Mathematics of Information Technology and Complex Systems





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Publications
NOTE: Publications listed pertain to algorithms and/or bioinformatics

THESES, Nov 2008 - March 2010

  1. Mirela Andronescu . "Computational approaches for RNA energy parameter estimation", November 2008.
  2. Alireza Khodabakhsi . "The structure approximating inverse protein folding in 2D and 3D HPC models", December 2008.
REFEREED CONTRIBUTIONS

  • Articles in Refereed Publications:

    November 2008 to March 2010
      W. Li, B. Ma, K. Zhang. "Amino Acid Classification and Hash Seeds for Homology Search". BICoB 2009: 44-51.
    1. P. Dao, A. Schonhuth, F.. Hormozdiari, I. Hajirasouliha, S. C. Sahinalp, M. Ester. "Quantifying systemic evolutionary changes by color coding confidence-sored PPI networks". The 9th Workshop on Algorithms in Bioinformatics, 2009.
    2. R. Salari, R. Backofen, and S. C. Sahinalp. "Fast prediction of RNA-RNA interaction." Journal of Algorithms for Molecular Biology 2009.
    3. H. Chitsaz, R. Backofen, S. C. Sahinalp. "biRNA: Fast RNA-RNA Binding Sites Prediction". The 9th Workshop on Algorithms in Bioinformatics, 2009.
    4. P. Dao, F. Hormozdiari, H. Jowhari, K. Byler, A. Cherkasov, S. C. Sahinalp. Improved Small Molecule Activity Determination via Centroid Nearest Neighbor s Classification The 8th Annual Conference on Computational Systems Bioinformatics, 2009.
    5. H. Chitsaz, R. Salari, S. C. Sahinalp, R. Backofen. "A Partition Function Algorithm for Interacting Nucleic Acid Strands". Bioinformatics 25(12):i365-i373.
    6. F. Hormozdiari, C. Alkan, E. Eichler and S. C. Sahinalp. "Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes". Genome Research, Jul, 19(7):1270-8, 2009.
    7. R. Colak, F. Hormozdiari, F. Moser, A. Schonhuth, J. Holman, M. Ester and S. C. Sahinalp. "Dense graphlet statistics of protein interaction networks and random networks". Pacific Symposium on Biocomputing, 2009.
    8. F. Hormozdiari, M. Hsing, R. Salari, A. Schonhuth, S. C. Sahinalp and A. Cherkasov. "The effect of insertion and deletions (indels) on wirings in protein interaction networks: a large scale study". Journal of Computational Biology, February 1, 2009, 16(2): 159-167.
    9. R. Salari, A. Schonhuth, F. Hormozdiari, A. Cherkasov and S. C. Sahinalp. "The relation between indel length and functional divergence: a formal study". 8th Workshop on Algorithms in Bioinformatics 2008.
    10. N. Alon, P. Dao, I. Hajirasouliha, F. Hormozdiari, S. C. Sahinalp. "Biomolecular Network Motif Counting and Discovery by Color Coding". Bioinformatics 2008 24: i241-i249.
    11. C. Thachuk, J. Manuch, A. Rafiey, L.-A. Mathieson, L. Stacho and A. Condon. "An algorithm for the energy barrier problem without pseudoknots and temporary arcs". Pacific Symposium on Biocomputing, 2010.
    12. M. S. Andronescu, C. Pop, and A. Condon. "Improved free energy parameters for RNA pseudoknotted secondary structure prediction". RNA 2010;16 26-42.
    13. C. Thachuk, J. Manuch, L. Stacho, and A. Condon. "NP-completeness of the direct energy barrier height problem without pseudoknots". Proc. 15th International Meeting on DNA Computing and Molecular Programming, 2009.
    14. H.L. Chen, H. Jabbari and A. Condon. "An O(n^5) algorithm for MFE prediction of kissing hairpins and 4-chains in nucleic acids". J. Comput. Biol., 803-815 2009.
    15. A. Condon and H. Jabbari. "Computational prediction of nucleic acid secondary structure: Methods, applications and challenges", Theoretical Computer Science, 9:340 (10 pages), 2009.
