Walter L. Ruzzo

Nathaniel McVicar, Walter L. Ruzzo, Scott Hauck: Accelerating ncRNA homology search with FPGAs. FPGA 2013: 43-52

Daniel C. Jones, Walter L. Ruzzo, Xinxia Peng, Michael G. Katze: A new approach to bias correction in RNA-Seq. Bioinformatics 28(7): 921-928 (2012)

Hamid Bolouri, Walter L. Ruzzo: Integration of 198 ChIP-seq Datasets Reveals Human cis-Regulatory Regions. Journal of Computational Biology 19(9): 989-997 (2012)

Corey B. Olson, Maria Kim, Cooper Clauson, Boris Kogon, Carl Ebeling, Scott Hauck, Walter L. Ruzzo: Hardware Acceleration of Short Read Mapping. FCCM 2012: 161-168

Daniel C. Jones, Walter L. Ruzzo, Xinxia Peng, Michael G. Katze: Compression of next-generation sequencing reads aided by highly efficient de novo assembly. CoRR abs/1207.2424 (2012)

Parvez Anandam, Elfar Torarinsson, Walter L. Ruzzo: Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies. Bioinformatics 25(5): 668-669 (2009)

Huei-Hun Tseng, Zasha Weinberg, Jeremy Gore, Ronald R. Breaker, Walter L. Ruzzo: Finding Non-Coding RNAs through genome-Scale Clustering. J. Bioinformatics and Computational Biology 7(2): 373-388 (2009)

Huei-Hun Tseng, Zasha Weinberg, Jeremy Gore, Ronald R. Breaker, Walter L. Ruzzo: Finding Non-coding RNAs Through Genome-Scale Clustering. APBC 2008: 199-210

Adrienne X. Wang, Walter L. Ruzzo, Martin Tompa: How accurately is ncRNA aligned within whole-genome multiple alignments? BMC Bioinformatics 8 (2007)

Zizhen Yao, Jeffrey Barrick, Zasha Weinberg, Shane Neph, Ronald R. Breaker, Martin Tompa, Walter L. Ruzzo: A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes. PLoS Computational Biology 3(7) (2007)

Zasha Weinberg, Walter L. Ruzzo: Sequence-based heuristics for faster annotation of non-coding RNA families. Bioinformatics 22(1): 35-39 (2006)

Zizhen Yao, Zasha Weinberg, Walter L. Ruzzo: CMfinder - a covariance model based RNA motif finding algorithm. Bioinformatics 22(4): 445-452 (2006)

Zizhen Yao, Walter L. Ruzzo: A Regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data. BMC Bioinformatics 7(S-1) (2006)

Walter L. Ruzzo: Searching for Non-coding RNA. BSB 2005: 9-10

Zasha Weinberg, Walter L. Ruzzo: Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy. ISMB/ECCB (Supplement of Bioinformatics) 2004: 334-341

Zasha Weinberg, Walter L. Ruzzo: Faster genome annotation of non-coding RNA families without loss of accuracy. RECOMB 2004: 243-251

J. Jaeger, Rimli Sengupta, Walter L. Ruzzo: Improved Gene Selection for Classification of Microarrays. Pacific Symposium on Biocomputing 2003: 53-64

Donald J. Patterson, Ken Yasuhara, Walter L. Ruzzo: Pre-mRNA Secondary Structure Prediction Aids Splice Site Prediction. Pacific Symposium on Biocomputing 2002: 223-234

Ka Yee Yeung, David R. Haynor, Walter L. Ruzzo: Validating clustering for gene expression data. Bioinformatics 17(4): 309-318 (2001)

Ka Yee Yeung, Walter L. Ruzzo: Principal component analysis for clustering gene expression data. Bioinformatics 17(9): 763-774 (2001)

Ka Yee Yeung, Chris Fraley, A. Murua, Adrian E. Raftery, Walter L. Ruzzo: Model-based clustering and data transformations for gene expression data. Bioinformatics 17(10): 977-987 (2001)

