A quantitative framework for characterizing the evolutionary history of mammalian gene expression
Open accessPublished version of a preprint
Abstract
The evolutionary history of a gene helps predict its function and relationship to phenotypic traits. Although sequence conservation is commonly used to decipher gene function and assess medical relevance, methods for functional inference from comparative expression data are lacking. Here, we use RNA-seq across seven tissues from 17 mammalian species to show that expression evolution across mammals is accurately modeled by the Ornstein–Uhlenbeck process, a commonly proposed model of continuous trait evolution. We apply this model to identify expression pathways under neutral, stabilizing, and directional selection. We further demonstrate novel applications of this model to quantify the extent of stabilizing selection on a gene's expression, parameterize the distribution of each gene's optimal expression level, and detect deleterious expression levels in expression data from individual patients. Our work provides a statistical framework for interpreting expression data across species and in disease.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Previous reports show high constraints of brain gene expression variance across evolution.
“This is in accordance with previous reports showing high constraints of brain gene expression variance across evolution”
From Cross-Species Single-Cell Analysis Reveals Divergence of the Primate Microglia Program (2019) · cites this paper as Chen et al., 2019
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709 · see citing works
Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp616 · Cited by 41,364 · see citing works
Richards, S., Aziz, N., Bale, S., Bick, D., Das, S., Gastier-Foster, J., Grody, W. W., Hegde, M., Lyon, E., Spector, E., et al. (2015) · Genetics in Medicine · doi:10.1038/gim.2015.30 · Cited by 32,594 · see citing works
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Li, B., & Dewey, C. N. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-323 · Cited by 22,179 · see citing works
A scaling normalization method for differential expression analysis of RNA-seq data
Robinson, M. D., & Oshlack, A. (2010) · Genome Biology · doi:10.1186/gb-2010-11-3-r25 · Cited by 7,876 · see citing works
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 4,408 · see citing works
Evolutionary Rate at the Molecular Level
KIMURA, M. (1968) · Nature · doi:10.1038/217624a0 · Cited by 3,747 · see citing works
GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists
Eden, E., Navon, R., Steinfeld, I., Lipson, D., & Yakhini, Z. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-48 · Cited by 3,356 · see citing works
King, M.-C., & Wilson, A. C. (1975) · Science · doi:10.1126/science.1090005 · Cited by 2,815 · see citing works
A comparative encyclopedia of DNA elements in the mouse genome
Yue, F., Cheng, Y., Breschi, A., Vierstra, J., Wu, W., Ryba, T., Sandstrom, R., Ma, Z., Davis, C., Pope, B. D., et al. (2014) · Nature · doi:10.1038/nature13992 · Cited by 1,781 · see citing works
Sequencing and comparison of yeast species to identify genes and regulatory elements
Kellis, M., Patterson, N. J., Endrizzi, M. G., Birren, B. W., & Lander, E. S. (2003) · Nature · doi:10.1038/nature01644 · Cited by 1,731 · see citing works
Comparative Genomics of the Eukaryotes
Rubin, G. M., Yandell, M. D., Wortman, J. R., Gabor, G. L., Miklos, Nelson, C. R., Hariharan, I. K., Fortini, M. E., Li, P. W., Apweiler, R., et al. (2000) · Science · doi:10.1126/science.287.5461.2204 · Cited by 1,698 · cited 1× · see citing works
“Comparative genomicshas identified andannotated functional genetic elements by their evolutionary patterns across species (Rubin et al. 2000; Kellis et al. 2003; Siepel et al. 2005; Pollard et al. 2006; Lindblad-Toh et al. 2011).”
BackgroundClinGen — The Clinical Genome Resource
Rehm, H. L., Berg, J. S., Brooks, L. D., Bustamante, C. D., Evans, J. P., Landrum, M. J., Ledbetter, D. H., Maglott, D. R., Martin, C. L., Nussbaum, R. L., et al. (2015) · New England Journal of Medicine · doi:10.1056/nejmsr1406261 · Cited by 1,496 · see citing works
Phylogenetic comparative analysis: a modeling approach for adaptive evolution
Butler, M. A., & King, A. A. (2004) · The American Naturalist · doi:10.1086/426002 · Cited by 1,438 · see citing works
Stabilizing selection and the comparative analysis of adaptation
Hansen, T. F. (1997) · Evolution · doi:10.1111/j.1558-5646.1997.tb01457.x · Cited by 1,361 · see citing works
Genetic diagnosis by whole exome capture and massively parallel DNA sequencing
Choi, M., Scholl, U. I., Ji, W., Liu, T., Tikhonova, I. R., Zumbo, P., Nayır, A., Bakkaloğlu, A., Özen, S., Sanjad, S. A., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0910672106 · Cited by 1,327 · see citing works
The evolution of gene expression levels in mammalian organs
Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csárdi, G., Harrigan, P., Weier, M., Liechti, A., Aximu-Petri, A., Kircher, M., et al. (2011) · Nature · doi:10.1038/nature10532 · Cited by 1,248 · see citing works