    16. M. Andronescu, V. Bereg, H.H. Hoos, and A. Condon. "RNA STRAND: The RNA secondary structure and statistical analysis database". BMC Bioinformatics 2008 9:340, 2008.
    17. A. Condon, J. Manuch, and C. Thachuk. "Complexity of a collision-aware string partition problem and its relation to oligo design for gene synthesis". The 14th Annual International Computing and Combinatorics Conference (COCOON), Lecture Notes in Computer Science, (LNBI 5092), Springer, 265-275, 2008.
    18. J. Manuch, L. Stacho, C. Stoll. "Two lower bounds for self-assemblies at temperature 1." SAC 2009, 808-809.
    19. A. Gupta, J. Manuch, L. Stacho, X. Zhao. "Haplotype inferring via galled-tree networks using a hypergraph covering problem for special genotype matrices". Discrete Applied Mathematics, 2310-2324 (2009).
    20. A. Gupta, J. Manuch, L. Stacho, X. Zhao. "Haplotype Inferring Via Galled-Tree Networks Is NP-Complete". Lecture Notes in Computer Science Volume 5092/2008, 287-298.
    21. R. Salari, C. Aksay, E. Karakoc, P.J. Unrau, I. Hajirasouliha and S.C. Sahinalp. "smyRNA: A Novel Ab Initio ncRNA Gene Finder". PLoS ONE (2009), 4(5), e5433.
    22. E. Dolgosheina, R.D. Morin, G. Aksay, S.C. Sahinalp, V. Magrini, E.R. Mardis, J. Mattsson and P.J. Unrau. "Conifers have a unique small RNA silencing signature". RNA (2008), 14(8), 1-8.
    23. R.D. Morin, G. Aksay, E. Dolgosheina, H.A. Ebhardt, V. Magrini, E.R. Mardis, S.C. Sahinalp and P.J. Unrau. "Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa". Genome Research (2008), 18(4), 571-84.
    24. B. Brejova, T. Vinar, Y. Chen, S. Wang, G. Zhao, D. G. Brown, M. Li, Yan Zhou. "Finding genes in Schistosoma japonicum: annotating novel genomes with help of extrinsic evidence". Nucleic acids research, 37(7):e52. 2009.
    25. T.Y. Lam, I.M. Meyer "HMMCONVERTER 1.0: a toolbox for hidden Markov models". Nucleic Acids Research (2009) 37(21):e139.

    November 2007 to October 2008
    1. J. Zhang, X. Gao, J. Xu, and M. Li . "Rapid and Accurate Protein Side Chain Packing using Local Backbone Information. RECOMB 2008.
    2. B. Brejova, T. Vinar, Y. Cheng, D. Brown, M. Li, and Y. Zhou. "Finding genes in Schistosoma Japonicum: annotating novel genomes with help of extrinsic evidence". Nucleic Acids Research. Accepted Nov. 2008
    3. H. Lin, Z. Zhang, M.Q. Zhang, B. Ma, M. Li. "ZOOM! Zillions of oligos mapped". Bioinformatics. 24:21, 2431-2437, 2008.
    4. S.C. Li, D. Bu, J. Xu, and M. Li, "Fragment-HMM: a new approach to protein structure prediction". Protein Science, 17(2008) 1925-1934, 2008.
    5. Z. Zhang, H. Lin, M. Li, "MANGO: multiple alignment with n gapped oligos". Journal of Bioinformatics and Computational Biology, 6:3, 521-541, 2008.
    6. S.C. Li, D. Bu, J. Xu, and M. Li, "Designing succinct structural alphabet". Bioinformatics, ISMB Special Issue, 2008.
    7. A. Condon, J. Manuch, and C. Thachuk. "Complexity of a Collision-Aware String Partition Problem and Its Relation to Oligo Design for Gene Synthesis". The 14th Annual International Computing and Combinatorics Conference (COCOON), Lecture Notes in Computer Science, (LNBI 5092), Springer 2008.
    8. L. Wang and K. Zhang. "Space Efficient Algorithms for Ordered Tree Comparison". Algorithmica 51(3) 2008.
    9. B. Shan, B Ma, K. Zhang , and G. Lajoie. "Complexities and Algorithms for Glycan Sequencing Using Tandem Mass Spectrometry". J. Bioinformatics and Computational Biology 6(1) 2008.
