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University of Louisville Bioinformatics

Sample Bioinformatics Publications

1998 | 1999 | 2000 | 2001 | 2002 | 2003 | 2004 | 2005 | 2006 | 2007 | 2008 | 2009 | 2010 | 2011 | 2012

(Bioinformatics faculty/staff in UPPERCASE)


Alton TM, BROCK GN, Yang D, Wilking DA, Hertweck SP, Loveless MB: "Retrospective review of intrauterine device in adolescent and young women," J Pediatr Adolesc Gynecol, vol. 25, pp. 195-200, Jun 2012.

Cannon RM, BROCK GN, Marvin MR, Slakey DP, Buell JF: "The contribution of donor quality to differential graft survival in african american and caucasian renal transplant recipients," Am J Transplant, vol. 12, pp. 1776 -83, Jul 2012.

CHARIKER JH, Naaz F, PANI JR: Item difficulty in the evaluation of computer-based instruction: an example from neuroanatomy. Anatomical sciences education 2012, 5(2):63-75.

Fan TW, Lorkiewicz PK, Sellers K, MOSELEY HN, Higashi RM, LANE AN: "Stable isotope-resolved metabolomics and applications for drug development," Pharmacol Ther, vol. 133, pp. 366-91, Mar 2012.

Heaton MP, Clawson ML, Chitko-Mckown CG, Leymaster KA, Smith TP, Harhay GP, White SN, Herrmann-Hoesing LM, Mousel MR, Lewis GS, KALBFLEISCH TS, Keen JE, Laegreid WW: "Reduced lentivirus susceptibility in sheep with TMEM154 mutations," PLoS Genet, vol. 8, p. e1002467, Jan 2012.

Hertweck SP, Yoost JL, McClure ME, Siow Y, BROCK GN, Wintergerst KA, Fallat ME: "Ferriman-Gallwey Scores, Serum Androgen and Mullerian Inhibiting Substance Levels in Hirstute Adolescent Girls," J Pediatr Adolesc Gynecol, Jul 24 2012.

Lavender NA, Rogers EN, Yeyeodu S, Rudd J, Hu T, Zhang J, BROCK GN, Kimbro KS, Moore JH, Hein DW, Kidd LC: "Interaction among apoptosis-associated sequence variants and joint effects on aggressive prostate cancer," BMC Med Genomics, vol. 5, p. 11, 2012.

MAHDI RN and ROUCHKA EC, "Codon usage bias as a function of generation time and life expectancy," Bioinformation, vol. 8, pp. 158-62, 2012.

MOSELEY HN, LANE AN, Belshoff AC, Higashi RM, Fan TW: "Correction: A novel deconvolution method for modeling UDP-GlcNAc biosynthetic pathways based on 13C mass isotopologue profiles under non steady-state conditions," BMC Biol, vol. 10, p. 74, Aug 17 2012.

Muenyi CS, Pinhas AR, Fan TW, BROCK GN, Helm CW, States JC: "Sodium arsenite +/- hyperthermia sensitizes p53-expressing human ovarian cancer cells to cisplatin by modulating platinum-DNA damage responses," Toxicol Sci, vol. 127, pp. 139-49, May 2012.

PANI JR, CHARIKER JH, Naaz F: Computer-based learning: Interleaving whole and sectional representation of neuroanatomy. Anatomical sciences education 2012.

ROUCHKA EC, FLIGHT RM, MOSELEY HNB, "Proceedings of the Eleventh Annual UT-ORNL-KBRIN Bioinformatics Summit 2012," BMC Bioinformatics, vol. 13 Suppl 12, p. A1, Jul 31 2011.

States JC, A. V. Singh AV, Knudsen TB, ROUCHKA EC, Ngalame NO, Arteel GE, Piao Y, Ko MS: "Prenatal arsenic exposure alters gene expression in the adult liver to a proinflammatory state contributing to accelerated atherosclerosis," PLoS One, vol. 7, p. e38713, 2012.


Battisti AJ, Chu YK, Chipman PR, Kaufmann B, JONSSON CB, Rossmann MG: Structural studies of Hantaan virus. J Virol 2011, 85:835-841.

BROCK GN, Mostajabi F, Ferguson N, Carrubba CJ, Eng M, Buell JF, Marvin MR: Prophylaxis against de novo hepatitis B for liver transplantation utilizing hep B core (+) donors: does hepatitis B immunoglobulin provide a survival advantage? Transpl Int 2011, 24:570-581. BROCK GN, Barnes C, Ramirez JA, Myers J: "How to handle mortality when investigating length of hospital stay and time to clinical stability," BMC Med Res Methodol, vol. 11, p. 144, 2011.

Cannon RM, BROCK GN, Marvin MR, Buell JF: Laparoscopic Liver Resection: An Examination of Our First 300 Patients. J Am Coll Surg 2011.

Danesh A, Cameron CM, Leon AJ, Ran L, Xu L, Fang Y, Kelvin AA, Rowe T, Chen H, Guan Y, et al: Early gene expression events in ferrets in response to SARS coronavirus infection versus direct interferon-alpha2b stimulation. Virology 2011, 409:102-112.

