Nathaniel J Evans bio photo

Nathaniel J Evans

Bioinformatics Ph.D. Student

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Nathaniel J Evans

Nathaniel J Evans

Currently

Nate is a Bioinformatics and Computational Biomedicine PhD student at Oregon Health and Science University (OHSU). He is actively engaged in various precision oncology projects and has special interest in predicting cell line and patient response to drug combinations.

Education

2018 - 2023 Oregon Health and Science University Ph.D. Bioinformatics and Computational Biomedicine

2010 - 2015 University of Washington B.S. Biological Physics

Patents

2017 METHOD AND APPARATUS FOR PRE-POSITIONING A STATIC, RADIALLY SYMMETRIC, COAXIAL SAMPLE AND SHEATH COMBINATION TO PROVIDE UNIFORM SAMPLE DELIVERY DURING FLOW

Awards

2019 1st Place BMI651 Kaggle Challenge: Classify breast cancer cell lines as resistant or susceptible to drug treatment. (Members: Nate Evans, Gareth Harman)

Publications

  1. Choonoo G, Blucher AS, Higgins S, Boardman M, Jeng S, Zheng C, et al. Illuminating biological pathways for drug targeting in head and neck squamous cell carcinoma. PLOS ONE. 2019 Oct 9;14(10):e0223639.

Presentations

MAY 2019 Identification of Atypical Dose-response Curves and Implications for Drug Sensitivity Designations (Authors: Nathaniel Evans, Aurora Blucher, Shannon McWeeney)

Occupation

Current Bioinformatics and Computational Biomedicine Ph.D Student
Oregon Health and Science University

  • RA2 position in the Mills lab
    • Developing image registration pipeline for CyclicIF

  • Collaborating with the Kulesz-Martin Lab on precision oncology research in HNSCC patients.

  • Covered QC/QA techniques for dose-response data, dose-response feature extraction techniques (including AUC, IC50) and compared fitting methods used by the beatAML project under mentorship of Drs. Shannon McWeeney and Aurora Blucher. Currently extending this by developing metrics of curve similarity for automated detection of toxicologically uncharacteristic dose-response observations that may be misrepresented by classical sensitivity metrics.

  • Development, testing and validation of a Single Particle Tracking (SPT) pipeline for application of Total Internal Reflection Fluorescence (TIRF) super-resolution imaging of actin monomers under the mentorship of Drs. James & Catherine Galbraith.

2013-Current Visiongate, Inc.
Visiongate is a Biotechnology company dedicated to the early detection and prevention of cancer. Visiongate is developing a lung cancer diagnostic aid, employing high-throughput 3D imaging of cells from liquid biopsy using Optical Projection Tomography Microscopy (OPTM). For more information: www.visiongate3d.com.

Consultant 2018-Current

  • Consulting on various projects in development awaiting patent submission.
  • Ran Cell-CT instruments for 4 week Pilot Clinical Accuracy Study

Mechanical Design Engineer 2015-2018

  • Cell delivery from storage chamber to imaging axis has a plethora of difficulties including cell-chamber adhesion and temporal non-uniform delivery, to mitigate this: designed, prototype and implemented an automated precision sample dispensing device for use loading sample in a pressure-cycled microfluidic pump. Implementation led to decreased clogging, higher cell-throughput, and an automated prep. process. Co-inventor on the pending patent.
  • Testing and validation of the Cell-CT and auxiliary systems are highly dependant on sample particle density (i.e. how many cells/objects per uL). Built an automated counting microscope using a brightfield upright microscope, motorized stage and high-resolution CCD to scan slides. Developed custom software to scan slide, segment, classify and count biological and non-biological objects (~10ums) using density based clustering and convolutional neural networks built in Tensorflow. Significantly reduced technician time required to manually count objects and produced a more automated prep. process.
  • Industry standard process to mix particulate into small volume, high-reynolds number fluids has significant overhead and poor yield percentage. To improve upon this required developing a novel process employing Dual Asymmetric Centrifugal (DAC) mixing with custom component integration. Resulted in a highly scalable process with much improved yield efficiency over industry standards. Co-inventor on pending patent.
  • Provided systems engineering and data analysis support for development of the Cell-CT. Specifically, diagnosing and treating aberrant motion-control of microfluidics during cell delivery in the Cell-CT. Designed and managed production of specific components for the Cell-CT, with emphasis on adjustability, repeatability and manufacturability.
  • Designed, tested and managed vendor manufacturing iterations for extremely critical high-pressure microfluidic cell-delivery device. Experience emphasis on pressure-cycled sealing, component deformation/failure and microfluidic optimization. Expected to be listed as co-inventor on future patent submission. Lab Work & Process development: degassing optical media, creating RI matched cell suspensions and process improvement. Developed rudimentary database GUI, written in java for internal sample tracking. For use in sample preparation process optimization.
  • Collaborated on a multidisciplinary team dedicated to the eradication of lung cancer through early detection and treatment.

Mechanical Engineer Intern 2013-2015

  • Designed Cell-CT auxiliary components, prepared cell samples, developed sterile environment procedures and manufactured low-volume components.
  • Developed and used hardware for inspection of 60 micron inner diameter glass capillary internal surfaces for defects as a quality control step. Significantly increased instrument operation time by reducing artifact hangups.
  • Characterized component failure rates and extrapolated future needs. Increased Cell-CT throughput by maintaining comprehensive inventory.

2014-2015 Student Researcher
University of Wasington (UW) Human Phtonics Lab (HPL)

  • Optical Projection Tomography Microscopy (OPTM) is inherently limited to narrow imaging thicknesses by commercially available Numerical Apertures (NA), however, by axially stitching, there is no limit to tissue length that can be imaged. This implies imaging of needle biopsies are an excellent application for this imaging technique. As a plausible data acquisition model, designed in CAD a OPTM module allowing needle biopsy translations necessary for OPTM imaging. Mentored by Dr. Eric Seibel.
  • Re-designed and prototyped a modular cartridge for index matched, large sample imaging, compatible with OPT microscope. Mentored by Dr. Ronnie Das.

Technical Skills

Programming Languages

  • Python
  • R
  • Java
  • C/C++
  • MATLAB
  • Mathematica
  • bash
  • mySQL
  • git

Software

  • SolidWorks
  • Altium
  • FIJI (ImageJ)
  • CorelDraw
  • Adobe Photoshop CC & Lightroom
  • Perforce

Manufacturing

  • Competent machinist (CNC lathe & Mill)
  • Proficient with various forms of additive manufacturing
  • Experienced with water-jetting and laser-cutting