Matthew Pearson
 

Summary   

 Software engineer with nine years’ experience working in R&D and computational biology. Excellent object-oriented design and development skills with a solid background in genomics and computer science.

Employment   

Broad Institute of MIT and Harvard
2008–
Senior Software Engineer
2005–7
Software Engineer II–III
Design and develop gene prediction and validation software. Lead a small team of software engineers. Work with a team of biologists to publish high-quality whole-genome annotations.
  • Wrote a program that uses homology and EST evidence to arbitrate among predictions from several gene prediction tools, including augustus, fgenesh, geneid and genewise.
  • Designed and implemented a whole-genome EST assembler that builds full gene models (and alternate splice forms, when present) from alignments of captured RNA. Start and stop codons are predicted when the evidence supports complete reading frames.
  • These tools have annotated nearly twenty published fungal genomes, as well as Culex pipiens, a mosquito.

Sun Microsystems, Enterprise Server Products
2001–5
Member of Technical Staff III
Designed low-latency network libraries for scientific codes and other demanding applications. Focus on usability and memory management.
  • Co-chaired an Open Group working group that defined ITAPI, a high-performance RDMA API industry standard.
  • Devised an algorithm to match work requests and completions on a proprietary network ASIC.
  • Received Sun's highest performance rating in 2003.

Sun Microsystems, High Performance Computing
1999–2001
Member of Technical Staff II
Developed, documented and maintained portions of MPI (a library that supports parallel applications on server clusters) and PFS (a parallel filesystem optimized for scientific workloads).
  • Led team of four engineers in implementing portions of MPI-2.
  • Designed and implemented an extended filesystem test harness with a heavy emphasis on integrity and reliability.
  • Wrote and debugged production code, including functions within the Solaris kernel vnode interface.
  • Wrote library interfaces, technical documentation and code examples for collective operations over intercommunicators and other obscure topics in parallel programming.

Education   

Stanford University

2006
Certificate in Computational Genomics
  • Studied sequence alignments, hidden Markov models, Gibbs sampling, phylogenetic trees and microarrays.
  • Term paper on searching microarray data for possible promoter motifs.
  • Cumulative GPA 4.0.

Dartmouth College

1999
A.B. cum laude, honors in computer science, minor in philosophy
  • Honors thesis research on out-of-core sorting of large data sets.
  • Received academic citation for an outstanding graphical editor and GUI in CS23 – Software Design and Implementation.
  • Studied computer architecture, algorithms, operating systems, networks, formal logic, probability, multivariable calculus, ethics and intellectual property.
  • Major GPA 3.85, cumulative GPA 3.5.
 

Papers &   
standards   

McGuire AM*, Pearson MD*, Neafsey DE, Galagan JE. Cross-kingdom patterns of alternative splicing and splice recognition. Genome Biol. 2008 Mar 5;9(3):R50.
*these authors contributed equally

DeCaprio D, Vinson JP, Pearson MD, Montgomery P, Doherty M, Galagan JE:
Conrad: gene prediction using conditional random fields. Genome Res. 2007 Sep;17(9):1389–98.

Dunlap JC, et al. Enabling a community to dissect an organism: overview of the Neurospora functional genomics project. Adv Genet. 2007;57:49–96.

Rosser J, Pearson MD, et al: Interconnect Transport API Technical Standard.
Open Group 2004;4679, Open Group 2005;9143.

Pearson MD: Fast out-of-core sorting on parallel disk systems.
Dart Coll Tech Rep. 1999;PCS-TR99-351.

 

Talks &   
posters   

Cross-kingdom patterns of alternative splicing and splice site recognition. Advances in Genome Biology and Technology 2008, Marco Island, Florida.

High-throughput genome annotation using Calhoun. Microbial Genomes 2007, Cambridge, UK.
 

Skills   

Programming languages: Fluent in Java, Jython, Python, shell scripting (Bourne/Korn/C/bash). Proficient with C, C++, HTML/CSS and sed/awk. Some experience with R and Bioconductor. Fading memories of [GNU]make, JavaScript, MIPS assembler, Perl, nroff and Tcl/Tk.

Operating systems: Extensive experience with Solaris and Mac OS X; familiar with BSD, Linux, Digital UNIX and IRIX. Not very good with Windows.

 

Interests   

Photography, swimming, backpacking, scuba diving, traveling.