Software Engineer

• Nov 2018 - Present

I analyze, develop, and improve algorithms used to sequence DNA. I analyze, develop, and improve algorithms used to sequence DNA.

Founder, Principal Data Scientist

• Jan 2017 - Present

I create and use software to analyze complex data sets, particularly proteomics and multi-omics data. I am especially strong on multiple hypothesis testing issues and translating analysis into biologically meaningful results. I create and use software to analyze complex data sets, particularly proteomics and multi-omics data. I am especially strong on multiple hypothesis testing issues and translating analysis into biologically meaningful results.

Data Scientist

• Jun 2015 - Sep 2016

Associate Lecturer in Statistics

• Sep 2014 - May 2015

I designed and taught the curriculum for Intro. Statistics for Engineers (224), based on recommendations from prior lecturers. This included extensive use of R, RStudio, and RMarkdown for homework assignments. I designed and taught the curriculum for Intro. Statistics for Engineers (224), based on recommendations from prior lecturers. This included extensive use of R, RStudio, and RMarkdown for homework assignments.

Senior Scientist in Stem Cell Research

• Nov 2013 - Apr 2014

I analyzed data and metadata from the Progenitor Cell Biology Consortium (PCBC), designed a reusable genomics processing pipeline for stem cell data to allow comparisons between disparate datasets, and taught the proteomics section of a stem cell biology training course, offered on the Stanford campus. I analyzed data and metadata from the Progenitor Cell Biology Consortium (PCBC), designed a reusable genomics processing pipeline for stem cell data to allow comparisons between disparate datasets, and taught the proteomics section of a stem cell biology training course, offered on the Stanford campus.

Assistant Scientist

• Jan 2013 - Oct 2013

I am developing a bioinformatics approach to integrate large-scale biological data sets -- consisting of clinical traits, mRNA transcripts, protein levels and DNA-chromatin interactions -- from a factorial experiment to discover how molecular pathways are involved in autoimmune T-cell biology. I will extend my new software suite, COMPASS Reader, to relate these multiple data sets to each other and to T-cell pathways available from public and private databases. This work involves an integration of statistical methodology for high throughput testing with bioinformatics infrastructure to manage, visualize and relate massive data sets.

Associate Lecturer

• Jan 2013 - Oct 2013

I ran one of the lectures for Statistics 301, Introductory Statistics. I also started development of an online version of Statistics 224, Introductory Statistics for Engineers.

Bioinformaticist

• Jul 2011 - Dec 2012

I created a prototype analysis system (COMPASS Reader) that incorporated data from a custom microarray study with a quantitative proteomics/phospho-proteomics study of 48 mice, representing two separate analysis studies (2 technical replicates on one, 5 biological replicates on the other), which investigated the interaction of genotype and environment on mitochondrial dysfunction in a diabetic model of mice (eight total conditions). The latter study included 3.5 million total comparisons, 100,000 of which I found to be significant (FDR<10%). I also implemented a custom protein database that stored relationships between proteins genes, and many of their descriptors (such as short descriptions, gene symbols, and various identifiers). In particular, this database included metadata about the type of file loaded, when it was loaded, storage of specific workflows for adding more information, and methods to modify or delete pieces that were not added correctly. I have also applied this methodology to analyzing SUMOylation stress response in Arabidopsis and in analyzing pathogenic T-cell response to calcitriol.

NLM Trainee

• Nov 2010 - Oct 2011

Designed and implemented a model of protein translation on measured proteins and transcripts (approx. 2000) to identify systemic stress response in yeast. The model allowed us to explain, in particular, the lack of correlation between down-regulated transcripts and their corresponding proteins.

NLM Trainee (pre-doctoral)

• Feb 2007 - Jan 2010

NLM Trainees in the Computation and Informatics in Biology and Medicine (CIBM) program are required to take extensive cross-disciplinary coursework, train in computation and biology, attend CIBM seminar every week, and attend the NLM Trainee conference every year, and perform research in a cross-disciplinary area. I investigated advantages of high mass accuracy applied to Electron Transfer Dissociation (mass spectrometry). Created dynamic progrmaming algorithm for de novo identification of peptide sMS spectra, Rigorously investigated combinatorics of number of peptides with a particular mass. Investigated issues with reverse decoy as a method of estimating false discovery rate.

Programmer / Analyst II and Database Specialist

• Nov 1999 - May 2006

The Klein research group receives nearly all of its money from research grants. Dr. Hubler designed, developed, tested, and supported the databases used by the Eye Grading group for the Los Angeles Latino Eye Study (LALES), five databases for the Wisconsin Eye Study of Cardiovascular disease In Diabetes (WESCID), five databases for the Wisconsin Eye Study in Diabetic Retinopathy (WESDR), five databases for the Beaver Dam Eye Study (BDES) and individual databases for over thirty other research projects. These systems all had complex data entry and reporting requirements with varying structures. In spite of this, Dr. Hubler was able to design and implement a general purpose interface for most of these databases. Dr. Hubler also developed several software development protocols and gave instructional seminars on Microsoft Access and programming practices.