Bioinformatics Lab UofL

Publications

Journal Articles

2016

Park JW, Jung S, Rouchka EC, Tseng YT, Xing Y. (2016) “rMAPS: RNA map analysis and plotting server for alternative exon regulation.” Nucleic Acids Research, epub ahead of print. (pdf).
Cieply B, Park JW, Nakauka-Ddamba A, Bebee TW, Guo Y, Shang X, Lengner CJ, Xing Y, Carstens RP. (2016) “Multiphasic and Dynamic Changes in Alternative Splicing during Induction of Pluripotency Are Coordinated by Numerous RNA-Binding Proteins.” Cell Reports, 15(2):247-255. (pdf).
Yang Y, Park JW, Bebee TW, Warzecha CC, Guo Y, Shang X, Xing Y, Carstens RP. (2016) “Determination of a Comprehensive Alternative Splicing Regulatory Network and Combinatorial Regulation by Key Factors during the Epithelial-to-Mesenchymal Transition.” Molecular and Cellular Biology, 36(11):1704-1719. (pdf).
Ji X, Park JW, Bahrami-Samani E, Lin L, Duncan-Lewis C, Pherribo G, Xing Y, Liebhaber SA. 2016. “αCP binding to a cytosine-rich subset of polypyrimidine tracts drives a novel pathway of cassette exon splicing in the mammalian transcriptome.” Nucleic Acids Research, 44(5):2283-2297. (pdf).
Lin L, Jiang P, Park JW, Wang J, Lu ZX, Lam MP, Ping P, Xing Y. 2016. “The contribution of Alu exons to the human proteome.” Genome Biology, 17:15. (pdf).
Rouchka EC, Jeoung M, Jang ER, Liu J, Wang C, Li X, Galperin E. 2016. “Data set for transcriptional response to depletion of the Shoc2 scaffolding protein.” Data in Brief, 7:770-778. (pdf).
Flight RM, Harrison BJ, Mohammad F, Bunge MB, Moon LDF, Petruska JC, Rouchka EC, Flight RM. (2014) “categoryCompare, an analytical tool based on ffeature annotations.” Frontiers in Genetics, 5:98. (pdf).
Harrison BJ, Flight RM, Gomes C, Venkat G, Ellis SR, Sankar U, Twiss JL, Rouchka EC, Petruska JC. (2014)“IB4-binding sensory neurons in the adult rat express a novel 3' UTR-extended isoform of CAMK4 that is associated with its localization to axons.” The Journal of Comparative Neurology, 522(2):308-336. (pdf).
Rouchka EC, Flight RM. (2013) “Proceedings of the Twelfth Annual UT-ORNL-KBRIN Bioinformatics Summit 2013.” BMC Bioinformatics, 14(Suppl 17):A1. (pdf).
Hougland MT, Harrison BJ, Magnuson DSK, Rouchka EC, Petruska JC. (2013) “The transcriptional response of neurotrophins and their tyrosine kinase receptors in lumbar sensorimotor circuits to spinal cord contusion is affected by injury severity and survival time.” Frontiers in Integrative Physiology, 3:478. (pdf).
Eteleeb AM, Rouchka EC. (2013) “Differential expression analysis methods for ribonucleic acid-sequencing data.” OA Bioinformatics, 1(1):3. (pdf).
Rouchka EC, Flight RM, Moseley HNB. (2012) “Proceedings of the Eleventh Annual UT-ORNL-KBRIN Bioinformatics Summit 2012.” BMC Bioinformatics, 13(Suppl 12):A1. (pdf).
Mohammad F, Robert M Flight, Benjamin J Harrison, Jeffrey C Petruska and Eric C Rouchka. “AbsIDconvert: an absolute approach for converting genetic identifiers at different granularities.” BMC Bioinformatics, 2012, 13:229. (pdf).
States JC, Singh AV, Knudsen TB, Rouchka EC, Ngalame NO, Beier JI, Arteel GE, Miller H, Pia Y, Ko MSH. (2012) “Transplacental arsenic exposure induces gene expression changes in adult liver showing linkages to systemic inflammatory diseases and contributing to a proinflammatory state contributing to athersclerosis.” PLoS One, 7(6):e38713. (pdf).
