Profiling cellular diversity in sponges informs animal cell type and nervous system evolution

Random Forests

Breiman, L. (2001) · Machine Learning · doi:10.1023/a:1010933404324 · Cited by 133,538 · see citing works

Image quality assessment: from error visibility to structural similarity

Wang, Z., Bovik, A. C., Sheikh, H. R., & Simoncelli, E. P. (2004) · IEEE Transactions on Image Processing · doi:10.1109/tip.2003.819861 · Cited by 57,892 · see citing works

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu033 · Cited by 32,291 · see citing works

WGCNA: an R package for weighted correlation network analysis

Langfelder, P., & Horvath, S. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-559 · Cited by 27,252 · see citing works

Summary for Policymakers

(2014) · Climate Change 2013 – The Physical Science Basis · doi:10.1017/cbo9781107415324.004 · Cited by 23,880 · see citing works

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1883 · Cited by 20,776 · see citing works

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

Sievers, F., Wilm, A., Dineen, D., Gibson, T., Karplus, K., Li, W.-Z., Lopez, R., McWilliam, H., Remmert, M., Söding, J., et al. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.75 · Cited by 15,576 · see citing works

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv351 · Cited by 13,344 · see citing works

Integrating single-cell transcriptomic data across different conditions, technologies, and species

Butler, A., Hoffman, P., Smibert, P., Papalexi, E., & Satija, R. (2018) · Nature Biotechnology · doi:10.1038/nbt.4096 · Cited by 13,174 · see citing works

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

Capella-Gutiérrez, S., Silla-Martinez, J., & Gabaldón, T. (2009) · Bioinform. · doi:10.1093/bioinformatics/btp348 · Cited by 12,052 · see citing works

Nitric oxide release accounts for the biological activity of endothelium-derived relaxing factor

Palmer, R. M. J., Ferrige, A. G., & Moncada, S. (1987) · Nature · doi:10.1038/327524a0 · Cited by 10,704 · see citing works

SCANPY: large-scale single-cell gene expression data analysis

Wolf, F. A., Angerer, P., & Theis, F. J. (2018) · Genome Biology · doi:10.1186/s13059-017-1382-0 · Cited by 8,881 · see citing works

Application of Phylogenetic Networks in Evolutionary Studies

Huson, D. H., & Bryant, D. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj030 · Cited by 8,751 · see citing works

Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets.

Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A. R., Kamitaki, N., Martersteck, E. M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.002 · Cited by 7,110 · see citing works

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

Letunic, I., & Bork, P. (2016) · Nucleic Acids Res. · doi:10.1093/nar/gkw290 · Cited by 4,851 · see citing works

Molecular Architecture of the Mouse Nervous System

Zeisel, A., Hochgerner, H., Lönnerberg, P., Johnsson, A., Memic, F., van der Zwan, J., Häring, M., Braun, E., Borm, L. E., La Manno, G., et al. (2018) · Cell · doi:10.1016/j.cell.2018.06.021 · Cited by 2,995 · see citing works

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

Huerta-Cepas, J., Forslund, K., Coelho, L. P., Szklarczyk, D., Jensen, L. J., von Mering, C., & Bork, P. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx148 · Cited by 2,709 · see citing works

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

Huerta‐Cepas, J., Serra, F., & Peer Bork, B. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw046 · Cited by 2,239 · see citing works

The InterPro protein families and domains database: 20 years on

Blum, M., Chang, H.-Y., Chuguransky, S., Grego, T., Kandasaamy, S., Mitchell, A., Nuka, G., Paysan-Lafosse, T., Qureshi, M., Raj, S., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa977 · Cited by 2,231 · see citing works

PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells

Wolf, F. A., Hamey, F. K., Plass, M., Solana, J., Dahlin, J. S., Göttgens, B., Rajewsky, N., Simon, L., & Theis, F. J. (2019) · Genome Biology · doi:10.1186/s13059-019-1663-x · Cited by 1,698 · see citing works

Ilastik: Interactive learning and segmentation toolkit

Sommer, C., Straehle, C., Köthe, U., & Hamprecht, F. A. (2011) · IEEE International Symposium on Biomedical Imaging (ISBI) · doi:10.1109/isbi.2011.5872394 · Cited by 1,145 · see citing works

Holotomography: Quantitative phase tomography with micrometer resolution using hard synchrotron radiation x rays

Cloetens, P., Ludwig, W., Baruchel, J., Dyck, D. V., Landuyt, J. V., Guigay, J. P., & Schlenker, M. (1999) · Applied Physics Letters · doi:10.1063/1.125225 · Cited by 1,078 · see citing works

The Presynaptic Active Zone

Südhof, T. C. (2012) · Neuron · doi:10.1016/j.neuron.2012.06.012 · Cited by 1,062 · see citing works

The Amphimedon queenslandica genome and the evolution of animal complexity

Srivastava, M., Simakov, O., Chapman, J., Fahey, B., Gauthier, M. E. A., Mitros, T., Richards, G. S., Conaco, C., Dacre, M., Hellsten, U., et al. (2010) · Nature · doi:10.1038/nature09201 · Cited by 1,049 · see citing works

TomoPy: a framework for the analysis of synchrotron tomographic data

Gürsoy, D., Carlo, F. D., Xiao, X., & Jacobsen, C. J. (2014) · Journal of Synchrotron Radiation · doi:10.1107/s1600577514013939 · Cited by 962 · see citing works

The Cell Biology of Sponges

Simpson, T. L. (1984) · Springer eBooks · doi:10.1007/978-1-4612-5214-6 · Cited by 827 · see citing works

Evaluation of time profile reconstruction from complex two-color microarray designs

Fierro, A. C., Thuret, R., Engelen, K., Bernot, G., Kathleen Marchal, D., & Pollet, N. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-1 · Cited by 713 · see citing works

Diffusion maps for high-dimensional single-cell analysis of differentiation data

Haghverdi, L., Buettner, F., & Theis, F. J. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv325 · Cited by 649 · see citing works

The Postsynaptic Organization of Synapses

Sheng, M., & Kim, E. (2011) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a005678 · Cited by 603 · see citing works

Notch signaling modulates proliferation and differentiation of intestinal crypt base columnar stem cells

VanDussen, K. L., Carulli, A. J., Keeley, T. M., Patel, S. R., Puthoff, B. J., Magness, S. T., Tran, I., Maillard, I. P., Siebel, C. W., Kolterud, Å., et al. (2011) · Development · doi:10.1242/dev.070763 · Cited by 579 · see citing works

CED-12/ELMO, a Novel Member of the CrkII/Dock180/Rac Pathway, Is Required for Phagocytosis and Cell Migration

Gumienny, T. L., Brugnera, E., Tosello-Trampont, A.-C., Kinchen, J. M., Haney, L. B., Nishiwaki, K., Walk, S. F., Nemergut, M. E., Macara, I. G., Francis, R., et al. (2001) · Cell · doi:10.1016/s0092-8674(01)00520-7 · Cited by 568 · see citing works

Drishti: a volume exploration and presentation tool

Limaye, A. C. (2012) · Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE · doi:10.1117/12.935640 · Cited by 541 · see citing works

mv morph : an r package for fitting multivariate evolutionary models to morphometric data

Clavel, J., Escarguel, G., & Merceron, G. (2015) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12420 · Cited by 524 · see citing works

A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals

Simion, P., Philippe, H., Baurain, D., Jager, M., Richter, D. J., Di Franco, A., Roure, B., Satoh, N., Quéinnec, É., Ereskovsky, A., et al. (2017) · Current Biology · doi:10.1016/j.cub.2017.02.031 · Cited by 518 · see citing works

Synaptic Vesicle ExocytosisPreprint

Südhof, T. C., & Rizo, J. (2011) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a005637 · Cited by 502 · see citing works

Serum response factor: master regulator of the actin cytoskeleton and contractile apparatus

