Harvard Catalyst Profiles

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Allon Moshe Klein, Ph.D.


The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. R01HD096755 (MEGASON, SEAN G) Aug 20, 2018 - Apr 30, 2023
    Mapping the signaling landscape of vertebrate development at single cell resolution
    Role: Co-Principal Investigator
  2. R01CA218579 (KLEIN, ALLON MOSHE) Jul 18, 2018 - Jun 30, 2023
    Single Cell Genome-Wide Myeloid Response Profiling in Immunotherapy
    Role: Principal Investigator
  3. R01HL141402 (SOCOLOVSKY, MERAV) Apr 15, 2018 - Mar 31, 2022
    Novel Growth Factor Regulators of Early Erythropoieisis
    Role: Co-Principal Investigator
  4. R33CA212697 (KLEIN, ALLON MOSHE) Feb 16, 2017 - Jan 31, 2021
    Droplet microfluidic technology for single cell cancer genomics
    Role: Principal Investigator

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Siwicki M, Gort-Freitas NA, Messemaker M, Bill R, Gungabeesoon J, Engblom C, Zilionis R, Garris C, Gerhard GM, Kohl A, Lin Y, Zou AE, Cianciaruso C, Bolli E, Pfirschke C, Lin YJ, Piot C, Mindur JE, Talele N, Kohler RH, Iwamoto Y, Mino-Kenudson M, Pai SI, deVito C, Koessler T, Merkler D, Coukos A, Wicky A, Fraga M, Sempoux C, Jain RK, Dietrich PY, Michielin O, Weissleder R, Klein AM, Pittet MJ. Resident Kupffer cells and neutrophils drive liver toxicity in cancer immunotherapy. Sci Immunol. 2021 Jul 02; 6(61). PMID: 34215680.
    Citations:    Fields:    
  2. Tallapragada NP, Cambra HM, Wald T, Keough Jalbert S, Abraham DM, Klein OD, Klein AM. Inflation-collapse dynamics drive patterning and morphogenesis in intestinal organoids. Cell Stem Cell. 2021 09 02; 28(9):1516-1532.e14. PMID: 33915079.
    Citations: 1     Fields:    Translation:Cells
  3. Maroni G, Bassal MA, Krishnan I, Fhu CW, Savova V, Zilionis R, Maymi VA, Pandell N, Csizmadia E, Zhang J, Storti B, Castaño J, Panella R, Li J, Gustafson CE, Fox S, Levy RD, Meyerovitz CV, Tramontozzi PJ, Vermilya K, De Rienzo A, Crucitta S, Bassères DS, Weetall M, Branstrom A, Giorgetti A, Ciampi R, Del Re M, Danesi R, Bizzarri R, Yang H, Kocher O, Klein AM, Welner RS, Bueno R, Magli MC, Clohessy JG, Ali A, Tenen DG, Levantini E. Identification of a targetable KRAS-mutant epithelial population in non-small cell lung cancer. Commun Biol. 2021 04 14; 4(1):370. PMID: 33854168.
    Citations:    Translation:HumansAnimalsCells
  4. Gerhard GM, Bill R, Messemaker M, Klein AM, Pittet MJ. Tumor-infiltrating dendritic cell states are conserved across solid human cancers. J Exp Med. 2021 01 04; 218(1). PMID: 33601412.
    Citations: 2     Fields:    Translation:HumansCells
  5. Pfirschke C, Engblom C, Gungabeesoon J, Lin Y, Rickelt S, Zilionis R, Messemaker M, Siwicki M, Gerhard GM, Kohl A, Meylan E, Weissleder R, Klein AM, Pittet MJ. Tumor-Promoting Ly-6G+ SiglecFhigh Cells Are Mature and Long-Lived Neutrophils. Cell Rep. 2020 09 22; 32(12):108164. PMID: 32966785.
    Citations: 6     Fields:    Translation:AnimalsCells
  6. Rodriguez-Fraticelli AE, Weinreb C, Wang SW, Migueles RP, Jankovic M, Usart M, Klein AM, Lowell S, Camargo FD. Single-cell lineage tracing unveils a role for TCF15 in haematopoiesis. Nature. 2020 07; 583(7817):585-589. PMID: 32669716.
