Management Development
Resume:
Leandro Hermida
Email: *********@********.***
Address: ***** ********** **
City: Germantown
State: MD
Zip: 20876
Country: USA
Phone: 301-***-****
Skill Level: Experienced
Salary Range: $140,000
Primary Skills/Experience:
See Resume
Educational Background:
See Resume
Job History / Details:
LEANDRO C. HERMIDA
11307 Willowdale Dr
Germantown, MD 20876
*********@********.***
DOB 15 July 1975
Citizenship USA
TECHNICAL SKILLS
Knowledge and expertise in the following areas:
* High-throughput omics technologies, data management and analysis
o Affymetrix, Agilent, Nimblegen and Illumina microarray platforms
o Illumina next-generation sequencing (NGS) platforms
* Bioinformatics workflow management frameworks
o Galaxy, GenePattern, Taverna
* Bioinformatics data mining frameworks
o BioMart
* Omics experimental data and metadata standards
o MAGE-TAB, MAGE-ML, ISA-Tab, FuGE-ML
* Programming languages
o Perl, Python, Java, PHP, C, C++, JavaScript
* Database systems and programming
o MySQL, PostgreSQL, Oracle, SQL Server
o Object-relational mapping (ORM) and persistence using JPA, Hibernate, DBIx::Class, SQL Alchemy
* Formal software development and project management methodologies
o Scrum, ICE, Dynamic ICE
* Project management, collaboration, issue/task tracking and resolution tools
o Atlassian JIRA, Atlassian Confluence
PROFESSIONAL EXPERIENCE
PHILIP MORRIS INTERNATIONAL RESEARCH & DEVELOPMENT Neuchatel, Switzerland
Bioinformatics Scientist (January 2012 - November 2012)
Worked as a lead bioinformatics scientist as well as scientific and IT specialist within the Computational Disease Biology and Genomics Research and Technology teams. Major disease areas of focus where COPD, CVD, and lung cancer. Previous projects include:
* Design, development and implementation of a systems biology data integration and analysis platform, including:
o Development and implementation of a high-throughput (microarray, next-generation sequencing) raw data and metadata management system and integration with data acquisition systems
o Customization of platform system to support reverse phase protein microarrays (RPA) data and metadata
o Design, development, and implementation of integrated analysis workflow framework and components along with computational biologists
o Design, development and implementation of an integrated contrast and gene set management and analysis platform for downstream analysis and biological interpretation of experimental data
o Design, development and implementation of integrated query-oriented data warehouse system for knowledge acquisition and integration of systems biology data
LEANDRO HERMIDA CONSULTING Ruschlikon, Switzerland
Bioinformatics/Scientific Consultant (September 2009 - January 2012)
Worked as an independent bioinformatics, scientific, and IT consultant. Clients and projects included:
* Philip Morris Research & Development, Neuchatel, Switzerland
o Design, development and implementation of a systems biology data integration and analysis platform, including:
* Development and implementation of a high-throughput (microarray, next-generation sequencing) raw data and metadata management system and integration with data acquisition systems
* Customization of platform system to support reverse phase protein microarrays (RPA) data and metadata
* Design, development, and implementation of integrated analysis workflow framework and components along with computational biologists
* Design, development and implementation of an integrated contrast and gene set management and analysis platform for downstream analysis and biological interpretation of experimental data
* Design, development and implementation of integrated query-oriented data warehouse system for knowledge acquisition and integration of systems biology data
* Swiss Institute of Bioinformatics, Basel, Switzerland
o Design, development and implementation of new components to the Protein Model Portal (http://www.proteinmodelportal.org/)
* Design, development and implementation of entire full-text searching infrastructure including processing and creation of indexes and web application and web service components
* Redesign, development and implementation of entire portal back-end database infrastructure, data loading and transformation programs, as well as web application interface and web services to use BioMart data mining framework and data marts
* Friedrich Miescher Institute, Basel, Switzerland
o Design, development and implementation of data processing infrastructure and application platform to visualize and report on institute-wide, large scale biological data storage
FRIEDRICH MIESCHER INSTITUTE - NOVARTIS RESEARCH FOUNDATION Basel, Switzerland
Lead Scientific Software Developer (March 2006 - July 2009)
Served as software development project leader and lead developer. Responsibilities include:
* Planning, management, design, development and implementation of software solutions which serve strategic, integrative or institute-wide goals.
