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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: regev a. 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.
Dynamic regulatory network controlling TH17 cell differentiation.
Yosef N, Shalek AK, Gaublomme JT, Jin H, Lee Y, Awasthi A, Wu C, Karwacz K, Xiao S, Jorgolli M, Gennert D, Satija R, Shakya A, Lu DY, Trombetta JJ, Pillai MR, Ratcliffe PJ, Coleman ML, Bix M, Tantin D, Park H, Kuchroo VK, Regev A. Yosef N, et al. Among authors: regev a. Nature. 2013 Apr 25;496(7446):461-8. doi: 10.1038/nature11981. Epub 2013 Mar 6. Nature. 2013. PMID: 23467089 Free PMC article.
Comparative analysis of RNA sequencing methods for degraded or low-input samples.
Adiconis X, Borges-Rivera D, Satija R, DeLuca DS, Busby MA, Berlin AM, Sivachenko A, Thompson DA, Wysoker A, Fennell T, Gnirke A, Pochet N, Regev A, Levin JZ. Adiconis X, et al. Among authors: regev a. Nat Methods. 2013 Jul;10(7):623-9. doi: 10.1038/nmeth.2483. Epub 2013 May 19. Nat Methods. 2013. PMID: 23685885 Free PMC article.
Spatial reconstruction of single-cell gene expression data.
Satija R, Farrell JA, Gennert D, Schier AF, Regev A. Satija R, et al. Among authors: regev a. Nat Biotechnol. 2015 May;33(5):495-502. doi: 10.1038/nbt.3192. Epub 2015 Apr 13. Nat Biotechnol. 2015. PMID: 25867923 Free PMC article.
Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace.
Qu K, Garamszegi S, Wu F, Thorvaldsdottir H, Liefeld T, Ocana M, Borges-Rivera D, Pochet N, Robinson JT, Demchak B, Hull T, Ben-Artzi G, Blankenberg D, Barber GP, Lee BT, Kuhn RM, Nekrutenko A, Segal E, Ideker T, Reich M, Regev A, Chang HY, Mesirov JP. Qu K, et al. Among authors: regev a. Nat Methods. 2016 Mar;13(3):245-247. doi: 10.1038/nmeth.3732. Epub 2016 Jan 18. Nat Methods. 2016. PMID: 26780094 Free PMC article.
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.
Tirosh I, Izar B, Prakadan SM, Wadsworth MH 2nd, Treacy D, Trombetta JJ, Rotem A, Rodman C, Lian C, Murphy G, Fallahi-Sichani M, Dutton-Regester K, Lin JR, Cohen O, Shah P, Lu D, Genshaft AS, Hughes TK, Ziegler CG, Kazer SW, Gaillard A, Kolb KE, Villani AC, Johannessen CM, Andreev AY, Van Allen EM, Bertagnolli M, Sorger PK, Sullivan RJ, Flaherty KT, Frederick DT, Jané-Valbuena J, Yoon CH, Rozenblatt-Rosen O, Shalek AK, Regev A, Garraway LA. Tirosh I, et al. Among authors: regev a. Science. 2016 Apr 8;352(6282):189-96. doi: 10.1126/science.aad0501. Science. 2016. PMID: 27124452 Free PMC article.
Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma.
Tirosh I, Venteicher AS, Hebert C, Escalante LE, Patel AP, Yizhak K, Fisher JM, Rodman C, Mount C, Filbin MG, Neftel C, Desai N, Nyman J, Izar B, Luo CC, Francis JM, Patel AA, Onozato ML, Riggi N, Livak KJ, Gennert D, Satija R, Nahed BV, Curry WT, Martuza RL, Mylvaganam R, Iafrate AJ, Frosch MP, Golub TR, Rivera MN, Getz G, Rozenblatt-Rosen O, Cahill DP, Monje M, Bernstein BE, Louis DN, Regev A, Suvà ML. Tirosh I, et al. Among authors: regev a. Nature. 2016 Nov 10;539(7628):309-313. doi: 10.1038/nature20123. Epub 2016 Nov 2. Nature. 2016. PMID: 27806376 Free PMC article.
605 results