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Steven Skiena

Papers on DiSC'04


Parsing Without a Grammar: Making Sense of Unknown File Formats

Publications


Note: Links lead to the DBLP on the Web.

Steven Skiena

Vladimir Filkov , Steven Skiena: Heterogeneous Data Integration with the Consensus Clustering Formalism. DILS 2004 : 110-123

Michael A. Bender , Dongdong Ge , Simai He , Haodong Hu , Ron Y. Pinter , Steven Skiena, Firas Swidan : Improved bounds on sorting with length-weighted reversals. SODA 2004 : 919-928

Vinhthuy T. Phan , Steven Skiena: An Improved Time-Sensitive Metaheuristic Framework for Combinatorial Optimization. WEA 2004 : 432-445

Levon Lloyd , Steven Skiena: Parsing Without a Grammar: Making Sense of Unknown File Formats. ICDM 2003 : 195-202

Vladimir Filkov , Steven Skiena: Integrating Microarray Data by Consensus Clustering. ICTAI 2003 : 418-425

Vinhthuy T. Phan , Steven Skiena, Pavel Sumazin : A Model for Analyzing Black-Box Optimization. WADS 2003 : 424-438

Esther M. Arkin , Michael A. Bender , Joseph S. B. Mitchell , Steven Skiena: The Lazy Bureaucrat scheduling problem. Inf. Comput. 184 (1): 129-146 (2003)

Mirela Andronescu , Danielle Dees , Laura Slaybaugh , Yinglei Zhao , Anne Condon , Barry Cohen , Steven Skiena: Algorithms for testing that sets of DNA words concatenate without secondary structure. Natural Computing 2 (4): 391-415 (2003)

Vinhthuy T. Phan , Pavel Sumazin , Steven Skiena: A Time-Sensitive System for Black-Box Combinatorial Optimization. ALENEX 2002 : 16-18

Mirela Andronescu , Danielle Dees , Laura Slaybaugh , Yinglei Zhao , Anne Condon , Barry Cohen , Steven Skiena: Algorithms for Testing That Sets of DNA Words Concatenate without Secondary Structure. DNA 2002 : 182-195

Rohan J. Fernandes , Steven Skiena: Microarray synthesis through multiple-use PCR primer design. ISMB 2002 : 128-135

Barry Cohen , Steven Skiena: Designing RNA structures: natural and artificial selection. RECOMB 2002 : 109-116

Andy Wildenberg , Steven Skiena, Pavel Sumazin : Deconvolving sequence variation in mixed DNA populations. RECOMB 2002 : 311-320

Steven Skiena, Sagi Snir : Restricting SBH Ambiguity via Restriction Enzymes. WABI 2002 : 404-417

Vladimir Filkov , Steven Skiena, Jizu Zhi : Analysis Techniques for Microarray Time-Series Data. Journal of Computational Biology 9 (2): 317-330 (2002)

Steven Skiena: Designing better phages. ISMB (Supplement of Bioinformatics) 2001 : 253-261

Vladimir Filkov , Steven Skiena, Jizu Zhi : Analysis techniques for microarray time-series data. RECOMB 2001 : 124-131

Michael A. Bender , Giridhar Pemmasani , Steven Skiena, Pavel Sumazin : Finding least common ancestors in directed acyclic graphs. SODA 2001 : 845-854

Esther M. Arkin , Michael A. Bender , Erik D. Demaine , Martin L. Demaine , Joseph S. B. Mitchell , Saurabh Sethia , Steven Skiena: When Can You Fold a Map? WADS 2001 : 401-413

Vinhthuy T. Phan , Steven Skiena: Dealing with errors in interactive sequencing by hybridization. Bioinformatics 17 (10): 862-870 (2001)

Ting Chen , Vladimir Filkov , Steven Skiena: Identifying gene regulatory networks from experimental data. Parallel Computing 27 (1-2): 141-162 (2001)

Steven Skiena, Pavel Sumazin : Shift Error Detection in Standardized Exams. CPM 2000 : 264-276

Esther M. Arkin , Ferran Hurtado , Joseph S. B. Mitchell , Carlos Seara , Steven Skiena: Some Separability Problems in the Plane. EWCG 2000 : 51-54

Michael A. Bender , Saurabh Sethia , Steven Skiena: Data Structures for Maintaining Set Partitions. SWAT 2000 : 83-96

Ting Chen , Steven Skiena: A case study in genome-level fragment assembly. Bioinformatics 16 (6): 494-500 (2000)

