John R. Rose,
Storey Engineering and Inovation Center, RM 2257
BMus: Music, Immaculate
MS: Computer Science, SUNY at Stony Broo
PhD: Computer Science, SUNY at Stony Broo
Distributed Artificial Intelligence and Multiagent Systems
Knowledge Discovery in Databases
I am a professor of computer science in the Department of Computer Science and Engineering
at the University of South Carolina. Prior to
this position, I was a postdoctoral fellow at the Laboratory for Computational
Chemistry at the Technical University of Munich. Before that, I labored as a
research assistant in data mining in chemical reaction databases at SUNY-Stony
I am currently a member of IEEE. I am the author of over 60 technical papers, and book chapters
in bioinformatics, machine intelligence, and computational science. My research
interests are in the areas of bioinformatics, normative reasoning and planning,
DAI and multiagent systems, and computational chemistry.
I have conducted research funded by NSF, NIH, NASA, DOD/ONR, Alexander von
Humboldt Foundation, BMFT (German NSF equivalent), as well as the South
A. V. Kish, J. R. Rose, C. Farkas, “Efficient Partitioning and Allocation of Data for Workload Queries,”
in Proc. of The 9th Annual International Joint Conferences on Computer, Information, Systems Sciences, & Engineering (CISSE) E-Conference,
J. Cleveland, J.R. Rose, “Identification of b-/y-ions in MS/MS Spectra Using a Two Stage Neural Network”,
Proteome Science 2013, 11(Suppl 1):S4 doi:10.1186/1477-5956-11-S1-S4. Epub 2013 Nov 7.
A. El Allali, J.R. Rose, “MGC: A Metagenomic Gene Caller”, BMC Bioinformatics,
14 Suppl 9:S6. doi: 10.1186/1471-2105-14-S9-S6. Epub 2013 Jun 28.
J. Cleveland, J.R. Rose, “A Neural Network Approach to the Identi?cation of b-/y-ions in MS/MS Spectra.”
Proceedings of the 6th IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012) 2012:588-592.
“MGC: Gene calling in metagenomic sequences, ” (with A. El Allali) 8th International Symposium on Bioinformatics Research and Applications, Dallas, ISBRA 2012 Short Abstracts pp. 55-58.
“A Neural Network Approach to Pre-filtering MS/MS spectra,” (with J. Cleveland) 8th International Symposium on Bioinformatics Research and Applications, Dallas, TX. ISBRA 2012 Short Abstracts pp. 82-84.
Speciation of coagulase negative staphylococci, isolated from indoor air, using SDS page gel bands of expressed proteins followed by MALDI TOF MS and MALDI TOF-TOF MS-MS analysis of tryptic peptides.(with K. Fox, A. Fox, and M. Walla) J. Micro. Meth. 84:243-250. 2011.
“An Information Theoretic Approach to Rescoring Peptides Produced by De Novo Peptide Sequencing,” (with J. Cleveland) in Proceedings of the ICBCB 2010 : International Conference on Bioinformatics and Computational Biology, Paris, World Academy of Science, Engineering and Technology 71:2010, pp. 265–270.
“Mim: A Species Independent Approach For Classifying Coding And Non-coding Dna Sequences In Bacterial And Archaeal Genomes,” (with A. El Allali) in Proceedings of the ICBCB 2010 : International Conference on Bioinformatics and Computational Biology, Paris, edited by C. Ardil, World Academy of Science, Engineering and Technology 71:2010, pp. 136–143.
“Mutual Information Measure for Distinguishing Coding and Non-Coding DNA Sequences,” (with A. El Allali) BIOCOMP08, 2008.
“Evidence for Protein Fragment Homology in
Viral Genome Types”,(with R. Mu
“Gene Family Content-Based Phylogeny of Pro
“Exploiting Belief Locality in Run-Time
Decision-Theoretic Planners”, (with W.H. Tur
“Correlation of Amino Acid Preference and
Mammalian Viral Genome Type”, (with
“Dblox: a genome-wide test for ancient segmental
duplication,” (with R. Friedman, V. E
“Social Organization in a Software
Agent Community with a Non-zero-Sum Game Interaction Model,” in Regulated
Agent-Based Social Systems,” (with M. Vanninen) G. Lindemann, D. Moldt, M. Paolucci (Eds.) LNAI 2934,
"Non-Random Association of Transposable Elements with Duplicated Genomic
"Machine Learning in Chemistry," in Chemoinformatics – From Data to Knowledge, Gasteiger, Engel (Eds.), Wiley-VCH, Weinheim, Germany Volume 3, pp1082-1097, Wiley-VCH, Weinheim, Germany, 2003.
“An Evaluation of Philosophical Agent Architectures for Mission Robustness,”, in Innovative
Concepts for Agent-Based Systems,” (with W. Tur
“Planning with Agents: An
Efficient Approach Using Hierarchical Dynamic Decision Networ
“Integrating Organizational Knowledge for Dynamic Scalable Multiagent Systems” (with W. A. Smith) IEEE KIMAS: Integration of Knowledge Intensive Multi-Agent Systems, Henry Hexmoor, editor, IEEE, 2003, p. 184-189.
“Parallel Algorithms for Bayesian Phylogenetic Inference” (with X. Feng, D. Buell, and P. Waddell) Journal of Parallel and Distributed Computing63, pp 707-718, 2003.
