Geometry of the Gene Expression Space of Individual Cells

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625 · see citing works

Density Estimation for Statistics and Data Analysis

Silverman, B. W. (2018) · Routledge eBooks · doi:10.1201/9781315140919 · Cited by 15,938 · see citing works

Individual Comparisons by Ranking Methods

Wilcoxon, F. (1945) · Biometrics Bulletin · doi:10.2307/3001968 · Cited by 15,354 · see citing works

Dendritic cells and the control of immunity

Banchereau, J., & Steinman, R. M. (1998) · Nature · doi:10.1038/32588 · Cited by 14,244 · see citing works

LIII. On lines and planes of closest fit to systems of points in space

Karl Pearson, F. R. S. (1901) · The London Edinburgh and Dublin Philosophical Magazine and Journal of Science · doi:10.1080/14786440109462720 · Cited by 13,658 · see citing works

Data clustering

Jain, A. K., Murty, M. N., & Flynn, P. J. (1999) · ACM Computing Surveys · doi:10.1145/331499.331504 · Cited by 13,532 · see citing works

Cluster analysis and display of genome-wide expression patterns

Eisen, M. B., Spellman, P. T., Brown, P. O., & Botstein, D. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.25.14863 · Cited by 12,617 · see citing works

Density Estimation for Statistics and Data Analysis

(1986) · Springer eBooks · doi:10.1007/978-1-4899-3324-9 · Cited by 8,478 · see citing works

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

Trapnell, C., Cacchiarelli, D., Grimsby, J., Pokharel, P., Li, S., Morse, M., Lennon, N. J., Livak, K. J., Mikkelsen, T. S., & Rinn, J. L. (2014) · Nature Biotechnology · doi:10.1038/nbt.2859 · Cited by 7,314 · see citing works

Immunobiology of Dendritic Cells

Banchereau, J., Brière, F., Caux, C., Davoust, J. M., Lebecque, S., Liu, Y., Pulendran, B., & Palucka, K. (2000) · Annual Review of Immunology · doi:10.1146/annurev.immunol.18.1.767 · Cited by 6,612 · see citing works

Identification of stem cells in small intestine and colon by marker gene Lgr5

Barker, N., van Es, J. H., Kuipers, J., Kujala, P., van den Born, M., Cozijnsen, M., Haegebarth, A., Korving, J., Begthel, H., Peters, P. J., et al. (2007) · Nature · doi:10.1038/nature06196 · Cited by 5,687 · see citing works

The Ants

Hölldobler, B., & Wilson, E. O. (1990) · Springer eBooks · doi:10.1007/978-3-662-10306-7 · Cited by 5,531 · see citing works

Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays

Alon, U. S., Barkai, N., Notterman, D. A., Gish, K., Ybarra, S. E., Mack, D. H., & Levine, A. J. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.12.6745 · Cited by 4,170 · see citing works

mRNA-Seq whole-transcriptome analysis of a single cell

Tang, F., Barbacioru, C., Wang, Y., Nordman, E., Lee, C., Xu, N., Wang, X., Bodeau, J., Tuch, B. B., Siddiqui, A., et al. (2009) · Nature Methods · doi:10.1038/nmeth.1315 · Cited by 3,969 · see citing works

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

Zeisel, A., Muñoz-Manchado, A. B., Codeluppi, S., Lönnerberg, P., La Manno, G., Juréus, A., Marques, S., Munguba, H., He, L., Betsholtz, C., et al. (2015) · Science · doi:10.1126/science.aaa1934 · Cited by 3,124 · see citing works

Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation

Tamayo, P., Slonim, D. K., Mesirov, J. P., Zhu, Q., Kitareewan, S., Dmitrovsky, E., Lander, E. S., & Golub, T. R. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.6.2907 · Cited by 2,924 · see citing works

Modelling spatial patterns.

Ripley, B. D. (1977) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1977.tb01615.x · Cited by 2,511 · see citing works

Renal and Extrarenal Effects of Gum Arabic (Acacia Senegal) - What Can be Learned from Animal Experiments?

Nasir, O. (2013) · Kidney & Blood Pressure Research · doi:10.1159/000350152 · Cited by 2,331 · see citing works

The dendritic cell lineage: ontogeny and function of dendritic cells and their subsets in the steady state and the inflamed setting

Merad, M., Sathe, P., Helft, J., Miller, J., & Mortha, A. (2013) · Annual Review of Immunology · doi:10.1146/annurev-immunol-020711-074950 · Cited by 2,309 · see citing works

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

Bendall, S. C., Simonds, E. F., Qiu, P., Amir, E.-A. D., Krutzik, P. O., Finck, R., Bruggner, R. V., Melamed, R., Trejo, A., Ornatsky, O. I., et al. (2011) · Science · doi:10.1126/science.1198704 · Cited by 2,279 · see citing works

Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing

Usoskin, D., Furlan, A., Islam, S., Abdo, H., Lönnerberg, P., Lou, D., Hjerling-Leffler, J., Haeggström, J., Kharchenko, O., Kharchenko, P. V., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.3881 · Cited by 2,136 · see citing works

Caste and ecology in the social insects

Brian, M. V. (1979) · Animal Behaviour · doi:10.1016/0003-3472(79)90042-3 · Cited by 1,888 · see citing works

Stem cells, self-renewal, and differentiation in the intestinal epithelium.

van der Flier, L. G., & Clevers, H. (2009) · Annual Review of Physiology · doi:10.1146/annurev.physiol.010908.163145 · Cited by 1,859 · see citing works

Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types

Jaitin, D. A., Kenigsberg, E., Keren-Shaul, H., Elefant, N., Paul, F., Zaretsky, I., Mildner, A., Cohen, N., Jung, S., Tanay, A., et al. (2014) · Science · doi:10.1126/science.1247651 · Cited by 1,795 · see citing works

Wnt/β-Catenin/Tcf Signaling Induces the Transcription of Axin2, a Negative Regulator of the Signaling Pathway

Jho, E., Zhang, T., Domon–Dell, C., Joo, C., Freund, J., & Costantini, F. D. (2002) · Molecular and Cellular Biology · doi:10.1128/mcb.22.4.1172-1183.2002 · Cited by 1,683 · see citing works

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

Ramsköld, D., Luo, S., Wang, Y.-C., Li, R., Deng, Q., Faridani, O. R., Daniels, G. A., Khrebtukova, I., Loring, J. F., Laurent, L. C., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2282 · Cited by 1,609 · see citing works