Miano, J. M., Long, X., & Fujiwara, K. (2006) · American Journal of Physiology-Cell Physiology · doi:10.1152/ajpcell.00386.2006 · Cited by 482 · see citing works

Synaptic Vesicle Endocytosis

Saheki, Y., & De Camilli, P. (2012) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a005645 · Cited by 457 · see citing works

Regulated secretion of conventional lysosomes

Andrews, N. W. (2000) · Trends in Cell Biology · doi:10.1016/s0962-8924(00)01794-3 · Cited by 354 · see citing works

Molecular evolution of the reactive oxygen-generating NADPH oxidase (Nox/Duox) family of enzymes

Kawahara, T., Quinn, M. T., & Lambeth, J. D. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-109 · Cited by 336 · see citing works

Early evolution of animal cell signaling and adhesion genes

Nichols, S., Dirks, W., Pearse, J. S., & King, N. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0604065103 · Cited by 327 · see citing works

Mapping single-cell atlases throughout Metazoa unravels cell type evolution

Tarashansky, A. J., Musser, J. M., Khariton, M., Li, P., Arendt, D., Quake, S. R., & Wang, B. (2021) · eLife · doi:10.7554/elife.66747 · Cited by 299 · see citing works

High-contrast en bloc staining of neuronal tissue for field emission scanning electron microscopy

Tapia, J. C., Kasthuri, N., Hayworth, K. J., Schalek, R., Lichtman, J. W., Smith, S. J., & Buchanan, J. (2012) · Nature Protocols · doi:10.1038/nprot.2011.439 · Cited by 296 · see citing works

Early metazoan cell type diversity and the evolution of multicellular gene regulation

Sebé-Pedrós, A., Chomsky, E., Pang, K., Lara‐Astiaso, D., Gaiti, F., Mukamel, Z., Amit, I., Hejnol, A., Degnan, B. M., & Tanay, A. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0575-6 · Cited by 292 · see citing works

Synaptic Vesicle Pools and Dynamics

Alabi, A. A., & Tsien, R. W. (2012) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a013680 · Cited by 284 · see citing works

From nerve net to nerve ring, nerve cord and brain — evolution of the nervous system

Arendt, D., Tosches, M. A., & Marlow, H. (2016) · Nature Reviews Neuroscience · doi:10.1038/nrn.2015.15 · Cited by 279 · see citing works

The Analysis of Eight Transcriptomes from All Poriferan Classes Reveals Surprising Genetic Complexity in Sponges

Riesgo, A., Farrar, N., Windsor, P. J., Giribet, G., & Leys, S. P. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu057 · Cited by 266 · see citing works

Ctenophore relationships and their placement as the sister group to all other animals

Whelan, N. V., Kocot, K. M., Moroz, T. P., Mukherjee, K., Williams, P., Paulay, G., Moroz, L. L., & Halanych, K. M. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0331-3 · Cited by 263 · see citing works

The diverse functions of Krüppel‐like factors 4 and 5 in epithelial biology and pathobiology

McConnell, B. B., Ghaleb, A. M., Nandan, M. O., & Yang, V. W. (2007) · BioEssays · doi:10.1002/bies.20581 · Cited by 258 · see citing works

Protein tyrosine phosphatases PTPδ, PTPσ, and LAR: presynaptic hubs for synapse organization

Takahashi, H., & Craig, A. M. (2013) · Trends in Neurosciences · doi:10.1016/j.tins.2013.06.002 · Cited by 257 · see citing works

Synaptic Cell Adhesion

Missler, M., Sudhof, T. C., & Biederer, T. (2012) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a005694 · Cited by 255 · see citing works

Optimization of phase contrast imaging using hard x rays

Zabler, S., Cloetens, P., Guigay, J. P., Baruchel, J., & Schlenker, M. (2005) · Review of Scientific Instruments · doi:10.1063/1.1960797 · Cited by 189 · see citing works

Coordinated contractions effectively expel water from the aquiferous system of a freshwater sponge

Elliott, G. R. D., & Leys, S. P. (2007) · Journal of Experimental Biology · doi:10.1242/jeb.003392 · Cited by 189 · see citing works

Hydrogen sulfide in signaling pathways

Olas, B. (2014) · Clinica Chimica Acta · doi:10.1016/j.cca.2014.10.037 · Cited by 171 · see citing works

Independent origins of neurons and synapses: insights from ctenophores

Moroz, L. L., & Kohn, A. B. (2016) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2015.0041 · Cited by 171 · see citing works

Pax–Six–Eya–Dach network during amphioxus development: Conservation in vitro but context specificity in vivo

Kozmík, Z., Holland, N. D., Kreslova, J., Oliveri, D., Schubert, M., Jonasova, K., Holland, L. Z., Pestarino, M., Beneš, V., & Candiani, S. (2007) · Developmental Biology · doi:10.1016/j.ydbio.2007.03.009 · Cited by 170 · see citing works

Selective inference in complex research

Benjamini, Y., Heller, R., & Yekutieli, D. (2009) · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences · doi:10.1098/rsta.2009.0127 · Cited by 166 · see citing works

The use of osmium-thiocarbohydrazide-osmium (OTO) and ferrocyanide-reduced osmium methods to enhance membrane contrast and preservation in cultured cells.

Willingham, M. C., & Rutherford, A. V. (1984) · Journal of Histochemistry & Cytochemistry · doi:10.1177/32.4.6323574 · Cited by 162 · see citing works

Multicut brings automated neurite segmentation closer to human performance

Beier, T., Pape, C., Rahaman, N., Prange, T., Berg, S., Bock, D. D., Cardona, A., Knott, G. W., Plaza, S. M., Scheffer, L. K., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4151 · Cited by 159 · see citing works

Regional specification of muscle progenitors in Drosophila: the role of the msh homeobox gene

Nose, A., Isshiki, T., & Takeichi, M. (1998) · Development · doi:10.1242/dev.125.2.215 · Cited by 154 · see citing works

Myosin-X: a MyTH-FERM myosin at the tips of filopodia

Kerber, M. L., & Cheney, R. E. (2011) · Journal of Cell Science · doi:10.1242/jcs.023549 · Cited by 151 · see citing works

Enzymatic production of single-molecule FISH and RNA capture probes

Gáspár, I., Wippich, F., & Ephrussi, A. (2017) · RNA · doi:10.1261/rna.061184.117 · Cited by 150 · see citing works

Pluripotency and the origin of animal multicellularity

(2019) · doi:10.1038/s41586-019-1290-4 · Cited by 146 · see citing works

Whole-body integration of gene expression and single-cell morphology

Vergara, H. M., Pape, C., Meechan, K., Zinchenko, V., Genoud, C., Wanner, A. A., Mutemi, K. N., Titze, B., Templin, R., Bertucci, P. Y., et al. (2021) · Cell · doi:10.1016/j.cell.2021.07.017 · Cited by 142 · see citing works

Ultra-large alignments using phylogeny-aware profiles

Nguyen, N., Mirarab, S., Kumar, K., & Warnow, T. J. (2015) · Genome biology · doi:10.1186/s13059-015-0688-z · Cited by 141 · see citing works

Gut-like ectodermal tissue in a sea anemone challenges germ layer homology

Steinmetz, P. R. H., Aman, A. J., Kraus, J. E. M., & Technau, U. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0285-5 · Cited by 135 · see citing works

Evolutionary origins of sensation in metazoans: functional evidence for a new sensory organ in sponges

Ludeman, D. A., Farrar, N. R., Riesgo, A., Paps, J., & Leys, S. P. (2014) · BMC Evolutionary Biology · doi:10.1186/1471-2148-14-3 · Cited by 129 · see citing works

The Role of High Mobility Group Box 1 in Innate Immunity

Lee, S.-A., Kwak, M. S., Kim, S., & Shin, J. (2014) · Yonsei Medical Journal · doi:10.3349/ymj.2014.55.5.1165 · Cited by 123 · see citing works

