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Proceedings of the 2018 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference.

Wren JD, Doerkson RJ, Toby IT, Nanduri B, Homayouni R, Manda P, Thakkar S.

BMC Bioinformatics. 2019 Mar 14;20(Suppl 2):95. doi: 10.1186/s12859-019-2618-7. No abstract available.


Evaluation of Sirtuin-3 probe quality and co-expressed genes using literature cohesion.

Roy S, Zaman KI, Williams RW, Homayouni R.

BMC Bioinformatics. 2019 Mar 14;20(Suppl 2):104. doi: 10.1186/s12859-019-2621-z.


Memphis FitKids: implementing a mobile-friendly web-based application to enhance parents' participation in improving child health.

Ullmann G, Kedia SK, Homayouni R, Akkus C, Schmidt M, Klesges LM, Ward KD.

BMC Public Health. 2018 Aug 29;18(1):1068. doi: 10.1186/s12889-018-5968-6.


Age-associated increase in mnemonic strategy use is linked to prefrontal cortex development.

Yu Q, McCall DM, Homayouni R, Tang L, Chen Z, Schoff D, Nishimura M, Raz S, Ofen N.

Neuroimage. 2018 Nov 1;181:162-169. doi: 10.1016/j.neuroimage.2018.07.008. Epub 2018 Jul 4.


Proceedings of the 2017 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.

Wren JD, Dozmorov MG, Toby I, Nanduri B, Homayouni R, Manda P, Thakkar S.

BMC Bioinformatics. 2017 Dec 28;18(Suppl 14):498. doi: 10.1186/s12859-017-1887-2. No abstract available.


Navigating the Functional Landscape of Transcription Factors via Non-Negative Tensor Factorization Analysis of MEDLINE Abstracts.

Roy S, Yun D, Madahian B, Berry MW, Deng LY, Goldowitz D, Homayouni R.

Front Bioeng Biotechnol. 2017 Aug 28;5:48. doi: 10.3389/fbioe.2017.00048. eCollection 2017.


Loss of C-5 Sterol Desaturase Activity Results in Increased Resistance to Azole and Echinocandin Antifungals in a Clinical Isolate of Candida parapsilosis.

Rybak JM, Dickens CM, Parker JE, Caudle KE, Manigaba K, Whaley SG, Nishimoto AT, Luna-Tapia A, Roy S, Zhang Q, Barker KS, Palmer GE, Sutter TR, Homayouni R, Wiederhold NP, Kelly SL, Rogers PD.

Antimicrob Agents Chemother. 2017 Aug 24;61(9). pii: e00651-17. doi: 10.1128/AAC.00651-17. Print 2017 Sep.


MAP3K4 Controls the Chromatin Modifier HDAC6 during Trophoblast Stem Cell Epithelial-to-Mesenchymal Transition.

Mobley RJ, Raghu D, Duke LD, Abell-Hart K, Zawistowski JS, Lutz K, Gomez SM, Roy S, Homayouni R, Johnson GL, Abell AN.

Cell Rep. 2017 Mar 7;18(10):2387-2400. doi: 10.1016/j.celrep.2017.02.030.


An efficient Bayesian approach for Gaussian Bayesian network structure learning.

Han S, Zhang H, Homayouni R, Karmaus W.

Commun Stat Simul Comput. 2017;46(7):5070-5084. doi: 10.1080/03610918.2016.1143103. Epub 2017 Feb 28.


Prioritization, clustering and functional annotation of MicroRNAs using latent semantic indexing of MEDLINE abstracts.

Roy S, Curry BC, Madahian B, Homayouni R.

BMC Bioinformatics. 2016 Oct 6;17(Suppl 13):350.


Proceedings of the 2015 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.

Wren JD, Thakkar S, Homayouni R, Johann DJ, Dozmorov MG.

BMC Bioinformatics. 2015;16 Suppl 13:S1. doi: 10.1186/1471-2105-16-S13-S1. Epub 2015 Sep 25. No abstract available.


A Bayesian approach for inducing sparsity in generalized linear models with multi-category response.

Madahian B, Roy S, Bowman D, Deng LY, Homayouni R.