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

Amir, E.-A. D., Davis, K. L., Tadmor, M. D., Simonds, E. F., Levine, J. H., Bendall, S. C., Shenfeld, D. K., Krishnaswamy, S., Nolan, G. P., & Pe'er, D. (2013) · Nature Biotechnology · doi:10.1038/nbt.2594 · Cited by 1,550 · see citing works

Human UDP-Glucuronosyltransferases: Metabolism, Expression, and Disease

Tukey, R. H., & Strassburg, C. P. (2000) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev.pharmtox.40.1.581 · Cited by 1,525 · see citing works

The intestinal crypt, a prototype stem cell compartment

Clevers, H. (2013) · Cell · doi:10.1016/j.cell.2013.07.004 · Cited by 1,223 · see citing works

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

Shalek, A. K., Satija, R., Adiconis, X., Gertner, R. S., Gaublomme, J. T., Raychowdhury, R., Schwartz, S., Yosef, N., Malboeuf, C., Lu, D., et al. (2013) · Nature · doi:10.1038/nature12172 · Cited by 1,190 · see citing works

Gene Regulation at the Single-Cell Level

Rosenfeld, N., Young, J. W., Alon, U., Swain, P. S., & Elowitz, M. B. (2005) · Science · doi:10.1126/science.1106914 · Cited by 1,104 · see citing works

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

Shalek, A. K., Satija, R., Shuga, J., Trombetta, J. J., Gennert, D., Lu, D., Chen, P., Gertner, R. S., Gaublomme, J. T., Yosef, N., et al. (2014) · Nature · doi:10.1038/nature13437 · Cited by 1,000 · see citing works

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

Islam, S., Kjällquist, U., Moliner, A., Zajac, P., Fan, J.-B., Lönnerberg, P., & Linnarsson, S. (2011) · Genome Research · doi:10.1101/gr.110882.110 · Cited by 949 · see citing works

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

Bendall, S. C., Davis, K. L., Amir, E.-A. D., Tadmor, M. D., Simonds, E. F., Chen, T. J., Shenfeld, D. K., Nolan, G. P., & Pe’er, D. (2014) · Cell · doi:10.1016/j.cell.2014.04.005 · Cited by 906 · see citing works

Repair and Regeneration of the Respiratory System: Complexity, Plasticity, and Mechanisms of Lung Stem Cell Function

Hogan, B. L. M., Barkauskas, C. E., Chapman, H. A., Epstein, J. A., Jain, R., Hsia, C. C. W., Niklason, L., Calle, E., Le, A., Randell, S. H., et al. (2014) · Cell Stem Cell · doi:10.1016/j.stem.2014.07.012 · Cited by 876 · see citing works

Development and Function of Dendritic Cell Subsets

Mildner, A., & Jung, S. (2014) · Immunity · doi:10.1016/j.immuni.2014.04.016 · Cited by 762 · see citing works

The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent ‘+4’ cell markers

Muñoz, J., Stange, D. E., Schepers, A. G., van de Wetering, M., Koo, B., Itzkovitz, S., Volckmann, R., Kung, K. S., Köster, J., Radulescu, S., et al. (2012) · The EMBO Journal · doi:10.1038/emboj.2012.166 · Cited by 758 · see citing works

Transcription Factor Achaete Scute-Like 2 Controls Intestinal Stem Cell Fate

van der Flier, L. G., van Gijn, M. E., Hatzis, P., Kujala, P., Haegebarth, A., Stange, D. E., Begthel, H., van den Born, M., Guryev, V., Oving, I. M., et al. (2009) · Cell · doi:10.1016/j.cell.2009.01.031 · Cited by 718 · see citing works

Single-cell dissection of transcriptional heterogeneity in human colon tumors

Dalerba, P. D., Tomer Kalisky, C., Sahoo, D., Rajendran, P. S., Rothenberg, M. E., Leyrat, A. A., Sim, S., Okamoto, J., Johnston, D. M., Qian, D., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.2038 · Cited by 693 · see citing works

Evolutionary Trade-Offs, Pareto Optimality, and the Geometry of Phenotype Space

Shoval, O., Sheftel, H., Shinar, G., Hart, Y., Ramote, O., Mayo, A., Dekel, E., Kavanagh, K., & Alon, U. (2012) · Science · doi:10.1126/science.1217405 · Cited by 647 · see citing works

Nodal is a novel TGF-β-like gene expressed in the mouse node during gastrulation

Zhou, X., Sasaki, H., Lowe, L. A., Hogan, B. L. M., & Kuehn, M. R. (1993) · Nature · doi:10.1038/361543a0 · Cited by 615 · see citing works

Metabolic zonation of the liver: Regulation and implications for liver function

Gebhardt, R. (1992) · Pharmacology & Therapeutics · doi:10.1016/0163-7258(92)90055-5 · Cited by 607 · see citing works

Gene expression patterns of human colon tops and basal crypts and BMP antagonists as intestinal stem cell niche factors

Kosinski, C., Li, V. S. W., Chan, A. S. Y., Zhang, J., Ho, C., Tsui, W. Y., Chan, T. L., Mifflin, R. C., Powell, D. W., Yuen, S. T., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0707210104 · Cited by 596 · see citing works

Plasticity of epithelial stem cells in tissue regeneration

Blanpain, C., & Fuchs, E. (2014) · Science · doi:10.1126/science.1242281 · Cited by 589 · see citing works

Critical assessment of automated flow cytometry data analysis techniques

Aghaeepour, N., Finak, G., Hoos, H. H., Mosmann, T. R., Brinkman, R. R., Gottardo, R., & Scheuermann, R. H. (2013) · Nature Methods · doi:10.1038/nmeth.2365 · Cited by 589 · see citing works

Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes

Newell, E. W., Sigal, N., Bendall, S. C., Nolan, G. P., & Davis, M. M. (2012) · Immunity · doi:10.1016/j.immuni.2012.01.002 · Cited by 555 · see citing works

Caste and ecology in the social insects.

