Mark J. Clement

Publication Activity (10 Years)

Years Active: 1992-2023
Publications (10 Years): 14

Top Topics

Binary Classification

Single Nucleotide Polymorphisms

Ensemble Learning

Top Venues

Publications

Chetan Joshi, Lawry Sorenson, Ammon Wolfert, Mark J. Clement, Joseph Price, Kasey Buckles
CENSUS-HWR: a large training dataset for offline handwriting recognition. CoRR (2023)
Eric Burdett, Stanley Fujimoto, Timothy Brown, Ammon Shurtz, Daniel Segrera, Lawry Sorenson, Mark J. Clement, Joseph Price
Active Transfer Learning for Handwriting Recognition. ICFHR (2022)
M. Stanley Fujimoto, Cole A. Lyman, Mark J. Clement
Kcollections: A Fast and Efficient Library for K-mers. IPDPS Workshops (2020)
Cole A. Lyman, Mark J. Clement, Travis J. A. Craddock, Mary Fletcher, Nancy G. Klimas, Gordon Broderick
Feedback Regulation of Immune Response to Maximum Exercise in Gulf War Illness. BCB (2019)
Cole A. Lyman, Connor Anderson, Matthew Morris, Umesh K. Nandal, Marianna J. Martindale, Mark J. Clement, Gordon Broderick
When the How Outweighs the What: the Pivotal Importance of Context. BIBM (2019)
Tanner D. Jensen, Kristi A. Bresciano, Emma Dallon, M. Stanley Fujimoto, Cole A. Lyman, Enoch Stewart, Joel Griffitts, Mark J. Clement
The PepSeq Pipeline: Software for Antimicrobial Motif Discovery in Randomly-Generated Peptide Libraries. BCB (2018)
Cole A. Lyman, M. Stanley Fujimoto, Anton Suvorov, Paul M. Bodily, Quinn Snell, Keith A. Crandall, Seth M. Bybee, Mark J. Clement
Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs. BIBE (2017)
Masaki Stanley Fujimoto, Paul M. Bodily, Cole A. Lyman, Andrew J. Jacobsen, Quinn Snell, Mark J. Clement
Modeling Global and local Codon Bias with Deep Language Models. BIBE (2017)
Cole A. Lyman, M. Stanley Fujimoto, Anton Suvorov, Paul M. Bodily, Quinn Snell, Keith A. Crandall, Seth M. Bybee, Mark J. Clement
Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs. CoRR (2017)
M. Stanley Fujimoto, Anton Suvorov, Nicholas O. Jensen, Mark J. Clement, Quinn Snell, Seth M. Bybee
The OGCleaner: filtering false-positive homology clusters. Bioinform. 33 (1) (2017)
M. Stanley Fujimoto, Cole A. Lyman, Anton Suvorov, Paul M. Bodily, Quinn Snell, Keith A. Crandall, Seth M. Bybee, Mark J. Clement
Genome Polymorphism Detection Through Relaxed de Bruijn Graph Construction. BIBE (2017)
Paul M. Bodily, M. Stanley Fujimoto, Justin T. Page, Mark J. Clement, Mark T. W. Ebbert, Perry G. Ridge
A novel approach for multi-SNP GWAS and its application in Alzheimer's disease. BMC Bioinform. 17 (S-7) (2016)
M. Stanley Fujimoto, Anton Suvorov, Nicholas O. Jensen, Mark J. Clement, Seth M. Bybee
Detecting false positive sequence homology: a machine learning approach. BMC Bioinform. 17 (2016)
Paul M. Bodily, M. Stanley Fujimoto, Quinn Snell, Dan Ventura, Mark J. Clement
ScaffoldScaffolder: solving contig orientation via bidirected to directed graph reduction. Bioinform. 32 (1) (2016)
Paul M. Bodily, M. Stanley Fujimoto, Cameron Ortega, Nozomu Okuda, Jared C. Price, Mark J. Clement, Quinn Snell
Heterozygous genome assembly via binary classification of homologous sequence. BMC Bioinform. 16 (S-7) (2015)
Matthew Seeley, Mark J. Clement, Christophe G. Giraud-Carrier, Quinn Snell, Paul M. Bodily, Stanley Fujimoto
A structured approach to ensemble learning for Alzheimer's disease prediction. BCB (2014)
