Photo of Allon M Klein,  PhD

Allon M Klein, PhD

Harvard Medical School

Harvard Medical School
Phone: (617) 432-4996


allon_klein@hms.harvard.edu

Allon M Klein, PhD

Harvard Medical School

EDUCATIONAL TITLES

  • Associate Professor, Systems Biology, Harvard Medical School

DF/HCC PROGRAM AFFILIATION

Publications

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  • Zilionis R, Engblom C, Pfirschke C, Savova V, Zemmour D, Saatcioglu HD, Krishnan I, Maroni G, Meyerovitz CV, Kerwin CM, Choi S, Richards WG, De Rienzo A, Tenen DG, Bueno R, Levantini E, Pittet MJ, Klein AM. Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species. Immunity 2019; 50:1317-1334.e10. PubMed
  • Wolock SL, Lopez R, Klein AM. Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data. Cell Syst 2019. PubMed
  • Jones KB, Furukawa S, Marangoni P, Ma H, Pinkard H, D'Urso R, Zilionis R, Klein AM, Klein OD. Quantitative Clonal Analysis and Single-Cell Transcriptomics Reveal Division Kinetics, Hierarchy, and Fate of Oral Epithelial Progenitor Cells. Cell Stem Cell 2019; 24:183-192.e8. PubMed
  • Pellin D, Loperfido M, Baricordi C, Wolock SL, Montepeloso A, Weinberg OK, Biffi A, Klein AM, Biasco L. A comprehensive single cell transcriptional landscape of human hematopoietic progenitors. Nat Commun 2019; 10:2395. PubMed
  • Mesa KR, Kawaguchi K, Cockburn K, Gonzalez D, Boucher J, Xin T, Klein AM, Greco V. Homeostatic Epidermal Stem Cell Self-Renewal Is Driven by Local Differentiation. Cell Stem Cell 2018. PubMed
  • Murai K, Skrupskelyte G, Piedrafita G, Hall M, Kostiou V, Ong SH, Nagy T, Cagan A, Goulding D, Klein AM, Hall BA, Jones PH. Epidermal Tissue Adapts to Restrain Progenitors Carrying Clonal p53 Mutations. Cell Stem Cell 2018. PubMed
  • DiSpirito JR, Zemmour D, Ramanan D, Cho J, Zilionis R, Klein AM, Benoist C, Mathis D. Molecular diversification of regulatory T cells in nonlymphoid tissues. Sci Immunol 2018. PubMed
  • Klein AM. Technique to measure the expression dynamics of each gene in a single cell. Nature 2018; 560:434-435. PubMed
  • Plasschaert LW, Žilionis R, Choo-Wing R, Savova V, Knehr J, Roma G, Klein AM, Jaffe AB. A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte. Nature 2018; 560:377-381. PubMed
  • Weinreb C, Wolock S, Klein AM. SPRING: a kinetic interface for visualizing high dimensional single-cell expression data. Bioinformatics 2018; 34:1246-1248. PubMed
  • Raj B, Wagner DE, McKenna A, Pandey S, Klein AM, Shendure J, Gagnon JA, Schier AF. Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain. Nat Biotechnol 2018. PubMed
  • Weinreb C, Wolock S, Tusi BK, Socolovsky M, Klein AM. Fundamental limits on dynamic inference from single-cell snapshots. Proc Natl Acad Sci U S A 2018; 115:E2467-E2476. PubMed
  • Tusi BK, Wolock SL, Weinreb C, Hwang Y, Hidalgo D, Zilionis R, Waisman A, Huh JR, Klein AM, Socolovsky M. Population snapshots predict early haematopoietic and erythroid hierarchies. Nature 2018; 555:54-60. PubMed
  • Zemmour D, Zilionis R, Kiner E, Klein AM, Mathis D, Benoist C. Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR. Nat Immunol 2018; 19:291-301. PubMed
  • Rodriguez-Fraticelli AE, Wolock SL, Weinreb CS, Panero R, Patel SH, Jankovic M, Sun J, Calogero RA, Klein AM, Camargo FD. Clonal analysis of lineage fate in native haematopoiesis. Nature 2018; 553:212-216. PubMed