    10. B. Ma, L. Xin, and K. Zhang . "A new quartet approach for reconstructing phylogenetic trees: quartet joining method". J. Comb. Optim. 16(3) 2008.
    11. Pain et al. (incl. Irmtraud Meyer ). "The genome of the simian and human malaria parasite Plasmodium knowlesi". Nature 455(7214) 2008.
    12. I.M. Meyer . Predicting novel RNA-RNA interactions, Current Opinion in Structural Biology 18(3) 2008.
    13. M. Andronescu, V. Bereg, H.H. Hoos and A. Condon . "RNA Strand: The RNA Secondary Structure and Statistical Analysis Database". BMC Bioinformatics, 9:340, 2008.
    14. Sanja Rogic, Ben Montpetit, Holger H. Hoos , Alan K. Mackworth, B.F. Francis Ouellette, and Philip Hieter. "Correlation between the secondary structure of pre-mRNA and efficiency of splicing in Saccharomyces cerevisiae". BMC Bioinformatics, 9:355, 2008.
    15. R. Colak, F. Hormozdiari, F. Moser, A. Schonhuth, J. Holman, M. Ester and S.C. Sahinalp . "Dense graphlet statistics of protein interaction networks and random networks". Pacific Symposium on Biocomputing 2009.
    16. F. Hormozdiari, M. Hsing, R. Salari, A. Schonhuth, S.C. Sahinalp and A. Cherkasov. "The effect of insertion and deletions (indels) on wirings in protein interaction networks: a large scale study." RECOMB satellite conference on Systems Biology 2008.
    17. R. Salari, A. Schonhuth, F. Hormozdiari, A. Cherkasov and S.C. Sahinalp . "The relation between indel length and functional divergence: a formal study" 8th Workshop on Algorithms in Bioinformatics 2008.
    18. N. Alon, P. Dao, I. Hajirasouliha, F. Hormozdiari, and S.C. Sahinalp . "Biomolecular Network Motif Counting and Discovery by Color Coding", 16th Annual International Conference Intelligent Systems for Molecular Biology, 2008.
    19. I. Hajirasouliha, F. Hormozdiari, S.C. Sahinalp , and I. Birol. "Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies". 16th Annual International Conference Intelligent Systems for Molecular Biology. (ISMB 2008), Toronto, Canada.
    20. E.V. Dolgosheina, R.D. Morin, G. Aksay, S.C. Sahinalp , V. Magrini, E.R. Mardis, J. Mattsson, and P.J. Unrau . "Conifers have a unique small RNA silencing signature." RNA 2008.
    21. R.D. Morin, G. Aksay, E. Dolgosheina, H.A. Ebhardt, V. Magrini, E.R. Mardis, S.C. Sahinalp , and P.J. Unrau . "Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa." Genome Res. 18(4), 2008.

    November 2006 to November 2007
    1. Z.C. Yen, I.M. Meyer, S. Karalic, C.J. Brown. "A cross-species comparison of X-chromosome inactivation in Eutheria". Genomics. 2007.
    2. I.M. Meyer. "A practical guide to the art of RNA gene prediction". Briefings in Bioinformatics. 2007.
    3. I.M. Meyer, Miklos I. "Simulfold: Simultaneously Inferring an RNA Structure Including Pseudo-Knots, a Multiple Sequence Alignment and an Evolutionary Tree Using a Bayesian Markov Chain Monte Carlo Framework". PLoS Computational Biology. 2007.
    4. H.S. Zaher and P.J. Unrau. "Selection of an improved RNA polymerase ribozyme with superior extension and fidelity". RNA. 2007.
    5. C. Alkan, M. Ventura, N. Archidiacono, M. Rocchi, S.C. Sahinalp, and E.E. Eichler. "Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data". PLoS Comput Biol. 2007 Sep 28;3(9):1807-18.
    6. F. Hormozdiari, P. Berenbrink, N. Przulj, and S.C. Sahinalp. "Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution". PLoS Comput Biol. 2007 Jul 6;3(7):e118
    7. C. Aksay, R. Salari, E. Karakoc, C. Alkan, and S.C. Sahinalp. "taveRNA: a web suite for RNA algorithms and applications". Nucleic Acids Res. 2007 Jul 1;35(Web Server issue):W325-9. Epub 2007 May 8.
