Webb Miller

Giltae Song, Chih-Hao Hsu, Cathy Riemer, Webb Miller: Evaluation of methods for detecting conversion events in gene clusters. BMC Bioinformatics 12(S-1): S45 (2011)

Aakrosh Ratan, Yu Zhang, Vanessa M. Hayes, Stephan C. Schuster, Webb Miller: Calling SNPs without a reference sequence. BMC Bioinformatics 11: 130 (2010)

Giltae Song, Louxin Zhang, Tomás Vinar, Webb Miller: CAGE: Combinatorial Analysis of Gene-Cluster Evolution. Journal of Computational Biology 17(9): 1227-1242 (2010)

Chih-Hao Hsu, Yu Zhang, Ross C. Hardison, Eric D. Green, Webb Miller: An Effective Method for Detecting Gene Conversion Events in Whole Genomes. Journal of Computational Biology 17(9): 1281-1297 (2010)

Bernard M. E. Moret, Webb Miller, Pavel A. Pevzner, David Sankoff: Session Introduction. Pacific Symposium on Biocomputing 2010: 1-2

Webb Miller, Stephen J. Wright, Yu Zhang, Stephan C. Schuster, Vanessa M. Hayes: Optimization Methods for Selecting Founder Populations for Captive Breeding of Endangered Species. Pacific Symposium on Biocomputing 2010: 43-53

Charles Addo-Quaye, Webb Miller, Michael J. Axtell: CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics 25(1): 130-131 (2009)

Yu Zhang, Giltae Song, Tomás Vinar, Eric D. Green, Adam C. Siepel, Webb Miller: Evolutionary History Reconstruction for Mammalian Complex Gene Clusters. Journal of Computational Biology 16(8): 1051-1070 (2009)

Bernard M. E. Moret, Webb Miller, Pavel A. Pevzner, David Sankoff: Session Introduction. Pacific Symposium on Biocomputing 2009: 111-113

Yu Zhang, Giltae Song, Chih-Hao Hsu, Webb Miller: Simultaneous History Reconstruction for Complex Gene Clusters in Multiple Species. Pacific Symposium on Biocomputing 2009: 162-173

Minmei Hou, Cathy Riemer, Piotr Berman, Ross C. Hardison, Webb Miller: Aligning Two Genomic Sequences That Contain Duplications. RECOMB-CG 2009: 98-110

Giltae Song, Louxin Zhang, Tomás Vinar, Webb Miller: Inferring the Recent Duplication History of a Gene Cluster. RECOMB-CG 2009: 111-125

Chih-Hao Hsu, Yu Zhang, Ross C. Hardison, Webb Miller: Whole-Genome Analysis of Gene Conversion Events. RECOMB-CG 2009: 181-192

Jian Ma, Aakrosh Ratan, Brian J. Raney, Bernard B. Suh, Louxin Zhang, Webb Miller, David Haussler: DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications. Journal of Computational Biology 15(8): 1007-1027 (2008)

Donna Karolchik, Robert M. Kuhn, Robert Baertsch, Galt P. Barber, Hiram Clawson, Mark Diekhans, Belinda Giardine, Rachel A. Harte, Angela S. Hinrichs, Fan Hsu, Kord M. Kober, Webb Miller, Jakob Skou Pedersen, Andy Pohl, Brian J. Raney, Brooke L. Rhead, Kate R. Rosenbloom, Kayla E. Smith, Mario Stanke, Archana Thakkapallayil, Heather Trumbower, Ting Wang, Ann S. Zweig, David Haussler, W. James Kent: The UCSC Genome Browser Database: 2008 update. Nucleic Acids Research 36(Database-Issue): 773-779 (2008)

C. Thach Nguyen, Jian Shen, Minmei Hou, Li Sheng, Webb Miller, Louxin Zhang: Approximating the Spanning Star Forest Problem and Its Application to Genomic Sequence Alignment. SIAM J. Comput. 38(3): 946-962 (2008)

Yu Zhang, Giltae Song, Tomás Vinar, Eric D. Green, Adam C. Siepel, Webb Miller: Reconstructing the Evolutionary History of Complex Human Gene Clusters. RECOMB 2008: 29-49

Jian Ma, Aakrosh Ratan, Louxin Zhang, Webb Miller, David Haussler: A Heuristic Algorithm for Reconstructing Ancestral Gene Orders with Duplications. RECOMB-CG 2007: 122-135

C. Thach Nguyen, Jian Shen, Minmei Hou, Li Sheng, Webb Miller, Louxin Zhang: Approximating the spanning star forest problem and its applications to genomic sequence alignment. SODA 2007: 645-654

Jakob Skou Pedersen, Gill Bejerano, Adam C. Siepel, Kate R. Rosenbloom, Kerstin Lindblad-Toh, Eric S. Lander, Jim Kent, Webb Miller, David Haussler: Identification and Classification of Conserved RNA Secondary Structures in the Human Genome. PLoS Computational Biology 2(4) (2006)

Minmei Hou, Piotr Berman, Louxin Zhang, Webb Miller: Controlling Size When Aligning Multiple Genomic Sequences with Duplications. WABI 2006: 138-149

