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Scientist specializing in biotechnology. I work on transforming complex data into understanding, using computational tools to accomplish this, and helping others to do the same. Expertise centers on bioinformatics, genomics, chemistry, computer science, university-level curriculum development and instruction. My professional goals combine science, software & teaching, to improve the understanding and utility of science-driven systems, for example in biotechnology or teaching domains. More pragmatically, any work requiring skills and hands-on ability in bioinformatics, data analysis / machine learning, computer programming, chemistry or teaching could be a good fit.Specialties: • Bioinformatics: Assay / molecular design; Oligo thermodynamics; Genomics; Next-generation sequencing.• Data analysis: Python, Pandas, R scripts; Data mining, feature selection, machine learning.• Software engineering: Algorithm / script / pipeline development; Programming (C, Python, Bash); Linux admin• Computer chemistry: Cheminformatics; Modeling / docking; Property prediction; Library design. • Teaching: Course curriculum development, design; Classroom, Lab, Online.
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Computational BiologistParse Biosciences Oct 2019 - PresentSeattle, Washington, UsBuilding computational tools to help bring single cell sequencing to the masses -
Scientific Research Consultant & ContractorVerdascend Sciences Jan 2009 - PresentConsulting & contract projects.• Bioinformatics: Assay and oligo design, evaluation, troubleshooting and QC; Genomic data processing, data mining, feature selection, machine learning & model building.• Technical and strategic consulting. Evaluation of current / possible molecular systems, novel assays, etc; Review of manuscripts, literature, invention and potential patent positions; Concept simulation and modeling experiments.• Software engineering: (Python / Pandas, C/C++, Perl, shell) Process automation and scripting; Algorithm design and code writing, troubleshooting and refactoring; Database modeling, design and implementation; Documentation and technical writing. -
InstructorUc San Diego Extended Studies Jan 2009 - PresentLa Jolla, Ca, Us• Genomic Sequencing Technologies (UCSD Extension BIOL-40237)Developed and teach on-line course covering sequencing chemistry, bioinformatics, targeted work flows, challenges and potential medical applications.• Bioinformatics (UCSD Extension BIOL-40236)Developed and teach on-line course covering classic bioinformatics (e.g. literature searches, sequence alignments) and newer developing applications (e.g. next-gen sequencing). -
Principal Scientist, BioinformaticsToma Biosciences Oct 2015 - Jun 2019Foster City, Ca, Us• NGS data analysis, troubleshooting, diagnostic experimental design and analysis• Designed and refined probes for targeted NGS somatic (cancer) variant detection system.• Designed custom assays, analysis tools and pipelines to support R&D, including simulations and machine learning.• Assay optimization and troubleshooting via directed experiments and analysis; Bioinformatics lead -
Staff Scientist, BioinformaticsQuantalife / Bio-Rad Nov 2010 - Feb 2013Hercules, Ca, Us• Designed hundreds of custom assays, building ddPCR content and streamlining R&Dexperiments. Wide range of targets and customer applications.• Computational process development. Thermodynamic models via machine learning.• Patents, publications, customer presentations. QuantaLife Droplet Award. -
Staff Scientist, BioinformaticsApplied Biosystems Oct 1999 - Jan 2009Waltham, Ma, Us• Architect and bioinformatics lead for assay design pipeline software (TaqMan and SNPlex). Systems have generated millions of quality assays and millions of dollars in revenue.• Scientific manager and mentor. My group focused on software tool development, experimental data analysis, sequence-based data mining and rule discovery.• Team contributor on multiple projects, furnishing expert advice, hands-on code and data manipulation, simulations and decision support work for management.• Implemented pipelines for investigational assays and data analysis protocols, including discovery of copy number variants in SOLiD next generation sequencing data.• Invented algorithms and software addressing nucleotide thermodynamics, tag sequence selection, multiplex partitioning, sequence analysis and data mining challenges.• Software tools and methods have yielded product lines, trade secrets, patents, publications. Numerous invention disclosures, DNA awards, Trade Secret of the Year award. -
Associate ProfessorCalifornia State University, East Bay 2004 - 2005Hayward, Ca, Us* Advanced Bioinformatics / Chemoinformatics. Drug discovery focus covering protein targeting, structural docking and scoring, SAR development, general and focused chemical library design.Composed original course content and lecture materials, emphasizing job market needs and requiring team project participation. -
Scientist, Computational ChemistryTelik, Inc. Oct 1995 - Oct 1999* Supported drug discovery group with molecular modeling, target protein and binding site analysis, chemical and patent database work, virtual screening, compound prioritization.* Physico-chemical property predictions to guide medicinal chemistry efforts with prioritization and modification of drug leads.* Created web interface system to company compound and binding assay databases.* Devised general framework for chemical library design and prioritized acquisition.* Used docking simulations to emulate and rationalize protein affinity fingerprints. * Derived anti-cancer QSAR models using molecular modeling and protein alignments.
Ryan Koehler Skills
Ryan Koehler Education Details
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University Of California, Santa CruzChemistry (Organic / Computational) -
University Of California, DavisBiochemistry
Frequently Asked Questions about Ryan Koehler
What company does Ryan Koehler work for?
Ryan Koehler works for Parse Biosciences
What is Ryan Koehler's role at the current company?
Ryan Koehler's current role is Computational Scientist.
What is Ryan Koehler's email address?
Ryan Koehler's email address is ry****@****end.com
What is Ryan Koehler's direct phone number?
Ryan Koehler's direct phone number is +150396*****
What schools did Ryan Koehler attend?
Ryan Koehler attended University Of California, Santa Cruz, University Of California, Davis.
What are some of Ryan Koehler's interests?
Ryan Koehler has interest in Science And Technology, Education, Environment, Health.
What skills is Ryan Koehler known for?
Ryan Koehler has skills like Bioinformatics, Genomics, Assay Development, Biotechnology, Data Mining, Molecular Biology, Pcr, Dna, Computational Biology, Cheminformatics, Algorithms, R.
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