Lewontin, R. C., & Hubby, J. L. (1966) · Genetics · doi:10.1093/genetics/54.2.595 · Cited by 1,221 · see citing works
Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations
O'Roak, B. J., Deriziotis, P., Lee, C., Vives, L., Schwartz, J. J., Girirajan, S., Karakoc, E., MacKenzie, A. P., Ng, S. B., Baker, C., et al. (2011) · Nature Genetics · doi:10.1038/ng.835 · Cited by 1,203 · see citing works
A high-resolution map of human evolutionary constraint using 29 mammals
Broad Institute Sequencing Platform and Whole Genome Assembly Team, Lindblad-Toh, K., Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Genome Institute at Washington University, Garber, M., Zuk, O., Lin, M. F., Parker, B. J., Washietl, S., Kheradpour, P., et al. (2011) · Nature · doi:10.1038/nature10530 · Cited by 1,108 · see citing works
Self-citationEvolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues
Merkin, J., Russell, C., Chen, P., & Burge, C. B. (2012) · Science · doi:10.1126/science.1228186 · Cited by 972 · see citing works
RNA-SeQC: RNA-seq metrics for quality control and process optimization
DeLuca, D. S., Levin, J. Z., Sivachenko, A., Fennell, T., Nazaire, M.-D., Williams, C., Reich, M., Winckler, W., & Getz, G. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts196 · Cited by 899 · see citing works
Intra- and Interspecific Variation in Primate Gene Expression Patterns
Enard, W., Khaitovich, P., Klose, J., Zöllner, S. K., Heißig, F., Giavalisco, P., Nieselt, K., Muchmore, E. A., Varki, A. P., Ravid, R., et al. (2002) · Science · doi:10.1126/science.1068996 · Cited by 845 · see citing works
Improving genetic diagnosis in Mendelian disease with transcriptome sequencing
Cummings, B. B., Marshall, J. L., Tukiainen, T., Lek, M., Donkervoort, S., Foley, A. R., Bolduc, V., Waddell, L. B., Sandaradura, S. A., O’Grady, G. L., et al. (2017) · Science Translational Medicine · doi:10.1126/scitranslmed.aal5209 · Cited by 831 · see citing works
Self-citationComprehensive comparative analysis of strand-specific RNA sequencing methods
Levin, J. Z., Yassour, M., Adiconis, X., Nusbaum, C., Thompson, D. A., Friedman, N., Gnirke, A., & Regev, A. (2010) · Nature Methods · doi:10.1038/nmeth.1491 · Cited by 753 · see citing works
Self-citationAmberger, J. S., & Hamosh, A. (2017) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.27 · Cited by 741 · see citing works
Receptor-mediated endocytosis: insights from the lipoprotein receptor system.
Brown, M. S., & Goldstein, J. L. (1979) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.76.7.3330 · Cited by 711 · see citing works
Integrated physiology and systems biology of PPARα
Kersten, S. (2014) · Molecular Metabolism · doi:10.1016/j.molmet.2014.02.002 · Cited by 679 · see citing works
C. Genetics of Man Enzyme polymorphisms in man
Harris, H. (1966) · Proceedings of the Royal Society of London. Series B. Biological Sciences · doi:10.1098/rspb.1966.0032 · Cited by 611 · see citing works
Patterns of Positive Selection in Six Mammalian Genomes
Kosiol, C., Vinař, T., da Fonseca, R. R., Hubisz, M. J., Bustamante, C. D., Nielsen, R., & Siepel, A. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000144 · Cited by 576 · see citing works
Origins and functional evolution of Y chromosomes across mammals
Cortez, D., Marín, R. M., Toledo‐Flores, D., Froidevaux, L., Liechti, A., Waters, P. D., Grützner, F., & Kaessmann, H. (2014) · Nature · doi:10.1038/nature13151 · Cited by 530 · see citing works
Aken, B. L., Achuthan, P., Akanni, W., Amode, M. R., Bernsdorff, F., Bhai, J., Billis, K., Carvalho-Silva, D., Cummins, C., Clapham, P., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1104 · Cited by 512 · see citing works
Forces shaping the fastest evolving regions in the human genome
Pollard, K. S., Salama, S. R., King, B., Kern, A. D., Dreszer, T., Katzman, S., Siepel, A., Pedersen, J. S., Bejerano, G., Baertsch, R., et al. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020168 · Cited by 511 · see citing works
Systematic changes in gene expression patterns following adaptive evolution in yeast
Ferea, T., Botstein, D., Brown, P. O., & Rosenzweig, R. F. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.17.9721 · Cited by 479 · see citing works
Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals
Swanson, W. J., Yang, Z., Wolfner, M. F., & Aquadro, C. F. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.051605998 · Cited by 441 · see citing works
Gene expression divergence recapitulates the developmental hourglass model
Kalinka, A. T., Varga, K. M., Gerrard, D. T., Preibisch, S., Corcoran, D. L., Jarrells, J., Ohler, U., Bergman, C., & Tomančák, P. (2010) · Nature · doi:10.1038/nature09634 · Cited by 415 · see citing works
Measuring error rates in genomic perturbation screens: gold standards for human functional genomics
Hart, T., Brown, K. R., Sircoulomb, F., Rottapel, R. K., & Moffat, J. (2014) · Molecular Systems Biology · doi:10.15252/msb.20145216 · Cited by 389 · see citing works
SFARI Gene: an evolving database for the autism research community
Banerjee-Basu, S., & Packer, A. (2010) · Disease Models & Mechanisms · doi:10.1242/dmm.005439 · Cited by 357 · see citing works
