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
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
|Software Engineering Intern, Mountain View CA
||May 2014 - Aug 2014|
|Software Engineering Intern, Boston MA
||May 2013 - Aug 2013|
||Sep 2011 - Dec 2012|
|Research Assistant, supervised by Bernard Mourrain|
|Jun 2015 - Aug 2015|
University of Texas at Austin
|Research Assistant; supervised by Dr. Chandrajit Bajaj||Sep 2013 - Present|
|Research Assistant; supervised by Dr. Daniel Miranker||Aug 2011 - Aug 2013|
|Research Assistant; supervised by Dr. Tandy Warnow||Dec 2010 - Jul 2011|
Brigham Young University
|Research Assistant; Computational Sciences Laboratory||Apr 2008 - Aug 2013||Research Assistant; supervised by Dr. Keith Crandall||Sep 2007 - Jan 2011|
Harvard University / Massachusetts Institute of Technology
|Internship; Harvard/MIT Department of Health, Sciences and Technology; supervised by Dr. Peter Park||Jun 2009 - Aug 2009|
|CS 312: Introduction to Programming (Java)||Spring 2016, Fall 2016|
|ACES Java I and II: Introduction to Programming (Java)||Spring 2016, Fall 2016||CS 302: Computer Fluency (Python)||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||Spring 2014|
|Teaching Assistant; CS388: Natural Language Processing||Spring 2013|
|Teaching Assistant; CS378: Mobile Computing||Spring, Fall 2012|
|Teaching Assistant; CS303E: Elements of Computers and Programming||Fall 2011|
|Teaching Assistant; CS360: Internet Programming (Brigham Young University)||Spring 2010|
- N. Clement, "Viral Capsid Assembly: A Quantified Uncertainty Approach." Journal of Computational Biology, Vol 25, No 1, Jan 2018; Open-access HTML version available here.
- M. Rasheed, N. Clement, A. Bhowmick, and C.L. Bajaj. "Statistical framework for uncertainty quantification in computational molecular modeling." IEEE/ACM Transactions on Computational Biology and Bioinformatics, Nov 2012; PDF available here.
- 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
|"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, UT||Dec 6, 2013|
|"Next-Generation Sequence Mapping Techniques." Invited presentation at Beijing Genomics Institute (BGI); BGI- Shenzhen; Shenzhen, China||May 24, 2012|
|"Pairallel Pair-HMM SNP Detection." Eleventh IEEE International Workshop on High Performance Computational Biology (HiCOMB '12); Shanghai, China||May 21, 2012|
|"Parallel Mapping Approaches for GNUMAP." Tenth IEEE International Workshop on High Performance Computational Biology (HiCOMB '11); Anchorage, AK||May 16, 2012|
|"The Needle in a Haystack: Finding what makes you unique." Spring Research Conference; Brigham Young University; Provo, UT||Mar 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, UT||Dec 4, 2009|
|"GNUMAP: Unbiased Probabilistic Mapping of Next-Generation Sequencing Reads." 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB '09); Stockholm, Sweden||Jul 1, 2009|
Refereed Journal Reviews
|Invited reviewer for PLOS ONE||2016 (x2)||Invited reviewer for Bioinformatics||2015 (x2)||Invited reviewer for BMC Bioinformatics||2014|
- 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)
|Executive Committee Chair for Graduate Representative Association of Computer Sciences (GRACS) executive committee at the University of Texas at Austin||Jan 2011 - Dec 2013|
|Mentor at Boys and Girls Club of Austin||Sep 2011 - Dec 2011|
|Co-President of Brigham Young University Bioinformatics Research Group||Aug 2009 - Aug 2010|
|Full-time Volunteer Representative for The Church of Jesus Christ of Latter-day Saints||Aug 2005 - Aug 2007|