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A
Zhou J, Troyanskaya OG. An analytical framework for interpretable and generalizable single-cell data analysis. Nat Methods. 2021 ;18(11):1317-1321.
Drescher K, Dunkel J, Nadell CD, van Teeffelen S, Grnja I, Wingreen NS, et al. Architectural transitions in Vibrio cholerae biofilms at single-cell resolution. Proc Natl Acad Sci U S A. 2016 ;113(14):E2066-72.
Meyer M, Wang Y, Edwards D, Smith GR, Rubenstein AB, Ramanathan P, et al. Attenuated activation of pulmonary immune cells in mRNA-1273-vaccinated hamsters after SARS-CoV-2 infection. J Clin Invest. 2021 ;131(20).
C
Qin B, Fei C, Bridges AA, Mashruwala AA, Stone HA, Wingreen NS, et al. Cell position fates and collective fountain flow in bacterial biofilms revealed by light-sheet microscopy. Science. 2020 ;369(6499):71-77.
Replogle JM, Norman TM, Xu A, Hussmann JA, Chen J, J Cogan Z, et al. Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing. Nat Biotechnol. 2020 ;38(8):954-961.
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Posfai E, Schell JPaul, Janiszewski A, Rovic I, Murray A, Bradshaw B, et al. Evaluating totipotency using criteria of increasing stringency. Nat Cell Biol. 2021 ;23(1):49-60.
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Batut PJ, Bing XYang, Sisco Z, Raimundo J, Levo M, Levine MS. Genome organization controls transcriptional dynamics during development. Science. 2022 ;375(6580):566-570.
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Ing-Simmons E, Vaid R, Bing XYang, Levine M, Mannervik M, Vaquerizas JM. Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning. Nat Genet. 2021 ;53(4):487-499.
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Chan MM, Smith ZD, Grosswendt S, Kretzmer H, Norman TM, Adamson B, et al. Molecular recording of mammalian embryogenesis. Nature. 2019 ;570(7759):77-82.
Adamson B, Norman TM, Jost M, Cho MY, Nuñez JK, Chen Y, et al.. A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response. Cell. 2016 ;167(7):1867-1882.e21.
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Chacha PPaul, Horie R, Kusakabe TG, Sasakura Y, Singh M, Horie T, et al. Neuronal identities derived by misexpression of the POU IV sensory determinant in a protovertebrate. Proc Natl Acad Sci U S A. 2022 ;119(4).
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Harder JL, Menon R, Otto EA, Zhou J, Eddy S, Wys NL, et al. Organoid single cell profiling identifies a transcriptional signature of glomerular disease. JCI Insight. 2019 ;4(1).
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Goyal Y, Levario TJ, Mattingly HH, Holmes S, Shvartsman SY, Lu H. Parallel imaging of embryos for quantitative analysis of genetic perturbations of the Ras pathway. Dis Model Mech. 2017 ;10(7):923-929.
Dixit A, Parnas O, Li B, Chen J, Fulco CP, Jerby-Arnon L, et al. Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. Cell. 2016 ;167(7):1853-1866.e17.
Scheffler RJ, Sugimoto Y, Bratton BP, Ellison CK, Koch MD, Donia MS, et al. Pseudomonas aeruginosa detachment from surfaces via a self-made small molecule. J Biol Chem. 2021 ;296:100279.
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Horie R, Hazbun A, Chen K, Cao C, Levine M, Horie T. Shared evolutionary origin of vertebrate neural crest and cranial placodes. Nature. 2018 ;560(7717):228-232.
Quinn JJ, Jones MG, Okimoto RA, Nanjo S, Chan MM, Yosef N, et al. Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts. Science. 2021 ;371(6532).
Douam F, Hrebikova G, Albrecht YESoto, Sellau J, Sharon Y, Ding Q, et al. Single-cell tracking of flavivirus RNA uncovers species-specific interactions with the immune system dictating disease outcome. Nat Commun. 2017 ;8:14781.
Lindström NO, Sealfon R, Chen X, Parvez RK, Ransick A, Brandine GDe Sena, et al.. Spatial transcriptional mapping of the human nephrogenic program. Dev Cell. 2021 ;56(16):2381-2398.e6.
Wang L, Xing X, Zeng X, S Jackson RE, TeSlaa T, Al-Dalahmah O, et al. Spatially resolved isotope tracing reveals tissue metabolic activity. Nat Methods. 2022 ;19(2):223-230.
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Wilson MZ, Ravindran PT, Lim WA, Toettcher JE. Tracing Information Flow from Erk to Target Gene Induction Reveals Mechanisms of Dynamic and Combinatorial Control. Mol Cell. 2017 ;67(5):757-769.e5.
Levo M, Raimundo J, Bing XYang, Sisco Z, Batut PJ, Ryabichko S, et al. Transcriptional coupling of distant regulatory genes in living embryos. Nature. 2022 ;605(7911):754-760.
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Yan J, Sharo AG, Stone HA, Wingreen NS, Bassler BL. Vibrio cholerae biofilm growth program and architecture revealed by single-cell live imaging. Proc Natl Acad Sci U S A. 2016 ;113(36):E5337-43.