Evolution of neuronal types and families

Arendt, D., Bertucci, P. Y., Achim, K., & Musser, J. M. (2019) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2019.01.022 · Cited by 121 · see citing works

Kinetics and rhythm of body contractions in the spongeTethya wilhelma(Porifera: Demospongiae)

Nickel, M. (2004) · Journal of Experimental Biology · doi:10.1242/jeb.01289 · Cited by 120 · see citing works

The ancestral gene repertoire of animal stem cells

Alié, A., Hayashi, T., Sugimura, I., Manuel, M., Sugano, W., Mano, A., Satoh, N., Agata, K., & Funayama, N. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1514789112 · Cited by 119 · see citing works

From insect eye to vertebrate muscle: redeployment of a regulatory networkPreprint

Relaix, F., & BUCKINGHAM, M. E. (1999) · Genes & Development · doi:10.1101/gad.13.24.3171 · Cited by 118 · see citing works

Gastric pouches and the mucociliary sole: setting the stage for nervous system evolution

Arendt, D., Benito-Gutierrez, E., Brunet, T., & Marlow, H. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2015.0286 · Cited by 112 · see citing works

Automation of sample mounting for macromolecular crystallography

Cipriani, F., Felisaz, F., Launer, L., Aksoy, J., Caserotto, H., Cusack, S., Dallery, M., di-Chiaro, F., Guijarro, M., Huet, J., et al. (2006) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444906030587 · Cited by 111 · see citing works

Evidence for glutamate, GABA and NO in coordinating behaviour in the sponge, Ephydatia muelleri (Demospongiae, Spongillidae)

Elliott, G. R. D., & Leys, S. P. (2010) · Journal of Experimental Biology · doi:10.1242/jeb.039859 · Cited by 106 · see citing works

Fast and precise targeting of single tumor cells in vivo by multimodal correlative microscopy

Karreman, M. A., Mercier, L., Schieber, N. L., Solecki, G. M., Allio, G., Winkler, F., Ruthensteiner, B., Goetz, J. G., & Schwab, Y. (2015) · Journal of Cell Science · doi:10.1242/jcs.181842 · Cited by 106 · see citing works

Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes

Fortunato, S., Adamski, M., Ramos, O. M., Leininger, S., Liu, J. L., Ferrier, D. E. K., & Adamska, M. (2014) · Nature · doi:10.1038/nature13881 · Cited by 104 · see citing works

SLC18: Vesicular neurotransmitter transporters for monoamines and acetylcholine

Lawal, H. O., & Krantz, D. E. (2013) · Molecular Aspects of Medicine · doi:10.1016/j.mam.2012.07.005 · Cited by 104 · see citing works

How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology

Marioni, J. C., & Arendt, D. (2017) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100616-060818 · Cited by 104 · see citing works

Syntrophins and Dystrobrevins: Defining the Dystrophin Scaffold at Synapses

Albrecht, D. E., & Froehner, S. C. (2002) · Neurosignals · doi:10.1159/000065053 · Cited by 97 · see citing works

Physiology of coordination in sponges

Leys, S. P., & Meech, R. W. (2006) · Canadian Journal of Zoology · doi:10.1139/z05-171 · Cited by 96 · see citing works

The architecture of cell differentiation in choanoflagellates and sponge choanocytes

Laundon, D., Larson, B. T., McDonald, K., King, N., & Burkhardt, P. (2019) · PLOS Biology · doi:10.1371/journal.pbio.3000226 · Cited by 93 · see citing works

Evolutionary emergence of synaptic nervous systems: what can we learn from the non‐synaptic, nerveless Porifera?

Nickel, M. (2010) · Invertebrate Biology · doi:10.1111/j.1744-7410.2010.00193.x · Cited by 93 · see citing works

WNT/β-Catenin Signalling and Epithelial Patterning in the Homoscleromorph Sponge Oscarella

Lapébie, P., Gazave, E., Ereskovsky, A. V., Derelle, R., Bézac, C., Renard, E., Houliston, E., & Borchiellini, C. (2009) · PLoS ONE · doi:10.1371/journal.pone.0005823 · Cited by 91 · see citing works

The contractile sponge epitheliumsensu lato– body contraction of the demospongeTethya wilhelmais mediated by the pinacoderm

Nickel, M., Scheer, C., Hammel, J. U., Herzen, J., & Beckmann, F. (2011) · Journal of Experimental Biology · doi:10.1242/jeb.049148 · Cited by 89 · see citing works

My worries are no longer behind me

Petsko, G. A. (2007) · Genome biology · doi:10.1186/gb-2007-8-8-109 · Cited by 88 · see citing works

GABA and glutamate specifically induce contractions in the sponge Tethya wilhelma

Ellwanger, K., Eich, A., & Nickel, M. (2006) · Journal of Comparative Physiology A · doi:10.1007/s00359-006-0165-y · Cited by 81 · see citing works

Neuroactive substances specifically modulate rhythmic body contractions in the nerveless metazoon Tethya wilhelma (Demospongiae, Porifera)

Ellwanger, K., & Nickel, M. (2006) · Frontiers in Zoology · doi:10.1186/1742-9994-3-7 · Cited by 79 · see citing works

Notch-mediated patterning and cell fate allocation of pancreatic progenitor cells

Afelik, S., Qu, X., Hasrouni, E., Bukys, M. A., Deering, T. G., Nieuwoudt, S., Rogers, W., MacDonald, R. J., & Jensen, J. N. (2012) · Development · doi:10.1242/dev.075804 · Cited by 79 · see citing works

The blood/vascular system in a phylogenetic perspective

Hartenstein, V., & Mandal, L. (2006) · BioEssays · doi:10.1002/bies.20497 · Cited by 77 · see citing works

Elementary nervous systems

Arendt, D. (2021) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2020.0347 · Cited by 72 · see citing works

The Evolutionary Assembly of Neuronal Machinery

Arendt, D. (2020) · Current Biology · doi:10.1016/j.cub.2020.04.008 · Cited by 67 · see citing works

The SNX-PX-BAR Family in Macropinocytosis: The Regulation of Macropinosome Formation by SNX-PX-BAR Proteins

Wang, J. T. H., Kerr, M. C., Karunaratne, S. M., Jeanes, A., Yap, A. S., & Teasdale, R. D. (2010) · PLoS ONE · doi:10.1371/journal.pone.0013763 · Cited by 67 · see citing works

Deletion of Ia-2 and/or Ia-2β in mice decreases insulin secretion by reducing the number of dense core vesicles

Cai, T., Hirai, H., Zhang, G., Zhang, M., Takahashi, N. K., Kasai, H., Satin, L. S., Leapman, R. D., & Notkins, A. L. (2011) · Diabetologia · doi:10.1007/s00125-011-2221-6 · Cited by 67 · see citing works

Stem cells and lineages of the intestine: a developmental and evolutionary perspective

Takashima, S., Gold, D., & Hartenstein, V. (2013) · Development Genes and Evolution · doi:10.1007/s00427-012-0422-8 · Cited by 67 · see citing works

Functions of Rab Proteins at Presynaptic Sites

Binotti, B., Jahn, R., & Chua, J. J. E. (2016) · Cells · doi:10.3390/cells5010007 · Cited by 62 · see citing works

Isolation of Ef silicatein and Ef lectin as Molecular Markers Sclerocytes and Cells Involved in Innate Immunity in the Freshwater Sponge Ephydatia fluviatilis

Funayama, N., Nakatsukasa, M., Kuraku, S., Takechi, K., Dohi, M., Iwabe, N., Miyata, T., & Agata, K. (2005) · ZOOLOGICAL SCIENCE · doi:10.2108/zsj.22.1113 · Cited by 61 · see citing works

Rethinking the Role of the Nervous System: Lessons From the Hydra Holobiont

Klimovich, A. V., & Bosch, T. C. G. (2018) · BioEssays · doi:10.1002/bies.201800060 · Cited by 61 · see citing works

Unbiased View of Synaptic and Neuronal Gene Complement in Ctenophores: Are There Pan-neuronal and Pan-synaptic Genes across Metazoa?

