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Accelerating drug discovery and repurposing by combining transcriptional signature connectivity with docking.
Thorman AW, Reigle J, Chutipongtanate S, Yang J, Shamsaei B, Pilarczyk M, Fazel-Najafabadi M, Adamczak R, Kouril M, Bhatnagar S, Hummel S, Niu W, Morrow AL, Czyzyk-Krzeska MF, McCullumsmith R, Seibel W, Nassar N, Zheng Y, Hildeman DA, Medvedovic M, Herr AB, Meller J. Thorman AW, et al. Among authors: pilarczyk m. Sci Adv. 2024 Aug 30;10(35):eadj3010. doi: 10.1126/sciadv.adj3010. Epub 2024 Aug 30. Sci Adv. 2024. PMID: 39213358 Free PMC article.
piNET: a versatile web platform for downstream analysis and visualization of proteomics data.
Shamsaei B, Chojnacki S, Pilarczyk M, Najafabadi M, Niu W, Chen C, Ross K, Matlock A, Muhlich J, Chutipongtanate S, Zheng J, Turner J, Vidović D, Jaffe J, MacCoss M, Wu C, Pillai A, Ma'ayan A, Schürer S, Kouril M, Medvedovic M, Meller J. Shamsaei B, et al. Among authors: pilarczyk m. Nucleic Acids Res. 2020 Jul 2;48(W1):W85-W93. doi: 10.1093/nar/gkaa436. Nucleic Acids Res. 2020. PMID: 32469073 Free PMC article.
Connecting omics signatures and revealing biological mechanisms with iLINCS.
Pilarczyk M, Fazel-Najafabadi M, Kouril M, Shamsaei B, Vasiliauskas J, Niu W, Mahi N, Zhang L, Clark NA, Ren Y, White S, Karim R, Xu H, Biesiada J, Bennett MF, Davidson SE, Reichard JF, Roberts K, Stathias V, Koleti A, Vidovic D, Clarke DJB, Schürer SC, Ma'ayan A, Meller J, Medvedovic M. Pilarczyk M, et al. Nat Commun. 2022 Aug 9;13(1):4678. doi: 10.1038/s41467-022-32205-3. Nat Commun. 2022. PMID: 35945222 Free PMC article.
GRcalculator: an online tool for calculating and mining dose-response data.
Clark NA, Hafner M, Kouril M, Williams EH, Muhlich JL, Pilarczyk M, Niepel M, Sorger PK, Medvedovic M. Clark NA, et al. Among authors: pilarczyk m. BMC Cancer. 2017 Oct 24;17(1):698. doi: 10.1186/s12885-017-3689-3. BMC Cancer. 2017. PMID: 29065900 Free PMC article.
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. Koleti A, et al. Among authors: pilarczyk m. Nucleic Acids Res. 2018 Jan 4;46(D1):D558-D566. doi: 10.1093/nar/gkx1063. Nucleic Acids Res. 2018. PMID: 29140462 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: pilarczyk m. Nucleic Acids Res. 2020 Jan 8;48(D1):D431-D439. doi: 10.1093/nar/gkz1023. Nucleic Acids Res. 2020. PMID: 31701147 Free PMC article.
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. Keenan AB, et al. Among authors: pilarczyk m. Cell Syst. 2018 Jan 24;6(1):13-24. doi: 10.1016/j.cels.2017.11.001. Epub 2017 Nov 29. Cell Syst. 2018. PMID: 29199020 Free PMC article. Review.
Air pollution might affect the clinical course of COVID-19 in pediatric patients.
Rzymski P, Poniedziałek B, Rosińska J, Ciechanowski P, Peregrym M, Pokorska-Śpiewak M, Talarek E, Zaleska I, Frańczak-Chmura P, Pilarczyk M, Figlerowicz M, Kucharek I, Flisiak R. Rzymski P, et al. Among authors: pilarczyk m. Ecotoxicol Environ Saf. 2022 Jul 1;239:113651. doi: 10.1016/j.ecoenv.2022.113651. Epub 2022 May 17. Ecotoxicol Environ Saf. 2022. PMID: 35594828 Free PMC article.
64 results