Comparative studies of gene expression and the evolution of gene regulation

RNA-Seq: a revolutionary tool for transcriptomics

Wang, Z., Gerstein, M., & Snyder, M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2484 · Cited by 13,174 · see citing works

Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals

Jaenisch, R., & Bird, A. (2003) · Nature Genetics · doi:10.1038/ng1089 · Cited by 6,325 · see citing works

Life-History Tactics: A Review of the Ideas

Stearns, S. C. (1976) · The Quarterly Review of Biology · doi:10.1086/409052 · Cited by 3,557 · see citing works

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., et al. (2007) · Nature Genetics · doi:10.1038/ng1966 · Cited by 3,398 · see citing works

A Map of Recent Positive Selection in the Human Genome

Voight, B. F., Kudaravalli, S., Wen, X., & Pritchard, J. K. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040072 · Cited by 2,912 · see citing works

Mapping and analysis of chromatin state dynamics in nine human cell types

Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B., Zhang, X., Wang, L., Issner, R., Coyne, M., et al. (2011) · Nature · doi:10.1038/nature09906 · Cited by 2,898 · see citing works

Evolution at Two Levels in Humans and Chimpanzees: Their macromolecules are so alike that regulatory mutations may account for their biological differences

King, M.-C., & Wilson, A. C. (1975) · Science · doi:10.1126/science.1090005 · Cited by 2,815 · see citing works

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

Marioni, J. C., Mason, C. E., Mane, S. M., Stephens, M., & Gilad, Y. (2008) · Genome Research · doi:10.1101/gr.079558.108 · Cited by 2,771 · see citing works

Genome-wide detection and characterization of positive selection in human populations

The International HapMap Consortium, Sabeti, P. C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., Xie, X., Byrne, E. H., McCarroll, S. A., et al. (2007) · Nature · doi:10.1038/nature06250 · Cited by 2,131 · see citing works

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

Carroll, S. B. (2008) · Cell · doi:10.1016/j.cell.2008.06.030 · Cited by 2,067 · see citing works

Gene Regulation for Higher Cells: A Theory

Britten, R. J., & Davidson, E. H. (1969) · Science · doi:10.1126/science.165.3891.349 · Cited by 2,049 · see citing works

Natural selection and random genetic drift in phenotypic evolution

Lande, R. (1976) · Evolution · doi:10.1111/j.1558-5646.1976.tb00911.x · Cited by 1,828 · see citing works

Molecular evolution of FOXP2, a gene involved in speech and language

Enard, W., Przeworski, M., Fisher, S. E., Lai, C. S. L., Wiebe, V., Kitano, T., Monaco, A. P., & Pääbo, S. (2002) · Nature · doi:10.1038/nature01025 · Cited by 1,603 · see citing works

The evolutionary significance of cis-regulatory mutations

Wray, G. A. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2063 · Cited by 1,521 · see citing works

Genetic Dissection of Transcriptional Regulation in Budding Yeast

Brem, R. B., Yvert, G., Clinton, R., & Kruglyak, L. (2002) · Science · doi:10.1126/science.1069516 · Cited by 1,392 · 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

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a <i>Pitx1</i> Enhancer

Chan, Y. F., Marks, M. E., Jones, F. C., Villarreal, G., Shapiro, M. D., Brady, S. D., Southwick, A. M., Absher, D. M., Grimwood, J., Schmutz, J., et al. (2010) · Science · doi:10.1126/science.1182213 · Cited by 1,020 · see citing works

An RNA gene expressed during cortical development evolved rapidly in humans

Pollard, K. S., Salama, S. R., Lambert, N., Lambot, M.-A., Coppens, S., Pedersen, J. S., Katzman, S., King, B., Onodera, C., Siepel, A., et al. (2006) · Nature · doi:10.1038/nature05113 · Cited by 1,005 · see citing works

THE LOCUS OF EVOLUTION: EVO DEVO AND THE GENETICS OF ADAPTATION

Hoekstra, H. E., & Coyne, J. A. (2007) · Evolution · doi:10.1111/j.1558-5646.2007.00105.x · Cited by 962 · see citing works

Long-Range Control of Gene Expression: Emerging Mechanisms and Disruption in Disease

Kleinjan, D. A., & van Heyningen, V. (2004) · The American Journal of Human Genetics · doi:10.1086/426833 · Cited by 868 · 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

Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks

Shapiro, M. D., Marks, M. E., Peichel, C. L., Blackman, B. K., Nereng, K. S., Jónsson, B., Schluter, D., & Kingsley, D. M. (2004) · Nature · doi:10.1038/nature02415 · Cited by 843 · see citing works

Identification of a functional transposon insertion in the maize domestication gene tb1

Studer, A. J., Zhao, Q., Ross‐Ibarra, J., & Doebley, J. (2011) · Nature Genetics · doi:10.1038/ng.942 · Cited by 805 · see citing works

Histone H3 lysine 4 methylation patterns in higher eukaryotic genes

Schneider, R., Bannister, A. J., Myers, F. A., Thorne, A. W., Crane‐Robinson, C., & Kouzarides, T. (2003) · Nature Cell Biology · doi:10.1038/ncb1076 · Cited by 792 · see citing works

Repetitive and Non-Repetitive DNA Sequences and a Speculation on the Origins of Evolutionary Novelty

Britten, R. J., & Davidson, E. H. (1971) · The Quarterly Review of Biology · doi:10.1086/406830 · Cited by 789 · see citing works

teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance.

