PROFESSIONAL EXPERIENCE
Cajal Corporation, San Jose, CA
2019- CEO & Technical Founder
- Stealth startup using ML, AR, and NLP to build technology that can read for you.
Synthego Corporation, Redwood City, CA
2016-2019 Chief Scientific Officer
- Responsible for the creation, implementation, and stewardship of Synthego's scientific vision. Represented Synthego publicly in press, at investor conferences, and KOL retreats. Relevant examples: Founders Fund F50 2016 Summit (attendee), AWS Reinvent: How to build a cloud laboratory (presenter), AI in Life Science: Allen & Co (presenter).
- Lead organization-wide transition from core product (synthetic sgRNA) to broad genome engineering products and services ('full-stack genome engineering') through automated mammalian cell culture and editing.
- Personally built and launched web-based CRISPR guide design and analysis software tools, including the Synthego Design Tool, and Synthego ICE Analysis. Utilized modern software patterns and cloud services (AWS, EC2/ECS/ELK/Lambda/Athena).
- Built a multidisciplinary research team of 35 scientists and engineers from scratch - integrating hardware, software, chemistry, genomics, cell biology, machine learning, and preclinical therapeutic design. We generated 40 patents (at various stages) and multiple publications.
- Played a central role in Synthego's series B, B+, and C fundraise activities, totaling $150MM+ in funding from top tier VCs. Generated decks, participated in pitches, and was point person on technical due diligence.
2014-2016 'Position' / Engineer
- Early employee ~#10, recruited to write workflow software and learn how a startup worked.
- Personally architected, built, and supported Synthego's RNA factory software (fully integrated LIMS, workflow, QC analysis, mobile client, and instrument interfaces). Shipped orders #1 to $10M total revenue.
WholeSlide, Inc., San Diego, CA
2011-2014 CEO & Technical Founder
- Built and licensed white-label digital pathology software for iOS devices
2011-2014 Consulting Technical Lead
- Dermoscopic image annotation tools with browser-based image segmentation. Memorial Sloan Kettering Cancer Center. 2014
- Web-based patient report generation; Applications for viewing high resolution images remotely. Emory University, Department of Neurology, 2014
- Custom iOS application development for virtual slide microscopy. MBF Biosciences, 2013-2014
- Virtual slide viewer integration into legacy medical education portal. University of California San Diego, School of Medicine, 2013-2014
- Custom user interface for wireless embedded BCI hardware Kendall Research Systems, 2013-2014
- Disaster recovery simulation game for resource distribution education. Red Cross, Red Crescent Climate Center. A collaboration with TankThink Labs. 2013
- Native & cross-platform applications to display geo-located photos on stylized map data. En Ville publishing. 2011-2014
- Cloud application for building analysis cohorts and visualizing neuroimaging data. National Database for Autism Research. 2013
- Cloud application for exploring neuroimaging data. International Neuroinformatics Coordinating Facility. 2011-2013
- Reverse-engineered USB ultrasound transducer; built a working USB-OTG adapter and Android client. Distributed Health Lab. 2012-2013
- iOS GLKit port of android open-body-browser to create OpenWorm viewer for iPhone & iPad. For http://openworm.org project. Sponsored by MetaCell, LLC, 2012
- Created a hematology reference application for iPhone and iPad; #4 free iPad Medical app. Hematology Outlines, 2012
ACADEMIC EXPERIENCE
University of California, San Diego School of Medicine, La Jolla, CA
2013-2014 Project Scientist, Neurosciences, Townsend Lab
- Developed gaze-based technologies to assist in autism evaluation and intervention.
o Built a head-mounted gaze tracking setup to record active gaze interactions in 2-person conversation.
o Used AR to map subject gaze from a head mounted pupil tracker to user input for a 3D gaming environment.
2009-2013 Postdoctoral Fellow, Neurosciences, Courchesne Lab
• Focused on identification of early biomarkers of autism. Used multiple modalities to assess risk in children, including but not limited to MRI (structure and functional), histology and immunohistochemistry, and eye tracking for gaze preference.
• Developed a novel reconstruction method of three-dimensional cortical laminar architecture; Published results in NEJM (first author), along with open software pipeline (cloud-based) with emphasis on reproducibility.
