Selected publications are shown below. Please visit Allon’s Google Scholar for a full list of publications!
2022
Wang SW#, Herriges MJ, Hurley K, Kotton DN, Klein AM#. CoSpar identifies early cell fate biases from single cell transcriptomic and lineage information. Nature Biotechnology. 2022 Feb 21. (# correspondence)
Cambra HM, Tallapragada NP, Mannam P, Breault DT, Klein AM. Triple-Decker Sandwich Cultures of Intestinal Organoids for Long-Term Live Imaging, Uniform Perturbation, and Statistical Sampling. Current Protocols. 2022 Jan 14.
2021
Siwicki M, Gort-Freitas NA, Messemaker M, Bill R, Gungabeesoon J, Engblom C, Zilionis R, Garris C, Gerhard GM, Kohl A, Lin Y, …, Pittet MJ, Klein AM. Resident Kupffer cells and neutrophils drive liver toxicity in cancer immunotherapy. Science Immunology. 2021 Jul 2;6(61).
Tallapragada NP, Cambra HM, Wald T, Jalbert SK, Abraham DM, Klein OD, Klein AM. Inflation-collapse dynamics drive patterning and morphogenesis in intestinal organoids. Cell Stem Cell. 2021 Apr 28.
Wang SW, Klein AM. Learning dynamics by computational integration of single cell genomic and lineage information. bioRxiv. 2021 Jan 1.
2020
Weinreb C, Klein AM. Lineage reconstruction from clonal correlations. Proc Natl Acad Sci U S A. 2020 Jul 21;117(29):17041-17048. doi: 10.1073/pnas.2000238117. Epub 2020 Jul 6. PubMed PMID: 32632001; PubMed Central PMCID: PMC7382289.
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 Jul;583(7817):585-589. doi: 10.1038/s41586-020-2503-6. Epub 2020 Jul 15. PubMed PMID: 32669716; NIHMSID:NIHMS1589128.
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 Jul 9;. doi: 10.1016/j.exphem.2020.07.002. [Epub ahead of print] PubMed PMID: 32653531.
Wagner DE, Klein AM. Lineage tracing meets single-cell omics: opportunities and challenges. Nat Rev Genet. 2020 Jul;21(7):410-427. doi: 10.1038/s41576-020-0223-2. Epub 2020 Mar 31. Review. PubMed PMID: 32235876; PubMed Central PMCID: PMC7307462.
Weissleder R, Pittet MJ. The expanding landscape of inflammatory cells affecting cancer therapy. Nat Biomed Eng. 2020 May;4(5):489-498. doi: 10.1038/s41551-020-0524-y. Epub 2020 Mar 18. Review. PubMed PMID: 32203281; PubMed Central PMCID: PMC7405944.
Weinreb C, Rodriguez-Fraticelli A, Camargo FD, Klein AM. Lineage tracing on transcriptional landscapes links state to fate during differentiation. Science. 2020 Feb 14;367(6479). Epub 2020 Jan 23.
Sharma N, Flaherty K, Lezgiyeva K, Wagner DE, Klein AM, Ginty DD. The emergence of transcriptional identity in somatosensory neurons. Nature. 2020 Jan;577(7790):392-398. Epub 2020 Jan 8.
2019
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 Sep;21(9):1102-1112. Epub 2019 Sep 2.
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 Jul 9;28(2):302-311.e5.
Klein AM, Treutlein B. Single cell analyses of development in the modern era. Development. 2019 Jun 27;146(12).
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. (2019). Immunity. 50(5), 1317-1334.
Wolock SL , Lopez R, Klein AM. Scrublet: computational identification of cell doublets in single-cell transcriptomic data. Cell systems 8 (4), 281-291. e9
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. (2019) Cell Stem Cell 24(1), 183-192.
2018
Wagner DE, Weinreb C, Zollins ZM, Briggs JA, Megason SG, Klein AM. Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo. Science. 2018;Epubc.
Weinreb C, Wolock S, Klein AM. SPRING: a kinetic interface for visualizing high dimensional single-cell expression data. Bioinfomatics. 2018;34 (7) :1246-8.
Kailin R Mesa, Kyogo Kawaguchi, Katie Cockburn, David Gonzalez, Jonathan Boucher, Tianchi Xin, Allon M Klein, Valentina Greco. Homeostatic Epidermal Stem Cell Self-Renewal Is Driven by Local Differentiation. Cell Stem Cell 23, 677 (2018)
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;Epub.