OSTER, G. F., & Wilson, E. O. (1978) · PubMed · Cited by 510 · see citing works

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

Amit, I., Garber, M., Chevrier, N., Leite, A. P., Donner, Y., Eisenhaure, T., Guttman, M., Grenier, J. K., Li, W., Zuk, O., et al. (2009) · Science · doi:10.1126/science.1179050 · Cited by 488 · see citing works

Intestinal crypt homeostasis revealed at single-stem-cell level by in vivo live imaging

Ritsma, L., Ellenbroek, S. I. J., Zomer, A., Snippert, H. J. G., de Sauvage, F. J., Simons, B. D., Clevers, H. C., & van Rheenen, J. (2014) · Nature · doi:10.1038/nature12972 · Cited by 481 · see citing works

Transmembrane proteins of tight junctions

Chiba, H., Osanai, M., Murata, M., Kojima, T., & Sawada, N. (2008) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2007.08.017 · Cited by 464 · see citing works

Archetypal Analysis

Cutler, A., & Breiman, L. (1994) · Technometrics · doi:10.1080/00401706.1994.10485840 · Cited by 447 · see citing works

Cdkn1a deletion improves stem cell function and lifespan of mice with dysfunctional telomeres without accelerating cancer formation

Choudhury, A. R., Ju, Z., Djojosubroto, M. W., Schienke, A., Lechel, A., Schaetzlein, S., Jiang, H., Stepczynska, A., Wang, C., Buer, J., et al. (2007) · Nature Genetics · doi:10.1038/ng1937 · Cited by 426 · cited 1× · see citing works

Mutations of the Down–regulated in adenoma (DRA) gene cause congenital chloride diarrhoea

Höglund, P., Haila, S., Socha, J., Tomaszewski, L., Saarialho‐Kere, U., Karjalainen‐Lindsberg, M., Airola, K., Holmberg, C., de la Chapelle, A., & Kere, J. (1996) · Nature Genetics · doi:10.1038/ng1196-316 · Cited by 426 · see citing works

The Genetic Program of Hematopoietic Stem Cells

Phillips, R. L., Ernst, R., Brunk, B. P., Ivanova, N. B., Mahan, M. A., Deanehan, J. K., Moore, K. A., Overton, G. C., & Lemischka, I. R. (2000) · Science · doi:10.1126/science.288.5471.1635 · Cited by 411 · see citing works

Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments

McDavid, A., Finak, G., Chattopadyay, P. K., Dominguez, M., Lamoreaux, L., Ma, S. S., Roederer, M., & Gottardo, R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts714 · Cited by 395 · see citing works

Loss-of-function mutations in the EGF-CFC gene CFC1 are associated with human left-right laterality defects

Bamford, R. N., Roessler, E., Burdine, R. D., Şaplakoǧlu, U., Cruz-Racelis, J. D., Splitt, M. P., Towbin, J. A., Bowers, P. N., Marino, B., Schier, A. F., et al. (2000) · Nature Genetics · doi:10.1038/81695 · Cited by 348 · see citing works

Universal patterns of stem cell fate in cycling adult tissues

Klein, A. M., & Simons, B. D. (2011) · Development · doi:10.1242/dev.060103 · Cited by 329 · see citing works

CD14 regulates the dendritic cell life cycle after LPS exposure through NFAT activation

Zanoni, I., Ostuni, R., Capuano, G., Collini, M., Caccia, M., Ronchi, A. E., Rocchetti, M., Mingozzi, F., Foti, M., Chirico, G. G., et al. (2009) · Nature · doi:10.1038/nature08118 · Cited by 319 · see citing works

The promise of single-cell sequencing

Eberwine, J. H., Sul, J., Bartfai, T., & Kim, J. (2013) · Nature Methods · doi:10.1038/nmeth.2769 · Cited by 305 · see citing works

Identification of a cKit(+) colonic crypt base secretory cell that supports Lgr5(+) stem cells in mice

Rothenberg, M. E., Nusse, Y., Kalisky, T., Lee, J. J., Dalerba, P., Scheeren, F., Lobo, N., Kulkarni, S., Sim, S., Qian, D., et al. (2012) · Gastroenterology · doi:10.1053/j.gastro.2012.02.006 · Cited by 263 · see citing works

The Ets-Domain Transcription Factor Spdef Promotes Maturation of Goblet and Paneth Cells in the Intestinal Epithelium

Gregorieff, A., Stange, D. E., Kujala, P., Begthel, H., van den Born, M., Korving, J., Peters, P. J., & Clevers, H. C. (2009) · Gastroenterology · doi:10.1053/j.gastro.2009.06.044 · Cited by 263 · see citing works

Dynamics extracted from fixed cells reveal feedback linking cell growth to cell cycle

Kafri, R., Levy, J., Ginzberg, M. B., Oh, S., Lahav, G., & Kirschner, M. W. (2013) · Nature · doi:10.1038/nature11897 · Cited by 232 · see citing works

Archetypal analysis for machine learning and data mining

Mørup, M., & Hansen, L. K. (2011) · Neurocomputing · doi:10.1016/j.neucom.2011.06.033 · Cited by 228 · see citing works

SAM pointed domain ETS factor (SPDEF) regulates terminal differentiation and maturation of intestinal goblet cells

Noah, T. K., Kazanjian, A. A., Whitsett, J. A., & Shroyer, N. F. (2009) · Experimental Cell Research · doi:10.1016/j.yexcr.2009.09.020 · Cited by 203 · see citing works

Identification and functional characterization of NODAL rare variants in heterotaxy and isolated cardiovascular malformations

Mohapatra, B., Casey, B. M., Li, H., Ho-Dawson, T., Smith, L., Fernbach, S. D., Molinari, L., Niesh, S. R., Jefferies, J. L., Craigen, W. J., et al. (2008) · Human Molecular Genetics · doi:10.1093/hmg/ddn411 · Cited by 175 · see citing works

Theories of Optimization, Form and Function in Branching Architecture in Plants

Farnsworth, K. D., & Niklas, K. J. (1995) · Functional Ecology · doi:10.2307/2389997 · Cited by 175 · see citing works

Inferring biological tasks using Pareto analysis of high-dimensional data

Hart, Y., Sheftel, H., Hausser, J., Székely, P., Moshe, N. B. B., Kohanim, Y. K., Tendler, A., Mayo, A., & Alon, U. S. (2015) · Nature Methods · doi:10.1038/nmeth.3254 · Cited by 174 · see citing works

Single-Cell Transcriptome Analysis Reveals Dynamic Changes in lncRNA Expression during Reprogramming

