Welcome
I'm an engineer, scientist, and musician located in the area of Boston, MA.
Currently I'm a Principal Software Engineer and Staff Scientist in the DSP Methods group at The Broad Institute of MIT and Harvard.
I enjoy building, creating, reverse-engineering, and trying to build a better future through technology.
While extremely serious about my work, I believe that a certain amount of whimsy is often helpful to get things done.
Engineering
To me the distinction between engineering and science is that science is the acquisition of knowledge and engineering is the application of knowledge to solve problems. In practice they are typically closely coupled.
While primarily a Software Engineer, I dabble in electronics and general making/repairing/hacking/reverse engineering. I have repaired amplifiers and guitars, created special effects for use onstage at performances, fixed electric bicycles, and built up many other projects.
I am a strong proponent of free software (free as in speech), and am delighted that as a corollary to working at the Broad, all of my work is open source and available on github.
Eden e300t master volume pot repair
Red Red Rockit opened for The Trews at the Middle East Upstairs sometime in 2016 and just after loading our gear into the club I found that the master volume pot had been broken off my Eden tube head.
It took some time but I eventually found the schematics and replaced the pot. Now it works as well as ever. Someday when I'm feeling adventurous I'll replace the caps.
In the future I'll post the step-by-step process.
Beyerdynamic dt-770 cable replacement
At the studio we had a set of Beyerdynamic dt770 headphones that had a faulty cable. I watched this video and then performed a similar operation on my headphones (except with a 1/8" jack instead of a mini XLR).
As an aside, these are the most comfortable and best sounding headphones I have ever found (a good tradeoff between sound and comfort, erring on the side of comfort). I highly recommend them.
(I may or may not have liberated this picture from an ebay listing, but it shows the details. My cable is not woven fabric - just a standard rubberized version.)
Science
Throughout my career I've been involved in many applied research projects - those projects which both require new knowledge/techniques and have a specific problem in mind.
Here I have listed a subset of the research I've been involved in - either in the form of links or a research artifact. One of these things is not like the others.
High-throughput RNA isoform sequencing using programmable cDNA concatenation
Co-first author paper where we introduce the MAS-seq and MAS-ISO-seq methods. We show a ~20x improvement in yield for long read transcriptome sequencing on PacBio instruments. Currently in review.
MAS-ISO-seq: A 20x yield increase in accurate, long-read RNA isoform sequencing data
My MAS-ISO-seq talk at Cold Spring Harbor Lab's Genome Informatics 2021. The conference was virtual, so we were able to easily record the presentations. I was running on very little sleep, so my presentation did not flow as well as I'd have liked.
Highly efficient full-length isoform sequencing using intramolecular multiplexed cDNAs: a 16-22x yield increase on PacBio sequencers
Poster I presented at AGBT Precision Health 2021 in San Diego.
Repeat expansions confer WRN dependence in microsatellite-unstable cancers
Paper to which I contributed as part of the Long Reads team at the Broad. Published in October of 2020 in Nature.
Squad X Infrastructure Study
While at BAE Systems I was Principal Investigator for the Squad X Infrastructure Study program funded by DARPA. I led the proposal effort and won funding for a team of 6 engineers for a year.
Scaling to 1M genomic samples for the All of Us research program
I was the initial author of a tool to perform joint calling in the cloud for the All of Us a program (based on an existing prototype for scalable joint calling by Laura Gauthier). After about 6 months I moved on from that project. My colleague Andrea Haessly virtually presented this "poster" at ASHG 2020 based on the work we did on the joint calling for All of Us.
Somatic small variant and copy number alteration calling with the Genome Analysis Toolkit
My functional annotation tool, Funcotator, was incorproated into the GATK and is now in use as part of the Broad's standard Somatic Variant Discovery Pipeline. This is a poster my colleague Lee Lichtenstein presented at AACR in 2019.
Graph-based read correction reclaims 40-90% of reads originally rejected from PacBio HiFi data without resequencing
This is a small piece of the research I pursued at the Broad. I presented this at our annual retreat in 2019 (essentially an internal scientific conference with about 2000 people in attendance).
On the Temperature Acclimation of Crab Musculature
My honors thesis from the Marder Lab. I show some differences in the excitatory junctional potentials (EJPs - i.e. muscle responses) of crabs acclimated to warmer temperatures. It's a decent undergraduate capstone work.
My Bands
Sidewalk Driver
We've had some moderate successes - many shows around the Boston and New York areas and a short tour of London in 2012. In 2018 we opened for Bon Jovi at The Boston Garden in front of 15067 people.
My Role: Bass and B-Vox
Music: Imagine David Bowie meets The Cars with some Hendrix and Zep thrown in for good measure and a glam stage presence.
Red Red Rockit
Three piece rock and roll band. This is the latest iteration of a band that traces its roots back to my first high school band.
My Role: Lead Vox and Bass
Music: Firmly rooted in the power trio days of yesteryear, yet manages to sound fresh as a daisy. One moment, you'll hear a bluesy, dirty James Gang groove and the next, a tight, bouncy Beatles-esque melody - each song delivering hooks that are somehow simultaneously unexpected and familiar.
Moxie Fever
My College band. We played lots of shows at small clubs around Boston. Once we played at CBGB in New York City.
My Role: Bass and B-Vox
Music: Poppy and catchy songs with great hooks. Reminiscent of Weezer and other mid 90s bands.
The Futon Police
My High School band. We had a handful of shows around Boston. Our largest was our last - in front of about 600 people.
My Role: Bass and B-Vox
Music: Poppy and angsty rock. Heavily Beatles, Hendrix, and Weezer influenced.