Florea L, Souvorov A, KALBFLEISCH TS, Salzberg SL: "Genome assembly has a major impact on gene content: a comparison of annotation in two Bos taurus assemblies," PLoS One, vol. 6, p. e21400, 2011.

Gobejishvili L, Avila DV, Barker DF, Ghare S, Henderson D, BROCK GN, Kirpich IA, Joshi-Barve S, Mokshagundam SP, McClain CJ, Barve S: S-adenosylmethionine decreases lipopolysaccharide-induced phosphodiesterase 4B2 and attenuates tumor necrosis factor expression via cAMP/protein kinase A pathway. J Pharmacol Exp Ther 2011, 337:433-443.

Hurley JM, Cruz JW, OUYANG M, Woychik NA: Bacterial toxin RelE mediates frequent codon-independent mRNA cleavage from the 5' end of coding regions in vivo. J Biol Chem 2011, 286:14770-14778.

Kidd LC, Vancleave TT, Doll MA, Srivastava DS, Thacker B, Komolafe O, Pihur V, BROCK GN, Hein DW: "No association between variant N-acetyltransferase genes, cigarette smoking and Prostate Cancer susceptibility among men of African descent," Biomark Cancer, vol. 2011, pp. 1-13, Feb 3 2011.

LI X, Gill R, COOPER NG, Yoo JK, DATTA S: Modeling microRNA-mRNA Interactions Using PLS Regression in Human Colon Cancer. BMC Med Genomics 2011, 4:44.

Maddry JA, Chen X, JONSSON CB, Ananthan S, Hobrath J, Smee DF, Noah JW, Noah D, Xu X, Jia F, et al: Discovery of novel benzoquinazolinones and thiazoloimidazoles, inhibitors of influenza H5N1 and H1N1 viruses, from a cell-based high-throughput screen. J Biomol Screen 2011, 16:73-81.

Mahdi RN, ROUCHKA EC: Reduced HyperBF Networks: Regularization by Explicit Complexity Reduction and Scaled Rprop-Based Training. Ieee Transactions on Neural Networks 2011, 22:673-686.

Manavalan TT, Teng Y, Appana SN, DATTA S, KALBFLEISCH TS, Li Y, Klinge CM: "Differential expression of microRNA expression in tamoxifen-sensitive MCF-7 versus tamoxifen-resistant LY2 human breast cancer cells," Cancer Lett, vol. 313, pp. 26-43, Dec 26 2011.

MOHAMMAD F, FLIGHT RM, HARRISON BJ, PETRUSKA JC, ROUCHKA EC: "A Heuristic Algorithm for Detecting Intercellular Interactions," in Bioinformatics and Bioengineering (BIBE), 2011 IEEE 11th International Conference on, 2011, pp. 1-8.

MOHAMMAD F, FLIGHT RM, HARRISON BJ, PETRUSKA JC, ROUCHKA EC: "Interval Trees for Detection of Overlapping Genetic Entities," in Bioinformatics and Bioengineering (BIBE), 2011 IEEE 11th International Conference on, 2011, pp. 278-281.

MOSELEY HN, LANE AN, Belshoff AC, Higashi RM, Fan TW: A novel deconvolution method for modeling UDP-GlcNAc biosynthetic pathways based on 13C mass isotopologue profiles under non steady-state conditions. BMC Biol 2011, 9:37.

Ndukum J, Atlas M, DATTA S: pkDACLASS: Open source software for analyzing MALDI-TOF data. Bioinformation 2011, 6:45-47.

Ndukum J, Fonseca LL, Santos H, Voit EO, DATTA S: Statistical inference methods for sparse biological time series data. BMC Syst Biol 2011, 5:57.

Oh S, Kang DD, BROCK GN, Tseng GC: Biological impact of missing-value imputation on downstream analyses of gene expression profiles. Bioinformatics 2011, 27:78-86.

Pihur V, DATTA S: Meta analysis of Chronic Fatigue Syndrome through integration of clinical, gene expression, SNP and proteomic data. Bioinformation 2011, 6:120-124.

Ramsey TL, Meltzer HY, BROCK GN, Mehrotra B, Jayathilake K, Bobo WV, Brennan MD: Evidence for a SULT4A1 haplotype correlating with baseline psychopathology and atypical antipsychotic response. Pharmacogenomics 2011, 12:471-480.

ROUCHKA EC, FLIGHT RM, Homayouni R, "Proceedings of the Tenth Annual UT-ORNL-KBRIN Bioinformatics Summit 2011," BMC Bioinformatics, vol. 12 Suppl 7, p. A1, Aug 5 2011.

Schuck JB, Sun H, Penberthy WT, COOPER NG, LI X, Smith ME: "Transcriptomic analysis of the zebrafish inner ear points to growth hormone mediated regeneration following acoustic trauma," BMC Neurosci, vol. 12, p. 88, 2011.

Warner DR, Mukhopadhyay P, BROCK GN, Pihur V, Pisano MM, Greene RM: TGFbeta-1 and Wnt-3a interact to induce unique gene expression profiles in murine embryonic palate mesenchymal cells. Reprod Toxicol 2011, 31:128-133.


