Publications

Single-cell and clonal analysis of AL amyloidosis plasma cells and their bone marrow microenvironment
Gort-Freitas NA, Moscvin M, Da Viá MC, Lazzaroni F, Nevone A, Sadigh S, Boullt S, Evans B, Chen T, Karagiannis TT, et al. (2025). Blood, 146(12): 1476-1492.

Immune cell type divergence in a basal chordate
Scully TD, Pickett CJ, Gort-Freitas NA, Davidson B, Klein AM (2025). bioRxiv.

Multi-stage single-cell atlas of Botryllus schlosseri asexual development unveils dedifferentiating bud founder cells
Lebel M, Sancerini T, Rabiteau S, Marchal S, Sharma P, Scully TD, Balissat E, Hiebert LS, De Tomaso AW, Klein AM, et al. (2025). bioRxiv.

Multi-step genomics on single cells and live cultures in sub-nanoliter capsules
Mazelis I, Sun H, Kulkarni A, Torre T, Klein AM (2025). bioRxiv.

Tissue fluidity: A double-edged sword for multicellular patterning
Garner RM, McGeary SE, Klein AM, Megason SG (2025). bioRxiv.

Linker minimization and characterization of Fc-fused interleukin-17A for increased in vivo half-life
Wu QC, Lee J, Swaminathan A, Winward A, Hwang Y, Socolovsky M, Way JC, Klein AM (2025). Protein Engineering, Design and Selection, 38, gzaf009.

A map of signaling responses in the human airway epithelium
McCauley KB, Kukreja K, Tovar Walker AE, Jaffe AB, Klein AM (2024). Cell Systems, 15(4): 307-321.e10.

Approximating mutual information of high-dimensional variables using learned representations
Gowri G, Lun X-K, Klein AM, Yin P (2024). Advances in Neural Information Processing Systems.

Cell state transitions are decoupled from cell division during early embryo development
Kukreja K, Jia BZ, McGeary SE, Patel N, Megason SG, Klein AM (2024). Nature Cell Biology, 26(12): 2035-2045.

IL-17A primes an early progenitor compartment to tune the erythropoietic feedback circuit
Wu QC, Swaminathan A, Winward A, Lalonde L, Hwang Y, Littman N, Socolovsky M, Klein AM (2024). bioRxiv.

scDiffEq: drift-diffusion modeling of single-cell dynamics with neural stochastic differential equations
Vinyard ME, Rasmussen AW, Li R, Klein AM, Getz G, Pinello L (2023). bioRxiv.

A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells
Li L, Bowling S, McGeary SE, Yu Q, Lemke B, Alcedo K, Jia Y, Liu X, Ferreira M, Klein AM, et al. (2023) Cell, 186(23): 5183-5199.e22.

CXCL9:SPP1 macrophage polarity identifies a network of cellular programs that control human cancers
Bill R, Wirapati P, Messemaker M, Roh W, Zitti B, Duval F, Kiss M, Park JC, Saal TM, Hoelzl J, et al. (2023). Science, 381(6657): 515-524.

The secreted neuronal signal Spock1 promotes blood-brain barrier development
O'Brown NM, Patel NB, Hartmann U, Klein AM, Gu C, Megason SG (2023). Developmental Cell, 58(17): 1534-1547.e6.

Global decoupling of cell differentiation from cell division in early embryo development
Kukreja K, Patel N, Megason SG, Klein AM (2023). bioRxiv.

A neutrophil response linked to tumor control in immunotherapy
Gungabeesoon J, Gort-Freitas NA, Kiss M, Bolli E, Messemaker M, Siwicki M, Hicham M, Bill R, Koch P, Cianciaruso C, et al. (2023). Cell, 186(7): 1448-1464.e20.

CoSpar identifies early cell fate biases from single-cell transcriptomic and lineage information
Wang S-W, Herriges MJ, Hurley K,  Kotton DN,  Klein AM (2022). Nature Biotechnology, 40: 1066-1074.