A Neutral Model of Transcriptome Evolution
Khaitovich, P., Weiß, G., Lachmann, M., Hellmann, I., Enard, W., Muetzel, B., Wirkner, U., Ansorge, W. J., & Pääbo, S. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020132 · Cited by 339 · see citing works
The Genotype-Tissue Expression (GTEx) project
Lonsdale, J., Thomas, J., Salvatore, M., Phillips, R., Lo, E., Shad, S., Hasz, R., Walters, G., Garcia, F., Young, N., et al. (2013) · Nature Genetics · doi:10.1038/ng.2653 · Cited by 263 · see citing works
Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse
Blake, J. A., Eppig, J. T., Kadin, J. A., Richardson, J. E., Smith, C. L., Bult, C. J., & the Mouse Genome Database Group (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1040 · Cited by 262 · see citing works
Guerra, R., Wang, J., Grundy, S. M., & Cohen, J. C. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.9.4532 · Cited by 242 · see citing works
Torgerson, D. G., Kulathinal, R. J., & Singh, R. S. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004021 · Cited by 231 · see citing works
Applications and Limitations of Mouse Models for Understanding Human Atherosclerosis
von Scheidt, M., Zhao, Y., Kurt, Z., Pan, C., Zeng, L., Yang, X., Schunkert, H., & Lusis, A. J. (2016) · Cell Metabolism · doi:10.1016/j.cmet.2016.11.001 · Cited by 220 · see citing works
Natural selection on gene expression
Gilad, Y., Oshlack, A., & Rifkin, S. A. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.06.002 · Cited by 218 · see citing works
Optimization of gene expression by natural selection
Bedford, T., & Hartl, D. L. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0812009106 · Cited by 191 · see citing works
Conservation of core gene expression in vertebrate tissues
Chan, E. T., Quon, G. T., Chua, G., Babak, T., Trochesset, M., Zirngibl, R. A., Aubin, J., Ratcliffe, M. J., Wilde, A., Brudno, M., et al. (2009) · Journal of Biology · doi:10.1186/jbiol130 · Cited by 190 · see citing works
From Mouse to Human: Evolutionary Genomics Analysis of Human Orthologs of Essential Genes
Georgi, B., Voight, B. F., & Bućan, M. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003484 · Cited by 186 · see citing works
Comparative genomics as a tool to understand evolution and diseasePreprint
Alföldi, J., & Lindblad‐Toh, K. (2013) · Genome Research · doi:10.1101/gr.157503.113 · Cited by 186 · see citing works
Self-citationSignatures of positive selection in Toll-like receptor (TLR) genes in mammals
Areal, H., Abrantes, J., & Esteves, P. J. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-368 · Cited by 167 · see citing works
Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures
Blekhman, R., Oshlack, A., Chabot, A. E., Smyth, G. K., & Gilad, Y. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000271 · Cited by 158 · see citing works
Evidence for widespread adaptive evolution of gene expression in budding yeast
Fraser, H. B., Moses, A. M., & Schadt, E. E. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0912245107 · Cited by 154 · see citing works
Comparative RNA sequencing reveals substantial genetic variation in endangered primatesPreprint
Perry, G. H., Melsted, P., Marioni, J. C., Wang, Y., Bainer, R. O., Pickrell, J. K., Michelini, K., Zehr, S. M., Yoder, A. D., Stephens, M., et al. (2011) · Genome Research · doi:10.1101/gr.130468.111 · Cited by 147 · see citing works
Rohlfs, R. V., Harrigan, P., & Nielsen, R. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst190 · Cited by 135 · see citing works
Yanai, I., Graur, D., & Ophir, R. (2004) · OMICS A Journal of Integrative Biology · doi:10.1089/153623104773547462 · Cited by 132 · see citing works
Identification of cis-suppression of human disease mutations by comparative genomics
Task Force for Neonatal Genomics, Jordan, D. M., Frangakis, S. G., Golzio, C., Cassa, C. A., Kurtzberg, J., Davis, E. E., Sunyaev, S. R., & Katsanis, N. (2015) · Nature · doi:10.1038/nature14497 · Cited by 115 · see citing works
Phylogenetic ANOVA: The Expression Variance and Evolution Model for Quantitative Trait Evolution
Rohlfs, R. V., & Nielsen, R. (2015) · Systematic Biology · doi:10.1093/sysbio/syv042 · Cited by 107 · see citing works
Measurement errors should always be incorporated in phylogenetic comparative analysis
Silvestro, D., Kostikova, A., Litsios, G., Pearman, P. B., & Salamin, N. (2015) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12337 · Cited by 107 · see citing works
Toward a Neutral Evolutionary Model of Gene Expression
Khaitovich, P., Pääbo, S., & Weiß, G. (2005) · Genetics · doi:10.1534/genetics.104.037135 · Cited by 106 · see citing works
Phylogenetic Analysis of Glycolytic Enzyme Expression
Pierce, V. A., & Crawford, D. L. (1997) · Science · doi:10.1126/science.276.5310.256 · Cited by 104 · see citing works
The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics
Pipes, L., Li, S., Bozinoski, M., Palermo, R. E., Peng, X., Blood, P., Kelly, S. M., Weiss, J. M., Thierry‐Mieg, J., Thierry‐Mieg, D., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1268 · Cited by 81 · see citing works
Adaptive Evolution of Gene Expression in Drosophila.
