Publication Search Results

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• Author=Keich U

1. Liachko I, Youngblood RA, Keich U, Dunham MJ. High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast, Genome Research, 23 (2013), no. 4, 698–704.

2. Ng P, Keich U. Alignment constrained sampling, Journal of computational biology, 18 (2011), no. 2, 155–168.

3. Tanaka E, Bailey T, Grant CE, Noble WS, Keich U. Improved similarity scors for comparing motifs, Bioinformatics, 27 (2011), no. 12, 1603–1609.

4. Gupta N, Bandeira N, Keich U, Pevzner PA. Target-Decoy Approach and False Discovery Rate: When Things May Go Wrong, Journal of the American Society for Mass Spectrometry, 22 (2011), 1111–1120.

5. Liachko I, Tanaka E, Cox K, Claire SC, Yang L, Seher A, Hallas L, Cha E, Kang G, Pace H, Barrow J, Inada M, Tye BK, Keich U. Novel features of ARS selection in budding yeast Lachancea kluyveri, BMC Genomics, 12 (2011), Art. 633.

6. Bhaskar A, Keich U. Confidently estimating the number of DNA replication origins, Statistical Applications in Genetics and Molecular Biology, 9 (2010), no. 1, 1–21.

7. Liachko I, Bhaskar A, Lee C, Chung SCC, Tye BK, Keich U. A Comprehensive Genome-Wide Map of Autonomously Replicating Sequences in a Naive Genome, PLoS Genetics, 6 (2010), no. 5, e1000946.

8. Nagarajan N, Keich U. Reliability and efficiency of algorithms for computing the significance of the Mann–Whitney test, Computational Statistics, 24 (2009), no. 4, 605–622.

9. Oliver HF, Orsi RH, Ponnala L, Keich U, Wang W, Sun Q, Cartinhour SW, Filiatrault MJ, Weidmann M, Boor KJ. Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs, BMC Genomics, 10 (2009), 641.

10. Ng P, Keich U. Factoring local sequence composition in motif significance analysis, Genome informatics, 21 (2008), 15–26.

11. Ng P, Keich U. GIMSAN: a Gibbs motif finder with significance analysis, Bioinformatics, 24 (2008), no. 19, 2256–2257.

12. Keich U, Gao H, Garretson JS, Bhaskar A, Liachko I, Donato J, Tye B. Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast, BMC Bioinformatics, 9 (2008), 372.

13. Nagarajan N, Keich U. FAST: Fourier transform based Algorithms for significance testing of ungapped multiple alignments, Bioinformatics, 24 (2008), no. 4, 577–578.

14. Nagaraj N, Ng P, Keich U. Refining motif finders with E-value calculations, , 3rd RECOMB Satellite Workshop on Regulatory Genomics, NA (ed.), NA, (2008), NA. MR2273480

15. Keich U, Ng P. A conservative parametric approach to motif significance analysis, Genome Informatics, 19 (2007), 61–72.

16. Zhi D, Keich U, Pevzner P, Heber S, Tang H. Checking for base-calling errors in repeats, IEEE/ACM Transactions on computational biology and bioinformatics, 4 (2007), no. 1, 54–64.

17. Nagarajan N, Ng P, Keich U. Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone, Bioinformatics, 22 (2006), no. 14, 393–401.

18. Keich U, Nagarajan N. A fast and numerically robust method for exact multinomial goodness-of-fit test, Journal of Computational and Graphical Statistics, 15 (2006), no. 4, 779–802. MR2273480

19. Nagarajan N, Jones N, Keich U. Computing the p-valueof the information content from an alignment of multiple sequence, Bioinformatics, 21 (2005), no. Suppl. 1, i311 – i318.

20. Buhler J, Keich U, Sun Y. Designing seeds for similarity search in genomic DNA, Journal of computer and system sciences, 70 (2005), no. 3, 342–363. MR2129866

21. Keich U. sFFT: a faster accurate computation of the p-value of the entropy score, Journal of computational Biology, 12 (2005), no. 4, 416–430.

22. Keich U, Li M, Ma B, Tromp J. On spaced seeds for similarity search, Discrete applied mathematics, 138 (2004), no. 3, 253–263. MR2049648

23. Keich U, Nagaraj N. A faster reliable algorithm to estimate the p-value of the multinomial llr statistic, Proceeding of the 4th International Workshop on Algorithms in Bioinformatics, WABI 2004, NA (ed.), NA, NA, (2004), NA.

24. Keich U. Stationary tangent - the discrete and non-smooth cases, Journal of time series analysis, 24 (2003), no. 2, 173–192. MR1965814

25. Buhler J, Keich U, Sun Y. Designing Seeds for Similarity Search in Genomic DNA, Proceedings of the Seventh Annual International Conference on Research in Computational Molecular Biology, RECOMB 2003, (2003),

26. Eskin E, Keich U, Gelfand MS, Pevzner P. Genome-Wide Analysis of Bacterial Promoter Regions, Proceedings of the Pacific Symposium on Biocomputing 2003, PSB 2003, NA (ed.), NA, (2003), NA.

27. Keich U, Pevzner PA. Subtle motifs: defining the limits of motif finding algorithms, Bioinformatics, 18 (2002), no. 10, 1382–1390.

28. Keich U, Pevzner PA. Finding motifs in the twilight zone, Bioinformatics, 18 (2002), no. 10, 1374–1381.

29. Keich U, Pevzner P. Finding motifs in the twilight zone, Proceedings of the Sixth Annual International Conference on Research in Computational Molecular Biology, RECOMB 2002, (2002),