**School of Mathematics and Statistics F07University of
Sydney NSW 2006Australia**

**+61 2 9351 2307 **uri@maths.usyd.edu.au

STAT 2911 - Probability and Statistical Models (Advanced): Semester 1, 2017 (past: 2009-2015)

STAT 3914 - Applied Statistics (Advanced): Semester 2, 2015 (past: 2010-2011, 2013-2014)

STAT 3014 - Applied Statistics (Advanced): Semester 2, 2015 (past: 2013-2014)

MATH 1907 - Mathematics (Special Studies Program) B: (past: 2010)

MSH8 - Statistical Methods in Bioinformatics: Semester 2, 2017 (past: 2009-2015)

MSH2 - Probability: Semester 1, 2017

**R code of aFFT-C and sisFFT**
– aFFT-C accurately convolves two non-negative vectors (see *Accurate pairwise convolutions of non-negative vectors via FFT* below), and sisFFT accurately computes tail probabilities (p-values) of a sum of iid lattice valued random variables (submitted).

**Python code of aFFT-C and sisFFT**
– Python version of above R code

**ALICO**
– alignment constrained sampling

**GIMSAN**
– a novel tool for de novo motif finding that includes a reliable
significance analysis

**SADMAMA (new version 17/2/2010)**
– computational tool for motif scanning and for detection of significant variation in
binding affinity across two sets of sequences

**The
FAST package** – Fourier transform based Algorithms for
Significance Testing of ungapped multiple alignments

**csFFT/sFFT**
– computing the p-value of the information content (entropy score)
of a sequence motif

**BagFFT**
– computing the exact p-value of the llr statistic for multinomial
goodness-of-fit test

**Ph.D.** in Mathematics, Courant Institute, New York
University

Thesis title: *Stationary Approximations to
Non-Stationary Stochastic Processes.*

Advisor: Prof. H . P.
McKean

**M.Sc.** in Mathematics, Department of Mathematics, Technion -
Israel Institute of Technology

Thesis title: *A Generalization
of the "Ahlswede Daykin Inequality".*

Advisor: Prof.
R. Aharoni

**B.Sc.** in Computer Science and Mathematics, Hebrew
University of Jerusalem

**2009 - present:**-
**Associate Professor in the School of Mathematics and Statistics at the University of Sydney (Senior Lecturer 2009-2015)** -

- 2003 - 2009:
- Assistant Professor at the Computer Science Department of Cornell University
- 2001 - 2003:
- Project scientist at the Department of Computer Science and Engineering of the University of California, San Diego
- 1999 - 2000:
- Assistant Professor at the Department of Mathematics of the University of California, Riverside
- 1996 - 1999:
- Von Karman Instructor at the Applied Mathematics Department of the California Institute of Technology
- 1991 - 1996:
- Research and Teaching assistant at the Courant Institute of New York University

Keich U. and Noble WS. ** Controlling the FDR in imperfect matches to an incomplete database.** *Journal of the American Statistical Association*, In Press.

Noble WS. and Keich U. ** Response to "Mass spectrometrists should search for all peptides, but assess only the ones they care about".** *Nature Methods*, 29;14(7):644, 2017 (response).

Keich U. and Noble WS. ** Progressive calibration and averaging for tandem mass spectrometry statistical confidence estimation: Why settle for a single decoy?** *Lecture Notes in Computer Science (LNCS, RECOMB 2017)*, 10229: 99-116, 2017 (paper).

Wilson H. and Keich U. ** Accurate Small Tail Probabilities of Sums of iid Lattice-Valued Random Variables via FFT**. *Journal of Computational and Graphical Statistics*, 26(1): 223-229, 2017 (paper).

Wilson H. and Keich U. ** Accurate pairwise convolutions of non-negative vectors via FFT**. *Computational Statistics & Data Analysis*, 101: 300-315, 2016 (paper).

Manescu D. and Keich U. **A Symmetric Length-Aware Enrichment Test.** *Journal of Computational Biology*, 23(6):508-25, 2016 (paper).

