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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: muhlich jl. 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.
MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging.
Schapiro D, Sokolov A, Yapp C, Chen YA, Muhlich JL, Hess J, Creason AL, Nirmal AJ, Baker GJ, Nariya MK, Lin JR, Maliga Z, Jacobson CA, Hodgman MW, Ruokonen J, Farhi SL, Abbondanza D, McKinley ET, Persson D, Betts C, Sivagnanam S, Regev A, Goecks J, Coffey RJ, Coussens LM, Santagata S, Sorger PK. Schapiro D, et al. Among authors: muhlich jl. Nat Methods. 2022 Mar;19(3):311-315. doi: 10.1038/s41592-021-01308-y. Epub 2021 Nov 25. Nat Methods. 2022. PMID: 34824477 Free PMC article.
Programming biological models in Python using PySB.
Lopez CF, Muhlich JL, Bachman JA, Sorger PK. Lopez CF, et al. Among authors: muhlich jl. Mol Syst Biol. 2013;9:646. doi: 10.1038/msb.2013.1. Mol Syst Biol. 2013. PMID: 23423320 Free PMC article.
Minerva: a light-weight, narrative image browser for multiplexed tissue images.
Hoffer J, Rashid R, Muhlich JL, Chen YA, Russell DPW, Ruokonen J, Krueger R, Pfister H, Santagata S, Sorger PK. Hoffer J, et al. Among authors: muhlich jl. J Open Source Softw. 2020;5(54):2579. doi: 10.21105/joss.02579. Epub 2020 Oct 15. J Open Source Softw. 2020. PMID: 33768192 Free PMC article.
Quality Control for Single Cell Analysis of High-plex Tissue Profiles using CyLinter.
Baker GJ, Novikov E, Zhao Z, Vallius T, Davis JA, Lin JR, Muhlich JL, Mittendorf EA, Santagata S, Guerriero JL, Sorger PK. Baker GJ, et al. Among authors: muhlich jl. bioRxiv [Preprint]. 2024 Mar 22:2023.11.01.565120. doi: 10.1101/2023.11.01.565120. bioRxiv. 2024. PMID: 37961235 Free PMC article. Preprint.
20 results