Moroz, L. L., & Kohn, A. B. (2015) · Integrative and Comparative Biology · doi:10.1093/icb/icv104 · Cited by 60 · see citing works

The statistical geometry of transcriptome divergence in cell-type evolution and cancer

Liang, C., the FANTOM Consortium, Forrest, A. R. R., & Wagner, G. P. (2015) · Nature Communications · doi:10.1038/ncomms7066 · Cited by 59 · see citing works

The role of Atonal transcription factors in the development of mechanosensitive cells

Jarman, A. P., & Groves, A. K. (2013) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2013.03.010 · Cited by 55 · see citing works

Conserved expression of vertebrate microvillar gene homologs in choanocytes of freshwater sponges

Peña, J. F., Alié, A., Richter, D. J., Wang, L., Funayama, N., & Nichols, S. (2016) · EvoDevo · doi:10.1186/s13227-016-0050-x · Cited by 54 · see citing works

Evolution of Animal Neural Systems

Liebeskind, B. J., Hofmann, H. A., Hillis, D. M., & Zakon, H. H. (2017) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-110316-023048 · Cited by 52 · see citing works

Kruppel-like factor 5 controls villus formation and initiation of cytodifferentiation in the embryonic intestinal epithelium

Bell, S. M., Zhang, L., Xu, Y. J., Besnard, V., Wert, S. E., Shroyer, N. F., & Whitsett, J. A. (2012) · Developmental Biology · doi:10.1016/j.ydbio.2012.12.010 · Cited by 51 · see citing works

The ontogeny of choanocyte chambers during metamorphosis in the demosponge Amphimedon queenslandica

Sogabe, S., Nakanishi, N., & Degnan, B. M. (2016) · EvoDevo · doi:10.1186/s13227-016-0042-x · Cited by 51 · see citing works

Evidence of Signaling and Adhesion Roles for β-Catenin in the Sponge Ephydatia muelleri

Schippers, K. J., & Nichols, S. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy033 · Cited by 49 · see citing works

A Rab21/LIM‐only/CH‐LIM complex regulates phagocytosis via both activating and inhibitory mechanisms

Khurana, T., Brzostowski, J. A., & Kimmel, A. R. (2005) · The EMBO Journal · doi:10.1038/sj.emboj.7600716 · Cited by 48 · see citing works

Ultrastructural localization of lysosomal digestion in the fresh water sponge Ephydatia fluviatilis

Willenz, P., & de Vyver, G. V. (1984) · Journal of Ultrastructure Research · doi:10.1016/s0022-5320(84)90112-6 · Cited by 48 · see citing works

Find your way with X-Ray

Karreman, M. A., Ruthensteiner, B., Mercier, L., Schieber, N. L., Solecki, G. M., Winkler, F., Goetz, J. G., & Schwab, Y. (2017) · Methods in cell biology · doi:10.1016/bs.mcb.2017.03.006 · Cited by 42 · see citing works

Animal Evolution: Convergent Nerve Cords?

Arendt, D. (2018) · Current Biology · doi:10.1016/j.cub.2018.01.056 · Cited by 40 · see citing works

Dynamic Transport and Cementation of Skeletal Elements Build Up the Pole-and-Beam Structured Skeleton of Sponges

Nakayama, S., 有馬, 和., Kawai, K., Mohri, K., Inui, C., Sugano, W., Koba, H., Tamada, K., Nakata, Y. J., Kishimoto, K., et al. (2015) · Current Biology · doi:10.1016/j.cub.2015.08.023 · Cited by 38 · see citing works

Requirement of the Tissue-Restricted Homeodomain Transcription Factor Nkx6.3 in Differentiation of Gastrin-Producing G Cells in the Stomach Antrum

Choi, M. Y., Romer, A. I., Wang, Y., Wu, M. P., Ito, S., Leiter, A. B., & Shivdasani, R. A. (2008) · Molecular and Cellular Biology · doi:10.1128/mcb.01737-07 · Cited by 38 · see citing works

Rbp‐j regulates expansion of pancreatic epithelial cells and their differentiation into exocrine cells during mouse development

Fujikura, J., Hosoda, K., Kawaguchi, Y., Noguchi, M., Iwakura, H., Odori, S., Mori, E., Tomita, T., Hirata, M., Ebihara, K., et al. (2007) · Developmental Dynamics · doi:10.1002/dvdy.21310 · Cited by 38 · see citing works

The Origin of the Integrative Systems: A Change in View Derived from Research on Coelenterates and Sponges

de Ceccatty, M. P. (1974) · Perspectives in biology and medicine · doi:10.1353/pbm.1974.0060 · Cited by 36 · see citing works

The evolution and function of the Pax/ S ix regulatory network in sponges

Rivera, A. M. Q., Winters, I. P., Rued, A. C., Ding, S. S., Posfai, D., Cieniewicz, B., Cameron, K., Gentile, L., & Hill, A. (2013) · Evolution & Development · doi:10.1111/ede.12032 · Cited by 35 · see citing works

Conserved gene regulatory module specifies lateral neural borders across bilaterians

Li, Y., Zhao, D., Horie, T., Chen, G., Bao, H., Chen, S., Liu, W., Horie, R., Liang, T., Dong, B., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1704194114 · Cited by 34 · see citing works

A New Flow-Regulating Cell Type in the Demosponge Tethya wilhelma – Functional Cellular Anatomy of a Leuconoid Canal System

Hammel, J. U., & Nickel, M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0113153 · Cited by 34 · see citing works

Mind bomb 2, a founder myoblast-specific protein, regulates myoblast fusion and muscle stability

Carrasco‐Rando, M., & Ruiz‐Gómez, M. (2008) · Development · doi:10.1242/dev.015529 · Cited by 32 · see citing works

Evolution of the Pax-Six-Eya-Dach network: the calcisponge case study

Fortunato, S., Leininger, S., & Adamska, M. (2014) · EvoDevo · doi:10.1186/2041-9139-5-23 · Cited by 32 · see citing works

Modern Approaches for Ultrastructural Analysis of the Zebrafish Embryo

Schieber, N. L., Nixon, S. J., Webb, R. I., Oorschot, V. M. J., & Parton, R. G. (2010) · Methods in cell biology · doi:10.1016/s0091-679x(10)96018-4 · Cited by 30 · see citing works

Solving Large Multicut Problems for Connectomics via Domain Decomposition

Pape, C., Beier, T., Li, P., Jain, V., Bock, D. D., & Kreshuk, A. (2017) · IEEE International Conference on Computer Vision Workshops · doi:10.1109/iccvw.2017.7 · Cited by 29 · see citing works

Analysis and Optimization of Graph Decompositions by Lifted MulticutsPreprint

Horňáková, A., Lange, J.-H., & Andres, B. (2015) · arXiv (Cornell University) · doi:10.48550/arxiv.1503.03791 · Cited by 28 · see citing works

Reconstructing complex lineage trees from scRNA-seq data using MERLoT

Parra, R. G., Παπαδόπουλος, Ν., Ahumada-Arranz, L., Kholtei, J. E., Mottelson, N., Horokhovsky, Y., Treutlein, B., & Söding, J. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz706 · Cited by 27 · see citing works

Visualization of protein crystals by high-energy phase-contrast X-ray imaging

Polikarpov, M., Bourenkov, G. P., Snigireva, I. I., Snigirev, A. A., Zimmermann, S., Csankó, K., Brockhauser, S., & Schneider, T. R. (2019) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798319011379 · Cited by 26 · see citing works

Krüppel-like factor gene function in the ctenophore Mnemiopsis leidyi assessed by CRISPR/Cas9-mediated genome editing