Nourmohammad, A., Rambeau, J., Held, T., Kováčová, V., Berg, J., & Lässig, M. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.07.033 · Cited by 74 · see citing works
Genome‐wide analysis of alternative splicing evolution among Mus subspecies
Harr, B., & Turner, L. M. (2010) · Molecular Ecology · doi:10.1111/j.1365-294x.2009.04490.x · Cited by 62 · see citing works
Deleterious Mutations and Neutral Substitutions
Jukes, T. H., & King, J. L. (1971) · Nature · doi:10.1038/231114a0 · Cited by 57 · see citing works
Decoupling of evolutionary changes in transcription factor binding and gene expression in mammalsPreprint
Wong, E. S. W., Thybert, D., Schmitt, B. M., Stefflova, K., Odom, D. T., & Flicek, P. (2014) · Genome Research · doi:10.1101/gr.177840.114 · Cited by 47 · see citing works
Wang, D., Marsh, J., & Ayala, F. J. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.14.7103 · Cited by 41 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- Benjamini Y, Hochberg Y. 1995 Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B Methodol 57: 289– 300. 10.2307/2346101 · DOI
Cited by
Sorted by citations
Cross-Species Single-Cell Analysis Reveals Divergence of the Primate Microglia Program
Geirsdottir, L., David, E., Keren-Shaul, H., Weiner, A., Bohlen, S. C., Neuber, J., Balic, A., Giladi, A., Sheban, F., Dutertre, C.-A., et al. (2019) · Cell · doi:10.1016/j.cell.2019.11.010 · Cited by 461 · see citing works
The evolution, evolvability and engineering of gene regulatory DNA
Vaishnav, E. D., de Boer, C. G., Molinet, J., Yassour, M., Fan, L., Adiconis, X., Thompson, D. A., Levin, J. Z., Cubillos, F. A., & Regev, A. (2022) · Nature · doi:10.1038/s41586-022-04506-6 · Cited by 279 · see citing works
Self-citationConservation, acquisition, and functional impact of sex-biased gene expression in mammals
Naqvi, S., Godfrey, A. K., Hughes, J. F., Goodheart, M. L., Mitchell, R. N., & Page, D. C. (2019) · Science · doi:10.1126/science.aaw7317 · Cited by 258 · see citing works
Evolution of neuronal cell classes and types in the vertebrate retina
Hahn, J., Monavarfeshani, A., Qiao, M., Kao, A. H., Kölsch, Y., Kumar, A., Kunze, V. P., Rasys, A. M., Richardson, R., Wekselblatt, J. B., et al. (2023) · Nature · doi:10.1038/s41586-023-06638-9 · Cited by 218 · see citing works
A comparison of gene expression and DNA methylation patterns across tissues and speciesPreprint
Blake, L. E., Roux, J., Hernando-Herraez, I., Banovich, N. E., García-Pérez, R., Hsiao, C. J., Eres, I. E., Chavarria, C., Marquès‐Bonet, T., & Gilad, Y. (2020) · Genome Research · doi:10.1101/gr.254904.119 · Cited by 127 · see citing works
Innovation, Conservation and Repurposing of Gene Function in Plant Root Cell Type Development
Kajala, K., Gouran, M., Shaar‐Moshe, L., Mason, G. A., Rodríguez-Medina, J., Kawa, D., Pauluzzi, G. C., Reynoso, M. A., Cantó‐Pastor, A., Manzano, C., et al. (2020) · Cell · doi:10.1016/j.cell.2021.04.024 · Cited by 112 · see citing works
Atlas of ACE2 gene expression reveals novel insights into transmission of SARS-CoV-2
Sun, K., Gu, L., Ma, L., & Duan, Y. (2020) · Heliyon · doi:10.1016/j.heliyon.2020.e05850 · Cited by 94 · see citing works
Detecting signatures of selection on gene expression
Price, P. D., Droguett, D. H. P., Taylor, J. A., Kim, D. W., Place, E., Rogers, T. F., Mank, J. E., Cooney, C. R., & Wright, A. E. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01761-8 · Cited by 83 · see citing works
Gene expression dynamics during rapid organismal diversification in African cichlid fishes
Taher, A. E., Böhne, A., Boileau, N., Ronco, F., Indermaur, A., Widmer, L., & Salzburger, W. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-01354-3 · Cited by 70 · see citing works
Fukushima, K., & Pollock, D. D. (2020) · Nature Communications · doi:10.1038/s41467-020-18090-8 · Cited by 67 · see citing works
Evidence for Weak Selective Constraint on Human Gene Expression
Glassberg, E. C., Gao, Z., Harpak, A., Lan, X., & Pritchard, J. K. (2018) · Genetics · doi:10.1534/genetics.118.301833 · Cited by 63 · see citing works
Cis and trans effects differentially contribute to the evolution of promoters and enhancers
Mattioli, K., Oliveros, W., Gerhardinger, C., Andergassen, D., Maass, P., Rinn, J., & Melé, M. (2020) · Genome Biology · doi:10.1186/s13059-020-02110-3 · Cited by 41 · see citing works
Evolution of tissue-specific expression of ancestral genes across vertebrates and insects
Mantica, F., Iñiguez, L., Márquez, Y., Permanyer, J., Torres-Méndez, A., Cruz, J., Franch‐Marro, X., Tulenko, F. J., Burguera, D., Bertrand, S., et al. (2024) · Nature Ecology & Evolution · doi:10.1038/s41559-024-02398-5 · Cited by 50 · see citing works
Winkelmüller, T. M., Entila, F. D., Anver, S., Piasecka, A., Song, B., Dahms, E., Sakakibara, H., Gan, X., Kułak, K., Sawikowska, A., et al. (2021) · The Plant Cell · doi:10.1093/plcell/koab073 · Cited by 47 · see citing works
