Allon M. Klein - Publications

Affiliations: 
2015 Systems Biology Harvard Medical School, Boston, MA, United States 

75 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 McCauley KB, Kukreja K, Tovar Walker AE, Jaffe AB, Klein AM. A map of signaling responses in the human airway epithelium. Cell Systems. PMID 38508187 DOI: 10.1016/j.cels.2024.02.005  0.64
2023 Li L, Bowling S, McGeary SE, Yu Q, Lemke B, Alcedo K, Jia Y, Liu X, Ferreira M, Klein AM, Wang SW, Camargo FD. A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells. Cell. PMID 37852258 DOI: 10.1016/j.cell.2023.09.019  0.452
2023 Kukreja K, Patel N, Megason SG, Klein AM. Global decoupling of cell differentiation from cell division in early embryo development. Biorxiv : the Preprint Server For Biology. PMID 37546736 DOI: 10.1101/2023.07.29.551123  0.511
2023 Scully T, Klein A. A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells. Biorxiv : the Preprint Server For Biology. PMID 37163054 DOI: 10.1101/2023.04.26.538465  0.38
2022 Mccauley KB, Kukreja K, Jaffe AB, Klein AM. A map of signaling responses in the human airway epithelium. Biorxiv : the Preprint Server For Biology. PMID 36597531 DOI: 10.1101/2022.12.21.521460  0.643
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. PMID 35190690 DOI: 10.1038/s41587-022-01209-1  0.481
2021 Cable J, Elowitz MB, Domingos AI, Habib N, Itzkovitz S, Hamidzada H, Balzer MS, Yanai I, Liberali P, Whited J, Streets A, Cai L, Stergachis AB, Hong CKY, Keren L, ... ... Klein AM, et al. Single cell biology-a Keystone Symposia report. Annals of the New York Academy of Sciences. PMID 34605044 DOI: 10.1111/nyas.14692  0.436
2021 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. PMID 33915079 DOI: 10.1016/j.stem.2021.04.002  0.384
2020 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. 583: 585-589. PMID 32669716 DOI: 10.1038/S41586-020-2503-6  0.781
2020 Loughran S, Haas S, Wilkinson AC, Klein A, Brand M. Lineage commitment of hematopoietic stem cells and progenitors: insights from recent single cell and lineage tracing technologies. Experimental Hematology. PMID 32653531 DOI: 10.1016/J.Exphem.2020.07.002  0.555
2020 Weinreb C, Klein AM. Lineage reconstruction from clonal correlations. Proceedings of the National Academy of Sciences of the United States of America. PMID 32632001 DOI: 10.1073/Pnas.2000238117  0.777
2020 Wagner DE, Klein AM. Lineage tracing meets single-cell omics: opportunities and challenges. Nature Reviews. Genetics. PMID 32235876 DOI: 10.1038/S41576-020-0223-2  0.704
2020 Weinreb C, Rodriguez-Fraticelli A, Camargo FD, Klein AM. Lineage tracing on transcriptional landscapes links state to fate during differentiation. Science (New York, N.Y.). PMID 31974159 DOI: 10.1126/Science.Aaw3381  0.806
2020 Sharma N, Flaherty K, Lezgiyeva K, Wagner DE, Klein AM, Ginty DD. The emergence of transcriptional identity in somatosensory neurons. Nature. PMID 31915380 DOI: 10.1038/S41586-019-1900-1  0.555
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. Nature Cell Biology. 21: 1102-1112. PMID 31481792 DOI: 10.1038/S41556-019-0378-2  0.516
2019 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 Reports. 28: 302-311.e5. PMID 31291568 DOI: 10.1016/J.Celrep.2019.06.031  0.466
2019 Klein AM, Treutlein B. Single cell analyses of development in the modern era. Development (Cambridge, England). 146. PMID 31249004 DOI: 10.1242/Dev.181396  0.496
