2012

• Y. Liu, S. Maxwell, T. Feng, X. Zhu, R. C. Elston, M. Koyuturk, and M. R. Chance. Gene, pathway and network frameworks to identify epistatic interactions of single nucleotide polymorphisms derived from GWAS data. BMC Systems Biology, in press.


• S. Erten, M. Ayati, Y. Liu, M. R. Chance, and M. Koyuturk. Algorithms for detecting complementary SNPs within a region of interest that are associated with diseases, 3rd ACM Conf. Bioinformatics, Computational Biology and Biomedicine (ACM-BCB'12), 3:194-201, 2012. pdf


• S. Erten, S. A. Chowdhury, X. Guan, R. K. Nibbe, J. Barnholtz-Sloan, M. R. Chance, and M. Koyuturk. Identifying stage-specific protein subnetworks for colorectal cancer, BMC Proceedings, 6(Suppl 7):S1, 2012. pdf


• M. Ruffalo, M. Koyuturk, S. Ray, and T. LaFramboise. Accurate estimation of short read mapping quality for next generation genome sequencing, Bioinformatics Suppl. on 11th European Conference on Computational Biology (ECCB), 28(18):i349-i355, 2012. pdf


• S. Saha, T. Roman, A. Galante, M. Koyuturk, and R. Ewing. Network-based approaches for extending the Wnt signaling pathway and identifying context-specific subnetworks, International Journal of Computational Biology and Drug Design, 5 (3-4):185-205. pdf


• Y.Liu, M. Koyuturk, J. Barnholtz-Sloan, and M. R. Chance. Gene interaction enrichment and network analysis to identify dysregulated pathways in cancer, BMC Systems Biology, 6:65, 2012. pdf


• G. Bebek, M. Koyuturk, N. D. Price, and M. R. Chance. Network biology methods integrating biological data for translational science, Briefings in Bioinformatics, 13(4): 446-459, 2012. pdf


• Y. Liu, M. Koyuturk, S. Maxwell, Z. Zhao, and M. R. Chance. Integrative analysis of common neurodegenerative diseases using gene association, interaction network, and mRNA expression data. AMIA Summit on Translational Bioinformatics, pp. 62-71, 2012. pdf


• M. Koyuturk. Using protein interaction networks to understand complex diseases, IEEE Computer, 45(3):31-38, 2012. pdf

2011

• S. Erten, G. Bebek, and M. Koyuturk. VAVIEN: An algorithm for prioritizing candidate disease genes based on topological similarity in protein interaction networks. Journal of Computational Biology, 18(11):1561-1574, 2011. pdf


• M. Ruffalo, T. LaFramboise, and M. Koyuturk. Comparative analysis of algorithms for next generation sequencing read alignment. Bioinformatics, 27(20): 2790-2796, 2011. pdf


• S. A. Chowdhury, R. K. Nibbe, M. R. Chance, and M. Koyuturk. Subnetwork state functions define dysregulated subnetworks in cancer. Journal of Computational Biology, 18(3):263-281, 2011. pdf


• S. Erten, G. Bebek, R. Ewing, and M. Koyuturk. DADA: Degree-aware algorithms for network-based disease gene prioritization., BMC BioData Mining, 4:19, 2011. pdf


• R. K. Nibbe, S. A. Chowdhury, M. Koyuturk, R. Ewing, and M. R. Chance. Protein-protein interaction networks and subnetworks in the biology of disease, WIREs Systems Biology and Medicine, 3(3):357-367, 2011. pdf


• S. Erten, G. Bebek, and M. Koyuturk. Disease gene prioritization based on topological similarity in protein-protein interaction networks. RECOMB'11, 54-68, 2011. pdf


• Y. Liu, S. Patel, R. K. Nibbe, S. Maxwell, S. A. Chowdhury, M. Koyuturk, X. Zhu, E. K. Larkin, S. Buxbaum, N. M. Punjabi, S. A. Gharib, S. Redline, and M. R. Chance. Systems biology analysis of gene expression and genome-wide association study data in obstructive sleep apnea. Pacific Symposium on Biocomputing, 16:14-25, 2011. pdf

2010

• G. Yavas, M. Koyuturk, and T. LaFramboise. Optimization algorithms for identification and genotyping of copy number polymorphisms in human populations. PRIB'10, 74-85, 2010. pdf