On the Decoupling of Evolutionary Changes in mRNA and Protein Levels
Jiang, D., Cope, A. L., Zhang, J., & Pennell, M. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad169 · Cited by 53 · see citing works
Correlated evolution of social organization and lifespan in mammals
Zhu, P., Liu, W., Zhang, X., Li, M., Liu, G., Yu, Y., Li, X., Li, X., Du, J., Wang, X., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-35869-7 · Cited by 48 · see citing works
Unusual sequence characteristics of human chromosome 19 are conserved across 11 nonhuman primates
Harris, R. A., Raveendran, M., Worley, K. C., & Rogers, J. (2020) · BMC Evolutionary Biology · doi:10.1186/s12862-020-1595-9 · Cited by 40 · see citing works
Atlas of ACE2 gene expression in mammals reveals novel insights in transmisson of SARS-Cov-2Preprint
Sun, K., Gu, L., Ma, L., & Duan, Y. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.03.30.015644 · Cited by 40 · see citing works
Schraiber, J. G., Edge, M. D., & Pennell, M. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002847 · Cited by 37 · see citing works
Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF
Yang, Y., Zhang, Y., Ren, B., Dixon, J. R., & Ma, J. (2019) · Cell Systems · doi:10.1016/j.cels.2019.05.011 · Cited by 37 · see citing works
Artificial intelligence for neurodegenerative experimental models
Marzi, S. J., Schilder, B. M., Nott, A., Frigerio, C. S., Willaime‐Morawek, S., Bucholc, M., Hanger, D. P., James, C. R., Lewis, P. A., Lourida, I., et al. (2023) · Alzheimer s & Dementia · doi:10.1002/alz.13479 · Cited by 34 · see citing works
Liu, W., Zhu, P., Li, M., Li, Z., Yu, Y., Liu, G., Du, J., Wang, X., Yang, J., Tian, R., et al. (2023) · The EMBO Journal · doi:10.15252/embj.2022112740 · Cited by 29 · see citing works
Catalán, A., Briscoe, A. D., & Höhna, S. (2019) · Genetics · doi:10.1534/genetics.119.302493 · Cited by 30 · see citing works
Layered evolution of gene expression in “superfast” muscles for courtship
Pease, J. B., Driver, R. J., de la Cerda, D. A., Day, L. B., Lindsay, W. R., Schlinger, B. A., Schuppe, E. R., Balakrishnan, C. N., & Fuxjager, M. J. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2119671119 · Cited by 28 · see citing works
Perspectives on studying molecular adaptations of amphibians in the genomic era
Sun, Y., 650091，中国, 云. 昆., Zhang, Y., Wang, K., 650223，中国, 中. 昆., & 诺曼73072，美国, 俄. (2020) · 动物学研究 · doi:10.24272/j.issn.2095-8137.2020.046 · Cited by 25 · see citing works
Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae
Large, C. R. L., Khanal, R., Hillier, L., Huynh, C., Kubo, C. A., Kim, J., Waterston, R., & Murray, J. I. (2025) · Science · doi:10.1126/science.adu8249 · Cited by 24 · see citing works
Predicting Archaic Hominin Phenotypes from Genomic Data
Brand, C. M., Colbran, L. L., & Capra, J. A. (2022) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-111521-121903 · Cited by 23 · see citing works
Macroevolutionary divergence of gene expression driven by selection on protein abundance
Cope, A. L., Schraiber, J. G., & Pennell, M. W. (2025) · Science · doi:10.1126/science.ads2658 · Cited by 20 · see citing works
Extracellular matrix gene expression signatures as cell type and cell state identifiers
Sacher, F., Feregrino, C., Tschopp, P., & Ewald, C. Y. (2021) · Matrix Biology Plus · doi:10.1016/j.mbplus.2021.100069 · Cited by 23 · see citing works
Evaluating the Performance of Widely Used Phylogenetic Models for Gene Expression Evolution
Dimayacyac, J. R., Wu, S., Jiang, D., & Pennell, M. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad211 · Cited by 21 · see citing works
Ahsan, A., Monir, M. M., Meng, X., Rahaman, M. M., Chen, H., & Chen, M. (2018) · DNA Research · doi:10.1093/dnares/dsy043 · Cited by 22 · see citing works
CAGEE: Computational Analysis of Gene Expression Evolution
Bertram, J., Fulton, B., Tourigny, J. P., Peña-García, Y., Moyle, L. C., & Hahn, M. W. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad106 · Cited by 21 · see citing works
Implementation and validation of single-cell genomics experiments in neuroscience
Colonna, M., Konopka, G., Liddelow, S. A., Nowakowski, T. J., Awatramani, R. B., Bateup, H. S., Cadwell, C. R., Caglayan, E., Chen, J. L., Gillis, J., et al. (2024) · Nature Neuroscience · doi:10.1038/s41593-024-01814-0 · Cited by 22 · see citing works
Self-citationEvolution of regulatory networks associated with traits under selection in cichlids
Mehta, T. K., Koch, C., Nash, W. J., Knaack, S., Sudhakar, P., Olbei, M. L., Bastkowski, S., Penso-Dolfin, L., Korcsmaros, T. D., Haerty, W., et al. (2021) · Genome biology · doi:10.1186/s13059-020-02208-8 · Cited by 21 · see citing works
Self-citationMugal, C. F., Mi, W., Backström, N., Wheatcroft, D. J., Ålund, M., Sémon, M., McFarlane, S. E., Dutoit, L., Qvarnström, A., & Ellegren, H. (2020) · Genome Research · doi:10.1101/gr.254508.119 · Cited by 21 · see citing works
Eutherian-Specific Gene TRIML2 Attenuates Inflammation in the Evolution of Placentation
