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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: yu t. 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.
Cell-to-cell and type-to-type heterogeneity of signaling networks: insights from the crowd.
Gabor A, Tognetti M, Driessen A, Tanevski J, Guo B, Cao W, Shen H, Yu T, Chung V; Single Cell Signaling in Breast Cancer DREAM Consortium members; Bodenmiller B, Saez-Rodriguez J. Gabor A, et al. Among authors: yu t. Mol Syst Biol. 2021 Oct;17(10):e10402. doi: 10.15252/msb.202110402. Mol Syst Biol. 2021. PMID: 34661974 Free PMC article.
A Crowdsourcing Approach to Develop Machine Learning Models to Quantify Radiographic Joint Damage in Rheumatoid Arthritis.
Sun D, Nguyen TM, Allaway RJ, Wang J, Chung V, Yu TV, Mason M, Dimitrovsky I, Ericson L, Li H, Guan Y, Israel A, Olar A, Pataki BA, Stolovitzky G, Guinney J, Gulko PS, Frazier MB, Chen JY, Costello JC, Bridges SL Jr; RA2-DREAM Challenge Community. Sun D, et al. JAMA Netw Open. 2022 Aug 1;5(8):e2227423. doi: 10.1001/jamanetworkopen.2022.27423. JAMA Netw Open. 2022. PMID: 36036935 Free PMC article.
Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics.
Yang M, Petralia F, Li Z, Li H, Ma W, Song X, Kim S, Lee H, Yu H, Lee B, Bae S, Heo E, Kaczmarczyk J, Stępniak P, Warchoł M, Yu T, Calinawan AP, Boutros PC, Payne SH, Reva B; NCI-CPTAC-DREAM Consortium; Boja E, Rodriguez H, Stolovitzky G, Guan Y, Kang J, Wang P, Fenyö D, Saez-Rodriguez J. Yang M, et al. Among authors: yu t, yu h. Cell Syst. 2020 Aug 26;11(2):186-195.e9. doi: 10.1016/j.cels.2020.06.013. Epub 2020 Jul 24. Cell Syst. 2020. PMID: 32710834 Free 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: yu t. 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.
A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery.
Creason A, Haan D, Dang K, Chiotti KE, Inkman M, Lamb A, Yu T, Hu Y, Norman TC, Buchanan A, van Baren MJ, Spangler R, Rollins MR, Spellman PT, Rozanov D, Zhang J, Maher CA, Caloian C, Watson JD, Uhrig S, Haas BJ, Jain M, Akeson M, Ahsen ME; SMC-RNA Challenge Participants; Stolovitzky G, Guinney J, Boutros PC, Stuart JM, Ellrott K. Creason A, et al. Among authors: yu t. Cell Syst. 2021 Aug 18;12(8):827-838.e5. doi: 10.1016/j.cels.2021.05.021. Epub 2021 Jun 18. Cell Syst. 2021. PMID: 34146471 Free PMC article.
Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth.
Tarca AL, Pataki BÁ, Romero R, Sirota M, Guan Y, Kutum R, Gomez-Lopez N, Done B, Bhatti G, Yu T, Andreoletti G, Chaiworapongsa T; DREAM Preterm Birth Prediction Challenge Consortium; Hassan SS, Hsu CD, Aghaeepour N, Stolovitzky G, Csabai I, Costello JC. Tarca AL, et al. Among authors: yu t. Cell Rep Med. 2021 Jun 15;2(6):100323. doi: 10.1016/j.xcrm.2021.100323. eCollection 2021 Jun 15. Cell Rep Med. 2021. PMID: 34195686 Free PMC article.
A Continuously Benchmarked and Crowdsourced Challenge for Rapid Development and Evaluation of Models to Predict COVID-19 Diagnosis and Hospitalization.
Yan Y, Schaffter T, Bergquist T, Yu T, Prosser J, Aydin Z, Jabeer A, Brugere I, Gao J, Chen G, Causey J, Yao Y, Bryson K, Long DR, Jarvik JG, Lee CI, Wilcox A, Guinney J, Mooney S; DREAM Challenge Consortium. Yan Y, et al. Among authors: yu t. JAMA Netw Open. 2021 Oct 1;4(10):e2124946. doi: 10.1001/jamanetworkopen.2021.24946. JAMA Netw Open. 2021. PMID: 34633425 Free PMC article.
Evaluation of crowdsourced mortality prediction models as a framework for assessing artificial intelligence in medicine.
Bergquist T, Schaffter T, Yan Y, Yu T, Prosser J, Gao J, Chen G, Charzewski Ł, Nawalany Z, Brugere I, Retkute R, Prusokas A, Prusokas A, Choi Y, Lee S, Choe J, Lee I, Kim S, Kang J, Mooney SD, Guinney J; Patient Mortality Prediction DREAM Challenge Consortium. Bergquist T, et al. Among authors: yu t. J Am Med Inform Assoc. 2023 Dec 22;31(1):35-44. doi: 10.1093/jamia/ocad159. J Am Med Inform Assoc. 2023. PMID: 37604111
9,502 results