Patrick W. Dymond, Walter L. Ruzzo: Parallel RAMs with owned global memory and deterministic context-free language recognition. J. ACM 47(1): 16-45 (2000)

Joshua Redstone, Walter L. Ruzzo: Algorithms for a Simple Point Placement Problem. CIAC 2000: 32-43

Paul Beame, Allan Borodin, Prabhakar Raghavan, Walter L. Ruzzo, Martin Tompa: A Time-Space Tradeoff for Undirected Graph Traversal by Walking Automata. SIAM J. Comput. 28(3): 1051-1072 (1999)

Walter L. Ruzzo, Martin Tompa: A Linear Time Algorithm for Finding All Maximal Scoring Subsequences. ISMB 1999: 234-241

Greg Barnes, Jonathan F. Buss, Walter L. Ruzzo, Baruch Schieber: A Sublinear Space, Polynomial Time Algorithm for Directed s-t Connectivity. SIAM J. Comput. 27(5): 1273-1282 (1998)

Greg Barnes, Walter L. Ruzzo: Undirected s-t Connectivity in Polynomial Time and Sublinear Space. Computational Complexity 6(1): 1-28 (1997)

Ashok K. Chandra, Prabhakar Raghavan, Walter L. Ruzzo, Roman Smolensky, Prasoon Tiwari: The Electrical Resistance of a Graph Captures its Commute and Cover Times. Computational Complexity 6(4): 312-340 (1997)

Paul Beame, Allan Borodin, Prabhakar Raghavan, Walter L. Ruzzo, Martin Tompa: Time-Space Tradeoffs for Undirected Graph Traversal by Graph Automata. Inf. Comput. 130(2): 101-129 (1996)

Patrick W. Dymond, Faith E. Fich, Naomi Nishimura, Prabhakar Ragde, Walter L. Ruzzo: Pointers versus Arithmetic in PRAMs. J. Comput. Syst. Sci. 53(2): 218-232 (1996)

Patrick W. Dymond, Faith E. Fich, Naomi Nishimura, Prabhakar Ragde, Walter L. Ruzzo: Pointers versus Arithmetic in PRAMs. Structure in Complexity Theory Conference 1993: 239-252

Tak Wah Lam, Walter L. Ruzzo: Results on Communication Complexity Classes. J. Comput. Syst. Sci. 44(2): 324-342 (1992)

Allan Borodin, Walter L. Ruzzo, Martin Tompa: Lower Bounds on the Length of Universal Traversal Sequences. J. Comput. Syst. Sci. 45(2): 180-203 (1992)

Greg Barnes, Jonathan F. Buss, Walter L. Ruzzo, Baruch Schieber: A Sublinear Space, Polynomial Time Algorithm for Directed s-t Connectivity. Structure in Complexity Theory Conference 1992: 27-33

Greg Barnes, Walter L. Ruzzo: Deterministic Algorithms for Undirected s-t Connectivity Using Polynomial Time and Sublinear Space (Extended Abstract). STOC 1991: 43-53

Paul Beame, Allan Borodin, Prabhakar Raghavan, Walter L. Ruzzo, Martin Tompa: Time-Space Tradeoffs for Undirected Graph Traversal. FOCS 1990: 429-438

Richard J. Anderson, Paul Beame, Walter L. Ruzzo: Low Overhead Parallel Schedules for Task Graphs. SPAA 1990: 66-75

Howard J. Karloff, Walter L. Ruzzo: The Iterated Mod Problem. Inf. Comput. 80(3): 193-204 (1989)

Allan Borodin, Stephen A. Cook, Patrick W. Dymond, Walter L. Ruzzo, Martin Tompa: Two Applications of Inductive Counting for Complementation Problems. SIAM J. Comput. 18(3): 559-578 (1989)