Presnell, J. S., & Browne, W. E. (2021) · Development · doi:10.1242/dev.199771 · Cited by 21 · see citing works

Leveraging Domain Knowledge to Improve Microscopy Image Segmentation With Lifted Multicuts

Pape, C., Matskevych, A., Wolny, A., Hennies, J., Mizzon, G., Louveaux, M., Musser, J. M., Maizel, A., Arendt, D., & Kreshuk, A. (2019) · Frontiers in Computer Science · doi:10.3389/fcomp.2019.00006 · Cited by 20 · see citing works

The central cells of sponges

Reiswig, H. M., & Brown, M. J. (1977) · Zoomorphology · doi:10.1007/bf01880648 · Cited by 16 · see citing works

A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC

Gopalan, V., Singh, A., Mehrabadi, F. R., Wang, L., Ruppin, E., Arda, H. E., & Hannenhalli, S. S. (2021) · Cancer Research · doi:10.1158/0008-5472.can-21-0427 · Cited by 16 · see citing works

Krüppel-like factor gene function in the ctenophore Mnemiopsis leidyi assessed by CRISPR/Cas9-mediated genome editing

(2019) · doi:10.1101/527002 · Cited by 9 · see citing works

Ancient gene linkages support ctenophores as sister to other animals

Schultz, D. T., Haddock, S. H. D., Bredeson, J. V., Green, R. E., Simakov, O., & Rokhsar, D. S. (2023) · Nature · doi:10.1038/s41586-023-05936-6 · Cited by 362 · see citing works

Segment Anything for Microscopy

Archit, A., Freckmann, L., Nair, S., Khalid, N., Hilt, P., Rajashekar, V., Freitag, M., Teuber, C., Spitzner, M., Contreras, C. T., et al. (2025) · Nature Methods · doi:10.1038/s41592-024-02580-4 · Cited by 354 · see citing works

The energy balance model of obesity: beyond calories in, calories out

Hall, K. D., Farooqi, I. S., Friedman, J. M., Klein, S., Loos, R. J., Mangelsdorf, D. J., O’Rahilly, S., Ravussin, E., Redman, L. M., Ryan, D. H., et al. (2022) · The American Journal of Clinical Nutrition · doi:10.1093/ajcn/nqac031 · Cited by 315 · see citing works

Mapping single-cell atlases throughout Metazoa unravels cell type evolution

Tarashansky, A. J., Musser, J. M., Khariton, M., Li, P., Arendt, D., Quake, S. R., & Wang, B. (2021) · eLife · doi:10.7554/elife.66747 · Cited by 299 · see citing works

Single-cell analysis of shared signatures and transcriptional diversity during zebrafish development

Sur, A., Wang, Y., Capar, P., Margolin, G., Prochaska, M. K., & Farrell, J. A. (2023) · Developmental Cell · doi:10.1016/j.devcel.2023.11.001 · Cited by 273 · see citing works

Spatiotemporal omics for biology and medicine

Liu, L., Chen, A., Li, Y., Mulder, J., Heyn, H., & Xu, X. (2024) · Cell · doi:10.1016/j.cell.2024.07.040 · Cited by 239 · see citing works

A stony coral cell atlas illuminates the molecular and cellular basis of coral symbiosis, calcification, and immunity

Levy, S., Elek, A., Grau‐Bové, X., Menéndez-Bravo, S., Iglesias, M., Tanay, A., Mass, T., & Sebé-Pedrós, A. (2021) · Cell · doi:10.1016/j.cell.2021.04.005 · Cited by 226 · see citing works

Volume electron microscopy

Peddie, C. J., Genoud, C., Kreshuk, A., Meechan, K., Micheva, K. D., Narayan, K., Pape, C., Parton, R. G., Schieber, N. L., Schwab, Y., et al. (2022) · Nature Reviews Methods Primers · doi:10.1038/s43586-022-00131-9 · Cited by 226 · see citing works

Single-cell transcriptomic profiling of the zebrafish inner ear reveals molecularly distinct hair cell and supporting cell subtypes

Shi, T., Beaulieu, M. O., Saunders, L. M., Fábián, P., Trapnell, C., Segil, N., Crump, J. G., & Raible, D. W. (2023) · eLife · doi:10.7554/elife.82978 · Cited by 173 · see citing works

The origin of animals: an ancestral reconstruction of the unicellular-to-multicellular transition

Ros-Rocher, N., Pérez-Posada, A., Leger, M. M., & Ruiz‐Trillo, I. (2021) · Open Biology · doi:10.1098/rsob.200359 · Cited by 160 · see citing works

Construction of a cross-species cell landscape at single-cell level

Wang, R., Zhang, P., Wang, J., Ma, L., Weigao, E., Suo, S., Jiang, M., Li, J., Chen, H., Sun, H., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac633 · Cited by 146 · see citing works

Looking Down on NF- κ B

Williams, L. M., & Gilmore, T. D. (2020) · Molecular and Cellular Biology · doi:10.1128/mcb.00104-20 · Cited by 128 · see citing works

Highly processed foods can be considered addictive substances based on established scientific criteria

Gearhardt, A. N., & DiFeliceantonio, A. G. (2022) · Addiction · doi:10.1111/add.16065 · Cited by 128 · see citing works

Single-cell transcriptomics identifies conserved regulators of neuroglandular lineages

Steger, J., Cole, A. G., Denner, A., Lebedeva, T. S., Genikhovich, G., Ries, A., Reischl, R., Taudes, E., Lassnig, M., & Technau, U. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111370 · Cited by 120 · see citing works

Benchmarking strategies for cross-species integration of single-cell RNA sequencing data

Song, Y., Miao, Z., Brāzma, A., & Papatheodorou, I. (2023) · Nature Communications · doi:10.1038/s41467-023-41855-w · Cited by 106 · see citing works

Heterotrophy in the earliest gut: a single-cell view of heterotrophic carbon and nitrogen assimilation in sponge-microbe symbioses

Rix, L. N., Ribes, M., Coma, R., Jahn, M. T., de Goeij, J. M., van Oevelen, D., Escrig, S., Meibom, A., & Hentschel, U. (2020) · The ISME Journal · doi:10.1038/s41396-020-0706-3 · Cited by 109 · see citing works

ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics

García-Castro, H., Kenny, N. J., Iglesias, M., Álvarez‐Campos, P., Mason, V., Elek, A., Schönauer, A., Sleight, V. A., Neiro, J., Aboobaker, A. A., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02302-5 · Cited by 108 · see citing works

Volume EM: a quiet revolution takes shape

Collinson, L., Bosch, C., Bullen, A., Burden, J. J., Carzaniga, R., Cheng, C., Darrow, M. C., Fletcher, G., Johnson, E., Narayan, K., et al. (2023) · Nature Methods · doi:10.1038/s41592-023-01861-8 · Cited by 100 · see citing works

Harmonizing model organism data in the Alliance of Genome Resources

Agapite, J., Albou, L., Aleksander, S., Alexander, M., Anagnostopoulos, A. V., Antonazzo, G., Argasinska, J., Arnaboldi, V., Attrill, H. L., Becerra, A., et al. (2022) · Genetics · doi:10.1093/genetics/iyac022 · Cited by 90 · see citing works

Stepwise emergence of the neuronal gene expression program in early animal evolution

Najle, S. R., Grau‐Bové, X., Elek, A., Navarrete, C., Cianferoni, D., Chiva, C., Cañas-Armenteros, D., Mallabiabarrena, A., Kamm, K., Sabidó, E., et al. (2023) · Cell · doi:10.1016/j.cell.2023.08.027 · Cited by 86 · see citing works

Evolutionary cell type mapping with single-cell genomics

Tanay, A., & Sebé-Pedrós, A. (2021) · Trends in Genetics · doi:10.1016/j.tig.2021.04.008 · Cited by 75 · see citing works

scDFC: A deep fusion clustering method for single-cell RNA-seq data

Hu, D., Liang, K., Zhou, S., Tu, W., Liu, M., & Liu, X. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad216 · Cited by 80 · see citing works