• S. A. Chowdhury, R. K. Nibbe, M. R. Chance, and M. Koyuturk. Subnetwork state functions define dysregulated subnetworks in cancer. RECOMB'10, 80-95, 2010. pdf supplement


• S. Erten and M. Koyuturk. Role of centrality in network-based prioritization of disease genes. EVOBIO'10, 13-25, 2010. (Best Paper Award) pdf


• M. Koyuturk. Algorithmic and analytical methods in network biology. WIREs Systems Biology & Medicine, 2(3):277-292, 2010. pdf


• R. K. Nibbe, M. Koyuturk, and M. R. Chance. An integrative -omics approach to identify functional subnetworks in human colorectal cancer. PLoS Computational Biology, 6(1):e1000639, 2010. pdf


• S. A. Chowdhury and M. Koyuturk. Identification of coordinately dysregulated subnetworks in complex phenotypes. Pacific Symposium on Biocomputing (PSB'10), 133-144, 2010. pdf


• G. Yavas, M. Koyuturk, M. Ozsoyoglu, M. P. Gould, and T. LaFramboise. COKGEN: A software for the identification of rare copy number variation from SNP microarrays. Pacific Symposium on Biocomputing (PSB'10), 371-382, 2010. pdf


• J. Pandey, M. Koyuturk, and A. Grama. Functional characterization and topological modularity of molecular interaction networks. BMC Bioinformatics Suppl. on APBC'10, 11(Suppl 1):S35. pdf


• M. Manguoglu, M. Koyuturk, A. Grama, and A. H. Sameh. Weighted matrix ordering and parallel banded preconditioners for iterative linear system solvers., SIAM Journal on Scientific Computing, 32(3):1201-1216, 2010. pdf

2009

• S. Erten, X. Li, G. Bebek, J. Li, and M. Koyuturk. Phylogenetic analysis of modularity in protein interaction networks. BMC Bioinformatics, 10:333, 2009. pdf


• G. Yavas, M. Koyuturk, M. Ozsoyoglu, M. P. Gould, and T. LaFramboise. An optimization framework for unsupervised identification of rare copy number variation from SNP array data. Genome Biology, 10:R119, 2009. pdf


• B. Carbunar, M. K. Ramanathan, M. Koyuturk, S. Jagannathan, and A. Grama, Efficient tag detection in RFID systems, Journal of Parallel & Distributed Computing, 69(2): 180-196, 2009. pdf


• X. Li, S. Erten, G. Bebek, M. Koyuturk and J. Li. Comparative analysis of modularity in biological systems. Ohio Collaborative Conference in Bioinformatics (OCCBIO'09), 104-109, 2009. pdf

2008

• J. Pandey, M. Koyuturk, S. Subramaniam, and A. Grama. Functional coherence in domain interaction networks, Bioinformatics Suppl. on ECCB'08, 24(16):i28-i34, 2008. pdf


• R. A. Ferreira, M. Koyuturk, S. Jagannathan, and A. Grama, Semantic indexing in structured peer-to-peer networks, Journal of Parallel and Distributed Computing, 68(1):64-77, 2008. pdf


• J. Pandey, M. Koyuturk, W. Szpankowski, and A. Grama, Annotating pathways in interaction networks, Pacific Symposium on Biocomputing (PSB'08), 13:153-165, 2008. pdf


• M. K. Ramanathan, M. Koyuturk, A. Grama, and S. Jagannathan, PHALANX: A graph theoretic framework for test case prioritization, SAC'08, 667-673, 2008. pdf

2007

• M. Koyuturk, W. Szpankowski, and A. Grama, Assessing significance of connectivity and conservation in protein interaction networks, Journal of Computational Biology, 14(6), 747-764, 2007. pdf


• J. Pandey, M. Koyuturk, Y. Kim, W. Szpankowski, S. Subramaniam, and A. Grama, Functional annotation of regulatory pathways, Bioinformatics Suppl. on ISMB/ECCB'07, 23(13), i377-i386, 2007. pdf


• J. Pandey, M. Koyuturk, W. Szpankowski, and A. Grama, A statistical model for functional characterization of regulatory pathways, Workshop on Data Mining for Biomedical Informatics, SIAM DM'07, 2007. pdf

