BioinformaticsA complete list of publications can be found in my CV. Recent papers on the following subjects are available below.
Notice: Copyrights to some of the following papers are held by the publishers. Copies made available here are preprints. Please treat these materials in a way consistent with the "fair use" provisions of appropriate copyright law.
BioinformaticsJD Welch, MK Slevin, DC Tatomer, RJ Duronio, JF Prins, WF Marzluff, "EnD-Seq and AppEnD: sequencing 3' ends to identify nontemplated tails and degradation intermediates", RNA 21:1375-1389, July 2015.
JD Welch, J Baran-Gale, CM Perou, P Sethupathy, JF Prins, "Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential", BMC Genomics 16:113, doi:10.1186/s12864-015-1227-8, PMID:25765044, 22 Feb 2015.
Cancer Genome Atlas Network, "Comprehensive genomic characterization of head and neck squamous cell carcinomas", Nature 517:576-582, doi:10.1038/nature14129, PMID: 25313082, PMCID: PMC4217452, 29 Jan 2015.
M. Parfenov et al., "Characterization of HPV and host genome interactions in primary head and neck cancers", PNAS 111:15544 - 15549, PMID: 25313082, 28 Oct 2014.
Cancer Genome Atlas Network, "Integrated Genomic Characterization of Papillary Thyroid Carcinoma", Cell 159(3), 676-90, PMID: 25417114, PMCID:PMC4243044, 23 Oct 2014.
Cancer Genome Atlas Network, Comprehensive molecular profiling of lung adenocarcinoma, Nature 511:543-550, doi:10.1038/nature13385, PMID: 25079552, 31 July 2014.
M.K. Slevin, S. Meaux, J.D. Welch, R. Bigler,P.L. Miliani de Marval,W. Su, R.E. Rhoads, J.F. Prins, W.F. Marzluff, "Deep Sequencing Shows Multiple Oligouridylations Are Required for 3' to 5' Degradation of Histone mRNAs on Polyribosomes", Molecular Cell 53:1020-1030, March 20, 2014, http://dx.doi.org/10.1016/j.molcel.2014.02.027.
P. Engstrom, et al., Systematic evaluation of spliced aligners for RNA-seq, Nature Methods, doi:10.1038/nmeth.2722, Nov 2013.
J. Simon, K. Hacker, D. Singh, R. Brannon, J. Parker, M. Weiser, T. Ho, P.-F. Kuan, E. Jonasch, T. Furey, J. Prins, J. Lieb, K. Rathmell, I. Davis, Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects, Genome Research, doi:10.1101/gr.158253.113, October 2013.
C. R. Cabanski, M. D. Wilkerson, M. Soloway, J. S. Parker, J. Liu, J. F. Prins, J. S. Marron, C. M. Perou, D. N. Hayes, BlackOPs: increasing confidence in variant detection through mappability filtering, Nucleic Acids Research, doi: 10.1093/nar/gkt692, Aug 2013.
Y. Huang, Y. Hu, C.D. Jones, J.N. MacLeod, D.Y. Chiang, Y. Liu, J.F. Prins, J. Liu, A Robust Method for Transcript Quantification with RNA-Seq Data, Journal of Computational Biology 20(3):167-187, PMID: 23461570, March 2013.
Y. Hu, Y. Huang, Y. Du, C. Orellana, D. Singh, A. Johnson, A. Monroy, P.-F. Kuan, S. Hammond, L. Makowski, S. Randell, D. Chiang, D. Hayes, C. Jones, Y. Liu, J. Prins, J. Liu, DiffSplice: the Genome-Wide Detection of Differential Splicing Events with RNA-seq, Nucleic Acids Research 41(2):e39, DOI: 10.1093/nar/gks1026, Oxford Journals, PMID: 23155066, January 2013.
Cancer Genome Atlas Network, Comprehensive genomic characterization of squamous cell lung cancers, Nature 489(7417):519–525, DOI:10.1038/nature11404, PMID: 22960745, 27 September 2012.
Cancer Genome Atlas Network, Comprehensive molecular characterization of human colon and rectal cancer , Nature 487(7407):330–337, DOI:10.1038/nature11252, PMID: 22810696, 18 July 2012.
Y. Huang, Y. Hu, C. Jones, J. MacLeod, D. Chiang, Y. Liu, J. Prins, J. Liu, “A Robust Method for Transcript Quantification with RNA-seq Data”, Research in Computational Molecular Biology (RECOMB), Lecture Notes in Computer Science 7262, Springer, 2012.
