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Single-Cell Analysis

  • 1.
    Levo M, Raimundo J, Bing X, Sisco Z, Batut P, Ryabichko S, Gregor T, Levine M. Transcriptional coupling of distant regulatory genes in living embryos. Nature. 2022;605(7911):754–760. PMCID: PMC9886134
    Reference Link
  • 1.
    Wang L, Xing X, Zeng X, Jackson R, TeSlaa T, Al-Dalahmah O, Samarah L, Goodwin K, Yang L, McReynolds M, Li X, Wolff J, Rabinowitz J, Davidson S. Spatially resolved isotope tracing reveals tissue metabolic activity. Nat Methods. 2022;19(2):223–230. PMID: 35132243
    Reference Link
  • 1.
    Batut P, Bing X, Sisco Z, Raimundo J, Levo M, Levine M. Genome organization controls transcriptional dynamics during development. Science. 2022;375(6580):566–570. PMID: 35113722
    Reference Link
  • 1.
    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. PMCID: PMC6390964
    Reference Link
  • 1.
    Chacha P, Horie R, Kusakabe T, Sasakura Y, Singh M, Horie T, Levine M. Neuronal identities derived by misexpression of the POU IV sensory determinant in a protovertebrate. Proc Natl Acad Sci U S A. 2022;119(4). PMCID: PMC8794889
    Reference Link
  • 1.
    Zhou J, Troyanskaya O. An analytical framework for interpretable and generalizable single-cell data analysis. Nat Methods. 2021;18(11):1317–1321. PMCID: PMC8959118
    Reference Link
  • 1.
    Meyer M, Wang Y, Edwards D, Smith G, Rubenstein A, Ramanathan P, Mire C, Pietzsch C, Chen X, Ge Y, Cheng W, Henry C, Woods A, Ma L, Stewart-Jones G, Bock K, Minai M, Nagata B, Periasamy S, Shi P-Y, Graham B, Moore I, Ramos I, Troyanskaya O, Zaslavsky E, Carfi A, Sealfon S, Bukreyev A. Attenuated activation of pulmonary immune cells in mRNA-1273-vaccinated hamsters after SARS-CoV-2 infection. J Clin Invest. 2021;131(20). PMCID: PMC8516449
    Reference Link
  • 1.
    Lindström N, Sealfon R, Chen X, Parvez R, Ransick A, Brandine G, Guo J, Hill B, Tran T, Kim A, Zhou J, Tadych A, Watters A, Wong A, Lovero E, Grubbs B, Thornton M, McMahon J, Smith A, Ruffins S, Armit C, Troyanskaya O, McMahon A. Spatial transcriptional mapping of the human nephrogenic program. Dev Cell. 2021;56(16):2381–2398.e6. PMCID: PMC8396064
    Reference Link
  • 1.
    Ing-Simmons E, Vaid R, Bing X, Levine M, Mannervik M, Vaquerizas J. Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning. Nat Genet. 2021;53(4):487–499. PMCID: PMC8035076
    Reference Link
  • 1.
    Quinn J, Jones M, Okimoto R, Nanjo S, Chan M, Yosef N, Bivona T, Weissman J. Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts. Science. 2021;371(6532). PMCID: PMC7983364
    Reference Link
  • 1.
    Goodwin K, Nelson C. Uncovering cellular networks in branching morphogenesis using single-cell transcriptomics. Curr Top Dev Biol. 2021;143:239–280. PMID: 33820623
    Reference Link
  • 1.
    Posfai E, Schell J, Janiszewski A, Rovic I, Murray A, Bradshaw B, Yamakawa T, Pardon T, Bakkali M, Talon I, De Geest N, Kumar P, To S, Petropoulos S, Jurisicova A, Pasque V, Lanner F, Rossant J. Evaluating totipotency using criteria of increasing stringency. Nat Cell Biol. 2021;23(1):49–60. PMCID: 2846056
    Reference Link
  • 1.
    Scheffler R, Sugimoto Y, Bratton B, Ellison C, Koch M, Donia M, Gitai Z. Pseudomonas aeruginosa detachment from surfaces via a self-made small molecule. J Biol Chem. 2021;296:100279. PMCID: PMC7949062
    Reference Link
  • 1.