How can Waddington-like landscapes facilitate insights beyond developmental biology?
Shakiba N, Li C, Garcia-Ojalvo J, Cho KH, Patil K, Walczak A, Liu YY, Kuehn S, Nie Q, Klein A, et al. (2022). Cell Systems, 13(1): 4-9.

Triple-decker sandwich cultures of intestinal organoids for long-term live imaging, uniform perturbation, and statistical sampling
Cambra HM, Tallapragada NP, Mannam P, Breault DT, Klein AM (2022). Current Protocols, 2, e330.

Tumor-infiltrating dendritic cell states are conserved across solid human cancers
Gerhard GM, Bill R, Messemaker M, Klein AM, Pittet MJ (2021). Journal of Experimental Medicine, 218 (1), e20200264.

Macrophage-targeted therapy unlocks antitumoral cross-talk between IFNγ-secreting lymphocytes and IL12-producing dendritic cells
Pfirschke C, Zilionis R, Engblom C, Messemaker M, Zou AE, Rickelt S, Gort-Freitas NA, Lin Y, Bill R, Siwicki M, et al. (2021). Cancer Immunology Research, 10(1): 40-55.

Single cell biology—a Keystone Symposia report
Cable J, Elowitz MB, Domingos AI, Habib N, Itzkovitz S, Hamidzada H, Balzer MS, Yanai I, Liberali P, Whited J, et al. (2021). Annals of the New York Academy of Sciences, 1506(1): 74-97.

Resident Kupffer cells and neutrophils drive liver toxicity in cancer immunotherapy
Siwicki M, Gort-Freitas NA, Messemaker M, Bill R, Gungabeesoon J, Engblom C, Zilionis R, Garris C, Gerhard GM, Kohl A, et al. (2021). Science Immunology, 6, eabi7083.

Identification of a targetable KRAS-mutant epithelial population in non-small cell lung cancer
Maroni G, Bassal MA, Krishnan I, Fhu CW, Savova V, Zilionis R, Maymi VA, Pandell N, Csizmadia E, Zhang J, et al. (2021). Communications Biology, 4, 370.

Inflation-collapse dynamics drive patterning and morphogenesis in intestinal organoids
Tallapragada NP, Cambra HM, Wald T, Keough Jalbert S, Abraham DM, Klein OD, Klein AM (2021). Cell Stem Cell, 28(9): 1516-1532.e14.

Lineage reconstruction from clonal correlations
Weinreb C., Klein A.M. (2020). Proceedings of the National Academy of Sciences of the United States of America, 117(29): 17041-17048.

Lineage tracing meets single-cell omics: opportunities and challenges
Wagner DE, Klein AM (2020). Nature Reviews Genetics, 21: 410-427.

Lineage tracing on transcriptional landscapes links state to fate during differentiation
Weinreb C, Rodriguez-Fraticelli A, Camargo FD, Klein AM (2020). Science, 367, eaaw3381.

Single-cell lineage tracing unveils a role for TCF15 in haematopoiesis
Rodriguez-Fraticelli AE, Weinreb C, Wang S-W, Migueles RP, Jankovic M, Usart M, Klein AM, Lowell S, Camargo FD (2020). Nature, 583: 585-589.

Tumor-promoting Ly-6G+ SiglecFhigh cells are mature and long-lived neutrophils
Pfirschke C, Engblom C, Gungabeesoon J, Lin Y, Rickelt S, Zilionis R, Messemaker M, Siwicki M, Gerhard GM, Kohl A, et al. (2020). Cell Reports, 32(12), 108164.

Lineage commitment of hematopoietic stem cells and progenitors: insights from recent single cell and lineage tracing technologies
Loughran SJ, Haas S, Wilkinson AC, Klein AM, Brand M (2020). Experimental Hematology, 88: 1-6.


The emergence of transcriptional identity in somatosensory neurons
Sharma N, Flaherty K, Lezgiyeva K, Wagner DE, Klein AM, Ginty DD (2020). Nature, 577: 392-398

A comprehensive single cell transcriptional landscape of human hematopoietic progenitors
Pellin D, Loperfido M, Baricordi C, Wolock SL, Montepeloso A, Weinberg OK, Biffi A, Klein AM, Biasco L (2019). Nature Communications, 10, 2395.