D. Singh, C.F. Orellana, Y. Hu, C.D. Jones, Y. Liu, D.Y. Chiang, J. Liu, J.F. Prins, FDM: A Graph-based Statistical Method to Detect Differential Transcription using RNA-seq data, Bioinformatics DOI:10.1093/bioinformatics/btr458, Oxford Journals, PMID: 21824971, 2011.
K. Wang, D. Singh, Z. Zeng, S. Coleman, Y. Huang, G. L. Savich, X. He, P. Mieczkowski, S. Grimm, C. Perou, J. MacLeod, D. Chiang, J. F. Prins, J. Liu, MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery Nucleic Acids Research, DOI: 10.1093/nar/gkq622, Oxford Journals, PMID: 20802226, 2010.
Y. Hu, K. Wang, X. He, D. Y. Chiang, J. F. Prins, J. Liu, A probabilistic framework for aligning paired-end RNA-seq data Bioinformatics 26:1950-1957, DOI: 10.1093/bioinformatics/btq336, Oxford Journals, PMID: 20576625, 2010.
D. Bandyopadhyay, J. Huan, J. Liu, J. Prins, J. Snoeyink, W. Wang, A. Tropsha, Functional Neighbors: Relationships between Non-homologous Protein Families Inferred Using Family-Specific Fingerprints, IEEE Transaction on Information Technology in Biomedicine 14(5):1137-1143, 2010
D. Bandyopadhyay, J. Huan, J. Prins, J. Snoeyink, W. Wang, A. Tropsha, Identification of Family-Specific Residue Packing Motifs and their use for Structure-Based Protein Function Prediction: I. Method Development and II. Case Studies and Applications Journal of Computer Aided Molecular Design 23(11):773-797, DOI: 10.1007/s10822-009-9273-4, 2009.
Q. Zhang, W. Wang, L. McMillan, J. Prins, F. Pardo-Manuel de Villena, D. Threadgill, Genotype Sequence Segmentation: Handling Constraints and Noise, Proceedings of the 8th Workshop on Algorithms in Bioinformatics (WABI), 2008.
J. Liu, Q. Zhang, W. Wang, L. McMillan, J. Prins, "Poclustering: lossless clustering of dissimilarity data", Proc 7th SIAM Conference on Data Mining (SDM), 2007. PDF
J. Huan, J. Prins, W. Wang, "Local Structure Comparison of Proteins", Computational Biology and Bioinformatics , C.-W. Tseng (ed.), Advances in Computers 68, pp 178 - 251, Elsevier AP, 2006. PDF
J. Huan, D. Bandyopadhyay, J. Snoeyink, J. Prins, A. Tropsha, W. Wang, "Distance-based Identification of Spatial Motifs in Proteins Using Constrained Frequent Subgraph Mining", IEEE Computational Systems Bioinformatics (CSB), 2006. PDF
J. Liu, Q. Zhang, W. Wang, L. McMillan, J. Prins, "Clustering pair-wise dissimilarity data into partially ordered sets", Proc. 12th ACM International Conference on Knowledge Discovery and Data Mining (SIGKDD), 2006. PDF
D. Bandyopadhyay, J. Huan, J. Liu, J. Prins, J. Snoeyink, W. Wang, A. Tropsha, "Structure-based function inference using protein family-specific fingerprints", Protein Science 15, pp 1537 - 1543, 2006. PDF
J. Liu, S. Paulsen, X. Sun, W. Wang, A. Nobel, J. Prins, Mining Approximate Frequent Itemsets In the Presence of Noise: Algorithm and Analysis, SIAM Conference on Data Mining (SDM), 2006. PDF
J. Huan, W. Wang, D. Bandyopadhyay, J. Snoeyink, J. Prins, A. Tropsha, "Comparing graph representations of protein structure for mining family-specific residue-based packing motifs", Journal of Computational Biology (JCB) 12(6), 2005. PDF
J. Huan, D. Bandyopadhyay, J. Liu, J. Prins, J. Snoeyink, A. Tropsha, W. Wang, "Rapid determination of local structural features common to a set of proteins" (demo), Proceedings of the 13th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2005. PDF
