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Items: 44

1.

Deep Learning data integration for better risk stratification models of bladder cancer.

Poirion OB, Chaudhary K, Garmire LX.

AMIA Jt Summits Transl Sci Proc. 2018 May 18;2017:197-206. eCollection 2018.

2.

Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data.

Ching T, Zhu X, Garmire LX.

PLoS Comput Biol. 2018 Apr 10;14(4):e1006076. doi: 10.1371/journal.pcbi.1006076. eCollection 2018 Apr.

3.

Using single-cell multiple omics approaches to resolve tumor heterogeneity.

Ortega MA, Poirion O, Zhu X, Huang S, Wolfgruber TK, Sebra R, Garmire LX.

Clin Transl Med. 2017 Dec 28;6(1):46. doi: 10.1186/s40169-017-0177-y. Review.

4.
5.

Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists.

Zhu X, Wolfgruber TK, Tasato A, Arisdakessian C, Garmire DG, Garmire LX.

Genome Med. 2017 Dec 5;9(1):108. doi: 10.1186/s13073-017-0492-3.

6.

Deep Learning Accurately Predicts Estrogen Receptor Status in Breast Cancer Metabolomics Data.

Alakwaa FM, Chaudhary K, Garmire LX.

J Proteome Res. 2018 Jan 5;17(1):337-347. doi: 10.1021/acs.jproteome.7b00595. Epub 2017 Nov 27.

7.

Deep Learning-Based Multi-Omics Integration Robustly Predicts Survival in Liver Cancer.

Chaudhary K, Poirion OB, Lu L, Garmire LX.

Clin Cancer Res. 2018 Mar 15;24(6):1248-1259. doi: 10.1158/1078-0432.CCR-17-0853. Epub 2017 Oct 5.

PMID:
28982688
8.

Corrigendum: Alternative splicing promotes tumour aggressiveness and drug resistance in African American prostate cancer.

Wang BD, Ceniccola K, Hwang S, Andrawis R, Horvath A, Freedman JA, Olender J, Knapp S, Ching T, Garmire L, Patel V, Garcia-Blanco MA, Patierno SR, Lee NH.

Nat Commun. 2017 Sep 27;8:16161. doi: 10.1038/ncomms16161.

9.

More Is Better: Recent Progress in Multi-Omics Data Integration Methods.

Huang S, Chaudhary K, Garmire LX.

Front Genet. 2017 Jun 16;8:84. doi: 10.3389/fgene.2017.00084. eCollection 2017. Review.

10.

Alternative splicing promotes tumour aggressiveness and drug resistance in African American prostate cancer.

Wang BD, Ceniccola K, Hwang S, Andrawis R, Horvath A, Freedman JA, Olender J, Knapp S, Ching T, Garmire L, Patel V, Garcia-Blanco MA, Patierno SR, Lee NH.

Nat Commun. 2017 Jun 30;8:15921. doi: 10.1038/ncomms15921. Erratum in: Nat Commun. 2017 Sep 27;8:16161.

11.

Human DBR1 modulates the recycling of snRNPs to affect alternative RNA splicing and contributes to the suppression of cancer development.

Han B, Park HK, Ching T, Panneerselvam J, Wang H, Shen Y, Zhang J, Li L, Che R, Garmire L, Fei P.

Oncogene. 2017 Sep 21;36(38):5382-5391. doi: 10.1038/onc.2017.150. Epub 2017 May 15.

12.

Celebrating parasites.

Greene CS, Garmire LX, Gilbert JA, Ritchie MD, Hunter LE.

Nat Genet. 2017 Mar 30;49(4):483-484. doi: 10.1038/ng.3830. No abstract available.

13.

Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization.

Zhu X, Ching T, Pan X, Weissman SM, Garmire L.

PeerJ. 2017 Jan 19;5:e2888. doi: 10.7717/peerj.2888. eCollection 2017.

14.

Genome-wide analysis of DNA methylation and their associations with long noncoding RNA/mRNA expression in non-small-cell lung cancer.

Feng N, Wang Y, Zheng M, Yu X, Lin H, Ma RN, Shi O, Zheng X, Gao M, Yu H, Garmire L, Qian B.

Epigenomics. 2017 Jan 23. doi: 10.2217/epi-2016-0120. [Epub ahead of print]

PMID:
28111977
15.

Single cell transcriptomics reveals unanticipated features of early hematopoietic precursors.

Yang J, Tanaka Y, Seay M, Li Z, Jin J, Garmire LX, Zhu X, Taylor A, Li W, Euskirchen G, Halene S, Kluger Y, Snyder MP, Park IH, Pan X, Weissman SM.

Nucleic Acids Res. 2017 Feb 17;45(3):1281-1296. doi: 10.1093/nar/gkw1214.

16.

Time Series miRNA-mRNA integrated analysis reveals critical miRNAs and targets in macrophage polarization.

Lu L, McCurdy S, Huang S, Zhu X, Peplowska K, Tiirikainen M, Boisvert WA, Garmire LX.