2019 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. Nature Communications. 10: 2395. PMID 31160568 DOI: 10.1038/S41467-019-10291-0  0.534
2019 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, ... ... Klein AM, et al. Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species. Immunity. PMID 30979687 DOI: 10.1016/J.Immuni.2019.03.009  0.442
2019 Wolock SL, Lopez R, Klein AM. Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data. Cell Systems. PMID 30954476 DOI: 10.1016/J.Cels.2018.11.005  0.514
2019 Rodriguez-Fraticelli AE, Weinreb CS, Klein AM, Wang S, Camargo FD. Combined Single Cell Lineage and Transcriptome Sequencing Unveils Cell-Autonomous Regulators of Hematopoietic Stem Cell Fate Blood. 134: 446-446. DOI: 10.1182/Blood-2019-123447  0.804
2018 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. PMID 30472156 DOI: 10.1016/J.Stem.2018.10.015  0.485
2018 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. PMID 30269904 DOI: 10.1016/J.Stem.2018.08.017  0.363
2018 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. PMID 30269903 DOI: 10.1016/J.Stem.2018.09.005  0.536
2018 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. Science Immunology. 3. PMID 30217811 DOI: 10.1126/Sciimmunol.Aat5861  0.318
2018 Klein AM. Technique to measure the expression dynamics of each gene in a single cell. Nature. 560: 434-435. PMID 30127477 DOI: 10.1038/D41586-018-05882-8  0.424
2018 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. PMID 30069046 DOI: 10.1038/S41586-018-0394-6  0.733
2018 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. Nature Neuroscience. PMID 29752482 DOI: 10.1038/S41593-018-0112-6  0.384
2018 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. Nature Immunology. PMID 29725080 DOI: 10.1038/S41590-018-0104-4  0.354
2018 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 (New York, N.Y.). PMID 29700229 DOI: 10.1126/Science.Aar4362  0.815
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 (New York, N.Y.). PMID 29700227 DOI: 10.1126/Science.Aar5780  0.814
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. Nature Biotechnology. PMID 29608178 DOI: 10.1038/Nbt.4103  0.687
2018 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. PMID 29466336 DOI: 10.1038/Nature25741  0.793
2018 Weinreb C, Wolock S, Tusi BK, Socolovsky M, Klein AM. Fundamental limits on dynamic inference from single-cell snapshots. Proceedings of the National Academy of Sciences of the United States of America. PMID 29463712 DOI: 10.1073/Pnas.1714723115  0.778
2018 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. Nature Immunology. PMID 29434354 DOI: 10.1038/S41590-018-0051-0  0.451
2018 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. 553: 212-216. PMID 29323290 DOI: 10.1038/Nature25168  0.802
2018 Loperfido M, Pellin D, Baricordi C, Wolock SL, Klein AM, Biasco L. The Single-Cell Transcriptional Landscape of Human Hematopoietic Progenitors Blood. 132: 1266-1266. DOI: 10.1182/Blood-2018-99-116327  0.492
2018 Rodriguez-Fraticelli AE, Weinreb C, Klein AM, Camargo F. Transcriptional and Functional Description of Stem Cell Heterogeneity in Native and Transplantation Hematopoiesis Blood. 132: 3844-3844. DOI: 10.1182/Blood-2018-99-113646  0.753
2018 Krishnan I, Maroni G, Clohessy S, Savova V, Bassal M, Zilionis R, Csizmadia E, Kerwin CM, Choi S, Meyerovitz CV, Pandell N, Fhu CW, Zhang J, Basseres DS, Magli CM, ... ... Klein AM, et al. Abstract 5864: Novel anti-BMI-1 therapy in non-small cell lung cancer Cancer Research. 78: 5864-5864. DOI: 10.1158/1538-7445.Am2018-5864  0.33
