Simon Kasif

Richard J. Roberts, Yi-Chien Chang, Zhenjun Hu, John Rachlin, Brian P. Anton, Revonda M. Pokrzywa, Han-Pil Choi, Lina L. Faller, Jyotsna Guleria, Genevieve Housman, Niels Klitgord, Varun Mazumdar, Mark G. McGettrick, Lais Osmani, Rajeswari Swaminathan, Kevin R. Tao, Stanley Letovsky, Dennis Vitkup, Daniel Segrè, Steven L. Salzberg, Charles DeLisi, Martin Steffen, Simon Kasif: COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. Nucleic Acids Research 39(Database-Issue): 11-14 (2011)

Antonina Mitrofanova, Samantha Kleinberg, Jane Carlton, Simon Kasif, Bud Mishra: Predicting malaria interactome classifications from time-course transcriptomic data along the intraerythrocytic developmental cycle. Artificial Intelligence in Medicine 49(3): 167-176 (2010)

Dikla Dotan-Cohen, Simon Kasif, Avraham A. Melkman: Seeing the forest for the trees: using the Gene Ontology to restructure hierarchical clustering. Bioinformatics 25(14): 1789-1795 (2009)

Peter J. Park, Sek Won Kong, Toma Tebaldi, Weil R. Lai, Simon Kasif, Isaac S. Kohane: Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance. Bioinformatics 25(23): 3121-3127 (2009)

Xiaoyu Jiang, Naoki Nariai, Martin Steffen, Simon Kasif, Eric D. Kolaczyk: Integration of relational and hierarchical network information for protein function prediction. BMC Bioinformatics 9 (2008)

John H. Reif, Simon Kasif, Deepak Sherlekar: Formula dissection: A parallel algorithm for constraint satisfaction. Computers & Mathematics with Applications 55(6): 1170-1177 (2008)

Antonina Mitrofanova, Samantha Kleinberg, Jane Carlton, Simon Kasif, Bud Mishra: Systems Biology via Redescription and Ontologies (III): Protein Classification Using Malaria Parasite's Temporal Transcriptomic Profiles. BIBM 2008: 278-283

Xiaoyu Jiang, Naoki Nariai, Martin Steffen, Simon Kasif, David Gold, Eric D. Kolaczyk: Combining Hierarchical Inference in Ontologies with Heterogeneous Data Sources Improves Gene Function Prediction. BIBM 2008: 411-416

Dikla Dotan-Cohen, Avraham A. Melkman, Simon Kasif: Hierarchical tree snipping: clustering guided by prior knowledge. Bioinformatics 23(24): 3335-3342 (2007)

Noga Alon, Vera Asodi, Charles Cantor, Simon Kasif, John Rachlin: Multi-Node Graphs: A Framework for Multiplexed Biological Assays. Journal of Computational Biology 13(10): 1659-1672 (2006)

Yu Zheng, Brian P. Anton, Richard J. Roberts, Simon Kasif: Phylogenetic detection of conserved gene clusters in microbial genomes. BMC Bioinformatics 6: 243 (2005)

John Rachlin, Chunming Ding, Charles Cantor, Simon Kasif: MuPlex: multi-objective multiplex PCR assay design. Nucleic Acids Research 33(Web-Server-Issue): 544-547 (2005)

Chang-Jiun Wu, Simon Kasif: GEMS: a web server for biclustering analysis of expression data. Nucleic Acids Research 33(Web-Server-Issue): 596-599 (2005)

Joseph D. Szustakowski, Simon Kasif, Zhiping Weng: Less is more: towards an optimal universal description of protein folds. ECCB/JBI 2005: 71

Satoru Miyano, Jill P. Mesirov, Simon Kasif, Sorin Istrail, Pavel A. Pevzner, Michael S. Waterman (Eds.): Research in Computational Molecular Biology, 9th Annual International Conference, RECOMB 2005, Cambridge, MA, USA, May 14-18, 2005, Proceedings. Lecture Notes in Computer Science 3500, Springer 2005, isbn 3-540-25866-3

Nathan O. Stitziel, T. Andrew Binkowski, Yan Yuan Tseng, Simon Kasif, Jie Liang: topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association. Nucleic Acids Research 32(Database-Issue): 520-522 (2004)