    8. R. Backofen, S. Chen, D. Hermelin, G. Landau, M.A. Roytberg, O. Weimann, and K. Zhang. "Locality and gaps in RNA comparison". Journal of Computational Biology.
    9. B. Shan, B. Ma, K. Zhang, and G. Lajoie. "Complexities and algorithms for glycan structure sequencing using tandem mass spectrometry". Journal of Bioinformatics and Computational Biology.
    10. X. Cui, T. Vinar, B. Brejova, D. Shasha, and M. Li. "Homology search for genes". Bioinformatics 2007 Jul 1;23(13):i97-i103. (Proc. of the 15th Annual International conference on Intelligent Systems for Molecular Biology, 2007.)
    11. B. Ma, L. Wang, and M. Li. "Near optimal alignment within a band in polynomial time". J. Comput. Syst. Sci. 73(2007):997-1011.
    12. M. Andronescu, A. Condon, H.H. Hoos, D.H. Mathews and K.P. Murphy. "Efficient parameter estimation for RNA secondary structure prediction". Bioinformatics 2007 Jul 1;23(13):i19-28. (Proc. of the 15th Annual International conference on Intelligent Systems for Molecular Biology, 2007.)
    13. R. Aguirre-Hernandez, H.H. Hoos and A. Condon. "Computational RNA secondary structure design: empirical complexity and improved methods". BMC Bioinformatics, 8:34, 2007.
    14. C. Thachuk, A. Shmygelska, and H.H. Hoos. "A replica exchange Monte Carlo algorithm for protein folding in the HP model". BMC Bioinformatics, 8:342, 2007.
    15. A. Shmygelska and H.H. Hoos. "An Adaptive Bin Framework Search Method for a Beta-Sheet Protein Homopolymer Model". BMC Bioinformatics, 8:136, 2007.
    16. J. Zhang, B. Jiang, M. Li, J. Tromp, X. Zhang, and M.Q. Zhang. "Computing exact P-values for DNA motifs". Bioinformatics, 23(5):531-537. 2007.
    17. M. Farach-Colton, G. Landau, S.C. Sahinalp, D. Tsur. ''Optimal spaced seed selection for approximate string search'' Journal of Computer and Systems Sciences, (accepted).
    18. S.C. Sahinalp, A. Utis. ''Hardness of sequence similarity search and other indexing problems'' Journal of Computer and Systems Sciences, (accepted).
    19. G. Bebek, P. Berenbrink, C. Cooper, T. Friedetzky, S.C. Sahinalp. ''Topological properties of proteome networks''. Theoretical Computer Science, (in press).
    20. A. F. Ergun, S. Muthukrishnan and S.C. Sahinalp. ''Sublinear Methods for Determining Representative Trends in Time Series Data Streams''. ACM Transactions on Algorithms (accepted).
    21. S.C. Sahinalp. "Edit distance under block operations". Encyclopedia of Algorithms (Ming Yang Kao, ed.), Springer (forthcoming).
    22. E. Karakoc, A. Cherkasov, S.C. Sahinalp. "Novel Approaches for Small Biomolecule Classification and Structural Similarity Search", Explorations, Volume 9, Issue 1, pages 14-21, June 2007.
    23. F. Hormozdiari , P. Berenbrink, N. Przulj, and S.C. Sahinalp. "Not all scale-free networks are born equal: The role of the seed graph in PPI network evolution", Computational Biology 3(7).
    24. C. Aksay, R. Salari, E. Karakoc, C. Alkan, and S.C. Sahinalp. "taveRNA: a web suite for RNA algorithms and applications", Nucleic Acids Research , Web Server Issue, 2007.
    25. S.C. Sahinalp. "The intelligence in developing systems for molecular biology", Genome Biology, 8:301, 2007.
    26. J. Liu, B. Ma, and K. Zhang, "An Algorithm for Searching RNA Motifs in Genomic Sequences", To appear, Biomolecular Engineering
    27. L. Wang and K. Zhang, Space efficient algorithms for ordered tree comparison, To appear, Algorithmica
    28. B. Ma, L. Wu, and K. Zhang, Improving the sensitivity and specificity of protein homology search by incorporating predicted secondary structures, To appear, Journal of Bioinformatics and Computational Biology.