"Massive Deliberation." (with
"Emergent Planning with Philosophical Agents" (with W. Tur
"An Agent Architecture for Long-Term Robustness" (with M. Huhns,
S. Roy, and W. Tur
"Social Organization in a Software Agent Community with a Non-Zero-Sum
Game Interaction Model" (with M Vanninen) in Proceedings
of International Wor
"An Agent Architecture for Comprehensive Mission Robustness" (with
M. Huhns) in Proceedings of the Goddard/JPL Wor
` "Philosophical Agents" (with M. Huhns) IEEE Internet Computing, Vol. 5, No. 3, 2001, pp. 104-106.
"An Information Model for the Representation of Multiple Biological
Classifications" (with Neville Yoon) In: Alexandrov
VN, Dongarra JJ, Juliano
BA, Renner RS, Tan CJK, editors. Computational Science - ICCS 2001:
International Conference, San Francisco, CA, USA, May 2001 Proceesings, Part 1.
"A Biologically-Motivated Approach to Direction Sensitive Velocity-Tuned Motion Detectors" (with Dudley Girard) Proceedings of SCI2000/ISAS2000, Orlando, Florida, 2000, Vol. 6, pp. 173-178.
" Neural Systems for Motion Analysis: Single Neuron and Networ
"Behavior-based Control for Autonomous Mobile Robots" (with Terry Huntsberger) Proceedings of Robotics 2000 Conference
"A Distributed Agent Environment System for Simulating a Naive Sensor/Emitter Model" Proceedings of the 1999 Summer Computer Simulation Conference (SCSC 31), 1999, pp. 359-363.
"Integrated Vision/Control System for Autonomous Planetary Rovers"
(with Terry Hunstberger and Toshiro Kubota) IAPR
"Machine Learning Techniques in Chemistry" Encyclopedia of Computational Chemistry Paul von Rague Schleyer, Editor (John Wiley & Sons, Ltd.), 1998.
"BISMARC: a biologically inspired system for map-based autonomous rover
control" (with Terry Huntsberger) Neural
"Fuzzy-Face: A Hybrid Wavelet/Fuzzy Self-Organizing Feature Map System
for Face Processing" (with Terry Huntsberger and
"Characterization of a Reaction Database in Terms of a Lower Bound on
the Number of Reaction Classes" (with Ra
"Computer Simulations of Bimodal Neurons and Networ
"Hierarchical Classification as an Aid to Browsing" (with Caroline Eastman) Informatica 21:49-57, 1997.
"Hierarchical Support for Browsing" (with Caroline Eastman) National
Online Meeting Proceedings pages 91-100, New Yor
"Automatic Extraction of Chemical Knowledge from Organic Reaction Data: Addtion of Carbon-Hydrogen Bonds to Carbon-Carbon Bonds" (with Lingran Chen and Johann Gasteiger) Journal of Organic Chemistry 60:8002-8014, 1995.
"Learning from Reaction Databases" (with Johann Gasteiger, Peter Roese, Ulrich Hondelmann and Wolfgang Witzenbichler) AIPS Conference Proceedings 330: E.C.C.C. 1: Computational Chemistry, F.E.C.S. Conference, F. Bernardi, J. L. Rivail, Editors, AIP Press, Woodbury, NY, pp. 667-685, 1995.
"Extraction of Chemical Knowledge from Organic Reaction Bata by
Automatic Hierarchical Classification and Generalization" (with Lingran Chen and Johann Gasteiger),
Software-Development in Chemistry Rainer Moll, Ed., Vol. 9, pp. 129-139,
1995 (Springer GmbH & Co.,
"Hierarchical Classification as an Aid to Browsing" (with Caroline Eastman) Second International Symposium on Knowledge Acquisition, Representation and Processing (KARP-95), Abstracts , Pages 105-107, 1995.
"HORACE: An Automatic System for the Hierarchical Classification of Chemical REactions" (with Johann Gasteiger), ACS Jour. Chemical Information and Computer Science (34):74-90, 1994.
Klassifizierung von Rea
"Hierarchical Classification as an Aid to Database and Hit-List Browsing" (with Johann Gasteiger) Third International Conference on Information and Knowledge Management, Gaithersburg, Maryland, pages 408-414, 1994.
"Hierarchical Classification as an Aid to Browsing" (with Caroline
Eastman) Fifth ASIS SIG/CR Classification Research Wor
" Knowledge Discovery in Reaction Databases" (with Herbert Gelernter) Proceedings of the Second International Conference on Information and Knowledge Management, pages 714-716, 1993.
"Similarity Concepts for the Planning of Organic Reactions and
Syntheses" (with J. Gasteiger, W. Ihlenfeldt and R. Fic
"Building and Refining a Knowledge Base for Synthetic Organic Chemistry via the Methodology of Inductive and Deductive Machine Learning" (with H. Gelernter and C. Chen) ACS Jour. Chemical Information and Computer Science (30):492-504, 1990.
"ISOLDE: A System for Learning Organic Chemistry through
Induction" (with H. Gelernter) Proceedings of EKAW-89: Third European
"HYDRA: A Knowledge Acquisition Tool for Experts Systems that Critique
"Critiquing the Process of Radiological Differential Diagnosis" (with P. Miller, C. Shaw and H. Swett) Computer Methods and Programs in Biomedicine, (22):21- 25, 1986.