Publications

Protein Interactions

Vacic V, Oldfield CJ, Mohan A, Radivojac P, Cortese MS, Uversky VN, and Dunker AK. "Characterization of molecular recognition features, MoRFs, and their binding partners." Journal of Proteome Research. 6(6):2351-66. (2007)

Vacic V, Oldfield CJ, Mohan A, Radivojac P, Cortese MS, Uversky VN, and Dunker AK. "Analysis of molecular recognition feature complexes." Poster presented at the 51st Biophysical Society Annual Meeting, Baltimore, Maryland. (2007)

Mohan A, Oldfield CJ, Radivojac P, Vacic V, Cortese MS, Dunker AK, and Uversky VN. "Analysis of molecular recognition features (MoRFs)." Journal of Molecular Biology, 362(5):1043-59. (2006)

Dunker AK, Mohan A, Vacic V, Radivojac P, Oldfield CJ, Cortese MS, and Uversky VN. "Molecular Recognition Features, MoRFs." Poster presented at the 50th Biophysical Society Annual Meeting, Salt Lake City, Utah. (2006)

Small RNAs

Vacic V, Jin H, Zhu J-K, and Lonardi S. "A probabilistic method for small RNA flowgram matching." Pacific Symposium on Biocomputing, PSB'08, 13:75-86. (2008) slides   web site

Jin H, Vacic V, Girke T, Lonardi S, and Zhu J-K. "Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis." BMC Molecular Biology. 9:6. (2008)

Visual Data Mining

Vacic V, Uversky VN, Dunker AK, and Lonardi S. "Composition Profiler: a tool for discovery and visualization of amino acid composition differences." BMC Bioinformatics. 8:211. (2007) web site

Vacic V, Iakoucheva LM, and Radivojac P. "Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments." Bioinformatics, 22(12):1536-7. (2006) web site

Comparative Genomics

Fu Z, Chen X, Vacic V, Nan P, Zhong Y, and Jiang T. "MSOAR: a high-throughput ortholog assignment system based on genome rearrangement." Journal of Computational Biology. 14(9):1160-75. (2007) web site

Fu Z, Chen X, Vacic V, Nan P, Zhong Y, and Jiang T. "A parsimony approach to genome-wide ortholog assignment." ACM Annual Conference on Research in Computational Molecular Biology, RECOMB'06, Venice, Italy. (2006)

Protein Disorder

Sickmeier M, Hamilton JA, LeGall T, Vacic V, Cortese MS, Tantos A, Szabo B, Tompa P, Chen J, Uversky VN, Obradovic Z, and Dunker AK. "DisProt: the database of disordered proteins." Nucleic Acids Research. 35:D786-93. (2007). web site

Vucetic S, Obradovic Z, Vacic V, Radivojac P, Peng K, Iakoucheva LM, Cortese MS, Lawson JD, Brown CJ, Sikes JG, Newton CD, and Dunker AK. "Disprot: a database of protein disorder." Bioinformatics, 21(1): 137-140. (2005)

Vacic V, Riggen S, Lewis A, Patterson E, Sickmeier M, Baird J, Hamilton J, Kim D, Cortese MS, Chen J, Radivojac P, Uversky VN, Vucetic S, Obradovic Z, and Dunker AK. "DisProt: a database of protein disorder." Poster presented at the Indiana Proteomics Symposium, Bloomington, Indiana. (2004)