On Protection in Operating System. - Michael A. Harrison; Walter L. Ruzzo; Jeffrey D. Ullman (SOSP, 1975)

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

Protection in Operating Systems. - Michael A. Harrison; Walter L. Ruzzo; Jeffrey D. Ullman (Commun. ACM, 1976)

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

On Uniform Circuit Complexity (Extended Abstract) - Walter L. Ruzzo (FOCS, 1979)

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

Tree-Size Bounded Alternation. - Walter L. Ruzzo (J. Comput. Syst. Sci., 1980)

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

Bounds on Minimax Edge Length for Complete Binary Trees (Extended Abstract) - Mike Paterson; Walter L. Ruzzo; Lawrence Snyder 001 (STOC, 1981)

On Uniform Circuit Complexity. - Walter L. Ruzzo (J. Comput. Syst. Sci., 1981)

Space-Bounded Hierarchies and Probabilistic Computations. - Walter L. Ruzzo; Janos Simon; Martin Tompa (J. Comput. Syst. Sci., 1984)

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

Two applications of complementation via inductive counting. - Allan Borodin; Stephen A. Cook; Patrick W. Dymond; Walter L. Ruzzo; Martin Tompa (SCT, 1988)

The Power of Parallel Pointer Manipulation. - Tak Wah Lam; Walter L. Ruzzo (SPAA, 1989)

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

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

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

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

The Iterated Mod Problem - Howard J. Karloff; Walter L. Ruzzo (Inf. Comput., 1989)

Time-Space Tradeoffs for Undirected Graph Traversal - Paul Beame; Allan Borodin; Prabhakar Raghavan; Walter L. Ruzzo; Martin Tompa (FOCS, 1990)

Low Overhead Parallel Schedules for Task Graphs. - Richard J. Anderson 001; Paul Beame; Walter L. Ruzzo (SPAA, 1990)

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

A Sublinear Space, Polynomial Time Algorithm for Directed s-t Connectivity - Greg Barnes; Jonathan F. Buss; Walter L. Ruzzo; Baruch Schieber (SCT, 1992)

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

Results on Communication Complexity Classes. - Tak Wah Lam; Walter L. Ruzzo (J. Comput. Syst. Sci., 1992)

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

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

Undirected s-t Connectivity in Polynomial Time and Sublinear Space. - Greg Barnes; Walter L. Ruzzo (Comput. Complex., 1997)

The Electrical Resistance of a Graph Captures its Commute and Cover Times. - Ashok K. Chandra; Prabhakar Raghavan; Walter L. Ruzzo; Roman Smolensky; Prasoon Tiwari (Comput. Complex., 1997)

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

A Linear Time Algorithm for Finding All Maximal Scoring Subsequences. - Walter L. Ruzzo; Martin Tompa (ISMB, 1999)

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

Algorithms for a Simple Point Placement Problem. - Joshua Redstone; Walter L. Ruzzo (CIAC, 2000)

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

Model-based clustering and data transformations for gene expression data. - Ka Yee Yeung; Chris Fraley; Alejandro Murua; Adrian E. Raftery; Walter L. Ruzzo (Bioinform., 2001)

Validating clustering for gene expression data. - Ka Yee Yeung; David R. Haynor; Walter L. Ruzzo (Bioinform., 2001)

Principal component analysis for clustering gene expression data. - Ka Yee Yeung; Walter L. Ruzzo (Bioinform., 2001)

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

Improved Gene Selection for Classification of Microarrays. - Jochen Jaeger; Rimli Sengupta; Walter L. Ruzzo (Pacific Symposium on Biocomputing, 2003)

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

Faster genome annotation of non-coding RNA families without loss of accuracy. - Zasha Weinberg; Walter L. Ruzzo (RECOMB, 2004)

Searching for Non-coding RNA. - Walter L. Ruzzo (BSB, 2005)

Sequence-based heuristics for faster annotation of non-coding RNA families. - Zasha Weinberg; Walter L. Ruzzo (Bioinform., 2006)

CMfinder - a covariance model based RNA motif finding algorithm. - Zizhen Yao; Zasha Weinberg; Walter L. Ruzzo (Bioinform., 2006)

A Regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data. - Zizhen Yao; Walter L. Ruzzo (BMC Bioinform., 2006)

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

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

Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies. - Parvez Anandam; Elfar Torarinsson; Walter L. Ruzzo (Bioinform., 2009)

Finding Non-Coding RNAs through genome-Scale Clustering. - Huei-Hun Elizabeth Tseng; Zasha Weinberg; Jeremy Gore; Ronald R. Breaker; Walter L. Ruzzo (J. Bioinform. Comput. Biol., 2009)

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

A new approach to bias correction in RNA-Seq. - Daniel C. Jones; Walter L. Ruzzo; Xinxia Peng; Michael G. Katze (Bioinform., 2012)

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

Integration of 198 ChIP-seq Datasets Reveals Human cis-Regulatory Regions. - Hamid Bolouri; Walter L. Ruzzo (J. Comput. Biol., 2012)

Accelerating ncRNA homology search with FPGAs. - Nathaniel McVicar; Walter L. Ruzzo; Scott Hauck (FPGA, 2013)

Discriminative motif analysis of high-throughput dataset. - Zizhen Yao; Kyle L. MacQuarrie; Abraham P. Fong; Stephen J. Tapscott; Walter L. Ruzzo; Robert Gentleman (Bioinform., 2014)

FPGA Acceleration of Short Read Alignment. - Nathaniel McVicar; Akina Hoshino; Anna La Torre; Thomas A. Reh; Walter L. Ruzzo; Scott Hauck (CoRR, 2018)