Bevan AK, Hutchinson KR, Foust KD, Braun L, McGovern VL, Schmelzer L, Ward JG, PETRUSKA JC, Lucchesi PA, Burghes AH, Kaspar BK: Early heart failure in the SMNDelta7 model of spinal muscular atrophy and correction by postnatal scAAV9-SMN delivery. Hum Mol Genet 2010, 19:3895-3905.

Bhatnagar S, PANGULURI SK, Gupta SK, Dahiya S, Lundy RF, KUMAR A: Tumor necrosis factor-alpha regulates distinct molecular pathways and gene networks in cultured skeletal muscle cells. PLoS One 2010, 5:e13262.

Bruder CE, Yao S, Larson F, Camp JV, Tapp R, McBrayer A, Powers N, Granda WV, JONSSON CB: Transcriptome sequencing and development of an expression microarray platform for the domestic ferret. BMC Genomics 2010, 11:251.

Cave M, Appana S, Patel M, Falkner KC, McClain CJ, BROCK G: Polychlorinated biphenyls, lead, and mercury are associated with liver disease in American adults: NHANES 2003-2004. Environ Health Perspect 2010, 118:1735-1742.

Cunningham AR, Qamar S, Carrasquer CA, Holt PA, Maguire JM, Cunningham SL, TRENT JO: Mammary carcinogen- protein binding potentials: novel and biologically relevant structure-activity relationship model descriptors. SAR QSAR Environ Res 2010, 21:463-479.

Dailey MM, Miller MC, Bates PJ, LANE AN, TRENT JO: Resolution and characterization of the structural polymorphism of a single quadruplex-forming sequence. Nucleic Acids Res 2010, 38:4877-4888.

DATTA S, Kim S, Chakraborty S, Gill RS: Statistical Analyses of Next Generation Sequence Data: A Partial Overview. J Proteomics Bioinform 2010, 3:183-190.

DATTA S, Pihur V: An adaptive optimal ensemble classifier via bagging and rank aggregation with applications to high dimensional data. BMC Bioinformatics 2010, 11:427.

Fan TW, Yuan P, LANE AN, Higashi RM, Wang Y, Hamidi AB, Zhou R, Guitart X, Chen G, Manji HK, Kaddurah-Daouk R: Stable isotope-resolved metabolomic analysis of lithium effects on glial-neuronal metabolism and interactions. Metabolomics 2010, 6:165-179.

Fan W, LI X, Wang W, Mo JS, Kaplan H, COOPER NG: Early Involvement of Immune/Inflammatory Response Genes in Retinal Degeneration in DBA/2J Mice. Ophthalmol Eye Dis 2010, 1:23-41.

FLIGHT RM, Wentzell PD: Preliminary exploration of time course DNA microarray data with correlation maps. OMICS 2010, 14:99-107.

Gill R, DATTA S: A statistical framework for differential network analysis from microarray data. BMC Bioinformatics 2010, 11:95.

Heaton MP, Leymaster KA, KALBFLEISCH TS, Freking BA, Smith TP, Clawson ML, Laegreid WW: Ovine reference materials and assays for prion genetic testing. BMC Vet Res 2010, 6:23.

Hill CE, HARRISON BJ, Rau KK, Hougland MT, Bunge MB, Mendell LM, PETRUSKA JC: Skin incision induces expression of axonal regeneration-related genes in adult rat spinal sensory neurons. J Pain 2010, 11:1066-1073.

Kidd LR, BROCK GN, Vancleave TT, Benford ML, Lavender NA, Kruer TL, Wittliff JL: Angiogenesis-associated sequence variants relative to breast cancer recurrence and survival. Cancer Causes Control 2010.

Kumar M, Lu Z, Takwi AA, Chen W, Callander NS, RAMOS KS, Young KH, Li Y: Negative regulation of the tumor suppressor p53 gene by microRNAs. Oncogene 2010.

LI D, ROUCHKA EC, SHAFTO P: Phylogenomic analysis using Bayesian congruence measuring. In Second International Conference on Bioinformatics and Computational Biology. pp. 30-37. Honolulu, HI; 2010:30-37.

Miller MC, Buscaglia R, Chaires JB, LANE AN, TRENT JO: Hydration Is a Major Determinant of the G- Quadruplex Stability and Conformation of the Human Telomere 3' Sequence of d(AG(3)(TTAG(3))(3)). J Am Chem Soc 2010.

Montoya-Durango DE, RAMOS KS: L1 retrotransposon and retinoblastoma: molecular linkages between epigenetics and cancer. Curr Mol Med 2010, 10:511-521.

MOSELEY HN: Correcting for the effects of natural abundance in stable isotope resolved metabolomics experiments involving ultra-high resolution mass spectrometry. BMC Bioinformatics 2010, 11:139.

MOSELEY HN, Sperling LJ, Rienstra CM: Automated protein resonance assignments of magic angle spinning solid-state NMR spectra of beta1 immunoglobulin binding domain of protein G (GB1). J Biomol NMR 2010, 48:123-128.

Mukhopadhyay P, BROCK G, Pihur V, Webb C, Pisano MM, Greene RM: Developmental microRNA expression profiling of murine embryonic orofacial tissue. Birth Defects Res A Clin Mol Teratol 2010, 88:511-534.