Doebley, J., Stec, A. O., & Gustus, C. D. (1995) · Genetics · doi:10.1093/genetics/141.1.333 · Cited by 768 · see citing works

Insights into hominid evolution from the gorilla genome sequence

Scally, A., Dutheil, J. Y., Hillier, L. W., Jordan, G. E., Goodhead, I., Herrero, J., Hobolth, A., Lappalainen, T., Mailund, T., Marquès‐Bonet, T., et al. (2012) · Nature · doi:10.1038/nature10842 · Cited by 760 · see citing works

THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?

Stern, D. L., & Courtier‐Orgogozo, V. (2008) · Evolution · doi:10.1111/j.1558-5646.2008.00450.x · Cited by 747 · see citing works

Signals of recent positive selection in a worldwide sample of human populations

Pickrell, J. K., Coop, G., Novembre, J., Kudaravalli, S., Li, J. Z., Absher, D., Srinivasan, B. S., Barsh, G. S., Myers, R. M., Feldman, M. W., et al. (2009) · Genome Research · doi:10.1101/gr.087577.108 · Cited by 717 · see citing works

A Single Amino Acid Mutation Contributes to Adaptive Beach Mouse Color Pattern

Hoekstra, H. E., Hirschmann, R. J., Bundey, R. A., Insel, P. A., & Crossland, J. P. (2006) · Science · doi:10.1126/science.1126121 · Cited by 716 · see citing works

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

Schmidt, D., Wilson, M. D., Ballester, B., Schwalie, P. C., Brown, G. D., Marshall, A., Kutter, C., Watt, S., Martinez-Jimenez, C. P., Mackay, S., et al. (2010) · Science · doi:10.1126/science.1186176 · Cited by 700 · see citing works

The Raw and the Stolen

Wrangham, Jones, Laden, Pilbeam, & Conklin-Brittain (1999) · Current Anthropology · doi:10.2307/3596391 · Cited by 700 · see citing works

DNase I sensitivity QTLs are a major determinant of human expression variation

Degner, J. F., Pai, A. A., Piqué-Regi, R., Veyrieras, J., Gaffney, D. J., Pickrell, J. K., Leon, S. D., Michelini, K., Lewellen, N., Crawford, G. E., et al. (2012) · Nature · doi:10.1038/nature10808 · Cited by 633 · see citing works

Variation in Transcription Factor Binding Among Humans

Kasowski, M. M., Grubert, F., Heffelfinger, C., Hariharan, M., Asabere, A., Waszak, S., Habegger, L., Rozowsky, J., Shi, M.-Y., Urban, A., et al. (2010) · Science · doi:10.1126/science.1183621 · Cited by 625 · see citing works

A humanized version of Foxp2 affects cortico-basal ganglia circuits in mice

Enard, W., Gehre, S., Hammerschmidt, K., Hölter, S. M., Blass, T., Somel, M., Brückner, M. K., Schreiweis, C., Winter, C., Sohr, R., et al. (2009) · Cell · doi:10.1016/j.cell.2009.03.041 · Cited by 605 · see citing works

Evolution of the mammalian transcription factor binding repertoire via transposable elementsPreprint

Bourque, G., Leong, B., Vega, V. B., Chen, X., Lee, Y. L., Srinivasan, K. G., Chew, J.-L., Ruan, Y., Wei, C., Ng, H., et al. (2008) · Genome Research · doi:10.1101/gr.080663.108 · Cited by 588 · see citing works

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

Cooper, G. M., & Shendure, J. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3046 · Cited by 563 · see citing works

Molecular spandrels: tests of adaptation at the genetic level

Barrett, R. D. H., & Hoekstra, H. E. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3015 · Cited by 562 · see citing works

Human-specific loss of regulatory DNA and the evolution of human-specific traits

McLean, C. Y., Reno, P. L., Pollen, A. A., Bassan, A. I., Capellini, T. D., Guenther, C., Indjeian, V. B., Lim, X., Menke, D. B., Schaar, B. T., et al. (2011) · Nature · doi:10.1038/nature09774 · Cited by 535 · see citing works

Revealing the architecture of gene regulation: the promise of eQTL studies

Gilad, Y., Rifkin, S. A., & Pritchard, J. K. (2008) · Trends in Genetics · doi:10.1016/j.tig.2008.06.001 · Cited by 531 · see citing works

Localizing Recent Adaptive Evolution in the Human Genome.