Keich U., Kertesz-Farkas A., Noble WS. ** Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics**. *Journal of Proteome Research*, 14 (8): 3148-61, 2015 (paper).

Kertesz-Farkas A., Keich U, Noble WS. ** Tandem Mass Spectrum Identification via Cascaded Search**. *Journal of Proteome Research*, 14 (8): 3027-38, 2015 (paper).

Manescu D. and Keich U. **A symmetric length-aware enrichment test.** *Best Paper Award, RECOMB 2015*, LNBI 9029: 224–242, 2015 (preprint).

Keich U. and Noble WS. ** On the Importance of Well-Calibrated Scores for Identifying Shotgun Proteomics Spectra**. *Journal of Proteome Research*, 14(2):1147–1160, 2015 (paper).

Tanaka E., Bailey TL., Keich U. ** Improving MEME via a two-tiered significance analysis**. *Bioinformatics*, 30(14): 1965-1973, 2014
(paper).

Liachko I., Youngblood RA., Keich U., Dunham MJ. ** High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast**. *Genome Research*, 23(4):698-704, 2013 (paper) (co-corresponding author).

Liachko I., Tanaka E., Cox K., Chung 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**.

Tanaka E., Bailey T., Grant CE., Noble WS., Keich U. ** Improved similarity scores for comparing motifs**. *Bioinformatics*, 27(12):1603-9, 2011 (abstract).

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*, Vol. 22, No. 7: 1111 - 1120, 2011(paper).

Ng P,. and Keich U. **Alignment Constrained Sampling**. *Journal of Computational Biology*, Vol. 18: No. 2, 2011 (paper).

Bhaskar A,. and Keich U. **Confidently Estimating the Number of DNA Replication Origins**. *Statistical Applications in Genetics and Molecular Biology*, Vol. 9: Iss. 1, Article 28, 2010 (paper).

Liachko I., Bhaskar A., Li C., Chung S.C.C., Tye B.K., and Keich
U. **A Comprehensive Genome-Wide Map of Autonomously Replicating
Sequences in a Naive Genome.** *PLoS Genetics*, May 2010 Issue. (paper).

Oliver H.F., Orsi R.H., Ponnala L., Keich U., Wang W., Sun Q.,
Cartinhour S.W., Filiatrault M.J., Wiedmann M., and Boor K.J. **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*, 10:641, 2009. (paper).

Nagarajan N. and Keich U. **Reliability and efficiency of algorithms
for computing the significance of the Mann-Whitney test.**
*Computational Statistics*, 24(4):605-622, 2009. (paper).

Ng P. and Keich U. **Factoring local sequence composition in motif significance analysis.** *Genome Informatics*, 21:15-26, 2008. (preprint).

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*,
9:372, 2008. (paper).

Ng P. and Keich U. **GIMSAN: a Gibbs motif finder with significance
analysis.** *Bioinformatics*, 24(19):2256-7, 2008. (paper).

Keich U. and Ng P. **A conservative parametric approach to motif
significance analysis.** *Genome Informatics*, 19:61-72, 2007.
(preprint)

Nagarajan N. and Keich U. **FAST: Fourier transform based Algorithms
for Significance Testing of ungapped multiple alignments.**
*Bioinformatics*, 24(4):577-8, 2008. (paper).

Ng P., Nagarajan N., Jones N., and Keich U. **Apples to apples:
improving the performance of motif finders and their significance
analysis in the Twilight Zone.** *Bioinformatics*,
22(14):e393-401, ISMB 2006. (preprint)

Nagarajan N., Ng P., Keich U. **Refining motif finders with
E-value calculations. ***Proceedings of the 3rd RECOMB Satellite
Workshop on Regulatory Genomics*, Singapore. 73-84, 2006. (preprint)

Keich U., Nagarajan N. **A fast and numerically robust method for
exact multinomial goodness-of-fit test.** *Journal of
Computational and Graphical Statistics,* , 15(4):779-802, 2006.
(preprint)