• Designed, deployed, and supported UCSD Autism Center of Excellence on-prem cluster for batch MRI analysis; Awarded an AWS Research grant and built cloud-based architectures for data federation and visualization with national (NIMH, NDAR) and international collaborators (INCF).
• Won Grand Prize at Qualcomm Uplinq 2012 hackathon with gaze-based autism screening tool on an Android device
• Developed a set of methods to analyze infant eye-tracking data for pre-clinical applications. Implemented methods in matlab and in openCV with Android and iOS targets.
• Deployed and configured a 48-node ROCKS cluster to automate current structural MRI processing pipelines and facilitate rapid iterative development of novel workflows. Operated infant MRI scan sessions; operator trained on GE 1.5T.
• Launched several science-focused technology projects: Cognitive Consilience - publication regarding cortical anatomy with accompanying mobile and web-based interactive visualization, Hematology Outlines - popular iOS medical education reference, Peaked at #4 in free medical in App Store, FigureZero - digital poster sharing tool with spatial annotation and presentation tools.
Center for the Neural Basis of Cognition, University of Pittsburgh & Carnegie Mellon University, Pittsburgh PA
2005-2009 PhD Neural Engineering / Bioengineering
- Center for Neural Basis of Cognition, joint program with Carnegie Mellon University
- Thesis: Engineering Approaches for Neurobiology. Emphasis on microfluidic cell culture platforms with closed-loop video control and annotation.
o Designed and built a microfluidic hardware/software platform for future study of chemotaxic and axonal guidance cues in dissociated cell culture with high precision and repeatability in a low-shear environment.
o Developed a computational model of recurrent neural network activity propagation in geometrically constrained networks.
o Developed a calcium reaction-diffusion biophysical model to study spike-timing dependent spatiotemporal profile detection using representative calcium signaling pathways.
- Served as President of Bioengineering Graduate Student Council. Represented 150+ graduate bioengineering students in matters of curriculum, teaching, and funding. Directly responsible for incoming recruitment, orientation, and faculty-student relations.
2001-2005 BSc Bioengineering
- Concentration in Biomechanics
- Built a 3D engine using C#.NET & DirectX 9 to visualize and replay complex robot kinematics. Part of a larger project to evaluate graft options and reconstruction techniques for ACL repair.
PUBLICATIONS
ORCID ID: https://orcid.org/0000-0002-5198-0825
Inference of CRISPR Edits from Sanger Trace Data Tim Hsiau, David Conant, Nicholas Rossi, Travis Maures, Kelsey Waite, Joyce Yang, Sahil Joshi, Reed Kelso, Kevin Holden, Brittany L Enzmann, Rich Stoner. bioRxiv 251082; doi: https://doi.org/10.1101/251082
Patches of Disorganization in the Neocortex of Children with Autism R Stoner ML Chow, MP Boyle, SM Sunkin, PR Mouton, S Roy, A Wynshaw-Boris, SA Colamarino, ES Lein, E Courchesne N Engl J Med. 2014 Mar 27;370(13):1209-19. doi: 10.1056/NEJMoa1307491
Patches of disorganization in the neocortex of children with autism We examined several areas of the brain from children with autism. Using a new technique, we found small areas of abnormal cells in parts of the brain associated with autism. These regions, called patches, support the idea that brain abnormalities in children with autism can be traced back to prenatal development. DOI 10.1056/NEJMoa1307491.
Cognitive Consilience: primate non-primary neuroanatomical circuits underlying cognition Soren Van Hout Solari and Rich Stoner Front. Neuroanat, 5:65, 2011.
Cognitive Consilience was a tool built to organize and present the principles of neuroanatomical organization within general model of cortex. Working with Soren Solari, he and I distilled and synthesized hundreds of primate neuroanatomy facts into a single interactive visualization. The resulting picture represents the fundamental neuroanatomical blueprint upon which cognitive functions must be implemented. We focus on neuroanatomy related to primate non-primary cortical systems to elucidate the basis underlying the distinct homotypical cognitive architecture.
