R. Paul Nobrega

Biophysical Scientist
Automation Consultant
Scientific Programmer


PhD in Biophysics

University of Massachusetts
Medical School

BS in Biotechnology

University of Massachusetts
at Lowell
2004 - 2008

Career profile

PhD with 5 years of industry experience, over 15 years of laboratory experience, and 5 years of professional programming and laboratory automation experience.

Proven track record for novel research, leading multidisciplinary collaborative projects, and synthesizing large datasets into succinct conclusions.


Senior Scientist

2019 - Present

Institute for Protein Innovation, Boston MA

  • Manage development of LIMS system
  • Automate data acquisition and analysis, lab-wide (python, c#)
  • Build custom microservices for custom functions/user interfaces
  • Apply data science techniques to interrogate biological data
  • Contribute to protein engineering projects
  • Mass spectrometery of biomolecules
Scientist I / Scientist II

2015 - 2019

Adimab, Lebanon NH

  • Conduct and evaluate accelerated stability assays on drug-candidate mAb molecules via MS/MS
  • Automate data acquisition and analysis (python, c#)
  • Use BLI for measuring binding kinetics and epitope mapping experiments
  • Lead exploratory protein engineering projects
Automation Consultant, Co-Founder

2015 - Present

Boston AutoLytics, LLC

  • Evaluate, prescribe, and develop automated solutions for data acquisition and analysis
  • Projects are biopharma focused with clients including: Adimab, Avitide, and Eli Lilly


Check out these on-going software projects:

PyVuka - A flexible and general purpose global fitting software for analyzing scientific data, written in python

ForteBioPKG - A python package for the automated analysis of high-throughput ForteBio BLI data. Automation includes kinetic and epitope mapping analyses


Data Analysis

Mass Spectrometry

Moelcular Kinetics

Chromatographic and Light Scattering/Absorption Techniques

Protein Engineering

Web Design & App production (php, html, javascript, jquery, etc)

Computer programming (Python & C#)

Specific Laboratory Techniques

NMR, Peptide Mapping, LCMS, MALDI, SPR, BLI, DSF, Micro-fluidic mixing, SAXS, CD, FL, PCR, HIC, CEX, SEC, Binding Kinetics, Folding Kinetics, MD, Intein Chemistry, Protein Engineering, Protein Purification, FRET, SDS-PAGE, DLS


Most of my professional publications are indexed on PubMed [Here]. Direct download links:

[14] Networks of electrostatic and hydrophobic interactions modulate the complex folding free energy surface of a designed βα protein (2019)

[13] Deamidation and isomerization liability analysis of 131 clinical-stage antibodies (2019)

[12] Database-Centric Method for Automated High-Throughput Deconvolution and Analysis of Kinetic Antibody Screening Data (2017)

[11] Rapid assessment of oxidation via middle-down LCMS correlates with methionine side-chain solvent-accessible surface area for 121 clinical stage monoclonal antibodies (2017)

[10] Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY (2017)

[9] Clusters of isoleucine, leucine, and valine side chains define cores of stability in high-energy states of globular proteins: Sequence determinants of structure and stability (2016)

[7] Early folding biases in the folding free-energy surface of βα-repeat proteins: A dissertation (2014)

[6] Modulation of frustration in folding by sequence permutation (2014)

[5] Microsecond barrier-limited chain collapse observed by time-resolved FRET and SAXS (2014)

[4] Sub-millisecond time-resolved SAXS using a continuous-flow mixer and X-ray microbeam (2013)

[3] Minireview: Advances in turbulent mixing techniques to study microsecond protein folding reactions (2013)

[2] Complementary techniques enhance the quality and scope of information obtained from SAXS (2013)

[1] Minireview: structural insights into early folding events using continuous-flow time-resolved small-angle X-ray scattering (2011)