    Citations: 14     Fields:    Translation:AnimalsCells
  7. Loughran SJ, Haas S, Wilkinson AC, Klein AM, Brand M. Lineage commitment of hematopoietic stem cells and progenitors: insights from recent single cell and lineage tracing technologies. Exp Hematol. 2020 08; 88:1-6. PMID: 32653531.
    Citations: 4     Fields:    Translation:HumansAnimalsCells
  8. Weinreb C, Klein AM. Lineage reconstruction from clonal correlations. Proc Natl Acad Sci U S A. 2020 07 21; 117(29):17041-17048. PMID: 32632001.
    Citations: 2     Fields:    Translation:AnimalsCells
  9. Wagner DE, Klein AM. Lineage tracing meets single-cell omics: opportunities and challenges. Nat Rev Genet. 2020 07; 21(7):410-427. PMID: 32235876.
    Citations: 46     Fields:    Translation:HumansAnimalsCells
  10. Weinreb C, Rodriguez-Fraticelli A, Camargo FD, Klein AM. Lineage tracing on transcriptional landscapes links state to fate during differentiation. Science. 2020 02 14; 367(6479). PMID: 31974159.
    Citations: 67     Fields:    Translation:AnimalsCells
  11. Sharma N, Flaherty K, Lezgiyeva K, Wagner DE, Klein AM, Ginty DD. The emergence of transcriptional identity in somatosensory neurons. Nature. 2020 01; 577(7790):392-398. PMID: 31915380.
    Citations: 48     Fields:    Translation:AnimalsCells
  12. Sharir A, Marangoni P, Zilionis R, Wan M, Wald T, Hu JK, Kawaguchi K, Castillo-Azofeifa D, Epstein L, Harrington K, Pagella P, Mitsiadis T, Siebel CW, Klein AM, Klein OD. A large pool of actively cycling progenitors orchestrates self-renewal and injury repair of an ectodermal appendage. Nat Cell Biol. 2019 09; 21(9):1102-1112. PMID: 31481792.
    Citations: 16     Fields:    Translation:AnimalsCells
  13. Wolock SL, Krishnan I, Tenen DE, Matkins V, Camacho V, Patel S, Agarwal P, Bhatia R, Tenen DG, Klein AM, Welner RS. Mapping Distinct Bone Marrow Niche Populations and Their Differentiation Paths. Cell Rep. 2019 07 09; 28(2):302-311.e5. PMID: 31291568.
    Citations: 43     Fields:    Translation:Humans
  14. Klein AM, Treutlein B. Single cell analyses of development in the modern era. Development. 2019 06 27; 146(12). PMID: 31249004.
    Citations: 3     Fields:    Translation:HumansAnimals
  15. 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 06 03; 10(1):2395. PMID: 31160568.
    Citations: 47     Fields:    Translation:HumansAnimalsCells
  16. 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 05 21; 50(5):1317-1334.e10. PMID: 30979687.
    Citations: 194     Fields:    Translation:HumansAnimalsCells
  17. Wolock SL, Lopez R, Klein AM. Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data. Cell Syst. 2019 04 24; 8(4):281-291.e9. PMID: 30954476.
    Citations: 184     Fields:    Translation:HumansAnimalsCells
  18. 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 01 03; 24(1):183-192.e8. PMID: 30472156.
    Citations: 14     Fields:    Translation:AnimalsCells
  19. 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 11 01; 23(5):687-699.e8. PMID: 30269904.
    Citations: 18     Fields:    Translation:AnimalsCells
  20. 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 11 01; 23(5):677-686.e4. PMID: 30269903.
    Citations: 45     Fields:    Translation:AnimalsCells
  21. 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 09 14; 3(27). PMID: 30217811.
    Citations: 39     Fields:    Translation:AnimalsCells
  22. 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 08; 560(7718):377-381. PMID: 30069046.
    Citations: 217     Fields:    Translation:HumansAnimalsCells
  23. Klein AM. Technique to measure the expression dynamics of each gene in a single cell. Nature. 2018 08; 560(7719):434-435. PMID: 30127477.
    Citations:    Fields:    
  24. Hrvatin S, Hochbaum DR, Nagy MA, Cicconet M, Robertson K, Cheadle L, Zilionis R, Ratner A, Borges-Monroy R, Klein AM, Sabatini BL, Greenberg ME. Publisher Correction: Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex. Nat Neurosci. 2018 Jul; 21(7):1017. PMID: 29752482.