Preference for geometric patterns early in life as a risk factor for autism K Pierce, D Conant, R Hazin, R Stoner, and J Desmond Arch Gen Psychiatry, 68(1):101-109, Jan 2011
Uniaxial and biaxial properties of terminally sterilized porcine urinary bladder matrix scaffolds DO Freytes, RM Stoner, SF Badylak J Biomed Mater Res B Appl Biomater, 84(2):408-414, Feb 2008
POSTERS AND PRESENTATIONS
Computing, querying, and visualizing brains, shape features, metrics, and templates: A prototype webapp infrastructure built on NIDM Stoner, R., Nichols, N., Klein,. A, Ghosh, S. Society for Neurosciences, San Diego CA 2013
A white matter projection atlas of the mouse brain: first steps towards an automated pipeline R. Stoner, Society for Neurosciences, San Diego CA 2013
Mapping neuroimaging resources into the NIDASH Data Model for federated information retrieval Nichols, B. Nolan and Steffener, Jason and Haselgrove, Christian and Keator, David B and Stoner, Richard Martin and Poline, Jean-Baptiste and Ghosh, Satrajit S. OHBM, Seattle, WA 2013
Demonstrating Cloud Computing Capabilities Using NDAR, Piplines and the Autism Informatics Grid Hall, D. Stoner RM, Farber, G. IMFAR, Toronto, ON 2012
Three-Dimensional Reconstruction and Analysis of Laminar Microstructure in Young Autistic Males Stoner RM, Courchesne E. International Meeting For Autism Research, San Diego CA 2011
Modeling Early Brain Growth in Autism Using MRI Stoner RM, Campbell K, Solso S, Courchesne E. International Society for Developmental Neuroscience, Estoril, Pt 2010
A Preference for Geometric Patterns Early in Life is a Risk Factor for Autism Pierce K, Conant D, Hazin R, Stoner RM, Desmond J. International Meeting For Autism Research, Philadelphia PA, 2009
High-Resolution Spatiotemporal Cell Stimulation Using Dynamic Targeting in a Microfluidic Device Stoner RM, Zeringue HC. Biomedical Engineering Society meeting, Pittsburgh, PA 2009
A Microphysiological Simulation of Spatiotemporal Calcium Detection for Synaptic Plasticity Stoner RM. Pitt/CMU Biophysical Journal Club, 2009
In silico and in vitro Characterization of Recurrent Activity in Patterned Neural Networks Stoner RM, Vishwanathan A, Zeringue HC. Society for Neuroscience, Washington, D.C. 2008
Physiologic detection of STDP-based spatiotemporal Calcium signals Stoner RM, Rubin J. Coherent Behavior in Neural Networks workshop, Mallorca, ES 2007
The Effect of Terminal Sterilization on the Mechanical and Material Properties of Lyophilized UBM Sheets Stoner RM, Fretyes D, Badylak SF. Midwest Tissue Engineering Conference, Pittsburgh, PA 2003
INDEPENDENT PROJECTS
CRISPR CRISPR Revolution – A CRISPR editing simulation packaged into a Unity game. Locate the PAM site before the strand passes you by! Released internally within Synthego as an April fools release.
Sphere One – an immersive shared virtual reality experience. A 12-foot geodesic sphere with dual projector setup driven by custom graphics projection. Unfinished.
A 21st Century Map of the Brain - Using the Allen Institute mouse connectivity data set, I rendered a series of generative projection atlases with each projections colored by origin.
WholeSlide Open was an attempt to build an open source medical education tool for students around the world.
ISIC Annotation Tool - In collaboration with Emory University and Memorial Sloan-Kettering Cancer Center, we built a web-based dermatology annotation tool around a very large collection of annotated melanoma images.
OpenWorm Browser for iOS - Working with the Openworm.org team, I ported the open-3d-viewer (Google Body Browser) to iOS & GLKit. The app allowed a user to explore the anatomy of c. elegans. It is open-source and available on the app store.
Cerebrii – First 3D brain atlas for iPhone. Interactive visualization of the SPL brain atlas with medical study guide and quiz. Extended to display fiber bundles from DTI. Featured in iPhone development book(s).
