Mark J. Clement

88 papers A 13B 3C 13Misc 4Journal 27Unranked 28
YearRankTypeTitle / Venue / Authors
2024 — conf
Head Tail Open: Open Tailed Classification of Imbalanced Document Data.
SAI (1)
Chetan Joshi, Daniel Segrera, Lawry Sorenson, Mark J. Clement, Bryan S. Morse, Porter Jenkins, Taylor Archibald, M. J. Ghorbani
2023 J jnl
CENSUS-HWR: a large training dataset for offline handwriting recognition.
CoRR
Chetan Joshi, Lawry Sorenson, Ammon Wolfert, Mark J. Clement, Joseph Price, Kasey Buckles
2022 B conf
Active Transfer Learning for Handwriting Recognition.
ICFHR
Eric Burdett, Stanley Fujimoto, Timothy Brown, Ammon Shurtz, Daniel Segrera, Lawry Sorenson, Mark J. Clement, Joseph Price
2020 — conf
Kcollections: A Fast and Efficient Library for K-mers.
IPDPS Workshops
M. Stanley Fujimoto, Cole A. Lyman, Mark J. Clement
2019 — conf
Feedback Regulation of Immune Response to Maximum Exercise in Gulf War Illness.
BCB
Cole A. Lyman, Mark J. Clement, Travis J. A. Craddock, Mary Fletcher, Nancy G. Klimas, Gordon Broderick
2019 — conf
When the How Outweighs the What: the Pivotal Importance of Context.
BIBM
Cole A. Lyman, Connor Anderson, Matthew C. Morris, Umesh K. Nandal, Marianna J. Martindale, Mark J. Clement, Gordon Broderick
2018 — conf
The PepSeq Pipeline: Software for Antimicrobial Motif Discovery in Randomly-Generated Peptide Libraries.
BCB
Tanner D. Jensen, Kristi A. Bresciano, Emma Dallon, M. Stanley Fujimoto, Cole A. Lyman, Enoch Stewart, Joel Griffitts, Mark J. Clement
2017 C conf
Genome Polymorphism Detection Through Relaxed de Bruijn Graph Construction.
BIBE
M. Stanley Fujimoto, Cole A. Lyman, Anton Suvorov, Paul M. Bodily, Quinn Snell, Keith A. Crandall, Seth M. Bybee, Mark J. Clement
2017 C conf
Modeling Global and local Codon Bias with Deep Language Models.
BIBE
Masaki Stanley Fujimoto, Paul M. Bodily, Cole A. Lyman, Andrew J. Jacobsen, Quinn Snell, Mark J. Clement
2017 J jnl
The OGCleaner: filtering false-positive homology clusters.
Bioinform.
M. Stanley Fujimoto, Anton Suvorov, Nicholas O. Jensen, Mark J. Clement, Quinn Snell, Seth M. Bybee
2017 C conf
Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs.
BIBE
Cole A. Lyman, M. Stanley Fujimoto, Anton Suvorov, Paul M. Bodily, Quinn Snell, Keith A. Crandall, Seth M. Bybee, Mark J. Clement
2017 J jnl
Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs.
CoRR
Cole A. Lyman, M. Stanley Fujimoto, Anton Suvorov, Paul M. Bodily, Quinn Snell, Keith A. Crandall, Seth M. Bybee, Mark J. Clement
2016 J jnl
A novel approach for multi-SNP GWAS and its application in Alzheimer's disease.
BMC Bioinform.
Paul M. Bodily, M. Stanley Fujimoto, Justin T. Page, Mark J. Clement, Mark T. W. Ebbert, Perry G. Ridge
2016 J jnl
Detecting false positive sequence homology: a machine learning approach.
BMC Bioinform.
M. Stanley Fujimoto, Anton Suvorov, Nicholas O. Jensen, Mark J. Clement, Seth M. Bybee
2016 J jnl
ScaffoldScaffolder: solving contig orientation via bidirected to directed graph reduction.
Bioinform.
Paul M. Bodily, M. Stanley Fujimoto, Quinn Snell, Dan Ventura, Mark J. Clement
2015 J jnl
Heterozygous genome assembly via binary classification of homologous sequence.
BMC Bioinform.
Paul M. Bodily, M. Stanley Fujimoto, Cameron Ortega, Nozomu Okuda, Jared C. Price, Mark J. Clement, Quinn Snell
2014 — conf
A structured approach to ensemble learning for Alzheimer's disease prediction.