Laura Elnitski, Belinda Giardine, Prachi Shah, Yi Zhang, Cathy Riemer, Matthew Weirauch, Richard Burhans, Webb Miller, Ross C. Hardison: Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results. Nucleic Acids Research 33(Database-Issue): 466-470 (2005)

Ji-Ping Z. Wang, Bruce G. Lindsay, James Leebens-Mack, Liying Cui, P. Kerr Wall, Webb C. Miller, Claude W. dePamphilis: EST clustering error evaluation and correction. Bioinformatics 20(17): 2973-2984 (2004)

George P. Patrinos, Belinda Giardine, Cathy Riemer, Webb Miller, David H. K. Chui, Nicholas P. Anagnou, Henri Wajcman, Ross C. Hardison: Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies. Nucleic Acids Research 32(Database-Issue): 537-541 (2004)

Vamsi Veeramachaneni, Piotr Berman, Webb Miller: Aligning two fragmented sequences. Discrete Applied Mathematics 127(1): 119-143 (2003)

Jia Li, Webb Miller: Significance of Interspecies Matches when Evolutionary Rate Varies. Journal of Computational Biology 10(3/4): 537-554 (2003)

Scott Schwartz, Laura Elnitski, Mei Li, Matthew Weirauch, Cathy Riemer, Arian Smit, Eric D. Green, Ross C. Hardison, Webb Miller: MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Research 31(13): 3518-3524 (2003)

Liliana Florea, Michael McClelland, Cathy Riemer, Scott Schwartz, Webb Miller: EnteriX 2003: visualization tools for genome alignments of Enterobacteriaceae. Nucleic Acids Research 31(13): 3527-3532 (2003)

Vamsi Veeramachaneni, Piotr Berman, Webb Miller: Aligning Two Fragmented Sequences. IPDPS 2002

Jia Li, Webb Miller: Significance Of inter-species matches when evolutionary rate varies. RECOMB 2002: 216-224

Webb Miller: Comparison of genomic DNA sequences: solved and unsolved problems. Bioinformatics 17(5): 391-397 (2001)

Thomas Wiehe, Roderic Guigó, Webb Miller: Genome Sequence Comparisons: Hurdles in the Fast Lane to Functional Genomics. Briefings in Bioinformatics 1(4): 381-388 (2000)

Zheng Zhang, Scott Schwartz, Lukas Wagner, Webb Miller: A Greedy Algorithm for Aligning DNA Sequences. Journal of Computational Biology 7(1-2): 203-214 (2000)

Piotr Berman, Zheng Zhang, Yuri I. Wolf, Eugene V. Koonin, Webb Miller: Winnowing Sequences from a Database Search. Journal of Computational Biology 7(1-2): 293-302 (2000)

Zheng Zhang, Piotr Berman, Thomas Wiehe, Webb Miller: Post-processing long pairwise alignments. Bioinformatics 15(12): 1012-1019 (1999)

Piotr Berman, Zheng Zhang, Yuri I. Wolf, Eugene V. Koonin, Webb Miller: Winnowing sequences from a database search. RECOMB 1999: 50-58

Zheng Zhang, Piotr Berman, Webb Miller: Alignments without Low-Scoring Regions. Journal of Computational Biology 5(2): 197-210 (1998)

Zheng Zhang, Piotr Berman, Webb Miller: Alignments without low-scoring regions. RECOMB 1998: 294-301

Kun-Mao Chao, Jinghui Zhang, James Ostell, Webb Miller: A tool for aligning very similar DNA sequences. Computer Applications in the Biosciences 13(1): 75-80 (1997)

Zheng Zhang, William R. Pearson, Webb Miller: Aligning a DNA Sequence with a Protein Sequence. Journal of Computational Biology 4(3): 339-349 (1997)

Gene Myers, Sanford Selznick, Zheng Zhang, Webb Miller: Progressive multiple alignment with constraints. RECOMB 1997: 220-225

Zheng Zhang, William R. Pearson, Webb Miller: Aligning a DNA sequence with a protein sequence. RECOMB 1997: 337-343

Nikola Stojanovic, Piotr Berman, Deborah Gumucio, Ross C. Hardison, Webb Miller: A Linear-Time Algorithm for the 1-Mismatch Problem. WADS 1997: 126-135

Z. Zhang, B. He, Webb C. Miller: Local Multiple Alignment Via Subgraph Enumeration. Discrete Applied Mathematics 71(1-3): 337-365 (1996)

Gene Myers, Sanford Selznick, Zheng Zhang, Webb Miller: Progressive Multiple Alignment with Constraints. Journal of Computational Biology 3(4): 563-572 (1996)

Kun-Mao Chao, Webb Miller: Linear-Space Algorithms that Build Local Alignments from Fragments. Algorithmica 13(1/2): 106-134 (1995)

Kun-Mao Chao, Jinghui Zhang, James Ostell, Webb Miller: A local alignment tool for very long DNA sequences. Computer Applications in the Biosciences 11(2): 147-153 (1995)

