Publications

Ladunga, I. (2010) (Editor) Computational Biology of Transcription Factor Binding.In the series: Methods in Molecular Biology. Springer, Berlin.ISBN: 978-1-60761-853-9
Belch Y, Yang J, Liu Y, Malkaram SA, Liu R, Riethoven JJ, Ladunga I. (2010) Weakly positioned nucleosomes enhance the transcriptional competency of chromatin. PloS One 5(9):e12984. Full text
Ladunga, I. (2010) An overview of the computational analyses and discovery of transcription factor binding sites. Methods Mol Biol. 674:1-22.
Jiao S, Bailey CP, Zhang S, Ladunga I. (2010) Probabilistic peak calling and controlling false discovery rate estimations in transcription factor binding site mapping from ChIP-seq. Methods Mol Biol. 674:161-177.
Gonzalez, M, Sealls, W., Jesch, E.D., Brosnan, M.J., Ladunga, I., Ding, X, Black, P.N., DiRusso, C.C. (2010) Defining a relationship between dietary fatty acids and the cytochrome P450 system in a mouse model of fatty liver disease. Physiol Genomics doi:10.1152/physiolgenomics.00209.2010
Ruscher, K.; Shamloo, M.; Rickhag, M.; Ladunga, I.; Soriano, L.; Gisselsson, L.; Toresson, H.; Ruslim-Litrus, L.; Oksenberg, D.; Urfer, R.; Johansson, B.; Nikolich, K.; Wieloch, T. (2010) The sigma-1 receptor enhances brain plasticity and functional recovery after experimental stroke. Brain Accepted for publication.
van Dijk K, Ding Y, Malkaram S, Riethoven JJ, Liu R, Yang J, Laczko P, Chen H, Xia Y, Ladunga I, Avramova Z, Fromm M.(2010) Dynamic Changes in Genome-Wide Histone H3 Lysine 4 Methylation Patterns in Response to Dehydration Stress in Arabidopsis thaliana. BMC Plant Biol. 10(1):238.
Prokupek, A.M., Kachman, S.D., Ladunga, I., Harshman, L.G. (2009)
Transcriptional profiling of the sperm storage organs of Drosophila melanogaster. Insect Mol. Biol. 18(4):465-75. Epub 2009 Apr 24. PMID: 19453766.
Ladunga I. (2009)
Finding similar nucleotide sequences using network BLAST searches. Curr. Protoc. Bioinformatics. Chapter 3:Unit 3.3. PMID: 19496060.
Ladunga I. (2009)
Finding homologs in amino acid sequences using network BLAST searches. Curr. Protoc. Bioinformatics. Chapter 4:Unit 3.4. PMID: 19274633.
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. (2007)
More Complete Gene Silencing by Fewer siRNAs: Transparent Optimized Design and Biophysical Signature. Nucleic Acids Res. 35(2):433-440, Epub: 2006 Dec 14.
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.
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.
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., CzakÃ³, 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.

Patents and copyrights

134 patents and copyrights listed >here<.

Ladunga, I., Smith, R.F and Wiese B.A. (1996)
FASTA-SWAP and FASTA-PAT: pattern database searches using combinations. 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.
Canadian online pharmacy 365
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.