Gearheart CM, Rouchka EC, Arazi B. (2012) “DNA-based active logic design and its implications.” Journal of Emerging Trends in Computing and Information Sciences, 3(5):756-766. (pdf).
Mahdi RN, Rouchka EC. (2012) “Codon usage bias as a function of generation time and life expectancy..” Bioinformation, 8(3):158-162. (pdf).
Rouchka EC, Flight RM, Homayouni R. (2011) “Proceedings of the Tenth Annual UT-ORNL-KBRIN Bioinformatics Summit 2011.” BMC Bioinformatics, 12(Suppl 7):A1. (pdf).
Mahdi RN, Rouchka EC. (2011) “Reduced hyperBF networks: regularization by explicit complexity reductioon and scaled Rprop-based training.” IEEE Transactions on Neural Networks, 22(5):673-686. (pdf).
Rouchka E, Montoya-Durango DE, Stribinskis V, Ramos K, Kalbfleisch T. (2010) “Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data.” BMC Bioinformatics, 11(Suppl 9):S12. (pdf).
Rouchka EC, Flight RM, Rinehart C. (2010) “Proceedings of the Ninth Annual UT-ORNL-KBRIN Bioinformatics Summit 2010.” BMC Bioinformatics, 11(Suppl 4):I1. (pdf).
Rouchka EC. (2010) “Database of exact tandem repeats in the Zebrafish genome.” BMC Genomics, 11:347. (pdf)
Bogard C, Arazi B, Rouchka EC. (2010) “DNA-based random number generator in security circuitry.” BioSystems, 100(3):208-214. (pdf).
Rouchka EC, Krushkal J. (2009) “Proceedings of the Eighth Annual UT-ORNL-KBRIN Bioinformatics Summit 2009.” BMC Bioinformatics, 10(Suppl 7):I1. (pdf).
Rouchka EC, Cha IE. (2009) “Current Trends in Pseudogene Detection and Characterization.” Current Bioinformatics, 4(2):112-119. (pdf).
Mahdi RN, Rouchka EC. (2009) “RBF-TSS: Identification of transcription start site in human using radial basis functions network and oligonucleotide positional frequencies.” PLoS One, 4(3):e4878. (pdf)
Rouchka EC, Phatak AW, Singh AV. (2008) “Effect of single nucleotide polymorphisms on Affymetrix(R) match-mismatch probe pairs.” Bioinformation, 2(9);405-411. (pdf)
Rouchka EC, Krushkal J, Goldowitz D. (2008) “Proceedings of the Seventh Annual UT-ORNL-KBRIN Bioinformatics Summit 2008.” BMC Bioinformatics, 9(Suppl 7):11. (pdf).
Bogard CM, Rouchka EC, Arazi B.  (2008)  “DNA Media Storage.”  Progress in Natural Sciences, 18(5):603-609. (pdf)
Winchester JS, Rouchka EC, Rowland NS, Rice NA.   (2007)  “In silico characterization of phosphorylase kinase: evidence for an alternative intronic polyadenylation site in PHKG1.”  Molecular Genetics and Metabolism, 92(2007):234-242. (pdf)
Rouchka EC, Hardin CT.   (2007)  “rMotifGen: random motif generator for DNA and protein sequences.”  BMC Bioinformatics, 8:292. (pdf)
Singh AV, Rouchka EC, Rempala GA, Bastian CD, Knudsen TB.   (2007)  “Integrative Database Management for Mouse Development: Systems and Concepts.”  Brith Defects Research (Part C), 81:1-19. (pdf)
Rouchka EC.  (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)
Thompson W, Rouchka EC, Lawrence CE.  (2003)  “Gibbs Recursive Sampler: finding transcription factor binding sites.”  Nucleic Acids Research, 31(13):3580-3585. (pdf)
Rouchka EC, Gish W, States DJ. (2002) “Comparison of Whole Genome Assemblies of the Human Genome.”  Nucleic Acids Research, 30(22):5004-5014. (pdf)
Kan Z, Rouchka EC, Gish WR, States DJ.  (2001) "Gene structure prediction and alternative splicing analysis using genomically aligned ESTs." Genome Research, 11(5):889-900. (pdf)