PANGULURI SK, BHATNAGAR S, KUMAR A, McCarthy JJ, Srivastava AK, COOPER NG, Lundy RF: Genomic profiling of messenger RNAs and microRNAs reveals potential mechanisms of TWEAK-induced skeletal muscle wasting in mice. PLoS One 2010, 5:e8760.

Paul PK, Gupta SK, Bhatnagar S, PANGULURI SK, Darnay BG, Choi Y, KUMAR A: Targeted ablation of TRAF6 inhibits skeletal muscle wasting in mice. J Cell Biol 2010, 191:1395-1411.

Petraccone L, Garbett NC, Chaires JB, TRENT JO: An integrated molecular dynamics (MD) and experimental study of higher order human telomeric quadruplexes. Biopolymers 2010, 93:533-548.

PETRUSKA JC, Kitay B, Boyce VS, Kaspar BK, Pearse DD, Gage FH, Mendell LM: Intramuscular AAV delivery of NT-3 alters synaptic transmission to motoneurons in adult rats. Eur J Neurosci 2010, 32:997-1005.

Riley PC, Gough SE, He J, Jandhyala SS, Kennedy B, Orcun S, Ouzzani M, Buck C, Roumani AM, ZHANG X: The Proteome Discovery Pipeline -- A data analysis pipeline for mass spectrometry-based differential proteomics discovery. Open Proteomics Journal 2010, 3:8-19.

ROUCHKA EC: Database of exact tandem repeats in the Zebrafish genome. BMC Genomics 2010, 11:347.

ROUCHKA EC, FLIGHT RM, Rinehart C: Proceedings of the Ninth Annual UT-ORNL-KBRIN Bioinformatics Summit 2010. BMC Bioinformatics 2010, 11:I1.

ROUCHKA E, Montoya-Durango DE, Stribinskis V, RAMOS K, KALBFLEISCH T: Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data. BMC Bioinformatics 2010, 11 Suppl 9:S12.

Wang B, Fang A, Heim J, Bogdanov B, Pugh S, LIbardoni M, ZHANG X: DISCO: distance and spectrum correlation optimization alignment for two-dimensional gas chromatography time-of-flight mass spectrometry-based metabolomics. Anal Chem 2010, 82:5069-5081.

Wang B, Valentine S, Plasencia M, Raghuraman S, ZHANG X: Artificial neural networks for the prediction of peptide drift time in ion mobility mass spectrometry. BMC Bioinformatics 2010, 11:182.

ZHANG X, Fang A, Riley CP, Wang M, Regnier FE, Buck C: Multi-dimensional liquid chromatography in proteomics--a review. Anal Chim Acta 2010, 664:101-113.


Allen LJ, Wesley CL, Owen RD, Goodin DG, Koch D, JONSSON CB, Chu YK, Shawn Hutchinson JM, Paige RL: A habitat-based model for the spread of hantavirus between reservoir and spillover species. J Theor Biol 2009, 260:510-522.

BROCK GN, Beavis W, L. S: Fuzzy logic and alternate methods for detecting gene regulatory Networks. Information Fusion 2009, 10:250-259.

BROCK GN, Pihur V, Kubatko L: Detecting gene regulatory networks from microarray data using fuzzy logic. In Fuzzy Systems in Bioinformatics, Bioengineering and Computational Biology (Studies in Fuzziness and Soft Computing). Edited by Y. J, L. W. Berlin, Heidelberg: Springer-Verlag; 2009

Chang DJ, Kantardzic M, OUYANG M: Hierarchical clustering with CUDA/GPU. In ISCA 22nd International Conference on Parallel and Distributed Computing and Communication Systems (PDCCS 2009). pp. 7-12; 2009:7-12.

Chernatynskaya AV, Deleeuw L, TRENT JO, Brown T, LANE AN: Structural analysis of the DNA target site and its interaction with Mbp1. Org Biomol Chem 2009, 7:4981-4991.

Chu YK, Goodin D, Owen RD, Koch D, JONSSON CB: Sympatry of 2 hantavirus strains, paraguay, 2003-2007. Emerg Infect Dis 2009, 15:1977-1980.

DATTA S: Computational biology touches all bases. A report of the 6th Annual Rocky Mountain Bioinformatics Conference, Aspen, USA, 4-7 December 2008. Genome Biol 2009, 10:303.

FLIGHT RM, Wentzell PD: Potential bias in GO::TermFinder. Brief Bioinform 2009, 10:289-294.

Gray RD, Petraccone L, TRENT JO, Chaires JB: Characterization of a K+-induced conformational switch in a human telomeric DNA oligonucleotide using 2-aminopurine fluorescence. Biochemistry 2009, 49:179-194.

Holt PA, Ragazzon P, Strekowski L, Chaires JB, TRENT JO: Discovery of novel triple helical DNA intercalators by an integrated virtual and actual screening platform. Nucleic Acids Res 2009, 37:1280-1287.

LI J, Kuang Y: Systemically modeling the dynamics of plasma insulin in subcutaneous injection of insulin analogues for type 1 diabetes. Math Biosci Eng 2009, 6:41-58.

Mahdi RN, ROUCHKA EC: Feature selection in cancer classification from mRNA data based on localized dimension reduction. In Eighth International Conference on Machine Learning and Applications (ICMLA 2009). pp. 443-448. Miami, Florida; 2009:443-448.

