Walter L. Ruzzo

发表

Finding Non-coding RNAs Through Genome-Scale Clustering

Huei-Hun Tseng, Zasha Weinberg, Jeremy Gore, 2008, APBC.

Pointers versus Arithmetic in PRAMs

Faith Ellen, Naomi Nishimura, Prabhakar Ragde, 1996, J. Comput. Syst. Sci..

Discriminative motif analysis of high-throughput dataset

Robert Gentleman, Walter L. Ruzzo, Zizhen Yao, 2014, Bioinform..

Lower bounds on the length of universal traversal sequences

Allan Borodin, Walter L. Ruzzo, Martin Tompa, 1989, STOC '89.

Hardware Acceleration of Short Read Mapping

Carl Ebeling, Walter L. Ruzzo, Scott Hauck, 2012, 2012 IEEE 20th International Symposium on Field-Programmable Custom Computing Machines.

Two Applications of Inductive Counting for Complementation Problems

Allan Borodin, Stephen A. Cook, Walter L. Ruzzo, 1989, SIAM J. Comput..

Pointers versus arithmetic in PRAMs

Faith Ellen, Naomi Nishimura, Prabhakar Ragde, 1993, [1993] Proceedings of the Eigth Annual Structure in Complexity Theory Conference.

Parallel RAMs with Owned Global Memory and Deterministic Context-Free Language Recognition (Extended Abstract)

Walter L. Ruzzo, Patrick W. Dymond, W. L. Ruzzo, 1986, ICALP.

Protection in operating systems

Jeffrey D. Ullman, Walter L. Ruzzo, Michael A. Harrison, 1976, CACM.

On the Complexity of General Context-Free Language Parsing and Recognition (Extended Abstract)

Walter L. Ruzzo, W. L. Ruzzo, 1979, ICALP.

On Uniform Circuit Complexity

Walter L. Ruzzo, 1981, J. Comput. Syst. Sci..

RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods

Jan Gorodkin, Walter L. Ruzzo, W. L. Ruzzo, 2014, Methods in Molecular Biology.

Two applications of complementation via inductive counting

Allan Borodin, Stephen A. Cook, Walter L. Ruzzo, 1988, [1988] Proceedings. Structure in Complexity Theory Third Annual Conference.

Searching for Non-coding RNA

Walter L. Ruzzo, W. L. Ruzzo, 2005, BSB.

Isolator: accurate and stable analysis of isoform-level expression in RNA-Seq experiments

Walter L. Ruzzo, Xinxia Peng, Daniel C. Jones, 2016, bioRxiv.

A Linear Time Algorithm for Finding All Maximal Scoring Subsequences

Walter L. Ruzzo, Martin Tompa, W. L. Ruzzo, 1999, ISMB.

Lower Bounds on the Length of Universal Traversal Sequences

Allan Borodin, Walter L. Ruzzo, Martin Tompa, 1992, J. Comput. Syst. Sci..

How accurately is ncRNA aligned within whole-genome multiple alignments?

Walter L. Ruzzo, Martin Tompa, Adrienne X. Wang, 2007, BMC Bioinformatics.

A Compendium of Problems Complete for P (Preliminary)

Walter L. Ruzzo, Raymond Greenlaw, James Hoover, 1991 .

A Time-Space Tradeoff for Undirected Graph Traversal by Walking Automata

Allan Borodin, Prabhakar Raghavan, Walter L. Ruzzo, 1999, SIAM J. Comput..

A Sublinear Space, Polynomial Time Algorithm for Directed s-t Connectivity

Baruch Schieber, Walter L. Ruzzo, Jonathan F. Buss, 1998, SIAM J. Comput..

Faster genome annotation of non-coding RNA families without loss of accuracy

Zasha Weinberg, Walter L. Ruzzo, W. L. Ruzzo, 2004, RECOMB.

A sublinear space, polynomial time algorithm for directed s-t connectivity

Baruch Schieber, Walter L. Ruzzo, Jonathan F. Buss, 1992, [1992] Proceedings of the Seventh Annual Structure in Complexity Theory Conference.

Results on communication complexity classes

Tak Wah Lam, Walter L. Ruzzo, 1989, [1989] Proceedings. Structure in Complexity Theory Fourth Annual Conference.

