 2008 to March 2009 (10 months)

PhD, Biomedical Sciences @ Mount Sinai School of Medicine of New York University From 1999 to 2008 PhD, Biomedical Sciences @ Universidade do Porto From 1998 to 2008 BSc, Biology @ Universidade do Porto From 1993 to 1997 Luis PhD is skilled in: Biochemistry, Molecular Biology, Protein Purification, DNA sequencing, X-ray crystallography, Protein Expression, Bioinformatics, Cell Biology, Cancer, Protein Chemistry, PCR, Computational Biology, Tissue Culture, Western Blotting, Site-directed..., Python, Molecular Dynamics, Protein Crystallization, recombinant DNA..., Enzyme Assays, Web Development, Web Applications, PHP, MySQL, Computer Science, Assay Development, Biophysics, Purification, Docking, Enzyme Kinetics, Java, Grant Writing, Programming Languages, Unix, Unix Shell Scripting, Manuscript Development, Photoshop, Microsoft Excel, NAMD, Autodock, Dreamweaver, Arduino, LAMP, Science, Ansible