Kim, D. H., Marinov, G. K., Pepke, S., Singer, Z. S., He, P., Williams, B. A., Schroth, G. P., Elowitz, M. B., & Wold, B. J. (2015) · Cell stem cell · doi:10.1016/j.stem.2014.11.005 · Cited by 163 · see citing works

Microfluidic single-cell real-time PCR for comparative analysis of gene expression patterns

Sánchez-Freire, V., Ebert, A., Tomer Kalisky, C., Quake, S. R., & Wu, J. C. (2012) · Nature Protocols · doi:10.1038/nprot.2012.021 · Cited by 162 · see citing works

A Continuum of Cell States Spans Pluripotency and Lineage Commitment in Human Embryonic Stem Cells

Hough, S. R., Laslett, A. L., Grimmond, S. M., Kolle, G., & Pera, M. F. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007708 · Cited by 159 · see citing works

c-Myc Is Required for the Formation of Intestinal Crypts but Dispensable for Homeostasis of the Adult Intestinal Epithelium

Bettess, M. D., Dubois, N. C., Murphy, M., Dubey, C., Roger, C., Robine, S., & Trumpp, A. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.17.7868-7878.2005 · Cited by 149 · see citing works

Stem cell self-renewal in intestinal crypt

Simons, B. D., & Clevers, H. C. (2011) · Experimental Cell Research · doi:10.1016/j.yexcr.2011.07.010 · Cited by 143 · see citing works

Establishment of a Normal Hematopoietic and Leukemia Stem Cell HierarchyPreprint

Chao, M. P., Seita, J., & Weissman, I. L. (2008) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2008.73.031 · Cited by 135 · see citing works

Upon dendritic cell (DC) activation chemokines and chemokine receptor expression are rapidly regulated for recruitment and maintenance of DC at the inflammatory site

Foti, M., Granucci, F., Aggujaro, D., Liboi, E., Luini, W., Minardi, S. P., Mantovani, A., Sozzani, S., & Ricciardi‐Castagnoli, P. (1999) · International Immunology · doi:10.1093/intimm/11.6.979 · Cited by 126 · see citing works

Developmental bias in the evolution of phalanges

Kavanagh, K. D., Shoval, O., Winslow, B., Alon, U., Leary, B. P., Kan, A., & Tabin, C. J. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1315213110 · Cited by 125 · see citing works

Dendritic Cell Apoptosis: Regulation of Tolerance versus Immunity

Kushwah, R., & Hu, J. (2010) · Journal of Immunology · doi:10.4049/jimmunol.1000325 · Cited by 116 · see citing works

Robust Cre-Mediated Recombination in Small Intestinal Stem Cells Utilizing the Olfm4 Locus

Schuijers, J., van der Flier, L. G., van Es, J. H., & Clevers, H. C. (2014) · Stem Cell Reports · doi:10.1016/j.stemcr.2014.05.018 · Cited by 115 · see citing works

Tmem176B and Tmem176A are associated with the immature state of dendritic cells

Condamine, T., Texier, L. L., Howie, D., Lavault, A., Hill, M., Halary, F., Cobbold, S. P., Waldmann, H., Cuturi, M. C., & Chiffoleau, E. (2010) · Journal of Leukocyte Biology · doi:10.1189/jlb.1109738 · Cited by 102 · see citing works

Dissecting genomic diversity, one cell at a time

Blainey, P. C., & Quake, S. R. (2013) · Nature Methods · doi:10.1038/nmeth.2783 · Cited by 102 · see citing works

Differential expression of Aquaporin 8 in human colonic epithelial cells and colorectal tumors

Fischer, H., Stenling, R., Rubio‐Terres, C., & Lindblom, A. (2001) · BMC Physiology · doi:10.1186/1472-6793-1-1 · Cited by 100 · see citing works

Mapping Differentiation under Mixed Culture Conditions Reveals a Tunable Continuum of T Cell Fates

Antebi, Y. E., Reich-Zeliger, S., Hart, Y., Mayo, A., Eizenberg, I., Rimer, J., Putheti, P., Pe'er, D., & Friedman, N. (2013) · PLoS Biology · doi:10.1371/journal.pbio.1001616 · Cited by 100 · see citing works

The Geometry of Locomotive Behavioral States in C. elegans

Gallagher, T., Bjorness, T., Greene, R., You, Y.-J., & Avery, L. (2013) · PLoS ONE · doi:10.1371/journal.pone.0059865 · Cited by 85 · see citing works

The geometry of the <scp>P</scp> areto front in biological phenotype space

Sheftel, H., Shoval, O., Mayo, A., & Alon, U. (2013) · Ecology and Evolution · doi:10.1002/ece3.528 · Cited by 79 · see citing works

MS4A12 Is a Colon-Selective Store-Operated Calcium Channel Promoting Malignant Cell Processes

Koslowski, M., Şahin, U., Dhaene, K., Huber, C., & Türeci, Ö. (2008) · Cancer Research · doi:10.1158/0008-5472.can-07-5768 · Cited by 73 · see citing works

Stem Cells Handbook

Sell, S. (2004) · DIAL (Catholic University of Leuven) · doi:10.1007/978-1-4614-7696-2 · Cited by 73 · see citing works

Optofluidic Cell Selection from Complex Microbial Communities for Single-Genome Analysis

Landry, Z., Giovannoni, S. J., Quake, S. R., & Blainey, P. C. (2013) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-407863-5.00004-6 · Cited by 65 · see citing works

Evolutionary Tradeoffs between Economy and Effectiveness in Biological Homeostasis Systems

Székely, P., Sheftel, H., Mayo, A., & Alon, U. S. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003163 · Cited by 64 · see citing works

Mathematical model of adult stem cell regeneration with cross-talk between genetic and epigenetic regulation

Lei, J., Levin, S. A., & Nie, Q. H. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1324267111 · Cited by 60 · see citing works

Evaluation of Phagocytic Activity in Human Monocyte-Derived Dendritic Cells

Kiama, S. G., Cochand, L., Karlsson, L., Nicod, L. P., & Gehr, P. (2001) · Journal of Aerosol Medicine · doi:10.1089/089426801316970240 · Cited by 59 · see citing works

Isolation and characterization of the CRIPTO autosomal gene and its X-linked related sequence.

