# sabareesh subramaniam

> Software Engineer

Location: San Francisco Bay Area, United States
Profile: https://flows.cv/sabareesh

I obtained my PhD in Computational Biology from the University of Wisconsin-Madison in Feb 2014. Prior to this, I obtained a Master's degree in Computer Sciences also from the UW-Madison in May 2010. I have also held full-time software engineering positions at Cisco and Qualcomm where I developed C/C++ software for network devices.

I worked on dynamic resource management for cloud applications at VMWare. My team focused on auto scaling (add/drop virtual machines) using reinforcement learning.

At Box, I work on the core platform team. My duties include leading a team of developers developing and operating the php monolith which process of millions of requests every minute. I also lead the development of microservices to extract functionality from the monolith and modernize the Box software stack.


Computational Biology:
My thesis is on computational protein modeling with an emphasis on algorithm and software development. Under the direction of Dr. Alessandro Senes, I have developed computational methods to predict membrane protein structure from sequence [Mueller 2014]. I have also worked in collaboration with experimentalists to predict protein structure based on experimentally derived constraints [LaPointe 2013]. 

I have developed flexible energy-based rotamer libraries [Subramaniam and Senes 2012,2014] that outperform state-of-the-art libraries in terms of prediction quality as well as computational efficiency.

A major component of my research is the development of efficient algorithms and software to facilitate protein modeling. I have been one of the primary developers of the Molecular Software Library (MSL) which is an open-source C++ software library developed from scratch by a small group of collaborators [Kulp 2012]. I have implemented sidechain optimization algorithms, force fields, solvation models, molecular surface area calculators and a variety of protein modeling applications that are an integral part of MSL.

## Work Experience
### Staff Software Engineer @ Box
Jan 2019 – Present

### Senior Member Of Technical Staff @ VMware
Jan 2014 – Jan 2019 | Palo Alto, CA
Automated, dynamic resource management, particularly auto scaling, for applications in the Cloud.

### Research Assistant @ UW-Madison
Jan 2008 – Jan 2014
Working on protein design and structure prediction with Dr.Alessandro Senes, Department of Biochemistry.
Developing an open-source molecular modeling library in C++ - MSL.

### Graduate Student @ UW-Madison
Jan 2008 – Jan 2010
Graduate Student with the Computer Sciences Department.

### Interim Engineering Intern @ Qualcomm
Jan 2009 – Jan 2009
Worked with LTE Modem SW group.
1. Developed a test framework using XML/C++ data binding to enable testing of connected mode measurement reporting.
2. Profiled the peformance of shared memory message transfer between the two QDSP6 processors on the LTE system.

### Software Engineer and Project Intern @ Cisco
Jan 2005 – Jan 2008
Software Engineer with the Optical Technology Business Unit. 
Developed a command-line interface (TL1)  to switching hardware using C/C++. 
Developed a TCL-based regression testing suite.


## Education
### Doctor of Philosophy (PhD) in Computational Biology
University of Wisconsin-Madison

### Master of Science (MS) in Computer Science
University of Wisconsin-Madison

### BE in Electronics and Communication
PSG College of Technology


## Contact & Social
- LinkedIn: https://linkedin.com/in/sabareeshsubramaniam
- Portfolio: http://pages.cs.wisc.edu/~sabarees/

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Source: https://flows.cv/sabareesh
JSON Resume: https://flows.cv/sabareesh/resume.json
Last updated: 2026-04-12