    Citations:    Fields:    
  25. Zemmour D, Zilionis R, Kiner E, Klein AM, Mathis D, Benoist C. Publisher Correction: Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR. Nat Immunol. 2018 06; 19(6):645. PMID: 29725080.
    Citations:    Fields:    
  26. 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 06 01; 360(6392):981-987. PMID: 29700229.
    Citations: 169     Fields:    Translation:Animals
  27. 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 06 01; 360(6392). PMID: 29700227.
    Citations: 108     Fields:    Translation:AnimalsCells
  28. Weinreb C, Wolock S, Klein AM. SPRING: a kinetic interface for visualizing high dimensional single-cell expression data. Bioinformatics. 2018 04 01; 34(7):1246-1248. PMID: 29228172.
    Citations: 79     Fields:    Translation:HumansCells
  29. 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 06; 36(5):442-450. PMID: 29608178.
    Citations: 130     Fields:    Translation:HumansAnimalsCells
  30. 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 03 01; 555(7694):54-60. PMID: 29466336.
    Citations: 100     Fields:    Translation:AnimalsCells
  31. 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 03 06; 115(10):E2467-E2476. PMID: 29463712.
    Citations: 54     Fields:    Translation:AnimalsCells
  32. 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 03; 19(3):291-301. PMID: 29434354.
    Citations: 109     Fields:    Translation:HumansAnimalsCells
  33. 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 01 11; 553(7687):212-216. PMID: 29323290.
    Citations: 119     Fields:    Translation:AnimalsCells
  34. Hrvatin S, Hochbaum DR, Nagy MA, Cicconet M, Robertson K, Cheadle L, Zilionis R, Ratner A, Borges-Monroy R, Klein AM, Sabatini BL, Greenberg ME. Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex. Nat Neurosci. 2018 01; 21(1):120-129. PMID: 29230054.
    Citations: 124     Fields:    Translation:AnimalsCells
  35. 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. 2017 12 12; 114(50):E10838-E10847. PMID: 29183978.
    Citations: 15     Fields:    Translation:AnimalsCells
  36. Klein AM, Macosko E. InDrops and Drop-seq technologies for single-cell sequencing. Lab Chip. 2017 07 25; 17(15):2540-2541. PMID: 28721415.
    Citations: 8     Fields:    Translation:HumansAnimals
  37. Wagner DE, Klein AM. Genetic screening enters the single-cell era. Nat Methods. 2017 02 28; 14(3):237-238. PMID: 28245215.
    Citations: 4     Fields:    
  38. Zilionis R, Nainys J, Veres A, Savova V, Zemmour D, Klein AM, Mazutis L. Single-cell barcoding and sequencing using droplet microfluidics. Nat Protoc. 2017 Jan; 12(1):44-73. PMID: 27929523.
    Citations: 154     Fields:    
  39. 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 10 26; 3(4):346-360.e4. PMID: 27667365.
    Citations: 273     Fields:    Translation:HumansAnimalsCells
  40. 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 Jun 17; 352(6292):1471-4. PMID: 27229141.
    Citations: 69     Fields:    Translation:AnimalsCells
  41. Peshkin L, Wühr M, Pearl E, Haas W, Freeman RM, Gerhart JC, Klein AM, Horb M, Gygi SP, Kirschner MW. On the Relationship of Protein and mRNA Dynamics in Vertebrate Embryonic Development. Dev Cell. 2015 Nov 09; 35(3):383-94. PMID: 26555057.
    Citations: 77     Fields:    Translation:AnimalsCells
  42. 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 May 21; 161(5):1187-1201. PMID: 26000487.
    Citations: 847     Fields:    Translation:AnimalsCells
  43. 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(7):e101085. PMID: 24991805.
    Citations: 14     Fields:    Translation:AnimalsCells
  44. Lim X, Tan SH, Koh WL, Chau RM, Yan KS, Kuo CJ, van Amerongen R, Klein AM, Nusse R. Interfollicular epidermal stem cells self-renew via autocrine Wnt signaling. Science. 2013 Dec 06; 342(6163):1226-30. PMID: 24311688.
    Citations: 138     Fields:    Translation:HumansAnimalsCells
  45. Hernández AR, Klein AM, Kirschner MW. Kinetic responses of ß-catenin specify the sites of Wnt control. Science. 2012 Dec 07; 338(6112):1337-40. PMID: 23138978.