Lindsey W Plasschaert, Rapolas Žilionis, Rayman Choo-Wing, Virginia Savova, Judith Knehr, Guglielmo Roma, Allon M Klein, Aron B Jaffe. A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte. Nature 560, 377 (2018)
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;Epub.
Tusi BK, Wolock SL, Weinreb C, Hwang Y, Hildalgo D, Zilionis R, Waisman A, Huh JR, Klein AM, Socolovsky M. Population snapshots predict early haematopoietic and erythroid hierarchies. Nature. 2018;555 (7694) :50-64.
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 (10) :E2467-E2476.
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 (7687) :212-16.
Hrvatin S, Hochbaum DR, Nagy MA, Cicconet M, Robertson K, Cheadle L, Zillionis R, Ratner A, Borges-Monroy R, Klein AM, et al. Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex. Nat Neuro Science. 2018;21 (1) :120-129.
Zemmour D, Zillionis 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 (3) :291-301.
2017
Klein, AM, Macosko, E. InDrops and Drop-seq technologies for single-cell sequencing. Lab Chip. 2017;17 (15).
Wagner, BK, Klein AM. Genetic screening enters the single-cell era. . Nature Methods. 2017;14 (3) :237-38.
Zilionis R, Nainys J, Veres A, Savova V, Zemmour D, Klein AM, L. M. Single-cell barcoding and sequencing using droplet microfluidics. Nature Protocols. 2017;12 (1) :44-73.
2016
Baron, M, Veres, A, Wolock, SL, Faust, AL, Gaujoux, R, Vetere, A, Yu R, Wagner, BK, Shen-Orr, SS, Klein, AM, et al. single-Cell Transciptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure. . Cell Systems. 2016;4712 (16).
Derr, A, Yang, C, Zilionis, R, Sergushichev, A, Blodgett, DM, Redick, S, Bortell, R, Luban, J, Harlan, DM, Kadener, S, et al. End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data. Genome Res . 2016;26 (10) :1397-1410.
Rompolas, P, Mesa, KR, Kawaguchi, K, Park, D, Gonzalez, D, Brown, S, Boucher, J, Klein, AM, Greco V. Spatiotemporal coordination of stem cell commitment during epidermal homeostasis. Science. 2016;352 (6292) :Epub.
2015
Peshkin, L, Wühr, M, Pearl, E, Haas, W, Freeman, RM Jr, Gerhart, JC, Klein, AM, Horb, M, Gygi, SP, Kirschner MW. On the Relationship of Protein and mRNA Dynamics in Vertebrate Embryonic Development. Developmental Cell. 2015;35 (33) :383-94.
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 (5) :1187-201.Abstract
2014
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.Abstract
2013
Lim X, Tan SH, Koh WLC, Chau RMW, Yan KS, Kuo CJ, van Amerongen R, Klein AM, Nusse R. Interfollicular epidermal stem cells self-renew via autocrine Wnt signaling. Science. 2013;342 (6163) :1226-30.Abstract
2012
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;337 (6098) :1091-3.Abstract
Hernández AR, Klein AM, Kirschner MW. Kinetic responses of β-catenin specify the sites of Wnt control. Science. 2012;338 (6112) :1337-40.Abstract
2011
Waks Z, Klein AM, Silver PA. Cell-to-cell variability of alternative RNA splicing. Mol Syst Biol. 2011;7 :506.Abstract
Klein AM, Lande-Diner L. The critical discussion group: fostering personal and scientific growth. Mol Cell. 2011;44 (2) :167-9.Abstract
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;359 (1) :26-36.Abstract
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 (65) :1815-24.Abstract
Klein AM, Simons BD. Universal patterns of stem cell fate in cycling adult tissues. Development. 2011;138 (15) :3103-11.Abstract
2010
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 (1) :270-5.Abstract
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;137 (19) :3205-13.Abstract
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, et al. Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells. Cell. 2010;143 (1) :134-44.Abstract
Lopez-Garcia C, Klein AM, Simons BD, Winton DJ. Intestinal stem cell replacement follows a pattern of neutral drift. Science. 2010;330 (6005) :822-5.Abstract
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 (2) :214-24.Abstract
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;18 (2) :317-23.Abstract
2008
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;77 (3 Pt 1) :031907.Abstract
2007
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 (2 Pt 1) :021910.Abstract
Clayton E, Doupé DP, Klein AM, Winton DJ, Simons BD, Jones PH. A single type of progenitor cell maintains normal epidermis. Nature. 2007;446 (7132) :185-9.Abstract