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Showing 1 to 12 of 236 entries
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Identification of sample annotation errors in gene expression datasets.

Archives of toxicology

Lohr M, Hellwig B, Edlund K, Mattsson JS, Botling J, Schmidt M, Hengstler JG, Micke P, Rahnenführer J.
PMID: 26608184
Arch Toxicol. 2015 Dec;89(12):2265-72. doi: 10.1007/s00204-015-1632-4. Epub 2015 Nov 25.

The comprehensive transcriptomic analysis of clinically annotated human tissue has found widespread use in oncology, cell biology, immunology, and toxicology. In cancer research, microarray-based gene expression profiling has successfully been applied to subclassify disease entities, predict therapy response, and...

Pleurochrysome: A Web Database of Pleurochrysis Transcripts and Orthologs Among Heterogeneous Algae.

Plant & cell physiology

Yamamoto N, Kudo T, Fujiwara S, Takatsuka Y, Hirokawa Y, Tsuzuki M, Takano T, Kobayashi M, Suda K, Asamizu E, Yokoyama K, Shibata D, Tabata S, Yano K.
PMID: 26746174
Plant Cell Physiol. 2016 Jan;57(1):e6. doi: 10.1093/pcp/pcv195. Epub 2016 Jan 07.

Pleurochrysis is a coccolithophorid genus, which belongs to the Coccolithales in the Haptophyta. The genus has been used extensively for biological research, together with Emiliania in the Isochrysidales, to understand distinctive features between the two coccolithophorid-including orders. However, molecular...

Estimating gene regulatory networks with pandaR.

Bioinformatics (Oxford, England)

Schlauch D, Paulson JN, Young A, Glass K, Quackenbush J.
PMID: 28334344
Bioinformatics. 2017 Jul 15;33(14):2232-2234. doi: 10.1093/bioinformatics/btx139.

CONTACT: [email protected] or [email protected] AND IMPLEMENTATION: PandaR is provided as a Bioconductor R Package and is available at bioconductor.org/packages/pandaR.

Integrating transcriptome and epigenome: putting together the pieces of the type 2 diabetes pathogenesis puzzle.

Diabetes

Das SK.
PMID: 25146470
Diabetes. 2014 Sep;63(9):2901-3. doi: 10.2337/db14-0757.

No abstract available.

The common ground of genomics and systems biology.

BMC systems biology

Conesa A, Mortazavi A.
PMID: 25033072
BMC Syst Biol. 2014;8:S1. doi: 10.1186/1752-0509-8-S2-S1. Epub 2014 Mar 13.

The rise of systems biology is intertwined with that of genomics, yet their primordial relationship to one another is ill-defined. We discuss how the growth of genomics provided a critical boost to the popularity of systems biology. We describe...

Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes by using DNA microarray and next-generation sequencing technologies.

Applied and environmental microbiology

Leimena MM, Wels M, Bongers RS, Smid EJ, Zoetendal EG, Kleerebezem M.
PMID: 22492454
Appl Environ Microbiol. 2012 Jun;78(12):4141-8. doi: 10.1128/AEM.00470-12. Epub 2012 Apr 06.

RNA sequencing is starting to compete with the use of DNA microarrays for transcription analysis in eukaryotes as well as in prokaryotes. The application of RNA sequencing in prokaryotes requires additional steps in the RNA preparation procedure to increase...

MassTRIX reloaded: combined analysis and visualization of transcriptome and metabolome data.

PloS one

Wägele B, Witting M, Schmitt-Kopplin P, Suhre K.
PMID: 22815716
PLoS One. 2012;7(7):e39860. doi: 10.1371/journal.pone.0039860. Epub 2012 Jul 06.

Systems Biology is a field in biological science that focuses on the combination of several or all "omics"-approaches in order to find out how genes, transcripts, proteins and metabolites act together in the network of life. Metabolomics as analog...

Mantra 2.0: an online collaborative resource for drug mode of action and repurposing by network analysis.

Bioinformatics (Oxford, England)

Carrella D, Napolitano F, Rispoli R, Miglietta M, Carissimo A, Cutillo L, Sirci F, Gregoretti F, Di Bernardo D.
PMID: 24558125
Bioinformatics. 2014 Jun 15;30(12):1787-8. doi: 10.1093/bioinformatics/btu058. Epub 2014 Feb 20.

SUMMARY: Elucidation of molecular targets of a compound [mode of action (MoA)] and its off-targets is a crucial step in drug development. We developed an online collaborative resource (MANTRA 2.0) that supports this process by exploiting similarities between drug-induced...

Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin.

Cell

Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, Leiserson MDM, Niu B, McLellan MD, Uzunangelov V, Zhang J, Kandoth C, Akbani R, Shen H, Omberg L, Chu A, Margolin AA, Van't Veer LJ, Lopez-Bigas N, Laird PW, Raphael BJ, Ding L, Robertson AG, Byers LA, Mills GB, Weinstein JN, Van Waes C, Chen Z, Collisson EA, Benz CC, Perou CM, Stuart JM.
PMID: 25109877
Cell. 2014 Aug 14;158(4):929-944. doi: 10.1016/j.cell.2014.06.049. Epub 2014 Aug 07.

Recent genomic analyses of pathologically defined tumor types identify "within-a-tissue" disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform...

System network analysis of genomics and transcriptomics data identified type 1 diabetes-associated pathway and genes.

Genes and immunity

Lu JM, Chen YC, Ao ZX, Shen J, Zeng CP, Lin X, Peng LP, Zhou R, Wang XF, Peng C, Xiao HM, Zhang K, Deng HW.
PMID: 30245508
Genes Immun. 2019 Jul;20(6):500-508. doi: 10.1038/s41435-018-0045-9. Epub 2018 Sep 24.

Genome-wide association studies (GWASs) have discovered >50 risk loci for type 1 diabetes (T1D). However, those variations only have modest effects on the genetic risk of T1D. In recent years, accumulated studies have suggested that gene-gene interactions might explain...

ST viewer: a tool for analysis and visualization of spatial transcriptomics datasets.

Bioinformatics (Oxford, England)

Fernández Navarro J, Lundeberg J, Ståhl PL.
PMID: 30875427
Bioinformatics. 2019 Mar 15;35(6):1058-1060. doi: 10.1093/bioinformatics/bty714.

MOTIVATION: Spatial Transcriptomics (ST) is a technique that combines high-resolution imaging with spatially resolved transcriptome-wide sequencing. This novel type of data opens up many possibilities for analysis and visualization, most of which are either not available with standard tools...

GO FEAT: a rapid web-based functional annotation tool for genomic and transcriptomic data.

Scientific reports

Araujo FA, Barh D, Silva A, Guimarães L, Ramos RTJ.
PMID: 29379090
Sci Rep. 2018 Jan 29;8(1):1794. doi: 10.1038/s41598-018-20211-9.

Downstream analysis of genomic and transcriptomic sequence data is often executed by functional annotation that can be performed by various bioinformatics tools and biological databases. However, a full fast integrated tool is not available for such analysis. Besides, the...

Showing 1 to 12 of 236 entries