* Guidance and integration of scientific data management efforts.
* Mentoring, advising and assisting technical reports in the area of software development, database development, and programming.
* Overall software development and programming architecture and strategy.
* Guidance and integration of software development and programming efforts.
* Design, implementation and maintenance of central systems and tools involved in software development and programming.
* Design, implementation and maintenance of best practices, formal processes and controls involved in software development and programming.
* Management of software and related systems projects through entire software/systems development lifecycle (SDLC).
* 3rd level support of production software installations.
Major projects and accomplishments include:
* Led project design, management and assisted in software development and customization of an institute-wide web-based animal management system.
* Led project design, management and software development of a life sciences data management framework for annotation of experimental workflows from high-throughput instruments in functional genomics and proteomics platforms (http://fuge.sf.net/dev/)
* Led project design, management and software development of a web-based multi-omics data mining software and data repository.
* Implemented integrated collaboration, software development project management, testing, and issue/task management platform.
* Implemented source control system including code repository design and integration with project and issue/task management platform.
* Designed, wrote and implemented institute standard policies, procedures and controls for development, deployment, and maintenance of software applications.
* Served as expert consultant on a number of major institute-wide IT infrastructure and systems projects.
* Delivered technical presentations at meetings, workshops, and conferences to directors and senior-level managers. These presentations often involved collaborating on recommendations, requirements, and solutions as well as preparation of my organization's positions or research on specific subjects.
* Written extensive technical documentation and manuals. Created project plans, disaster recovery plans, standard operating procedures, working instructions, installation procedures, etc.
* Co-led IT team to two successful Novartis internal audits of IT and software development.
* Worked on various collaborative software development projects with research groups and technology platforms and served as an expert advisor.
* Continue to develop and teach lectures and practical exercises at the Biozentrum and SIB.
BIOZENTRUM, UNIVERSITY OF BASEL & SWISS INSTITUTE OF BIOINFORMATICS Basel Switzerland
Lead Bioinformatics Software Developer (November 2002 - March 2006)
Primary responsibilities involved software development, system and database administration for SIB Bioinformatics division and Basel Computational Biology Center ([BC]2). Additional responsibilities involved collaborative projects with other research groups at the Biozentrum. Major projects and accomplishments include:
* Designed, developed and administered the Microarray Information Management and Analysis System (MIMAS), a microarray data repository and annotation system used by facilities in the Swiss Array Consortium (http://mimas.vital-it.ch/)
* Installed, administered and customized GeneSpring GX Workgroup analysis platform (formerly Signet) for Swiss Array Consortium. Designed and developed software which connects GeneSpring to MIMAS repository data and annotations
* Designed, developed and administered the Ashbya Genome Database (AGD), a genome browser and information resource for the yeast community and evolutionary biologists (http://agd.vital-it.ch/)
* Assisted in design, development and strategy of GermOnline, a cross-species community annotation knowledgebase on germ cell differentiation (http://www.germonline.org/)
* Co-designed and developed a web-based microRNA data atlas and warehouse (http://www.mirz.unibas.ch/cloningprofiles/)
* Developed long-term strategy for microarray data management and annotation solutions for Swiss Array Consortium.
* Installed and configured Oracle, MySQL and PostgreSQL database servers and environments for bioinformatics division and [BC]2.
* Performed database administration duties for bioinformatics division and [BC]2. Responsibilities included database server system administration and monitoring, backup and recovery implementation, hardware configurations, database infrastructure planning and future strategy and support for DBMS users.
* Installed and customized Macromolecular Structure Database Search Database (MSDSD), a 400GB+ Oracle database used by the protein structure informatics group.
* Worked on external projects and provided programming and development support for groups at the Biozentrum.
* Developed and taught lectures and practical exercises that are part of the Biozentrum's Bioinformatics curriculum. Also gave workshops associated with microarray data management and analysis (see TEACHING section below).
NEURALSTEM, INC. Gaithersburg, Maryland USA
Bioinformatics Programmer & Database Developer (October 2000 - November 2002)
Led bioinformatics software development projects under principal scientist of Gene Discovery group. Accomplishments included:
* Developed innovative method to rapidly mine novel transcripts along with molecular biology principal scientist Dr. Babru Samal. Submitted patent application. [USPTO patent link]
* Developed and wrote bioinformatics software required by new gene discovery platform. Software and database tools written in Perl, Visual Basic, C++, T-SQL, and SQL Server 2000.
