User:Istvan Ladunga
NAME Ladunga, Istvan (Steve) POSITION TITLE
Full Professor
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) INSTITUTION AND LOCATION DEGREE (if applicable) YEAR(s) FIELD OF STUDY
Budapest (Eotvos) University of Sciences,
Budapest, Hungary
BS and MS
1971-1976
Biology
Budapest (Eotvos) University of Sciences, Budapest, Hungary
Ph.D.
1978
Molecular Biology
Institute for Computer Science, Hungarian Academy of Sciences, Budapest, Hungary
Postdoctoral
1978-1981
Mathematical models in biology
A. Professional Interests Computational biology (bioinformatics), biostatistics including chromatin structure, regulation of gene expression, genome compaction, next-generation sequencing including RNA sequencing and chromatin immunoprecipitation, experimental design. Collaboration with experimental biologists on high-throughput experiments. http://compbio.unl.edu/steve_ladunga.html B. Positions and Honors.
1979-1986 Research Associate, Institute for Computer Science, Hungarian Acad. Sciences, Budapest. 1986-1989 Head of Department, Department of International Cooperation, National Committee for Technological Development, Budapest. 1989-1993 Senior Research Associate, Department of Genetics, Budapest University of Sciences, 1993-1994 Visiting Research Associate, Department of Mathematics, Stanford University. 1994-1996 Visiting Res. Associate, Human Genome Center, Baylor College of Medicine, Houston, TX. 1996-2000 Principal Investigator, SmithKline Beecham Pharmaceuticals (now GlaxoSmithKline), Bioinformatics Department, King of Prussia, PA. 2000-2004 Senior Staff Scientist, Celera Genomics/Applied Biosystems, Foster City, CA. 2004-2005 Consultant, AGY Therapeutics, Inc., South San Francisco, CA. 2005-present Professor, Department of Statistics, University of Nebraska-Lincoln.
Honors 1977 First Prize of the Faculty of Natural Sciences, Budapest University. 1978 Grand Prix of the Ministry of Education. 1978 Special Prize of the Hungarian Society for Biology.
Other Experience and Professional Memberships
1979-1981 Member, Committee for the Nationwide Agro-Ecological Survey, Budapest, Hungary 1986-1989 Chair, Department of International Collaboration, Natl. Committee for Technological Development, Budapest. 1990-1991 Organizing Committee for the Third Congress of the European Society for Evol. Biology. 1994-present International Society for Computational Biology 1996-2002 Protein Society 1998-present American Association for the Advancement of Science 2002-present Computer Society, Inst. Electric and Electronic Engineers 2007-2008 Organization Committee, Internatl. Symp. on Bioinformatics Research. & Applications 2010-present Committee for Research, Academic Senate, UNL 2011-present Committee for Information Technology, UNL
C. Publications
1. Panda, D., Das, A. Dinh, P.X., Subramaniam, S., Nayak, D., Barrows, N.J., Pearson, J.L., Kelly, D.L., Ladunga, I., Pattnaik, A.K. (2011) RNAi Screening Reveals A Requirement for Host Cell Secretory Pathway in Infection by Diverse Families of Negative-Strand RNA Viruses. Submitted to Proc. Natl. Acad. Sci. U.S.A. 2. Ruscher, K, Shamloo, M, Rickhag, M, Deierborg, T, Ladunga, I, Gisselsson, L, Toresson, H, Johansson, B, Helenius, A, Nikolich, K, Urfer, R, Wieloch, T. (2011) Sigma-1 receptor activation enhances brain plasticity and functional recovery after experimental stroke. Brain, 134:732-746. 3. Belch, Y, Yang, J, Malkaram, SA , Liu, R , Riethoven, JJM , Ladunga, I. (2010). Weakly positioned nucleosomes enhance the transcriptional competency of chromatin. PLoS One. 5(9):e12984. 4. Ladunga I (Editor) (2010) Computational Biology of Transcription Factor Binding. In the series “Methods in Molecular Biology”, Vol. 674, Series Editor John Walker, Springer/Humana Press. New York. 5. Ladunga, I. (2010) An overview of the computational biology of transcription factor binding. In: Computational Biology of Transcription Factor Binding (Editor: Ladunga, I), pp. 1-Springer/Humana Press, New York. 6. 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. 7. Jiao, S, Bailey, CB, Zhang, S, Ladunga, I (2010) Probabilistic peak calling and controlling false discovery rate estimations in transcription factor binding site mapping from ChIP-seq. In: Computational Biology of Transcription Factor Binding (Editor: Ladunga, I), pp. 161-77. Humana Press, New York 8. 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. 9. Prokoupek A, Kachman SD, Ladunga I, Harshman LG. (2009) Transcriptional profiling of the sperm storage organs of Drosophila melanogaster. Insect Mol. Biol., 18(4):465-475. 10. Wang Y, Ladunga I, Miller AR, Horken KM, Plucinak T, Weeks DP, Bailey CP. (2008) The small ubiquitin-like modifier (SUMO) and SUMO-conjugating system of C. reinhardtii. Genetics, 179(1):177-192. 