    Citations: 61     Fields:    Translation:HumansCells
  46. Doupé DP, Alcolea MP, Roshan A, Zhang G, Klein AM, Simons BD, Jones PH. A single progenitor population switches behavior to maintain and repair esophageal epithelium. Science. 2012 Aug 31; 337(6098):1091-3. PMID: 22821983.
    Citations: 125     Fields:    Translation:AnimalsCells
  47. Klein AM, Lande-Diner L. The critical discussion group: fostering personal and scientific growth. Mol Cell. 2011 Oct 21; 44(2):167-9. PMID: 22017864.
    Citations:    Fields:    Translation:Humans
  48. Magenheim J, Klein AM, Stanger BZ, Ashery-Padan R, Sosa-Pineda B, Gu G, Dor Y. Ngn3(+) endocrine progenitor cells control the fate and morphogenesis of pancreatic ductal epithelium. Dev Biol. 2011 Nov 01; 359(1):26-36. PMID: 21888903.
    Citations: 37     Fields:    Translation:AnimalsCells
  49. Klein AM, Simons BD. Universal patterns of stem cell fate in cycling adult tissues. Development. 2011 Aug; 138(15):3103-11. PMID: 21750026.
    Citations: 124     Fields:    Translation:AnimalsCells
  50. Waks Z, Klein AM, Silver PA. Cell-to-cell variability of alternative RNA splicing. Mol Syst Biol. 2011 Jul 05; 7:506. PMID: 21734645.
    Citations: 47     Fields:    Translation:HumansCells
  51. 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 Dec 07; 8(65):1815-24. PMID: 21632613.
    Citations: 4     Fields:    Translation:HumansCells
  52. Snippert HJ, van der Flier LG, Sato T, van Es JH, van den Born M, Kroon-Veenboer C, Barker N, Klein AM, van Rheenen J, Simons BD, Clevers H. Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells. Cell. 2010 Oct 01; 143(1):134-44. PMID: 20887898.
    Citations: 765     Fields:    Translation:AnimalsCells
  53. Salpeter SJ, Klein AM, Huangfu D, Grimsby J, Dor Y. Glucose and aging control the quiescence period that follows pancreatic beta cell replication. Development. 2010 Oct; 137(19):3205-13. PMID: 20823063.
    Citations: 39     Fields:    Translation:AnimalsCells
  54. Lopez-Garcia C, Klein AM, Simons BD, Winton DJ. Intestinal stem cell replacement follows a pattern of neutral drift. Science. 2010 Nov 05; 330(6005):822-5. PMID: 20929733.
    Citations: 270     Fields:    Translation:AnimalsCells
  55. Klein AM, Nakagawa T, Ichikawa R, Yoshida S, Simons BD. Mouse germ line stem cells undergo rapid and stochastic turnover. Cell Stem Cell. 2010 Aug 06; 7(2):214-24. PMID: 20682447.
    Citations: 102     Fields:    Translation:AnimalsCells
  56. Doupé DP, Klein AM, Simons BD, Jones PH. The ordered architecture of murine ear epidermis is maintained by progenitor cells with random fate. Dev Cell. 2010 Feb 16; 18(2):317-23. PMID: 20159601.
    Citations: 110     Fields:    Translation:AnimalsCells
  57. 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 Jan 05; 107(1):270-5. PMID: 20018764.
    Citations: 34     Fields:    Translation:HumansAnimalsCells
  58. Klein AM, Doupé DP, Jones PH, Simons BD. Mechanism of murine epidermal maintenance: cell division and the voter model. Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Mar; 77(3 Pt 1):031907. PMID: 18517422.
    Citations: 10     Fields:    Translation:Animals
  59. Klein AM, Doupé DP, Jones PH, Simons BD. Kinetics of cell division in epidermal maintenance. Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Aug; 76(2 Pt 1):021910. PMID: 17930068.
    Citations: 22     Fields:    Translation:HumansAnimals
  60. Clayton E, Doupé DP, Klein AM, Winton DJ, Simons BD, Jones PH. A single type of progenitor cell maintains normal epidermis. Nature. 2007 Mar 08; 446(7132):185-9. PMID: 17330052.
    Citations: 349     Fields:    Translation:AnimalsCells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.