A large pool of actively cycling progenitors orchestrates self-renewal and injury repair of an ectodermal appendage
Sharir A, Marangoni P, Zilionis R, Wan M, Wald T, Hu JK, Kawaguchi K, Castillo-Azofeifa D, Epstein L, Harrington K, et al. (2019). Nature Cell Biology, 21: 1102-1112. 

Mapping distinct bone marrow niche populations and their differentiation paths
Wolock SL, Krishnan I, Tenen DE, Matkins V, Camacho V, Patel S, Agarwal P, Bhatia R, Tenen DG, Klein AM, et al. (2019). Cell Reports, 28(2): 302-311.e5.

Single cell analyses of development in the modern era
Klein AM, Treutlein B (2019). Development, 146(12), dev181396.

Scrublet: Computational identification of cell doublets in single-cell transcriptomic data
Wolock SL, Lopez R, Klein AM (2019). Cell Systems, 8(4): 281-291.e9.

Single-cell transcriptomics of human and mouse lung cancers reveals conserved myeloid populations across individuals and species
Zilionis R, Engblom C, Pfirschke C, Savova V, Zemmour D, Saatcioglu HD, Krishnan I, Maroni G, Meyerovitz CV, Kerwin CM, et al. (2019). Immunity, 50(5): 1317-1334.e10

Emergence of the erythroid lineage from multipotent hematopoiesis
Khoramian Tusi B, Wolock SL, Weinreb C, Hwang Y, Hidalgo D, Zilionis R, Waisman A, Huh J, Klein AM, Socolovsky M. (2018). bioRxiv. 

Fundamental limits on dynamic inference from single-cell snapshots
Weinreb C, Wolock S, Tusi BK, Socolovsky M, Klein AM (2018). Proceedings of the National Academy of Sciences of the United States of America, 115(10): E2467-E2476.

Molecular diversification of regulatory T cells in nonlymphoid tissues
DiSpirito JR, Zemmour D, Ramanan D, Cho J, Zilionis R, Klein AM, Benoist C, Mathis D (2018). Science Immunology, 3, eaat5861.

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain
Raj B, Wagner DE, McKenna A, Pandey S, Klein AM, Shendure J, Gagnon JA, Schier AF (2018). Nature Biotechnology, 36: 442-450.

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo
Wagner DE, Weinreb C, Collins ZM, Briggs JA, Megason SG, Klein AM (2018). Science, 360(6392): 981-987.

The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution
Briggs JA, Weinreb C, Wagner DE, Megason S, Peshkin L, Kirschner MW, Klein AM (2018). Science, 360(6392), eaar5780.

Quantitative clonal analysis and single-cell transcriptomics reveal division kinetics, hierarchy, and fate of oral epithelial progenitor cells
Jones KB, Furukawa S, Marangoni P, Ma H, Pinkard H, D'Urso R, Zilionis R, Klein AM, Klein OD (2018). Cell Stem Cell, 24(1): 183-192.e8.

Epidermal tissue adapts to restrain progenitors carrying clonal p53 mutations
Murai K, Skrupskelyte G, Piedrafita G, Hall M, Kostiou V, Ong SH, Nagy T, Cagan A, Goulding D, Klein AM, et al. (2018). Cell Stem Cell, 23(5): 687-699.e8.

Homeostatic epidermal stem cell self-renewal is driven by local differentiation
Mesa KR, Kawaguchi K, Cockburn K, Gonzalez D, Boucher J, Xin T, Klein AM, Greco V (2018). Cell Stem Cell, 23(5): 677- 686.e4.

A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte
Plasschaert LW, Žilionis R, Choo-Wing R, Savova V, Knehr J, Roma G, Klein AM, Jaffe AB (2018). Nature, 560: 377-381.

Publisher Correction: Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex
Hrvatin S, Hochbaum DR, Nagy MA, Cicconet M, Robertson K, Cheadle L, Zilionis R, Ratner A, Borges-Monroy R, Klein AM, et al. (2018). Nature Neuroscience, 21, 1017.

