ANSHUL NIGHAM

Profile

	Computer Science Ph.D. with  1 year product development experience at IBM
	Over 5 years of development experience in C/C++/Java
	Strong research background in algorithm design with an excellent publication record
	Proven writing, presenting and public speaking skills

Education

	Ph.D, Singapore--MIT Alliance / NUS (Computer Science, 2009)
		GPA: 5.0/5.0
		President's Scholar (NUS), 2005--2006

	B. Eng, Nanyang Technological University, Singapore (Electrical/Electronic Engg, 2003)
		First Class Honours (GPA 3.8/4.0)
		Awarded the SIA--NOL scholarship for undergraduate studies

Skills

	Programming: Strong C/C++ background. Experience in Java/J2EE, C#, Win32, .NET, MATLAB, R, PHP, Ruby, XML/XPath/XSLT, Shell scripting
	Development tools: gcc, gdb, make, doxygen, Eclipse, svn, git, XCode, Visual Studio
	Platforms: Linux, Windows, Mac OS X
	Publishing: HTML/CSS, Javascript, PHP, 
	CS Courses: Algorithm design, Databases, Artificial Intelligence, Machine Learning, Computer Language Engineering, Computer Graphics, Research Methodology
	Communication: Fluent public speaker and presenter, good technical writing skills
	Teamwork: Part of technical/research collaborations, as well as organizational projects

Experience

	Staff Software Engineer, IBM Singapore (Aug 2008 -- present)
	
		Developed components of a Win32-based agent for an enterprise single sign-on application
		Developed and improved components of Windows GUI applications using C#/.NET
		Designed and developed a prototype centralized versioning repository system using Axis web-services framework and Java
		Provided development-side support to enterprise customers
	
	Internship at Texas Instruments, Singapore (Jan 2002 -- Jun 2002)
	
		Developed firmware for a portable MP3 player based on the C55x DSP platform
		Improved the real-time operating system to improve usability and efficiency
	
Projects

	Research work components
	
		Implemented a generic, parallelizing class in
		C++ using the Boost threads library
		Developed a PHP front-end and Ruby daemon to allow web-based
		access to a back-end algorithm developed in C++
		Implemented various graph algorithms, including the Bron-Kerbosch clique finder
		Implemented an efficient dynamic programming algorithm to
		compute substructure similarities between molecular structures
		Rewrote MATLAB prototype code involving statistics and linear
		algebra in C++ for better performance
	
	Graduate course projects
	
		Developed the LPASSO method to improve regression regularization using numerical optimization
		Implemented a compiler for the decaf programming language for SPARC processors
		Implemented algorithms for solving and learning Bayesian Networks
		Implemented image-rendering code using ray-tracing techniques
	
	Final Year Project, NTU: Medical Image Processing (Jan--Dec 2002)
	
		Developed useful-pixel extraction algorithm for non-lossy compression of medical images
		Implemented a digital image watermarking scheme
	
Research
	
	Computational tools for automated analysis of macromolecules 
	
		Developed an algorithm to detect structural flexibility in protein structures
		Used statistical modeling to eliminate inherent experimental noise in atomic coordinate data
		Applied clustering to group rigid but discontinuous molecular fragments
		Implemented in C++ with a web-based front-end
		Interfaced results with popular molecular visualization tools like PyMol/JMol
		Parallelized algorithm for speedup on multi-core hardware
	
	Graph-theoretic study of generic molecular structures 
	
		Developed a general approach to explore the space of all possible protein structures
		Used a graphical representation with hierarchical ordering to store structures
		Used clustering and graph manipulation to identify key bifurcation points
		Improved scalability by using a compact clustered representation of the space
		Investigated branching properties of the graph for compact structures
	
	Localized sampling for optimizing protein structure prediction 
	
		Designed a method to sample neighborhood conformations of a compact protein structure
		Exploited kinematic loop-closure techniques to efficiently generate local changes
		Performed energy minimization of molecular structures using Monte Carlo methods
		Applied method to last-stage refinement of protein structure prediction methods
		Improved convergence over standard sampling and gradient descent methods

	Exchange visits
	
		Stanford University, under Prof. Jean-Claude Latombe (Jul--Aug 2005)
		Massachusetts Institute of Technology, under Prof. Tomas Lozano-Perez (Sep-Dec 2005)

	Publications
	
		Characterizing Protein Conformation Space. SMA Symposium, 2007.
		Protein Conformation Flexibility Analysis with Noisy Data. Journal of Computational Biology 15(7):813--828 (2007).
		Protein Conformation Flexibility Analysis with Noisy Data. RECOMB 2007, pp. 396--411.
		pFlexAna: Detecting Conformational Changes in Remotely Related Proteins. Nucleic Acids Research, 36:W246--W251 (2008).
	
	Teaching Assistant, NUS (Aug 2007 -- Jun 2007)
	
		Assisted in teaching Data Structures and Algorithms at undergraduate level
		Conducted tutorial/recitation sessions with a combined class strength of over 100 students
		Conducted help sessions for labs and examinations
		Marked exam scripts and performed other administrative duties
		
	Teaching Assistant, SMA (2003 -- 2004)
	
		Assisted with Pervasive Human-Centric Computing (Spring 2003) and Computational Biology (Spring 2004)
		Set up course projects and provided hardware and software support
		Assisted with project evaluations and marking
		
Activities and interests

	Represented NTU in international debating tournaments for three years
	Led a team to organize the Singapore World Universities Debating Championship in 2004
	Hobbyist photographer and active photoblogger