Williamson, S. H., Hubisz, M. J., Clark, A. G., Payseur, B. A., Bustamante, C. D., & Nielsen, R. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030090 · Cited by 507 · see citing works

Predicting expression patterns from regulatory sequence in Drosophila segmentation

Segal, E., Raveh-Sadka, T., Schroeder, M., Unnerstall, U., & Gaul, U. (2008) · Nature · doi:10.1038/nature06496 · Cited by 466 · see citing works

optix Drives the Repeated Convergent Evolution of Butterfly Wing Pattern Mimicry

Reed, R. D., Papa, R., Martin, A., Hines, H. M., Counterman, B. A., Pardo‐Díaz, C., Jiggins, C. D., Chamberlain, N. L., Kronforst, M. R., Chen, R., et al. (2011) · Science · doi:10.1126/science.1208227 · Cited by 462 · see citing works

An Aneuploid Mouse Strain Carrying Human Chromosome 21 with down Syndrome Phenotypes.

O'Doherty, A., Ruf, S., Mulligan, C., Hildreth, V., Errington, M. L., Cooke, S., Sesay, A., Modino, S., Vanes, L., Hernandez, D., et al. (2005) · Science · doi:10.1126/science.1114535 · Cited by 434 · see citing works

Constructing genomic maps of positive selection in humans: Where do we go from here?Preprint

Akey, J. M. (2009) · Genome Research · doi:10.1101/gr.086652.108 · Cited by 422 · see citing works

Sperm Methylation Profiles Reveal Features of Epigenetic Inheritance and Evolution in Primates

Molaro, A., Hodges, E. C., Fang, F., Song, Q., McCombie, W. R., Hannon, G. J., & Smith, A. D. (2011) · Cell · doi:10.1016/j.cell.2011.08.016 · Cited by 418 · see citing works

Neutral and adaptive variation in gene expression

Whitehead, A., & Crawford, D. L. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0507648103 · Cited by 414 · see citing works

Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals

Lynch, V. J., Leclerc, R. D., May, G. E., & Wagner, G. P. (2011) · Nature Genetics · doi:10.1038/ng.917 · Cited by 413 · see citing works

Transcriptional neoteny in the human brain

Somel, M., Franz, H., Zheng, Y., Lorenc, A., Guo, S., Giger, T., Kelso, J. F., Nickel, B., Dannemann, M., Bahn, S., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0900544106 · Cited by 409 · see citing works

A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture

Clark, R. M., Wagler, T. N., Quijada, P., & Doebley, J. (2006) · Nature Genetics · doi:10.1038/ng1784 · Cited by 407 · see citing works

PHENOTYPIC EVOLUTION BY NEUTRAL MUTATION

Lynch, M., & Hill, W. G. (1986) · Evolution · doi:10.1111/j.1558-5646.1986.tb00561.x · Cited by 403 · see citing works

A Yeast Hybrid Provides Insight into the Evolution of Gene Expression Regulation

Tirosh, I., Reikhav, S., Levy, A. A., & Barkai, N. (2009) · Science · doi:10.1126/science.1169766 · Cited by 399 · see citing works

How reliable are empirical genomic scans for selective sweeps?Preprint

Teshima, K. M., Coop, G., & Przeworski, M. (2006) · Genome Research · doi:10.1101/gr.5105206 · Cited by 398 · see citing works

Genetic variability maintained in a finite population due to mutational production of neutral and nearly neutral isoalleles

Kimura, M. (1968) · Genetics Research · doi:10.1017/s0016672300011459 · Cited by 390 · see citing works

Regulatory changes underlying expression differences within and between Drosophila species

Wittkopp, P. J., Haerum, B. K., & Clark, A. G. (2008) · Nature Genetics · doi:10.1038/ng.77 · Cited by 373 · see citing works

Unstable Tandem Repeats in Promoters Confer Transcriptional Evolvability

Vinces, M. D., Legendre, M., Caldara, M., Hagihara, M., & Verstrepen, K. J. (2009) · Science · doi:10.1126/science.1170097 · Cited by 372 · see citing works

Human-Specific Gain of Function in a Developmental Enhancer

Prabhakar, S., Visel, A., Akiyama, J. A., Shoukry, M. I., Lewis, K. D., Holt, A., Plajzer-Frick, I., Morrison, H., FitzPatrick, D. R., Afzal, V., et al. (2008) · Science · doi:10.1126/science.1159974 · Cited by 363 · see citing works

Evolution of gene expression in the Drosophila melanogaster subgroup

Rifkin, S. A., Kim, J., & White, K. P. (2003) · Nature Genetics · doi:10.1038/ng1086 · Cited by 351 · see citing works

Evolution of primate gene expression

Khaitovich, P., Enard, W., Lachmann, M., & Pääbo, S. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1940 · Cited by 341 · 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

Expression profiling in primates reveals a rapid evolution of human transcription factors

Gilad, Y., Oshlack, A., Smyth, G. K., Speed, T. P., & White, K. P. (2006) · Nature · doi:10.1038/nature04559 · Cited by 323 · see citing works