BMC Bioinformatics. 2015;16 Suppl 13:S13. doi: 10.1186/1471-2105-16-S13-S13. Epub 2015 Sep 25.


A Pilot Study of Demographic and Dopaminergic Genetic Contributions to Weight Change in Kidney Transplant Recipients.

Stanfill A, Hathaway D, Cashion A, Homayouni R, Cowan P, Thompson C, Madahian B, Conley Y.

PLoS One. 2015 Sep 25;10(9):e0138885. doi: 10.1371/journal.pone.0138885. eCollection 2015.


Expression of mouse Dab2ip transcript variants and gene methylation during brain development.

Salami F, Qiao S, Homayouni R.

Gene. 2015 Aug 15;568(1):19-24. doi: 10.1016/j.gene.2015.05.012. Epub 2015 May 7.


Dab2IP Regulates Neuronal Positioning, Rap1 Activity and Integrin Signaling in the Developing Cortex.

Qiao S, Homayouni R.

Dev Neurosci. 2015;37(2):131-41. doi: 10.1159/000369092. Epub 2015 Feb 25.


Neurogenetic and Neuroimaging Evidence for a Conceptual Model of Dopaminergic Contributions to Obesity.

Stanfill AG, Conley Y, Cashion A, Thompson C, Homayouni R, Cowan P, Hathaway D.

Biol Res Nurs. 2015 Jul;17(4):413-21. doi: 10.1177/1099800414565170. Epub 2015 Jan 9. Review.


CbGRiTS: cerebellar gene regulation in time and space.

Ha T, Swanson D, Larouche M, Glenn R, Weeden D, Zhang P, Hamre K, Langston M, Phillips C, Song M, Ouyang Z, Chesler E, Duvvurru S, Yordanova R, Cui Y, Campbell K, Ricker G, Phillips C, Homayouni R, Goldowitz D.

Dev Biol. 2015 Jan 1;397(1):18-30. doi: 10.1016/j.ydbio.2014.09.032. Epub 2014 Oct 23.


Group A streptococcus expresses a trio of surface proteins containing protective epitopes.

Niedermeyer SE, Penfound TA, Hohn C, Li Y, Homayouni R, Zhao J, Dale JB.

Clin Vaccine Immunol. 2014 Oct;21(10):1421-5. doi: 10.1128/CVI.00448-14. Epub 2014 Jul 30.


Tetraspanin CD9 modulates human lymphoma cellular proliferation via histone deacetylase activity.

Herr MJ, Longhurst CM, Baker B, Homayouni R, Speich HE, Kotha J, Jennings LK.

Biochem Biophys Res Commun. 2014 May 16;447(4):616-20. doi: 10.1016/j.bbrc.2014.04.046. Epub 2014 Apr 18.


Functionally enigmatic genes: a case study of the brain ignorome.

Pandey AK, Lu L, Wang X, Homayouni R, Williams RW.

PLoS One. 2014 Feb 11;9(2):e88889. doi: 10.1371/journal.pone.0088889. eCollection 2014.


Glutamate dysfunction associated with developmental cerebellar damage: relevance to autism spectrum disorders.

McKimm E, Corkill B, Goldowitz D, Albritton LM, Homayouni R, Blaha CD, Mittleman G.

Cerebellum. 2014 Jun;13(3):346-53. doi: 10.1007/s12311-013-0541-4.


Expression levels of obesity-related genes are associated with weight change in kidney transplant recipients.

Cashion A, Stanfill A, Thomas F, Xu L, Sutter T, Eason J, Ensell M, Homayouni R.

PLoS One. 2013;8(3):e59962. doi: 10.1371/journal.pone.0059962. Epub 2013 Mar 27.


Dab2IP GTPase activating protein regulates dendrite development and synapse number in cerebellum.

Qiao S, Kim SH, Heck D, Goldowitz D, LeDoux MS, Homayouni R.

PLoS One. 2013;8(1):e53635. doi: 10.1371/journal.pone.0053635. Epub 2013 Jan 9.


Literature aided determination of data quality and statistical significance threshold for gene expression studies.

Xu L, Cheng C, George EO, Homayouni R.

BMC Genomics. 2012;13 Suppl 8:S23. doi: 10.1186/1471-2164-13-S8-S23. Epub 2012 Dec 17.


