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Research Interests

Generating probabilistic uncertainty models for complex functionals computed on objects with native error/uncertainty. Focus on generating intelligent (low-discrepancy) samples in high-dimensional spaces. Applications to protein-protein docking and protein homology modeling.

I have recently entered into candidacy for my PhD. Please see here for a link to my PhD Proposal presentation slides (best viewed in Adobe Reader), and here for a link to my PhD Proposal document.

University of Texas at Austin: 2010-2016
M.S. Computer Science; Dec 2014 Ph.D. Computer Science; In candidacy as of Jan 2016

Brigham Young University: 2004-2010
B.S. Computer Science with Bioinformatics emphasis
Industry Experience

Google, Inc

Software Engineering Intern, Mountain View CA
  • Worked on Google Ads infrastructure to increase benefit frome broad match keywords
  • Created a pipeline to determine relevancy of words from "next queries"—those commonly seen next in a given session
May 2014 - Aug 2014
Software Engineering Intern, Boston MA
  • Integrated vast collection of Google knowledge into Google Play to improve Books' genre search.
May 2013 - Aug 2013

Cipher Systems, LLC

Bioinformatics Consultant
  • Developed industrial software for fast DNA matching and organism characterization
Sep 2011 - Dec 2012
Research Projects


Research Assistant, supervised by Bernard Mourrain
Sophia-Antipolis, France
  • Developed methodology for efficiently determining offset surfaces for parametric algebraic curves
  • Implemented 2-d curve offset surface algorithm in the Axel package
  • Extending 2-d implementation to parametric surfaces in 3 dimensions
Jun 2015 - Aug 2015

University of Texas at Austin

Research Assistant; supervised by Dr. Chandrajit Bajaj
  • Generating probabilistic uncertainty quantification models for functions computed on objects with inherent error
  • Creating atomic-resolution graphical and interaction models for proteins and viral capsids
Sep 2013 - Present
Research Assistant; supervised by Dr. Daniel Miranker
  • Implemented metric space indexing and other database techniques as applied to short DNA sequences
Aug 2011 - Aug 2013
Research Assistant; supervised by Dr. Tandy Warnow
  • Producing relevant phylogenetic alignments from gappy data
Dec 2010 - Jul 2011

Brigham Young University

Research Assistant; Computational Sciences Laboratory
  • The GNUMAP project: designed, developed, and tested program currently used by many individuals for processing massive amounts of sequencing data
  • Used phtreads and MPI to distribute the workload on a cluster
Apr 2008 - Aug 2013
Research Assistant; supervised by Dr. Keith Crandall
  • Evaluated phylogenetic profiling tools
Sep 2007 - Jan 2011
Teaching Assistant; CS360: Internet Programming
  • Assisted students in building a web server in C++ with threading
Spring 2010