Species-Specific Transcription in Mice Carrying Human Chromosome 21

Wilson, M. D., Barbosa‐Morais, N. L., Schmidt, D., Conboy, C. B., Vanes, L., Tybulewicz, V. L. J., Fisher, E., Tavaré, S., & Odom, D. T. (2008) · Science · doi:10.1126/science.1160930 · Cited by 280 · see citing works

Sex-specific and lineage-specific alternative splicing in primatesPreprint

Blekhman, R., Marioni, J. C., Zumbo, P., Stephens, M., & Gilad, Y. (2009) · Genome Research · doi:10.1101/gr.099226.109 · Cited by 266 · see citing works

From DNA sequence to transcriptional behaviour: a quantitative approach

Segal, E., & Widom, J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2591 · Cited by 262 · see citing works

The Developmental Role of Agouti in Color Pattern Evolution

Manceau, M., Domingues, V. S., Mallarino, R., & Hoekstra, H. E. (2011) · Science · doi:10.1126/science.1200684 · Cited by 233 · see citing works

The study of eQTL variations by RNA-seq: from SNPs to phenotypes

Majewski, J., & Pastinen, T. (2011) · Trends in Genetics · doi:10.1016/j.tig.2010.10.006 · Cited by 232 · see citing works

MicroRNA-driven developmental remodeling in the brain distinguishes humans from other primates

Somel, M., Liu, X., Tang, L., Yan, Z., Hu, H., Guo, S., Jiang, X., Zhang, X., Xu, G., Xie, G., et al. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001214 · Cited by 232 · see citing works

Compensatory cis-trans Evolution and the Dysregulation of Gene Expression in Interspecific Hybrids of Drosophila

Landry, C. R., Wittkopp, P. J., Taubes, C. H., Ranz, J. M., Clark, A. G., & Hartl, D. L. (2005) · Genetics · doi:10.1534/genetics.105.047449 · Cited by 228 · 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

The Role of Nucleosome Positioning in the Evolution of Gene Regulation

Tsankov, A. M., Thompson, D. A., Socha, A. L., Regev, A., & Rando, O. J. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000414 · Cited by 217 · see citing works

Meat‐Adaptive Genes and the Evolution of Slower Aging in Humans

Finch, C. E., & Stanford, C. B. (2004) · The Quarterly Review of Biology · doi:10.1086/381662 · Cited by 214 · see citing works

A Genome-Wide Study of DNA Methylation Patterns and Gene Expression Levels in Multiple Human and Chimpanzee Tissues

Pai, A. A., Bell, J. T., Marioni, J. C., Pritchard, J. K., & Gilad, Y. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001316 · Cited by 209 · see citing works

Functional Evolution of a cis-Regulatory Module

Ludwig, M. Z., Pálsson, A., Alekseeva, E. A., Bergman, C., Nathan, J., & Kreitman, M. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030093 · Cited by 207 · see citing works

Genetic Interactions Between Transcription Factors Cause Natural Variation in Yeast

Gerke, J., Lorenz, K., & Cohen, B. A. (2009) · Science · doi:10.1126/science.1166426 · Cited by 198 · see citing works

Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene

Janssens, H., Hou, S., Jaeger, J., Kim, A.-R., Марковна, М. Е., Sharp, D., & Reinitz, J. (2006) · Nature Genetics · doi:10.1038/ng1886 · Cited by 198 · see citing works

Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species

Bradley, R. K., Li, X., Trapnell, C., Davidson, S. M., Pachter, L. S., Chu, H. C., Tonkin, L. A., Biggin, M. D., & Eisen, M. B. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000343 · Cited by 190 · see citing works

A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression

Rifkin, S. A., Houle, D., Kim, J., & White, K. P. (2005) · Nature · doi:10.1038/nature04114 · Cited by 187 · see citing works

From genome to epigenome

Murrell, A., Rakyan, V. K., & Beck, S. (2005) · Human Molecular Genetics · doi:10.1093/hmg/ddi110 · Cited by 183 · see citing works

Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain

Nowick, K., Gernat, T., Almaas, E., & Stubbs, L. J. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0911376106 · Cited by 162 · see citing works

RATES OF DIVERGENCE IN GENE EXPRESSION PROFILES OF PRIMATES, MICE, AND FLIES: STABILIZING SELECTION AND VARIABILITY AMONG FUNCTIONAL CATEGORIES

Lemos, B., Meiklejohn, C. D., Cáceres, M., & Hartl, D. L. (2005) · Evolution · doi:10.1111/j.0014-3820.2005.tb00900.x · Cited by 162 · 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

Local Regulatory Variation in Saccharomyces cerevisiae

Ronald, J., Brem, R. B., Whittle, J., & Kruglyak, L. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0010025 · Cited by 157 · see citing works

Frequent Gain and Loss of Functional Transcription Factor Binding Sites

Doniger, S. W., & Fay, J. C. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030099 · Cited by 153 · 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

Evolutionary origin of a novel gene expression pattern through co-option of the latent activities of existing regulatory sequences