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Conference Papers and Presentations
Beck MB, Desoky A, Rouchka EC, Yampolskiy RV. (2014) “Decoding Methods for DNA Steganalysis.”Proceedings of the 6th International Conference on Bioinformatics and Computational Biology (BICOB-2014), pp. xxx-xxx. March 24-26, 2014, Las Vegas, NV. (pdf).
Eteleeb AM, Flight RM, Harrison BJ, Petruska JC, Rouchka EC. (2013) “An Island-Based Approach for Differential Expression Analysis.” Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics (ACM-BCB'13), pp. 419-429. September 22-25, 2013, Washington, DC. (pdf)
Flight RM, Eteleeb AM, Rouchka EC. “Affymetrix® Mismatch(MM) Probes: Useful After All. ”Proceedings of the 2012 ASE/IEEE International Conference on BioMedical Computing (BioMedCom 2012), pp. 561-568. December 14-16, 2012, Washington, DC. (pdf).
Mohammad F, Flight RM, Harrison BJ, Petruska JC, Rouchka EC. (2011) “A Heuristic Algorithm for Detecting Intercellular Interactions.” Proceedings of the 11th IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2011), pp. 1-8. October 24-26, 2011, Taichung, Taiwan. (pdf).
Mohammad F, Flight RM, Harrison BJ, Petruska JC, Rouchka EC. (2011) “Interval Trees for Detection of Overlapping Genetic Entities.” Proceedings of the 11th IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2011), pp. 278-281. October 24-26, 2011, Taichung, Taiwan. (pdf).
Dazhuo Li, Patrick Shafto. (2011) “Bayesian Hierarchical Cross-Clustering.” Proceedings of the 14th International Conference on Artificial Intelligence and Statistics (AISTATS), Geoffrey Gordon, David Dunson, and Miroslav Dudk, eds. JMLR W&CP, vol. 15, 2011. (pdf).
Li D, Fahim M, Rouchka EC. (2010) “A Bayesian nonparametric model for joint relation integration and domain clustering.” In Proceedings of the Ninth International Conference on Machine Learning and Applications (ICMLA 2010). December 12-14, 2010, Washington, DC. (pdf)
Gearheart CM, Rouchka EC, Arazi B. (2010) “DNA-based dyanmic logic circuitry.” in Proceedings of the 53rd IEEE International Midwest Symposium on Circuits and Systems (MWSCAS). pp. 248-251. August 1-4, 2010, Seattle, WA. (doi).
Li D, Rouchka EC, Shafto P. (2010) “Phylogenomic analysis using Bayesian congruence measuring.” in Proceedings of the Second International Conference on Bioinformatics and Computational Biology (BICoB-2010). pp. 30-37. March 24-26, 2010, Honolulu, HI. (pdf).
Rouchka E, Montoya D, Stribinskis V, Ramos K, Kalbfleisch T. (2010) “Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data.” in Proceedings of the AMIA 2010 Summit on Translational Bioinformatics, March 10-12, 2010, San Francisco, CA.
Mahdi RN, Rouchka EC. (2009) “Feature selection in cancer classification from mRNA data based on localized dimension reduction.” in Proceedings of the Eith International Conference on Machine Learning and Applications (ICMLA '09). pp. 443-448. December 13-15, 2009, Miami, FL. (pdf).
Chang D-J, Desoky AH, Ouyang M, Rouchka EC. (2009) “Compute pairwise Manhattan distance and Pearson correlation coefficient of data points with GPU.” in proceedings of the 10th ACIS International Conference on Software Engineering, Artificial Intelligence, Networking and Parallel/Distributed Computing (SNPD) 2009. May 27-29, 2009, Daegu, Korea. (pdf)
Mahdi R, Rouchka EC. (2008) “Evidence of bias towards buffered codons in human transcripts.” in Proceedings of the 8th IEEE International Symposium on Signal Processing and Information Technology (ISSPIT 2008) pp 29-34. December 16-19, 2008, Sarajevo, Bosnia & Herzegovina. (pdf).
Mahdi R, Rouchka EC. (2008) “Model based unsupervised learning guided by abundant background samples.” in Proceedings of the Seventh International Conference on Machine Learning and Applications (ICMLA 2008), pp 203-210. December 11-13, 2008, San Diego, CA. (pdf).
Bogard C, Arazi B, Rouchka EC. (2008) “Towards DNA-based Security Circuitry: First Step . Random Number Generation.” in Proceedings of the 51st Midwest Symposium on Circuits and Systems (MWSCAS 2008). pp 597-600. August 10-13, 2008, Knoxville, TN. (pdf).
Bogard CM, Rouchka EC, Arazi B.  (2007)  “DNA media storage.”   In Prodeedings of the Second International Conference on Bio-inspired Computing: Theories and Applications (BIC-TA). pp 236-239, Zhengzhou, China, September 2007. (pdf)
Li K, Chang D, Rouchka E, Chen YY.   (2007)  “Biological Sequence Mining using Plausible Neural Network and its Application to Exon/intron Boundaries Prediction.”   In Proceedings of the 2007 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2007). 165-169. Honolulu, HI, April, 2007. (pdf)
Hardin CT, Rouchka EC.,   “DNA Motif Detection Using Particle Swarm Optimization and Expectation-Maximization.” Proceedings of the 2005 IEEE Swarm Intelligence Symposium, Pasedina, California, June 2005. (pdf).
Cha IE, Rouchka EC.,   “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).
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 TW, Rouchka EC, States DJ. (1999) "Identity by Descent Genome Segmentation Based on Single Nucleotide Polymorphism Distributions."  ISMB, 7:54-59. (pdf)
Rouchka EC, States DJ. (1998) "Sequence Assembly Validation by Multiple Restriction Digest Fragment Coverage Analysis" ISMB, 6:140-147. (pdf)

