Daniel Cuevas Email & Phone Number

Madison, Wisconsin, Us

R&D, variant/biomarker discovery and detection, algorithm development, software development

Madison, Wisconsin, Us

R&D, biomarker discovery, product innovation, concept to commercial product development, algorithm & analysis pipeline development. Below are the mix of skills, tools, and activities I exercised:**Early product development**- Disease biomarker discovery- Proof-of-concept predictive modeling- Data characterization- R&D-centric software development- Technical reports and presentations- Project risk assessment**Data types**- NGS: targeted, whole genome, bisulfite, cfDNA- 16S rRNA sequencing- Fluorescent small molecule imaging- ELISA protein concentrations- Patient characteristics and covariates (categorical and quantitative)**Data analysis and modeling**- Ad-hoc data analysis- Data management, organization, and documentation- AWS data storage and management- Summary statistics and visualizations- Hypothesis testing- Predictive modeling and classification- Modeling performance reports and visualizations**Software development**- Git/GitHub version tagging, code review, pair-programming- Unit/regression testing in CI environments- Sphinx code documentation and user documentation- Data processing parallelization using high performance computing (HPC) SLURM scheduler- Poetry packaging manager- Docker containerization- RMarkdown and Jupyter Notebooks**Programming languages, libraries, and visualization tools**- Python: SciPy, NumPy, pandas, scikit-image, scikit-learn, statsmodels, seaborn, plotnine, matplotlib- R: ggplot2, caret, glmnet, bioconductor, dada2, phyloseq- Bash, shell, Perl

San Diego, Ca, Us

Generated a diverse set of bacterial genome-scale metabolic models to perform comparative analyses alongside investigation into common and unique difficulties in metabolism-based annotationsDeveloped automated pipeline named PMAnalyzer that performs logistic model fitting onto bacterial growth curves using Python’s SciPy optimization libraries and Pandas data structures, eliminating manual execution and increasing throughputDeveloped genome-scale metabolic model software named PyFBA that performs Flux-Balance Analysis and a customizable model reconciliation heuristic to improve bacterial metabolism accuracy and robustnessLed a team of student researchers to produce a bacterial database and API that consist of a variety of data, including taxonomic-based phenotypes, experimental observations, and model-predicted resultsPerformed various statistical and machine learning techniques (e.g., regressions, SVM, random forest) on numerous biological data sets, such as DNA/amino acid sequences, mass spectroscopy-based metabolomics data, optical density biomass measurements, DNA microarray expression levels, and other quantitative biological/environmental measurements

Waltham, Ma, Us

Developed a web-interface serving as a hub that aggregated the entirety of experimental results and analysis conducted by all Ion Torrent R&D sites across the country and was absorbed as an integral tool for comparative studies throughout the companyPerformed deep analysis on sequence quality and mapping statistics (e.g., GC bias, primer-strand preferences, targeted sequencing efficacy) that identified deficiencies in the sequencing protocols and the Ion Torrent AmpliSeq primer design algorithmTrained team members to use bioinformatics tools (e.g., in-house bash scripts, the Integrated Genomics Viewer, Torrent Suite plugins) for investigations within various aspects of the Ion Torrent technologyExercised interdisciplinary skills by bridging communication between molecular biology and bioinformatics scientists to assess the effectiveness of library preparation procedures in producing longer read lengths, higher quality sequences, and other far reaching goals

Waltham, Ma, Us

Performed multiple studies to measure the quality of several sequencing experiments by focusing on the performance of various sequencing polymerase mutantsLed projects through supervision of sequencing and mapping runs to produce variant calls, mapping statistics, and mapping quality summaries for Collaborations groupAssisted team members with sequencing runs, prepared and initialized PGM sequencing instruments, and resolved server-related issues to improve the flow of experimentsMajor ProjectsIon Report Generator: A Perl script that is automatically run every night on the Linux Ion Torrent server to produce a web page displaying a compilation of sequence data, results, tables, figures, and analytics. These daily reports enable the group to closely examine specific metrics produced from the PGM sequencer and allow scientists to easily and quickly compare outcomes and draw conclusions.Bioscope Mapping Analysis Pipeline: After sequencing completes, raw sequencing data must be mapped to a reference genome using Bioscope software. Bioscope provides bioinformaticians with simple tools in generating valuable information about the sequencing data and how well the library sample performed. Secondary mapping analysis is executed through Bioscope software on the Linux computing cluster, followed by tertiary analysis to find other key biological features such as small and large indels, SNPs, and other specific metrics.

San Diego, Ca, Us

Constructed a search hash-algorithm used to accurately identify DNA sequence similarity among multiple filesCollaborated with a group member in developing an Android mobile application that effectively extracted metagenomic information from a DNA sequence fileDeveloped a social network web application to access and distribute metagenomic data while leveraging the network’s facilities to connect with colleagues and collaboratorsMajor ProjectsAccessing the SEED genome database via Web services API: A group of Web services that provide programmers access to the SEED genome sequences database. My involvement in this project was writing example method calls for users and programmers who had interest in using the Java programming language to access these Web services. I utilized a SOAP methodology to exchange information between the programmer and the SEED database.Real-Time Metagenomics: A group of applications which perform annotation of DNA sequences for biologists. These applications use new technologies, such as Web 2.0, orkut's social networking platform, and the Android mobile operating system. My main focus was developing a social network application that would allow a user and their "friends" to share and distribute their DNA annotations among themselves. Using JSON-RPC method calls to a remote server, this application successfully updates colleagues, who are using either the Android implementation or orkut, about new annotated information. The app was developed using XML, JavaScript, and CSS.Rapid Sequence Searching Tool Using Hashing: A Java program that compares two DNA sequence files and finds matching sequences and subsequences. My main focus was to use a hash-table data structure for determining areas where a query sequence file had similarities in comparison to a reference sequence file. This process had to execute and run in a short amount of time and must output detailed results of where these sequence matches were located in each data file.

Doctor Of Philosophy - Phd, Bioinformatics And Computational Biology

Doctor Of Philosophy - Phd, Bioinformatics And Computational Biology

Bachelor Of Science - Bs, Computer Science