Publisher Correction: Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR
Zemmour D, Zilionis R, Kiner E, Klein AM, Mathis D, Benoist C (2018). Nature Immunology, 19, 645.

SPRING: a kinetic interface for visualizing high dimensional single-cell expression data
Weinreb C, Wolock S, Klein AM (2018). Bioinformatics, 34(7): 1246-1248.

Population snapshots predict early haematopoietic and erythroid hierarchies
Tusi BK, Wolock SL, Weinreb C, Hwang Y, Hidalgo D, Zilionis R, Waisman A, Huh JR, Klein AM, Socolovsky M (2018). Nature, 555: 54-60.

Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR
Zemmour D, Zilionis R, Kiner E, Klein AM, Mathis D, Benoist C (2018). Nature Immunology, 9: 291-301.

Clonal analysis of lineage fate in native haematopoiesis
Rodriguez-Fraticelli AE, Wolock SL, Weinreb CS, Panero R, Patel SH, Jankovic M, Sun J, Calogero RA, Klein AM, Camargo FD (2018). Nature, 553: 212-216.

Genetic screening enters the single-cell era
Wagner DE, Klein AM (2017). Nature Methods, 14: 237-238.

Osteoblasts remotely supply lung tumors with cancer-promoting SiglecFhigh neutrophils
Engblom C, Pfirschke C, Zilionis R, Da Silva Martins J, Bos SA, Courties G, Rickelt S, Severe N, Baryawno N, Baryawno N, et al. (2017). Science, 358, eaal5081.

Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex
Hrvatin S, Hochbaum DR, Nagy MA, Cicconet M, Robertson K, Cheadle L, Zilionis R, Ratner A, Borges-Monroy R, Klein AM, et al. (2017). Nature Neuroscience, 21: 120-129.

Proteomics of phosphorylation and protein dynamics during fertilization and meiotic exit in the Xenopus egg
Presler M, Van Itallie E, Klein AM, Kunz R, Coughlin ML, Peshkin L, Gygi SP, Wühr M, Kirschner MW (2017). Proceedings of the National Academy of Sciences of the United States of America, 114(50): E10838-E10847.

Mouse embryonic stem cells can differentiate via multiple paths to the same state
Briggs JA, Li VC, Lee S, Woolf CJ, Klein A, Kirschner MW (2017). eLife, 6, e26945.

InDrops and Drop-seq technologies for single-cell sequencing
Klein AM, Macosko E (2017). Lab on a Chip, 17: 2540-2541.

Epidermal stem cells self-renew upon neighboring differentiation
Mesa KR, Kawaguchi K, Gonzalez DG, Cockburn K, Boucher J, Xin T, Klein AM, Greco V (2017). bioRxiv.

Single-cell barcoding and sequencing using droplet microfluidics
Zilionis R, Nainys J, Veres A, Savova V, Zemmour D, Klein AM, Mazutis L (2016). Nature Protocols, 12: 44-73.

A single-cell transcriptomic map of the human and mouse pancreas reveals inter- and intra-cell population structure
Baron M, Veres A, Wolock SL, Faust AL, Gaujoux R, Vetere A, Ryu JH, Wagner BK, Shen-Orr SS, Klein AM, et al. (2016). Cell Systems, 3(4): 346-360.e4.

End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data
Derr A, Yang C, Zilionis R, Sergushichev A, Blodgett DM, Redick S, Bortell R, Luban J, Harlan DM, Kadener S, et al. (2016). Genome Research, 26: 1397-1410.

Spatiotemporal coordination of stem cell commitment during epidermal homeostasis
Rompolas P, Mesa KR, Kawaguchi K, Park S, Gonzalez D, Brown S, Boucher J, Klein AM, Greco V (2016). Science, 352: 1471-1474.

On the relationship of protein and mRNA dynamics in vertebrate embryonic development
Peshkin L, Wühr M, Pearl E, Haas W, Freeman RM, Gerhart JC, Klein AM, Horb M, Gygi SP, Kirschner MW (2015). Developmental Cell, 35(3): 383-394.

Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells
Klein AM, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, Peshkin L, Weitz DA, Kirschner MW (2015). Cell, 161(5): 1187-1201.

Clonal dynamics of native haematopoiesis
Sun J, Ramos A, Chapman B, Johnnidis JB, Le L, Ho YJ, Klein A, Hofmann O, Camargo FD (2014). Nature, 514: 322-327.

Basolateral junction proteins regulate competition for the follicle stem cell niche in the Drosophila ovary
Kronen MR, Schoenfelder KP, Klein AM, Nystul TG (2014). PLoS ONE, 9(7), e101085.

Interfollicular epidermal stem cells self-renew via autocrine Wnt signaling
Lim X, Tan SH, Koh WL, Chau RM, Yan KS, Kuo CJ, van Amerongen R, Klein AM, Nusse R (2013). Science, 342: 1226-1230.

Kinetic responses of β-catenin specify the sites of Wnt control
Hernández AR, Klein AM, Kirschner MW (2012). Science, 338: 1337-1340.

A single progenitor population switches behavior to maintain and repair esophageal epithelium
Doupé DP, Alcolea MP, Roshan A, Zhang G, Klein AM, Simons BD, Jones PH (2012). Science, 337: 1091-1093.

The critical discussion group: fostering personal and scientific growth
Klein AM, Lande-Diner L (2011). Molecular Cell, 44(2): 167-169.

Ngn3(+) endocrine progenitor cells control the fate and morphogenesis of pancreatic ductal epithelium
Magenheim J, Klein AM, Stanger BZ, Ashery-Padan R, Sosa-Pineda B, Gu G, Dor Y (2011). Developmental Biology, 359(1): 26-36.

Universal patterns of stem cell fate in cycling adult tissues
Klein AM, Simons BD (2011). Development, 138(15): 3103–3111.

Cell-to-cell variability of alternative RNA splicing
Waks Z, Klein AM, Silver PA (2011). Molecular Systems Biology, 7, 506.

Patterning as a signature of human epidermal stem cell regulation
Klein AM, Nikolaidou-Neokosmidou V, Doupé DP, Jones PH, Simons BD (2011). Journal of the Royal Society, Interface, 8: 1815-1824.

Glucose and aging control the quiescence period that follows pancreatic beta cell replication
Salpeter SJ, Klein AM, Huangfu D, Grimsby J, Dor Y (2010). Development, 137(19): 3205-3213.

Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells
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. (2010). Cell, 143(1): 134-144.

Intestinal stem cell replacement follows a pattern of neutral drift
Lopez-Garcia C, Klein AM, Simons BD, Winton DJ (2010). Science, 330: 822-825.

Mouse germ line stem cells undergo rapid and stochastic turnover
Klein AM, Nakagawa T, Ichikawa R, Yoshida S, Simons BD (2010). Cell Stem Cell, 7(2): 214-224.

The ordered architecture of murine ear epidermis is maintained by progenitor cells with random fate
Doupé DP, Klein AM, Simons BD, Jones PH (2010). Developmental Cell, 18(2): 317-323.

Stochastic fate of p53-mutant epidermal progenitor cells is tilted toward proliferation by UV B during preneoplasia
Klein AM, Brash DE, Jones PH, Simons BD (2009). Proceedings of the National Academy of Sciences of the United States of America, 107(1): 270-275.

Mechanism of murine epidermal maintenance: cell division and the voter model
Klein AM, Doupé DP, Jones PH, Simons BD (2008). Physical Review E, Statistical, Nonlinear, and Soft Matter Physics, 77, 031907.

Kinetics of cell division in epidermal maintenance
Klein AM, Doupé DP, Jones PH, Simons BD (2007). Physical Review E, Statistical, Nonlinear, and Soft Matter Physics, 76, 021910.

A single type of progenitor cell maintains normal epidermis
Clayton E, Doupé DP, Klein AM, Winton DJ, Simons BD, Jones PH (2007). Nature, 446: 185-189. 

 
See publications on ORCID