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A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses.
Gross SM, Dane MA, Smith RL, Devlin KL, McLean IC, Derrick DS, Mills CE, Subramanian K, London AB, Torre D, Evangelista JE, Clarke DJB, Xie Z, Erdem C, Lyons N, Natoli T, Pessa S, Lu X, Mullahoo J, Li J, Adam M, Wassie B, Liu M, Kilburn DF, Liby TA, Bucher E, Sanchez-Aguila C, Daily K, Omberg L, Wang Y, Jacobson C, Yapp C, Chung M, Vidovic D, Lu Y, Schurer S, Lee A, Pillai A, Subramanian A, Papanastasiou M, Fraenkel E, Feiler HS, Mills GB, Jaffe JD, Ma'ayan A, Birtwistle MR, Sorger PK, Korkola JE, Gray JW, Heiser LM. Gross SM, et al. Among authors: clarke djb. Commun Biol. 2022 Oct 7;5(1):1066. doi: 10.1038/s42003-022-03975-9. Commun Biol. 2022. PMID: 36207580 Free PMC article.
FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources.
Clarke DJB, Wang L, Jones A, Wojciechowicz ML, Torre D, Jagodnik KM, Jenkins SL, McQuilton P, Flamholz Z, Silverstein MC, Schilder BM, Robasky K, Castillo C, Idaszak R, Ahalt SC, Williams J, Schurer S, Cooper DJ, de Miranda Azevedo R, Klenk JA, Haendel MA, Nedzel J, Avillach P, Shimoyama ME, Harris RM, Gamble M, Poten R, Charbonneau AL, Larkin J, Brown CT, Bonazzi VR, Dumontier MJ, Sansone SA, Ma'ayan A. Clarke DJB, et al. Cell Syst. 2019 Nov 27;9(5):417-421. doi: 10.1016/j.cels.2019.09.011. Epub 2019 Oct 30. Cell Syst. 2019. PMID: 31677972 Free PMC article.
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. Stathias V, et al. Among authors: clarke djb. Nucleic Acids Res. 2020 Jan 8;48(D1):D431-D439. doi: 10.1093/nar/gkz1023. Nucleic Acids Res. 2020. PMID: 31701147 Free PMC article.
Interoperable RNA-Seq analysis in the cloud.
Lachmann A, Clarke DJB, Torre D, Xie Z, Ma'ayan A. Lachmann A, et al. Among authors: clarke djb. Biochim Biophys Acta Gene Regul Mech. 2020 Jun;1863(6):194521. doi: 10.1016/j.bbagrm.2020.194521. Epub 2020 Mar 7. Biochim Biophys Acta Gene Regul Mech. 2020. PMID: 32156561 Review.
EnrichrBot: Twitter bot tracking tweets about human genes.
Bartal A, Lachmann A, Clarke DJB, Seiden AH, Jagodnik KM, Ma'ayan A. Bartal A, et al. Among authors: clarke djb. Bioinformatics. 2020 Jun 1;36(12):3932-3934. doi: 10.1093/bioinformatics/btaa240. Bioinformatics. 2020. PMID: 32277816 Free PMC article.
The COVID-19 Gene and Drug Set Library.
Kuleshov MV, Clarke DJB, Kropiwnicki E, Jagodnik KM, Bartal A, Evangelista JE, Zhou A, Ferguson LB, Lachmann A, Ma'ayan A. Kuleshov MV, et al. Among authors: clarke djb. Res Sq [Preprint]. 2020 May 13:rs.3.rs-28582. doi: 10.21203/rs.3.rs-28582/v1. Res Sq. 2020. PMID: 32702729 Free PMC article. Updated. Preprint.
The COVID-19 Drug and Gene Set Library.
Kuleshov MV, Stein DJ, Clarke DJB, Kropiwnicki E, Jagodnik KM, Bartal A, Evangelista JE, Hom J, Cheng M, Bailey A, Zhou A, Ferguson LB, Lachmann A, Ma'ayan A. Kuleshov MV, et al. Among authors: clarke djb. Patterns (N Y). 2020 Sep 11;1(6):100090. doi: 10.1016/j.patter.2020.100090. Epub 2020 Jul 25. Patterns (N Y). 2020. PMID: 32838343 Free PMC article.
Appyters: Turning Jupyter Notebooks into data-driven web apps.
Clarke DJB, Jeon M, Stein DJ, Moiseyev N, Kropiwnicki E, Dai C, Xie Z, Wojciechowicz ML, Litz S, Hom J, Evangelista JE, Goldman L, Zhang S, Yoon C, Ahamed T, Bhuiyan S, Cheng M, Karam J, Jagodnik KM, Shu I, Lachmann A, Ayling S, Jenkins SL, Ma'ayan A. Clarke DJB, et al. Patterns (N Y). 2021 Mar 4;2(3):100213. doi: 10.1016/j.patter.2021.100213. eCollection 2021 Mar 12. Patterns (N Y). 2021. PMID: 33748796 Free PMC article.
33 results