Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 61

1.

A Critical Role of the IL-1β-IL-1R Signaling Pathway in Skin Inflammation and Psoriasis Pathogenesis.

Cai Y, Xue F, Quan C, Qu M, Liu N, Zhang Y, Fleming C, Hu X, Zhang HG, Weichselbaum R, Fu YX, Tieri D, Rouchka EC, Zheng J, Yan J.

J Invest Dermatol. 2018 Aug 16. pii: S0022-202X(18)32478-3. doi: 10.1016/j.jid.2018.07.025. [Epub ahead of print]

PMID:
30120937
2.

A combined approach with gene-wise normalization improves the analysis of RNA-seq data in human breast cancer subtypes.

Li X, Rouchka EC, Brock GN, Yan J, O'Toole TE, Tieri DA, Cooper NGF.

PLoS One. 2018 Aug 8;13(8):e0201813. doi: 10.1371/journal.pone.0201813. eCollection 2018.

3.

Transcriptomic response of breast cancer cells to anacardic acid.

Schultz DJ, Krishna A, Vittitow SL, Alizadeh-Rad N, Muluhngwi P, Rouchka EC, Klinge CM.

Sci Rep. 2018 May 23;8(1):8063. doi: 10.1038/s41598-018-26429-x.

4.

Identification of G-quadruplex forming sequences in three manatee papillomaviruses.

Zahin M, Dean WL, Ghim SJ, Joh J, Gray RD, Khanal S, Bossart GD, Mignucci-Giannoni AA, Rouchka EC, Jenson AB, Trent JO, Chaires JB, Chariker JH.

PLoS One. 2018 Apr 9;13(4):e0195625. doi: 10.1371/journal.pone.0195625. eCollection 2018.

5.

Yersinia pestis Targets the Host Endosome Recycling Pathway during the Biogenesis of the Yersinia-Containing Vacuole To Avoid Killing by Macrophages.

Connor MG, Pulsifer AR, Chung D, Rouchka EC, Ceresa BK, Lawrenz MB.

MBio. 2018 Feb 20;9(1). pii: e01800-17. doi: 10.1128/mBio.01800-17.

6.

Transcriptome-wide identification of the RNA-binding landscape of the chromatin-associated protein PARP1 reveals functions in RNA biogenesis.

Melikishvili M, Chariker JH, Rouchka EC, Fondufe-Mittendorf YN.

Cell Discov. 2017 Nov 28;3:17043. doi: 10.1038/celldisc.2017.43. eCollection 2017.

7.

Framework for reanalysis of publicly available Affymetrix® GeneChip® data sets based on functional regions of interest.

Saka E, Harrison BJ, West K, Petruska JC, Rouchka EC.

BMC Genomics. 2017 Dec 6;18(Suppl 10):875. doi: 10.1186/s12864-017-4266-5.

8.

Leukotriene B4-receptor-1 mediated host response shapes gut microbiota and controls colon tumor progression.

Jala VR, Maturu P, Bodduluri SR, Krishnan E, Mathis S, Subbarao K, Wang M, Jenson AB, Proctor ML, Rouchka EC, Knight R, Haribabu B.

Oncoimmunology. 2017 Aug 10;6(12):e1361593. doi: 10.1080/2162402X.2017.1361593. eCollection 2017.

9.

Pas de deux: An Intricate Dance of Anther Smut and Its Host.

San Toh S, Chen Z, Rouchka EC, Schultz DJ, Cuomo CA, Perlin MH.

G3 (Bethesda). 2018 Feb 2;8(2):505-518. doi: 10.1534/g3.117.300318.

10.

Dietary copper-fructose interactions alter gut microbial activity in male rats.

Song M, Li X, Zhang X, Shi H, Vos MB, Wei X, Wang Y, Gao H, Rouchka EC, Yin X, Zhou Z, Prough RA, Cave MC, McClain CJ.

Am J Physiol Gastrointest Liver Physiol. 2018 Jan 1;314(1):G119-G130. doi: 10.1152/ajpgi.00378.2016. Epub 2017 Oct 12.

PMID:
29025734
11.

Genome-wide miRNA response to anacardic acid in breast cancer cells.