Noga Alon, Richard Beigel, Simon Kasif, Steven Rudich, Benny Sudakov: Learning a Hidden Matching. SIAM J. Comput. 33(2): 487-501 (2004)

Jie Wu, Simon Kasif, Charles DeLisi: Identification of functional links between genes using phylogenetic profiles. Bioinformatics 19(12): 1524-1530 (2003)

Yang Su, T. M. Murali, Vladimir Pavlovic, Michael Schaffer, Simon Kasif: RankGene: identification of diagnostic genes based on expression data. Bioinformatics 19(12): 1578-1579 (2003)

Stanley Letovsky, Simon Kasif: Predicting protein function from protein/protein interaction data: a probabilistic approach. ISMB (Supplement of Bioinformatics) 2003: 197-204

T. M. Murali, Simon Kasif: Extracting Conserved Gene Expression Motifs from Gene Expression Data. Pacific Symposium on Biocomputing 2003: 77-88

Vladimir Pavlovic, Ashutosh Garg, Simon Kasif: A Bayesian framework for combining gene predictions. Bioinformatics 18(1): 19-27 (2002)

Noga Alon, Richard Beigel, Simon Kasif, Steven Rudich, Benny Sudakov: Learning a Hidden Matching. FOCS 2002: 197-

Richard Beigel, Noga Alon, Simon Kasif, Mehmet Serkan Apaydin, Lance Fortnow: An optimal procedure for gap closing in whole genome shotgun sequencing. RECOMB 2001: 22-30

Deyou Cai, Arthur L. Delcher, Ben Kao, Simon Kasif: Modeling splice sites with Bayes networks. Bioinformatics 16(2): 152-158 (2000)

Simon Kasif, Steven Salzberg, David L. Waltz, John Rachlin, David W. Aha: A Probabilistic Framework for Memory-Based Reasoning. Artif. Intell. 104(1-2): 287-311 (1998)

Simon Kasif: Towards a Constraint-Based Engineering Framework for Algorithm Design and Application. Constraints 2(1): 75-82 (1997)

Simon Kasif: Towards a Constraint-Based Engineering Framework for Algorithm Design and Application. ACM Comput. Surv. 28(4es): 66 (1996)

Arthur L. Delcher, Adam J. Grove, Simon Kasif, Judea Pearl: Logarithmic-Time Updates and Queries in Probabilistic Networks. J. Artif. Intell. Res. (JAIR) 4: 37-59 (1996)

David G. Heath, Simon Kasif, S. Rao Kosaraju, Steven Salzberg, Gregory F. Sullivan: Learning nested concept classes with limited storage. J. Exp. Theor. Artif. Intell. 8(2): 129-147 (1996)

Truxton Fulton, Simon Kasif, Steven Salzberg, David L. Waltz: Local Induction of Decision Trees: Towards Interactive Data Mining. KDD 1996: 14-19

Arthur L. Delcher, Adam J. Grove, Simon Kasif, Judea Pearl: Logarithmic-Time Updates and Queries in Probabilistic Networks. CoRR cs.AI/9602102 (1996)

Arthur L. Delcher, Simon Kasif: Term Matching on a Mesh-Connected Array of Processors. Ann. Math. Artif. Intell. 14(2-4): 177-186 (1995)

David L. Waltz, Simon Kasif: On Reasoning From Data. ACM Comput. Surv. 27(3): 356-359 (1995)

Steven Salzberg, Arthur L. Delcher, David G. Heath, Simon Kasif: Best-Case Results for Nearest-Neighbor Learning. IEEE Trans. Pattern Anal. Mach. Intell. 17(6): 599-608 (1995)

Truxton Fulton, Simon Kasif, Steven Salzberg: Efficient Algorithms for Finding Multi-way Splits for Decision Trees. ICML 1995: 244-251

Arthur L. Delcher, Adam J. Grove, Simon Kasif, Judea Pearl: Logarithmic-Time Updates and Queries in Probabilistic Networks. UAI 1995: 116-124