Mahdi RN, ROUCHKA EC: RBF-TSS: identification of transcription start site in human using radial basis functions network and oligonucleotide positional frequencies. PLoS One 2009, 4:e4878.

Montoya-Durango DE, LIu Y, Teneng I, KALBFLEISCH T, Lacy ME, Steffen MC, RAMOS KS: Epigenetic control of mammalian LINE-1 retrotransposon by retinoblastoma proteins. Mutat Res 2009, 665:20-28.

Murray HM, Lall SP, Rajaselvam R, Boutilier LA, FLIGHT RM, Blanchard B, Colombo S, Mohindra V, Yufera M, Douglas SE: Effect of early introduction of microencapsulated diet to larval Atlantic halibut, Hippoglossus hippoglossus L. assessed by microarray analysis. Mar Biotechnol (NY) 2009, 12:214-229.

PANGULURI S, Saggu S, Lundy R: Comparison of somatostatin and corticotrophin-releasing hormone immunoreactivity in forebrain neurons projecting to taste-responsive and non-responsive regions of the parabrachial nucleus in rat. Brain Res 2009, 1298:57-69.

PANGULURI SK, Kakar SS: Effect of PTTG on endogenous gene expression in HEK 293 cells. BMC Genomics 2009, 10:577.

Pihur V, DATTA S: RankAggreg, an R package for weighted rank aggregation. BMC Bioinformatics 2009, 10:62.

RAMOS KS: Unraveling genetic regulatory networks of mammalian retroelements. BMC Proc 2009, 3 Suppl 2:S3.

RAMOS KS, Nanez A: Genetic regulatory networks of nephrogenesis: deregulation of WT1 splicing by benzo(a)pyrene. Birth Defects Res C Embryo Today 2009, 87:192-197.

ROUCHKA EC, Cha IE: Current trends in pseudogene detection and characterization. Current Bioinformatics 2009, 4:112-119.

ROUCHKA EC, Krushkal J: Proceedings of the Eighth Annual UT-ORNL-KBRIN Bioinformatics Summit 2009. BMC Bioinformatics 2009, 10:I1.

ROUCHKA EC, Wang X, Graham JH, COOPER NGF: Computational prediction of genes translationally regulated by cytoplasmic polyadenylation elements. In Lecture Notes in Computer Science, Lecture Notes in Bioinformatics. Volume 5462. Edited by Rajasekaran S. New Orleans, LA.; 2009: 353-361.

Wang H, LI J, Kuang Y: Enhanced modeling of the glucose-insulin system and its applications in insulin therapies. J Biol Dynamics 2009, 3:22-38.

Wang XP, COOPER NG: Characterization of the transcripts and protein isoforms for cytoplasmic polyadenylation element binding protein-3 (CPEB3) in the mouse retina. BMC Mol Biol 2009, 10:109.

Xu P, BROCK GN, Parrish RS: Modified linear discriminant analysis approaches for classification of high-dimensional microarray data. Computational Statistics and Data Analysis 2009, 53:1674-1687.

ZHANG X, Oh C, Riley CP, Buck C, Cho H: Computational approaches to peptide retention time prediction for proteomics. In Biological Data Mining. 2009: 337-349

Zhu Y, KALBFLEISCH T, Brennan MD, LI Y: A MicroRNA gene is hosted in an intron of a schizophrenia-susceptibility gene. Schizophr Res 2009, 109:86-89.


BROCK GN, Pihur V, DATTA S, Datta S: clValid, an R package for cluster validation. Journal of Statistical Software 2008, 25.

BROCK GN, Shaffer JR, Blakesley RE, Lotz MJ, Tseng GC: Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes. BMC Bioinformatics 2008, 9:12.

Burd RS, OUYANG M, Madigan D: Bayesian logistic injury severity score: a method for predicting mortality using international classification of disease-9 codes. Acad Emerg Med 2008, 15:466-475.

Chu YK, Owen RD, Sanchez-Hernandez C, Romero-Almaraz Mde L, JONSSON CB: Genetic characterization and phylogeny of a hantavirus from Western Mexico. Virus Res 2008, 131:180-188.

DATTA S: Computational biology touches all bases. A report of the 6th Annual Rocky Mountain Bioinformatics Conference, Aspen, USA, 4-7 December 2008. Genome Biol 2009, 10:303.

DATTA S, Turner D, Singh R, Ruest LB, Pierce WM, Jr., Knudsen TB: Fetal alcohol syndrome (FAS) in C57BL/6 mice detected through proteomics screening of the amniotic fluid. Birth Defects Res A Clin Mol Teratol 2008, 82:177-186.

Heaton MP, Keele JW, Harhay GP, Richt JA, Koohmaraie M, Wheeler TL, Shackelford SD, Casas E, King DA, Sonstegard TS, et al: Prevalence of the prion protein gene E211K variant in U.S. cattle. BMC Vet Res 2008, 4:25.

Holt PA, Chaires JB, TRENT JO: Molecular docking of intercalators and groove-binders to nucleic acids using Autodock and Surflex. J Chem Inf Model 2008, 48:1602-1615.

LANE AN, Chaires JB, Gray RD, TRENT JO: Stability and kinetics of G-quadruplex structures. Nucleic Acids Res 2008, 36:5482-5515.