    29. B. Rastegari and A. Condon. Parsing nucleic acid pseudoknotted secondary structure: algorithm and applications, J. Computational Biology, to appear. (A preliminary version appeared in Algorithms in Bioinformatics: 5th International Workshop, Lecture Notes in Computer Science. 2005 3692:341-352.)
    30. James King, Warren Cheung and Holger H. Hoos: Neighbourhood Thresholding for Projection-Based Motif Discovery. Accepted for publication in Bioinformatics, 2006/06.
    31. A. Gupta, J. Manuch, and L. Stacho, Structure-approximating inverse protein folding problem in 2D HP model, Journal of Computational Biology, accepted.
    32. P. Clote, E. Kranakis, D. Krizanc, and L. Stacho, Asymptotics of random RNA, Discrete Applied Mathematics, accepted.
    33. E. Chavez, S. Dobrev, E. Kranakis, J. Opatrny, L. Stacho, J. Urrutia, Traversal of a quasi-planar subdivision without using mark bits, Journal of Interconnection Networks, accepted.
    34. D. Kral, and L. Stacho, Closure for the property of having hamiltonian prism, Journal of Graph Theory, accepted.

    November 2005 to November 2006
    1. E. Karakoc, C. Sahinalp, A. Cherkasov. Comparative QSAR and Fragments Distribution Analysis of Drugs, Drug Likes, Metabolic Substances and Antimicrobial Compounds. Journal of Chemical Information and Modeling, 46(5), pp 2167-2182, Sep 2006.
    2. E. Karakoc, A. Cherkasov, C. Sahinalp. Distance based algorithms for small biomolecule classification and structural similarity search. Bioinformatics, (22)14, pp 243-251, Jul 2006.
    3. C. Alkan, E. Karakoc, J. Nadeau, C. Sahinalp, K. Zhang. ''RNA-RNA interactions and miRNA target prediction''. Journal of Computational Biology, 13(2), pp 267-282,  (RECOMB'05 special issue), Mar 2006.
    4. M. Andronescu and A. Condon. Finding MFE Structures Formed by Nucleic Acid Strands in a Combinatorial Set, Nanotechnology: Science and Computing, J. Chen, N. Jonoska. G. Rozenberg (Eds.), G. Rozenberg (Eds.), Natural Computing Series, Springer, 121-136, 2006.
    5. Wayne Pullan and Holger H. Hoos: Dynamic Local Search for the Maximum Clique Problem. Journal of Artificial Intelligence Research, Volume 25, pages 159-185, 2006.
    6. M. Li, B. Ma, L. Zhang, Superiority and complexity of the spaced seeds. SODA, 2006, pp. 444-453.
    7. J. Liu, B. Ma, M. Li. PRIMA: Peptide robust identification from MS/MS spectra. Bioinform. Comput. Biol., 4:1(2006) 125-138.
    8. A. Gupta, J. Manuch, and L. Stacho, Fault tolerant forwarding and optical indexes: a design theory approach, Journal of Combinatorial Designs 14 (2006), 25--40.
    9. E. Chavez, S. Dobrev, E. Kranakis, J. Opatrny, L. Stacho, J. Urrutia, Route Discovery with Constant Memory in Oriented Planar Geometric Networks, Networks 48 (2006), 7--15.
    10. L. Goddyn, and L. Stacho, Edge disjoint cycles through prescribed vertices, Journal of Graph Theory 50 (2005), 246--260.
    11. G. Fertin, A. Liestman, T. Shermer, and L. Stacho, Edge-disjoint spanners in Cartesian products of graphs, Discrete Mathematics 296 (2005), 167--186.
    12. P. Berenbrink, T. Friedetzky, J. Manuch, and L. Stacho, (Quasi) spanner in mobile ad hoc networks, Journal of Interconnection Networks 6 (2005), 63--84.
