Mark J. Clement

发表

Large Grain Size Stochastic Optimization Alignment

Perry G. Ridge, Hyrum Carroll, Dan Sneddon, 2006, Sixth IEEE Symposium on BioInformatics and BioEngineering (BIBE'06).

Learning the Language of Genes: Representing Global Codon Bias with Deep Language Models

Mark J. Clement, M. Stanley Fujimoto, Paul M. Bodily, 2017 .

Mark J. Clement, Quinn Snell, John Jardine, 2001, Proceedings 10th IEEE International Symposium on High Performance Distributed Computing.

An open source phylogenetic search and alignment package

Hyrum Carroll, Mark J. Clement, Quinn Snell, 2009, Int. J. Bioinform. Res. Appl..

A novel approach for multi-SNP GWAS and its application in Alzheimer’s disease

Perry G. Ridge, Mark J. Clement, Paul Bodily, 2016, BMC Bioinformatics.

On the use of cartographic projections in visualizing phylo-genetic tree space

Mark J. Clement, Quinn Snell, Kenneth Sundberg, 2010, Algorithms for Molecular Biology.

Modeling Global and local Codon Bias with Deep Language Models

Mark J. Clement, Quinn Snell, Cole A. Lyman, 2017, 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE).

Parallel Algorithm and Processor Selection Based on Fuzzy Logic

Mark J. Clement, Quinn Snell, Bryan S. Morse, 1999, HPCN Europe.

Design issues for efficient implementation of MPI in Java

Mark J. Clement, Quinn Snell, Vladimir Getov, 1999, JAVA '99.

The Chordal Spoke ATM Interconnection Network

Mark J. Clement, Wei Wei, Bryan S. Morse, 1997, PDPTA.

Parallel Mapping Approaches for GNUMAP

Mark J. Clement, Quinn Snell, Nathan L. Clement, 2011, 2011 IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum.

Parallel Phylogenetic Inference

Mark J. Clement, Quinn Snell, David McLaughlin, 2000, ACM/IEEE SC 2000 Conference (SC'00).

Additional file 2: of Detecting false positive sequence homology: a machine learning approach

Mark J. Clement, M. Fujimoto, Anton Suvorov, 2016 .

Visualizing Phylogenetic Treespace Using Cartographic Projections

Mark J. Clement, Quinn Snell, Kenneth Sundberg, 2009, WABI.

Core Algorithms of the Maui Scheduler

Mark J. Clement, Quinn Snell, David B. Jackson, 2001, JSSPP.

Medium Grain Size Applications on Distributed Memory Multicomputers

Mark J. Clement, Michael J. Quinn, Brent Baxter, 1993 .

The Performance Impact of Advance Reservation Meta-scheduling

Mark J. Clement, Quinn Snell, David B. Jackson, 2000, JSSPP.

The PepSeq Pipeline: Software for Antimicrobial Motif Discovery in Randomly-Generated Peptide Libraries

Mark J. Clement, Cole A. Lyman, M. Stanley Fujimoto, 2018, BCB.

PsodaScript: Applying Advanced Language Constructs to Open-source Phylogenetic Search

Hyrum Carroll, Mark J. Clement, Adam R. Teichert, 2007 .

Identification and correction of substitution errors in Moleculo long reads

Mark J. Clement, Quinn Snell, Jared C. Price, 2013, 13th IEEE International Conference on BioInformatics and BioEngineering.

Haplotype-centered mapping for improved alignments and genetic association studies

Perry G. Ridge, Mark J. Clement, Quinn Snell, 2014, BCB.

Heterozygous genome assembly via binary classification of homologous sequence

Mark J. Clement, Quinn Snell, Paul Bodily, 2015, BMC Bioinformatics.

Kcollections: A Fast and Efficient Library for K-mers

Mark J. Clement, M. Stanley Fujimoto, Cole A. Lyman, 2020, 2020 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW).

Analyzing Gene Relationships for Down Syndrome with Labeled Transition Graphs

Hyrum Carroll, Mark J. Clement, Quinn Snell, 2007, Formal Methods in Computer Aided Design (FMCAD'07).

Distributed polyphonic music synthesis

Mark J. Clement, J. Williams, 1997, Proceedings. The Sixth IEEE International Symposium on High Performance Distributed Computing (Cat. No.97TB100183).