M. Stanley Fujimoto, Paul M. Bodily, Nozomu Okuda, Mark J. Clement, Quinn Snell
Effects of error-correction of heterozygous next-generation sequencing data. BMC Bioinform. 15 (S-7) (2014)
Paul M. Bodily, Mark J. Clement, Quinn Snell, M. Stanley Fujimoto, Perry G. Ridge
Haplotype-centered mapping for improved alignments and genetic association studies. BCB (2014)
James D. Jensen, Daniel M. Jensen, Mark J. Clement, Quinn O. Snell
Probabilistic inference and ranking of gene regulatory pathways as a shortest-path problem. BMC Bioinform. 14 (S-13) (2013)
Matt Seeley, Mark J. Clement, Quinn Snell
Feature identification and reduction for improved generalization accuracy in secondary-structure prediction. BIBE (2013)
Changjin Hong, Nathan L. Clement, Spencer Clement, Saher Sue Hammoud, Douglas T. Carrell, Bradley R. Cairns, Quinn Snell, Mark J. Clement, William Evan Johnson
Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data. BMC Bioinform. 14 (2013)
Paul M. Bodily, Mark J. Clement, Quinn Snell, Jared C. Price, Stanley Fujimoto, Nozomu Okuda
Application of a MAX-CUT Heuristic to the Contig Orientation Problem in Genome Assembly. BCB (2013)
Jared C. Price, Judson Ward, Joshua Udall, Quinn Snell, Mark J. Clement
Identification and correction of substitution errors in Moleculo long reads. BIBE (2013)
Kenneth Sundberg, Mark J. Clement, Quinn Snell, Dan Ventura, Michael Whiting, Keith A. Crandall
Phylogenetic search through partial tree mixing. BMC Bioinform. 13 (S-13) (2012)
Nathan L. Clement, Brent A. Shepherd, Paul M. Bodily, Sukhbat Tumur-Ochir, Younghoon Gim, Quinn Snell, Mark J. Clement, W. Evan Johnson
Parallel Pair-HMM SNP Detection. IPDPS Workshops (2012)
Mark J. Clement, Quinn Snell, Srinivas Aluru, David A. Bader
HiCOMB Introduction. IPDPS Workshops (2012)
Nathan L. Clement, Mark J. Clement, Quinn Snell, W. Evan Johnson
Parallel Mapping Approaches for GNUMAP. IPDPS Workshops (2011)
Kendell Clement, Nathaniel Gustafson, Amanda Berbert, Hyrum Carroll, Christopher Merris, Ammon Olsen, Mark J. Clement, Quinn Snell, Jared Allen, Randall J. Roper
PathGen: a transitive gene pathway generator. Bioinform. 26 (3) (2010)
Mike Eagar, Mark J. Clement, Quinn Snell
Spatially Indexing Sequences using Hashes. BIOCOMP (2010)
Kenneth Sundberg, Mark J. Clement, Quinn Snell
On the use of cartographic projections in visualizing phylo-genetic tree space. Algorithms Mol. Biol. 5 (2010)
Lukas Olson, Mark J. Clement, Quinn Snell
The Impact of Equally-Optimal Pairwise Alignments. BIOCOMP (2010)
Nathan L. Clement, Quinn Snell, Mark J. Clement, Peter C. Hollenhorst, Jahnvi Purwar, Barbara J. Graves, Bradley R. Cairns, W. Evan Johnson
The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing. Bioinform. 26 (1) (2010)
Timothy O'Connor, Kenneth Sundberg, Hyrum Carroll, Mark J. Clement, Quinn Snell
Analysis of Long Branch Extraction. BIOCOMP (2009)
Hyrum Carroll, Mark J. Clement, Quinn Snell, David A. McClellan
ChemAlign: Biologically Relevant Multiple Sequence Alignment Using Physicochemical Properties. BIBM (2009)
David Oviatt, Mark J. Clement, Quinn Snell, Kenneth Sundberg, Jared Allen, Randall J. Roper
Inferring Gene Regulatory Networks from Asynchronous Microarray Data. BIOCOMP (2009)
Hyrum Carroll, Adam R. Teichert, Jonathan Krein, Kenneth Sundberg, Quinn Snell, Mark J. Clement
