Publications

Search Publications
Export 25 results:
Author Title [ Year(Asc)]
Filters: Keyword is Single-Cell Analysis  [Clear All Filters]
2022
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.
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).
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.
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.
2021
Zhou J, Troyanskaya OG. An analytical framework for interpretable and generalizable single-cell data analysis. Nat Methods. 2021 ;18(11):1317-1321.
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).
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.
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.
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.
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).
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.
Goodwin K, Nelson CM. Uncovering cellular networks in branching morphogenesis using single-cell transcriptomics. Curr Top Dev Biol. 2021 ;143:239-280.
2020
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.
2019
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.
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).
2018
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.
2017
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.
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.
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.
2016
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.
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.
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.
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.
2013
Toettcher JE, Weiner OD, Lim WA. Using optogenetics to interrogate the dynamic control of signal transmission by the Ras/Erk module. Cell. 2013 ;155(6):1422-34.