Rebeiz, M., Jikomes, N., Kassner, V. A., & Carroll, S. B. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1105937108 · Cited by 142 · see citing works

Gene Expression Differences Among Primates Are Associated With Changes in a Histone Epigenetic Modification

Cain, C. E., Blekhman, R., Marioni, J. C., & Gilad, Y. (2011) · Genetics · doi:10.1534/genetics.110.126177 · Cited by 138 · see citing works

Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization

Field, Y., Fondufe‐Mittendorf, Y. N., Moore, I. K., Mieczkowski, P. A., Kaplan, N., Lubling, Y., Lieb, J. D., Widom, J., & Segal, E. (2009) · Nature Genetics · doi:10.1038/ng.324 · Cited by 136 · see citing works

MicroRNA Expression and Regulation in Human, Chimpanzee, and Macaque Brains

Hu, H. Y., Guo, S., Xi, J., Yan, Z., Fu, N., Zhang, X., Menzel, C., Liang, H., Yang, H., Zhao, M., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002327 · Cited by 130 · see citing works

Sequence features that drive human promoter function and tissue specificity.Preprint

Landolin, J., Johnson, D. S., Trinklein, N., Aldred, S. F., Medina, C., Shulha, H., Weng, Z., & Myers, R. (2010) · Genome Research · doi:10.1101/gr.100370.109 · Cited by 114 · see citing works

Changes in exon–intron structure during vertebrate evolution affect the splicing pattern of exonsPreprint

Gelfman, S., Burstein, D. E., Penn, O., Savchenko, A., Amit, M., Schwartz, S., Pupko, T., & Ast, G. (2011) · Genome Research · doi:10.1101/gr.119834.110 · Cited by 109 · see citing works

An ensemble model of competitive multi-factor binding of the genomePreprint

Wasson, T., & Hartemink, A. J. (2009) · Genome Research · doi:10.1101/gr.093450.109 · Cited by 107 · see citing works

Incipient Balancing Selection through Adaptive Loss of Aquaporins in Natural Saccharomyces cerevisiae Populations

Will, J., Kim, H. S., Clarke, J., Painter, J. C., Fay, J. C., & Gasch, A. P. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000893 · Cited by 99 · see citing works

Incorporating nucleosomes into thermodynamic models of transcription regulationPreprint

Raveh-Sadka, T., Levo, M., & Segal, E. (2009) · Genome Research · doi:10.1101/gr.088260.108 · Cited by 99 · see citing works

The molecular elements that underlie developmental evolution

Alonso, C. R., & Wilkins, A. S. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1676 · Cited by 97 · see citing works

Incorporating Nucleosomes into Thermodynamic Models of Transcription Regulation

Raveh-Sadka, T., Levo, M., & Segal, E. (2009) · Lecture notes in computer science · doi:10.1007/978-3-642-02008-7_15 · Cited by 97 · see citing works

Coupled Evolution of Transcription and mRNA Degradation

Dori-Bachash, M., Shema, E., & Tirosh, I. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001106 · Cited by 96 · see citing works

Evolution Acts on Enhancer Organization to Fine-Tune Gradient Threshold Readouts

Crocker, J., Tamori, Y., & Erives, A. J. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060263 · Cited by 89 · see citing works

Polygenic and directional regulatory evolution across pathways in Saccharomyces

Bullard, J. H., Mostovoy, Y., Dudoit, S., & Brem, R. B. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0912959107 · Cited by 87 · see citing works

Exudativory in the Bengal slow loris (Nycticebus bengalensis) in Trishna Wildlife Sanctuary, Tripura, northeast India

Swapna, N., Radhakrishna, S., Gupta, A. K., & Kumar, A. (2009) · American Journal of Primatology · doi:10.1002/ajp.20760 · Cited by 87 · see citing works

Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organizationPreprint

Tsankov, A. M., Yanagisawa, Y., Rhind, N., Regev, A., & Rando, O. J. (2011) · Genome Research · doi:10.1101/gr.122267.111 · Cited by 86 · see citing works

Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences

Tirosh, I., Sigal, N., & Barkai, N. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.20 · Cited by 79 · see citing works

Evidence of Tree Gouging and Exudate Eating in Pygmy Slow Lorises (Nycticebus pygmaeus)

Tan, C. L., & Drake, J. H. (2001) · Folia Primatologica · doi:10.1159/000049918 · Cited by 75 · see citing works

Consequences of Eukaryotic Enhancer Architecture for Gene Expression Dynamics, Development, and Fitness

Ludwig, M. Z., Manu, Kittler, R., White, K. P., & Kreitman, M. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002364 · Cited by 73 · see citing works

Genomic and chromatin signals underlying transcription start-site selection

Valen, E., & Sandelin, A. (2011) · Trends in Genetics · doi:10.1016/j.tig.2011.08.001 · Cited by 69 · see citing works

Regulatory Variation Within and Between Species

Zheng, W., Gianoulis, T. A., Karczewski, K. J., Zhao, H., & Snyder, M. P. (2011) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-082908-150139 · Cited by 69 · see citing works