Single-cell RNA sequencing of the Strongylocentrotus purpuratus larva reveals the blueprint of major cell types and nervous system of a non-chordate deuterostome

Paganos, P., Voronov, D., Musser, J. M., Arendt, D., & Arnone, M. I. (2021) · eLife · doi:10.7554/elife.70416 · Cited by 73 · see citing works

Cell type diversity in a developing octopus brain

Styfhals, R., Zolotarov, G., Hulselmans, G. J., Spanier, K. I., Poovathingal, S. K., Elagoz, A. M., Winter, S. D., Deryckere, A., Rajewsky, N., Ponte, G., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-35198-1 · Cited by 76 · see citing works

Articulating the “stem cell niche” paradigm through the lens of non-model aquatic invertebrates

Martı́nez, P., Ballarin, L., Ereskovsky, A. V., Gazave, E., Hobmayer, B., Manni, L., Röttinger, É., Sprecher, S. G., Tiozzo, S., Coelho, A. V., et al. (2022) · BMC Biology · doi:10.1186/s12915-022-01230-5 · Cited by 73 · see citing works

Multiple Origins of Neurons From Secretory Cells

Moroz, L. L. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.669087 · Cited by 67 · see citing works

Elementary nervous systems

Arendt, D. (2021) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2020.0347 · Cited by 72 · see citing works

The Evolutionary Assembly of Neuronal Machinery

Arendt, D. (2020) · Current Biology · doi:10.1016/j.cub.2020.04.008 · Cited by 67 · see citing works

A chromosome-scale epigenetic map of the <i>Hydra</i> genome reveals conserved regulators of cell state

Cazet, J. F., Siebert, S., Little, H. M., Bertemes, P., Primack, A. S., Ladurner, P., Achrainer, M., Fredriksen, M. T., Moreland, R. T., Singh, S., et al. (2023) · Genome Research · doi:10.1101/gr.277040.122 · Cited by 66 · see citing works

Single-cell RNA sequencing analysis of shrimp immune cells identifies macrophage-like phagocytes

Yang, P., Chen, Y., Huang, Z., Xia, H., Cheng, L., Wu, H., Zhang, Y., & Wang, F. (2022) · eLife · doi:10.7554/elife.80127 · Cited by 55 · see citing works

Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories

Piovani, L., Leite, D. J., Yáñez-Guerra, L. A., Simpson, F., Musser, J. M., Salvador‐Martínez, I., Marlétaz, F., Jékely, G., & Telford, M. J. (2023) · Science Advances · doi:10.1126/sciadv.adg6034 · Cited by 50 · see citing works

MRTF specifies a muscle-like contractile module in Porifera

Colgren, J. J., & Nichols, S. (2022) · Nature Communications · doi:10.1038/s41467-022-31756-9 · Cited by 47 · see citing works

The neuronal cilium – a highly diverse and dynamic organelle involved in sensory detection and neuromodulation

Jurisch‐Yaksi, N., Wachten, D., & Gopalakrishnan, J. (2024) · Trends in Neurosciences · doi:10.1016/j.tins.2024.03.004 · Cited by 50 · see citing works

Evolution of synapses and neurotransmitter systems: The divide-and-conquer model for early neural cell-type evolution

Burkhardt, P., & Jékely, G. (2021) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2021.11.002 · Cited by 48 · see citing works

Cell differentiation: What have we learned in 50 years?

Newman, S. A. (2019) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2019.110031 · Cited by 40 · 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

Annelid adult cell type diversity and their pluripotent cellular origins

Álvarez‐Campos, P., García-Castro, H., Emili, E., Pérez-Posada, A., del Olmo, I., Péron, S., Salamanca-Díaz, D. A., Mason, V., Metzger, B. M., Bely, A. E., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-47401-6 · Cited by 39 · see citing works

Evolutionary assembly of cooperating cell types in an animal chemical defense system

Brückner, A., Badroos, J. M., Learsch, R. W., Yousefelahiyeh, M., Kitchen, S. A., & Parker, J. (2021) · Cell · doi:10.1016/j.cell.2021.11.014 · Cited by 36 · see citing works

Alternative neural systems: What is a neuron? (Ctenophores, sponges and placozoans)

Moroz, L. L., & Romanova, D. Y. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.1071961 · Cited by 39 · see citing works

Cell Atlas technologies and insights into tissue architecture

Wilbrey-Clark, A., Roberts, K., & Teichmann, S. A. (2020) · Biochemical Journal · doi:10.1042/bcj20190341 · Cited by 36 · see citing works

Stem Cells and Innate Immunity in Aquatic Invertebrates: Bridging Two Seemingly Disparate Disciplines for New Discoveries in Biology

Ballarin, L., Karahan, A., Salvetti, A., Rossi, L., Manni, L., Rinkevich, B., Rosner, A., Voskoboynik, A., Rosental, B., Canesi, L., et al. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.688106 · Cited by 37 · see citing works

Cross-phyla protein annotation by structural prediction and alignment

Ruperti, F., Papadopoulos, N., Musser, J. M., Mirdita, M., Steinegger, M., & Arendt, D. (2023) · Genome Biology · doi:10.1186/s13059-023-02942-9 · Cited by 38 · see citing works

Cell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data

Mah, J. L., & Dunn, C. W. (2024) · Nature Ecology & Evolution · doi:10.1038/s41559-023-02281-9 · Cited by 37 · see citing works

Evolution of Sensory Receptors

Valencia‐Montoya, W. A., Pierce, N. E., & Bellono, N. W. (2024) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-120123-112853 · Cited by 35 · see citing works

Crustacean leg regeneration restores complex microanatomy and cell diversity

Almazán, A., Çevrim, Ç., Musser, J. M., Averof, M., & Paris, M. (2022) · Science Advances · doi:10.1126/sciadv.abn9823 · Cited by 35 · see citing works

Inherency and agency in the origin and evolution of biological functions

Newman, S. A. (2022) · Biological Journal of the Linnean Society · doi:10.1093/biolinnean/blac109 · Cited by 31 · see citing works

Benchmarking cross-species single-cell RNA-seq data integration methods: towards a cell type tree of life

Hua-wen, Z., Han, W., Gómez-Cabrero, D., Tegner, J. N., Gao, X., Cui, G., & Aranda, M. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1316 · Cited by 31 · see citing works

Amino acids integrate behaviors in nerveless placozoans

Nikitin, M. A., Romanova, D. Y., Borman, S. I., & Moroz, L. L. (2023) · Frontiers in Neuroscience · doi:10.3389/fnins.2023.1125624 · Cited by 31 · see citing works

MorphoFeatures for unsupervised exploration of cell types, tissues, and organs in volume electron microscopy

Zinchenko, V., Hugger, J., Uhlmann, V., Arendt, D., & Kreshuk, A. (2023) · eLife · doi:10.7554/elife.80918 · Cited by 30 · see citing works

Choanoflagellates and the ancestry of neurosecretory vesicles

Göhde, R., Naumann, B. T., Laundon, D., Imig, C., McDonald, K. L., Cooper, B. H., Varoqueaux, F., Fasshauer, D., & Burkhardt, P. (2021) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2019.0759 · Cited by 28 · see citing works

Contraction-Expansion and the Effects on the Aquiferous System in the Demosponge Halichondria panicea

Goldstein, J., Bisbo, N., Funch, P., & Riisgård, H. U. (2020) · Frontiers in Marine Science · doi:10.3389/fmars.2020.00113 · Cited by 27 · see citing works

Phylomitogenomics bolsters the high-level classification of Demospongiae (phylum Porifera)

