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Research Interests

• Multiple Sequence Alignment
• Algorithms and Data Structures
• Complexity Theory
• Linear and Non-Linear Optimization Problems
• Combinatorics
• Software Engineering and Architecture

Publications

Journal Articles

• Amarendran R. Subramanian, Suvrat Hiran, Rasmus Steinkamp, Peter Meinicke, Eduardo Corel, Burkhard Morgenstern DIALIGN-TX and multiple protein alignment using secondary structure information at GOBICS, Nucleic Acids Research 2010, DOI 10.1093/nar/gkq442



• Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern: DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment, Algorithms for Molecular Biology 2008, 3:6



• Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann, Burkhard Morgenstern: DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment, BMC Bioinformatics 2005, 6:66



• B. Morgenstern, N. Werner, S.J. Prohaska, R. Steinkamp, I. Schneider, A.R. Subramanian, P.F. Stadler, J. Weyer-Menkhoff : Multiple sequence alignment with user-defined constraints @ GOBICS, Bioinformatics 21, 1271-1273.

Conference Proceedings

• Michael Kaufmann, Jan Kratochvil, Katharina Lehmann and Amarendran R. Subramanian: Max-Tolerance Graphs as Intersection Graphs: Cliques, Cycles, and Recognition Proceedings of the 17th ACM-SIAM Symposium on Discrete Algorithms (SODA) 2006, pp. 832-841

• B. Morgenstern, S.J. Prohaska, N. Werner, J. Weyer-Menkhoff, I. Schneider, A.R. Subramanian, P.F. Stadler: Multiple sequence alignment with user-defined constraints, German Conference on Bioinformatics 2004, Lecture Notes in Informatics, P-53, pp. 25-36

Thesis work

• Amarendran R. Subramanian: Segment-based Multiple Sequence Alignment, Dissertation (PhD thesis), 2009.


• Amarendran R. Subramanian: Zeichnungen planarer partitionierter Graphen, Diplomarbeit (Informatik), 2001.


• Amarendran R. Subramanian: Monopole und Kontaktstrukturen, Diplomarbeit (Mathematik), 2003.

Software

• DIALIGN-TX, DIRMBASE 1 and IRMBASE 2 are now available at http://dialign-tx.gobics.de
• DIALIGN-T and IRMBASE are available at http://dialign-tx.gobics.de


• Anchored DIALIGN is available at http://dialign.gobics.de/anchor/index.php