De Novo Genesis of Enhancers in Vertebrates

Eichenlaub, M., & Ettwiller, L. M. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001188 · Cited by 64 · see citing works

Chromatin regulators as capacitors of interspecies variations in gene expression

Tirosh, I., Reikhav, S., Sigal, N., Assia, Y., & Barkai, N. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.84 · Cited by 62 · see citing works

Tempo and Mode in Evolution of Transcriptional Regulation

Gordon, K. L., & Ruvinsky, I. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002432 · Cited by 62 · see citing works

Intergenic and Repeat Transcription in Human, Chimpanzee and Macaque Brains Measured by RNA-Seq

Xu, A. G., He, L., Li, Z., Xu, Y., Li, M., Fu, X., Zheng, Y., Yuan, Y., Menzel, C., Li, N., et al. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000843 · Cited by 58 · see citing works

Gene–Environment Interactions at Nucleotide Resolution

Gerke, J., Lorenz, K., Ramnarine, S., & Cohen, B. A. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001144 · Cited by 55 · see citing works

Expression of androgen receptor mRNA during mouse embryogenesis

Crocoll, A., Zhu, C. C., Cato, A. C. B., & Blum, M. (1998) · Mechanisms of Development · doi:10.1016/s0925-4773(98)00007-0 · Cited by 53 · see citing works

A Conserved Developmental Patterning Network Produces Quantitatively Different Output in Multiple Species of Drosophila

Fowlkes, C. C., Eckenrode, K. B., Bragdon, M. D. J., Meyer, M., Wunderlich, Z., Simirenko, L., Hendriks, C. L. L., Keränen, S. V. E., Henriquez, C., Knowles, D. W., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002346 · Cited by 50 · see citing works

Gene regulation and the origins of human biological uniqueness

Sholtis, S. J., & Noonan, J. P. (2010) · Trends in Genetics · doi:10.1016/j.tig.2009.12.009 · Cited by 47 · see citing works

Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation statesPreprint

Martin, D. I. K., Singer, M., Dhahbi, J. M., Mao, G., Zhang, L., Schroth, G. P., Pachter, L. S., & Boffelli, D. (2011) · Genome Research · doi:10.1101/gr.122721.111 · Cited by 42 · see citing works

A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activityPreprint

Smith, A. M., Sánchez, M. J., Follows, G., Kinston, S., Donaldson, I. J., Green, A. R., & Göttgens, B. (2008) · Genome Research · doi:10.1101/gr.077008.108 · Cited by 37 · see citing works

Evolution of Nucleosome Occupancy: Conservation of Global Properties and Divergence of Gene-Specific Patterns

Tsui, K., Dubuis, S., Gebbia, M., Morse, R. H., Barkai, N., Tirosh, I., & Nislow, C. (2011) · Molecular and Cellular Biology · doi:10.1128/mcb.05276-11 · Cited by 31 · see citing works

Effects of Testosterone on the Sternal Cutaneous Glands and Genitalia of the Male Greater Galago (Galago crassicaudatus crassicaudatus)

Dixson, A. F. (1976) · Folia Primatologica · doi:10.1159/000155751 · Cited by 30 · see citing works

Distinct Functional Constraints Partition Sequence Conservation in a cis-Regulatory Element

Barrière, A., Gordon, K. L., & Ruvinsky, I. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002095 · Cited by 30 · see citing works

Epistasis in a quantitative trait captured by a molecular model of transcription factor interactions

Gertz, J., Gerke, J., & Cohen, B. A. (2009) · Theoretical Population Biology · doi:10.1016/j.tpb.2009.10.002 · Cited by 29 · see citing works

Genome‐wide maps of transcription regulatory elements

Sakabe, N. J., & Nóbrega, M. A. (2010) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.70 · Cited by 26 · see citing works

Early Developmental Conditioning of Later Health and Disease: Physiology or Pathophysiology?

Hanson, M. A., & Gluckman, P. D. (2014) · Physiological Reviews · doi:10.1152/physrev.00029.2013 · Cited by 1,188 · see citing works

Detecting Natural Selection in Genomic Data

Vitti, J. J., Grossman, S. R., & Sabeti, P. C. (2013) · Annual Review of Genetics · doi:10.1146/annurev-genet-111212-133526 · Cited by 694 · see citing works

Signatures of negative selection in the genetic architecture of human complex traits

Zeng, J., de Vlaming, R., Wu, Y., Robinson, M. R., Lloyd-Jones, L. R., Yengo, L., Yap, C. X., Xue, A., Sidorenko, J., McRae, A. F., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0101-4 · Cited by 391 · see citing works

Aging increases cell-to-cell transcriptional variability upon immune stimulation

Martinez-Jimenez, C. P., Eling, N., Chen, H.-C., Vallejos, C. A., Kolodziejczyk, A. A., Connor, F., Stojic, L., Rayner, T. F., Stubbington, M. J. T., Teichmann, S. A., et al. (2017) · Science · doi:10.1126/science.aah4115 · Cited by 339 · see citing works

Comparative transcriptomics in human and mouse

Breschi, A., Gingeras, T., & Guigó, R. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.19 · Cited by 368 · see citing works

Where Are the Disease-Associated eQTLs?