Schultz DJ, Muluhngwi P, Alizadeh-Rad N, Green MA, Rouchka EC, Waigel SJ, Klinge CM.

PLoS One. 2017 Sep 8;12(9):e0184471. doi: 10.1371/journal.pone.0184471. eCollection 2017.

12.

Detecting and accounting for multiple sources of positional variance in peak list registration analysis and spin system grouping.

Smelter A, Rouchka EC, Moseley HNB.

J Biomol NMR. 2017 Aug;68(4):281-296. doi: 10.1007/s10858-017-0126-5. Epub 2017 Aug 16.

13.

Identification of successful mentoring communities using network-based analysis of mentor-mentee relationships across Nobel laureates.

Chariker JH, Zhang Y, Pani JR, Rouchka EC.

Scientometrics. 2017;111(3):1733-1749. doi: 10.1007/s11192-017-2364-4. Epub 2017 Mar 27.

14.

A comparison of per sample global scaling and per gene normalization methods for differential expression analysis of RNA-seq data.

Li X, Brock GN, Rouchka EC, Cooper NGF, Wu D, O'Toole TE, Gill RS, Eteleeb AM, O'Brien L, Rai SN.

PLoS One. 2017 May 1;12(5):e0176185. doi: 10.1371/journal.pone.0176185. eCollection 2017.

15.

Identification of a plasma metabolomic signature of thrombotic myocardial infarction that is distinct from non-thrombotic myocardial infarction and stable coronary artery disease.

DeFilippis AP, Trainor PJ, Hill BG, Amraotkar AR, Rai SN, Hirsch GA, Rouchka EC, Bhatnagar A.

PLoS One. 2017 Apr 17;12(4):e0175591. doi: 10.1371/journal.pone.0175591. eCollection 2017.

16.

Systems characterization of differential plasma metabolome perturbations following thrombotic and non-thrombotic myocardial infarction.

Trainor PJ, Hill BG, Carlisle SM, Rouchka EC, Rai SN, Bhatnagar A, DeFilippis AP.

J Proteomics. 2017 May 8;160:38-46. doi: 10.1016/j.jprot.2017.03.014. Epub 2017 Mar 22.

17.

Perspectives and expectations in structural bioinformatics of metalloproteins.

Yao S, Flight RM, Rouchka EC, Moseley HN.

Proteins. 2017 May;85(5):938-944. doi: 10.1002/prot.25263. Epub 2017 Mar 15.

18.

Aberrant coordination geometries discovered in the most abundant metalloproteins.

Yao S, Flight RM, Rouchka EC, Moseley HN.

Proteins. 2017 May;85(5):885-907. doi: 10.1002/prot.25257. Epub 2017 Mar 7.

19.

Regulation of miR-29b-1/a transcription and identification of target mRNAs in CHO-K1 cells.

Muluhngwi P, Richardson K, Napier J, Rouchka EC, Mott JL, Klinge CM.

Mol Cell Endocrinol. 2017 Mar 15;444:38-47. doi: 10.1016/j.mce.2017.01.044. Epub 2017 Jan 28.

20.

Computational Analysis of G-Quadruplex Forming Sequences across Chromosomes Reveals High Density Patterns Near the Terminal Ends.

Chariker JH, Miller DM, Rouchka EC.

PLoS One. 2016 Oct 24;11(10):e0165101. doi: 10.1371/journal.pone.0165101. eCollection 2016.

21.

Discovery of a Family of Genomic Sequences Which Interact Specifically with the c-MYC Promoter to Regulate c-MYC Expression.

Rezzoug F, Thomas SD, Rouchka EC, Miller DM.

PLoS One. 2016 Aug 23;11(8):e0161588. doi: 10.1371/journal.pone.0161588. eCollection 2016.

22.

Nuclear respiratory factor-1 and bioenergetics in tamoxifen-resistant breast cancer cells.

Radde BN, Ivanova MM, Mai HX, Alizadeh-Rad N, Piell K, Van Hoose P, Cole MP, Muluhngwi P, Kalbfleisch TS, Rouchka EC, Hill BG, Klinge CM.

Exp Cell Res. 2016 Sep 10;347(1):222-31. doi: 10.1016/j.yexcr.2016.08.006. Epub 2016 Aug 8.

