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Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees.
Gong W, Granados AA, Hu J, Jones MG, Raz O, Salvador-Martínez I, Zhang H, Chow KK, Kwak IY, Retkute R, Prusokiene A, Prusokas A, Khodaverdian A, Zhang R, Rao S, Wang R, Rennert P, Saipradeep VG, Sivadasan N, Rao A, Joseph T, Srinivasan R, Peng J, Han L, Shang X, Garry DJ, Yu T, Chung V, Mason M, Liu Z, Guan Y, Yosef N, Shendure J, Telford MJ, Shapiro E, Elowitz MB, Meyer P. Gong W, et al. Among authors: meyer p. Cell Syst. 2021 Aug 18;12(8):810-826.e4. doi: 10.1016/j.cels.2021.05.008. Epub 2021 Jun 18. Cell Syst. 2021. PMID: 34146472 Free article.
Evaluation and optimization of sequence-based gene regulatory deep learning models.
Rafi AM, Nogina D, Penzar D, Lee D, Lee D, Kim N, Kim S, Kim D, Shin Y, Kwak IY, Meshcheryakov G, Lando A, Zinkevich A, Kim BC, Lee J, Kang T, Vaishnav ED, Yadollahpour P; Random Promoter DREAM Challenge Consortium; Kim S, Albrecht J, Regev A, Gong W, Kulakovskiy IV, Meyer P, de Boer C. Rafi AM, et al. Among authors: meyer p. bioRxiv [Preprint]. 2024 Feb 17:2023.04.26.538471. doi: 10.1101/2023.04.26.538471. bioRxiv. 2024. PMID: 38405704 Free PMC article. Preprint.
Predicting human olfactory perception from chemical features of odor molecules.
Keller A, Gerkin RC, Guan Y, Dhurandhar A, Turu G, Szalai B, Mainland JD, Ihara Y, Yu CW, Wolfinger R, Vens C, Schietgat L, De Grave K, Norel R; DREAM Olfaction Prediction Consortium; Stolovitzky G, Cecchi GA, Vosshall LB, Meyer P. Keller A, et al. Among authors: meyer p. Science. 2017 Feb 24;355(6327):820-826. doi: 10.1126/science.aal2014. Epub 2017 Feb 20. Science. 2017. PMID: 28219971 Free PMC article.
Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data.
Tanevski J, Nguyen T, Truong B, Karaiskos N, Ahsen ME, Zhang X, Shu C, Xu K, Liang X, Hu Y, Pham HV, Xiaomei L, Le TD, Tarca AL, Bhatti G, Romero R, Karathanasis N, Loher P, Chen Y, Ouyang Z, Mao D, Zhang Y, Zand M, Ruan J, Hafemeister C, Qiu P, Tran D, Nguyen T, Gabor A, Yu T, Guinney J, Glaab E, Krause R, Banda P; DREAM SCTC Consortium; Stolovitzky G, Rajewsky N, Saez-Rodriguez J, Meyer P. Tanevski J, et al. Among authors: meyer p. Life Sci Alliance. 2020 Sep 24;3(11):e202000867. doi: 10.26508/lsa.202000867. Print 2020 Nov. Life Sci Alliance. 2020. PMID: 32972997 Free PMC article.
Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models.
Karr JR, Williams AH, Zucker JD, Raue A, Steiert B, Timmer J, Kreutz C; DREAM8 Parameter Estimation Challenge Consortium; Wilkinson S, Allgood BA, Bot BM, Hoff BR, Kellen MR, Covert MW, Stolovitzky GA, Meyer P. Karr JR, et al. Among authors: meyer p. PLoS Comput Biol. 2015 May 28;11(5):e1004096. doi: 10.1371/journal.pcbi.1004096. eCollection 2015 May. PLoS Comput Biol. 2015. PMID: 26020786 Free PMC article.
2,902 results