BCB
Matthew Seeley, Mark J. Clement, Christophe G. Giraud-Carrier, Quinn Snell, Paul M. Bodily, Stanley Fujimoto
2014 J jnl
Effects of error-correction of heterozygous next-generation sequencing data.
BMC Bioinform.
M. Stanley Fujimoto, Paul M. Bodily, Nozomu Okuda, Mark J. Clement, Quinn Snell
2014 — conf
Haplotype-centered mapping for improved alignments and genetic association studies.
BCB
Paul M. Bodily, Mark J. Clement, Quinn Snell, M. Stanley Fujimoto, Perry G. Ridge
2013 — conf
Application of a MAX-CUT Heuristic to the Contig Orientation Problem in Genome Assembly.
BCB
Paul M. Bodily, Mark J. Clement, Quinn Snell, Jared C. Price, Stanley Fujimoto, Nozomu Okuda
2013 C conf
Feature identification and reduction for improved generalization accuracy in secondary-structure prediction.
BIBE
Matt Seeley, Mark J. Clement, Quinn Snell
2013 C conf
Identification and correction of substitution errors in Moleculo long reads.
BIBE
Jared C. Price, Judson Ward, Joshua Udall, Quinn Snell, Mark J. Clement
2013 J jnl
Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data.
BMC Bioinform.
Changjin Hong, Nathan L. Clement, Spencer Clement, Saher Sue Hammoud, Douglas T. Carrell, Bradley R. Cairns, Quinn Snell, Mark J. Clement, William Evan Johnson
2013 J jnl
Probabilistic inference and ranking of gene regulatory pathways as a shortest-path problem.
BMC Bioinform.
James D. Jensen, Daniel M. Jensen, Mark J. Clement, Quinn O. Snell
2012 — conf
HiCOMB Introduction.
IPDPS Workshops
Mark J. Clement, Quinn Snell, Srinivas Aluru, David A. Bader
2012 — conf
Parallel Pair-HMM SNP Detection.
IPDPS Workshops
Nathan L. Clement, Brent A. Shepherd, Paul M. Bodily, Sukhbat Tumur-Ochir, Younghoon Gim, Quinn Snell, Mark J. Clement, W. Evan Johnson
2012 J jnl
Phylogenetic search through partial tree mixing.
BMC Bioinform.
Kenneth Sundberg, Mark J. Clement, Quinn Snell, Dan Ventura, Michael Whiting, Keith A. Crandall
2011 — conf
Parallel Mapping Approaches for GNUMAP.
IPDPS Workshops
Nathan L. Clement, Mark J. Clement, Quinn Snell, W. Evan Johnson
2010 J jnl
On the use of cartographic projections in visualizing phylo-genetic tree space.
Algorithms Mol. Biol.
Kenneth Sundberg, Mark J. Clement, Quinn Snell
2010 J jnl
PathGen: a transitive gene pathway generator.
Bioinform.
Kendell Clement, Nathaniel Gustafson, Amanda Berbert, Hyrum Carroll, Christopher Merris, Ammon Olsen, Mark J. Clement, Quinn Snell, Jared Allen, Randall J. Roper
2010 — conf
Spatially Indexing Sequences using Hashes.
BIOCOMP
Mike Eagar, Mark J. Clement, Quinn Snell
2010 J jnl
The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing.
Bioinform.
Nathan L. Clement, Quinn Snell, Mark J. Clement, Peter C. Hollenhorst, Jahnvi Purwar, Barbara J. Graves, Bradley R. Cairns, W. Evan Johnson
2010 — conf
The Impact of Equally-Optimal Pairwise Alignments.
BIOCOMP
Lukas Olson, Mark J. Clement, Quinn Snell
2009 J jnl
An open source phylogenetic search and alignment package.
Int. J. Bioinform. Res. Appl.
Hyrum Carroll, Adam R. Teichert, Jonathan Krein, Kenneth Sundberg, Quinn Snell, Mark J. Clement
2009 — conf
Analysis of Long Branch Extraction.
BIOCOMP
Timothy O'Connor, Kenneth Sundberg, Hyrum Carroll, Mark J. Clement, Quinn Snell
2009 — conf
ChemAlign: Biologically Relevant Multiple Sequence Alignment Using Physicochemical Properties.
BIBM
Hyrum Carroll, Mark J. Clement, Quinn Snell, David A. McClellan
2009 — conf
Inferring Gene Regulatory Networks from Asynchronous Microarray Data.
