7. Katsutomo Okamura^*, Sudha Balla^*, Raquel Martin, Na Liu, Eric C. Lai, Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster, Nature Structural & Molecular Biology (NSMB), (June 2008, Volume 15 No. 6), pp. 581-590.

6. Sudha Balla, Sanguthevar Rajasekaran, Ion I. Mandoiu, Efficient Algorithms for Degenerate Primer Search, International Journal of Foundations of Computer Science (IJFCS), (Aug 2007, Vol. 18, No. 4), pp 899-910.

5. Jaime Davila, Sudha Balla, Sanguthevar Rajasekaran, Fast and Practical Algorithms for Planted (l, d) Motif Search, IEEE Transactions on Computational Biology and Bioinformatics (TCBB), (Oct-Dec 2007, Vol. 4, No. 4), pp. 544-552.

4. Sudha Balla, Sanguthevar Rajasekaran, An Efficient Algorithm for Minimum Degeneracy Primer Selection, IEEE Transactions on Nanobioscience (TNB), (March 2007, Vol. 6 No. 1), pp 12-17.

3. Sudha Balla, Vishal Thapar, Snigdha Verma, ThaiBinh Luong, Tanaz Faghri, Chun-Hsi Huang, Sanguthevar Rajasekaran, Jacob J del Campo, Jessica H Shinn, William A Mohler, Mark W Maciejewski, Michael R Gryk, Bryan Piccirillo, Stanley R Schiller, Martin R Schiller, Minimotif Miner: a tool for investigating protein function, Nature Methods, (March 2006, Vol. 3 No. 3), pp 175-177.

Short notes:
Matchmaker, Science, (17 February 2006, Vol. 311), page 925.
Minimotif Miner, Journal of Proteome Research, (April 2006, Vol. 5 Issue 4), pp 736-737.

2. Rajasekaran S, Balla S, Huang C-H, Thapar V, Gryk M, Maciejewski M, Schiller M, High-performance Exact Algorithms for Motif Search, Journal of Clinical Monitoring and Computing (Springer), (October 2005, Vol. 19, No. 4-5), pp 319-328.

1. S. Rajasekaran, S. Balla and C.-H. Huang, Exact Algorithms for Planted Motif Problems, Journal of Computational Biology, (October 2005, Vol. 12, No. 8), pp 1117-1128.

6. Sudha Balla, Sanguthevar Rajasekaran and Ion I. Mandoiu, Faster Greedy Algorithms for Multiple Degenerate Primer Selection, 8th IEEE International Conference on BioInformatics and BioEngineering (BIBE 2008), accepted.

5. Jaime Davila, Sudha Balla and Sanguthevar Rajasekaran, Fast Algorithms for Selecting Specific siRNA in Complete mRNA Data, Workshop on Algorithms in Bioinformatics (WABI 2007), (LNCS 4645 (2007)), pp 302-309.

4. Sudha Balla, Sanguthevar Rajasekaran, Space and Time Efficient Algorithms to Discover Endogenous RNAi Patterns In Complete Genome Data, 3rd International Symposium on Bioinformatics Research and Applications (ISBRA 2007), (LNBI 4463 (2007)), pp 260-269.

3. Jaime Davila, Sudha Balla and Sanguthevar Rajasekaran, Space and Time Efficient Algorithms For Planted Motif Search, Proc. 6th International Conference on Computational Science (ICCS 2006)/ 2nd International Workshop on Bioinformatics Research and Applications (IWBRA 2006), (LNCS 3992 (2006)), pp 822-829.

2. S. Rajasekaran, S. Balla, C.-H. Huang, V. Thapar, M. Gryk, M. Maciejewski, M. Schiller, Exact Algorithms for Motif Search, Proc. of the Third Asia-Pacific Bioinformatics Conference, 2005, (APBC 2005), pp 239-248.

1. Sanguthevar Rajasekaran, Sudha Balla, Chun-Hsi Huang, Exact Algorithms for Planted Motif Challenge Problems, Proc. of the Third Asia-Pacific Bioinformatics Conference, 2005, (APBC 2005), pp 249-260.

2. Sudha Balla, Sanguthevar Rajasekaran, Sorting and FFT Based Techniques in the Discovery of Biopatterns, In Ion Mandoiu and Alexander Zelikovsky, editors, Bioinformatics Algorithms: Techniques and Applications. Wiley Book Series on Bioinformatics (Series Editors: Yi Pan and Albert Y. Zomaya). pp 93-116.

1. Sudha Balla, Jaime Davila, Sanguthevar Rajasekaran, Approximation Algorithms for Primer Selection, Planted Motif Search and Related Problems, In T.E. Gonzalez, editor, Approximation Algorithms and Metaheuristics. CRC Press. pp 75-1.

3. Sudha Balla, Sanguthevar Rajasekaran and Ion I. Mandoiu, Greedy Heuristics for Degenerate Primer Selection, BECAT/CSE-TR-07-4.

2. Shireesh Thota, Sudha Balla, Sanguthevar Rajasekaran, Algorithms for Motif Discovery Based on Edit Distance, BECAT/CSE-TR-07-3.

1. Sudha Balla, Jaime Davila, Sanguthevar Rajasekaran, On the Challenging Instances of the Planted Motif Problem, BECAT/CSE-TR-07-2.

6. Alliance Innovation Fair, (October 19, 2006), CT Convention Center, Hartford. [POSTER]
5. Molecular, Microbial and Structural Biology Departmental Retreat, (March 16, 2006), UConn. [POSTER]
4. Neuroscience Departmental Retreat and Quinquennial Celebration, (October 23-24, 2005), Interlaken Inn, Lakeville, Ct. [POSTER]
3. Detecting and Processing Regularities in High Throughput Biological Data (June 20-22, 2005), DIMACS, Rutgers. [TALK]
2. UCONN Neuroscience Department Annual Retreat (October 15, 2004), UConn. [POSTER]
1. Proteomics: Sequence, Structure, Function (May 10 - 14, 2004), IPAM, UCLA.