Publications
Papers in international, peer-reviewed journals
- Ladunga, I. (2008) (Editor) The Computational Biology of Transcription Factor Binding.In the series: Methods in Molecular Biology. Springer, Berlin.In preparation
- Y. Wang, I. Ladunga, A.R. Miller, K. M. Horken, T. Plucinak, D. P. Weeks, and C. P. Bailey. (2008)
The Small Ubiquitin-like Modifier (SUMO) and SUMO
Conjugating System of Chlamydomonas reinhardtii. Genetics,179(1):177-192.
- Abdelaty S, Alvarez-Venegas R, Yilmaz M, Le O, Hou Q, Sader M, Al-Abdallat A, Xia Y, Lu G, Ladunga I, Avramova Z. (2008). The highly similar Arabidopsis homologs of Trithorax atx1 and atx2 encode divergent biochemical functions. Plant Cell, 20(3):568-579.
- Ladunga, I. (2006) More Complete Gene Silencing by Fewer siRNAs: Transparent Optimized Design and Biophysical Signature. Nucleic Acids Res. Epub: 2006 Dec 14.
- Ladunga, I. (1999) PHYSEAN: PHYsical SEquence ANalysis of Proteins. Bioinformatics, 15: 128-138.
- Ladunga, I. (2000) Large-scale discovery of secretory proteins from nucleic acid sequences. Current Opinion in Biotechnology,11:13-18, invited paper.
- Ladunga, I., and Smith, R.F.(1997) Amino acid substitution patterns conserve folding of proteins by preserving steric and hydrophobicity properties. Protein Engineering 10: 187-196.
- Ladunga, I., Wiese, B.A. and Smith, R.F. (1996) FASTA-SWAP and FASTA-PAT: pattern database searches using combinations of aligned amino acids and a novel scoring theory. Journal of Molecular Biology. 259: 840-854.
- Ladunga, I. (2002) Finding homologs in amino acid sequences using network BLAST searches. Curr. Prot. Bioinf., Chapter 3.4. Published online November 2002
- Ladunga, I. (2002) Finding homologs in nucleic acid sequences using network BLAST searches. Curr. Prot. Bioinf., Chapter 3.3. Published online August 2002
- Karlin, S., and Ladunga, I. (1994). Novel comparisons of genomic sequences in Eukaryotes. Proc. Natl. Acad. Sci. U.S.A., 91: 2832-12836.
- Karlin, S., Ladunga, I., and Blaisdell, B.E.(1994). Heterogeneity of genomes: measures and values. Proc. Natl. Acad. Sci. U.S.A., 91: 12837-12841.
- Ladunga, I. (1992) Phylogenetic continuum indicates "galaxies" in the protein universe. Journal of Molecular Evolution, 34: 358-375.
- Ladunga, I., Czakó, F, Csabai, I., and Geszti, T. (1991) Improving prediction accuracy of signal peptides by simulated neural networks. Computer Applications in the BioSciences, 7: 485-487.
- Ladunga, I. (1999). OLIGOPAT: Oligopeptide Pattern Analysis and Prediction of Proteins by Mathematical Programming Protein Sci,.8, Suppl. 1., 157.
- Ladunga, I. (1998) A Novel Sequence Analysis Based on Weighted Physicochemical Properties of Amino Acid Residues. Protein Sci. 7: 75.
- Thomas, P.D., Kejariwal, A., Campbell, M.J., Mi, H., Diemer, K., Guo, N., Ladunga, I., Ulitsky-Lazareva, B., Muruganujan, A., Rabkin, S., Vandergriff, J.A., and Doremieux, O. (2003) PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids. Res., 31: 334-341.
Patents and copyrights
134 patents and copyrights listed >here<.
- Ladunga, I., Smith, R.F and Wiese B.A.: FASTA-SWAP and FASTA-PAT: pattern database searches using combinations, filed in June, 1996. Copyright.
- Methods and systems for identification of protein classes
Patent Number: US5987390, 1999, Industry, United States of America.
- A browsable database for biological use
Patent Number: WO2004053769 (A3) , 2004, Industry, United States of America.
- A browsable database for biological use
Patent Number: US2005149269, 2005, Industry, United States of America.
- A browsable database for biological use
Patent Number: WO2004053769 (A2) , 2004, Industry, United States of America.
- A browsable database for biological use
Patent Number: EP1576524 (A3), 2004, Industry, United States of America.
- A browsable database for biological use
Patent Number: EP1576524 (A2), 2004, Industry, United States of America.
- A browsable database for biological use
Patent Number: EP1576524 (A0), 2004, Industry, United States of America.
- A browsable database for biological use
Patent Number: AU2003299589 (A1), 2004, Industry, United States of America.
- A browsable database for biological use
Patent Number: WO2004053769, 2004, Industry, United States of America.
- Isolated human secreted proteins, nucleic acid molecules encoding human secreted proteins, and uses thereof
Patent Number: US2005048560, 2005, Industry, United States of America.
- Isolated human secreted proteins, nucleic acid molecules encoding human secreted proteins, and uses thereof
Patent Number: US2005043229, 2005, Industry, United States of America.
Book chapters and dissertations
- Ladunga, I. (1982) Molecular evolution. In: Vida G.(ed.): The Genetic Basis of Evolution. (in Hungarian), pp. 157-207, Natura, Budapest.
- Ladunga, I. Computer Analyses of Protein Evolution. Ph.D. Thesis (in Hungarian). Budapest University of Sciences.
- Ladunga I. Computer Analysis and Simulation of Protein Evolution. Master’s Thesis (in Hungarian). Budapest University of Sciences.