Mahdi RN, ROUCHKA EC: Evidence of bias towards buffered codons in human transcripts. Proc IEEE Int Symp Signal Proc Inf Tech 2008, 2008:29-34.

Mahdi RN, ROUCHKA EC: Model Based Unsupervised Learning Guided by Abundant Background Samples. Proc Int Conf Mach Learn 2008, 7:203-210.

Mekmaysy CS, Petraccone L, Garbett NC, Ragazzon PA, Gray R, TRENT JO, Chaires JB: Effect of O6-methylguanine on the stability of G-quadruplex DNA. J Am Chem Soc 2008, 130:6710-6711.

PANGULURI SK, Yeakel C, Kakar SS: PTTG: an important target gene for ovarian cancer therapy. J Ovarian Res 2008, 1:6.

Partridge CR, He Q, Brun M, RAMOS KS: Genetic networks of cooperative redox regulation of osteopontin. Matrix Biol 2008, 27:462-474.

Pihur V, DATTA S: Finding common genes in multiple cancer types through meta-analysis of microarray experiments: a rank aggregation approach. Genomics 2008, 92:400-403.

Pihur V, DATTA S: Reconstruction of genetic association networks from microarray data: a partial least squares approach. Bioinformatics 2008, 24:561-568.

ROUCHKA EC, Krushkal J, Goldowitz D: Proceedings of the Seventh Annual UT-ORNL-KBRIN Bioinformatics Summit 2008. BMC Bioinformatics 2008, 9:11.

ROUCHKA EC, Phatak AW, Singh AV: Effect of single nucleotide polymorphisms on Affymetrix match-mismatch probe pairs. Bioinformation 2008, 2:405-411.

Walraven JM, TRENT JO, Hein DW: Structure-function analyses of single nucleotide polymorphisms in human N-acetyltransferase 1. Drug Metab Rev 2008, 40:169-184.

Walraven JM, Zang Y, TRENT JO, Hein DW: Structure/function evaluations of single nucleotide polymorphisms in human N-acetyltransferase 2. Curr Drug Metab 2008, 9:471-486.


Boratyn GM, DATTA S: Incorporation of biological knowledge into distance for clustering genes. Bioinformation 2007, 1:396-405.

BROCK GN, Weeks DE, Sobel E, Feingold E: A novel method for estimating significance levels in NPL scores for large pedigrees. Genet Epidemiol 2007, 31:417-430.

Cambon AC, Khalyfa A, COOPER NG, Thompson CM: Analysis of probe level patterns in Affymetrix microarray data. BMC Bioinformatics 2007, 8:146.

Chu YK, Goodin D, Owen RD, Koch D, JONSSON CB: Sympatry of 2 hantavirus strains, paraguay, 2003-2007. Emerg Infect Dis 2009, 15:1977-1980.

DATTA S, Le-Rademacher J: Predicting patient survival from microarray data by accelerated failure time modeling using partial least squares and LASSO. Biometrics 2007, 63:259-271.

Jornsten R, OUYANG M, Wang HY: A meta-data based method for DNA microarray imputation. BMC Bioinformatics 2007, 8:109.

KALBFLEISCH T, Cambon A, Wattenberg BW: A bioinformatics approach to identifying tail-anchored proteins in the human genome. Traffic 2007, 8:1687-1694.

Karakach TK, FLIGHT RM, Wentzell PD: Bootstrap method for the estimation of measurement uncertainty in spotted dual-color DNA microarrays. Anal Bioanal Chem 2007, 389:2125-2141.

LI J, Liu ZJ, Pan YC, Liu Q, Fu X, COOPER NG, Li Y, Qiu M, Shi T: Regulatory module network of basic/helix-loop-helix transcription factors in mouse brain. Genome Biol 2007, 8:R244.

LI K, Chang DJ, ROUCHKA E, Chen YY: Biological Sequence Mining Using Plausible Neural Network and its Application to Exon/intron Boundaries Prediction. Proc IEEE Symp Comput Intell Bioinforma Comput Biol 2007, 2007:165-169.

PANGULURI SK, LI B, Hormann RE, Palli SR: Effect of ecdysone receptor gene switch ligands on endogenous gene expression in 293 cells. FEBS J 2007, 274:5669-5689.

Pihur V, DATTA S: Weighted rank aggregation of cluster validation measures: a Monte Carlo cross-entropy approach. Bioinformatics 2007, 23:1607-1615.

RAMOS KS, He Q, KALBFLEISCH T, Montoya-Durango DE, Teneng I, Stribinskis V, Brun M: Computational and biological inference of gene regulatory networks of the LINE-1 retrotransposon. Genomics 2007, 90:176-185.

Rempala GA, RAMOS KS, KALBFLEISCH T, Teneng I: Validation of a mathematical model of gene transcription in aggregated cellular systems: application to l1 retrotransposition. J Comput Biol 2007, 14:339-349.

ROUCHKA EC, Hardin CT: rMotifGen: random motif generator for DNA and protein sequences. BMC Bioinformatics 2007, 8:292.

Singh AV, ROUCHKA EC, Rempala GA, Bastian CD, Knudsen TB: Integrative database management for mouse development: systems and concepts. Birth Defects Res C Embryo Today 2007, 81:1-19.

