• Singh, A., U. Keswani, D. Levine, C. Feschotte and N. Stojanovic (2009) An algorithm for the reconstruction of consensus sequences of ancient segmental duplication and transposon copies in eukaryotic genomes. To appear in the International Journal of Bioinformatics Research and Applications.
• Tendulkar, A., N. Stojanovic and R. Barber (2008) Web-enabled classification of SNPs for genome-wide association studies. To appear in Proceedings of the 11th International Conference on Information Technology, ICIT-2008.
• Singh, A., U. Keswani, D. Levine, C. Feschotte and N. Stojanovic (2008) Reconstructing the sequences of broken transposable elements. In Proceedings of the 5th Biotechnology and Bioinformatics Symposyum, Biot-2008, 27-33.
• Stojanovic, N. (2008) On the futility of interpreting over-representation of motifs in genomic sequences as functional signals. In Proceedings of BIOSIGNALS 2008, International Conference on Bio-inspired Systems and Signal Processing, 2, 464-471.
• Singh, A. and N. Stojanovic (2008) An algorithm for finding substantially broken repeated sequences in newly sequenced genomes. In Proceedings of ICMB 2007, International Conference on Mathematical Biology, American Institute of Physics, 971(1), 79-88.
• Ji, F., J. Fu, R. Elmasri, N. Stojanovic and G. Grant (2007) Mediated taxonomy system for bioinformatics data integration. In Proceedings of DMB 2007, 2nd IEEE International Workshop on Data Mining in Bioinformatics.
• Singh, A., C. Feschotte and N. Stojanovic (2007) Micro-repetitive structure of genomic sequences and the identification of ancient repeat elements. In Proceedings of BIBM 2007, The IEEE International Conference on Bioinformatics and Biomedicine, 165-171.
• Singh, A., C. Feschotte and N. Stojanovic (2007) A study of the repetitive structure and distribution of short motifs in human genomic sequences. International Journal of Bioinformatics Research and Applications 3, 523-535.
• Stojanovic, N. (editor, 2007) Computational Genomics: Current Methods. Horizon Scientific Press.
• Singh, A. and N. Stojanovic (2006) An Efficient Algorithm for the Identification of Repetitive Variable Motifs in the Regulatory Sequences of Co-expressed Genes. In Proceedings of ISCIS 2006, the 21st International Symposyum on Computer and Information Sciences, ed. by A. Levi, H. Yenigun, E. Savas, S. Balcisoy and Y. Saygin, Springer-Verlag LNCS 4263, 182-191.
• Singh, A. and N. Stojanovic (2006) Computational Analysis of the Distribution of Short Repeated Motifs in Human Genomic Sequences. In Proceedings of the Biotechnology and Bioinformatics Symposyum, Biot-2006, 25-34.
• Stojanovic, N. and P. Berman (2006) A linear-time algorithm for studying genetic variation. In Algorithms in Bioinformatics, Proceedings of WABI 2006, ed. by P. Bucher and B. Moret, Springer-Verlag LNBI 4175, 344-354.
• Stojanovic, N. (2006) An Algorithm for the Automated Verification of DNA Supercontig Assemblies. In Applications of Evolutionary Computing, Proceedings of EvoWorkshops 2006, ed. by F. Rothlauf et al., Springer-Verlag LNCS 3907, 196-207.
• Stojanovic, N. and K. Dewar (2005) A Probabilistic Approach to the Assessment of Phylogenetic Conservation in Mammalian Hox Gene Clusters. In Proceedings of BIOINFO-2005, Joint Conference of InCoB, AASBi and KSBI, 118-123.
• Stojanovic, N. (2005) The Human Genome Project: Software Challenges and Future Directions. In Proceedings of the 3rd ACS/IEEE International Conference on Computer Systems and Applications, CD.
• Stojanovic, N. (2004) Computational methods for the analysis of differential conservation in groups of similar DNA sequences. Genome Informatics 15(2), 21-30.
