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Items: 9

1.

LINCS Data Portal 2.0: next generation access point for perturbation-response signatures.

Stathias V, Turner J, Koleti A, Vidovic D, Cooper D, Fazel-Najafabadi M, Pilarczyk M, Terryn R, Chung C, Umeano A, Clarke DJB, Lachmann A, Evangelista JE, Ma'ayan A, Medvedovic M, Schürer SC.

Nucleic Acids Res. 2019 Nov 8. pii: gkz1023. doi: 10.1093/nar/gkz1023. [Epub ahead of print]

PMID:
31701147
2.

Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center.

Stathias V, Koleti A, Vidović D, Cooper DJ, Jagodnik KM, Terryn R, Forlin M, Chung C, Torre D, Ayad N, Medvedovic M, Ma'ayan A, Pillai A, Schürer SC.

Sci Data. 2018 Jun 19;5:180117. doi: 10.1038/sdata.2018.117.

3.

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.

Keenan AB, Jenkins SL, Jagodnik KM, Koplev S, He E, Torre D, Wang Z, Dohlman AB, Silverstein MC, Lachmann A, Kuleshov MV, Ma'ayan A, Stathias V, Terryn R, Cooper D, Forlin M, Koleti A, Vidovic D, Chung C, Schürer SC, Vasiliauskas J, Pilarczyk M, Shamsaei B, Fazel M, Ren Y, Niu W, Clark NA, White S, Mahi N, Zhang L, Kouril M, Reichard JF, Sivaganesan S, Medvedovic M, Meller J, Koch RJ, Birtwistle MR, Iyengar R, Sobie EA, Azeloglu EU, Kaye J, Osterloh J, Haston K, Kalra J, Finkbiener S, Li J, Milani P, Adam M, Escalante-Chong R, Sachs K, Lenail A, Ramamoorthy D, Fraenkel E, Daigle G, Hussain U, Coye A, Rothstein J, Sareen D, Ornelas L, Banuelos M, Mandefro B, Ho R, Svendsen CN, Lim RG, Stocksdale J, Casale MS, Thompson TG, Wu J, Thompson LM, Dardov V, Venkatraman V, Matlock A, Van Eyk JE, Jaffe JD, Papanastasiou M, Subramanian A, Golub TR, Erickson SD, Fallahi-Sichani M, Hafner M, Gray NS, Lin JR, Mills CE, Muhlich JL, Niepel M, Shamu CE, Williams EH, Wrobel D, Sorger PK, Heiser LM, Gray JW, Korkola JE, Mills GB, LaBarge M, Feiler HS, Dane MA, Bucher E, Nederlof M, Sudar D, Gross S, Kilburn DF, Smith R, Devlin K, Margolis R, Derr L, Lee A, Pillai A.

Cell Syst. 2018 Jan 24;6(1):13-24. doi: 10.1016/j.cels.2017.11.001. Epub 2017 Nov 29. Review.

4.

Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data.

Koleti A, Terryn R, Stathias V, Chung C, Cooper DJ, Turner JP, Vidovic D, Forlin M, Kelley TT, D'Urso A, Allen BK, Torre D, Jagodnik KM, Wang L, Jenkins SL, Mader C, Niu W, Fazel M, Mahi N, Pilarczyk M, Clark N, Shamsaei B, Meller J, Vasiliauskas J, Reichard J, Medvedovic M, Ma'ayan A, Pillai A, Schürer SC.

Nucleic Acids Res. 2018 Jan 4;46(D1):D558-D566. doi: 10.1093/nar/gkx1063.

5.

Drug target ontology to classify and integrate drug discovery data.

Lin Y, Mehta S, Küçük-McGinty H, Turner JP, Vidovic D, Forlin M, Koleti A, Nguyen DT, Jensen LJ, Guha R, Mathias SL, Ursu O, Stathias V, Duan J, Nabizadeh N, Chung C, Mader C, Visser U, Yang JJ, Bologa CG, Oprea TI, Schürer SC.

J Biomed Semantics. 2017 Nov 9;8(1):50. doi: 10.1186/s13326-017-0161-x.

7.

Evolving BioAssay Ontology (BAO): modularization, integration and applications.

Abeyruwan S, Vempati UD, Küçük-McGinty H, Visser U, Koleti A, Mir A, Sakurai K, Chung C, Bittker JA, Clemons PA, Brudz S, Siripala A, Morales AJ, Romacker M, Twomey D, Bureeva S, Lemmon V, Schürer SC.

J Biomed Semantics. 2014 Jun 3;5(Suppl 1 Proceedings of the Bio-Ontologies Spec Interest G):S5. doi: 10.1186/2041-1480-5-S1-S5. eCollection 2014.

8.

Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS).

Vempati UD, Chung C, Mader C, Koleti A, Datar N, Vidović D, Wrobel D, Erickson S, Muhlich JL, Berriz G, Benes CH, Subramanian A, Pillai A, Shamu CE, Schürer SC.

J Biomol Screen. 2014 Jun;19(5):803-16. doi: 10.1177/1087057114522514. Epub 2014 Feb 11.

PMID:
24518066
9.

GPCR ontology: development and application of a G protein-coupled receptor pharmacology knowledge framework.

Przydzial MJ, Bhhatarai B, Koleti A, Vempati U, Schürer SC.

Bioinformatics. 2013 Dec 15;29(24):3211-9. doi: 10.1093/bioinformatics/btt565. Epub 2013 Sep 29.

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