SELECTED BRG PUBLICATIONS

JOURNALS | CONFERENCES | DISSERTATIONS AND THESES | TECHNICAL REPORTS

 

JOURNAL ARTICLES

  • Rouchka, E.C.  (2006)  “Aligning DNA sequences using dynamic programming.”  ACM Crossroads, 13(1):18-22. (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)
  • Knudsen, T.B.  (2004)  “Computational systems Biology.”  Reproductive Toxicology, 19(1):1-2. (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)
  • 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)

  • 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.

 

CONFERENCE PAPERS AND PRESENTATIONS

  • 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).
  • 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)

 


DISSERTATIONS, THESES AND PROJECTS
  • Thai, A.  (2007)  Evaluation of Using Swarm Intelligence to Produce Facility Layout Solutions..  Tim Hardin and Eric Rouchka, advisors. CECS Master's of Engineering Thesis.(pdf)
  • Yachim, Y.  (2007)  YMAGE: A Resource for Real-Time Sharing of High-Resolution Digital Images .  Eric Rouchka, advisor. CECS Master's of Engineering Thesis.(pdf)
  • Graves, P.  (2007)  EST Visualizer.  Eric Rouchka, advisor. CECS Master's of Engineering Project.(pdf)
  • Akkineni, V.  (2006)  Microarray Data Analysis Using Java and R.  Eric Rouchka, advisor. CECS Master's of Science Thesis.(pdf)
  • Rudraraju, Y.  (2006)  Degenerate Primer Design.  Eric Rouchka, advisor. CECS Master's of Science Project.(pdf)
  • Koparkar, A.  (2006)  Computational Detection of CPE Elements.  Eric Rouchka, advisor. CECS Master's of Science Project.(pdf)
  • Gundlapalli, R.  (2005)  Microarray Database Resource for Designing Custom Microarrays.  Eric Rouchka, advisor. CECS Master's of Science Thesis.(pdf)
  • Phatak, A.  (2005)  Using Relational Databases to Analyze Micorarray Probes and Single Nucleotide Polymorphisms.  Eric Rouchka, advisor. CECS Master's of Engineering Project.(pdf)
  • El-Hadik, S.  (2005)  .  Ahmed Desoky, advisor. CECS Master's Thesis.(pdf)
  • Hornsby, J.  (2005)  Implementation of Data Management Portion of MiDaR Project.  Eric Rouchka, advisor. CECS Master's Thesis.(pdf)
  • Mann, N.  (2004)  Developing a Database for GenBank Information.  Dar-jen Chang, advisor. CECS Master's Thesis.(pdf)
  • Sahasubrushe, P.  (2004)  The Java COG Kit Desktop: A Simple and Central Approach to Grid Computing Using the Graphical Desktop Paradigm.  Rammohan Ragade, advisor. CECS Master's Thesis.(pdf 11.0 MB)
  • Choi, H.  (2003)  Processing and analysis of DNA microarrays.  Ahmed Desoky, advisor. CSE Ph.D. Thesis.(pdf 19.9 MB)

TECHNICAL REPORTS
  • 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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