Sci Rep. 2016 Dec 16;6:37446. doi: 10.1038/srep37446.

17.

THE TRAINING OF NEXT GENERATION DATA SCIENTISTS IN BIOMEDICINE.

Garmire LX, Gliske S, Nguyen QC, Chen JH, Nemati S, VAN Horn JD, Moore JH, Shreffler C, Dunn M.

Pac Symp Biocomput. 2017;22:640-645. doi: 10.1142/9789813207813_0059.

18.

Analysis of Microarray Data on Gene Expression and Methylation to Identify Long Non-coding RNAs in Non-small Cell Lung Cancer.

Feng N, Ching T, Wang Y, Liu B, Lin H, Shi O, Zhang X, Zheng M, Zheng X, Gao M, Zheng ZJ, Yu H, Garmire L, Qian B.

Sci Rep. 2016 Nov 16;6:37233. doi: 10.1038/srep37233.

19.

Single-Cell Transcriptomics Bioinformatics and Computational Challenges.

Poirion OB, Zhu X, Ching T, Garmire L.

Front Genet. 2016 Sep 21;7:163. eCollection 2016. Review.

20.

Meta-dimensional data integration identifies critical pathways for susceptibility, tumorigenesis and progression of endometrial cancer.

Wei R, De Vivo I, Huang S, Zhu X, Risch H, Moore JH, Yu H, Garmire LX.

Oncotarget. 2016 Aug 23;7(34):55249-55263. doi: 10.18632/oncotarget.10509.

21.

A Nomogram Derived by Combination of Demographic and Biomarker Data Improves the Noninvasive Evaluation of Patients at Risk for Bladder Cancer.

Huang S, Kou L, Furuya H, Yu C, Goodison S, Kattan MW, Garmire L, Rosser CJ.

Cancer Epidemiol Biomarkers Prev. 2016 Sep;25(9):1361-6. doi: 10.1158/1055-9965.EPI-16-0260. Epub 2016 Jul 6.

22.

Pan-Cancer Analyses Reveal Long Intergenic Non-Coding RNAs Relevant to Tumor Diagnosis, Subtyping and Prognosis.

Ching T, Peplowska K, Huang S, Zhu X, Shen Y, Molnar J, Yu H, Tiirikainen M, Fogelgren B, Fan R, Garmire LX.

EBioMedicine. 2016 May;7:62-72. doi: 10.1016/j.ebiom.2016.03.023. Epub 2016 Mar 19.

23.

Novel personalized pathway-based metabolomics models reveal key metabolic pathways for breast cancer diagnosis.

Huang S, Chong N, Lewis NE, Jia W, Xie G, Garmire LX.

Genome Med. 2016 Mar 31;8(1):34. doi: 10.1186/s13073-016-0289-9.

24.

Non-coding yet non-trivial: a review on the computational genomics of lincRNAs.

Ching T, Masaki J, Weirather J, Garmire LX.

BioData Min. 2015 Dec 22;8:44. doi: 10.1186/s13040-015-0075-z. eCollection 2015. Review.

25.

Lowered circulating aspartate is a metabolic feature of human breast cancer.

Xie G, Zhou B, Zhao A, Qiu Y, Zhao X, Garmire L, Shvetsov YB, Yu H, Yen Y, Jia W.

Oncotarget. 2015 Oct 20;6(32):33369-81. doi: 10.18632/oncotarget.5409.

26.

Th17 cells transdifferentiate into regulatory T cells during resolution of inflammation.

Gagliani N, Amezcua Vesely MC, Iseppon A, Brockmann L, Xu H, Palm NW, de Zoete MR, Licona-Limón P, Paiva RS, Ching T, Weaver C, Zi X, Pan X, Fan R, Garmire LX, Cotton MJ, Drier Y, Bernstein B, Geginat J, Stockinger B, Esplugues E, Huber S, Flavell RA.

Nature. 2015 Jul 9;523(7559):221-5. doi: 10.1038/nature14452. Epub 2015 Apr 29.

27.

Using epigenomics data to predict gene expression in lung cancer.

Li J, Ching T, Huang S, Garmire LX.

BMC Bioinformatics. 2015;16 Suppl 5:S10. doi: 10.1186/1471-2105-16-S5-S10. Epub 2015 Mar 18.

28.

Genome-scale hypomethylation in the cord blood DNAs associated with early onset preeclampsia.

Ching T, Ha J, Song MA, Tiirikainen M, Molnar J, Berry MJ, Towner D, Garmire LX.

Clin Epigenetics. 2015 Mar 13;7:21. doi: 10.1186/s13148-015-0052-x. eCollection 2015.

29.

mirMark: a site-level and UTR-level classifier for miRNA target prediction.

Menor M, Ching T, Zhu X, Garmire D, Garmire LX.

Genome Biol. 2014;15(10):500.

30.

Co-detection and sequencing of genes and transcripts from the same single cells facilitated by a microfluidics platform.

Han L, Zi X, Garmire LX, Wu Y, Weissman SM, Pan X, Fan R.