23.

Involvement of PARP1 in the regulation of alternative splicing.

Matveeva E, Maiorano J, Zhang Q, Eteleeb AM, Convertini P, Chen J, Infantino V, Stamm S, Wang J, Rouchka EC, Fondufe-Mittendorf YN.

Cell Discov. 2016 Feb 16;2:15046. doi: 10.1038/celldisc.2015.46. eCollection 2016.

24.

rMAPS: RNA map analysis and plotting server for alternative exon regulation.

Park JW, Jung S, Rouchka EC, Tseng YT, Xing Y.

Nucleic Acids Res. 2016 Jul 8;44(W1):W333-8. doi: 10.1093/nar/gkw410. Epub 2016 May 12.

25.

Data set for transcriptional response to depletion of the Shoc2 scaffolding protein.

Rouchka EC, Jeoung M, Jang ER, Liu J, Wang C, Li X, Galperin E.

Data Brief. 2016 Mar 9;7:770-8. doi: 10.1016/j.dib.2016.03.012. eCollection 2016 Jun.

26.

The Adaptor Protein CD2AP Is a Coordinator of Neurotrophin Signaling-Mediated Axon Arbor Plasticity.

Harrison BJ, Venkat G, Lamb JL, Hutson TH, Drury C, Rau KK, Bunge MB, Mendell LM, Gage FH, Johnson RD, Hill CE, Rouchka EC, Moon LD, Petruska JC.

J Neurosci. 2016 Apr 13;36(15):4259-75. doi: 10.1523/JNEUROSCI.2423-15.2016.

27.

Transcriptional profile of immediate response to ionizing radiation exposure.

Rouchka EC, Flight RM, Fasciotto BH, Estrada R, Eaton JW, Patibandla PK, Waigel SJ, Li D, Kirtley JK, Sethu P, Keynton RS.

Genom Data. 2015 Dec 1;7:82-5. doi: 10.1016/j.gdata.2015.11.027. eCollection 2016 Mar.

28.

Shoc2-tranduced ERK1/2 motility signals--Novel insights from functional genomics.

Jeoung M, Jang ER, Liu J, Wang C, Rouchka EC, Li X, Galperin E.

Cell Signal. 2016 May;28(5):448-459. doi: 10.1016/j.cellsig.2016.02.005. Epub 2016 Feb 11.

29.

Transcriptional changes in sensory ganglia associated with primary afferent axon collateral sprouting in spared dermatome model.

Harrison BJ, Venkat G, Hutson T, Rau KK, Bunge MB, Mendell LM, Gage FH, Johnson RD, Hill C, Rouchka EC, Moon L, Petruska JC.

Genom Data. 2015 Oct 23;6:249-52. doi: 10.1016/j.gdata.2015.10.005. eCollection 2015 Dec.

30.

Genome-Wide Profiling of PARP1 Reveals an Interplay with Gene Regulatory Regions and DNA Methylation.

Nalabothula N, Al-jumaily T, Eteleeb AM, Flight RM, Xiaorong S, Moseley H, Rouchka EC, Fondufe-Mittendorf YN.

PLoS One. 2015 Aug 25;10(8):e0135410. doi: 10.1371/journal.pone.0135410. eCollection 2015.

31.

A less-biased analysis of metalloproteins reveals novel zinc coordination geometries.

Yao S, Flight RM, Rouchka EC, Moseley HN.

Proteins. 2015 Aug;83(8):1470-87. doi: 10.1002/prot.24834. Epub 2015 Jun 13.

32.

Inorganic Arsenic-induced cellular transformation is coupled with genome wide changes in chromatin structure, transcriptome and splicing patterns.

Riedmann C, Ma Y, Melikishvili M, Godfrey SG, Zhang Z, Chen KC, Rouchka EC, Fondufe-Mittendorf YN.

BMC Genomics. 2015 Mar 19;16:212. doi: 10.1186/s12864-015-1295-9.

33.

An Island-Based Approach for Differential Expression Analysis.

Eteleeb AM, Flight RM, Harrison BJ, Petruska JC, Rouchka EC.

ACM Conf Bioinform Comput Biol Biomed Inform (2013). 2013 Dec 31;2013:419-429.

34.