Lavrov, D. V., Díaz, M. C., Maldonado, M., Morrow, C. C., Pérez, T., Pomponi, S. A., & THACKER, R. W. (2023) · PLoS ONE · doi:10.1371/journal.pone.0287281 · Cited by 26 · see citing works

Placozoan fiber cells: mediators of innate immunity and participants in wound healing

Mayorova, T. D., Hammar, K. M., Jung, J. H., Aronova, M. A., Zhang, G., Winters, C. A., Reese, T. S., & Smith, C. L. (2021) · Scientific Reports · doi:10.1038/s41598-021-02735-9 · Cited by 26 · see citing works

Tissue dissociation for single-cell and single-nuclei RNA sequencing for low amounts of input material

Wiegleb, G., Reinhardt, S., Dahl, A., & Posnien, N. (2022) · Frontiers in Zoology · doi:10.1186/s12983-022-00472-x · Cited by 22 · see citing works

Nitric oxide signaling in ctenophores

Moroz, L. L., Mukherjee, K., & Romanova, D. Y. (2023) · Frontiers in Neuroscience · doi:10.3389/fnins.2023.1125433 · Cited by 25 · see citing works

A New Model Organism to Investigate Extraocular Photoreception: Opsin and Retinal Gene Expression in the Sea Urchin Paracentrotus lividus

Paganos, P., Ullrich-Lüter, E., Caccavale, F., Zakrzewski, A.-C., Voronov, D., Fournon-Berodia, I., Cocurullo, M., Lüter, C., & Arnone, M. I. (2022) · Cells · doi:10.3390/cells11172636 · Cited by 23 · see citing works

The genome of the reef-building glass sponge Aphrocallistes vastus provides insights into silica biomineralization

Francis, W. R., Eitel, M., Vargas, S., García‐Escudero, C. A., Conci, N., Deister, F., Mah, J. L., Guiglielmoni, N., Krebs, S., Blum, H., et al. (2023) · Royal Society Open Science · doi:10.1098/rsos.230423 · Cited by 23 · see citing works

Expanding of Life Strategies in Placozoa: Insights From Long-Term Culturing of Trichoplax and Hoilungia

Romanova, D. Y., Nikitin, M. A., Shchenkov, S. V., & Moroz, L. L. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.823283 · Cited by 25 · see citing works

A Primer for Single-Cell Sequencing in Non-Model Organisms

Alfieri, J. M., Wang, G., Jonika, M. M., Gill, C. A., Blackmon, H., & Athrey, G. (2022) · Genes · doi:10.3390/genes13020380 · Cited by 23 · see citing works

Integrating single cell transcriptomics and volume electron microscopy confirms the presence of pancreatic acinar-like cells in sea urchins

Paganos, P., Ronchi, P., Carl, J., Mizzon, G., Martinez, P., Benvenuto, G., & Arnone, M. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.991664 · Cited by 15 · see citing works

Whole genome sequence of the deep-sea sponge Geodia barretti (Metazoa, Porifera, Demospongiae)

Steffen, K., Proux‐Wéra, E., Solér, L., Churcher, A. M., Sundh, J., & Cárdenas, P. (2023) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkad192 · Cited by 23 · see citing works

Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response

Ruperti, F., Becher, I., Stokkermans, A., Wang, L., Marschlich, N., Potel, C., Maus, E., Stein, F., Drotleff, B., Schippers, K. J., et al. (2024) · Current Biology · doi:10.1016/j.cub.2023.12.021 · Cited by 23 · see citing works

Orthology Clusters from Gene Trees with Possvm

Grau‐Bové, X., & Sebé-Pedrós, A. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab234 · Cited by 23 · see citing works

Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets

Müller, A., Schmidt, D., Albrecht, J. P., Rieckert, L., Otto, M., Garcia, L. E. G., Fabig, G., Solimena, M., & WEIGERT, M. G. (2024) · Nature Protocols · doi:10.1038/s41596-024-00957-5 · Cited by 21 · see citing works

Cell contractility in early animal evolution

Brunet, T. (2023) · Current Biology · doi:10.1016/j.cub.2023.07.054 · Cited by 20 · see citing works

Nitric oxide signaling controls collective contractions in a colonial choanoflagellate

Reyes-Rivera, J., Wu, Y., Guthrie, B. G. H., Marletta, M. A., King, N., & Brunet, T. (2022) · Current Biology · doi:10.1016/j.cub.2022.04.017 · Cited by 21 · see citing works

Krüppel-like factor gene function in the ctenophore Mnemiopsis leidyi assessed by CRISPR/Cas9-mediated genome editing

Presnell, J. S., & Browne, W. E. (2021) · Development · doi:10.1242/dev.199771 · Cited by 21 · see citing works

Methods of enhanced FIB-SEM sample preparation and image acquisition

Pang, S., & Xu, C. S. (2023) · Methods in cell biology · doi:10.1016/bs.mcb.2023.01.019 · Cited by 20 · see citing works

Leveraging Domain Knowledge to Improve Microscopy Image Segmentation With Lifted Multicuts

Pape, C., Matskevych, A., Wolny, A., Hennies, J., Mizzon, G., Louveaux, M., Musser, J. M., Maizel, A., Arendt, D., & Kreshuk, A. (2019) · Frontiers in Computer Science · doi:10.3389/fcomp.2019.00006 · Cited by 20 · see citing works

TranscriptFormer: A generative cell atlas across 1.5 billion years of evolution

Pearce, J. D., Simmonds, S. E., Mahmoudabadi, G., Krishnan, L., Palla, G., Istrate, A.-M., Tarashansky, A. J., Nelson, B. E., Valenzuela, O., Li, D., et al. (2026) · Science · doi:10.1126/science.aec8514 · Cited by 57 · see citing works

Crosshair, semi-automated targeting for electron microscopy with a motorised ultramicrotome

Meechan, K., Guan, W., Riedinger, A., Stankova, V., Yoshimura, A., Pipitone, R., Milberger, A., Schaar, H., Romero‐Brey, I., Templin, R., et al. (2022) · eLife · doi:10.7554/elife.80899 · Cited by 19 · see citing works

The Buds of Oscarella lobularis (Porifera, Homoscleromorpha): A New Convenient Model for Sponge Cell and Evolutionary Developmental Biology

Rocher, C., Vernale, A., Fierro‐Constaín, L., Séjourné, N., Chenesseau, S., Marschal, C., Issartel, J., Goff, E. L., Stroebel, D., Jouvion, J., et al. (2024) · Journal of Experimental Zoology Part B Molecular and Developmental Evolution · doi:10.1002/jez.b.23271 · Cited by 17 · see citing works

Marine Natural Products in Inflammation‐Related Diseases: Opportunities and Challenges

Zhang, T., Ouyang, Z., Zhang, Y., Sun, H., Kong, L., Xu, Q., Qu, J., & Sun, Y. (2025) · Medicinal Research Reviews · doi:10.1002/med.22109 · Cited by 18 · see citing works

Marine Invertebrates One Cell at A Time: Insights from Single-Cell Analysis

Bump, P. A., & Lubeck, L. (2023) · Integrative and Comparative Biology · doi:10.1093/icb/icad034 · Cited by 17 · see citing works

Archaeocytes in sponges: simple cells of complicated fate

Ereskovsky, A. V., Melnikov, N. P., & Lavrov, A. (2024) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.13162 · Cited by 17 · see citing works

The Biodiversity Cell Atlas: mapping the tree of life at cellular resolution

Sebé-Pedrós, A., Tanay, A., Lawniczak, M., Arendt, D., Aerts, S., Archibald, J. M., Arnone, M. I., Blaxter, M., Cleves, P. A., Coelho, S. M., et al. (2025) · Nature · doi:10.1038/s41586-025-09312-4 · Cited by 16 · see citing works

The cellular substrate of evolutionary novelty

Parker, J., & Pennell, M. W. (2025) · Current Biology · doi:10.1016/j.cub.2025.04.014 · Cited by 15 · see citing works