Sci Rep. 2014 Sep 26;4:6485. doi: 10.1038/srep06485.

31.

Power analysis and sample size estimation for RNA-Seq differential expression.

Ching T, Huang S, Garmire LX.

RNA. 2014 Nov;20(11):1684-96. doi: 10.1261/rna.046011.114. Epub 2014 Sep 22.

32.

A novel model to combine clinical and pathway-based transcriptomic information for the prognosis prediction of breast cancer.

Huang S, Yee C, Ching T, Yu H, Garmire LX.

PLoS Comput Biol. 2014 Sep 18;10(9):e1003851. doi: 10.1371/journal.pcbi.1003851. eCollection 2014 Sep.

33.

Genome-wide hypermethylation coupled with promoter hypomethylation in the chorioamniotic membranes of early onset pre-eclampsia.

Ching T, Song MA, Tiirikainen M, Molnar J, Berry M, Towner D, Garmire LX.

Mol Hum Reprod. 2014 Sep;20(9):885-904. doi: 10.1093/molehr/gau046. Epub 2014 Jun 18.

34.

The poor performance of TMM on microRNA-Seq.

Garmire LX, Subramaniam S.

RNA. 2013 Jun;19(6):735-6. doi: 10.1261/rna.039271.113. Epub 2013 Apr 24. No abstract available.

35.

Targeted, high-depth, next-generation sequencing of cancer genes in formalin-fixed, paraffin-embedded and fine-needle aspiration tumor specimens.

Hadd AG, Houghton J, Choudhary A, Sah S, Chen L, Marko AC, Sanford T, Buddavarapu K, Krosting J, Garmire L, Wylie D, Shinde R, Beaudenon S, Alexander EK, Mambo E, Adai AT, Latham GJ.

J Mol Diagn. 2013 Mar;15(2):234-47. doi: 10.1016/j.jmoldx.2012.11.006. Epub 2013 Jan 13.

PMID:
23321017
36.

Whole-genome microRNA screening identifies let-7 and mir-18 as regulators of germ layer formation during early embryogenesis.

Colas AR, McKeithan WL, Cunningham TJ, Bushway PJ, Garmire LX, Duester G, Subramaniam S, Mercola M.

Genes Dev. 2012 Dec 1;26(23):2567-79. doi: 10.1101/gad.200758.112. Epub 2012 Nov 14.

37.

Inter-cellular signaling network reveals a mechanistic transition in tumor microenvironment.

Wu Y, Garmire LX, Fan R.

Integr Biol (Camb). 2012 Dec;4(12):1478-86. doi: 10.1039/c2ib20044a.

38.

Regulated accumulation of desmosterol integrates macrophage lipid metabolism and inflammatory responses.

Spann NJ, Garmire LX, McDonald JG, Myers DS, Milne SB, Shibata N, Reichart D, Fox JN, Shaked I, Heudobler D, Raetz CR, Wang EW, Kelly SL, Sullards MC, Murphy RC, Merrill AH Jr, Brown HA, Dennis EA, Li AC, Ley K, Tsimikas S, Fahy E, Subramaniam S, Quehenberger O, Russell DW, Glass CK.

Cell. 2012 Sep 28;151(1):138-52. doi: 10.1016/j.cell.2012.06.054.

39.

Evaluation of normalization methods in mammalian microRNA-Seq data.

Garmire LX, Subramaniam S.

RNA. 2012 Jun;18(6):1279-88. doi: 10.1261/rna.030916.111. Epub 2012 Apr 24.

40.

A global clustering algorithm to identify long intergenic non-coding RNA--with applications in mouse macrophages.

Garmire LX, Garmire DG, Huang W, Yao J, Glass CK, Subramaniam S.

PLoS One. 2011;6(9):e24051. doi: 10.1371/journal.pone.0024051. Epub 2011 Sep 30.

41.

Regulatory network of microRNAs in RAW 264.7 macrophage cells.

Garmire LX, Shen Z, Briggs S, Yeo G, Subramaniam S, Glass C.

Conf Proc IEEE Eng Med Biol Soc. 2010;2010:6198-201. doi: 10.1109/IEMBS.2010.5627742.

PMID:
21097158
42.

Role of microRNA-23b in flow-regulation of Rb phosphorylation and endothelial cell growth.

Wang KC, Garmire LX, Young A, Nguyen P, Trinh A, Subramaniam S, Wang N, Shyy JY, Li YS, Chien S.

Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):3234-9. doi: 10.1073/pnas.0914825107. Epub 2010 Jan 27.

43.

In silico methods for unraveling the mechanistic complexities of intestinal absorption: metabolism-efflux transport interactions.

Garmire LX, Hunt CA.

Drug Metab Dispos. 2008 Jul;36(7):1414-24. doi: 10.1124/dmd.107.020164. Epub 2008 Apr 24.

44.

An in silico transwell device for the study of drug transport and drug-drug interactions.

Garmire LX, Garmire DG, Hunt CA.

Pharm Res. 2007 Dec;24(12):2171-86. Epub 2007 Aug 17.

PMID:
17703347

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