BIOCOMP
David Oviatt, Mark J. Clement, Quinn Snell, Kenneth Sundberg, Jared Allen, Randall J. Roper
2009 C conf
Visualizing Phylogenetic Treespace Using Cartographic Projections.
WABI
Kenneth Sundberg, Mark J. Clement, Quinn Snell
2008 — conf
Genomic Scale Reconstruction of Gene Regulatory Networks from Microarray Data.
BIOCOMP
Kenneth Sundberg, Daniel Ence, Daniel Wilcox, Quinn Snell, Mark J. Clement
2008 — conf
Incomparability of Results Between Phylogenetic Search Programs.
BIOCOMP
Kenneth Sundberg, Hyrum Carroll, Quinn Snell, Mark J. Clement
2008 J jnl
Parsimony accelerated Maximum Likelihood searches.
Int. J. Comput. Biol. Drug Des.
Kenneth Sundberg, Timothy O'Connor, Hyrum Carroll, Mark J. Clement, Quinn Snell
2007 B conf
Analyzing Gene Relationships for Down Syndrome with Labeled Transition Graphs.
FMCAD
Neha Rungta, Hyrum Carroll, Eric G. Mercer, Randall J. Roper, Mark J. Clement, Quinn Snell
2007 J jnl
DNA reference alignment benchmarks based on tertiary structure of encoded proteins.
Bioinform.
Hyrum Carroll, Wesley A. Beckstead, Timothy O'Connor, Mark T. W. Ebbert, Mark J. Clement, Quinn Snell, David A. McClellan
2007 J jnl
Pharmacogenomics: analysing SNPs in the CYP2D6 gene using amino acid properties.
Int. J. Bioinform. Res. Appl.
Mark T. W. Ebbert, Wesley A. Beckstead, Timothy O'Connor, Mark J. Clement, David A. McClellan
2007 J jnl
Phylogenies scores for exhaustive searches and parsimony scores searches.
Int. J. Bioinform. Res. Appl.
Hyrum Carroll, Perry G. Ridge, Mark J. Clement, Quinn Snell
2007 C conf
Using Parsimony to Guide Maximum Likelihood Searches.
BIBE
Kenneth Sundberg, Timothy O'Connor, Hyrum Carroll, Mark J. Clement, Quinn Snell
2006 J jnl
Jumpstarting phylogenetic analysis.
Int. J. Bioinform. Res. Appl.
Jesse Mecham, Mark J. Clement, Quinn Snell, Todd Freestone, Kevin D. Seppi, Keith A. Crandall
2006 C conf
Large Grain Size Stochastic Optimization Alignment.
BIBE
Perry G. Ridge, Hyrum Carroll, Dan Sneddon, Mark J. Clement, Quinn Snell
2004 — conf
A Survivable Multi-agent Approach to Network Routing.
Communications in Computing
Casey T. Deccio, Mark J. Clement, Quinn Snell
2004 C conf
Aggressive telecommunications overbooking ratios.
IPCCC
Robert Ball, Mark J. Clement, Feng Huang, Quinn Snell, Casey T. Deccio
2004 — conf
Temporal Difference Learning in Network Routing.
Communications in Computing
Reid Broadbent, Casey T. Deccio, Mark J. Clement
2002 A conf
An Enterprise-Based Grid Resource Management System.
HPDC
Quinn Snell, Kevin Tew, Joseph J. Ekstrom, Mark J. Clement
2002 C conf
Preemption Based Backfill.
JSSPP
Quinn Snell, Mark J. Clement, David B. Jackson
2002 A conf
TCS: Estimating Gene Genealogies.
IPDPS
Mark J. Clement, Quinn Snell, Peter Walker, David Posada, Keith A. Crandall
2001 C conf
Core Algorithms of the Maui Scheduler.
JSSPP
David B. Jackson, Quinn Snell, Mark J. Clement
2001 A conf
Livelock Avoidance for Meta-Schedulers.
HPDC
John Jardine, Quinn Snell, Mark J. Clement
2001 J jnl
Object Placement Using Performance Surfaces.
Clust. Comput.
André Turgeon, Quinn Snell, Mark J. Clement
2001 B conf
Performance of Finite Field Arithmetic in an Elliptic Curve Cryptosystem.
MASCOTS
Zhi Li, John Higgins, Mark J. Clement
2001 C conf
The YGuard access control model: set-based access control.
SACMAT
Ty van den Akker, Quinn Snell, Mark J. Clement
2000 A conf
Application Placement using Performance Surfaces.
HPDC
André Turgeon, Quinn Snell, Mark J. Clement
2000 A conf
Parallel Phylogenetic Inference.