Umans, B. D., Battle, A., & Gilad, Y. (2021) · Trends in Genetics · doi:10.1016/j.tig.2020.08.009 · Cited by 296 · see citing works

The Evolution of Gene Expression in cis and trans

Signor, S. A., & Nuzhdin, S. V. (2018) · Trends in Genetics · doi:10.1016/j.tig.2018.03.007 · Cited by 294 · see citing works

Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures

Khan, Z., Ford, M. J., Cusanovich, D. A., Mitrano, A., Pritchard, J. K., & Gilad, Y. (2013) · Science · doi:10.1126/science.1242379 · Cited by 240 · see citing works

Targeted genome-modification tools and their advanced applications in crop breeding

Li, B., Sun, C., Li, J., & Gao, C. (2024) · Nature Reviews Genetics · doi:10.1038/s41576-024-00720-2 · Cited by 259 · see citing works

Human brain evolution: transcripts, metabolites and their regulators

Somel, M., Liu, X., & Khaitovich, P. (2013) · Nature reviews. Neuroscience · doi:10.1038/nrn3372 · Cited by 243 · see citing works

Evolutionary dynamics of coding and non-coding transcriptomes

Necşulea, A., & Kaessmann, H. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3802 · Cited by 222 · see citing works

The power and promise of RNA ‐seq in ecology and evolution

Todd, E. V., Black, M. A., & Gemmell, N. J. (2016) · Molecular Ecology · doi:10.1111/mec.13526 · Cited by 233 · see citing works

Evolution of transcription factor binding in metazoans — mechanisms and functional implications

Villar, D., Flicek, P., & Odom, D. T. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3481 · Cited by 206 · see citing works

A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics

Romero, I. G., Pavlovic, B. J., Hernando-Herraez, I., Zhou, X., Ward, M. C., Banovich, N. E., Kagan, C. L., Burnett, J. E., Huang, C. H., Mitrano, A., et al. (2015) · eLife · doi:10.7554/elife.07103 · Cited by 194 · see citing works

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

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

Old Trade, New Tricks: Insights into the Spontaneous Mutation Process from the Partnering of Classical Mutation Accumulation Experiments with High-Throughput Genomic Approaches

Katju, V., & Bergthorsson, U. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy252 · Cited by 178 · see citing works

Comparative analysis of gene regulatory networks: from network reconstruction to evolution.

Thompson, D., Regev, A., & Roy, S. (2015) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100913-012908 · Cited by 160 · see citing works

Evolution of genetic and genomic features unique to the human lineage

O'Bleness, M., Searles, V. B., Varki, A., Gagneux, P., & Sikela, J. M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3336 · Cited by 168 · see citing works

The Genetic and Mechanistic Basis for Variation in Gene Regulation

Pai, A. A., Pritchard, J. K., & Gilad, Y. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1004857 · Cited by 158 · see citing works

Gene regulatory network inference resources: A practical overview

Mercatelli, D., Scalambra, L., Triboli, L., Ray, F., & Giorgi, F. M. (2019) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2019.194430 · Cited by 161 · see citing works

The strength and pattern of natural selection on gene expression in rice

Groen, S. C., Ćalić, I., Joly‐Lopez, Z., Platts, A. E., Choi, J. Y., Natividad, M. A., Dorph, K., Mauck, W. M., Bracken, B., Cabral, C. L. U., et al. (2020) · Nature · doi:10.1038/s41586-020-1997-2 · Cited by 138 · see citing works

Epigenetics and Cardiovascular Disease

Webster, A., Yan, M. S.-C., & Marsden, P. A. (2012) · Canadian Journal of Cardiology · doi:10.1016/j.cjca.2012.10.023 · Cited by 133 · 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., Cuevas, C., Marquès‐Bonet, T., & Gilad, Y. (2020) · Genome Research · doi:10.1101/gr.254904.119 · Cited by 131 · see citing works

Trm9-Catalyzed tRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation

Deng, W., Babu, I. R., Su, D., Yin, S., Begley, T. J., & Dedon, P. C. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005706 · Cited by 119 · see citing works

Gene pleiotropy constrains gene expression changes in fish adapted to different thermal conditions

Papakostas, S., Vøllestad, L. A., Bruneaux, M., Aykanat, T., Vanoverbeke, J., Ning, M., Primmer, C., & Leder, E. (2014) · Nature Communications · doi:10.1038/ncomms5071 · Cited by 96 · see citing works

The genomics of local adaptation in trees: are we out of the woods yet?

