A. Ivan, M.S. Halfon, S. Sinha (2008). Computational discovery of cis-regulatory modules in Drosophila, without prior knowledge of motifs. Genome Biology. (Accepted.)

M.B. Noyes, X. Meng, A. Wakabayashi, S. Sinha, M.H. Brodsky, S.A. Wolfe (2008). The systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Res. (Accepted.)

S. Sinha, A.S. Adler, Y. Field, H.Y. Chang, E. Segal (2008). Systematic Functional Characterization of cis-Regulatory Motifs in Human Core Promoters. Genome Research. (Accepted.)

S. Sinha and X. He (2007). MORPH: Probabilistic alignment combined with Hidden Markov Models of cis-regulatory modules. PLoS Computational Biology. 3(11):e216.

A. Adler, S. Sinha, E. Segal, H. Chang. (2007). Motif module map reveals enforcement of aging by continual NF-kB activity. Genes & Development, 21:3244-3257. Cover article. Recommended by Faculty of 1000.

L. Li, Q. Zhu, X. He, S. Sinha and M.S. Halfon. (2007) Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses. Genome Biology 8, R101. (Marked by journal as highly accessed.)

R. Kantorovitz, G. E. Robinson and S. Sinha (2007).  A statistical method for alignment-free comparison of regulatory sequences. Bioinformatics, 23(13). (Special Issue on ISMB 2007). (Acceptance rate: 15% in over 400.)

J. Kim and S. Sinha (2007) Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment. Bioinformatics, 23(3).

S. Sinha, X. Ling, C.W. Whitfield, C. Zhai, G.E. Robinson (2006) Genome scan for cis-regulatory DNA motifs associated with social behavior in honey bees. Proc. Nat. Acad. Sciences, 103(44).

S. Sinha (2006). On counting position weight matrix matches in a sequence, with application to discriminative motif finding. Bioinformatics, 22(14). (Special Issue on ISMB 2006). (Acceptance rate: 15% in over 400.)

S. Sinha, Y. Liang, E.D. Siggia (2006). Stubb: a program for discovery and analysis of cis-regulatory modules. Nucl. Acids Res, 34 (Web server issue): W555-9.

S. Sinha and E. D. Siggia (2005). Sequence Turnover and Tandem Repeats in cis-Regulatory Modules in Drosophila. Molecular Biology and Evolution, 22(4):874-85.

M. Tompa, N. Li, T. L. Bailey, G. M. Church, B. DeMoor, E. Eskin, A. V. Favorov,  M. C. Frith, Y. Fu, W. J. Kent, V. J. Makeev, A. A. Mironov, W. S. Noble, G. Pavesi, G. Pesole, M. Regnier, N. Simonis, S. Sinha, G. Thijs, J. van Helden, M. Vandenbogaert, Z. Weng, C. Workman, C. Ye, Z. Zhu. (2005) An Assessment of Computational Tools for the Discovery of Transcription Factor Binding Sites, Nature Biotechnology, Vol. 23, No. 1, pp. 137 – 144.

S. Sinha, M. Blanchette, and M. Tompa (2004). PhyME: A Probabilistic Algorithm for Finding Motifs in Sets of Orthologous Sequences. BMC Bioinformatics, 5(170). (Marked by journal as Research Highlight.)

S. Sinha, M. Schroeder, U. Unnerstall, U. Gaul, and E. D. Siggia (2004). Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila. BMC Bioinformatics, 5(129). Cited by the Faculty of 1000.

A. Prakash, M. Blanchette, S. Sinha, M. Tompa (2004). Motif Discovery in Heterogeneous Sequence Data, Ninth Pacific Symposium on Biocomputing (PSB).

S. Sinha, E. van Nimwegen, and E. D. Siggia (2003). A Probabilistic Method to Detect Regulatory Modules. Bioinformatics, 2003, 19(S1). (Special issue on ISMB 2003.) (Best paper award, 2^nd prize.)

S. Sinha (2003). Discriminative Motifs. Journal of Computational Biology, 10(3), 599-615. A preliminary version appeared in RECOMB, 2002.

S. Sinha, M. Tompa (2003) YMF, a Program for Discovery of Novel Transcription Factor Binding Sites by Statistical Overrepresentation, Nucleic Acids Research, Vol. 31, No. 13, pp. 3586-358.

S. Sinha, M. Tompa (2003) Performance Comparison of Algorithms for Finding Transcription Factor Binding Sites, Third IEEE Symposium on Bioinformatics and Bioengineering, (BIBE), pp. 214-220.

S. Sinha and M. Tompa (2002). Discovery of Novel Transcription Factor Binding Sites by Statistical Overrepresentation. Nucleic Acids Research, 30(24), 5549-60.

Y. Chen, R. Venkatesan, M. Cary, R. Pang, S. Sinha, M. Jakubowski. (2002) Oblivious hashing:  Silent Verification of Code Execution, Fifth International Workshop on Information Hiding (IHW).

M. Blanchette and S. Sinha (equal authors) (2001). Separating Real Motifs from their Artifacts. Bioinformatics, 17(S1). (Special issue on ISMB 2001.)

R. Venkatesan, V. Vazirani, S. Sinha. (2001) A Graph-Theoretic Approach to Software Watermarking, Fourth International Workshop on Information Hiding, (IHW), pp. 157-168.

S. Sinha and M. Tompa (2000). A Statistical Method for Finding Transcription Factor Binding Sites. Proc. Eighth Intl. Conf. on Intelligent Systems for Molecular Biology (ISMB) 2000, 8:344-54.