A structured approach to ensemble learning for Alzheimer's disease prediction

Mark J. Clement, Quinn Snell, Paul Bodily, 2014, BCB.

Performance comparison of desktop multiprocessing and workstation cluster computing

Mark J. Clement, Phyllis E. Crandall, Eranti V. Sumithasri, 1996, Proceedings of 5th IEEE International Symposium on High Performance Distributed Computing.

The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing

Mark J. Clement, Quinn Snell, Barbara J. Graves, 2010, Bioinform..

Multivariate statistical techniques for parallel performance prediction

Mark J. Clement, Michael J. Quinn, M. J. Quinn, 1995, Proceedings of the Twenty-Eighth Annual Hawaii International Conference on System Sciences.

A performance broker for CORBA

Mark J. Clement, Quinn Snell, Kevin Butler, 1999, Proceedings. The Eighth International Symposium on High Performance Distributed Computing (Cat. No.99TH8469).

PathGen: a transitive gene pathway generator

Hyrum Carroll, Mark J. Clement, Quinn Snell, 2010, Bioinform..

Additional file 1 of A novel approach for multi-SNP GWAS and its application in Alzheimerâ s disease

Perry G. Ridge, Mark J. Clement, Paul M. Bodily, 2016 .

Object Placement Using Performance Surfaces

Mark J. Clement, Quinn Snell, André Turgeon, 2004, Cluster Computing.

High performance phylogenetic inference

Mark J. Clement, Quinn Snell, Glenn Judd, 1999, Proceedings. The Eighth International Symposium on High Performance Distributed Computing (Cat. No.99TH8469).

Temporal Difference Learning in Network Routing

Mark J. Clement, Casey T. Deccio, Reid Broadbent, 2004, Communications in Computing.

High Performance Computing for the Masses

Mark J. Clement, Quinn Snell, Glenn Judd, 1999, IPPS/SPDP Workshops.

The Polygraph: A Data Structure for Genome Alignment and Variation Detection

Mark J. Clement, Cole A. Lyman, M. Fujimoto, 2019 .

Probabilistic inference and ranking of gene regulatory pathways as a shortest-path problem

Mark J. Clement, Quinn Snell, James D. Jensen, 2013, BMC Bioinformatics.

Parsimony accelerated Maximum Likelihood searches

Hyrum Carroll, Mark J. Clement, Quinn Snell, 2008, Int. J. Comput. Biol. Drug Des..

Parallel Pair-HMM SNP Detection

Mark J. Clement, Quinn Snell, Paul Bodily, 2012, 2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops & PhD Forum.

Aggressive telecommunications overbooking ratios

Mark J. Clement, Quinn Snell, Feng Huang, 2004, IEEE International Conference on Performance, Computing, and Communications, 2004.

Preemption Based Backfill

Mark J. Clement, Quinn Snell, David B. Jackson, 2002, JSSPP.

Incomparability of Results Between Phylogenetic Search Programs

Hyrum Carroll, Mark J. Clement, Quinn Snell, 2008, BIOCOMP.

Using the ParaGraph Visualization Tool on the Meiko CS-2

Mark J. Clement, Michael J. Quinn, Phyllis E. Crandall, 1994 .

Detecting false positive sequence homology: a machine learning approach

Mark J. Clement, M. Stanley Fujimoto, Anton Suvorov, 2016, BMC Bioinformatics.

Phylogenetic search through partial tree mixing

Mark J. Clement, Quinn Snell, Dan Ventura, 2012, BMC Bioinformatics.

DNA reference alignment benchmarks based on tertiary structure of encoded proteins

Hyrum Carroll, Mark J. Clement, Quinn Snell, 2007, Bioinform..

The Impact of Equally-Optimal Pairwise Alignments

Mark J. Clement, Quinn Snell, Lukas Olson, 2010, BIOCOMP.

Effects of error-correction of heterozygous next-generation sequencing data

Mark J. Clement, Quinn Snell, Paul Bodily, 2014, BMC Bioinformatics.

Inferring gene regulatory networks from asynchronous microarray data with AIRnet

Mark J. Clement, Quinn Snell, Kenneth Sundberg, 2010, BMC Genomics.

GNUMAP 4.0: Space and Time Efficient NGS Read Mapping Using the FM-Index

Mark J. Clement, Quinn Snell, M. Stanley Fujimoto, 2018 .