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Books and Books Chapters
Beck M, Rouchka EC, Yampolskiy R. (2013) “Finding data in DNA: Computer forensic investigations of living organisms.” Fourth International Conference on Digital Forensics and Cyber Crime (ICDF2C 2012), Rogers M, Seifried-Spellar KC. (Eds.), Lafayette, IN, USA, October 25-26, 2012, In Lecture Notes in Computer Science, Social Informatics and Telecommunications Engineering Series Vol. 0114, pp. 204-219. (pdf)
Rouchka EC, Wang X, Graham JH, Cooper NGF. (2009) “Computational prediction of genes translationally regulated by cytoplasmic polyadenylation elements.” First International Conference on Bioinformatics and Computational Biology, BICoB 2009, Rajasekaran, S. (Ed.), New Orleans, LA, USA, April 8-10, 2009, In Lecture Notes in Computer Science, Lecture Notes in Bioinformatics Vol. 5462, pp. 353-361, 2009. (ISBN 978-3-642-00726-2). (pdf)
Jacobs S, Lopez C. (2006) “Deciphering Human Chromosome 16: index to the report.” Information as material, ISBN: 0955309220. (cover art Eric Rouchka) (Amazon.com)

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DISSERTATIONS
Mohammad, F. (2012) A System-Based Approach for Detecting Molecular Interactions Across Tissues. Eric Rouchka, advisor. CSE Ph.D. Dissertation. (pdf)
Li D. (2012) Bayesian Nonparametric Clusterings in Relational and High-Dimensional Settings with Applications in Bioinformatics. Eric Rouchka, advisor. CSE Ph.D. Dissertation. (pdf)
Gearheart C. (2010) DNA-based Computing for Secure Circuitry Design. Eric Rouchka, advisor. CSE Ph.D. Dissertation. (pdf)
Mahdi, R. (2010) Reduced HyperBF Networks: Practical Optimization, Regularization, and Applications in Bioinformatics. Eric Rouchka, advisor. CSE Ph.D. Dissertation. (pdf)
Ghanta S. (2009) Diagnostic test for fetal chromosomal abnormalities using biallelic Single Nucleotide Polymorphisms. Adel Elmaghraby, advisor. CSE Ph.D. Dissertation. (pdf)
Cha IE. (2008) Computational Analysis of Expressed Sequence Tags for Understanding Gene Regulation. Eric Rouchka, advisor. CSE Ph.D. Dissertation. (pdf)
Wang X. (2008) The Expression and Localization of Cytoplasmic Polyadenylation Element Binding Proteins in the Retina. Nigel Cooper, advisor. ASNB Ph.D. Dissertation. (pdf) (Eric Rouchka -- Committee Member).
Choi H.  (2003)  Processing and analysis of DNA microarraysAhmed Desoky, advisor. CSE Ph.D. Thesis.(pdf 19.9 MB)
THESES AND PROJECTS
Saka E. (2011) Image Registration and Visualization of In Situ Gene Expression Images. Eric Rouchka, advisor. CECS Master of Science Thesis. (pdf)
Disibio M. (2010) Assessment and Performance of VSN-INV Normalization of the NCI-60 microRNA Expression Profiles. Eric Rouchka, advisor. CECS Master of Science Thesis. (pdf)
Morris J. (2009) An Analysis Pipeline for the Processing, Annotation, and Dissemination of Expressed Sequence Tags. Eric Rouchka, advisor. CECS Master of Engineering Thesis. (pdf)
Hoblitzell, K. (2008) Tissue Based Analysis of Gene Expression Using ESTs. Eric Rouchka, advisor. CECS Master of Engineering Project. (pdf)
Iwu S..  (2007)  KBRIN Publications Reference ManagerEric Rouchka, advisor. CECS Master of Engineering Project.(pdf)
Thai A..  (2007)  Evaluation of Using Swarm Intelligence to Produce Facility Layout SolutionsEric Rouchka and Tim Hardin, co-advisors. CECS Master of Engineering Thesis.(pdf)
Graves P..  (2007)  EST VisualizerEric Rouchka, advisor. CECS Master of Engineering Project.(pdf)
Yachim Y..  (2007)  An Alternative to Conventional Methods in Digital Image ViewingEric Rouchka, advisor. CECS Master of Engineering Thesis.(pdf)
Koparkar A..  (2006)  Computational Detection of CPE ElementsEric Rouchka, advisor. CECS Master of Science Project.(pdf)
Rudraraju YL..  (2006)  MPrime-DEG: Multiple Degenerate Primer Design for Amplifying Homologous SequencesEric Rouchka, advisor. CECS Master of Science Project.(pdf)
Akkineni V..  (2006)  Microarray Data Analysis Tool Using Java and REric Rouchka, advisor. CECS Master of Science Thesis.(pdf)
Phatak A..  (2005)  Using Relational Databases to Analyze Microarray Probes and Single Nucleotide Polymorphisms.Eric Rouchka, advisor. CECS Master of Engineering Project.(pdf)
Gundlapalli R..  (2005)  Microarray Database Resource for Designing Custom MicroarraysEric Rouchka, advisor. CECS Master of Science Thesis.(pdf)
El-Hadik S.  (2005)  Design and implementation of Affymetrix(R) data processing with Java ADPJAhmed Desoky, advisor. CECS Master's Thesis.(pdf)
Hornsby J.  (2005)  Implementation of Data Management Portion of MiDaR ProjectEric Rouchka, advisor. CECS Master's Thesis.(pdf)
Mann N.  (2004)  Developing a Database for GenBank InformationDar-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)

