- Rouchka, E.C. (2006) “Aligning DNA sequences using dynamic programming.” ACM Crossroads, 13(1):18-22. (pdf)
- Rempala GA, Ramos KS, Kalbfleisch T. (2006) “A stochastic model of gene transcription: an application to L1 retrotransposition events..” J Theor Biol., 242(1):101-116. (pdf)
- Datta S, Datta S. (2006) “Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes” BMC Bioinformatics, 7:397. (pdf)
- Datta S, Datta S. (2006) “Evaluation of clustering algorithms for gene expression data.” BMC Bioinformatics, 7(Suppl 4):S17. (pdf)
- Datta S, Le-Rademacher, J. and Datta, S. (2006) “Predicting patient survival from microarray data by accelerated failure time modeling using partial least squares and LASSO.” Biometrics, To appear2yy. (pdf)
- Datta S, de Padilla M. (2006) “Feature selection and machine learning with mass spectrometry data for distinguishing cancer and non-cancer samples.” Statistical Methodology, (Special Issue on Bioinformatics) 3:79-92. (pdf)
- Rouchka, E.C., Khalyfa, A., Cooper, N.G.F. (2005) “MPrime: efficient large scale multiple primer and oligonucleotide design for cutomized gene arrays.” BMC Bioinformatics, 6:175. (pdf)
- Nemeth, K.A., Singh, A.V., Knudsen, T.B. (2005) “Searching for biomarkers of developmental toxicity with microarrays: normal eye morphogenesis in rodent embryos.” Toxicology and Applied Pharmacology, 206(2005):219-228. ( pdf)
- Knudsen K.B., Singh, A.V., Knudsen, T.B. (2005) “Data input module for Birth Defects Systems Manager.”
Reproductive Toxicology, 20(3):369-375. (pdf)
- Singh, A.V., Knudsen, K.B., Knudsen, T.B. (2005) “Computational systems analysis of developmental toxicity: design, development and implementation of a Birth Defects Systems Manager (BDSM).”
Reproductive Toxicology, 19(3):421-439. (pdf)
- Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, Zheng H, Bakker E, Calabrese P, Gladstone J, Goyal R, Jakobsson M, Kim S, Morozov Y, Padhukasahasram B, Plagnol V, Rosenberg NA, Shah C, Wall JD, Wang J, Zhao K, Kalbfleisch T, Schulz V, Kreitman M, Bergelson J. (2005) “The pattern of polymorphism in Arabidopsis thaliana.”
PLos Biol., 3(7):e96. (pdf
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- Datta S, Datta S. (2005) “
Empirical Bayes screening (EBS) of many p-values with applications to microarray studies.” Bioinformatics, 21, 1987-1994. (pdf)
- Knudsen, T.B. (2004) “Computational systems Biology.”
Reproductive Toxicology, 19(1):1-2. (pdf)
- Warrenfeltz, Z., Pavlik, S., Datta, S., Kraemer, E., Benedict, B. Mcdonald, J. F. (2004) “
Gene expression profiling of epithelial ovarian tumors corelated with malignant potential.” Molecular Cancer, 3:27. (pdf)
- Datta, S., Satten, G. A., Benos, D. J., Xia, J., Heslin, M., and Datta, S. (2004) “
An empirical Bayes adjustment to increase the sensitivity of detecting differentially expressed genes in microarray experiments.” Bioinformatics, 20:235-242. (pdf)
- Thompson, W., Rouchka, E.C., Lawrence, C.E. (2003) “Gibbs Recursive Sampler: finding transcription factor binding sites.” Nucleic Acids Research, 31(13):3580-3585. (pdf)
- G., Brehm, S., Datta, S., and Adams, M. W. W. (2003) “
Whole Genome DNA microarray of a hyperthermophile and an archaeon: Pyrococcus furious grown on peptides and carbohydrate.” Journal of Bacteriology, 185:3935-3947. (pdf)
- Datta S, Datta S. (2003) “Comparisons and validation of statistical clustering techniques for microarray gene expression data.
” Bioinformatics, 19:459-466. (pdf)
- Datta S. (2003) “Statistical techniques for microarray data: A partial overview.
” Communications in Statistics-Theory and Methods, 32,263-280. (pdf)
- Rouchka, E.C., Gish, W., States, D.J. (2002) “Comparison of Whole Genome Assemblies of the Human Genome.” Nucleic Acids Research, 30(22):5004-5014. (pdf)
- Kan, Z., Rouchka, E.C., Gish, W.R., States, D.J. (2001) "Gene structure prediction and alternative splicing analysis using genomically aligned ESTs." Genome Research, 11(5):889-900. (abstract)
- Stephens JC, Schneider JA, Tanguay DA, Choi J, Acharya T, Stanley SE, Jiang R, Messer CJ, Chew A, Han JH, Duan J, Carr JL, Lee MS, Koshy B, Kumar AM, Zhang G, Newell WR, Windemuth A, Xu C, Kalbfleisch TS, Shaner SL, Arnold K, Schulz V, Drysdale CM, Nandabalan K, Judson RS, Ruano G, Vovis GF. (2001) "Haplotype variation and linkage disequilibrium in 313 human genes." Science, 293(5529):489-493. (pdf)
- Datta S. (2001) “Exploring relationships in gene expressions: A partial least squares approach.