Dab2ip regulates neuronal migration and neurite outgrowth in the developing neocortex.

Lee GH, Kim SH, Homayouni R, D'Arcangelo G.

PLoS One. 2012;7(10):e46592. doi: 10.1371/journal.pone.0046592. Epub 2012 Oct 4.


Developing a gene expression model for predicting ventilator-associated pneumonia in trauma patients: a pilot study.

Swanson JM, Wood GC, Xu L, Tang LE, Meibohm B, Homayouni R, Croce MA, Fabian TC.

PLoS One. 2012;7(8):e42065. doi: 10.1371/journal.pone.0042065. Epub 2012 Aug 15.


Latent Semantic Indexing of PubMed abstracts for identification of transcription factor candidates from microarray derived gene sets.

Roy S, Heinrich K, Phan V, Berry MW, Homayouni R.

BMC Bioinformatics. 2011 Oct 18;12 Suppl 10:S19. doi: 10.1186/1471-2105-12-S10-S19.


Proceedings of the Tenth Annual UT-ORNL-KBRIN Bioinformatics Summit 2011.

Rouchka EC, Flight RM, Homayouni R.

BMC Bioinformatics. 2011;12 Suppl 7:A1. Epub 2011 Aug 5. No abstract available.


A potential link between autoimmunity and neurodegeneration in immune-mediated neurological disease.

Lee S, Xu L, Shin Y, Gardner L, Hartzes A, Dohan FC, Raine C, Homayouni R, Levin MC.

J Neuroimmunol. 2011 Jun;235(1-2):56-69. doi: 10.1016/j.jneuroim.2011.02.007. Epub 2011 May 13.


Functional cohesion of gene sets determined by latent semantic indexing of PubMed abstracts.

Xu L, Furlotte N, Lin Y, Heinrich K, Berry MW, George EO, Homayouni R.

PLoS One. 2011 Apr 14;6(4):e18851. doi: 10.1371/journal.pone.0018851.


Genomewide expression profile analysis of the Candida glabrata Pdr1 regulon.

Caudle KE, Barker KS, Wiederhold NP, Xu L, Homayouni R, Rogers PD.

Eukaryot Cell. 2011 Mar;10(3):373-83. doi: 10.1128/EC.00073-10. Epub 2010 Dec 30.


Discovering gene functional relationships using FAUN (Feature Annotation Using Nonnegative matrix factorization).

Tjioe E, Berry MW, Homayouni R.

BMC Bioinformatics. 2010 Oct 7;11 Suppl 6:S14. doi: 10.1186/1471-2105-11-S6-S14.


Interaction of a novel mitochondrial protein, 4-nitrophenylphosphatase domain and non-neuronal SNAP25-like protein homolog 1 (NIPSNAP1), with the amyloid precursor protein family.

Tummala H, Li X, Homayouni R.

Eur J Neurosci. 2010 Jun;31(11):1926-34. doi: 10.1111/j.1460-9568.2010.07248.x. Epub 2010 May 24.


Using gene expression databases for classical trait QTL candidate gene discovery in the BXD recombinant inbred genetic reference population: mouse forebrain weight.

Lu L, Wei L, Peirce JL, Wang X, Zhou J, Homayouni R, Williams RW, Airey DC.

BMC Genomics. 2008 Sep 25;9:444. doi: 10.1186/1471-2164-9-444.


Bioinformatic analysis reveals cRel as a regulator of a subset of interferon-stimulated genes.

Wei L, Fan M, Xu L, Heinrich K, Berry MW, Homayouni R, Pfeffer LM.

J Interferon Cytokine Res. 2008 Sep;28(9):541-51. doi: 10.1089/jir.2007.0136.


Transcriptome profile of the vascular endothelial cell response to Candida albicans.

Barker KS, Park H, Phan QT, Xu L, Homayouni R, Rogers PD, Filler SG.

J Infect Dis. 2008 Jul 15;198(2):193-202. doi: 10.1086/589516.


A gain-of-function mutation in the transcription factor Upc2p causes upregulation of ergosterol biosynthesis genes and increased fluconazole resistance in a clinical Candida albicans isolate.

Dunkel N, Liu TT, Barker KS, Homayouni R, Morschhäuser J, Rogers PD.