Zhang, X., Pavličev, M., Jones, H. N., & Muglia, L. J. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz238 · Cited by 19 · see citing works
The 3D-Evo Space: Evolution of Gene Expression and Alternative Splicing Regulation
Mantica, F., & Irimia, M. (2022) · Annual Review of Genetics · doi:10.1146/annurev-genet-071719-020653 · Cited by 19 · see citing works
The metabolic domestication syndrome of budding yeast
Tengölics, R., Szappanos, B., Mülleder, M., Kalapis, D., Grézal, G., Sajben, C., Agostini, F., Mokochinski, J. B., Bálint, B., Nagy, L. G., et al. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2313354121 · Cited by 20 · see citing works
Hirsch, M. G., Pal, S., Mehrabadi, F. R., Malikić, S., Gruen, C., Sassano, A., Pérez‐Guijarro, E., Merlino, G. T., Şahinalp, S. C., Molloy, E. K., et al. (2024) · Cell Systems · doi:10.1016/j.cels.2024.11.013 · Cited by 19 · see citing works
Tempo and mode of gene expression evolution in the brain across primates
Rickelton, K., Zintel, T. M., Pizzollo, J., Miller, E., Ely, J. J., Raghanti, M. A., Hopkins, W. D., Hof, P. R., Sherwood, C. C., Bauernfeind, A. L., et al. (2024) · eLife · doi:10.7554/elife.70276 · Cited by 18 · see citing works
Pal, S., Oliver, B., & Przytycka, T. M. (2022) · Journal of Computational Biology · doi:10.1089/cmb.2022.0121 · Cited by 17 · see citing works
Boman, J., Qvarnström, A., & Mugal, C. F. (2024) · BMC Biology · doi:10.1186/s12915-024-01920-2 · Cited by 17 · 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
Viruses as Living Systems—A Metacybernetic View
Yolles, M. I., & Frieden, R. (2022) · Systems · doi:10.3390/systems10030070 · Cited by 15 · see citing works
Hibbins, M. S., & Hahn, M. W. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009892 · Cited by 14 · see citing works
Khalilimeybodi, A., Saucerman, J. J., & Rangamani, P. (2024) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2024.108499 · Cited by 14 · see citing works
Insights into the skin of caecilian amphibians from gene expression profiles
Torres‐Sánchez, M., Wilkinson, M., Gower, D. J., Creevey, C. J., & Mauro, D. S. (2020) · BMC Genomics · doi:10.1186/s12864-020-06881-8 · Cited by 12 · see citing works
Begum, T., & Robinson‐Rechavi, M. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa288 · Cited by 14 · see citing works
Zhong, X., Lundberg, M., & Råberg, L. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab023 · Cited by 12 · see citing works
Tracing the Evolution of Human Gene Regulation and Its Association with Shifts in Environment
Colbran, L. L., Johnson, M. R., Mathieson, I., & Capra, J. A. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab237 · Cited by 13 · see citing works
Evolutionary transcriptomics unveils rapid changes of gene expression patterns in flowering plants
Schuster, C., Gabel, A., Drost, H., Große, I., Leyser, O., & Meyerowitz, E. M. (2026) · Cell · doi:10.1016/j.cell.2025.12.015 · Cited by 16 · see citing works
Silva, C. C. D. S., Cirne, D., Freitas, O., & Campos, P. R. A. (2023) · Physical review. E · doi:10.1103/physreve.107.024417 · Cited by 11 · see citing works
Principles of metabolome conservation in animals
Liska, O., Boross, G. Z., Rocabert, C., Szappanos, B., Tengölics, R., & Papp, B. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2302147120 · Cited by 11 · see citing works
A Tale of Too Many Trees: A Conundrum for Phylogenetic Regression
Adams, R. H. J., Lozano, J. R., Duncan, M., Green, J. E., Assis, R., & DeGiorgio, M. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf032 · Cited by 11 · see citing works
Dickson, Z. W., & Golding, G. B. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac087 · Cited by 10 · see citing works
Gene expression supports a single origin of horns and antlers in hoofed mammals
Calamari, Z. T., & Flynn, J. J. (2024) · Communications Biology · doi:10.1038/s42003-024-06134-4 · Cited by 9 · see citing works
Ancestral splice variation is a key substrate for rapid diversification in African cichlids
Singh, P., Ahi, E. P., Duenser, A., Durdević, M., Gessl, W., Schäffer, S., Gallaun, J., D, O. S. C., & Sturmbauer, C. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2516477123 · Cited by 8 · see citing works
A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data
Bastide, P., Soneson, C., Stern, D., Lespinet, O., & Gallopin, M. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac269 · Cited by 8 · see citing works
SCSMRD: A database for single-cell skeletal muscle regeneration
Feng, X.-K., Xie, C., Li, Y.-Y., Wang, Z.-S., & Bai, L. (2022) · Journal of Integrative Agriculture · doi:10.1016/j.jia.2022.08.108 · Cited by 6 · see citing works
Screening of SLE-susceptible SNPs in One Chinese Family with Systemic Lupus Erythematosus
Luo, J., Meng, Y., Zhai, J., Zhu, Y., Li, Y., & Wu, Y. (2020) · Current Bioinformatics · doi:10.2174/1574893615666200120105153 · Cited by 7 · see citing works