Jihad El-Sana , Francine Evans , Aravind Kalaiah , Amitabh Varshney , Steven Skiena, Elvir Azanli : Efficiently computing and updating triangle strips for real-time rendering. Computer-Aided Design 32 (13): 753-772 (2000)

Jonathan Berry , Nathaniel Dean , Mark K. Goldberg , Gregory E. Shannon , Steven Skiena: LINK: a system for graph computation. Softw., Pract. Exper. 30 (11): 1285-1302 (2000)

Barry Cohen , Steven Skiena: Optimizing combinatorial library construction via split synthesis. RECOMB 1999 : 124-133

Ting Chen , Vladimir Filkov , Steven Skiena: Identifying gene regulatory networks from experimental data. RECOMB 1999 : 94-103

Esther M. Arkin , Michael A. Bender , Joseph S. B. Mitchell , Steven Skiena: The Lazy Bureaucrat Scheduling Problem. WADS 1999 : 122-133

Esther M. Arkin , Yi-Jen Chiang , Joseph S. B. Mitchell , Steven Skiena, Tae-Cheon Yang : On the Maximum Scatter Traveling Salesperson Problem. SIAM J. Comput. 29 (2): 515-544 (1999)

Steven Skiena: Who is Interested in Algorithms and why? Lessons from the Stony Brook Algorithms Repository. Algorithm Engineering 1998 : 204-212

Esther M. Arkin , Yi-Jen Chiang , Martin Held , Joseph S. B. Mitchell , Vera Sacristan , Steven Skiena, Tae-Heng Yang : On Minimum-Area Hulls. Algorithmica 21 (1): 119-136 (1998)

Esther M. Arkin , Martin Held , Joseph S. B. Mitchell , Steven Skiena: Recognizing polygonal parts from width measurements. Comput. Geom. 9 (4): 237-246 (1998)

Esther M. Arkin , Henk Meijer , Joseph S. B. Mitchell , David Rappaport , Steven Skiena: Decision trees for geometric models. Int. J. Comput. Geometry Appl. 8 (3): 343-364 (1998)

Ting Chen , Steven Skiena: Trie-Based Data Structures for Sequence Assembly. CPM 1997 : 206-223

Jonathan Berry , Nathaniel Dean , Mark K. Goldberg , Gregory E. Shannon , Steven Skiena: Graph Drawing and Manipulation with LINK . Graph Drawing 1997 : 425-437

Sanjeev Khanna , S. Muthukrishnan , Steven Skiena: Efficient Array Partitioning. ICALP 1997 : 616-626

Richa Agarwala , Serafim Batzoglou , Vlado Dancík , Scott E. Decatur , Martin Farach , Sridhar Hannenhalli , S. Muthukrishnan , Steven Skiena: Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model. RECOMB 1997 : 1-2

J. Richard Bradley , Steven Skiena: Fabricating arrays of strings. RECOMB 1997 : 57-66

Esther M. Arkin , Yi-Jen Chiang , Joseph S. B. Mitchell , Steven Skiena, Tae-Cheon Yang : On the Maximum Scatter TSP (Extended Abstract). SODA 1997 : 211-220

Richa Agarwala , Serafim Batzoglou , Vlado Dancík , Scott E. Decatur , Martin Farach , Sridhar Hannenhalli , Steven Skiena: Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model. SODA 1997 : 390-399

George N. Sazaklis , Esther M. Arkin , Joseph S. B. Mitchell , Steven Skiena: Geometric Decision Trees for Optical Character Recognition (Extended Abstract). Symposium on Computational Geometry 1997 : 394-396

Esther M. Arkin , Joseph S. B. Mitchell , Steven Skiena: Guest Editors' Foreword. Int. J. Comput. Geometry Appl. 7 (1/2): 1- (1997)

Richa Agarwala , Serafim Batzoglou , Vlado Dancík , Scott E. Decatur , Sridhar Hannenhalli , Martin Farach , S. Muthukrishnan , Steven Skiena: Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model. Journal of Computational Biology 4 (3): 275-296 (1997)

Esther M. Arkin , Yi-Jen Chiang , Martin Held , Joseph S. B. Mitchell , Vera Sacristan , Steven Skiena, Tae-Heng Yang : On Minimum-Area Hulls (Extended Abstract). ESA 1996 : 334-348

Francine Evans , Steven Skiena, Amitabh Varshney : Optimizing Triangle Strips for Fast Rendering. IEEE Visualization 1996 : 319-326

Steven Dawson , C. R. Ramakrishnan , Steven Skiena, Terrance Swift : Principles and Practice of Unification Factoring. ACM Trans. Program. Lang. Syst. 18 (5): 528-563 (1996)