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TECHNICAL REPORTS
Rouchka EC. (2014) “Accounting for regions of high and low G+C content found in human genomic DNA.” University of Louisville Bioinformatics Laboratory Technical Report Series, TR-ULBL-2014-01. (pdf).
Rouchka EC. (2008) “A brief overview of Gibbs sampling.” University of Louisville Bioinformatics Laboratory Technical Report Series, TR-ULBL-2008-02. (pdf).
Rouchka EC. (2008) “An algorithmic approach to gene regulatory sequence analysis.” University of Louisville Bioinformatics Laboratory Technical Report Series, TR-ULBL-2008-01. (pdf).
Phatak AW, Rouchka EC.(2007) “Using Relational Databases to Analyze Microarray Probes and Single Nucleotide Polymorphisms.”  University of Louisville Bioinformatics Technical Report Series, TR-ULBL-2007-04. (pdf)
Cha IE, Hoblitzell KL, Rouchka EC. (2007) “Alternative Splicing Events.”  University of Louisville Bioinformatics Technical Report Series, TR-ULBL-2007-03. (pdf)
Kelley R, Rouchka EC. (2007) “Bioinformatics Techniques Used in Diabetes Research.”  University of Louisville Bioinformatics Technical Report Series, TR-ULBL-2007-02. (pdf)
Rizzo J, Rouchka EC. (2007) “Review of Phylogenetic Tree Construction.”  University of Louisville Bioinformatics Technical Report Series, TR-ULBL-2007-01. (pdf)
Rouchka EC. (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 EC., States DJ.  (2002)  “Compositional Analysis of Homogeneous Regions in Human Genomic DNA.”  Technical Report, Washington University Department of Computer Science, WUCS-2002-02. (pdf)
Rouchka EC., (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 EC., States DJ. (1999) "Assembly and Analysis of Extended Human Genomic Contig Regions."  Technical Report, Washington University Department of Computer Science, WUCS-99-10. (pdf)
Rouchka EC, States DJ., (1997) "Sequence Assembly Validation by Restriction Digest Fingerprint Comparison." Technical Report, Washington University, Department of Computer Science, WUCS-97-40.(pdf)
Rouchka EC, Mazzarella R, States DJ. (1997) "Computational Detection of CpG Islands in DNA." Technical Report, Washington University, Department of Computer Science, WUCS-97-39. (pdf)

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