FigureZero was an interactive zoomable canvas on for poster authors to annotate their PDF poster. It was tested at the 2012 Society for Neuroscience meeting as a way to present and share digital posters.
WholeSlide DURA was a neuroscience visualization tool built for iPad. It supported a long list of neuroscience file types in several 2D and 3D environments.
PersonalEyes app guided users through a set of Ishihara plates and generated a color-blind correction ICC color profile based on user feedback.
Prism operated on the video stream from the iPad 2 camera, creating interesting image transforms on part of all of the image in real time. It looked like the first versions of Instagram, before Instagram ever existed.
NeuroResponse. A patient feedback app for neurosurgeons to use during DBS electrode placement. UCSF Department of Neurosurgery, 2010
LEADERSHIP AND PROFESSIONAL ORGANIZATIONS
2007-2009 President - Bioengineering Graduate Student Council (BMES)
University of Pittsburgh, PA
Served on Graduate Faculty Council, representing 150+ graduate bioengineering students in matters regarding curriculum, teaching requirements, and funding. Directed incoming student recruitment, orientation, and faculty-student pairing.
Member
American
Association for the Advancement of Science
Biomedical Engineering Society
National Foundation for Autism Research
Neuroethics Society
Society for Neuroscience
TEACHING EXPERIENCE
Fall 2008 BioE 1531/2531 Computer Applications in Bioengineering (TA)
University of Pittsburgh, Pittsburgh, PA
Course Topics: C++, image processing using ITK, reusable code
Spring 2008 BioE 2241 Issues in Bioengineering: Ethics and Concepts (TA)
University of Pittsburgh, Pittsburgh, PA
Course Topics: Biomedical and research ethics, case studies
Spring 2008 The Princeton Review MCAT Biology
Course Topics: Comprehensive cell / molecular biology and human physiology
Spring 2007 BioE 1002 Intramural Research Internship (TA)
University of Pittsburgh, Pittsburgh, PA
Course Topics: Research project development and presentation skill
PRESS
2/27/19 - Synthego to award $1M in CRISPR tools to genome innovators, SynBioBeta
3/19/19 - Grant for Genome Engineer Innovation Offered by Synthego. GEN Genetic Engineering & Biotechnology News
5/3/18 - Biology Will Be the Next Great Computing Platform. Wired
1/29/18 - Synthego Launches Powerful CRISPR Analysis Software To Make World-Class Genome Engineering Accessible. AP
10/19/17 - Synthego Receives Intel Capital Investment to Advance CRISPR Bioinformatics. AP
5/16/2017 - Synthego First to Offer Over 100,000 Genomes in Powerful New CRISPR Software. AP
5/16/2017 – Synthego’s genetic toolkit aims to make CRISPR more accessible. TechCrunch
3/26/14 - NIMH & UCSD press releases - NIH-funded Study Shows Disrupted Cell Layering Process in the Developing Brain. This publication was featured in over 400 articles around the world. Featured on BBC, NYT, SD Union Tribune, Chicago Tribune, Wired, and many more.
6/20/13 - Stony Brook University - Arno Klein and the Mindboggle Team Emerge Victorious at the Human Brain Mapping Hackathon in Seattle
7/13/12 - Puget Sound Business Journal - Allen Institute invites ‘hackers’ to help spread its knowledge
7/12/12 - Xconomy - Developers Go Head-to-Head in Hackathon
7/06/12 - SFARI - Brain hack
7/03/12 - Time Techland - Allen Institute: Microsoft Cofounder’s Organization Holds Brain Hackathon
6/27/12 - Qualcomm - San Diego’s Qualcomm Embraces Experiment in Incentive Prizes
12/11/11 - UCSD Health Sciences - Cognitive consilience
AWARDS
2013 Best Individual Presentation, Allen Institute for Brain Sciences MNA, OIST
Winner, Best MNI152 Mashup, OHBM hackathon
2012 Grand prize, Qualcomm Uplinq hackathon
"Most buttons", Allen Institute for Brain Sciences hackathon
2011 Amazon AWS in Research grant to build a cloud-backed neuroimaging pipeline for ASD-related MRI analysis
2007 Whitaker Bioengineering fellowship