Eukaryot Cell. 2008 Jul;7(7):1180-90. doi: 10.1128/EC.00103-08. Epub 2008 May 16.


Gene tree labeling using nonnegative matrix factorization on biomedical literature.

Heinrich KE, Berry MW, Homayouni R.

Comput Intell Neurosci. 2008:276535. doi: 10.1155/2008/276535.


The transcription factor Mrr1p controls expression of the MDR1 efflux pump and mediates multidrug resistance in Candida albicans.

Morschhäuser J, Barker KS, Liu TT, BlaB-Warmuth J, Homayouni R, Rogers PD.

PLoS Pathog. 2007 Nov;3(11):e164.


Genome-wide expression and location analyses of the Candida albicans Tac1p regulon.

Liu TT, Znaidi S, Barker KS, Xu L, Homayouni R, Saidane S, Morschhäuser J, Nantel A, Raymond M, Rogers PD.

Eukaryot Cell. 2007 Nov;6(11):2122-38. Epub 2007 Sep 28.


Blood gene expression profiling in liver transplant recipients with hepatitis C virus and posttransplantation diabetes mellitus.

Driscoll CJ, Cashion AK, Hathaway DK, Thompson C, Conley Y, Riely C, Xu L, Homayouni R.

Transplant Proc. 2006 Dec;38(10):3646-8.


The creatine kinase/creatine connection to Alzheimer's disease: CK-inactivation, APP-CK complexes and focal creatine deposits.

Bürklen TS, Schlattner U, Homayouni R, Gough K, Rak M, Szeghalmi A, Wallimann T.

J Biomed Biotechnol. 2006;2006(3):35936.


Murine central and peripheral nervous system transcriptomes: comparative gene expression.

LeDoux MS, Xu L, Xiao J, Ferrell B, Menkes DL, Homayouni R.

Brain Res. 2006 Aug 30;1107(1):24-41. Epub 2006 Jul 7.


Collaborative development of the Arrowsmith two node search interface designed for laboratory investigators.

Smalheiser NR, Torvik VI, Bischoff-Grethe A, Burhans LB, Gabriel M, Homayouni R, Kashef A, Martone ME, Perkins GA, Price DL, Talk AC, West R.

J Biomed Discov Collab. 2006 Jul 3;1:8.


Pdr1 regulates multidrug resistance in Candida glabrata: gene disruption and genome-wide expression studies.

Vermitsky JP, Earhart KD, Smith WL, Homayouni R, Edlind TD, Rogers PD.

Mol Microbiol. 2006 Aug;61(3):704-22. Epub 2006 Jun 27.


Combining gene expression QTL mapping and phenotypic spectrum analysis to uncover gene regulatory relationships.

Bao L, Wei L, Peirce JL, Homayouni R, Li H, Zhou M, Chen H, Lu L, Williams RW, Pfeffer LM, Goldowitz D, Cui Y.

Mamm Genome. 2006 Jun;17(6):575-83. Epub 2006 Jun 12.


NFkappaB negatively regulates interferon-induced gene expression and anti-influenza activity.

Wei L, Sandbulte MR, Thomas PG, Webby RJ, Homayouni R, Pfeffer LM.

J Biol Chem. 2006 Apr 28;281(17):11678-84. Epub 2006 Mar 3.


Stabilization of ubiquitous mitochondrial creatine kinase preprotein by APP family proteins.

Li X, Bürklen T, Yuan X, Schlattner U, Desiderio DM, Wallimann T, Homayouni R.

Mol Cell Neurosci. 2006 Feb;31(2):263-72. Epub 2005 Nov 2.


Genome-wide expression profiling of the response to azole, polyene, echinocandin, and pyrimidine antifungal agents in Candida albicans.

Liu TT, Lee RE, Barker KS, Lee RE, Wei L, Homayouni R, Rogers PD.

Antimicrob Agents Chemother. 2005 Jun;49(6):2226-36.


Gene clustering by latent semantic indexing of MEDLINE abstracts.

Homayouni R, Heinrich K, Wei L, Berry MW.

Bioinformatics. 2005 Jan 1;21(1):104-15. Epub 2004 Aug 12.


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