Jumpstarting phylogenetic analysis

Mark J. Clement, Quinn Snell, Kevin D. Seppi, 2006, Int. J. Bioinform. Res. Appl..

Cost Optimal Analysis for Workstation Clusters

Mark J. Clement, J. Kelly Flanagan, Michael R. Steed, 1996, PDPTA.

Spatially Indexing Sequences using Hashes

Mark J. Clement, Quinn Snell, Mike Eagar, 2010, BIOCOMP.

Genomic Scale Reconstruction of Gene Regulatory Networks from Microarray Data

Mark J. Clement, Quinn Snell, Kenneth Sundberg, 2008, BIOCOMP.

Symbolic performance prediction of scalable parallel programs

Mark J. Clement, Michael J. Quinn, M. J. Quinn, 1995, Proceedings of 9th International Parallel Processing Symposium.

An enterprise-based grid resource management system

Mark J. Clement, Quinn Snell, Kevin Tew, 2002, Proceedings 11th IEEE International Symposium on High Performance Distributed Computing.

Analytical performance prediction of data-parallel programs

Mark J. Clement, 1994 .

Genome Polymorphism Detection Through Relaxed de Bruijn Graph Construction

Mark J. Clement, Quinn Snell, Cole A. Lyman, 2017, 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE).

High Performance Scheduling for Windows NT

Mark J. Clement, Quinn Snell, David B. Jackson, 1999, PDPTA.

The YGuard access control model: set-based access control

Mark J. Clement, Quinn Snell, Ty van den Akker, 2001, SACMAT '01.

Feature identification and reduction for improved generalization accuracy in secondary-structure prediction

Mark J. Clement, Quinn Snell, Matt Seeley, 2013, 13th IEEE International Conference on BioInformatics and BioEngineering.

A Survivable Multi-agent Approach to Network Routing

Mark J. Clement, Quinn Snell, Casey T. Deccio, 2004, Communications in Computing.

Effective bandwidth for traffic engineering

Mark J. Clement, Quinn Snell, R. Kunz, 2001, 2001 IEEE Workshop on High Performance Switching and Routing (IEEE Cat. No.01TH8552).

Performance prediction of PVM programs

Mark J. Clement, Michael R. Steed, M. Clement, 1996, Proceedings of International Conference on Parallel Processing.

Editorial

Mark J. Clement, Xian-He Sun, 2004, The Journal of Supercomputing.

Automated Performance Prediction for Scalable Parallel Computing

Mark J. Clement, Michael J. Quinn, 1997, Parallel Comput..

ChemAlign: Biologically Relevant Multiple Sequence Alignment Using Physicochemical Properties

Hyrum Carroll, Mark J. Clement, Quinn Snell, 2009, 2009 IEEE International Conference on Bioinformatics and Biomedicine.

Analytical performance prediction on multicomputers

Mark J. Clement, Michael J. Quinn, 1993, Supercomputing '93. Proceedings.

TCS: estimating gene genealogies

Mark J. Clement, Quinn Snell, David Posada, 2002, Proceedings 16th International Parallel and Distributed Processing Symposium.

Phylogenies scores for exhaustive searches and parsimony scores searches

Perry G. Ridge, Hyrum Carroll, Mark J. Clement, 2007, Int. J. Bioinform. Res. Appl..

Using Parsimony to Guide Maximum Likelihood Searches

Hyrum Carroll, Mark J. Clement, Quinn Snell, 2007, 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering.

The OGCleaner: filtering false-positive homology clusters

Mark J. Clement, Quinn Snell, M. Stanley Fujimoto, 2017, Bioinform..

Network Performance Modeling for PVM Clusters

Mark J. Clement, Phyllis E. Crandall, Michael R. Steed, 1996, Proceedings of the 1996 ACM/IEEE Conference on Supercomputing.

Parallel programming in multi-paradigm clusters

Mark J. Clement, Phyllis E. Crandall, J. Leichtl, 1997, Proceedings. The Sixth IEEE International Symposium on High Performance Distributed Computing (Cat. No.97TB100183).

Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data

Mark J. Clement, Quinn Snell, Nathan L. Clement, 2013, BMC Bioinformatics.

HiCOMB Introduction

Srinivas Aluru, David A. Bader, Mark J. Clement, 2012, 2013 IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum.