Functional Optimization in Distinct Tissues and Conditions Constrains the Rate of Protein Evolution
Usmanova, D. R., Plata, G., & Vitkup, D. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae200 · Cited by 6 · see citing works
A gene-level test for directional selection on gene expression
Colbran, L. L., Ramos-Almodóvar, F., & Mathieson, I. (2023) · Genetics · doi:10.1093/genetics/iyad060 · Cited by 6 · see citing works
Majane, A. C., Cridland, J. M., Blair, L. K., & Begun, D. J. (2024) · Genetics · doi:10.1093/genetics/iyae039 · Cited by 5 · see citing works
Yang, Y., Xiao, S., Zhao, X., Sun, Y. H., Fang, Q., Fan, L., Yè, G., & Ye, X. (2024) · BMC Biology · doi:10.1186/s12915-024-01974-2 · Cited by 5 · see citing works
Evolutionary diversification of ancestral genes across vertebrates and insects
Mantica, F., & Irimia, M. (2025) · Genome biology · doi:10.1186/s13059-025-03699-z · Cited by 5 · see citing works
Kyritsis, K., Ouzounis, C. A., Angelis, L., & Vizirianakis, I. S. (2020) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqaa088 · Cited by 5 · see citing works
Adaptive cellular evolution in the intestine of hyperdiverse cichlid fishes
Fages, A., Luxey, M., Ronco, F., Huyghe, C. E. T., Fischer, S., Viktorin, G., Menon, P. N. K., Indermaur, A., Salzburger, W., & Tschopp, P. (2026) · Nature · doi:10.1038/s41586-026-10494-8 · Cited by 6 · see citing works
TAD conservation in vertebrate genomes is driven by stabilising selection
Patalano, F., Sandve, S. R., Aasland, R., & Paulsen, J. (2025) · BMC Biology · doi:10.1186/s12915-025-02362-0 · Cited by 4 · see citing works
Zambon, M., Mantica, F., Dias, M., Frazer, J., & Irimia, M. (2025) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2025.102387 · Cited by 4 · see citing works
Hirsch, M. G., Pal, S., Mehrabadi, F. R., Malikić, S., Gruen, C., Sassano, A., Pérez‐Guijarro, E., Merlino, G. T., Şahinalp, S. C., Molloy, E. K., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.17.588869 · Cited by 4 · see citing works
Rapid evolution of gene expression patterns in flowering plantsPreprint
Schuster, C., Gabel, A., Drost, H., Große, I., Leyser, O., & Meyerowitz, E. M. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.07.08.602577 · Cited by 4 · see citing works
The molecular evolution of vertebrate organs
Cardoso-Moreira, M. (2026) · Nature Ecology & Evolution · doi:10.1038/s41559-026-03003-7 · Cited by 3 · see citing works
Annotation depth confounds direct comparison of gene expression across species
Oziolor, E. M., Arat, S., & Martin, M. T. (2021) · BMC Bioinformatics · doi:10.1186/s12859-021-04414-y · Cited by 3 · see citing works
Dighe, A., Maziarz, J. D., Ibrahim‐Hashim, A., Gatenby, R. A., Gupta, K., Levchenko, A., & Wagner, G. P. (2023) · iScience · doi:10.1016/j.isci.2023.108593 · Cited by 3 · see citing works
Meyer, M. J., Falk, S., Römer, S., Prinzinger, C., Tacke, S., Geyer, J., Simm, S., & Tzvetkov, M. V. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23095100 · Cited by 3 · see citing works
Gallopin, M., Drevet, C., de la Torre, V. S. G., Jelassi, S., Michel, M., Ducos, C., Saule, C., Majorel, C., Sarramégna, V., Pillon, Y., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.09.28.509953 · Cited by 3 · see citing works
Seasonal and comparative evidence of adaptive gene expression in mammalian brain size plasticityPreprint
Thomas, W. R., Richter, T. A., O’Neil, E. T., Baldoni, C., Corthals, A., von Elverfeldt, D., Nieland, J. D., Dechmann, D. K. N., Hunter, R. G., & Dávalos, L. M. (2024) · eLife · doi:10.7554/elife.100788 · Cited by 3 · see citing works
Adaptive cellular evolution in the intestinal tracts of hyperdiverse African cichlid fishesPreprint
Fages, A., Luxey, M., Ronco, F., Huyghe, C. E. T., Menon, P. N. K., Indermaur, A., Salzburger, W., & Tschopp, P. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.28.625862 · Cited by 3 · see citing works
Seasonal and comparative evidence of adaptive gene expression in mammalian brain size plasticity
Thomas, W. R., Richter, T. A., O’Neil, E. T., Baldoni, C., Corthals, A., von Elverfeldt, D., Nieland, J. D., Dechmann, D. K. N., Hunter, R. G., & Dávalos, L. M. (2025) · eLife · doi:10.7554/elife.100788.3 · Cited by 2 · see citing works
Constraints on the optimization of gene product diversity
Jiang, D., Kejiou, N. S., Qiu, Y., Palazzo, A. F., & Pennell, M. W. (2025) · Molecular Systems Biology · doi:10.1038/s44320-025-00095-4 · Cited by 3 · see citing works
Measurement and meaning in gene expression evolution
Diaz, R., Wang, Z., & Townsend, J. P. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-91810-7.00008-x · Cited by 2 · see citing works
Smail, H. O. (2020) · International Journal of Applied Biology · doi:10.20956/ijab.v4i1.9914 · Cited by 2 · see citing works
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
Self-citationNetwork properties constrain natural selection on gene expression in Caenorhabditis elegansPreprint