    13. L. Stacho, and D. Szeszler, On a generalization of Chvatal's condition giving new hamiltonian degree sequences, Discrete Mathematics 292 (2005), 159--165.
    14. Tulpan D, Andronescu M, Chang SB, Shortreed MR, Condon A, Hoos HH, Smith LM. Thermodynamically based DNA strand design, Nucleic Acids Res. 2005 33(15):4951-64.
    15. Shortreed MR, Chang SB, Hong DG, Phillips M, Campion B, Tulpan DC, Andronescu M, Condon A, Hoos HH, Smith LM.  A thermodynamic approach to designing structure-free combinatorial DNA word sets, Nucleic Acids Research 2005 33(15):4965-4977. 
    16. Jihong Ren, Baharak Rastegari, Anne Condon and Holger H. Hoos. HotKnots: Heuristic Prediction of RNA Secondary Structures Including Pseudoknots, RNA, 11 (10): 1494-1504, 2005.
    17. Can Alkan, Eray Tüzün, Jerome Buard, Franck Lethiec, Evan E. Eichler, Jeffrey A. Bailey, S. Cenk Sahinalp . Manipulating Multiple Sequence Alignments via MaM and WebMaM. Nucleic Acids Research -  Web server issue (2005). 


  • Other Refereed Contributions:

    November 2006 to present
    1. E. Karakoc, S.C. Sahinalp, and A. Cherkasov. "Comparative QSAR Analysis of Bacterial-, Fungalplant- and Human Metabolites". Pacific Symposium on Biocomputing, 12:133-144, 2007.
    2. F. Hormozdiari, P. Berenbrink, N. Przulj, and S.C. Sahinalp. "Not All Scale Free Networks are Born Equal: the Role of the Seed Graph in PPI Network Emulation". RECOMB Satellite Conference on Systems Biology, San Diego, CA, USA (2006).
    3. S. Chen, B. Ma and K. Zhang. "The normalized similarity metric and its applications". To appear in the IEEE International Conference on Bioinformatics and Biomedicine, 2007.
    4. C. Thachuk and A. Condon. "On the design of oligos for gene synthesis". To appear in the IEEE 7th International Symposium on Bioinformatics and Bioengineering, 2007.
    5. H. Jabbari, A. Condon, A. Pop, C. Pop, and Y. Zhao. "HFold: RNA pseudoknotted secondary structure prediction using hierarchical folding". To appear in Algorithms in Bioinformatics: 5th International Workshop, 2007.
    6. B. Rastegari, A. Condon, and K. Leyton-Brown. "Revenue Monotonicity in Combinatorial Auctions". Proc. Twenty Second Conference on Artificial Intelligence (AAAI), 2007.
    7. F. Hutter, D. Babic, H.H. Hoos and A. Hu. "Boosting Verification by Automatic Tuning of Decision Procedures". Proceedings of the 7th International Conference on Formal Methods in Computer-Aided Design (FMCAD-07), 2007 (to appear).
    8. L. Xu, F. Hutter, H.H. Hoos and K. Leyton-Brown. "SATzilla-07: The Design and Analysis of an Algorithm Portfolio for SAT". Proceedings of the 13th International Conference on Principles and Practice of Constraint Programming (CP-07), 2007 (to appear).
    9. F. Hutter, H.H. Hoos and T. Stutzle. "Automatic Algorithm Configuration based on Local Search". Proceedings of the 22nd Conference on Artificial Intelligence (AAAI-07), pp. 1152-1157, 2007.
    10. H.H. Hoos and T. Stutzle. "Empirical Analysis of Randomized Algorithms". Chapter 14, Handbook of Approximation Algorithms and Metaheuristics, Chapman & Hall/CRC, 2007.
    11. H.H. Hoos and T. Stutzle. "Stochastic Local Search". Chapter 19, Handbook of Approximation Algorithms and Metaheuristics, Chapman & Hall/CRC, 2007.
    12. C. Rostoker, A. Wagner and H.H. Hoos. "A Parallel Workflow for Real-time Correlation and Clustering of High-Frequency Stock Market Data". Proceedings of the 21th International Parallel and Distributed Processing Symposium (IPDPS 2007), pp. 1-10, IEEE Computer Society, 2007.