2017 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. Nature Neuroscience. PMID 29230054 DOI: 10.1038/S41593-017-0029-5  0.419
2017 Weinreb C, Wolock S, Klein A. SPRING: a kinetic interface for visualizing high dimensional single-cell expression data. Bioinformatics (Oxford, England). PMID 29228172 DOI: 10.1093/Bioinformatics/Btx792  0.734
2017 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. Proceedings of the National Academy of Sciences of the United States of America. 114: E10838-E10847. PMID 29183978 DOI: 10.1073/Pnas.1709207114  0.677
2017 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. 6. PMID 28990928 DOI: 10.7554/Elife.26945  0.677
2017 Klein AM, Macosko E. InDrops and Drop-seq technologies for single-cell sequencing. Lab On a Chip. 17: 2540-2541. PMID 28721415 DOI: 10.1039/C7Lc90070H  0.371
2017 Wagner DE, Klein AM. Genetic screening enters the single-cell era. Nature Methods. 14: 237-238. PMID 28245215 DOI: 10.1038/Nmeth.4196  0.556
2017 Zilionis R, Nainys J, Veres A, Savova V, Zemmour D, Klein AM, Mazutis L. Single-cell barcoding and sequencing using droplet microfluidics. Nature Protocols. 12: 44-73. PMID 27929523 DOI: 10.1038/Nprot.2016.154  0.486
2017 Briggs JA, Li VC, Lee S, Woolf CJ, Klein A, Kirschner MW. Author response: Mouse embryonic stem cells can differentiate via multiple paths to the same state Elife. DOI: 10.7554/Elife.26945.028  0.72
2017 Rodriguez-Fraticelli A, Wolock S, Weinreb C, Sun J, Klein A, Camargo F. Clonal analysis of lineage fate in unperturbed hematopoiesis Experimental Hematology. 53. DOI: 10.1016/J.Exphem.2017.06.075  0.738
2017 Kawaguchi K, Klein AM. In Vitro Reconstitution of Tissue Homeostasis and Stochastic Cell Fate Choice Biophysical Journal. 112. DOI: 10.1016/J.Bpj.2016.11.2317  0.518
2016 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 Systems. PMID 27667365 DOI: 10.1016/J.Cels.2016.08.011  0.56
2016 Derr A, Yang C, Zilionis R, Sergushichev A, Blodgett DM, Redick S, Bortell R, Luban J, Harlan DM, Kadener S, Greiner DL, Klein A, Artyomov M, Garber M. End Sequence Analysis ToolKit (ESAT) expands the extractable from single cell RNA-seq experiments. Genome Research. PMID 27470110 DOI: 10.1101/Gr.207902.116  0.38
2016 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 (New York, N.Y.). PMID 27229141 DOI: 10.1126/Science.Aaf7012  0.581
2016 Weinreb C, Wolock S, Tusi BK, Socolovsky M, Klein AM. Population Balance Reconstruction of the Hematopoietic Differentiation Hierarchy Blood. 128: 3861-3861. DOI: 10.1182/Blood.V128.22.3861.3861  0.707
2016 Tusi BK, Wolock S, Weinreb C, Hwang Y, Hidalgo D, Klein AM, Socolovsky M. Reconstructing Early Erythroid Development In Vivo Using Single-Cell Transcriptomics Blood. 128: 1195-1195. DOI: 10.1182/Blood.V128.22.1195.1195  0.786
2015 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. Developmental Cell. 35: 383-94. PMID 26555057 DOI: 10.1016/J.Devcel.2015.10.010  0.734
2015 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. 161: 1187-201. PMID 26000487 DOI: 10.1016/J.Cell.2015.04.044  0.755
2014 Sun J, Ramos A, Chapman B, Johnnidis JB, Le L, Ho YJ, Klein A, Hofmann O, Camargo FD. Clonal dynamics of native haematopoiesis. Nature. 514: 322-7. PMID 25296256 DOI: 10.1038/Nature13824  0.482
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. 9: e101085. PMID 24991805 DOI: 10.1371/Journal.Pone.0101085  0.543