J. Liu, S. Paulsen, W. Wang, A. Nobel, J. Prins, "Mining approximate frequent itemset from noisy data", Proceedings of the 5th IEEE International Conference on Data Mining (ICDM), 2005. PDF
J. Huan, W, Wang, J. Prins, and J. Yang, "SPIN: Mining Maximal Frequent Subgraphs from Graph Databases", Proceedings of the 10th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), 2004. PDF
J. Huan, W. Wang, D. Bandyopadhyay, J. Snoeyink, J. Prins, A. Tropsha, "Mining Protein Family Specific Residue Packing Patterns From Protein Structure Graphs", in Proceedings of the Intl Conf on Research in Computational Molecular Biology (RECOMB), 2004. PDF
J. Huan, W. Wang, A. Washington, J. Prins, R. Shah, A. Tropsha, "Accurate Classification of Protein Structural Families Using Coherent Subgraph Analysis", in Proceedings of the Pacific Symposium on Biocomputing (PSB), 2004. PDF
J. Huan, W. Wang, J. Prins, "Efficient Mining of Frequent Subgraphs in the Presence of Isomorphism", in Proceedings of the 3rd IEEE International Conference on Data Mining (ICDM), 2003. PDF
J. Huan, J. Prins, W. Wang, T. Vision, "Reconstruction of Ancestral Gene Order Following Segmental Duplication and Gene Loss", in Proceedings of the IEEE Computer Society Bioinformatics Conference (CSB), 2003. PDF
Irregular Parallel Computation and Nested Data-ParallelismJ. Ichnowski, J.F. Prins, R. Alterovitz, "Cache-Aware Asymptotically-Optimal Sampling-Based Motion Planning", Proc. IEEE International Conference on Robotics and Automation (ICRA), IEEE, May 2014.
S. Olivier, B. de Supinski, M. Schulz, J. Prins, Characterizing and Mitigating Work Time Inflation in Task Parallel Programs, Proc. ACM/IEEE Intl. Conference on High Performance Computing, Networking, Storage, and Analysis (SC 12), IEEE, Salt Lake City, UT, Nov. 2012 (Named Best Student Paper). Reprinted in Scientific Programming 21(3):123-136, doi: 10.3233/SPR-130369, 2013.
A. Porterfield, S. Olivier, S. Balachandran, J.F. Prins, "Power Measurement and Energy-Saving Automatic Concurrency Throttling for OpenMP Programs", Proc. HP-PAC 2013 workshop (IPDPSW), IEEE, 2013.
S. Olivier, A. Porterfield, K. Wheeler, M. Spiegel, J. Prins, "OpenMP Task Scheduling Strategies for Multicore NUMA Systems", International Journal of High Performance Computing Applications 26(2):110-124, 2012. Available online through SAGE Journals Online, 2012.
S. Olivier, A. Porterfield, K. Wheeler, J. Prins, Scheduling Task Parallelism on Multi-Socket Multicore Systems, Proc. of Intl. Workshop on Runtime and Operating Systems for Supercomputers (ROSS), ACM, 2011.
S. Olivier, J. Prins, Comparison of OpenMP 3.0 and Other Task Parallel Frameworks on Unbalanced Task Graphs International Journal of Parallel Programming (IJPP) 38(5-6):341-460, DOI: 10.1007/s10766-010-0140-7, Springer, 2010.
S. Olivier, J. Prins, Evaluating OpenMP 3.0 Run Time Systems on Unbalanced Task Graphs, Proc. of 5th International Workshop on OpenMP (IWOMP 2009), Dresden, Germany, LNCS 5568, Springer , June 2009.
J. Dinan, S. Olivier, G. Sabin, J. Prins, P. Sadayappan, C.-W. Tseng, A Message Passing Benchmark for Unbalanced Applications, Simulation Modelling Practice and Theory, 16 (9), 1177-1189, October 2008.
S. Olivier, J. Prins, Scalable Dynamic Load Balancing Using UPC. Proc. of 37th International Conference on Parallel Processing (ICPP-08), Portland, OR, September 2008.