11. Ladunga I. (2008) More complete silencing by fewer siRNAs: Transparent optimized design and a biophysical signature. Nucl Acids Res 35(2):433-440. 12. Abdelaty S, Alvarez-Venegas R, Yilmaz M, Le O, Hou Q, Sader M, Al-Abdallat A, Xia Y, Lu G, Ladunga I, Avramova Z. The highly similar Arabidopsis homologs of Trithorax atx1 and atx2 encode divergent biochemical functions. Plant Cell, 2008 20:568-579. 13. Ladunga I (2009) Finding similar nucleotide sequences using network BLAST searches. Curr Protoc Bioinformatics. Chapter 3: Unit 3.3. 14. Ladunga I (2009) Finding homologs in amino acid sequences using network BLAST searches. Curr Protoc Bioinformatics. Chapter 4: Unit 3.4. 15. Ladunga, I. (2000) Large-scale discovery of secretory proteins from nucleic acid sequences. Current Opinion in Biotechnology,11:13-18. 16. 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. 17. 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. 18. Ladunga, I. (2002) Finding homologs in amino acid sequences using network BLAST searches. Curr. Prot. Bioinf., Chapter 3.4. 19. Ladunga, I. (2002) Finding homologs in nucleic acid sequences using network BLAST searches. Curr. Prot. Bioinf., Chapter 3.3.. 20. Karlin, S., and Ladunga, I. (1994). Novel comparisons of genomic sequences in Eukaryotes. Proc. Natl. Acad. Sci. U.S.A., 91: 2832-12836. 21. 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. 22. Ladunga, I. (1992) Phylogenetic continuum indicates "galaxies" in the protein universe. Journal of Molecular Evolution, 34: 358-375. 23. 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. 24. Ladunga, I. (1999). OLIGOPAT: Oligopeptide Pattern Analysis and Prediction of Proteins by Mathematical Programming. Protein Sci,.8, Suppl. 1., 157. 25. Ladunga, I. (1998) A Novel Sequence Analysis Based on Weighted Physicochemical Properties of Amino Acid Residues. Protein Sci. 7: 75. 26. 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 1. 134 patents and copyrights listed >here<. Selected patents/copyrights: 2. Ladunga, I., Smith, R.F and Wiese B.A.: FASTA-SWAP and FASTA-PAT: pattern database searches using combinations, 1996. Copyright. 3. Ladunga, I. Methods and systems for identification of protein classes. Patent Number: US5987390, 1999, Industry, United States of America. 4. A browsable database for biological use Patent Number: WO2004053769 (A3) , 2004, Industry, United States of America. 5. A browsable database for biological use.Patent Number: US2005149269, 2005, Industry, United States of America. 6. A browsable database for biological use. Patent Number: WO2004053769 (A2) , 2004, Industry, United States of America. 7. A browsable database for biological use Patent Number: EP1576524 (A3), 2004, Industry, United States of America. 8. A browsable database for biological use. Patent Number: EP1576524 (A2), 2004, Industry, United States of America. 9. A browsable database for biological use. Patent Number: EP1576524 (A0), 2004, Industry, United States of America. 10. A browsable database for biological use. Patent Number: AU2003299589 (A1), 2004, Industry, United States of America. 11. A browsable database for biological use. Patent Number: WO2004053769, 2004, Industry, United States of America. 12. Isolated human secreted proteins, nucleic acid molecules encoding human secreted proteins, and uses thereof. Patent Number: US2005048560, 2005, Industry, United States of America. 13. Isolated human secreted proteins, nucleic acid molecules encoding human secreted proteins, and uses thereof. Patent Number: US2005043229, 2005, Industry, United States of America.
Current Research Support IANR Life Sciences Initiative: MicroRNA regulators and Gene Co-Expression Networks as Models for the Enhancements of Algal Bioenergy Production. PI. Nebraska Research Initiative (NRI), “Advancing Nebraska Research through Supercomputing", Co-PI.
NSF MRI 0821538: Acquisition High Capacity DNA Sequencing System. Fromm, M.E. (PI), 2008-11. Co-PI
Completed Research Support Nanotechnology-Enhanced Epigenomics. NSF EPSCoR EPS-0701892 Choobineh (PI), Multi-investigator Grant, Role: Co-Investigator, 2008-2010 Nebraska Research Initiative (NRI) Enhancement of the UNL Bioinformatics Core Research Facility (BCRF) PI: Ladunga, I., 01/04/2007 –01/31/2008 UNL Strategic Research Cluster Grant, Chromatin Biology, PI: Fromm, M.E., 2007-2008 Role: Co-PI. UNL Cyberinfrastructure Development, PI: Ladunga, I. 2006-2007.
Advisor and Post Doctoral Advisor Graduate students and Research Assistants: Dayananda S. Gangadharaiah, Samuel McInturf, Yang Liu, Peter Laczko, Jingyi Yang, Jason Wendler, Shuo Jiao. Postdoctoral Associates: Matthew F. Cserhati, Sridhar A. Malkaram, Rong Liu, Jaime Davila, Baoqiang Cao, Ralph Brandenberger, Erika Lindquist, Ada Wong, Tony Ceccardi.