    Qin B, Fei C, Bridges A, Mashruwala A, Stone H, Wingreen N, Bassler B. Cell position fates and collective fountain flow in bacterial biofilms revealed by light-sheet microscopy. Science. 2020;369(6499):71–77. PMCID: PMC7426073
    Reference Link
  • 1.
    Replogle J, Norman T, Xu A, Hussmann J, Chen J, Cogan Z, Meer E, Terry J, Riordan D, Srinivas N, Fiddes I, Arthur J, Alvarado L, Pfeiffer K, Mikkelsen T, Weissman J, Adamson B. Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing. Nat Biotechnol. 2020;38(8):954–961. PMCID: PMC7416462
    Reference Link
  • 1.
    Chan M, Smith Z, Grosswendt S, Kretzmer H, Norman T, Adamson B, Jost M, Quinn J, Yang D, Jones M, Khodaverdian A, Yosef N, Meissner A, Weissman J. Molecular recording of mammalian embryogenesis. Nature. 2019;570(7759):77–82. PMCID: PMC7229772
    Reference Link
  • 1.
    Harder J, Menon R, Otto E, Zhou J, Eddy S, Wys N, O’Connor C, Luo J, Nair V, Cebrian C, Spence J, Bitzer M, Troyanskaya O, Hodgin J, Wiggins R, Freedman B, Kretzler M, European Renal cDNA Bank (ERCB), Nephrotic Syndrome Study Network (NEPTUNE). Organoid single cell profiling identifies a transcriptional signature of glomerular disease. JCI Insight. 2019;4(1). PMCID: PMC6485369
    Reference Link
  • 1.
    Dixit A, Parnas O, Li B, Chen J, Fulco C, Jerby-Arnon L, Marjanovic N, Dionne D, Burks T, Raychowdhury R, Adamson B, Norman T, Lander E, Weissman J, Friedman N, Regev A iv. Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. Cell. 2016;167(7):1853–1866.e17. PMCID: PMC5181115
    Reference Link
  • 1.
    Adamson B, Norman T, Jost M, Cho M, Nuñez J, Chen Y, Villalta J, Gilbert L, Horlbeck M, Hein M, Pak R, Gray A, Gross C, Dixit A, Parnas O, Regev A iv, Weissman J. A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response. Cell. 2016;167(7):1867–1882.e21. PMCID: PMC5315571
    Reference Link
  • 1.
    Wilson M, Ravindran P, Lim W, Toettcher J. Tracing Information Flow from Erk to Target Gene Induction Reveals Mechanisms of Dynamic and Combinatorial Control. Mol Cell. 2017;67(5):757–769.e5. PMCID: PMC5591080
    Reference Link
  • 1.
    Goyal Y, Levario T, Mattingly H, Holmes S, Shvartsman S, Lu H. Parallel imaging of embryos for quantitative analysis of genetic perturbations of the Ras pathway. Dis Model Mech. 2017;10(7):923–929. PMCID: PMC5536913
    Reference Link
  • 1.
    Douam F, Hrebikova G, Albrecht Y, Sellau J, Sharon Y, Ding Q, Ploss A. Single-cell tracking of flavivirus RNA uncovers species-specific interactions with the immune system dictating disease outcome. Nat Commun. 2017;8:14781. PMCID: PMC5424064
    Reference Link
  • 1.
    Yan J, Sharo A, Stone H, Wingreen N, Bassler B. 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. PMCID: PMC5018804
    Reference Link
  • 1.
    Toettcher J, Weiner O, Lim W. Using optogenetics to interrogate the dynamic control of signal transmission by the Ras/Erk module. Cell. 2013;155(6):1422–34. PMCID: PMC3925772
    Reference Link
  • 1.
    Drescher K, Dunkel J, Nadell C, van Teeffelen S, Grnja I, Wingreen N, Stone H, Bassler B. Architectural transitions in Vibrio cholerae biofilms at single-cell resolution. Proc Natl Acad Sci U S A. 2016;113(14):E2066–72. PMCID: PMC4833255
    Reference Link

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