Areas of Expertise: Computational Biology (Bioinformatics), Biostatistics, Epigenetics, Optimization, Machine Learning
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 Comp. Biol. 2013 Nov;9(11):e1003326. doi: 10.1371/journal.pcbi.1003326.
Brueggeman AJ, Gangadharaiah DS, Cserhati MF, Casero M, Weeks DP, Ladunga I. (2012) Activation of the carbon concentrating mechanism by CO2 deprivation coincides with massive transcriptional restructuring in Chlamydomonas… Plant Cell, 4(5):1860-75.
Fang W, Si Y, Douglass S, Casero D, Merchant, SS, Pellegrini M, Ladunga I, Liu P, Spalding MH. (2012) Genome-wide Changes in Chlamydomonas Gene Expression Regulated by Carbon Dioxide and the Transcription Regulator ... Plant Cell, 4(5):1876-93.
Blanc G, .., Ladunga I, …, Weeks D, Yamada T, Claverie JM, Grigoriev I, van Etten J (2012) The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation. Genome Biol., 13(5):R39.
Panda, D., …, 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. Proc. Natl. Acad. Sci. U.S.A. 108:19036-41.
Ruscher, K, .., 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.
Belch, Y, .. , Ladunga, I. (2010). Weakly positioned nucleosomes enhance the transcriptional competency of chromatin. PLoS One. 5(9):e12984.
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.
Ladunga I. (2010). An overview of the computational analyses and discovery of transcription factor binding sites. In: Ladunga, I. (ed.) Computational Biology of Transcription Factor Binding. pp. 1-22, Humana Press, New York.
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. . In: Ladunga, I. (ed.) Computational Biology of Transcription Factor Binding. pp. 161-77, Humana Press, New York.
Ladunga I. (2007) More complete silencing by fewer siRNAs: Transparent optimized design and a biophysical signature. Nucl Acids Res 35(2):433-440. 4.
Prokoupek A, Kachman SD, Ladunga I, Harshman LG. Transcriptional profiling of the sperm storage organs of Drosophila melanogaster. Insect Mol Biol, 18(4):465-475.
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, 20:568-579.
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 Chlamydomonas reinhardtii. Genetics, 179(1):177-192.
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.
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 RF(1997) Amino acid substitution patterns conserve folding of proteins by preserving steric and hydrophobicity properties. Protein Engineering 10: 187-196.
Ladunga I, Wiese BA and Smith RF (1996) FASTA-SWAP and FASTA-PAT: pattern database searches using combinations of aligned amino acids and a novel scoring theory. J. Mol. Biol. 259: 840-854.
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 BE (1994). Heterogeneity of genomes: measures and values. Proc. Natl. Acad. Sci. U.S.A., 91: 12837-12841.
Patents and Copyrights:
Ladunga I et al. (2000 - 2007) Over 100 patents on sequences of secreted proteins, filed by Celera Genomics Corp.
Ladunga I. Methods and Systems for the Identification of Protein Classes. Sole inventor, filed by SmithKline Beecham, Granted: Nov. 16, 1999, Patent Number: 5,987,390.
Muruganujan A; Guo N; Mi H; Rabkin S; Thomas PD; Diemer K; Kejariwal A; Ladunga I; et al.: A browsable database for biological use. 2004, Patent Number: WO2004053769.
Ladunga I, Smith RF and Wiese BA: FASTA-SWAP and FASTA-PAT: pattern database searches using combinations, 1996. Copyright.