Simon Kasif, Arthur L. Delcher: Local Consistency in Parallel Constraint Satisfaction Networks. Artif. Intell. 69(1-2): 307-327 (1994)

Sreerama K. Murthy, Simon Kasif, Steven Salzberg: A System for Induction of Oblique Decision Trees. J. Artif. Intell. Res. (JAIR) 2: 1-32 (1994)

Jonathan Bright, Simon Kasif, Lewis Stiller: Exploiting Algebraic Structure in Parallel State Space Search. AAAI 1994: 1341-1346

John Rachlin, Simon Kasif, Steven Salzberg, David W. Aha: Towards a Better Understanding of Memory-based Reasoning Systems. ICML 1994: 242-250

Simon Kasif, Saibal Banerjee, Arthur L. Delcher, Gregory F. Sullivan: Some Results on the Computational Complexity of Symmetric Connectionist Networks. Ann. Math. Artif. Intell. 9(3-4): 327-344 (1993)

David G. Heath, Simon Kasif: The Complexity of Finding Minimal Voronoi Covers with Applications to Machine Learning. Comput. Geom. 3: 289-305 (1993)

Arthur L. Delcher, Simon Kasif, Harry R. Goldberg, William H. Hsu: Probabilistic Prediction of Protein Secondary Structure Using Causal Networks (Extended Abstract). AAAI 1993: 316-321

Sreerama K. Murthy, Simon Kasif, Steven Salzberg, Richard Beigel: OC1: A Randomized Induction of Oblique Decision Trees. AAAI 1993: 322-327

David G. Heath, Simon Kasif, Steven Salzberg: Induction of Oblique Decision Trees. IJCAI 1993: 1002-1007

Arthur L. Delcher, Simon Kasif, Harry R. Goldberg, William H. Hsu: Protein Secondary-Structure Modeling with Probabilistic Networks. ISMB 1993: 109-117

Simon Kasif, Arthur L. Delcher: Local Consistency in Parallel Constraint-Satisfaction Networks. PPCP 1993: 139-145

Arthur L. Delcher, Simon Kasif: Efficient Parallel Term Matching and Anti-Unification. J. Autom. Reasoning 9(3): 391-406 (1992)

Arthur L. Delcher, Simon Kasif: Improved Decision-Making in Game Trees: Recovering from Pathology. AAAI 1992: 513-518

Steven Salzberg, Arthur L. Delcher, David G. Heath, Simon Kasif: Learning with a Helpful Teacher. IJCAI 1991: 705-711

David G. Heath, Simon Kasif, S. Rao Kosaraju, Steven Salzberg, Gregory F. Sullivan: Learning Nested Concept Classes with Limited Storage. IJCAI 1991: 777-782

Simon Kasif: On the Parallel Complexity of Discrete Relaxation in Constraint Satisfaction Networks. Artif. Intell. 45(3): 275-286 (1990)

Arthur L. Delcher, Simon Kasif: Efficient Parallel Term Matching and Anti-Unification. ICLP 1990: 355-369

Arthur L. Delcher, Simon Kasif: Some Results on the Complexity of Exploiting Data Dependency in Parallel Logic Programs. J. Log. Program. 6(3): 229-241 (1989)

Simon Kasif: Parallel Solutions to Constraint Satisfaction Problems. KR 1989: 180-188

Simon Kasif: Control and data driven execution of logic programs: A comparison. International Journal of Parallel Programming 15(1): 73-99 (1986)

Simon Kasif: On the Parallel Complexity of Some Constraint Satisfaction Problems. AAAI 1986: 349-353

Simon Kasif, Jack Minker: The Intelligent Channel: A Scheme for Result Sharing in Logic Programs. IJCAI 1985: 29-31

Simon Kasif, Madhur Kohli, Jack Minker: PRISM: A Parallel Inference System for Problem Solving. IJCAI 1983: 544-546

Norbert Eisinger, Simon Kasif, Jack Minker: Logic Programming: A Parallel Approach. ICLP 1982: 71-77

Upen S. Chakravarthy, Simon Kasif, Madhur Kohli, Jack Minker, D. Cao: Logic Programming on ZMOB: A Highly Parallel Machine. ICPP 1982: 347-349