Rosana, D., Montuori, N., Rocchi, M., DePonti-Zilli, L., Ciccodicola, A., & Persico, M. G. (1991) · Europe PMC (PubMed Central) · Cited by 59 · see citing works

Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells

McDavid, A., Dennis, L., Danaher, P., Finak, G., Krouse, M., Wang, A., Webster, P., Beechem, J., & Gottardo, R. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003696 · Cited by 58 · see citing works

MBLR, a new RING finger protein resembling mammalian Polycomb gene products, is regulated by cell cycle‐dependent phosphorylation

Akasaka, T., Takahashi, N., Suzuki, M., Koseki, H., Bodmer, R., & Koga, H. (2002) · Genes to Cells · doi:10.1046/j.1365-2443.2002.00565.x · Cited by 54 · see citing works

Sets of efficient points in a normed space

Durier, R., & Michelot, C. (1986) · Journal of Mathematical Analysis and Applications · doi:10.1016/0022-247x(86)90237-4 · Cited by 53 · see citing works

Archetypal analysis of diverse Pseudomonas aeruginosatranscriptomes reveals adaptation in cystic fibrosis airways

Thøgersen, J. C., Mørup, M., Damkiær, S., Molin, S., & Jelsbak, L. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-279 · Cited by 52 · see citing works

An adaptive decoder from spike trains to micro-stimulation using kernel least-mean-squares (KLMS)

Li, L., Park, I. M., Seth, S., Choi, J. S., Francis, J. T., Sanchez, J. C., & Príncipe, J. C. (2011) · Machine learning for signal processing ... · doi:10.1109/mlsp.2011.6064603 · Cited by 33 · see citing works

Modeling transcriptional networks in Drosophila development at multiple scales

Wunderlich, Z., & DePace, A. H. (2011) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2011.07.005 · Cited by 27 · see citing works

Serrated Adenoma of the Colorectum Undergoes a Proliferation versus Differentiation Process: New Conceptual Interpretation of Morphogenesis

Jiao, Y., Nakamura, S., Sugai, T., Yamada, N., & Habano, W. (2008) · Oncology · doi:10.1159/000151359 · Cited by 21 · see citing works

Erratum: Critical assessment of automated flow cytometry data analysis techniques

Aghaeepour, N., Finak, G., Hoos, H. H., Mosmann, T. R., Brinkman, R. R., Gottardo, R., & Scheuermann, R. H. (2013) · Nature Methods · doi:10.1038/nmeth0513-445c · Cited by 19 · see citing works

Archetypal analysis for machine learning

Mørup, M., & Hansen, L. K. (2010) · IEEE International Workshop on Machine Learning for Signal Processing (MLSP) · doi:10.1109/mlsp.2010.5589222 · Cited by 17 · see citing works

Gene expression in TGFbeta-induced epithelial cell differentiation in a three-dimensional intestinal epithelial cell differentiation model

Juuti‐Uusitalo, K., Kaukinen, K., Mäki, M., Tuimala, J., & Kainulainen, H. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-279 · Cited by 14 · see citing works

From Stem Cells to Functional Tissue Architecture

Huang, S., & Ingber, D. E. (2004) · doi:10.1007/978-1-59259-411-5_4 · Cited by 6 · see citing works

Can cell mortality determine division of labor in tissue organization?

Rodríguez‐Caso, C. (2013) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2013.05.001 · Cited by 5 · see citing works

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

van Dijk, D., Sharma, R., Nainys, J., Yim, K., Kathail, P., Carr, A. J., Burdziak, C., Moon, K. R., Chaffer, C. L., Pattabiraman, D., et al. (2018) · Cell · doi:10.1016/j.cell.2018.05.061 · Cited by 1,829 · see citing works

Revealing the vectors of cellular identity with single-cell genomics

Wagner, A., Regev, A., & Yosef, N. (2016) · Nature Biotechnology · doi:10.1038/nbt.3711 · Cited by 632 · see citing works

Joint probabilistic modeling of single-cell multi-omic data with totalVI

Gayoso, A., Steier, Z., Lopez, R., Regier, J., Nazor, K. L., Streets, A., & Yosef, N. (2021) · Nature Methods · doi:10.1038/s41592-020-01050-x · Cited by 592 · see citing works

Cancer-associated fibroblast compositions change with breast cancer progression linking the ratio of S100A4+ and PDPN+ CAFs to clinical outcome

Friedman, G., Levi-Galibov, O., David, E., Bornstein, C., Giladi, A., Dadiani, M., Mayo, A., Halperin, C., Pevsner‐Fischer, M., Lavon, H., et al. (2020) · Nature Cancer · doi:10.1038/s43018-020-0082-y · Cited by 344 · see citing works

Central dogma rates and the trade-off between precision and economy in gene expression

Hausser, J., Mayo, A., Keren, L., & Alon, U. (2019) · Nature Communications · doi:10.1038/s41467-018-07391-8 · Cited by 188 · see citing works

Tumour heterogeneity and the evolutionary trade-offs of cancer

Hausser, J., & Alon, U. S. (2020) · Nature reviews. Cancer · doi:10.1038/s41568-020-0241-6 · Cited by 209 · see citing works

Interpretable factor models of single-cell RNA-seq via variational autoencoders

Svensson, V., Gayoso, A., Yosef, N., & Pachter, L. S. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa169 · Cited by 192 · see citing works

Unsupervised Trajectory Analysis of Single-Cell RNA-Seq and Imaging Data Reveals Alternative Tuft Cell Origins in the Gut

Herring, C. A., Banerjee, A., McKinley, E. T., Simmons, A. J., Ping, J., Roland, J. T., Franklin, J. L., Liu, Q., Gerdes, M. J., Coffey, R. J., et al. (2017) · Cell Systems · doi:10.1016/j.cels.2017.10.012 · Cited by 178 · see citing works

Assessing rejection-related disease in kidney transplant biopsies based on archetypal analysis of molecular phenotypes

REEVE, J. P., Böhmig, G. A., Eskandary, F. A., Einecke, G., Lefaucheur, C., Loupy, A., Halloran, P. F., & the MMDx-Kidney study group (2017) · JCI Insight · doi:10.1172/jci.insight.94197 · Cited by 181 · see citing works

Principles of Cell Circuits for Tissue Repair and Fibrosis

Adler, M., Mayo, A., Zhou, X., Franklin, R. A., Meizlish, M. L., Medzhitov, R., Kallenberger, S. M., & Alon, U. (2020) · iScience · doi:10.1016/j.isci.2020.100841 · Cited by 177 · see citing works