J. Dinan, S. Olivier, J. Prins, G. Sabin, P. Sadayappan, C.-W. Tseng, "Dynamic Load Balancing of Unbalanced Computations Using Message Passing", Proc. of 6th Intl. Workshop on Performance Modeling, Evaluation, and Optimization of Parallel and Distributed Systems (PMEO-PDS 2007), Long Beach, CA, 2007. PDF
S. Olivier, J. Huan, J. Liu, J. Prins, J. Dinan, P. Sadayappan, C.-W. Tseng, "UTS: An Unbalanced Tree Search Benchmark", 19th International Workshop on Languages and Compilers for Parallel Computing (LCPC), 2006. PDF
C. Pan, J. Prins, C. Miller, "A High-performance Lattice Boltzmann Implementation to Model Flow in Porous Media", Computer Physics Communications 158, 2004. PDF
J. Prins, J. Huan, W. Pugh, C.-W. Tseng, P. Sadayappan, "UPC Implementation of an Unbalanced Tree Search Benchmark", UNC Dept. of Computer Science Technical Report 03-034, Oct 2003 PDF
K. Berlin, J. Huan, M. Jacob, G. Kochhar, J. Prins, W. Pugh, P. Sadayappan, J. Spacco, C.-W. Tseng, "Evaluating the Impact of Programming Language Features on the Performance of Parallel Applications on Cluster Architectures", in Languages and Compilers for Parallel Computing (LCPC), 2003 PDF
J. Riely, J. Prins, "Flattening is an Improvement", in Static Analysis Symposium 2000, LNCS 1824, Springer-Verlag 2000 (pp 360 - 376). PDF
J. Prins, S. Chatterjee, M. Simons, "Irregular Computations in Fortran Expression and Implementation Strategies", Scientific Programming 7, 1999 (pp 313-326). PDF
L. Nyland, J. Prins, R.H. Yun, J. Hermans, H.-C. Kum, L. Wang, "Modeling Dynamic Load Balancing in Molecular Dynamics to Achieve Scalable Parallel Execution", in Fifth International Symposium on Solving Irregularly Structured Problems in Parallel (Irregular 98), Ferrieira, A. and Rolim, J. and Simon, H. and Teng, S.-H, eds., LNCS 1457, Springer-Verlag, 1998. (pp 356-365) PDF, PostScript
J. Prins, S. Chatterjee, M. Simons, "Expressing Irregular Computations in Modern Fortran Dialects", in Languages, Compilers and Runtime Systems (LCR98), D. O'Hallaron, ed., LNCS 1511, Springer-Verlag, 1998 (pp 1-16). PDF
J. Prins, M. Ballabio, M. Boverat, M. Hodous, D. Maric, "Fast Primitives for Irregular Computations on the NEC SX-4", Crosscuts 6 (4), CSCS, 1997. (pp 6-10) PDF
L. Nyland, J. Prins, R.H. Yun, J. Hermans, H.-C. Kum, L. Wang, "Achieving Scalable Parallel Molecular Dynamics Using Domain Decomposition Techniques", Journal of Parallel and Distributed Computing, 47 (2), 1997. (pp 125-138) PDF, PostScript
S. Kumar, S. Goddard, J. Prins, "Connected Components Algorithms for Mesh-Connected Parallel Computers", in Parallel Algorithms, S. Bhatt, ed., AMS, 1997. (pp 43-58) PDF
L. Nyland, S. Chatterjee, J. Prins, "Parallel Solutions to Irregular Problems Using HPF", First HPF UG meeting, Santa Fe, NM, Feb. 1997.HTML
D. Palmer, J. Prins, S. Chatterjee, R. Faith, "Piecewise Execution of Nested Data-Parallel Programs", in Languages and Compilers for Parallel Computing (LCPC 95), Huang et al., eds., LNCS 1033, Springer-Verlag 1996. (pp 346-362) PDF
J. Riely, J. Prins, S. Iyer, "Provably Correct Vectorization of Nested Parallel Programs", Massively Parallel Programming Models: Suitability, Realization and Performance, Berlin, IEEE 1995. (pp 213-223) PDF
D. Palmer, J. Prins, "Work-efficient Nested Data-Parallelism", Proc. 5th Symposium on the Frontiers of Massively Parallel Processing, IEEE 1995. (pp 186-193) PDF
High-Performance Scientific ComputingJ.E. McClure, H. Wang, J.F. Prins, C.T. Miller, W.-C. Feng, Petascale Application of a Coupled CPU-GPU Algorithm for Simulation and Analysis of Multiphase Flow Solutions in Porous Medium Systems, Proc. 28th Intnl Parallel and Distributed Processing Symposium (IPDPS), IEEE, 2014.
J.E. McClure, J.F. Prins, C.T. Miller, "A novel heterogeneous algorithm to simulate multiphase flow in porous media on multicore CPU-GPU systems", Computer Physics Communications 185::1865-1874, http://dx.doi.org/10.1016/j.cpc.2014.03.012, 2014.
R.E. Overman, J.F. Prins, L.A. Miller, M.L. Minion, Dynamic Load Balancing of the Adaptive Fast Multipole Method in Heterogeneous Systems, Proc. ASHES 2013 workshop (IPDPSW), IEEE, 2013.
