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Items: 1 to 20 of 32

1.

Transcriptome Analysis of Salt Stress Responsiveness in the Seedlings of Dongxiang Wild Rice (Oryza rufipogon Griff.).

Zhou Y, Yang P, Cui F, Zhang F, Luo X, Xie J.

PLoS One. 2016 Jan 11;11(1):e0146242. doi: 10.1371/journal.pone.0146242. eCollection 2016.

2.

Differentially Expressed Genes and Signature Pathways of Human Prostate Cancer.

Myers JS, von Lersner AK, Robbins CJ, Sang QX.

PLoS One. 2015 Dec 18;10(12):e0145322. doi: 10.1371/journal.pone.0145322. eCollection 2015.

3.

aRrayLasso: a network-based approach to microarray interconversion.

Brown AS, Patel CJ.

Bioinformatics. 2015 Dec 1;31(23):3859-61. doi: 10.1093/bioinformatics/btv469. Epub 2015 Aug 17.

4.

New signaling pathways govern the host response to C. albicans infection in various niches.

Liu Y, Shetty AC, Schwartz JA, Bradford LL, Xu W, Phan QT, Kumari P, Mahurkar A, Mitchell AP, Ravel J, Fraser CM, Filler SG, Bruno VM.

Genome Res. 2015 May;25(5):679-89. doi: 10.1101/gr.187427.114. Epub 2015 Apr 9.

5.

Simultaneous transcriptional profiling of bacteria and their host cells.

Humphrys MS, Creasy T, Sun Y, Shetty AC, Chibucos MC, Drabek EF, Fraser CM, Farooq U, Sengamalay N, Ott S, Shou H, Bavoil PM, Mahurkar A, Myers GS.

PLoS One. 2013 Dec 4;8(12):e80597. doi: 10.1371/journal.pone.0080597. eCollection 2013.

6.

COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia.

Meysman P, Sonego P, Bianco L, Fu Q, Ledezma-Tejeida D, Gama-Castro S, Liebens V, Michiels J, Laukens K, Marchal K, Collado-Vides J, Engelen K.

Nucleic Acids Res. 2014 Jan;42(Database issue):D649-53. doi: 10.1093/nar/gkt1086. Epub 2013 Nov 8.

7.

Revealing of Mycobacterium marinum transcriptome by RNA-seq.

Wang S, Dong X, Zhu Y, Wang C, Sun G, Luo T, Tian W, Zheng H, Gao Q.

PLoS One. 2013 Sep 30;8(9):e75828. doi: 10.1371/journal.pone.0075828. eCollection 2013.

8.

Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data.

Guo Y, Sheng Q, Li J, Ye F, Samuels DC, Shyr Y.

PLoS One. 2013 Aug 20;8(8):e71462. doi: 10.1371/journal.pone.0071462. eCollection 2013.

9.

Comparative RNA-Seq and microarray analysis of gene expression changes in B-cell lymphomas of Canis familiaris.

Mooney M, Bond J, Monks N, Eugster E, Cherba D, Berlinski P, Kamerling S, Marotti K, Simpson H, Rusk T, Tembe W, Legendre C, Benson H, Liang W, Webb CP.

PLoS One. 2013 Apr 4;8(4):e61088. doi: 10.1371/journal.pone.0061088. Print 2013.

10.

Comparability and reproducibility of biomedical data.

Huang Y, Gottardo R.

Brief Bioinform. 2013 Jul;14(4):391-401. doi: 10.1093/bib/bbs078. Epub 2012 Nov 27. Review.

11.

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae.

Nookaew I, Papini M, Pornputtapong N, Scalcinati G, Fagerberg L, Uhlén M, Nielsen J.

Nucleic Acids Res. 2012 Nov 1;40(20):10084-97. doi: 10.1093/nar/gks804. Epub 2012 Sep 10.

12.

Global analysis of the small RNA transcriptome in different ploidies and genomic combinations of a vertebrate complex--the Squalius alburnoides.

Inácio A, Pinho J, Pereira PM, Comai L, Coelho MM.

PLoS One. 2012;7(7):e41158. doi: 10.1371/journal.pone.0041158. Epub 2012 Jul 18.

13.

RNA-seq analysis reveals that an ECF σ factor, AcsS, regulates achromobactin biosynthesis in Pseudomonas syringae pv. syringae B728a.

Greenwald JW, Greenwald CJ, Philmus BJ, Begley TP, Gross DC.

PLoS One. 2012;7(4):e34804. doi: 10.1371/journal.pone.0034804. Epub 2012 Apr 18.

14.

Discovery of novel microRNAs in rat kidney using next generation sequencing and microarray validation.

Meng F, Hackenberg M, Li Z, Yan J, Chen T.

PLoS One. 2012;7(3):e34394. doi: 10.1371/journal.pone.0034394. Epub 2012 Mar 28.

15.

Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis.

Llorens F, Hummel M, Pastor X, Ferrer A, Pluvinet R, Vivancos A, Castillo E, Iraola S, Mosquera AM, González E, Lozano J, Ingham M, Dohm JC, Noguera M, Kofler R, del Río JA, Bayés M, Himmelbauer H, Sumoy L.

BMC Genomics. 2011 Jun 23;12:326. doi: 10.1186/1471-2164-12-326.

16.

AnyExpress: integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm.

Kim J, Patel K, Jung H, Kuo WP, Ohno-Machado L.

BMC Bioinformatics. 2011 Mar 17;12:75. doi: 10.1186/1471-2105-12-75.

17.

Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments.

McCormick KP, Willmann MR, Meyers BC.

Silence. 2011 Feb 28;2(1):2. doi: 10.1186/1758-907X-2-2.

18.

Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.).

Mizuno H, Kawahara Y, Sakai H, Kanamori H, Wakimoto H, Yamagata H, Oono Y, Wu J, Ikawa H, Itoh T, Matsumoto T.

BMC Genomics. 2010 Dec 2;11:683. doi: 10.1186/1471-2164-11-683.

19.

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays.

Agarwal A, Koppstein D, Rozowsky J, Sboner A, Habegger L, Hillier LW, Sasidharan R, Reinke V, Waterston RH, Gerstein M.

BMC Genomics. 2010 Jun 17;11:383. doi: 10.1186/1471-2164-11-383.

20.

In plants, expression breadth and expression level distinctly and non-linearly correlate with gene structure.

Yang H.

Biol Direct. 2009 Nov 21;4:45; discussion 45. doi: 10.1186/1745-6150-4-45.

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