Webb Miller, Ahmed Elsherbini, Jamie Peck, Cathy Riemer, Scott Schwartz, Nikola Stojanovic, Ross C. Hardison: A database for globin gene expression data. HICSS (5) 1995: 62-71

Gene Myers, Webb Miller: Chaining Multiple-Alignment Fragments in Sub-Quadratic Time. SODA 1995: 38-47

Webb Miller, Mark Boguski: A note about computing all local alignments. Computer Applications in the Biosciences 10(4): 455-456 (1994)

Webb Miller, Mark Boguski, Balaji Raghavachari, Zheng Zhang, Ross C. Hardison: Constructing Aligned Sequence Blocks. Journal of Computational Biology 1(1): 51-64 (1994)

Zheng Zhang, Balaji Raghavachari, Ross C. Hardison, Webb Miller: Chaining Multiple-Alignment Blocks. Journal of Computational Biology 1(3): 217-226 (1994)

Kun-Mao Chao, Ross C. Hardison, Webb Miller: Recent Developments in Linear-Space Alignment Methods: A Survey. Journal of Computational Biology 1(4): 271-291 (1994)

Xiaoqiu Huang, Pavel A. Pevzner, Webb Miller: Parametric Recomuting in Alignment Graphs. CPM 1994: 87-101

Webb Miller: Building multiple alignments from pairwise alignments. Computer Applications in the Biosciences 9(2): 169-176 (1993)

Kun-Mao Chao, Ross C. Hardison, Webb Miller: Locating well-conserved regions within a pairwise alignment. Computer Applications in the Biosciences 9(4): 387-396 (1993)

Xiaoqiu Huang, Webb Miller, Scott Schwartz, Ross C. Hardison: Parallelization of a local similarity algorithm. Computer Applications in the Biosciences 8(2): 155-165 (1992)

Kun-Mao Chao, William R. Pearson, Webb Miller: Aligning two sequences within a specified diagonal band. Computer Applications in the Biosciences 8(5): 481-487 (1992)

Webb Miller, J. Barr, Kenneth E. Rudd: Improved algorithms for searching restriction maps. Computer Applications in the Biosciences 7(4): 447-456 (1991)

Webb Miller, James Ostell, Kenneth E. Rudd: An algorithm for searching restriction maps. Computer Applications in the Biosciences 6(3): 247-252 (1990)

Xiaoqiu Huang, Ross C. Hardison, Webb Miller: A space-efficient algorithm for local similarities. Computer Applications in the Biosciences 6(4): 373-381 (1990)

Sun Wu, Udi Manber, Gene Myers, Webb Miller: An O(NP) Sequence Comparison Algorithm. Inf. Process. Lett. 35(6): 317-323 (1990)

Eugene W. Myers, Webb Miller: Row Replacement Algorithms for Screen Editors. ACM Trans. Program. Lang. Syst. 11(1): 33-56 (1989)

Eugene W. Myers, Webb Miller: Optimal alignments in linear space. Computer Applications in the Biosciences 4(1): 11-17 (1988)

Webb Miller, Eugene W. Myers: A Simple Row-replacement Method. Softw., Pract. Exper. 18(7): 597-611 (1988)

Webb Miller, Eugene W. Myers: Side-effects in Automatic File Updating. Softw., Pract. Exper. 16(9): 809-820 (1986)

Webb Miller, Eugene W. Myers: A File Comparison Program. Softw., Pract. Exper. 15(11): 1025-1040 (1985)

Donald B. Johnson, Webb Miller, Brian Minnihan, Celia Wrathall: Reducibility Among Floating-Point Graphs. J. ACM 26(4): 739-760 (1979)

Webb Miller, David L. Spooner: Software for Roundoff Analysis II. ACM Trans. Math. Softw. 4(4): 369-387 (1978)

Webb Miller, David L. Spooner: Algorithm 532: Software for Roundoff Analysis [Z]. ACM Trans. Math. Softw. 4(4): 388-390 (1978)

Webb Miller: Graph Transformations for Roundoff Analysis. SIAM J. Comput. 5(2): 204-216 (1976)

Webb Miller, David L. Spooner: Automatic Generation of Floating-Point Test Data. IEEE Trans. Software Eng. 2(3): 223-226 (1976)

Webb Miller: Computer Search for Numerical Instability. J. ACM 22(4): 512-521 (1975)

Webb Miller: Computational Complexity and Numerical Stability. SIAM J. Comput. 4(2): 97-107 (1975)

Webb Miller: Software for Roundoff Analysis. ACM Trans. Math. Softw. 1(2): 108-128 (1975)

Webb Miller: The Error in Interval Arithmetic. Interval Mathematics 1975: 246-250

Webb Miller: Computational Complexity and Numerical Stability. STOC 1974: 317-322

Webb Miller: Toward Abstract Numerical Analysis. J. ACM 20(3): 399-408 (1973)

Webb Miller: Toward Mechanical Verification of Properties of Roundoff Error Propagation. STOC 1973: 50-58

Webb Miller: Recursive Function Theory and Numerical Analysis. J. Comput. Syst. Sci. 4(5): 465-472 (1970)