Signature of Pareto optimization in the Escherichia coli proteome

Koçillari, L., Fariselli, P., Trovato, A., Seno, F., & Maritan, A. (2018) · Scientific Reports · doi:10.1038/s41598-018-27287-3 · Cited by 175 · see citing works

Negative co-stimulation constrains T cell differentiation by imposing boundaries on possible cell states

Wei, S. C., Sharma, R., Anang, N.-A. A. S., Levine, J. H., Zhao, Y., Mancuso, J. J., Setty, M., Sharma, P., Wang, J., Pe’er, D., et al. (2019) · Immunity · doi:10.1016/j.immuni.2019.03.004 · Cited by 97 · see citing works

Single-Cell Transcriptional Archetypes of Airway Inflammation in Cystic Fibrosis

Schupp, J. C., Khanal, S., Gómez, J. L., Sauler, M., Adams, T. S., Chupp, G. L., Yan, X., Poli, S., Zhao, Y., Montgomery, R. R., et al. (2020) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.202004-0991oc · Cited by 87 · see citing works

Tumor diversity and the trade-off between universal cancer tasks

Hausser, J., Székely, P., Bar, N., Zimmer, A., Sheftel, H., Caldas, C., & Alon, U. (2019) · Nature Communications · doi:10.1038/s41467-019-13195-1 · Cited by 76 · see citing works

Optimal Regulatory Circuit Topologies for Fold-Change Detection

Adler, M., Székely, P., Mayo, A., & Alon, U. S. (2017) · Cell Systems · doi:10.1016/j.cels.2016.12.009 · Cited by 79 · see citing works

Mapping Phenotypic Plasticity upon the Cancer Cell State Landscape Using Manifold Learning

Burkhardt, D. B., Juan, B. P. S., Lock, J. G., Krishnaswamy, S., & Chaffer, C. L. (2022) · Cancer Discovery · doi:10.1158/2159-8290.cd-21-0282 · Cited by 74 · see citing works

Continuum of Gene-Expression Profiles Provides Spatial Division of Labor within a Differentiated Cell Type

Adler, M., Kohanim, Y. K., Tendler, A., Mayo, A., & Alon, U. S. (2019) · Cell Systems · doi:10.1016/j.cels.2018.12.008 · Cited by 72 · see citing works

Archetype tasks link intratumoral heterogeneity to plasticity and cancer hallmarks in small cell lung cancer

Groves, S. M., Ildefonso, G. V., McAtee, C. O., Ozawa, P. M. M., Ireland, A. S., Stauffer, P. E., Wasdin, P. T., Huang, X., Qiao, Y., Lim, J. S., et al. (2022) · Cell Systems · doi:10.1016/j.cels.2022.07.006 · Cited by 64 · see citing works

The Mass-Longevity Triangle: Pareto Optimality and the Geometry of Life-History Trait Space

Székely, P., Kohanim, Y. K., Moran, U., Mayo, A., & Alon, U. S. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004524 · Cited by 55 · see citing works

A brief review of single-cell transcriptomic technologies

Tomer Kalisky, C., Oriel, S., Bar-Lev, T. H., Ben-Haim, N., Trink, A., Wineberg, Y., Kanter, I., Gilad, S., & Pyne, S. (2017) · Briefings in Functional Genomics · doi:10.1093/bfgp/elx019 · Cited by 54 · see citing works

A geometric approach to characterize the functional identity of single cells

Mohammadi, S., Ravindra, V., Gleich, D. F., & Grama, A. Y. (2018) · Nature Communications · doi:10.1038/s41467-018-03933-2 · Cited by 51 · see citing works

Emergence of division of labor in tissues through cell interactions and spatial cues

Adler, M., Moriel, N., Goeva, A., Avraham‐Davidi, I., Mages, S., Adams, T. S., Kaminski, N., Macosko, E. Z., Regev, A., Medzhitov, R. M., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112412 · Cited by 50 · see citing works

Mathematics in modern immunology

Castro, M., Lythe, G., Molina-Parı́s, C., & Ribeiro, R. M. (2016) · Interface Focus · doi:10.1098/rsfs.2015.0093 · Cited by 46 · see citing works

Tissue Biology: In Search of a New Paradigm

Adler, M., Chavan, A. R., & Medzhitov, R. (2023) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-120420-113830 · Cited by 40 · see citing works

Sexually dimorphic oxytocin circuits drive intragroup social conflict and aggression in wild house mice

Sofer, Y., Zilkha, N., Gimpel, E., Wagner, S., Chuartzman, S. G., & Kimchi, T. (2024) · Nature Neuroscience · doi:10.1038/s41593-024-01685-5 · Cited by 38 · see citing works

How to address cellular heterogeneity by distribution biology

Komin, N., & Skupin, A. (2017) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2017.05.010 · Cited by 37 · see citing works

System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris

Navid, A., Jiao, Y., Wong, S., & Pett‐Ridge, J. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-2844-z · Cited by 35 · see citing works

Archetypes of human cognition defined by time preference for reward and their brain correlates: An evolutionary trade-off approach

Cona, G., Koçillari, L., Palombit, A., Bertoldo, A., Maritan, A., & Corbetta, M. (2018) · NeuroImage · doi:10.1016/j.neuroimage.2018.10.050 · Cited by 35 · see citing works

Sex-dependent control of pheromones on social organization within groups of wild house mice

Zilkha, N., Chuartzman, S. G., Sofer, Y., Pen, Y., Cum, M., Mayo, A., Alon, U. S., & Kimchi, T. (2023) · Current Biology · doi:10.1016/j.cub.2023.02.039 · Cited by 29 · see citing works

The geometry of clinical labs and wellness states from deeply phenotyped humans

Zimmer, A., Kohanim, Y. K., Rappaport, N., Wilmanski, T. M., Baloni, P., Jade, K., Robinson, M., Magis, A. T., Lovejoy, J. C., Gibbons, S. M., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23849-8 · Cited by 30 · see citing works

Evolutionary trade-offs and the structure of polymorphisms

Sheftel, H., Székely, P., Mayo, A., Sella, G., & Alon, U. (2018) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2017.0105 · Cited by 29 · see citing works

Geometry of Gene Expression Space of Wilms' Tumors From Human Patients

Trink, A., Kanter, I., Pode‐Shakked, N., Urbach, A., Dekel, B., & Tomer Kalisky, C. (2018) · Neoplasia · doi:10.1016/j.neo.2018.06.006 · Cited by 26 · see citing works