An open source phylogenetic search and alignment package. Int. J. Bioinform. Res. Appl. 5 (3) (2009)
Kenneth Sundberg, Mark J. Clement, Quinn Snell
Visualizing Phylogenetic Treespace Using Cartographic Projections. WABI (2009)
Kenneth Sundberg, Hyrum Carroll, Quinn Snell, Mark J. Clement
Incomparability of Results Between Phylogenetic Search Programs. BIOCOMP (2008)
Kenneth Sundberg, Daniel Ence, Daniel Wilcox, Quinn Snell, Mark J. Clement
Genomic Scale Reconstruction of Gene Regulatory Networks from Microarray Data. BIOCOMP (2008)
Kenneth Sundberg, Timothy O'Connor, Hyrum Carroll, Mark J. Clement, Quinn Snell
Parsimony accelerated Maximum Likelihood searches. Int. J. Comput. Biol. Drug Des. 1 (1) (2008)
Kenneth Sundberg, Timothy O'Connor, Hyrum Carroll, Mark J. Clement, Quinn Snell
Using Parsimony to Guide Maximum Likelihood Searches. BIBE (2007)
Neha Rungta, Hyrum Carroll, Eric G. Mercer, Randall J. Roper, Mark J. Clement, Quinn Snell
Analyzing Gene Relationships for Down Syndrome with Labeled Transition Graphs. FMCAD (2007)
Mark T. W. Ebbert, Wesley A. Beckstead, Timothy O'Connor, Mark J. Clement, David A. McClellan
Pharmacogenomics: analysing SNPs in the CYP2D6 gene using amino acid properties. Int. J. Bioinform. Res. Appl. 3 (4) (2007)
Hyrum Carroll, Wesley A. Beckstead, Timothy O'Connor, Mark T. W. Ebbert, Mark J. Clement, Quinn Snell, David A. McClellan
DNA reference alignment benchmarks based on tertiary structure of encoded proteins. Bioinform. 23 (19) (2007)
Hyrum Carroll, Perry G. Ridge, Mark J. Clement, Quinn Snell
Phylogenies scores for exhaustive searches and parsimony scores searches. Int. J. Bioinform. Res. Appl. 3 (4) (2007)
Jesse Mecham, Mark J. Clement, Quinn Snell, Todd Freestone, Kevin D. Seppi, Keith A. Crandall
Jumpstarting phylogenetic analysis. Int. J. Bioinform. Res. Appl. 2 (1) (2006)
Perry G. Ridge, Hyrum Carroll, Dan Sneddon, Mark J. Clement, Quinn Snell
Large Grain Size Stochastic Optimization Alignment. BIBE (2006)
Casey T. Deccio, Mark J. Clement, Quinn Snell
A Survivable Multi-agent Approach to Network Routing. Communications in Computing (2004)
Robert Ball, Mark J. Clement, Feng Huang, Quinn Snell, Casey T. Deccio
Aggressive telecommunications overbooking ratios. IPCCC (2004)
Reid Broadbent, Casey T. Deccio, Mark J. Clement
Temporal Difference Learning in Network Routing. Communications in Computing (2004)
Quinn Snell, Mark J. Clement, David B. Jackson
Preemption Based Backfill. JSSPP (2002)
Quinn Snell, Kevin Tew, Joseph J. Ekstrom, Mark J. Clement
An Enterprise-Based Grid Resource Management System. HPDC (2002)
Mark J. Clement, Quinn Snell, Peter Walker, David Posada, Keith A. Crandall
TCS: Estimating Gene Genealogies. IPDPS (2002)
John Jardine, Quinn Snell, Mark J. Clement
Livelock Avoidance for Meta-Schedulers. HPDC (2001)
David B. Jackson, Quinn Snell, Mark J. Clement
Core Algorithms of the Maui Scheduler. JSSPP (2001)
André Turgeon, Quinn Snell, Mark J. Clement
Object Placement Using Performance Surfaces. Clust. Comput. 4 (3) (2001)
Zhi Li, John Higgins, Mark J. Clement
Performance of Finite Field Arithmetic in an Elliptic Curve Cryptosystem. MASCOTS (2001)
Ty van den Akker, Quinn Snell, Mark J. Clement
The YGuard access control model: set-based access control. SACMAT (2001)
Quinn Snell, Michael Whiting, Mark J. Clement, David McLaughlin
Parallel Phylogenetic Inference. SC (2000)