” Gene Expression, 9:257-264. (pdf)
- Desoky, A., Rash, G., Wachowiak, M., Peter Quesada "Wavelet Based Noise Removal Techniques of Biomechanical Signals" IEEE Transactions on Biomedical Engineering,VOL 47, NO. 3, MARCH 2000.
- Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM. "A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae." Nature, 403(6770):623-627. (pdf)
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- Boratyn GM, Datta S, Datta S., “Biologically supervised hierarchical clustering algorithms for gene expression data.” Proceedings of the 28th IEEE EMBS Annual International Conference, New York, New York, 5515-5518, 2006.
- Datta S, Datta S., “Validation measures for clustering algorithms incorporating biological information.” IEEE Proceedings of International Multi-Symposiums on Computer and Computional Sciences (IMSCCS|06), 131-135, 2006.
- Hardin, C.T., Rouchka, E.C., “DNA Motif Detection Using Particle Swarm Optimization and Expectation-Maximization.” Proceedings of the 2005 IEEE Swarm Intelligence Symposium, Pasedina, California, June 2005. (pdf).
- Cha, I.E., Rouchka, E.C., “Comparison of Current BLAST Software on Nucleotide Sequences” Proceedings of the Fourth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2005), Denver, Colorado, April 4, 2005. (pdf).
- Datta S, Datta S., “An empirical Bayes adjustment to multiple p-values for the detection of differentially expressed genes in microarray experiments.” Bioinformatics 2004, Conferences in Research and Practice in Information Technology - Second Asia-Pacific Bioinformatics Conference, Sydney, Austraalia, 2004, 155-159.
- Eltonsy, N., Tourassi, G.,Desoky, A., Elmaghraby, A. “A Methodology for Analysis, Extraction, and Visualization of CT Scans ” ISSPIT-2003, Dermstadt, Germany, December 14 – 17.
- Chris Hall, Dar-jen Chang, Ahmed Desoky “Client/Server Application for the Analysis of Gene Expressions” ICIS-2002, Boston, MA, July 18 – 20.
- Ahmed Desoky, Eugenia Wang "Software System for DNA Fingerprinting" Research Louisville, Jewish Hospital Foundation, Norton Healthcare, and U of L Healthcare, October 29 - Nov 2, 2001, page F10.
- Ahmed H. Desoky, Hee Jun Choi "Hybrid Wavelet_Discerte Cosine Transform" 5 th International Conference on Engineering Design and Automation (EDA 2001), August 5 - 8, 2001, Las Vegas, Nevada.
- Kan, Z., Gish, W., Rouchka, E., Glasscock, J., States, D. (2000) "UTR Reconstruction and Analysis Using Genomically Aligned EST Sequences." ISMB, 8:218-227. (pdf)
- Blackwell, T.W., Rouchka, E. C., States, D.J. (1999) "Identity by Descent Genome Segmentation Based on Single Nucleotide Polymorphism Distributions." ISMB, 7:54-59. (pdf)
- Rouchka, E.C., States, D.J., (1998) "Sequence Assembly Validation by Multiple Restriction Digest Fragment Coverage Analysis" ISMB, 6:140-147. (pdf)
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- Rouchka, E.C. (2002) “Assembly and Compositional Analysis of Human Genomic Data.” D. Sc. Dissertation, Technical Report, Washington University Department of Computer Science, WUCS-2002-39.
(pdf 3.9MB)
- Rouchka, E.C., States, D.J. (2002) “Compositional Analysis of Homogeneous Regions in Human Genomic DNA.” Technical Report, Washington University Department of Computer Science, WUCS-2002-02. (pdf)
- Rouchka, E.C., (1999) "Pattern Matching Techniques and Their Applications to Computational Molecular Biology-- A Review." Technical Report, Washington University Department of Computer Science, WUCS-99-09. (pdf)
- Rouchka, E. C., States, D.J. (1999) "Assembly and Analysis of Extended Human Genomic Contig Regions." Technical Report, Washington University Department of Computer Science, WUCS-99-10. (pdf)
- Rouchka, E.C., States, D.J., (1997) "Sequence Assembly Validation by Restriction Digest Fingerprint Comparison." Technical Report, Washington University, Department of Computer Science, WUCS-97-40.
(pdf)
- Rouchka, E.C., Mazzarella, R., States, D.J., (1997) "Computational Detection of CpG Islands in DNA." Technical Report, Washington University, Department of Computer Science, WUCS-97-39. (pdf)
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