A data-driven classification of 3D foot types by archetypal shapes based on landmarks

Alcacer, A., Epifanio, I., Ibáñez, M. V., Simó, A., & Ballester, A. (2020) · PLoS ONE · doi:10.1371/journal.pone.0228016 · Cited by 24 · see citing works

Phenotypic heterogeneity in modeling cancer evolution

Mahdipour–Shirayeh, A., Kaveh, K., Kohandel, M., & Sivaloganathan, S. (2017) · PLoS ONE · doi:10.1371/journal.pone.0187000 · Cited by 21 · see citing works

Finding Archetypal Spaces Using Neural Networks

van Dijk, D., Burkhardt, D. B., Amodio, M., Tong, A., Wolf, G., & Krishnaswamy, S. (2019) · IEEE International Conference on Big Data (BigData) · doi:10.1109/bigdata47090.2019.9006484 · Cited by 17 · see citing works

Resource allocation in mammalian systems

Baghdassarian, H. M., & Lewis, N. E. (2024) · Biotechnology Advances · doi:10.1016/j.biotechadv.2023.108305 · Cited by 17 · see citing works

Bridging scales: From cell biology to physiology using in situ single-cell technologies

Nagle, M. P., Tam, G. S., Maltz, E., Hemminger, Z., & Wollman, R. (2021) · Cell Systems · doi:10.1016/j.cels.2021.03.002 · Cited by 15 · see citing works

A reduced-dimensionality approach to uncovering dyadic modes of body motion in conversations

Gaziv, G., Noy, L., Liron, Y., & Alon, U. S. (2017) · PLoS ONE · doi:10.1371/journal.pone.0170786 · Cited by 14 · see citing works

Gene expression rearrangements denoting changes in the biological state

Gonzalez, A., Nieves, J., Leon, D. A., Vega, M. L. B., & Sosa, P. V. (2021) · Scientific Reports · doi:10.1038/s41598-021-87764-0 · Cited by 14 · see citing works

Archetypal Analysis of Injury in Kidney Transplant Biopsies Identifies Two Classes of Early AKI

Halloran, P. F., Böhmig, G. A., Bromberg, J. S., Einecke, G., Eskandary, F. A., Gupta, G., Myślak, M., Viklický, O., Perkowska‐Ptasińska, A., Madill-Thomsen, K. S., et al. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.817324 · Cited by 14 · see citing works

Rampant False Detection of Adaptive Phenotypic Optimization by ParTI-Based Pareto Front Inference

Sun, M., & Zhang, J. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa330 · Cited by 12 · see citing works

Geometric analysis of pathways dynamics: Application to versatility of TGF-β receptors

Samal, S. S., Naldi, A., Grigoriev, D. Y., Weber⋆, A., Théret, N., & Radulescu, O. (2016) · Biosystems · doi:10.1016/j.biosystems.2016.07.004 · Cited by 11 · see citing works

Inferring metabolic objectives and trade-offs in single cells during embryogenesis

Lin, D.-W., Zhang, L., Zhang, J., & Chandrasekaran, S. (2025) · Cell Systems · doi:10.1016/j.cels.2024.12.005 · Cited by 10 · see citing works

A unified model for interpretable latent embedding of multi-sample, multi-condition single-cell data

Madrigal, A., Lu, T., Soto, L. M., & Najafabadi, H. (2023) · bioRxiv · doi:10.1038/s41467-024-50963-0 · Cited by 6 · see citing works

Transcriptomic Plasticity Is a Hallmark of Metastatic Pancreatic Cancer

Jiménez-Sánchez, A., Persad, S., Hayashi, A., Umeda, S., Sharma, R., Xie, Y., Mehta, A., Park, W., Masilionis, I., Chu, T., et al. (2025) · Cancer Research · doi:10.1158/0008-5472.can-25-1117 · Cited by 8 · see citing works

MIDAA: deep archetypal analysis for interpretable multi-omic data integration based on biological principles

Milite, S., Caravagna, G., & Sottoriva, A. (2025) · Genome biology · doi:10.1186/s13059-025-03530-9 · Cited by 8 · see citing works

The flipping t ‐ratio test: Phylogenetically informed assessment of the Pareto theory for phenotypic evolution

Mikami, T., & Iwasaki, W. (2021) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.13553 · Cited by 8 · see citing works

Pinpointing Cancer Sub-Type Specific Metabolic Tasks Facilitates Identification of Anti-cancer Targets

Gao, S., Dai, Z., Xu, H., & Lai, L. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.872024 · Cited by 7 · see citing works

The Geometry of Normal Tissue and Cancer Gene Expression Manifolds

Nieves, J., & González, A. (2024) · Acta Biotheoretica · doi:10.1007/s10441-024-09483-z · Cited by 5 · see citing works

AAnet Resolves a Continuum of Spatially Localized Cell States to Unveil Intratumoral Heterogeneity

Venkat, A., Youlten, S. E., Juan, B. P. S., Purcell, C., Gupta, S., Amodio, M., Neumann, D. P., Lock, J., Westacott, A. E., McCool, C. S., et al. (2025) · Cancer Discovery · doi:10.1158/2159-8290.cd-24-0684 · Cited by 8 · see citing works

Pareto optimality reveals an atlas of cellular archetypes

Crowley, G., Alon, U., & Quake, S. R. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2530194123 · Cited by 4 · see citing works

High accuracy gene expression profiling of sorted cell subpopulations from breast cancer PDX model tissue

Porter, W., Snowden, E., Hahn, F., Ferguson, M., Tong, F., Dillmore, W. S., & Blaesius, R. (2020) · PLoS ONE · doi:10.1371/journal.pone.0238594 · Cited by 3 · see citing works

New Insights into Initiation of Colon and Intestinal Cancer: The Significance of Central Stem Cells in the CryptPreprint

Mahdipour–Shirayeh, A., & Shahriyari, L. (2016) · arXiv (Cornell University) · doi:10.48550/arxiv.1610.04089 · Cited by 4 · see citing works

The architecture of functional lateralisation and its relationship to callosal connectivity in the human brainPreprint

Karolis, V. R., Corbetta, M., & de Schotten, M. T. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/372300 · Cited by 4 · see citing works

Casting Multiple Shadows: High-Dimensional Interactive Data Visualisation with Tours and EmbeddingsPreprint