    13. L. Xu, H.H. Hoos and K. Leyton-Brown. "Hierarchical Hardness Models for SAT". Proceedings of the 13th International Conference on Principles and Practice of Constraint Programming (CP-07), 2007 (to appear).
    14. Z. Zhang, H. Lin, and M. Li. "MANGO: A new approach to multiple sequence alignment". In San Diego, California, August 13-17 2007. Life Sciences Society, To appear.
    15. J. Zhang, X. Chen, and M. Li. "Calculate exact p-value for structured motif". In The 18th Annual Symposium on Combinatorial Pattern Matching (CPM 2007), London, Ontario, 2007. To appear.
    16. J. Qian, S.C. Li, D. Bu, M. Li, J. Xu. "Finding Compact Structural Motifs in Many Proteins". In 18th Annual Symposium on Combinatorial Pattern Matching (CPM 2007), London, Ontario, 2007. To appear.
    17. X. Cui, T. Vinar, B. Brejova, D. Shasha, and M. Li. "Homology Search for Genes". In Bioinformatics: ISMB/ECCB 2007 Conference Proceedings 21-25 July 2007, Vienna, number 13 in 23 volume of pp. i97-103, 2007.
    18. X. Gao, D. Bu, S.C. Li, M. Li, and J. Xu. "Consensus Contact Prediction by Linear Programming". In 6th Annual Conference on Computational Systems Bioinformatics Conference (CSB 2007), San Diego, California, April 30 2007. Accepted.
    19. E. Karakoc, C. Sahinalp, A. Cherkasov. ''Comparative QSAR Analysis of Bacterial, Fungal, Plant and Human Metabolites''. Proceedings of PSB'07, Pacific Symposium on Biocomputing, Hawaii (full paper), Jan 2007. (to appear)
    20. S.C. Sahinalp. ''Indexed Approximate String Matcing'' Encyclopedia of Algorithms (invited contribution), Ming Yang Kao (ed.), Springer, (to appear).
    21. B. Ma, and K. Zhang. "Combinatorial Pattern Matching". 18th Annual Symposium, CPM 2007, London, Canada, July 9-11, 2007, Proceedings Springer 2007.
    22. B. Shan, B. Ma, K. Zhang, and Gilles Lajoie. "Complexities and Algorithms for Glycan Structure Sequencing using Tandem Mass Spectrometry". APBC 2007: 297-306.
    23. L. Xin, B. Ma, and K. Zhang. "A New Quartet Approach for Reconstructing Phylogenetic Trees: Quartet Joining Method". COCOON 2007: 40-50.
    24. S. Chen, and K. Zhang. "An Improved Algorithm for Tree Edit Distance Incorporating Structural Linearity". COCOON 2007: 482-492.

    November 2005 to November 2006
    1. Dave A.D. Tompkins and Holger H. Hoos: On the Quality and Quantity of Random Decisions in Stochastic Local Search for SAT. Proceedings of the 19th Conference of the Canadian Society for Computational Studies of Intelligence, (AI-2006), Volume 4013 of Lecture Notes in Artificial Intelligence, pp. 146-158, 2006.
    2. Frank Hutter, Youssef Hamadi, Holger H. Hoos and Kevin Leyton-Brown: Performance Prediction and Automated Configuration of Randomized Algorithms. Accepted for publication in the Proceedings of the Twelfth International Conference on Principles and Practice of Constraint Programming (CP-06), 2006.
    3. E. Karakoc, A. Cherkasov, C. Sahinalp. ''Distance based algorithbms for small biomolecule classification and structural similarity search''. Proceedings of ISMB'06, Intelligent Systems for Molecular Biology, Fortaleza, Brazil, pp 243-251, Aug 2006.
    4. C. Alkan, E. Karakoc, C. Sahinalp, P. Unrau, A. Ebhardt, K. Zhang, J. Buhler. ''RNA Structure Prediction via Energy Density Minimization'' Proceedings of RECOMB'06, Research in Computational Molecular Biology, Venice, Italy, pp 130-142, Apr 2006.
    5. T. Batu, F. Ergun, C. Sahinalp. ''String embeddings and edit distance approximations'' Proceedings of SODA'06, ACM-SIAM Symposium on Discrete Algorithms, Miami, Fl, pp 792-801, Jan 2006.