Inskeep, T. R., & Groen, S. C. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.19.639144 · Cited by 2 · see citing works
Rickelton, K., Ely, J. J., Hopkins, W. D., Hof, P. R., Sherwood, C. C., Bauernfeind, A. L., & Babbitt, C. C. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.03.03.641249 · Cited by 2 · see citing works
SCOUT: Ornstein–Uhlenbeck modelling of gene expression evolution on single-cell lineage treesPreprint
Stuart, H., & McKenna, A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.12.688020 · Cited by 2 · see citing works
Coordinated shifts in gene expression and regulation during mole-rat evolutionPreprint
Daunesse, M., Liorzou, E., Parey, E., Villar, D., & Berthelot, C. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.24.690111 · Cited by 2 · see citing works
Phylogenomics and comparative genomics in ant-eating mammals
Allio, R. (2021) · theses.fr (ABES) · doi:10.70675/0b3fded9z0768z4976z9f7cz8b7e4a9f1114 · Cited by 2 · see citing works
Arzumanova, K., Rohlfs, R. V., Grønvold, L., Strand, M. A., Hvidsten, T. R., & Sandve, S. R. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-2561-3_11 · Cited by 1 · see citing works
An Empirical Bayes Approach for the Study of Phenotypic Evolution from High-Dimensional Data
Montoya, P., Fabre, A., Goswami, A., Morlon, H., & Clavel, J. (2026) · Systematic Biology · doi:10.1093/sysbio/syag051 · Cited by 1 · see citing works
Montoya, P., Joseph, J., Goswami, A., Morlon, H., & Clavel, J. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.27.728209 · Cited by 1 · see citing works
Lineage-aware stochastic modeling reveals gene-expression dynamics in development and diseasePreprint
Xing, J., Staklinski, S. J., Liu, Z., Nowak, D. G., & Siepel, A. C. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.25.734628 · Cited by 1 · see citing works
Interspecies Differential Gene Expression Analysis with Regularized Phylogenetic Linear ModelsPreprint
Gallopin, M., Daunesse, M., Lespinet, O., Liehrmann, A., & Bastide, P. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.30.734542 · Cited by 1 · see citing works
Evolutionary dynamics of neutral phenotypes under DNA substitution modelsPreprint
Zabad, S., & Moses, A. M. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.26.355438
Predicting gene regulatory changes across human evolution using ancient DNA
Colbran, L. L. (2020)
Begum, T., Duchen, P., Bucao, C. F., & Robinson‐Rechavi, M. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.12.29.571877
Characterizing patterns of selection pressure on mammalian antiviral immune response
Hawash, M. B. F. (2024) · Journal of Mammalian Evolution · doi:10.1007/s10914-024-09715-6
Genetic and selective constraints on the optimization of gene product diversityPreprint
Jiang, D., Kejiou, N. S., Qiu, Y., Palazzo, A. F., & Pennell, M. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.07.17.603951
Zintel, T., Ely, J., Raghanti, M., Hopkins, W., Hof, P., Sherwood, C., Kamilar, J., Bauernfeind, A., & Babbitt, C. C. (2020) · Genes · doi:10.3390/genes16020117
TAD conservation in vertebrate genomes is driven by stabilising selection.Preprint
Patalano, F., Sandve, S. R., Aasland, R., & Paulsen, J. (2025) · Research Square · doi:10.21203/rs.3.rs-5809117/v1
- Authors
- Chen, J., Swofford, R., Johnson, J., Cummings, B. B., Rogel, N., Lindblad-Toh, K., Haerty, W., Palma, F. D., & Regev, A.
- Affiliations
- Broad Institute (US)
- Earlham Institute (GB)
- University of East Anglia (GB)
- ORCID
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2018-12-14
- Volume
- 29
- Issue
- 1
- Pages
- 53-63
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- PMC
- PMC6314168
- OpenAlex
- W2949594216
- Cited by
- 128
- References
- 66
- Citations by year
- 2026: 18 · 2025: 18 · 2024: 18 · 2023: 14 · 2022: 13 · 2021: 24 · 2020: 16 · 2019: 5 · 2018: 2
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- UEA Digital Repository (University of East Anglia) (acceptedVersion)
- Uppsala University Publications (Uppsala University) (submittedVersion, other-oa)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- HighWire Press Open Archive (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- Broad Institute
- Vetenskapsrådet
- National Institutes of Health (5rm1hg006193-10)
- Klarman Cell Observatory, Broad Institute
- Biotechnology and Biological Sciences Research Council (BBS/E/T/000PR9817, BBS/E/T/000PR5885, BBS/E/T/000PR9818, BB/CSP1720/1)
- National Human Genome Research Institute (RM1‐HG006193, T32HG002295)
- National Institute of Neurological Disorders and Stroke
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- gene expression evolution, Ornstein-Uhlenbeck process, stabilizing selection, directional selection, neutral selection, comparative transcriptomics, mammals
- MeSH terms
- Animals, Dogs, Gene Expression Regulation, Models, Genetic, Rabbits, Evolution, Molecular
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