Lee, S. A., Laa, U., & Cook, D. (2020) · arXiv (Cornell University) · doi:10.48550/arxiv.2012.06077 · Cited by 4 · see citing works

CytoSimplex: visualizing single-cell fates and transitions on a simplex

Liu, J., Wang, Y., Li, C., Gu, Y., Ono, N., & Welch, J. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf119 · Cited by 3 · see citing works

ParTIpy: a scalable framework for archetypal analysis and Pareto task inference

Schäfer, P., Zimmermann, L., Burmedi, P. L., Walfisch, A., Goldenberg, N., Yonassi, S., Tamar, E. S., Adler, M., Tanevski, J., Flores, R. R., et al. (2025) · bioRxiv · doi:10.1038/s44320-026-00209-6 · Cited by 3 · see citing works

Role of Scar‐Associated Macrophages in Organ Fibrosis Diseases

Ding, R., Yang, Z., Chen, Y., Yu, Q., Ji, Y., Wang, Z., & Gu, M. (2026) · Journal of Immunology Research · doi:10.1155/jimr/8393673 · Cited by 3 · see citing works

Multi-cellular phenotypic dynamics during the progression of an immunocompetent breast cancer model

Gsell, L., Watson, S. S., Sutevski, I., Massara, M., Soukup, K., Eroğlu, A., Mold, J. E., Cougnoux, A., Joyce, J. A., & Hausser, J. (2025) · iScience · doi:10.1016/j.isci.2025.113808 · Cited by 3 · see citing works

Characterization of Continuous Transcriptional Heterogeneity in High-Risk Blastemal-Type Wilms’ Tumors Using Unsupervised Machine Learning

Trink, Y., Urbach, A., Dekel, B., Hohenstein, P., Goldberger, J., & Tomer Kalisky, C. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24043532 · Cited by 3 · see citing works

Characterization of Alternative Splicing in High-Risk Wilms’ Tumors

Trink, Y., Urbach, A., Dekel, B., Hohenstein, P., Goldberger, J., & Tomer Kalisky, C. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25084520 · Cited by 3 · see citing works

Asymmetric latent semantic indexing for gene expression experiments visualization

González, J., Muñoz, A., & Martos, G. (2016) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720016500232 · Cited by 3 · see citing works

Modeling Cell Dynamics in Colon and Intestinal Crypts: The Significance of Central Stem Cells in Tumorigenesis

Mahdipour–Shirayeh, A., & Shahriyari, L. (2018) · Bulletin of Mathematical Biology · doi:10.1007/s11538-018-0457-8 · Cited by 3 · see citing works

Model-free network control

Shulman, J., Malatino, F., & Gunaratne, G. H. (2020) · Physica D Nonlinear Phenomena · doi:10.1016/j.physd.2020.132467 · Cited by 2 · see citing works

A comprehensive fitness landscape model reveals the evolutionary history and future evolvability of eukaryotic cis -regulatory DNA sequencesPreprint

Vaishnav, E. D., de Boer, C. G., Yassour, M., Molinet, J., Fan, L., Adiconis, X., Thompson, D. A., Cubillos, F. A., Levin, J. Z., & Regev, A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.17.430503 · Cited by 2 · see citing works

The geometry of normal tissue and cancer gene expression manifoldsPreprint

Nieves, J., & González, A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.20.457160 · Cited by 2 · see citing works

Modeling combinatorial regulation from single-cell multi-omics provides regulatory units underpinning cell type landscape using cRegulon

Feng, Z., Chen, X. X., Duren, Z., Xin, J., Hao, M., Yuan, Q., Wang, Y., & Wong, W. H. (2025) · Genome biology · doi:10.1186/s13059-025-03680-w · Cited by 1 · see citing works

The cell as a token: high-dimensional geometry in language models and cell embeddings

Gilpin, W. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf595 · Cited by 3 · see citing works

Archetypal Curves in the Shape and Size Space: Discovering the Salient Features of Curved Big Data by Representative Extremes

Epifanio, I., Gimeno, V., Gual-Arnau, X., & Ibáñez, M. V. (2023) · La Matematica · doi:10.1007/s44007-023-00058-x · Cited by 1 · see citing works

Tradeoffs and cultural diversityPreprint

Karin, O., & Alon, U. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/263905 · Cited by 1 · see citing works

Universal cancer tasks, evolutionary tradeoffs, and the functions of driver mutationsPreprint

Hausser, J., Székely, P., Bar, N., Zimmer, A., Sheftel, H., Caldas, C., & Alon, U. S. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/382291 · Cited by 1 · see citing works

Characterization of the Continuous Transcriptional Heterogeneity in Wilms’ Tumors Using Unsupervised Machine LearningPreprint

Trink, Y., Urbach, A., Dekel, B., Hohenstein, P., Goldberger, J., & Tomer Kalisky, C. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.06.494924 · Cited by 1 · see citing works

An Integrated Bioinformatics Pipeline for Single Cell RNA-seq Analysis - Application in Natural Killer Cell Differentiation

Netskar, H. (2019) · NORA - Norwegian Open Research Archives

Faculty Opinions recommendation of Central dogma rates and the trade-off between precision and economy in gene expression.

Kuroda, S., & Hironaka, K. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.734774279.793555453

Casting multiple shadows: interactive data visualisation with tours and embeddings

Lee, S. A., Laa, U., & Cook, D. (2022) · Journal of Data Science Statistics and Visualisation · doi:10.52933/jdssv.v2i3.21

Multi-cellular phenotypic dynamics during the progression of breast tumorsPreprint

Gsell, L., Watson, S. S., Sutevski, I., Massara, M., Soukup, K., Eroğlu, A., Mold, J. E., Cougnoux, A., Joyce, J. A., & Hausser, J. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.16.649085

Chronic pain is linked to a resting-state neural archetype that optimizes learning from punishmentsPreprint

Scarlatti, F., Dormegny-Jeanjean, L. C., Schefzik, R., Banaschewski, T., Bokde, A. L. W., Brühl, R., Desrivières, S., Garavan, H., Gowland, P. A., Grigis, A., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.07.11.664303

Tissue-level division of labor is coordinated across organs through universal programs and context-specific adaptations

Yonassi, S., Goldenberg, N., Walfisch, A., Cohen, E., Tamar, E. S., Zhou, X., & Adler, M. (2026) · Cell Reports · doi:10.1016/j.celrep.2026.117851

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