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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.

Major emphasis on parallel implementations and on finding patterns through mining large datasets

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.

Education
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

INRIA

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
  • Developing high-dimensional sampling techniques and parallelized evaluations
  • Sep 2013 - Present
    Research Assistant; supervised by Dr. Daniel Miranker
    • Implemented metric space indexing and other database techniques as applied to short DNA sequences
    • Showed performance increases when using MPI-based map/reduce environment
    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

    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 (Java)
    • Teaches introductory programming course to students just starting the CS major
    • Prepares and presents lectures, assignments, and materials throughout the semester
    Spring 2016, Fall 2016
    ACES Java I and II: Introduction to Programming (Java)
    • Taught intro Java programming to middle- and high-school students
    • Developed curriculum based on needs and experience of students
    Spring 2016, Fall 2016
    CS 302: Computer Fluency (Python)
    • 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 (C++)
    Spring 2014, Spring 2015, Spring 2016
    SABIC Computer Fluency (Python)
    Spring 2014, Spring 2015, Spring 2016
    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
    Teaching Assistant; CS360: Internet Programming (Brigham Young University)
    • Assisted students in building a web server in C++ with threading
    Spring 2010
    Refereed Journal and Conference Publications
    • N. Clement, M. Rasheed, and C. Bajaj. "Uncertainty Quantified Computational Analysis of the Energetics of Virus Capsid Assembly." ArXiv e-prints, Oct 2016. PDF available here.
    • M. Rasheed, N. Clement, A. Bhowmick, and C. Bajaj, "Statistical Framework for Uncertainty Quantification in Computational Molecular Modeling." Proc. of the 7th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB '16); Seattle, WA; Oct 2016.
    • 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
    "Statistical Framework for Uncertainty Quantification in Computational Molecular Modeling." 2016 ACM-BCB; Seattle, WA (slides available here).Oct 3, 2016
    "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 PLOS ONE2016 (x2)
    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