Ankit Agrawal

Research and Publications

Book Chapter:

• Ankit Agrawal, Alok Choudhary, and Xiaoqiu Huang, "Sequence-Specific Sequence Comparison Using Pairwise Statistical Significance", In Software Tools and Algorithms for Biological Systems, Springer New York (In book series: Advances in Experimental Medicine and Biology, AEMB), 2011, Vol. 696, pp. 297-306.

Journal Publications:

• Ankit Agrawal, Sanchit Misra, Daniel Honbo, and Alok Choudhary, "Parallel Pairwise Statistical Significance Estimation of Local Sequence Alignment Using MPI Library", In Concurrency and Computation: Practice and Experience, Wiley-Blackwell publishers, 2011, to appear.

• Ankit Agrawal and Xiaoqiu Huang, "Pairwise Statistical Significance of Local Sequence Alignment Using Sequence-Specific and Position-Specific Substitution Matrices", In IEEE/ACM Transactions on Computational Biology and Bioinformatics,  vol. 8, no. 1, pp. 194-205, Sept. 2011.

• Sanchit Misra, Ankit Agrawal, Wei-keng Liao, and Alok Choudhary, "Anatomy of a Hash-based Long Read Sequence Mapping Algorithm for Next Generation DNA Sequencing", In Bioinformatics 2011, Vol. 27, no. 2, pp. 189-195 (first published online November 18, 2010 doi:10.1093/bioinformatics/btq648).

• Ankit Agrawal, Ankush Mittal, Rahul Jain and Raghav Takkar, "Fuzzy-Adaptive-Thresholding-Based Exon Prediction", In International Journal of Computational Biology and Drug Design, IJCBDD, 2010, vol. 3, no. 4, pp. 311-333.

• Ankit Agrawal and Xiaoqiu Huang, "Pairwise Statistical Significance of Local Sequence Alignment Using Multiple Parameter Sets and Empirical Justification of Parameter Set Change Penalty". In BMC Bioinformatics 2009, 10 (Suppl 3): S1, DOI doi:10.1186/1471-2105-10-S3-S1

• Ankit Agrawal and Xiaoqiu Huang, "PSIBLAST_PairwiseStatSig: Reordering PSI-BLAST Hits Using Pairwise Statistical Significance", In Bioinformatics, 2009, DOI 10.1093/bioinformatics/btp089.

• Ankit Agrawal, Volker Brendel and Xiaoqiu Huang, "Pairwise Statistical Significance and Empirical Determination of Effective Gap Opening Penalties for Protein Local Sequence Alignment", In International Journal of Computational Biology and Drug Design, IJCBDD, 2008, vol.1, no.4, pp. 347-367.

• Ankit Agrawal, Ankush Mittal and S. Gupta, "A Restrictive Mining Algorithm to Learn Multi Time Delay Gene Networks", In Bioinformatics Trends - A Journal of Bioinformatics and Its Applications, Vol. 2, Issue 3 & 4, pp. 125-140, 2007.

• Ankit Agrawal and Ankush Mittal, "A Dynamic Time-Lagged Correlation Based Method to Learn Multi-Time Delay Gene Networks", In Enformatika, vol. 9, November 2005, ISSN 1307-6884, pp. 167-174.

Conference/Workshop Publications:

• Nithin Nakka, Ankit Agrawal and Alok Choudhary, "Predicting Node Failure in High Performance Computing Systems from Failure and Usage Logs", in Proc. IEEE IPDPS Workshop on Dependable Parallel, Distributed and Network-Centric Systems (DPDNS), May 2011, to appear.

• Yuhong Zhang, Sanchit Misra, Daniel Honbo, Ankit Agrawal, Wei-keng Liao, and Alok Choudhary, "Efficient Pairwise Statistical Significance Estimation for Local Sequence Alignment Using GPU", In Proc. IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS), February 2011, pp. 226-231.

• Ankit Agrawal, Sanchit Misra, Ramanathan Narayanan, Lalith Polepeddi, and Alok Choudhary, "A Lung Cancer Mortality Risk Calculator Based on SEER Data", In Proc. IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS), February 2011, pp. 233-233.

• Ankit Agrawal, Sanchit Misra, Alok Choudhary, and Karl Bilimoria, "Risk Prediction for Post-operative Adverse Outcomes in Colorectal Cancer Surgery", In Proc. IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS), February 2011, pp. 232-232.

• Ankit Agrawal, Alok Choudhary, and Xiaoqiu Huang,  "Derived Distribution Points Heuristic for Fast Pairwise Statistical Significance Estimation", In Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology (BCB '10). ACM, New York, NY, USA, 2010, pp. 312-321.

• Ankit Agrawal, Sanchit Misra, Daniel Honbo, and Alok Choudhary, "MPIPairwiseStatSig: Parallel Pairwise Statistical Significance Estimation of Local Sequence Alignment", In Proc. HPDC ECMLS 2010, pp. 470-476.