* Used computational biology expertise in collaboration with laboratory scientists to create a number of other high-throughput computational tools that furthered gene discovery effort.
* Using Affymetrix U95 and U133 Human Genome expression data, developed novel automated method to extract transcripts and ESTs with targeted expression profiles in Neuralstem neuronal stem cells.
* Created Neuralstem Bioinformatics intranet web site, which included various CGI/ASP client tools for database mining.
* Performed all database and IT administration for the Gene Discovery group.
* Developed storage schemes and database design of all gene discovery data (raw mRNA sequences, computationally derived data from gene discovery pipeline, Affymetrix expression profiles, etc.).
MILLENNIUM PHARMACEUTICALS Boston, Massachusetts USA
Bioinformatics Associate (August 1999 - October 2000)
Served as a contractor for Millennium Pharmaceuticals, Inc. in Cambridge, MA. Role involved complete support of two departments, Target Gene Identification and Molecular Pathology. Accomplishments included:
* Performed database management using in-house software tools (Oracle, RS3, ISIS/Base, SQL*Plus, TOAD).
* Assisted in in-house software tech support/troubleshooting for department employees.
* Developed and designed department web site at request of cheminformatics group.
* Performed searches in medical literature and available databases for scientists to maintain knowledge base. Performed various administrative duties as needed. Maintained and added to internal sample and tissue database as lab data was generated.
KOCH-GLITSCH, INC. Wilmington, Massachusetts USA
Lead CFD & Software Engineer (August 1997 - August 1999)
Headed CFD Laboratory and research projects. Accomplishments and responsibilities included:
* Development of CAD and CFD models for simulation and processing simulations using FLUENT and FIDAP.
* Performed pilot plant experiments to obtain empirical data and analyzed both simulation and experimental data to optimize/troubleshoot design of chemical process systems.
* Assisted in development equipment rating software for use by Koch-Glitsch and administered technical support of software.
* Maintained contacts and exposure with other research labs and employees.
* Performed system administration of workstations and servers and maintained lab hardware, network, software licenses and security.
* Wrote reports of research findings and progress to department heads and others.
* Supervised two lab engineers to assist in research and traveled as representative of CFD laboratory.
EDUCATION
VANDERBILT UNIVERSITY Nashville, Tennessee
Bachelor of Engineering, Chemical Engineering
1993-1997, Overall GPA: 3.4/4.0 (incl. transferred courses)
UNIVERSITY OF BASEL Basel, Switzerland
Various graduate and PhD-level courses in bioinformatics
2003-2005, uncompleted PhD due to group leader move to France, no GPA in Switzerland
CERTIFICATIONS AND TRAINING
ICE Silver Project Management Certification (2008)
Java 5 Sun Certified Java Programmer (SCJP) (2007)
Applying UML 2.0 with MagicDraw (2006)
Oracle Application Developer Certification (2001)
LANGUAGES
English native speaker
Spanish advanced (Council of Europe C1)
German intermediate (Council of Europe Level B1) (http://en.wikipedia.org/wiki/Common_European_Framework_of_Reference_for_Languages)
PUBLICATIONS
Hermida L, Poussin C, Stadler MB, Gubian S, Sewer A, Gaidatzis D, Hotz HR, Martin F, Belcastro V, Petich MC, Hoeng J (2013). Confero: an Integrated Contrast and Gene Set Platform for Computational Analysis and Biological Interpretation of Omics Data. (submitted BMC Genomics 2012)
Gattiker A*, Hermida L*, Liechti R, Xenarios I, Collin O, Rougemont J, Primig M (2009). MIMAS 3.0 is a Multiomics Information Management and Annotation System. BMC Bioinformatics 2009 May 18; 10:151. * contributed equally
Jones AR, Lister AL, Hermida L, Wilkinson P, Eisenacher M, Belhajjame K, Gibson F, Lord P, Pocock M, Rosenfelder H, Santoyo-Lopez J, Wipat A, Paton NW (2008). Modelling and managing experimental data using FuGE. OMICS 2009 Jun; 13(3):239-51.
Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B, Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G, Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN, Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo JJ, Sander C, Zavolan M, Tuschl T (2007). A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129(7): 1401-14.
Hermida L, Schaad O, Demougin P, Descombes P, Primig M (2006). MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation. BMC Bioinformatics 7(1):190.
Hermida L, Brachat S, Voegeli S, Philippsen P, Primig M (2005). The Ashbya Genome Database (AGD) - a tool for the yeast community and genome biologists. Nucleic Acids Res 33 Database Issue: D348-52.
Loop T, Leemans R, Stiefel U, Hermida L, Egger B, Xie F, Primig M, Certa U, Fischbach KF, Reichert H, Hirth F (2004). Transcriptional signature of an adult brain tumor in Drosophila. BMC Genomics 5:24.
Wiederkehr C, Basavaraj R, Sarrauste de Menthiere C, Koch R, Schlecht U, Hermida L, Masdoua B, Ishii R, Cassen V, Yamamoto M, Lane C, Cherry M, Lamb B, Primig M (2004). Database model and specification of GermOnline Release 2.0, a cross-species community annotation knowledgebase on germ cell differentiation. Bioinformatics 20, 808-11.
Schlecht U, Demougin P, Koch R, Hermida L, Wiederkehr C, Descombes P, Pineau C, Jegou B and Primig M (2004). Expression profiling of mammalian male meiosis and gametogenesis identifies novel candidate genes for roles in the regulation of fertility. Mol. Biol. Cell 15, 1031-43.
Wiederkehr C, Basavaraj R, Sarrauste de Menthiere C, Hermida L, Koch R, Schlecht U, Amon A, Brachat S, Breitenbach M, Briza P, Caburet S, Cherry M, Davis R, Deutschbauer A, Dickinson HG, Dumitrescu T, Fellous M, Goldman A, Grootegoed JA, Hawley R, Ishii R, Jegou B, Kaufman RJ, Klein F, Lamb N, Maro B, Nasmyth K, Nicolas A, Orr-Weaver T, Philippsen P, Pineau C, Rabitsch KP, Reinke V, Roest H, Saunders W, Schroder M, Schedl T, Siep M, Villeneuve A, Wolgemuth DJ, Yamamoto M, Zickler D, Esposito RE, Primig M (2004). GermOnline, a cross-species community knowledgebase on germ cell differentiation. Nucleic Acids Res 32, Database issue: D560-7.
Primig N, Wiederkehr C, Basavaraj R, Sarrauste de Menthiere C, Hermida L, Koch R, Schlecht U, Dickinson HG, Fellous M, Grootegoed JA, Hawley RS, Jegou B, Maro B, Nicolas A, Orr-Weaver T, Schedl T, Villeneuve A, Wolgemuth DJ, Yamamoto M, Zickler D, Lamb N, Esposito RE (2003). GermOnline: a novel cross-species community annotation database on germ line development and gametogenesis. Nat. Genet 35, 291-2.
TEACHING
Perl Programming for Biomedical Researchers (2008), SIB EMBnet, Biozentrum, University of Basel
* Developed and taught lectures and practical exercises on Perl programming language and the use of regular expressions in biomedical research/bioinformatics programming.
Advanced Programming for Biologists (2007), SIB EMBnet, Biozentrum, University of Basel
* Developed and taught lectures and practical exercises on database systems, database programming and SQL and their use in biology and bioinformatics.
F10: Data Acquisition and Knowledge Representation (2005 -2006), Biozentrum, University of Basel
* Developed entire semester course plan, content and syllabus.
* Taught the Data Modeling and Database Design, Database Systems, Data Exchange Technologies and Middleware, Data Acquisition, and Microarray Databases lecture series.
F1-F2: Introduction to Bioinformatics I (2005-2006), Biozentrum, University of Basel
* Developed and taught Introduction to Programming in Perl lecture and co-developed and taught practical exercises.
* Gave Evolution of Genes and Genomes practical exercises.
* Gave Microarray Data Computation and Analysis practical exercises.
Neurogenomics (2004-2005), Biozentrum, University of Basel
* Developed and gave workshops on Affymetrix GCOS, microarray data management and microarray data standards.
REFERENCES
Available upon request.
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