2006

• M. Koyuturk, Y. Kim, S. Subramaniam, W. Szpankowski, and A. Grama, Detecting conserved interaction patterns in biological networks, Journal of Computational Biology, 13(7), 1299-1322, 2006. pdf


• M. Koyuturk, Y. Kim, U. Topkara, S. Subramaniam, W. Szpankowski, and A. Grama, Pairwise alignment of protein interaction networks, Journal of Computational Biology, 13(2), 182-199, 2006. pdf


• Y. Kim, M. Koyuturk, U. Topkara, A. Grama, and S. Subramaniam, Inferring functional information from domain co-evolution, Bioinformatics, 22(1), 40-49, 2006. pdf


• M. Koyuturk, A. Grama, and N. Ramakrishnan, Non-orthogonal decomposition of binary matrices for bounded-error data compression and analysis, ACM Transactions on Mathematical Software, 32(1), 33-69, 2006. pdf


• J. Chi, M. Koyuturk, and A. Grama, Conquest: A coarse-grained algorithm for constructing summaries of distributed discrete datasets, Algorithmica, 45(3), 377-401, 2006. pdf


• M. Koyuturk, A. Grama, and W. Szpankowski, Assessing significance of connectivity and conservation in protein interaction networks, RECOMB'06, 45-59, 2006. pdf

2005

• M. Koyuturk, A. Grama, and N. Ramakrishnan, Compression, clustering and pattern discovery in very high dimensional discrete-attribute datasets, IEEE Transactions on Knowledge and Data Engineering, 17(4), 447-461, 2005. pdf


• M. Koyuturk and C. Aykanat, Iterative-improvement-based declustering heuristics for multi-disk databases, Information Systems, 30(1), 47-70, 2005. pdf


• M. Koyuturk, A. Grama, and W. Szpankowski, Pairwise local alignment of protein interaction networks guided by models of evolution, RECOMB'05, 48-65, 2005. pdf


• B. Carbunar, M. K. Ramanathan, M. Koyuturk, C. Hoffmann, and A. Grama, Redundant reader elimination in RFID systems, SECON'05, 2005. pdf

2004

• M. Koyuturk, A. Grama, and W. Szpankowski, An efficient algorithm for detecting frequent subgraphs in biological networks, BioInformatics Suppl. on ISMB/ECCB'04, 20, i200-i207, 2004. pdf


• M. Koyuturk, W. Szpankowski, and A. Grama, Biclustering gene-feature matrices for statistically significant dense patterns, CSB'04, 2004. pdf


• J. Chi, M. Koyuturk, and A. Grama, CONQUEST: A distributed tool for constructing summaries of high-dimensional discrete-attributed datasets, SIAM DM'04, 154-165, 2004. pdf

2003 and Before

• M. Koyuturk and A. Grama, PROXIMUS: A framework for analyzing very high dimensional discrete-attributed datasets, KDD'03, 147-156, 2003. pdf


• M. Koyuturk, A. Grama, and W. Szpankowski, Algorithms for bounded-error correlation of high dimensional data in microarray experiments, CSB'03, 575-580, 2003. pdf


• M. Koyuturk, A. Grama and N. Ramakrishnan, Algebraic techniques for analysis of large discrete-valued datasets, PKDD'02, 311-324, 2002. pdf


• M. N. Gurcan, M. Koyuturk, H. S. Yildiz, R. Cetin-Atalay and A. E. Cetin, Identification of relative protein bands in Polyacrylamide Gel Electrophoresis (PAGE) images using multiresolution snake algorithm, Biotechniques, 26, 1162-1169, 1999.


• M. N. Gurcan, M. Koyuturk, H. S. Yildiz, R. Cetin-Atalay, A. E. Cetin, Identification of relative protein bands in Polyacrylamide Gel Electrophoresis (PAGE) images using multiresolution snake algorithm", TFTS'98, 277-280, 1998. pdf


• M. Koyuturk, M. N. Gurcan and A. E. Cetin, Mammogramlarda kutle lezyonlarinin yilan algoritmasiyla otomatik olarak sezimlenmesi [Automatic detection of mass lesions on mammograms using snake algorithm], SIU'98,334-340, 1998.

DBLP entry