SC
Quinn Snell, Michael Whiting, Mark J. Clement, David McLaughlin
2000 C conf
The Performance Impact of Advance Reservation Meta-scheduling.
JSSPP
Quinn Snell, Mark J. Clement, David B. Jackson, Chad Gregory
1999 A conf
A Performance Broker for CORBA.
HPDC
Kevin Butler, Mark J. Clement, Quinn Snell
1999 — conf
Design Issues for Efficient Implementation of MPI in Java.
Java Grande
Glenn Judd, Mark J. Clement, Quinn Snell, Vladimir Getov
1999 J jnl
Editorial.
J. Supercomput.
Mark J. Clement, Xian-He Sun
1999 — conf
High Performance Computing for the Masses.
IPPS/SPDP Workshops
Mark J. Clement, Quinn Snell, Glenn Judd
1999 A conf
High Performance Phylogenetic Inference.
HPDC
Mark J. Clement, Quinn Snell, Glenn Judd, Michael Whiting
1999 Misc conf
High Performance Scheduling for Windows NT.
PDPTA
Mark J. Clement, Quinn Snell, David B. Jackson, David Ashton
1999 — conf
Parallel Algorithm and Processor Selection Based on Fuzzy Logic.
HPCN Europe
Shuling Yu, Mark J. Clement, Quinn Snell, Bryan S. Morse
1999 J jnl
Performance Surface Prediction for WAN-Based Clusters.
J. Supercomput.
Mark J. Clement, Glenn Judd, Bryan S. Morse, J. Kelly Flanagan
1999 J jnl
The DOGMA Approach to Parallel and Distributed Computing.
Parallel Distributed Comput. Pract.
Quinn Snell, Glenn Judd, Mark J. Clement
1998 J jnl
DOGMA: distributed object group metacomputing architecture.
Concurr. Pract. Exp.
Glenn Judd, Mark J. Clement, Quinn Snell
1998 — conf
Performance Surface Prediction for WAN-Based Clusters.
HICSS (7)
Mark J. Clement, Glenn Judd, Joy L. Peterson, Bryan S. Morse, J. Kelly Flanagan
1998 A conf
The DOGMA Approach to High-Utilization Supercomputing.
HPDC
Glenn Judd, Mark J. Clement, Quinn Snell
1997 J jnl
Automated Performance Prediction for Scalable Parallel Computing.
Parallel Comput.
Mark J. Clement, Michael J. Quinn
1997 A conf
Distributed Polyphonic Music Synthesis.
HPDC
John Williams, Mark J. Clement
1997 A conf
Parallel Programming in Multi-Paradigm Clusters.
HPDC
Johann Leichtl, Phyllis Crandall, Mark J. Clement
1997 Misc conf
The Chordal Spoke ATM Interconnection Network.
PDPTA
Mark J. Clement, Bryan S. Morse, J. Kelly Flanagan, Wei Wei, Phyllis E. Crandall
1996 Misc conf
Cost Optimal Analysis for Workstation Clusters.
PDPTA
Mark J. Clement, J. Kelly Flanagan, Michael R. Steed
1996 A conf
Network Performance Modeling for PVM Clusters.
SC
Mark J. Clement, Michael R. Steed, Phyllis E. Crandall
1996 A conf
Performance Comparison of Desktop Multiprocessing and Workstation Cluster Computing.
HPDC
Phyllis Crandall, Eranti V. Sumithasri, Mark J. Clement
1996 — conf
Performance Prediction of PVM Programs.
IPPS
Michael R. Steed, Mark J. Clement
1995 — conf
Multivariate statistical techniques for parallel performance prediction.
HICSS (2)
Mark J. Clement, Michael J. Quinn
1995 J jnl
Overlapping Computations, Communications and I/O in parallel Sorting.
J. Parallel Distributed Comput.
Mark J. Clement, Michael J. Quinn
1995 — conf
Symbolic performance prediction of scalable parallel programs.
IPPS
Mark J. Clement, Michael J. Quinn
1995 Misc conf
The Round Table ATM Interconnection Network.
PDPTA
Wei Wei, Mark J. Clement, J. Kelly Flanagan
1993 A conf
Analytical performance prediction on multicomputers.
SC
Mark J. Clement, Michael J. Quinn
1992 — conf
Hyperweave: A Fault-Tolerant Expandable Interconnection Network.
SPDP
Gowri Ramanathan, Mark J. Clement, Phyllis Crandall