Nagarajan N., Jones N., and Keich U. **Computing the p-value of
the information content from an alignment of multiple sequences.**
*Bioinformatics*, Vol. 21, Suppl 1, i311-i318, ISMB 2005.
(preprint) (Erratum)

Buhler J., Keich U., Sun Y. **Designing Seeds for Similarity
Search in Genomic DNA.** *Journal of Computer and System
Sciences*, Volume 70, Issue 3, May 2005, Pages 342-363. (preprint)

Keich U., and Nagarajan N. **A Faster Reliable Algorithm to
Estimate the p-Value of the Multinomial llr Statistic**.
*Proceedings of the 4th International Workshop on Algorithms in
Bioinformatic (WABI 2004)*, September 2004, Bergen, Norway.
(preprint)

Keich U. **sFFT: a faster accurate computation of the p-value of
the entropy score.** *Journal of Computational Biology*,
Volume 12, Number 4, May 2005, Pages 416-430. (preprint)

Zhi D., Keich U., Pevzner P., Heber S., and Tang H. **Correcting base-assignment errors in repeat regions of shotgun assembly.** *IEEE/ACM Transactions on
Computational Biology and Bioinformatics*, 4(1):54-64, (2007).
(preprint)

Keich U., Li M., Ma B., and Tromp J. **On Spaced Seeds for
Similarity Search**. *Discrete Applied Mathematics*,
138(3):253--263. 2004. (preprint)

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)*, April 2003, Berlin, Germany. (preprint)

Eskin E., Keich U., Gelfand M.S., Pevzner P.A. **Genome-Wide
Analysis of Bacterial Promoter Regions**. *Proceedings of the
Pacific Symposium on Biocomputing (PSB-2003)*, January 2003,
Kaua'i, Hawaii. (preprint)

Keich U. and Pevzner, P.A. **Finding motifs in the twilight
zone.** *Bioinformatics*, Vol. 18 (2002), Issue 10, 1374-1381.
(preprint)

Keich U. and Pevzner P.A. **Subtle motifs: defining the limits
of motif finding algorithms.** *Bioinformatics*, Vol. 18
(2002), Issue 10, 1382-1390. (preprint)

Keich U. and Pevzner P.A. **Finding motifs in the twilight zone.**
*Proceedings of the Sixth Annual International Conference on
Research in Computational Molecular Biology (RECOMB-2002)*, April
2002, Washington DC, USA, ACM Press. (preprint)

Keich U. **A Stationary Tangent - the Discrete and Non-smooth
Cases.** *Journal of Time Series Analysis*, March 2003, vol.
24, no. 2, pp. 173-192(20). (preprint)

Cwikel M. and Keich U. **Optimal decompositions for the
K-functional for a couple of Banach lattices.** *Arkiv för
Matematik*, 39 (2001), No. 1, 27-64. (preprint)

Keich U. **A Possible Definition of A Stationary Tangent.**
*Stochastic Processes and Their Applications*, 88 (2000), No. 1,
1-36. (preprint)

Keich U. **Krein's Strings, the Symmetric Moment Problem, and
Extending a Real Positive Definite Function.**, *Communications
on Pure and Applied Mathematics*, 52 (1999), no. 10, 1315-1334.
(preprint)

Keich U. **On L**^{p} **Bounds for Kakeya
Maximal Functions and the Minkowski Dimension in R**^{2}**.**,
*Bulletin of the London Mathematical Society*, 31 (1999),
213-221. (preprint)

Keich U. **Absolute Continuity Between the Wiener and Stationary
Gaussian Measures.**, *Pacific Journal of Mathematics*, Vol.
88 (1999), No. 1, 95-108. (preprint)

Keich U. **The Entropy Distance Between the Wiener and
Stationary Gaussian Measures.**, *Pacific Journal of Mathematics*,
Vol. 88 (1999), No. 1, 109-128. (preprint)

Aharoni R. and Keich U. **A Generalization of the Ahlswede Daykin
Inequality.**, *Discrete Mathematics *, 152 (1996), 1-12. (preprint)