2013 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 (New York, N.Y.). 342: 1226-30. PMID 24311688 DOI: 10.1126/Science.1239730  0.554
2012 Hernández AR, Klein AM, Kirschner MW. Kinetic responses of β-catenin specify the sites of Wnt control. Science (New York, N.Y.). 338: 1337-40. PMID 23138978 DOI: 10.1126/Science.1228734  0.476
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 (New York, N.Y.). 337: 1091-3. PMID 22821983 DOI: 10.1126/Science.1218835  0.658
2011 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. Developmental Biology. 359: 26-36. PMID 21888903 DOI: 10.1016/J.Ydbio.2011.08.006  0.549
2011 Klein AM, Simons BD. Universal patterns of stem cell fate in cycling adult tissues. Development (Cambridge, England). 138: 3103-11. PMID 21750026 DOI: 10.1242/Dev.060103  0.697
2011 Waks Z, Klein AM, Silver PA. Cell-to-cell variability of alternative RNA splicing. Molecular Systems Biology. 7: 506. PMID 21734645 DOI: 10.1038/Msb.2011.32  0.456
2011 Klein AM, Nikolaidou-Neokosmidou V, Doupé DP, Jones PH, Simons BD. Patterning as a signature of human epidermal stem cell regulation. Journal of the Royal Society, Interface / the Royal Society. 8: 1815-24. PMID 21632613 DOI: 10.1098/Rsif.2011.0240  0.689
2010 Lopez-Garcia C, Klein AM, Simons BD, Winton DJ. Intestinal stem cell replacement follows a pattern of neutral drift. Science (New York, N.Y.). 330: 822-5. PMID 20929733 DOI: 10.1126/Science.1196236  0.7
2010 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. 143: 134-44. PMID 20887898 DOI: 10.1016/J.Cell.2010.09.016  0.716
2010 Salpeter SJ, Klein AM, Huangfu D, Grimsby J, Dor Y. Glucose and aging control the quiescence period that follows pancreatic beta cell replication. Development (Cambridge, England). 137: 3205-13. PMID 20823063 DOI: 10.1242/Jcs.080713  0.387
2010 Klein AM, Nakagawa T, Ichikawa R, Yoshida S, Simons BD. Mouse germ line stem cells undergo rapid and stochastic turnover. Cell Stem Cell. 7: 214-24. PMID 20682447 DOI: 10.1016/J.Stem.2010.05.017  0.704
2010 Doupé DP, Klein AM, Simons BD, Jones PH. The ordered architecture of murine ear epidermis is maintained by progenitor cells with random fate. Developmental Cell. 18: 317-23. PMID 20159601 DOI: 10.1016/J.Devcel.2009.12.016  0.71
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. Proceedings of the National Academy of Sciences of the United States of America. 107: 270-5. PMID 20018764 DOI: 10.1073/Pnas.0909738107  0.626
2009 Barbera M, Doupe DP, Klein AM, Simons BD, Jones PH, Fitzgerald RC. 250 Characterisation of Squamous Oesophageal Epithelium and Location of Epithelial Stem Cells Gastroenterology. 136: A-49. DOI: 10.1016/S0016-5085(09)60221-3  0.494
2008 Klein AM, Doupé DP, Jones PH, Simons BD. Mechanism of murine epidermal maintenance: cell division and the voter model. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 77: 031907. PMID 18517422 DOI: 10.1103/Physreve.77.031907  0.67
2007 Klein AM, Doupé DP, Jones PH, Simons BD. Kinetics of cell division in epidermal maintenance. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 76: 021910. PMID 17930068 DOI: 10.1103/Physreve.76.021910  0.654
2007 Clayton E, Doupé DP, Klein AM, Winton DJ, Simons BD, Jones PH. A single type of progenitor cell maintains normal epidermis. Nature. 446: 185-9. PMID 17330052 DOI: 10.1038/Nature05574  0.718
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