Sridhar Hannenhalli , W. Feldman , H. F. Lewis , Steven Skiena, Pavel A. Pevzner : Positional sequencing by hybridization. Computer Applications in the Biosciences 12 (1): 19-24 (1996)

Ting Chen , Steven Skiena: Sorting with Fixed-length Reversals. Discrete Applied Mathematics 71 (1-3): 269-295 (1996)

Harald Rau , Steven Skiena: Dialing for Documents: An Experiment in Information Theory. J. Vis. Lang. Comput. 7 (1): 79-95 (1996)

Esther M. Arkin , Martin Held , Joseph S. B. Mitchell , Steven Skiena: Hamiltonian triangulations for fast rendering. The Visual Computer 12 (9): 429-444 (1996)

Dimitris Margaritis , Steven Skiena: Reconstructing Strings from Substrings in Rounds. FOCS 1995 : 613-620

Steven Dawson , C. R. Ramakrishnan , I. V. Ramakrishnan , Konstantinos F. Sagonas , Steven Skiena, Terrance Swift , David Scott Warren : Unification Factoring for Efficient Execution of Logic Programs. POPL 1995 : 247-258

Y. Lin , Steven Skiena: Complexity aspects of visibility graphs. Int. J. Comput. Geometry Appl. 5 (3): 289-312 (1995)

Steven Skiena, Gopalakrishnan Sundaram : Reconstructing Strings from Substrings. Journal of Computational Biology 2 (2): 333-353 (1995)

Yaw-Ling Lin , Steven Skiena: Algorithms for Square Roots of Graphs. SIAM J. Discrete Math. 8 (1): 99-118 (1995)

Harald Rau , Steven Skiena: Dialing for Documents: An Experiment in Information Theory. ACM Symposium on User Interface Software and Technology 1994 : 147-155

Esther M. Arkin , Martin Held , Joseph S. B. Mitchell , Steven Skiena: Hamilton Triangulations for Fast Rendering. ESA 1994 : 36-47

Henk Meijer , Steven Skiena: Reconstructing Polygons From X-Rays. CCCG 1993 : 381-386

Steven Skiena, Gopalakrishnan Sundaram : A Partial Digest Approach to Restriction Site Mapping. ISMB 1993 : 362-370

Esther M. Arkin , Henk Meijer , Joseph S. B. Mitchell , David Rappaport , Steven Skiena: Decision Trees for Geometric Models. Symposium on Computational Geometry 1993 : 369-378

Michael Murphy , Steven Skiena: Ranger: A Tool for Nearest Neighbor Search in High Dimensions. Symposium on Computational Geometry 1993 : 403-404

Steven Skiena, Gopalakrishnan Sundaram : Reconstructing Strings from Substrings (Extended Abstract). WADS 1993 : 565-576

Esther M. Arkin , Michael T. Goodrich , Joseph S. B. Mitchell , David M. Mount , Christine D. Piatko , Steven Skiena: Point Probe Decision Trees for Geometric Concept Classes. WADS 1993 : 95-106

Eugene Joseph , Steven Skiena: Model-based Probing Strategies for Convex Polygons. Comput. Geom. 2 : 209-221 (1992)

W. H. Leung , Steven Skiena: Inducing Codes from Examples. Data Compression Conference 1991 : 267-276

Yaw-Ling Lin , Steven Skiena: Algorithms for Square Roots of Graphs. ISA 1991 : 12-21

Steven Skiena: Probing Convex Polygons with Half-Planes. J. Algorithms 12 (3): 359-374 (1991)

Steven Skiena, Warren D. Smith , Paul Lemke : Reconstructing Sets from Interpoint Distances (Extended Abstract). Symposium on Computational Geometry 1990 : 332-339

Scot W. Hornick , Sanjeev R. Maddila , Ernst P. Mücke , Harald Rosenberger , Steven Skiena, Ioannis G. Tollis : Searching on a Tape. IEEE Trans. Computers 39 (10): 1265-1272 (1990)

Steven Skiena: Problems in Geometric Probing. Algorithmica 4 (4): 599-605 (1989)

Steven Skiena: Encroaching Lists as a Measure of Presortedness. BIT 28 (4): 755-784 (1988)

Bartlett W. Mel , Stephen M. Omohundro , Arch D. Robinson , Steven Skiena, Kurt H. Thearling , Luke T. Young , Stephen Wolfram : Tablet: Personal Computer in the Year 2000. Commun. ACM 31 (6): 638-646 (1988)

Herbert Edelsbrunner , Steven Skiena: Probing Convex Polygons with X-Rays. SIAM J. Comput. 17 (5): 870-882 (1988)

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