Allan Borodin, Stephen A. Cook, Patrick W. Dymond, Walter L. Ruzzo, Martin Tompa: Erratum: Two Applications of Inductive Counting for Complementation Problems. SIAM J. Comput. 18(6): 1283 (1989)

Tak Wah Lam, Walter L. Ruzzo: Results on Communication Complexity Classes. Structure in Complexity Theory Conference 1989: 148-157

Tak Wah Lam, Walter L. Ruzzo: The Power of Parallel Pointer Manipulation. SPAA 1989: 92-102

Allan Borodin, Walter L. Ruzzo, Martin Tompa: Lower Bounds on the Length of Universal Traversal Sequences (Detailed Abstract). STOC 1989: 562-573

Ashok K. Chandra, Prabhakar Raghavan, Walter L. Ruzzo, Roman Smolensky, Prasoon Tiwari: The Electrical Resistance of a Graph Captures its Commute and Cover Times (Detailed Abstract). STOC 1989: 574-586

Allan Borodin, Stephen A. Cook, Patrick W. Dymond, Walter L. Ruzzo, Martin Tompa: Two applications of complementation via inductive counting. Structure in Complexity Theory Conference 1988: 116-125

Patrick W. Dymond, Walter L. Ruzzo: Parallel RAMs with Owned Global Memory and Deterministic Context-Free Language Recognition (Extended Abstract). ICALP 1986: 95-104

Walter L. Ruzzo, Janos Simon, Martin Tompa: Space-Bounded Hierarchies and Probabilistic Computations. J. Comput. Syst. Sci. 28(2): 216-230 (1984)

David S. Johnson, Ronald Fagin, Michael L. Fredman, David Harel, Richard M. Karp, Nancy A. Lynch, Christos H. Papadimitriou, Ronald L. Rivest, Walter L. Ruzzo, Joel I. Seiferas (Eds.): Proceedings of the 15th Annual ACM Symposium on Theory of Computing, 25-27 April, 1983, Boston, Massachusetts, USA. ACM 1983

Walter L. Ruzzo, Janos Simon, Martin Tompa: Space-Bounded Hierarchies and Probabilistic Computations. STOC 1982: 215-223

Walter L. Ruzzo: On Uniform Circuit Complexity. J. Comput. Syst. Sci. 22(3): 365-383 (1981)

Mike Paterson, Walter L. Ruzzo, Lawrence Snyder: Bounds on Minimax Edge Length for Complete Binary Trees (Extended Abstract). STOC 1981: 293-299

Walter L. Ruzzo: Tree-Size Bounded Alternation. J. Comput. Syst. Sci. 21(2): 218-235 (1980)

Susan L. Graham, Michael A. Harrison, Walter L. Ruzzo: An Improved Context-Free Recognizer. ACM Trans. Program. Lang. Syst. 2(3): 415-462 (1980)

Walter L. Ruzzo: On Uniform Circuit Complexity (Extended Abstract). FOCS 1979: 312-318

Walter L. Ruzzo: On the Complexity of General Context-Free Language Parsing and Recognition (Extended Abstract). ICALP 1979: 489-497

Walter L. Ruzzo: Tree-Size Bounded Alternation. STOC 1979: 352-359

Leonard M. Adleman, Kellogg S. Booth, Franco P. Preparata, Walter L. Ruzzo: Improved Time and Space Bounds for Boolean Matrix Multiplication. Acta Inf. 11: 61-77 (1978)

Michael A. Harrison, Walter L. Ruzzo, Jeffrey D. Ullman: Protection in Operating Systems. Commun. ACM 19(8): 461-471 (1976)

Susan L. Graham, Michael A. Harrison, Walter L. Ruzzo: On Line Context Free Language Recognition in Less than Cubic Time (Extended Abstract). STOC 1976: 112-120

Michael A. Harrison, Walter L. Ruzzo, Jeffrey D. Ullman: On Protection in Operating System. SOSP 1975: 14-24