About us

Members

Computational Biology Course: BIOC/STAT 442/842

Next-Generation Sequencing and Systems Biology Course: STAT 843

Projects

Publications

Patents / Copyrights

Optimal RNAi Design

Nucleosome Mapping

Istvan  (Steve) Ladunga, Ph.D.
Professor of Computational Biology
Head of the Computational Biology Research Lab
Department of Statistics
University of Nebraska - Lincoln

346C Hardin Hall North Wing, University of Nebraska-Lincoln
N. 33rd St., Lincoln, NE 68583-0963
Phone: (402) 472-6074    

Research

My Laboratory conducts research in the computational biology (you can call it bioinformatics) of:

•   Pluralistic and stochastic gene regulation
•   Regulation of genes that code for ribosomal proteins
•   Transcriptional regulation in the algae, including Chlamydomonas reinhardtii
•   Next generation sequencing including RNA-seq and ChIP-Seq
•   Structural principles of nucleosomes and nucleosome mapping,

Education

Ph.D. in Molecular Biology, summa cum laude, Budapest (Eotvos) University of Sciences, Hungary.
MS and BS in Biology, Budapest University of Sciences.

Professional Experience

Department of Statistics, University of Nebraska-Lincoln
Professor

Celera Genomics/Applied Biosystems, Foster City, CA
Senior Staff Scientist

AGY Therapeutics, Inc., South San Francisco, CA

SmithKline Beecham (now GlaxoSmithKine) Pharmaceuticals, King of Prussia, PA
Principal Investigator, Bioinformatics Dept.

Baylor College of Medicine, Human Genome Center, Houston
Visiting Research Associate

Department of Mathematics, Stanford University
Visiting Research Associate

Department of Genetics, Budapest University of Sciences
Research Associate

Institute for Computer Science and Automation (SZTAKI), Hungarian Academy of Sciences, Budapest
Postdoctoral

Selected Publications

• Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, Liu T, Madrigal P, Taslim C, Zhang J. (2013) Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data. PLoS Comput Biol. 9(11):e1003326.
• Brueggeman AJ, Gangadharaiah DS, Cserhati MF, Casero D, Weeks DP, Ladunga I. (2012) Activation of the Carbon Concentrating Mechanism by CO2 Deprivation Coincides with Massive Transcriptional Restructuring in Chlamydomonas reinhardtii. Plant Cell, epub ahead of print.
• Fang W, Si Y, Douglass S, Casero D, Merchant SS, Pellegrini M, Ladunga I, Liu P, Spalding MH. (2012) Transcriptome-Wide Changes in Chlamydomonas reinhardtii Gene Expression Regulated by Carbon Dioxide and the CO2-Concentrating Mechanism Regulator CIA5/CCM1. Plant Cell, epub ahead of print
• Blanc G, Agarkova I, Grimwood J, Kuo A, Brueggeman A, Dunigan D, Gurnon J, Ladunga I, Lindquist E, Lucas S, Pangilinan J, Proschold T, Salamov A, Schmutz J, Weeks D, Yamada T, Claverie JM, Grigoriev I, Van Etten J, Lomsadze A, Borodovsky M. (2012) The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation. Genome Biology, 13:R39
• Panda D, Das A, Dinh PX, Subramaniam S, Nayak D, Barrows NJ, Pearson JL, Thompson J, Kelly DL, Ladunga I, Pattnaik AK (2011). RNAi screening reveals requirement for host cell secretory pathway in infection by diverse families of negative-strand RNA viruses. Proc Natl Acad Sci U S A. 108(47):19036-41.
• Gonzalez, M, Sealls, W., Jesch, E.D., Brosnan, M.J., Ladunga, I., Ding, X, Black, P.N., DiRusso, C.C. (2011) Defining a relationship between dietary fatty acids and the cytochrome P450 system in a mouse model of fatty liver disease. Physiol Genomics 43(3):121-35. doi:10.1152/physiolgenomics.00209.
• 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. (2011) The sigma-1 receptor enhances brain plasticity and functional recovery after experimental stroke. Brain 134(Pt 3):732-46.
• 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.
• 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.
• 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 AM, Kachman SD, Ladunga I, Harshman LG. (2009) Transcriptional profiling of the sperm storage organs of Drosophila melanogaster. Insect Mol Biol. 18:465-475
• Ladunga I. (2009) Finding similar nucleotide sequences using network BLAST searches. Curr Protoc Bioinformatics. Chapter 3:Unit 3.3.
• Ladunga I. (2009) Finding homologs in amino acid sequences using network BLAST searches. Curr Protoc Bioinformatics. Chapter 3:Unit 3.4.
• 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.
• 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., 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. generic Viagra 31: 334-341.

Patents and copyrights

134 patents and copyrights listed >here<.
Selected patents/copyrights:

1. Ladunga, I., Smith, R.F and Wiese B.A.: FASTA-SWAP and FASTA-PAT: pattern database searches using combinations, filed in June, 1996. Copyright.
   
2. Ladunga, I. Methods and systems for identification of protein classes
   Patent Number: US5987390, 1999, Industry, United States of America.
3. A browsable database for biological use
   Patent Number: WO2004053769 (A3) , 2004, Industry, United States of America.
4. A browsable database for biological use
   Patent Number: US2005149269, 2005, Industry, United States of America.
5. A browsable database for biological use
   Patent Number: WO2004053769 (A2) , 2004, Industry, United States of America.
6. A browsable database for biological use
   Patent Number: EP1576524 (A3), 2004, Industry, United States of America.
7. A browsable database for biological use
   Patent Number: EP1576524 (A2), 2004, Industry, United States of America.
8. A browsable database for biological use
   Patent Number: EP1576524 (A0), 2004, Industry, United States of America.
9. A browsable database for biological use
   Patent Number: AU2003299589 (A1), 2004, Industry, United States of America.
10. A browsable database for biological use
    Patent Number: WO2004053769, 2004, Industry, United States of America.
11. Isolated human secreted proteins, nucleic acid molecules encoding human secreted proteins, and uses thereof
    Patent Number: US2005048560, 2005, Industry, United States of America.
12. Isolated human secreted proteins, nucleic acid molecules encoding human secreted proteins, and uses thereof
    Patent Number: US2005043229, 2005, Industry, United States of America.