Wang H, LI J, Kuang Y: Mathematical modeling and qualitative analysis of insulin therapies. Math Biosci 2007, 210:17-33.

Winchester JS, ROUCHKA EC, Rowland NS, Rice NA: In Silico characterization of phosphorylase kinase: evidence for an alternate intronic polyadenylation site in PHKG1. Mol Genet Metab 2007, 92:234-242.


Boratyn GM, DATTA S: Biologically supervised hierarchical clustering algorithms for gene expression data. Conf Proc IEEE Eng Med Biol Soc 2006, 1:5515-5518.

DATTA S: Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes. BMC Bioinformatics 2006, 7:397.

Goodin DG, Kocj DE, Owen RD, Chu YK, Hutchinson S, JONSSON CB: Land cover associated with hantavirus presence in Paraguay. Global Ecology and Biogeography 2006, 15:519-527.

LI J, Kuang Y, Mason CC: Modeling the glucose-insulin regulatory system and ultradian insulin secretory oscillations with two explicit time delays. J Theor Biol 2006, 242:722-735.

Makroglou A, LI J, Kuang Y: Mathematical models and software tools for the glucose-insulin regulatory system and diabetes: an overview. Applied Numerical Mathematics 2006, 56:559-573.

PANGULURI SK, KUMAR P, Palli SR: Functional characterization of ecdysone receptor gene switches in mammalian cells. FEBS J 2006, 273:5550-5563.

RAMOS KS: Transcriptional profiling and functional genomics reveal a role for AHR transcription factor in nephrogenesis. Ann N Y Acad Sci 2006, 1076:728-735.

RAMOS KS, Hadi Falahatpisheh M, Nanez A, He Q: Modulation of biological regulatory networks during nephrogenesis. Drug Metab Rev 2006, 38:677-683.

Rempala GA, RAMOS KS, KALBFLEISCH T: A stochastic model of gene transcription: an application to L1 retrotransposition events. J Theor Biol 2006, 242:101-116.

ROUCHKA EC: Dynamic programming approaches to sequence alignment. ACM Crossroads 2006, 13:18-22.

Zhu Y, Stribinskis V, RAMOS KS, LI Y: Sequence analysis of RNase MRP RNA reveals its origination from eukaryotic RNase P RNA. RNA 2006, 12:699-706.


Bhalla R, Dalal M, PANGULURI SK, Jagadish B, Mandaokar AD, Singh AK, KUMAR PA: Isolation, characterization and expression of a novel vegetative insecticidal protein gene of Bacillus thuringiensis. FEMS Microbiol Lett 2005, 243:467-472.

Cha IE, ROUCHKA EC: Comparison of different versions of current BLAST software on nucleotide sequences. In Fourth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2005); Denver, Colorado. 2005

DATTA S: Empirical Bayes screening of many p-values with applications to microarray studies. Bioinformatics 2005, 21:1987-1994.

Hardin CT, ROUCHKA EC: DNA Motif Detection Using Particle Swarm Optimization and Expectation-Maximization. Proc IEEE Swarm Intell Symp 2005, 2005:181-184.

Huang YJ, MOSELEY HN, Baran MC, Arrowsmith C, Powers R, Tejero R, Szyperski T, Montelione GT: An integrated platform for automated analysis of protein NMR structures. Methods Enzymol 2005, 394:111-141.

Jornsten R, Wang HY, Welsh WJ, OUYANG M: DNA microarray data imputation and significance analysis of differential expression. Bioinformatics 2005, 21:4155-4161.

Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, Zheng H, Bakker E, Calabrese P, Gladstone J, Goyal R, et al: The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol 2005, 3:e196.

PANGULURI SK, Sridhar J, Jagadish B, Sharma PC, KUMAR PA: Isolation and characterization of a green tissue-specific promoter from pigeonpea [Cajanus cajan (L.) Millsp.]. Indian J Exp Biol 2005, 43:369-372.

PANI JR, CHARIKER JH, Dawson TE, Johnson N: Acquiring new spatial intuitions: learning to reason about rotations. Cognitive psychology 2005, 51(4):285-333.

ROUCHKA EC, Khalyfa A, COOPER NG: MPrime: efficient large scale multiple primer and oligonucleotide design for customized gene microarrays. BMC Bioinformatics 2005, 6:175.

Weinberg MV, Schut GJ, Brehm S, DATTA S, Adams MW: Cold shock of a hyperthermophilic archaeon: Pyrococcus furiosus exhibits multiple responses to a suboptimal growth temperature with a key role for membrane-bound glycoproteins. J Bacteriol 2005, 187:336-348.


DATTA S, Satten GA, Benos DJ, Xia J, Heslin MJ: An empirical bayes adjustment to increase the sensitivity of detecting differentially expressed genes in microarray experiments. Bioinformatics 2004, 20:235-242.

Fan TW, LANE AN, Higashi RM: The promise of metabolomics in cancer molecular therapeutics. Curr Opin Mol Ther 2004, 6:584-592.

Johnson CD, Balagurunathan Y, Tadesse MG, Falahatpisheh MH, Brun M, Walker MK, Dougherty ER, RAMOS KS: Unraveling gene-gene interactions regulated by ligands of the aryl hydrocarbon receptor. Environ Health Perspect 2004, 112:403-412.