On protection in operating systems

Jeffrey D. Ullman, Walter L. Ruzzo, Michael A. Harrison, 1975, SOSP.

Improved time and space bounds for Boolean matrix multiplication

Franco P. Preparata, Leonard M. Adleman, Walter L. Ruzzo, 2004, Acta Informatica.

Tree-size bounded alternation(Extended Abstract)

Walter L. Ruzzo, 1979, STOC '79.

Time-space tradeoffs for undirected graph traversal

Allan Borodin, Prabhakar Raghavan, Walter L. Ruzzo, 1990, Proceedings [1990] 31st Annual Symposium on Foundations of Computer Science.

Proceedings of the fifteenth annual ACM symposium on Theory of computing

Nancy A. Lynch, Ronald Fagin, Richard M. Karp, 1983, STOC 1983.

The Iterated Mod Problem

Howard J. Karloff, Walter L. Ruzzo, W. L. Ruzzo, 1989, Inf. Comput..

Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies

Walter L. Ruzzo, Elfar Torarinsson, Parvez Anandam, 2009, Bioinform..

A Regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data

Walter L. Ruzzo, Zizhen Yao, W. L. Ruzzo, 2006, BMC Bioinformatics.

Space-bounded hierarchies and probabilistic computations

Janos Simon, Walter L. Ruzzo, Martin Tompa, 1982, STOC '82.

Deterministic algorithms for undirected s-t connectivity using polynomial time and sublinear space.

Walter L. Ruzzo, Greg Barnes, 1991, STOC '91.

Pre-mRNA Secondary Structure Prediction Aids Splice Site Prediction

Donald J. Patterson, Walter L. Ruzzo, Ken Yasuhara, 2001, Pacific Symposium on Biocomputing.

Validating clustering for gene expression data

Ka Yee Yeung, Walter L. Ruzzo, David R. Haynor, 2001, Bioinform..

Parallel RAMs with owned global memory and deterministic context-free language recognition

Walter L. Ruzzo, Patrick W. Dymond, W. L. Ruzzo, 2000, JACM.

Algorithms for a Simple Point Placement Problem

Walter L. Ruzzo, Joshua Redstone, W. L. Ruzzo, 2000, CIAC.

Sequence-based heuristics for faster annotation of non-coding RNA families

Zasha Weinberg, Walter L. Ruzzo, W. L. Ruzzo, 2006, Bioinform..

On uniform circuit complexity

Walter L. Ruzzo, W. L. Ruzzo, 1979, 20th Annual Symposium on Foundations of Computer Science (sfcs 1979).

Time-Space Tradeoffs for Undirected Graph Traversal by Graph Automata

Allan Borodin, Prabhakar Raghavan, Walter L. Ruzzo, 1996, Inf. Comput..

Results on Communication Complexity Classes

Tak Wah Lam, Walter L. Ruzzo, 1992, J. Comput. Syst. Sci..

A new approach to bias correction in RNA-Seq

Walter L. Ruzzo, Xinxia Peng, Michael G. Katze, 2012, Bioinform..

Cluster analysis of gene expression data

Ka Yee Yeung, Walter L. Ruzzo, 2001 .

On line context free language recognition in less than cubic time(Extended Abstract)

Walter L. Ruzzo, Michael A. Harrison, Susan L. Graham, 1976, STOC '76.

A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes

Zasha Weinberg, Ronald R. Breaker, Walter L. Ruzzo, 2007, PLoS Comput. Biol..

The power of parallel pointer manipulation

Tak Wah Lam, Walter L. Ruzzo, W. L. Ruzzo, 1989, SPAA '89.

Erratum: Two Applications of Inductive Counting for Complementation Problems

Allan Borodin, Stephen A. Cook, Walter L. Ruzzo, 1989, SIAM J. Comput..

FPGA Acceleration of Short Read Alignment pdf

Walter L. Ruzzo, Scott Hauck, Nathaniel McVicar, 2018, ArXiv.

Improved Gene Selection for Classification of Microarrays

Walter L. Ruzzo, Rimli Sengupta, W. L. Ruzzo, 2002, Pacific Symposium on Biocomputing.