Proceedings of the Thirteenth Annual UT- KBRIN Bioinformatics Summit 2014.

Rouchka EC, Chariker JH.

BMC Bioinformatics. 2014;15 Suppl 10:I1. Epub 2014 Sep 26. No abstract available.

35.

categoryCompare, an analytical tool based on feature annotations.

Flight RM, Harrison BJ, Mohammad F, Bunge MB, Moon LD, Petruska JC, Rouchka EC.

Front Genet. 2014 Apr 29;5:98. doi: 10.3389/fgene.2014.00098. eCollection 2014.

36.

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.

Harrison BJ, Flight RM, Gomes C, Venkat G, Ellis SR, Sankar U, Twiss JL, Rouchka EC, Petruska JC.

J Comp Neurol. 2014 Feb 1;522(2):308-36. doi: 10.1002/cne.23398.

37.

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.

Hougland MT, Harrison BJ, Magnuson DS, Rouchka EC, Petruska JC.

Front Physiol. 2013 Jan 9;3:478. doi: 10.3389/fphys.2012.00478. eCollection 2012.

38.

Proceedings of the 12th Annual UT-ORNL-KBRIN Bioinformatics Summit 2013.

Rouchka EC, Flight RM.

BMC Bioinformatics. 2013 Mar 22;14 Suppl 17:A1. No abstract available.

39.

AbsIDconvert: an absolute approach for converting genetic identifiers at different granularities.

Mohammad F, Flight RM, Harrison BJ, Petruska JC, Rouchka EC.

BMC Bioinformatics. 2012 Sep 12;13:229. doi: 10.1186/1471-2105-13-229.

40.

Prenatal arsenic exposure alters gene expression in the adult liver to a proinflammatory state contributing to accelerated atherosclerosis.

States JC, Singh AV, Knudsen TB, Rouchka EC, Ngalame NO, Arteel GE, Piao Y, Ko MS.

PLoS One. 2012;7(6):e38713. doi: 10.1371/journal.pone.0038713. Epub 2012 Jun 15.

41.

Codon usage bias as a function of generation time and life expectancy.

Mahdi RN, Rouchka EC.

Bioinformation. 2012;8(3):158-62. Epub 2012 Feb 3.

42.

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.

43.

Reduced HyperBF networks: regularization by explicit complexity reduction and scaled Rprop-based training.

Mahdi RN, Rouchka EC.

IEEE Trans Neural Netw. 2011 May;22(5):673-86. doi: 10.1109/TNN.2011.2109736. Epub 2011 Mar 17.

PMID:
21421438
44.

Database of exact tandem repeats in the Zebrafish genome.

Rouchka EC.

BMC Genomics. 2010 Jun 1;11:347. doi: 10.1186/1471-2164-11-347.

45.

DNA-based random number generation in security circuitry.

Gearheart CM, Arazi B, Rouchka EC.

Biosystems. 2010 Jun;100(3):208-14. doi: 10.1016/j.biosystems.2010.03.005. Epub 2010 Mar 18.

46.

RBF-TSS: identification of transcription start site in human using radial basis functions network and oligonucleotide positional frequencies.

Mahdi RN, Rouchka EC.

PLoS One. 2009;4(3):e4878. doi: 10.1371/journal.pone.0004878. Epub 2009 Mar 16.

47.

Evidence of bias towards buffered codons in human transcripts.

Mahdi RN, Rouchka EC.

Proc IEEE Int Symp Signal Proc Inf Tech. 2008 Dec 16;2008:29-34.

48.

Effect of single nucleotide polymorphisms on Affymetrix match-mismatch probe pairs.

Rouchka EC, Phatak AW, Singh AV.

Bioinformation. 2008 Jul 14;2(9):405-11.

49.

Toward DNA-based Security Circuitry: First Step - Random Number Generation.

Bogard CM, Arazi B, Rouchka EC.

Conf Proc (Midwest Symp Circuits Syst). 2008 Aug 10;51:597-600.

50.

Model Based Unsupervised Learning Guided by Abundant Background Samples.

Mahdi RN, Rouchka EC.

Proc Int Conf Mach Learn. 2008;7(4724976):203-210.

Supplemental Content

Loading ...
Support Center