  • Wagner DE, Weinreb C, Collins ZM, Briggs JA, Megason SG, Klein AM. Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo. Science 2018; 360:981-987. PubMed
  • Briggs JA, Weinreb C, Wagner DE, Megason S, Peshkin L, Kirschner MW, Klein AM. The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution. Science 2018. PubMed
  • Presler M, Van Itallie E, Klein AM, Kunz R, Coughlin ML, Peshkin L, Gygi SP, Wühr M, Kirschner MW. Proteomics of phosphorylation and protein dynamics during fertilization and meiotic exit in the Xenopus egg. Proc Natl Acad Sci U S A 2018; 114:E10838-E10847. PubMed
  • Briggs JA, Li VC, Lee S, Woolf CJ, Klein A, Kirschner MW. Mouse embryonic stem cells can differentiate via multiple paths to the same state. Elife 2017. PubMed
  • Klein AM, Macosko E. InDrops and Drop-seq technologies for single-cell sequencing. Lab Chip 2017; 17:2540-2541. PubMed
  • Wagner DE, Klein AM. Genetic screening enters the single-cell era. Nat Methods 2017; 14:237-238. PubMed
  • Zilionis R, Nainys J, Veres A, Savova V, Zemmour D, Klein AM, Mazutis L. Single-cell barcoding and sequencing using droplet microfluidics. Nat Protoc 2016; 12:44-73. PubMed
  • Baron M, Veres A, Wolock SL, Faust AL, Gaujoux R, Vetere A, Ryu JH, Wagner BK, Shen-Orr SS, Klein AM, Melton DA, Yanai I. A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure. Cell Syst 2016; 3:346-360.e4. PubMed
  • Rompolas P, Mesa KR, Kawaguchi K, Park S, Gonzalez D, Brown S, Boucher J, Klein AM, Greco V. Spatiotemporal coordination of stem cell commitment during epidermal homeostasis. Science 2016; 352:1471-4. PubMed
  • Klein AM, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, Peshkin L, Weitz DA, Kirschner MW. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 2015; 161:1187-201. PubMed
  • Kronen MR, Schoenfelder KP, Klein AM, Nystul TG. Basolateral junction proteins regulate competition for the follicle stem cell niche in the Drosophila ovary. PLoS ONE 2014; 9:e101085. PubMed
  • Hernández AR, Klein AM, Kirschner MW. Kinetic responses of β-catenin specify the sites of Wnt control. Science 2012; 338:1337-40. PubMed
  • Klein AM, Nikolaidou-Neokosmidou V, Doupé DP, Jones PH, Simons BD. Patterning as a signature of human epidermal stem cell regulation. J R Soc Interface 2011; 8:1815-24. PubMed
  • Klein AM, Simons BD. Universal patterns of stem cell fate in cycling adult tissues. Development 2011; 138:3103-11. PubMed
  • Waks Z, Klein AM, Silver PA. Cell-to-cell variability of alternative RNA splicing. Mol Syst Biol 2011; 7:506. PubMed
  • Lopez-Garcia C, Klein AM, Simons BD, Winton DJ. Intestinal stem cell replacement follows a pattern of neutral drift. Science 2010; 330:822-5. PubMed
  • Klein AM, Nakagawa T, Ichikawa R, Yoshida S, Simons BD. Mouse germ line stem cells undergo rapid and stochastic turnover. Cell Stem Cell 2010; 7:214-24. PubMed
  • Klein AM, Brash DE, Jones PH, Simons BD. Stochastic fate of p53-mutant epidermal progenitor cells is tilted toward proliferation by UV B during preneoplasia. Proc Natl Acad Sci U S A 2010; 107:270-5. PubMed
  • Klein AM, Doupé DP, Jones PH, Simons BD. Kinetics of cell division in epidermal maintenance. Phys Rev E Stat Nonlin Soft Matter Phys 2007; 76:021910. PubMed
  • Clayton E, Doupé DP, Klein AM, Winton DJ, Simons BD, Jones PH. A single type of progenitor cell maintains normal epidermis. Nature 2007; 446:185-9. PubMed
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