Space-Bounded Hierarchies and Probabilistic Computations

Janos Simon, Walter L. Ruzzo, Martin Tompa, 1984, J. Comput. Syst. Sci..

Accurate annotation of non-coding RNAs in practical time

Walter L. Ruzzo, Zasha Weinberg, Z. Weinberg, 2005 .

On Uniform Circuit Complexity (Extended Abstract)

Walter L. Ruzzo, 1979, FOCS 1979.

The electrical resistance of a graph captures its commute and cover times

Prabhakar Raghavan, Walter L. Ruzzo, Roman Smolensky, 1989, STOC '89.

Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy

Zasha Weinberg, Walter L. Ruzzo, W. L. Ruzzo, 2004, ISMB/ECCB.

Compression of next-generation sequencing reads aided by highly efficient de novo assembly

Walter L. Ruzzo, Xinxia Peng, Michael G. Katze, 2012, Nucleic acids research.

An Improved Context-Free Recognizer

Walter L. Ruzzo, Michael A. Harrison, Susan L. Graham, 1980, ACM Trans. Program. Lang. Syst..

Accelerating ncRNA homology search with FPGAs

Walter L. Ruzzo, Scott Hauck, Nathaniel McVicar, 2013, FPGA '13.

Low overhead parallel schedules for task graphs

Richard J. Anderson, Walter L. Ruzzo, Paul Beame, 1990, SPAA '90.

Limits to Parallel Computation: P-Completeness Theory

H. James Hoover, Walter L. Ruzzo, Raymond Greenlaw, 1995 .

Undirecteds-t connectivity in polynomial time and sublinear space

Walter L. Ruzzo, Greg Barnes, W. L. Ruzzo, 2005, computational complexity.

Limits to parallel computation

H. James Hoover, Walter L. Ruzzo, Raymond Greenlaw, 1995 .

Integration of 198 ChIP-seq Datasets Reveals Human cis-Regulatory Regions

Walter L. Ruzzo, Hamid Bolouri, W. L. Ruzzo, 2012, J. Comput. Biol..

Tree-Size Bounded Alternation

Walter L. Ruzzo, W. L. Ruzzo, 1980, J. Comput. Syst. Sci..

Bounds on minimax edge length for complete binary trees

Lawrence Snyder, Mike Paterson, Walter L. Ruzzo, 1981, STOC '81.

Low Overhead Parallel Schedules for Task. Graphs* (Extended Abstract)

Walter L. Ruzzo, Richard Anderson, Paul Beame, 1990 .

Polee: RNA-Seq analysis using approximate likelihood

Walter L. Ruzzo, W. L. Ruzzo, Daniel C. Jones, 2020, bioRxiv.

Principal component analysis for clustering gene expression data

Ka Yee Yeung, Walter L. Ruzzo, W. L. Ruzzo, 2001, Bioinform..

Model-based clustering and data transformations for gene expression data

Adrian E. Raftery, Ka Yee Yeung, Walter L. Ruzzo, 2001, Bioinform..

The electrical resistance of a graph captures its commute and cover times

Prabhakar Raghavan, Walter L. Ruzzo, Roman Smolensky, 2005, computational complexity.

CMfinder - a covariance model based RNA motif finding algorithm

Zasha Weinberg, Walter L. Ruzzo, Zizhen Yao, 2006, Bioinform..

Principal component analysis (PCA) for clustering gene expression data

Ka Yee Yeung, Walter L. Ruzzo, 2001 .

Algorithms for Ordering DNA Probes on Chromosomes

Walter L. Ruzzo, Joshua Redstone, 1998 .

Details of the Adjusted Rand index and Clustering algorithms Supplement to the paper “ An empirical study on Principal Component Analysis for clustering gene expression data ” ( to appear in Bioinformatics )

Ka Yee Yeung, Walter L. Ruzzo, W. L. Ruzzo, 2001 .

A Compendium of Problems Complete for P

H. James Hoover, Walter L. Ruzzo, Raymond Greenlaw, 1991 .

An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription

Robert Gentleman, Deepayan Sarkar, Walter L. Ruzzo, 2011, Nucleic acids research.

Bayesian Classification of DNA Array Expression Data

Walter L. Ruzzo, W. L. Ruzzo, L. Hood, 2000 .