• Daniel Honbo, Ankit Agrawal, and Alok Choudhary, "Efficient Pairwise Statistical Significance Estimation using FPGAs", In Proc. BIOCOMP 2010, pp. 571-577.

• Ankit Agrawal, Alok Choudhary, and Xiaoqiu Huang, "Non-Conservative Pairwise Statistical Significance of Local Sequence Alignment Using Position-Specific Substitution Matrices", In Proc. BIOCOMP 2010, pp. 262-268.

• Ankit Agrawal and Xiaoqiu Huang, "Pairwise Statistical Significance of Local Sequence Alignment Using Substitution Matrices with Sequence-Pair-Specific Distance", In Proc. IEEE International Conference on Information Technology ICIT 2008, pp. 94-99.

• Ankit Agrawal and Xiaoqiu Huang, "Pairwise DNA Alignment with Sequence Specific Transition-Transversion Ratio Using Multiple Parameter Sets", In Proc. IEEE International Conference on Information Technology  ICIT 2008, pp. 89-93.

• Ankit Agrawal and Xiaoqiu Huang, "Conservative, Non-Conservative and Average Pairwise Statistical Significance of Local Sequence Alignment", In Proc. IEEE International Conference on Bioinformatics and Biomedicine BIBM 2008, Philadelphia, PA, USA, Nov. 3-5, 2008 pp. 433-436.

• Ankit Agrawal and Xiaoqiu Huang, "Pairwise Statistical Significance of Local Sequence Alignment Using Multiple Parameter Sets", In Proc. 2nd International Workshop on Data and Text Mining in Bioinformatics (Napa Valley, California, USA, October 30, 2008). DTMBIO '08. ACM, New York, NY, pp. 53-60. DOI= http://doi.acm.org/10.1145/1458449.1458462

• Ankit Agrawal, Volker Brendel and Xiaoqiu Huang, "Pairwise Statistical Significance Versus Database Statistical Significance for Local Alignment of Protein Sequences", In: Mandoiu, I., Sunderraman, R., Zelikovsky, A. (eds.) International Symposium on Bioinformatics Research and Applications (ISBRA) 2008. Lecture Notes in Computer Science (Lecture Notes in Bioinformatics), vol. 4983, pp. 50-61. Springer, Heidelberg 2008.

• Ankit Agrawal, Arka Ghosh and Xiaoqiu Huang, "Estimating Pairwise Statistical Significance of Protein Local Alignments Using a Clustering-Classification Approach Based on Amino Acid Composition.  In: Mandoiu, I., Sunderraman, R., Zelikovsky, A. (eds.) International Symposium on Bioinformatics Research and Applications (ISBRA) 2008. Lecture Notes in Computer Science (Lecture Notes in Bioinformatics), vol. 4983, pp. 62-73. Springer, Heidelberg 2008.

• Ankit Agrawal and Xiaoqiu Huang, "DNAlignTT: Pairwise DNA Alignment with Sequence Specific Transition-Transversion Ratio", In Proc. IEEE International Conference EIT 2008, May 18-21 pp. 457-459.

• Ankit Agrawal and Siddhartha Khaitan, "A New Heuristic for Multiple Sequence Alignment", In Proc. IEEE International Conference EIT 2008, May 18-21 pp. 225-227.

• Ankit Agrawal, Ankush Mittal, Rahul Jain and Raghav Takkar, "An Adaptive Fuzzy Thresholding Algorithm for Exon Prediction", In proc. IEEE International Conference EIT 2008, May 18-21 pp. 221-224.

• Ankit Agrawal, Rahul Jain, Raghav Takkar and Ankush Mittal, "PCRPA: Protein-Coding Region Predictor and Analyzer - Exon Prediction Using Power Spectrum Estimation Methods", In Proc. National Conference on IT and Its Application 2006, pp. B107-B111, 2006.

• Ankit Agrawal and Ankush Mittal, "Identifying Temporal Gene Networks Using Signal Processing Metrics on Time-Series Gene Expression Data", In Proc. IEEE Third International Conference on Intelligent Sensing and Information Processing, 14-17 December 2005, Bangalore , India, pp. 87-92, 2005.

• Ankit Agrawal and Ankush Mittal and S. Gupta, "Identifying Temporal Gene Networks by Mining Gene Expression Data", In Proc. IEEE 12^th International Conference on Advanced Computing and Communications (ADCOM), Ahmedabad, India December 15^th-18^th, 2004, pp. 194-200, 2004.

• Ankush Mittal, Sumit Gupta, L.-F. Cheong and Ankit Agrawal, "Camera Motion Characterization of Establishment Shots and Video Signatures", In Proc. IEEE 12th International Conference on Advanced Computing and Communications (ADCOM), Ahmedabad, India December 15th-18th, 2004, pp. 663-668, 2004.

Posters :

• Ankit Agrawal, R. Jain, R. Takkar, A. Mittal, "Exon prediction using a novel fuzzy logic based adaptive thresholding algorithm",  International Conference in Bioinformatics (InCoB), December 18-20, pp. P043.1-6, 2006.