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Items: 1 to 20 of 102

1.

A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.

Subramanian A, Narayan R, Corsello SM, Peck DD, Natoli TE, Lu X, Gould J, Davis JF, Tubelli AA, Asiedu JK, Lahr DL, Hirschman JE, Liu Z, Donahue M, Julian B, Khan M, Wadden D, Smith IC, Lam D, Liberzon A, Toder C, Bagul M, Orzechowski M, Enache OM, Piccioni F, Johnson SA, Lyons NJ, Berger AH, Shamji AF, Brooks AN, Vrcic A, Flynn C, Rosains J, Takeda DY, Hu R, Davison D, Lamb J, Ardlie K, Hogstrom L, Greenside P, Gray NS, Clemons PA, Silver S, Wu X, Zhao WN, Read-Button W, Wu X, Haggarty SJ, Ronco LV, Boehm JS, Schreiber SL, Doench JG, Bittker JA, Root DE, Wong B, Golub TR.

Cell. 2017 Nov 30;171(6):1437-1452.e17. doi: 10.1016/j.cell.2017.10.049.

2.

Compound signature detection on LINCS L1000 big data.

Liu C, Su J, Yang F, Wei K, Ma J, Zhou X.

Mol Biosyst. 2015 Mar;11(3):714-22. doi: 10.1039/c4mb00677a. Epub 2015 Jan 22.

3.

A review of connectivity map and computational approaches in pharmacogenomics.

Musa A, Ghoraie LS, Zhang SD, Glazko G, Yli-Harja O, Dehmer M, Haibe-Kains B, Emmert-Streib F.

Brief Bioinform. 2018 May 1;19(3):506-523. doi: 10.1093/bib/bbw112. Review. Erratum in: Brief Bioinform. 2017 Sep 1;18(5):903.

4.

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures.

Duan Q, Flynn C, Niepel M, Hafner M, Muhlich JL, Fernandez NF, Rouillard AD, Tan CM, Chen EY, Golub TR, Sorger PK, Subramanian A, Ma'ayan A.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W449-60. doi: 10.1093/nar/gku476. Epub 2014 Jun 6.

5.

A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations.

Litichevskiy L, Peckner R, Abelin JG, Asiedu JK, Creech AL, Davis JF, Davison D, Dunning CM, Egertson JD, Egri S, Gould J, Ko T, Johnson SA, Lahr DL, Lam D, Liu Z, Lyons NJ, Lu X, MacLean BX, Mungenast AE, Officer A, Natoli TE, Papanastasiou M, Patel J, Sharma V, Toder C, Tubelli AA, Young JZ, Carr SA, Golub TR, Subramanian A, MacCoss MJ, Tsai LH, Jaffe JD.

Cell Syst. 2018 Apr 25;6(4):424-443.e7. doi: 10.1016/j.cels.2018.03.012. Epub 2018 Apr 11.

6.

Preparation of highly multiplexed small RNA sequencing libraries.

Persson H, S√łkilde R, Pirona AC, Rovira C.

Biotechniques. 2017 Aug 1;63(2):57-64. doi: 10.2144/000114574.

7.

Low-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing.

Mai Z, Xiao C, Jin J, Zhang G.

Sci Rep. 2017 Apr 21;7(1):1053. doi: 10.1038/s41598-017-01165-w.

8.

L1000CDS2: LINCS L1000 characteristic direction signatures search engine.

Duan Q, Reid SP, Clark NR, Wang Z, Fernandez NF, Rouillard AD, Readhead B, Tritsch SR, Hodos R, Hafner M, Niepel M, Sorger PK, Dudley JT, Bavari S, Panchal RG, Ma'ayan A.

NPJ Syst Biol Appl. 2016;2. pii: 16015. doi: 10.1038/npjsba.2016.15. Epub 2016 Aug 4.

9.

Systematic Quality Control Analysis of LINCS Data.

Cheng L, Li L.

CPT Pharmacometrics Syst Pharmacol. 2016 Nov;5(11):588-598. doi: 10.1002/psp4.12107. Epub 2016 Oct 31.

10.

Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data.

McArt DG, Dunne PD, Blayney JK, Salto-Tellez M, Van Schaeybroeck S, Hamilton PW, Zhang SD.

PLoS One. 2013 Jun 26;8(6):e66902. doi: 10.1371/journal.pone.0066902. Print 2013.

11.

A cost-effective RNA sequencing protocol for large-scale gene expression studies.

Hou Z, Jiang P, Swanson SA, Elwell AL, Nguyen BK, Bolin JM, Stewart R, Thomson JA.

Sci Rep. 2015 Apr 1;5:9570. doi: 10.1038/srep09570.

12.

Survival analysis of genome-wide profiles coupled with Connectivity Map database mining to identify potential therapeutic targets for cholangiocarcinoma.

Lin P, Zhong XZ, Wang XD, Li JJ, Zhao RQ, He Y, Jiang YQ, Huang XW, Chen G, He Y, Yang H.

Oncol Rep. 2018 Dec;40(6):3189-3198. doi: 10.3892/or.2018.6710. Epub 2018 Sep 18.

13.

Drug Signature Detection Based on L1000 Genomic and Proteomic Big Data.

Chen W, Zhou X.

Methods Mol Biol. 2019;1939:273-286. doi: 10.1007/978-1-4939-9089-4_15.

PMID:
30848467
14.

Comparative Analysis of Droplet-Based Ultra-High-Throughput Single-Cell RNA-Seq Systems.

Zhang X, Li T, Liu F, Chen Y, Yao J, Li Z, Huang Y, Wang J.

Mol Cell. 2019 Jan 3;73(1):130-142.e5. doi: 10.1016/j.molcel.2018.10.020. Epub 2018 Nov 21.

PMID:
30472192
15.

Systematic polypharmacology and drug repurposing via an integrated L1000-based Connectivity Map database mining.

Liu TP, Hsieh YY, Chou CJ, Yang PM.

R Soc Open Sci. 2018 Nov 28;5(11):181321. doi: 10.1098/rsos.181321. eCollection 2018 Nov.

16.

Transcriptomic Data Mining and Repurposing for Computational Drug Discovery.

Wang Y, Yella J, Jegga AG.

Methods Mol Biol. 2019;1903:73-95. doi: 10.1007/978-1-4939-8955-3_5.

PMID:
30547437
17.

New methods for next generation sequencing based microRNA expression profiling.

Buermans HP, Ariyurek Y, van Ommen G, den Dunnen JT, 't Hoen PA.

BMC Genomics. 2010 Dec 20;11:716. doi: 10.1186/1471-2164-11-716.

18.

l1kdeconv: an R package for peak calling analysis with LINCS L1000 data.

Li Z, Li J, Yu P.

BMC Bioinformatics. 2017 Jul 27;18(1):356. doi: 10.1186/s12859-017-1767-9.

19.

Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures.

Wang Z, He E, Sani K, Jagodnik KM, Silverstein MC, Ma'ayan A.

Bioinformatics. 2019 Apr 1;35(7):1247-1248. doi: 10.1093/bioinformatics/bty763.

PMID:
30169739
20.

RNA-Seq Atlas--a reference database for gene expression profiling in normal tissue by next-generation sequencing.

Krupp M, Marquardt JU, Sahin U, Galle PR, Castle J, Teufel A.

Bioinformatics. 2012 Apr 15;28(8):1184-5. doi: 10.1093/bioinformatics/bts084. Epub 2012 Feb 17.

PMID:
22345621

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