M. Gschwind, F. Gustavson, J. Prins, eds, "High Performance Computing on Cell B.E. Processors", special issue of Scientific Programming 17(1-2), IOS Press, 2009.
L. Nyland, M. Harris, J. Prins, "Fast N-Body Simulation with CUDA", in GPU Gems 3, H. Nguyen, ed., Addison Wesley (pp 677-696), 2007. PDF
S. Olivier, J. Prins, J.Derby, K. Vu, "Porting the GROMACS Molecular Dynamics Code to the Cell Processor", Proc. of 8th IEEE Intl. Workshop on Parallel and Distributed Scientific and Engineering Computing (PDSEC-07) Long Beach, CA, March 2007. PDF
C. Pan, J. Prins, C. Miller, "A High-performance Lattice Boltzmann Implementation to Model Flow in Porous Media", Computer Physics Communications 158, 2004. PDF
G. Mann, R. Yun, L. Nyland, J. Prins, J. Board, J. Hermans, "The Sigma MD program and a generic interface applicable to multi-functional programs with complex, hierarchical command structure", in Computational Methods for Macromolecules, T. Schlick, H.-H. Gan, eds., LNCSE 24 (pp 129 - 145), Springer - Verlag, 2002.
J. Prins, J. Hermans, G. Mann, L. Nyland, M. Simons, "A Virtual Environment for Steered Molecular Dynamics", Future Generation Computer Systems 15, 1999 (pp 485-495) PDF
L. Nyland, J. Prins, R.H. Yun, J. Hermans, H.-C. Kum, L. Wang, "Modeling Dynamic Load Balancing in Molecular Dynamics to Achieve Scalable Parallel Execution", in Fifth International Symposium on Solving Irregularly Structured Problems in Parallel (Irregular 98), Ferrieira, A. and Rolim, J. and Simon, H. and Teng, S.-H, eds., LNCS 1457, Springer-Verlag, 1998. (pp 356-365) PDF, PostScript
L. Nyland, J. Prins, R.H. Yun, J. Hermans, H.-C. Kum, L. Wang, "Achieving Scalable Parallel Molecular Dynamics Using Domain Decomposition Techniques", Journal of Parallel and Distributed Computing, 47 (2), Dec. 1997. (pp 125-138) PDF, PostScript
J. Leech, J. Prins, J. Hermans, "SMD: Visual Steering of Molecular Dynamics for Protein Design", Computational Science & Engineering 3 (4), IEEE, 1996. (pp 38-45) ( PDF with linked images ) ( monochrome scanned article in PDF )
Software Engineering issues in Parallel ProgrammingM. Farthing, C. Miller, D. Sassen, J. Prins, "A problem solving environment for subsurface flow and transport phenomena", to appear in International Conference on Computational Methods in Water Resources XV, Elsevier, 2004. PDF.
L. Nyland, J. Prins, A. Goldberg, P. Mills, "A Design Methodology for Data-Parallel Applications", Transactions on Software Engineering 26, IEEE, 1999 (pp 293-315) PDF
R. Faith, L. Nyland, J. Prins, "Khepera: A System for the Rapid Implementation of Domain Specific Languages" , Proc. ACM/USENIX conference on Domain Specific Languages, ACM, 1997. (pp 243-255) PDF
L. Nyland, J. Prins, A. Goldberg, P. Mills, J. Reif, R. Wagner, "A Refinement Methodology for Data-Parallel Applications", in Proc. EuroPar 96 Parallel Processing Conference, Lyon, France, LNCS 1123, Springer-Verlag, 1996. (pp 145-151) PDF
A. Goldberg, J. Prins, J. Reif, R. Faith, Z. Li, P. Mills, L. Nyland, D. Palmer, J. Riely, S. Westfold, "The Proteus System for the Development of Parallel Applications", in Prototyping Languages and Prototyping Technology, M. Harrison, ed., (to appear Aug 2000) Springer-Verlag (40 pp) PDF
A. Goldberg, P. Mills, L. Nyland, J. Prins, J. Reif, J. Riely, "Specification and Development of Parallel Algorithms with the Proteus System", in Specification of Parallel Algorithms, G. Blelloch, M. Chandy, S. Jagannathan, (eds), AMS, 1995. (pp 383-399) PDF
P. Mills, L.Nyland, J. Prins, J. Reif, "Software Issues in High-Performance Computing and a Framework for the Development of HPC Applications", in Computer Science Agendas for High Performance Computing, U. Vishkin, ed., ACM 1995. (pp 110-117) PDF