• Stojanovic, N. and K. Dewar (2004) Identifying multiple alignment regions satisfying simple formulas and patterns. Bioinformatics 20(13), 2140-2142.
• Stojanovic, N., J.L. Chang, J. Lehoczky, M.C. Zody and K. Dewar (2002) Identification of mixups among DNA sequencing plates. Bioinformatics 18(11), 1418-1426.
• International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409(6822), 860-921.
• Florea, L., C. Riemer, S. Schwartz, Z. Zhang, N. Stojanovic, W. Miller and M. McClelland (2000) Web-based visualization tools for bacterial genome alignments. Nucleic Acids Research 28(18), 3486-3496.
• Stojanovic, N., L. Florea, C. Riemer, D. Gumucio, J. Slightom, M. Goodman, W. Miller and R. Hardison (1999) Comparison of five methods for finding conserved sequence in multiple alignments of gene regulatory regions. Nucleic Acids Research 27(19), 3899-3910.
• Riemer, C., A. ElSherbini, N. Stojanovic, S. Schwartz, P. Kwitkin, W. Miller and R. Hardison (1998) A database of experimental results on globin gene expression. Genomics 53, 325-337.
• Stojanovic, N., P. Berman, D. Gumucio, R. Hardison and W. Miller (1997) A linear-time algorithm for the 1-mismatch problem. In Algorithms and Data Structures, Proceedings of WADS '97, ed. by F. Dehne, A. Rau-Chaplin, J.-R. Sack and R. Tamassia, Springer-Verlag LNCS 1272, 126-135.
• Hardison, R., J. Slightom, D. Gumucio, M. Goodman, N. Stojanovic and W. Miller (1997) Locus control regions of mammalian beta-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights. Gene 205, 73-94.
• Slightom, J., J. Bock, D. Tagle, D. Gumucio, M. Goodman, N. Stojanovic, J. Jackson, W. Miller and R. Hardison (1997) The complete sequences of galago and rabbit beta-globin locus control regions: extended sequence and functional conservation outside the cores of DNase hypersensitive sites. Genomics 39, 90-94.
• Hardison, R., L. Elnitski, A. ElSherbini, A. Goldstrom, J. Jackson, J. Peck, C. Riemer, S. Schwartz, N. Stojanovic and W. Miller (1995) The Globin Gene Server: an aid to studying the regulation of mammalian globin gene clusters. Molecular Biology of Hemoglobin Switching, Proceedings of the 9th Conference on Hemoglobin Switching, Vol. 1, ed. by G. Stamatoyannopoulos, Intercept, 405-426.
• Jackson, J., A. ElSherbini, C. Riemer, N. Stojanovic, W. Miller and R. Hardison (1995) Effects of hypersensitive sites from the beta-globin LCR on enhancement in transfected cells: synergism between HS2 and HS3. Molecular Biology of Hemoglobin Switching, Proceedings of the 9th Conference on Hemoglobin Switching, Vol. 1, ed. by G. Stamatoyannopoulos, Intercept, 87-109.
• Miller, W., A. ElSherbini, J. Peck, C. Riemer, S. Schwartz, N. Stojanovic and R. Hardison (1995) A database for globin gene expression data. Proceedings of the 28th Annual Hawaii International Conference on System Sciences, 62-71.
• Hardison, R., K.-M. Chao, S. Schwartz, N. Stojanovic, M. Ganetsky, and W. Miller (1994) Globin Gene Server: a prototype E-mail database server featuring extensive multiple alignments and data compilation for electronic genetic analysis. Genomics 21, 344-353.
• Hardison, R., K.-M. Chao, M. Adamkiewicz, D. Price, J. Jackson, T. Zeigler, N. Stojanovic and W. Miller (1993) Positive and negative regulatory elements of the rabbit embryonic epsilon-globin gene revealed by an improved multiple alignment program and by functional analysis. DNA Sequence 4, 163-176.