MOSELEY HN, Riaz N, Aramini JM, Szyperski T, Montelione GT: A generalized approach to automated NMR peak list editing: application to reduced dimensionality triple resonance spectra. J Magn Reson 2004, 170:263-277.

MOSELEY HN, Sahota G, Montelione GT: Assignment validation software suite for the evaluation and presentation of protein resonance assignment data. J Biomol NMR 2004, 28:341-355.

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PANI JR, CHARKIER JH: The psychology of error in relation to medical practice. Journal of surgical oncology 2004, 88(3):130-142.

RAMOS A, LANE AN, Hollingworth D, Fan TW: Secondary structure and stability of the selenocysteine insertion sequences (SECIS) for human thioredoxin reductase and glutathione peroxidase. Nucleic Acids Res 2004, 32:1746-1755.

Warrenfeltz S, Pavlik S, DATTA S, Kraemer ET, Benigno B, McDonald JF: Gene expression profiling of epithelial ovarian tumours correlated with malignant potential. Mol Cancer 2004, 3:27.


Chu YK, Goodin D, Owen RD, Koch D, JONSSON CB: Sympatry of 2 hantavirus strains, paraguay, 2003-2007. Emerg Infect Dis 2009, 15:1977-1980.

Dapic V, Abdomerovic V, Marrington R, Peberdy J, Rodger A, TRENT JO, Bates PJ: Biophysical and biological properties of quadruplex oligodeoxyribonucleotides. Nucleic Acids Res 2003, 31:2097-2107.

DATTA S: Comparisons and validation of statistical clustering techniques for microarray gene expression data. Bioinformatics 2003, 19:459-466.

Johnson CD, Balagurunathan Y, Lu KP, Tadesse M, Falahatpisheh MH, Carroll RJ, Dougherty ER, Afshari CA, RAMOS KS: Genomic profiles and predictive biological networks in oxidant-induced atherogenesis. Physiol Genomics 2003, 13:263-275.

Thompson W, ROUCHKA EC, Lawrence CE: Gibbs Recursive Sampler: finding transcription factor binding sites. Nucleic Acids Res 2003, 31:3580-3585.

Zheng D, Huang YJ, MOSELEY HN, Xiao R, Aramini J, Swapna GV, Montelione GT: Automated protein fold determination using a minimal NMR constraint strategy. Protein Sci 2003, 12:1232-1246.


Baran MC, MOSELEY HN, Sahota G, Montelione GT: SPINS: standardized protein NMR storage. A data dictionary and object-oriented relational database for archiving protein NMR spectra. J Biomol NMR 2002, 24:113-121.

Inge TH, Casson LK, Priebe W, TRENT JO, Georgeson KE, Miller DM, Bates PJ: Importance of Sp1 consensus motifs in the MYCN promoter. Surgery 2002, 132:232-238.

Monleon D, Colson K, MOSELEY HN, Anklin C, Oswald R, Szyperski T, Montelione GT: Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed LInux-based computing architecture, and an integrated set of spectral analysis tools. J Struct Funct Genomics 2002, 2:93-101.

ROUCHKA EC, Gish W, States DJ: Comparison of whole genome assemblies of the human genome. Nucleic Acids Res 2002, 30:5004-5014.

Szyperski T, Yeh DC, Sukumaran DK, MOSELEY HN, Montelione GT: Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment. Proc Natl Acad Sci U S A 2002, 99:8009-8014.


DATTA S: Exploring relationships in gene expressions: a partial least squares approach. Gene Expr 2001, 9:249-255.

Kan Z, ROUCHKA EC, Gish WR, States DJ: Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res 2001, 11:889-900.

LI J, Kuang Y, Li B: Analyses of IVGTT glucose-insulin interaction models with time delay. Discrete Contin Dynam Systems 2001, B:103-124.

MOSELEY HN, Monleon D, Montelione GT: Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data. Methods Enzymol 2001, 339:91-108.

Stephens JC, Schneider JA, Tanguay DA, Choi J, Acharya T, Stanley SE, Jiang R, Messer CJ, Chew A, Han JH, et al: Haplotype variation and linkage disequilibrium in 313 human genes. Science 2001, 293:489-493.

TRENT JO: Molecular modeling of drug-DNA complexes: an update. Methods Enzymol 2001, 340:290-326.


Kan Z, Gish W, ROUCHKA E, Glasscock J, States D: UTR reconstruction and analysis using genomically aligned EST sequences. Proc Int Conf Intell Syst Mol Biol 2000, 8:218-227.

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Blackwell TW, ROUCHKA E, States DJ: Identity by descent genome segmentation based on single nucleotide polymorphism distributions. Proc Int Conf Intell Syst Mol Biol 1999:54-59.

Mervis CB, Robinson BF, PANI JR: Visuospatial construction. Am J Hum Genet 1999, 65(5):1222-1229.

MOSELEY HN, Montelione GT: Automated analysis of NMR assignments and structures for proteins. Curr Opin Struct Biol 1999, 9:635-642.


ROUCHKA EC, States DJ: Sequence assembly validation by multiple restriction digest fragment coverage analysis. Proc Int Conf Intell Syst Mol Biol 1998, 6:140-147.

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