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Items: 14

1.

ChEA3: transcription factor enrichment analysis by orthogonal omics integration.

Keenan AB, Torre D, Lachmann A, Leong AK, Wojciechowicz ML, Utti V, Jagodnik KM, Kropiwnicki E, Wang Z, Ma'ayan A.

Nucleic Acids Res. 2019 Jul 2;47(W1):W212-W224. doi: 10.1093/nar/gkz446.

2.

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
3.

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.

4.

Massive mining of publicly available RNA-seq data from human and mouse.

Lachmann A, Torre D, Keenan AB, Jagodnik KM, Lee HJ, Wang L, Silverstein MC, Ma'ayan A.

Nat Commun. 2018 Apr 10;9(1):1366. doi: 10.1038/s41467-018-03751-6.

5.

Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses.

Torre D, Krawczuk P, Jagodnik KM, Lachmann A, Wang Z, Wang L, Kuleshov MV, Ma'ayan A.

Sci Data. 2018 Feb 27;5:180023. doi: 10.1038/sdata.2018.23.

6.

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.

7.

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.

8.

Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop.

Jagodnik KM, Koplev S, Jenkins SL, Ohno-Machado L, Paten B, Schurer SC, Dumontier M, Verborgh R, Bui A, Ping P, McKenna NJ, Madduri R, Pillai A, Ma'ayan A.

J Biomed Inform. 2017 Jul;71:49-57. doi: 10.1016/j.jbi.2017.05.006. Epub 2017 May 10.

9.

Training an Actor-Critic Reinforcement Learning Controller for Arm Movement Using Human-Generated Rewards.

Jagodnik KM, Thomas PS, van den Bogert AJ, Branicky MS, Kirsch RF.

IEEE Trans Neural Syst Rehabil Eng. 2017 Oct;25(10):1892-1905. doi: 10.1109/TNSRE.2017.2700395. Epub 2017 May 2.

PMID:
28475063
10.

GEN3VA: aggregation and analysis of gene expression signatures from related studies.

Gundersen GW, Jagodnik KM, Woodland H, Fernandez NF, Sani K, Dohlman AB, Ung PM, Monteiro CD, Schlessinger A, Ma'ayan A.

BMC Bioinformatics. 2016 Nov 15;17(1):461.

11.

Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd.

Wang Z, Monteiro CD, Jagodnik KM, Fernandez NF, Gundersen GW, Rouillard AD, Jenkins SL, Feldmann AS, Hu KS, McDermott MG, Duan Q, Clark NR, Jones MR, Kou Y, Goff T, Woodland H, Amaral FMR, Szeto GL, Fuchs O, Schüssler-Fiorenza Rose SM, Sharma S, Schwartz U, Bausela XB, Szymkiewicz M, Maroulis V, Salykin A, Barra CM, Kruth CD, Bongio NJ, Mathur V, Todoric RD, Rubin UE, Malatras A, Fulp CT, Galindo JA, Motiejunaite R, Jüschke C, Dishuck PC, Lahl K, Jafari M, Aibar S, Zaravinos A, Steenhuizen LH, Allison LR, Gamallo P, de Andres Segura F, Dae Devlin T, Pérez-García V, Ma'ayan A.

Nat Commun. 2016 Sep 26;7:12846. doi: 10.1038/ncomms12846.

12.

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.

Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A, McDermott MG, Monteiro CD, Gundersen GW, Ma'ayan A.

Nucleic Acids Res. 2016 Jul 8;44(W1):W90-7. doi: 10.1093/nar/gkw377. Epub 2016 May 3.

13.

An optimized proportional-derivative controller for the human upper extremity with gravity.

Jagodnik KM, Blana D, van den Bogert AJ, Kirsch RF.

J Biomech. 2015 Oct 15;48(13):3692-700. doi: 10.1016/j.jbiomech.2015.08.016. Epub 2015 Aug 29.

14.

Optimization and evaluation of a proportional derivative controller for planar arm movement.

Jagodnik KM, van den Bogert AJ.

J Biomech. 2010 Apr 19;43(6):1086-91. doi: 10.1016/j.jbiomech.2009.12.017. Epub 2010 Jan 25.

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