Non-Neuronal Transmitter Systems in Bacteria, Non-Nervous Eukaryotes, and Invertebrate Embryos

Shmukler, Y. B., & Никишин, Д. А. (2022) · Biomolecules · doi:10.3390/biom12020271 · Cited by 15 · see citing works

Plant-on-chip: Core morphogenesis processes in the tiny plant <i>Wolffia australiana</i>

Li, F., Yang, J.-J., Sun, Z.-Y., Wang, L., Qi, L.-Y., A, S., Liu, Y.-Q., Zhang, H.-M., Dang, L.-F., Wang, S.-J., et al. (2023) · PNAS Nexus · doi:10.1093/pnasnexus/pgad141 · Cited by 15 · see citing works

Why isn’t sex optional? Stem-cell competition, loss of regenerative capacity, and cancer in metazoan evolution

Fields, C., & Levin, M. G. (2020) · Communicative & Integrative Biology · doi:10.1080/19420889.2020.1838809 · Cited by 14 · see citing works

The premetazoan ancestry of the synaptic toolkit and appearance of first neurons

Colgren, J. J., & Burkhardt, P. (2022) · Essays in Biochemistry · doi:10.1042/ebc20220042 · Cited by 17 · see citing works

A Review on Genus Halichondria (Demospongiae, Porifera)

Goldstein, J., & Funch, P. (2022) · Journal of Marine Science and Engineering · doi:10.3390/jmse10091312 · Cited by 14 · see citing works

Jellyfish for the study of nervous system evolution and function

Cunningham, K. L., Anderson, D. J., & Weissbourd, B. (2024) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2024.102903 · Cited by 14 · see citing works

Advancing marine invertebrate cell line research: four key knowledge gaps

Rinkevich, B., & Pomponi, S. A. (2025) · In Vitro Cellular & Developmental Biology - Animal · doi:10.1007/s11626-025-01029-y · Cited by 13 · see citing works

Voltage-gated ion channel diversity underlies neuronal excitability and nervous system evolution

Dávila-Velderrain, J., & van Giesen, L. (2025) · Nature Communications · doi:10.1038/s41467-025-66641-8 · Cited by 14 · see citing works

Toxic Effect of Anionic Surfactants on Freshwater Sponge Lubomirskia baikalensis and Its Endosymbiotic Microalgae Chlorella sp.

Nikonova, A. A., Mizandrontsev, I. B., Bazhenov, B. N., Khanaev, I. V., Shabalina, O. V., Afanasyeva, A. A., Avezova, T. N., Chindyavskaya, A. N., Bityutsky, A. N., Kan, A. Y., et al. (2023) · Diversity · doi:10.3390/d15010077 · Cited by 13 · see citing works

Integrating phylogenies into single-cell RNA sequencing analysis allows comparisons across species, genes, and cells

Church, S. H., Mah, J. L., & Dunn, C. W. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002633 · Cited by 13 · see citing works

Neuronal and non-neuronal functions of the synaptic cell adhesion molecule neurexin in Nematostella vectensis

Guzman, C., Mohri, K., Nakamura, R., Miyake, M., Tsuchiya, Y., Tomii, K., & Watanabe, H. (2024) · Nature Communications · doi:10.1038/s41467-024-50818-8 · Cited by 13 · see citing works

Electrical signaling and coordinated behavior in the closest relative of animals

Colgren, J. J., & Burkhardt, P. (2025) · Science Advances · doi:10.1126/sciadv.adr7434 · Cited by 13 · see citing works

Form, Function, Agency: Sources of Natural Purpose in Animal Evolution

Newman, S. A. (2023) · The MIT Press eBooks · doi:10.7551/mitpress/14642.003.0014 · Cited by 13 · see citing works

A morphological cell atlas of the freshwater sponge Ephydatia muelleri with key insights from targeted single-cell transcriptomes

Leys, S. P., Grombacher, L., Field, D., Elliott, G. R. D., Ho, V., KAHN, A. S., Reid, P. J., Riesgo, A., Lanna, E., Bobkov, Y. V., et al. (2025) · EvoDevo · doi:10.1186/s13227-025-00237-7 · Cited by 12 · see citing works

Single-Cell Analysis for Whole-Organism Datasets

Pisco, A. O., Tojo, B. M., & McGeever, A. (2021) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-092820-031008 · Cited by 10 · see citing works

A cell-cell atlas approach for understanding symbiotic interactions between microbes.

Alacid, E., & Richards, T. (2021) · Current Opinion in Microbiology · doi:10.1016/j.mib.2021.09.001 · Cited by 11 · see citing works

The Semantic Mutex Watershed for Efficient Bottom-Up Semantic Instance Segmentation

Wolf, S., Li, Y., Pape, C., Bailoni, A., Kreshuk, A., & Hamprecht, F. A. (2020) · Lecture notes in computer science · doi:10.1007/978-3-030-58539-6_13 · Cited by 12 · see citing works

Potential for host-symbiont communication via neurotransmitters and neuromodulators in an aneural animal, the marine sponge Amphimedon queenslandica

Xiang, X., Gomez, A. A. V., Blomberg, S. P., Yuan, H., Degnan, B. M., & Degnan, B. M. (2023) · Frontiers in Neural Circuits · doi:10.3389/fncir.2023.1250694 · Cited by 11 · see citing works

Single-nucleus profiling highlights the all-brain echinoderm nervous system

Paganos, P., Ullrich-Lüter, J., Almazán, A., Voronov, D., Carl, J., Zakrzewski, A.-C., Zemann, B., Rusciano, M. L., Sancerni, T., Schauer, M., et al. (2025) · Science Advances · doi:10.1126/sciadv.adx7753 · Cited by 12 · see citing works

The contraction–expansion behaviour in the demosponge Tethya wilhelma is light controlled and follows a diurnal rhythm

Flensburg, S. B., Garm, A. L., & Funch, P. (2022) · Journal of Experimental Biology · doi:10.1242/jeb.244751 · Cited by 11 · see citing works

Mapping Cell Atlases at the Single‐Cell Level

Ye, F., Wang, J., Li, J., Mei, Y., & Guo, G. (2023) · Advanced Science · doi:10.1002/advs.202305449 · Cited by 11 · see citing works

Cell type innovation at the tips of the animal tree

Kishi, Y., & Parker, J. (2021) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2021.01.009 · Cited by 11 · see citing works

Electrical Signaling Beyond Neurons

Monk, T., Dennler, N., Ralph, N. O., Rastogi, S., Afshar, S., Urbizagastegui, P. A. D. A., Jarvis, R. J., André, V. S., & Adamatzky, A. (2024) · Neural Computation · doi:10.1162/neco_a_01696 · Cited by 11 · see citing works

Understanding the evolution of cell types to explain the roots of animal diversity

Callier, V. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2002403117 · Cited by 4 · see citing works

Evolution of the Sensory/Neural Cell Types

Leys, S. P., Mah, J. L., & Esposito, E. K. J. (2021) · CRC Press eBooks · doi:10.1201/b21831-6 · Cited by 1 · see citing works

Elements of a ‘nervous system’ in sponges

Leys, S. P. (2015) · Journal of Experimental Biology · doi:10.1242/jeb.110817 · Cited by 138 · see citing works

A morphological cell atlas of the freshwater sponge Ephydatia muelleri with key insights from targeted single-cell transcriptomes

Leys, S. P., Grombacher, L., Field, D., Elliott, G. R. D., Ho, V., KAHN, A. S., Reid, P. J., Riesgo, A., Lanna, E., Bobkov, Y. V., et al. (2025) · EvoDevo · doi:10.1186/s13227-025-00237-7 · Cited by 12 · see citing works

Calcareous sponge cell atlas provides support to homology between sponge and eumetazoan body plansPreprint

Pan, D., Rajapaksha, D. G., Caglar, C., Rathjen, R., Adamski, M., & Adamska, M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.26.708390