Experience

MicroByre

• United States
• Biotechnology Research
• 1 - 100 Employee

• Senior Data Scientist

  • Aug 2022 - Present



Alladapt Immunotherapeutics, Inc.

• United States
• Biotechnology Research
• 1 - 100 Employee

• Consultant - Predictive Modeling

  • Feb 2021 - Jul 2022

  + Development of computational tools to assess potential cross-reactivity amongst food allergens. + Development of visualizations to illuminate cross-reactivity patterns amongst multiple food allergens. + Analysis and visualization of data from multiplex ELISA-based in vitro allergy tests. + Supported efforts to identify key allergens for drug potency testing. + Development of computational tools to assess potential cross-reactivity amongst food allergens. + Development of visualizations to illuminate cross-reactivity patterns amongst multiple food allergens. + Analysis and visualization of data from multiplex ELISA-based in vitro allergy tests. + Supported efforts to identify key allergens for drug potency testing.



Fluxus Inc

• Santa Clara, California, United States

• Consultant - Predictive Modeling, Analysis Pipelines & Data Science

  • Apr 2018 - Jul 2020

  Small start-up developing new blood diagnostic technology. Led efforts focused on the two primary sub-systems as well as overall performance: Biomarker Capture and Labeling - Predictive Modeling + Built first-principles models of reaction kinetics: biomarker plus antibody coated beads. + Developed an interactive tool to predict on- and off-rates given user input of key parameters. Biomarker Label Detection - Predictive Modeling, Pipeline Building & Data Science + Built a first-principles model of the signal and developed a stochastic simulation of the signal. + Built end-to-end analysis pipeline using Python (with Numba, NumPy). + Identified/implemented three detection algorithms (CUSUM, HMM local and global decoding). + Identified/exported a wide variety of secondary/tertiary information, e.g. false positive estimate. + Designed/analyzed experiments and simulations to test algorithm performance. + Analyzed data generated by other teams for a variety of R&D tests; produced reports with relevant statistical analysis. Overall Instrument Performance - Predictive Modeling, System Integration + Built a first-principles model incorporating adjustable R&D parameters. + Mapped the instrument specification landscape for sensitivity to run-to-run variability. + Using theory and simulation estimated instrument/algorithms positive and negative predictive values (PPV, NPV) and limits of detection and quantification (LOD, LOQ). Supported efforts of scientists/engineers with decisions in a complex environment Chalk Talks, Presentations & Visualizations To aid in understanding of kinetics, rotational and translational diffusion, stochastic processes/signals, error sources/assessment, e.g. detector dead time, hidden Markov models (HMMs), algorithms associated with HMMs, e.g. forward-backward, the CUSUM algorithm. Show less



Roche Molecular Systems

• Principal Scientist II

  • Jun 2014 - Nov 2016

  Start-up developing new DNA sequencing technology; acquired by Roche partway through tenure. Led/initiated a wide variety of efforts focused on the main objectives of increasing (i) accuracy, (ii) read length, and (iii) yield of functional sensors. Biophysics, Computational Biology + Kinetics, Experiment: Devised methods to isolate, and therefore measure all three key kinetic rates. + Kinetics, Theory: Derived analytic expressions as function of voltage, salt concentration, temp, etc. + Sequencing Accuracy: Derived analytic expressions using a continuous-time Markov chain model. + Polymerase Function: Built signal analysis pipeline to compute kinetic rates, error rates and lifetime. + Nanopore Potential Drop: Ran analog circuit simulations of time-varying electric potential. Bioinformatics, Data Science + Multi-variant Data Analysis: Teasing apart component performance: polymerase, DNA, electrode, etc. + Cross-Checking: With model predictions and other measured parameters (in-house or literature). + Statistical Analysis: Designed for specific question(s) at hand. System Integration + Increased Sequencing Time: Drove effort to change the (i) electrode, (ii) electrochemical method of detection and (iii) analog circuit. This work was critical to acquisition. + Component & Instrument Specifications: Informed decision making by mapping interaction landscape. + Systems Engineering: Analysis of system-level of changes to the circuit, electrode and/or biology. Supported efforts of scientists/engineers with decisions in a complex environment. Upstream, Downstream Effects: Helped teams understand how their sub-system interacts with others so they could more effectively plan experiments/troubleshoot, extract useful information, assess error, etc. General Assistance, Teams and Individuals: Deep-dive chalk talks, experimental design, troubleshooting, interpreting results, relevant statistical analysis, and searching/reading literature. Show less



Genia Technologies

• Consultant

  • Jan 2013 - Jun 2014

  See above experience with Roche Molecular Systems See above experience with Roche Molecular Systems



Purdue University

• United States
• Higher Education
• 700 & Above Employee

• Assistant Professor of Chemistry

  • Jul 2002 - Dec 2008

  Five (5) Ph.D. students, one (1) M.S. student, 10 undergraduates. Students won awards at local, national and international level. 14 publications (all corresponding author), 42 invited talks. Experimental biophysics research α-Synuclein aggregation pathways (pathological hallmark of Parkinson's disease) Showed that α-synuclein bound to lipid bilayers can aggregate into several toxic structures, not just amyloid plaques. Established that the type of aggregate and propensity to aggregate is dependent on the protein, ion and anionic lipid concentrations. Built a simple physics-based model to account for complex behavior in multifactorial environments. Interplay of form and function in lipid bilayers Established a protein-free mechanism by which supported lipid bilayers can be transformed from two-dimensional to three-dimensional structures. Determined several mechanisms by which the electrostatic environment can be tuned to control the organization of lipid bilayers. Elucidated the effect of composition and ion concentration on the mechanical properties of liposomes. Show less



Stanford University

• United States
• Higher Education
• 700 & Above Employee

• Postdoctoral Fellow

  • May 1999 - Jun 2002

  Research: ­ Developed new methods for patterning lipid bilayers interfaced with hard surfaces without the need to engineer the hard surface; Developed new methods for the creation of hybrid protein-lipid bilayer surfaces; Interrogated the dynamic aspect of cell membrane organization by using electric fields to selectively move one lipid raft component, observing that other components exhibited correlated motion Communication: ­ Four journal articles Mentoring: ­ Direct supervision of two summer undergraduates and informal mentoring of several graduate students Show less



University of Wisconsin-Madison

• Higher Education
• 700 & Above Employee

• Graduate Research Assistant

  • Jun 1995 - May 1999

  Research: ­ Created some of the most highly ordered organic films on semiconductor surfaces and elucidated the mechanism of attachment Communication: ­ 18 journal articles, one patent and two invited talks Research: ­ Created some of the most highly ordered organic films on semiconductor surfaces and elucidated the mechanism of attachment Communication: ­ 18 journal articles, one patent and two invited talks