Analysis of Long Branch Extraction

Hyrum Carroll, Mark J. Clement, Quinn Snell, 2009, BIOCOMP.

Overlapping Computations, Communications and I/O in parallel Sorting

Mark J. Clement, Michael J. Quinn, M. J. Quinn, 1995, J. Parallel Distributed Comput..

DOGMA: Distributed Object Group Management Architecture

Mark J. Clement, Quinn Snell, Glenn Judd, 1998 .

Performance surface prediction for WAN-based clusters

Mark J. Clement, Glenn Judd, Bryan S. Morse, 1998, Proceedings of the Thirty-First Hawaii International Conference on System Sciences.

DOGMA: distributed object group metacomputing architecture

Mark J. Clement, Quinn Snell, Glenn Judd, 1998, Concurr. Pract. Exp..

Latency tolerant algorithms for WAN based workstation clusters

Mark J. Clement, B. Helzer, Q. Snell, 1999, Proceedings. Frontiers '99. Seventh Symposium on the Frontiers of Massively Parallel Computation.

The Round Table ATM Interconnection Network

Mark J. Clement, Wei Wei, J. Kelly Flanagan, 1995, PDPTA.

ScaffoldScaffolder: solving contig orientation via bidirected to directed graph reduction

Mark J. Clement, Quinn Snell, Dan Ventura, 2015, Bioinform..

NetLib Communication Performance on the iWarp Multicomputer

Mark J. Clement, Brent Baxter, 1993 .

Performance Surface Prediction for WAN-Based Clusters

Mark J. Clement, Glenn Judd, Bryan S. Morse, 2004, The Journal of Supercomputing.

The DOGMA approach to high-utilization supercomputing

Mark J. Clement, Quinn Snell, Glenn Judd, 1998, Proceedings. The Seventh International Symposium on High Performance Distributed Computing (Cat. No.98TB100244).

DOGMA: distributed object group metacomputing architecture

Mark J. Clement, Glenn Judd, Quinn Snell, 1998 .

Effects of Gap Open and Gap Extension Penalties

Perry G. Ridge, Hyrum Carroll, Mark J. Clement, 2006 .

Genome Sequence Assembly By Suffix Tree Branch Extension

Mark J. Clement, Justin T. Page, Joshua A. Udall, 2014 .

Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs

Mark J. Clement, Quinn Snell, Cole A. Lyman, 2017, 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE).

Phylogenetic Analysis of Large Sequence Data Sets

Hyrum Carroll, Mark J. Clement, Keith A. Crandall, 2005 .

Using Analytical Performance Prediction for Architectural Scaling

Mark J. Clement, Michael J. Quinn, 1994 .

Performance of finite field arithmetic in an elliptic curve cryptosystem

Mark J. Clement, John Higgins, Zhi Li, 2001, MASCOTS 2001, Proceedings Ninth International Symposium on Modeling, Analysis and Simulation of Computer and Telecommunication Systems.

Application of a MAX-CUT Heuristic to the Contig Orientation Problem in Genome Assembly

Mark J. Clement, Quinn Snell, Paul Bodily, 2013, BCB.

PSODA: Better Tasting and Less Filling Than PAUP

Hyrum Carroll, Mark J. Clement, Mark T. W. Ebbert, 2007 .

Pharmacogenomics: analysing SNPs in the CYP2D6 gene using amino acid properties

Mark J. Clement, Mark T. W. Ebbert, Wesley A. Beckstead, 2007, Int. J. Bioinform. Res. Appl..

Additional file 3: of Detecting false positive sequence homology: a machine learning approach

Mark J. Clement, M. Fujimoto, Anton Suvorov, 2016 .

The DOGMA Approach to Parallel and Distributed Computing

Mark J. Clement, Quinn Snell, Glenn Judd, 1999, Scalable Comput. Pract. Exp..

Phylogenetics The OGCleaner : filtering false-positive homology clusters

Mark J. Clement, Quinn Snell, M. Stanley Fujimoto, 2016 .

Directed next generation sequencing for phylogenetics: An example using Decapoda (Crustacea)

Mark J. Clement, Keith A. Crandall, Seth M. Bybee, 2011 .

Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics

Mark J. Clement, Keith A. Crandall, Seth M. Bybee, 2011, Genome biology and evolution.

Message from the workshop chairs

Srinivas Aluru, Nagiza F. Samatova, Albert Y. Zomaya, 2009 .