Harvard University / Massachusetts Institute of Technology

Internship; Harvard/MIT Department of Health, Sciences and Technology; supervised by Dr. Peter Park
  • Analyzed genome diversity and its impacts on short-read sequencing
Jun 2009 - Aug 2009
Teaching Experience
CS 312: Introduction to Programming
  • Teaches introductory programming course to students just starting the CS major
  • Prepares and presents lectures, assignments, and materials throughout the semester
Spring 2016 (present)
CS 302: Computer Fluency
  • Primary instructor for course introducing programming concepts (such as algorithms and computer design) to non-major students
  • Designs coursework, prepares and presents lectures, and supervises 3 teaching assistants throughout the semester
  • Class of roughly 200 students
Fall 2014, Spring 2015, Fall 2015
KAUST Computer Programming
Spring 2014, Spring 2015, Spring 2016 (present)
SABIC Computer Fluency
Spring 2014, Spring 2015, Spring 2016 (present)
CS 105 - Perl
  • Primary instructor for course teaching semantics and advanced properties of the Perl programming language
Spring 2014
Teaching Assistant; CS388: Natural Language Processing
  • Graduate course providing introduction to natural language processing, including topics such as part-of-speech tagging, semantic role labeling, and machine translation
Spring 2013
Teaching Assistant; CS378: Mobile Computing
  • Upper-lever undergraduat course helping students develop mobile applications on the Android device for the first time
Spring, Fall 2012
Teaching Assistant; CS303E: Elements of Computers and Programming
  • Lead discussion section for non computer science majors
Fall 2011
Refereed Journal and Conference Publications
  • M. Rasheed, N. Clement, A. Bhowmick, and C. Bajaj, "Quantifying and Visualizing Uncertainties in Molecular Models." ArXiv e-prints, Aug. 2015. PDF available here
  • N.L. Clement, L.P. Thompson, and D. Miranker, "ADaM: Augmenting existing approximate fast matching algorithms with efficient and exact range queries." BMC Bioinformatics, Vol 15, May 2014; Open-access publication available here.
  • C. Hong, N.L. Clement, ... and W.E. Johnson. "Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data." BMC Bioinformatics, Vol 14, No 337, Nov 2013. PDF available here.
  • Francis, O. E., Bendall, M., Manimaran, S., Hong, C., Clement, N. L., ... and Johnson, W. E. "Pathoscope: Species identification and strain attribution with unassembled sequencing data." Genome Research (2013); PDF available here.
  • Nathan L. Clement, Brent A. Shepherd, Paul Bodily, Sukhbat Tumur-Ochir, Younghoon Gim, Quinn Snell, Mark J. Clement, and W. Evan Johnson. "Parallel Pair-HMM SNP Detection." Conference proceedings for the Eleventh IEEE International Workshop on High Performance Computational Biology (HiCOMB '12), held in conjunction with the International Parallel and Distributed Processing Symposium; Shanghai, China; May 21, 2012; PDF available here.
  • N. L. Clement, M. J. Clement, Q. Snell, and W. E. Johnson "Parallel Mapping Approaches for GNUMAP." Conference proceedings for the Tenth IEEE International Workshop on High Performance Computational Biology (HiCOMB '11), held in conjunction with the International Parallel and Distributed Processing Symposium; Anchorage, Alaska; May 16, 2011; PDF available here
  • N. L. Clement, Q. Snell, M. J. Clement, P. C. Hollenhorst, J. Purwar, B. J. Graves, B. R. Cairns, and W. E. Johnson, "The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing," Bioinformatics, vol. 26, no. 1, pp. 38-45, 2010; PDF available here
Formal Presentations
"ADaM: Augmenting existing approximate fast matching algorithms with efficient and exact range queries." 2013 Biotechnology and Bioinformatics Symposium (BIOT); Provo, UTDec 6, 2013
"Next-Generation Sequence Mapping Techniques." Invited presentation at Beijing Genomics Institute (BGI); BGI- Shenzhen; Shenzhen, ChinaMay 24, 2012
"Pairallel Pair-HMM SNP Detection." Eleventh IEEE International Workshop on High Performance Computational Biology (HiCOMB '12); Shanghai, ChinaMay 21, 2012
"Parallel Mapping Approaches for GNUMAP." Tenth IEEE International Workshop on High Performance Computational Biology (HiCOMB '11); Anchorage, AKMay 16, 2012
"The Needle in a Haystack: Finding what makes you unique." Spring Research Conference; Brigham Young University; Provo, UTMar 20, 2010
"The GNUMAP Project: Unbiased Probabilistic Mapping of Oligonucleotides from Next-Generation Sequencing and Applications." Biology Department weekly seminar series; University of Utah; Salt Lake City, UTDec 4, 2009
"GNUMAP: Unbiased Probabilistic Mapping of Next-Generation Sequencing Reads." 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB '09); Stockholm, SwedenJul 1, 2009
Refereed Journal Reviews
Invited reviewer for Bioinformatics2015 (x2)
Invited reviewer for BMC Bioinformatics2014
Awards and Honors
  • Awarded Honorable Mention for 2012 National Science Foundation (NSF) Graduate Research Fellowship Program
  • Selected as American Association for the Advancement of Science (AAAS) member, Summer 2011 - Summer 2012
  • Awarded Honorable Mention for 2011 National Science Foundation (NSF) Graduate Research Fellowship Program
  • Received 2004 Heritage Scholarship (4-year, full-tuition)
Volunteer Experience
Executive Committee Chair for Graduate Representative Association of Computer Sciences (GRACS) executive committee at the University of Texas at AustinJan 2011 - Dec 2013
Mentor at Boys and Girls Club of AustinSep 2011 - Dec 2011
Co-President of Brigham Young University Bioinformatics Research GroupAug 2009 - Aug 2010
Full-time Volunteer Representative for The Church of Jesus Christ of Latter-day SaintsAug 2005 - Aug 2007