André Turgeon, Quinn Snell, Mark J. Clement
Application Placement using Performance Surfaces. HPDC (2000)
Quinn Snell, Mark J. Clement, David B. Jackson, Chad Gregory
The Performance Impact of Advance Reservation Meta-scheduling. JSSPP (2000)
Glenn Judd, Mark J. Clement, Quinn Snell, Vladimir Getov
Design Issues for Efficient Implementation of MPI in Java. Java Grande (1999)
Mark J. Clement, Xian-He Sun
Editorial. J. Supercomput. 13 (3) (1999)
Mark J. Clement, Quinn Snell, Glenn Judd, Michael Whiting
High Performance Phylogenetic Inference. HPDC (1999)
Mark J. Clement, Glenn Judd, Bryan S. Morse, J. Kelly Flanagan
Performance Surface Prediction for WAN-Based Clusters. J. Supercomput. 13 (3) (1999)
Mark J. Clement, Quinn Snell, David B. Jackson, David Ashton
High Performance Scheduling for Windows NT. PDPTA (1999)
Quinn Snell, Glenn Judd, Mark J. Clement
The DOGMA Approach to Parallel and Distributed Computing. Scalable Comput. Pract. Exp. 2 (2) (1999)
Kevin Butler, Mark J. Clement, Quinn Snell
A Performance Broker for CORBA. HPDC (1999)
Mark J. Clement, Quinn Snell, Glenn Judd
High Performance Computing for the Masses. IPPS/SPDP Workshops (1999)
Shuling Yu, Mark J. Clement, Quinn Snell, Bryan S. Morse
Parallel Algorithm and Processor Selection Based on Fuzzy Logic. HPCN Europe (1999)
Mark J. Clement, Glenn Judd, Joy L. Peterson, Bryan S. Morse, J. Kelly Flanagan
Performance Surface Prediction for WAN-Based Clusters. HICSS (7) (1998)
Glenn Judd, Mark J. Clement, Quinn Snell
The DOGMA Approach to High-Utilization Supercomputing. HPDC (1998)
Glenn Judd, Mark J. Clement, Quinn Snell
DOGMA: distributed object group metacomputing architecture. Concurr. Pract. Exp. 10 (11-13) (1998)
Johann Leichtl, Phyllis Crandall, Mark J. Clement
Parallel Programming in Multi-Paradigm Clusters. HPDC (1997)
John Williams, Mark J. Clement
Distributed Polyphonic Music Synthesis. HPDC (1997)
Mark J. Clement, Michael J. Quinn
Automated Performance Prediction for Scalable Parallel Computing. Parallel Comput. 23 (10) (1997)
Mark J. Clement, Bryan S. Morse, J. Kelly Flanagan, Wei Wei, Phyllis E. Crandall
The Chordal Spoke ATM Interconnection Network. PDPTA (1997)
Mark J. Clement, J. Kelly Flanagan, Michael R. Steed
Cost Optimal Analysis for Workstation Clusters. PDPTA (1996)
Michael R. Steed, Mark J. Clement
Performance Prediction of PVM Programs. IPPS (1996)
Mark J. Clement, Michael R. Steed, Phyllis E. Crandall
Network Performance Modeling for PVM Clusters. SC (1996)
Phyllis Crandall, Eranti V. Sumithasri, Mark J. Clement
Performance Comparison of Desktop Multiprocessing and Workstation Cluster Computing. HPDC (1996)
Mark J. Clement, Michael J. Quinn
Overlapping Computations, Communications and I/O in parallel Sorting. J. Parallel Distributed Comput. 28 (2) (1995)
Mark J. Clement, Michael J. Quinn
Multivariate statistical techniques for parallel performance prediction. HICSS (2) (1995)
Wei Wei, Mark J. Clement, J. Kelly Flanagan
The Round Table ATM Interconnection Network. PDPTA (1995)
Mark J. Clement, Michael J. Quinn
Symbolic performance prediction of scalable parallel programs. IPPS (1995)
Mark J. Clement, Michael J. Quinn
Analytical performance prediction on multicomputers. SC (1993)
Gowri Ramanathan, Mark J. Clement, Phyllis Crandall
Hyperweave: A Fault-Tolerant Expandable Interconnection Network. SPDP (1992)