    6. A. Condon. Designed DNA Molecules: Principles and Applications, Nature Reviews Genetics 7, 565-575, 2006.
    7. G. Bebek, P. Berenbrink, C. Cooper, T. Friedetzky, J. Nadeau, C. Sahinalp. ''Topological properties of proteome networks'' Proceedings of RECOMB Satellite Meeting on Systems Biology, San Diego, CA, (full paper), Dec 2005.
    8. E. Kranakis, T. Mott, L.Stacho, On-Line Routing in Quasi-Planar and Quasi-Polyhedral Graphs, 2nd IEEE PerCom Workshop on Pervasive Wireless Networking (PWN'06), March 2006, Pisa, Italy.
    9. E. Chavez, S. Dobrev, E. Kranakis, J. Opatrny, L. Stacho, J. Urrutia, Local Construction of Planar Spanners in Unit Disk Graphs with Irregular Transmission Ranges, 7th Latin American Theoretical Informatics Symposium (LATIN'06), March 2006, Valdivia, Chile.
    10. A. Gupta, J. Manuch, L. Stacho and X. Zhao, On intractability of haplotype inferring via galled-tree networks, Workshop on Networks in Computational Biology, Ankara, Turkey, September, 2006.
    11. C. Alkan, E. Karakoc, S. C. Sahinalp, P. Unrau, A. Ebhard, K. Zhang, and J. Buhler, RNA secondary structure prediction via energy density minimization, Proceedings of the Tenth ACM Annual International Conference on Computational Molecular Biology (RECOMB), pp. 130-142, Venice, Italy, Jan. 2006. 
    12. L. Wang and K. Zhang, Space efficient algorithms for ordered tree comparison, Proceedings of the Sixteenth International Symposium on Algorithms and Computation, pp. 380-391, Sanya, China, December 2005.
    13. J. Manuch, X. Zhao, and L. Stacho, A. Gupta. Characterization of the existence of galled-tree networks, 4th Asia Pacific Bioinformatics Conference (APBC'06), 13-16 Feb 2006, Taiwan.

    Before November 2005
    1. M. Farach-Colton, G. Landau, C. Sahinalp, D. Tsur. ''Optimal spaced seed selection for approximate string search'' Proceedings of ICALP, International Colloquium on Automata, Languages and Programming, Lisboa, Portugal, pp 1251-1262, LNCS 3580, Jul 2005
    2. T. Batu, S.C. Sahinalp. ''Approximate String Comparisons via Locally Consistent Parsing'' Proceedings of DLT'05, International Conference on Developments in Language Theory (invited paper), Palermo, Italy, pp 22-35, LNCS 3572, Jul 2005.
    3. C. Alkan, E. Karakoc, J. Nadeau, C. Sahinalp, K. Zhang. ''RNA-RNA interactions and miRNA target prediction'' Proceedings of RECOMB'05, Research in Computational Molecular Biology, Boston, MA, pp 152-171, LNBI 3500, Apr 2005.E. Tuzun, C. Alkan, J. Buard, F. Lethiec, E. Eichler, J. Bailey, S.C. Sahinalp. ''Manipulating Multiple Sequence Alignments with Mam and WebMam''. Nucleic Acids Research, 1;33 (Web Server Issue), W295-298, Jul 2005. [PIMD: 15980474]
    4. B. Rastegari and A. Condon. Linear Time Algorithm for Parsing RNA Secondary Structure, 5th Workshop on Algorithms in   Bioinformatics (WABI), Oct 2005.
    5. Can Alkan, Emre Karakoç, Joe Nadeau, S. Cenk Sahinalp, Kaizhong Zhang .  RNA-RNA Interaction Prediction and Antisense RNA Target Search.  RECOMB'05, Research in Computational Molecular Biology, pp. 152-171, Cambridge, Ma. (2005).
    6. J. Liu, B. Ma, and K. Zhang, Algorithms for searching RNA motifs in genomic sequences, Proceedings of the 6th Atlantic Symposium on Computational Biology and Genome Informatics, pp. 1303-1306, Salt Lake City, Utah, USA, July 2005.

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