Lind, B. M., Menon, M., Bolte, C. E., Faske, T. M., & Eckert, A. (2017) · bioRxiv · doi:10.1007/s11295-017-1224-y · Cited by 98 · see citing works

Trait Correlations in the Genomics Era

Saltz, J. B., Hessel, F. C., & Kelly, M. W. (2017) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2016.12.008 · Cited by 106 · see citing works

The evolution of duplicate gene expression in mammalian organsPreprint

Guschanski, K., Warnefors, M., & Kaessmann, H. (2017) · Genome Research · doi:10.1101/gr.215566.116 · Cited by 105 · see citing works

The genetic architecture of hybrid incompatibilities and their effect on barriers to introgression in secondary contact

Lindtke, D., & Buerkle, C. A. (2015) · Evolution · doi:10.1111/evo.12725 · Cited by 95 · see citing works

Antagonistic Pleiotropy in Human Disease

Byars, S., & Voskarides, K. (2019) · Journal of Molecular Evolution · doi:10.1007/s00239-019-09923-2 · Cited by 96 · see citing works

Differential expression of a WRKY gene between wild and cultivated soybeans correlates to seed size

Gu, Y., Li, W., Jiang, H., Wang, Y., Gao, H., Liu, M., Chen, Q., Lai, Y., & He, C. (2017) · Journal of Experimental Botany · doi:10.1093/jxb/erx147 · Cited by 97 · see citing works

Phenotypic plasticity in gene expression contributes to divergence of locally adapted populations of F undulus heteroclitus

Dayan, D. I., Crawford, D. L., & Oleksiak, M. F. (2015) · Molecular Ecology · doi:10.1111/mec.13188 · Cited by 96 · see citing works

Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish

Hu, P., Liu, M., Liu, Y., Wang, J., Zhang, D., Niu, H., Jiang, S., Wang, J., Zhang, D., Han, B., et al. (2016) · Scientific Reports · doi:10.1038/srep28952 · Cited by 95 · see citing works

Network‐based approaches for understanding gene regulation and function in plants

Ko, D. K., & Brandizzí, F. (2020) · The Plant Journal · doi:10.1111/tpj.14940 · Cited by 100 · see citing works

Dynamics of Transcription Factor Binding Site Evolution

Tuğrul, M., Paixão, T., Barton, N., & Tkačik, G. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005639 · Cited by 90 · see citing works

Differentially expressed genes match bill morphology and plumage despite largely undifferentiated genomes in a H olarctic songbird

Mason, N. A., & Taylor, S. A. (2015) · Molecular Ecology · doi:10.1111/mec.13140 · Cited by 92 · see citing works

A single‐nucleotide polymorphism in WRKY33 promoter is associated with the cold sensitivity in cultivated tomato

Guo, M., Yang, F., Liu, C., Zou, J., Qi, Z., Fotopoulos, V., Lu, G., Yu, J., & Zhou, J. (2022) · New Phytologist · doi:10.1111/nph.18403 · Cited by 93 · see citing works

Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features

Seki, R., Li, C., Fang, Q., Hayashi, S., Egawa, S., Hu, J. Y., Xu, L., Pan, H., Kondo, M., Sato, T., et al. (2017) · Nature Communications · doi:10.1038/ncomms14229 · Cited by 90 · 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., Cooney, C., & Wright, A. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01761-8 · Cited by 81 · see citing works

The roles ofcis- andtrans-regulation in the evolution of regulatory incompatibilities and sexually dimorphic gene expressionPreprint

Meiklejohn, C. D., Coolon, J. D., Hartl, D. L., & Wittkopp, P. J. (2013) · Genome Research · doi:10.1101/gr.156414.113 · Cited by 86 · 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

Comparative transcriptomics of the model mushroom Coprinopsis cinerea reveals tissue-specific armories and a conserved circuitry for sexual development

Plaza, D. F., Lin, C., van der Velden, N. S. J., Aebi, M., & Künzler, M. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-492 · Cited by 87 · see citing works

The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution

Traeger, S., Altegoer, F., Freitag, M., Gabaldón, T., Kempken, F., Kumar, A., Marcet‐Houben, M., Pöggeler, S., Stajich, J., & Nowrousian, M. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003820 · Cited by 83 · see citing works

The Role of Alternative Splicing and Differential Gene Expression in Cichlid Adaptive Radiation

Singh, P., Börger, C., More, H. L., & Sturmbauer, C. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx204 · Cited by 81 · see citing works

Human neuronal maturation comes of age: cellular mechanisms and species differences

Wallace, J. L., & Pollen, A. A. (2024) · Nature Reviews Neuroscience · doi:10.1038/s41583-023-00760-3 · Cited by 82 · see citing works

Transcriptome asymmetry in synthetic and natural allotetraploid wheats, revealed by RNA ‐sequencing

Wang, X., Zhang, H., Li, Y., Zhang, Z., Li, L., & Liu, B. (2015) · New Phytologist · doi:10.1111/nph.13678 · Cited by 80 · see citing works

Evolutionary principles of modular gene regulation in yeasts

Thompson, D. A., Roy, S., Chan, M., Styczynsky, M. P., Pfiffner, J., French, C., Socha, A., Thielke, A., Napolitano, S., Muller, P., et al. (2013) · eLife · doi:10.7554/elife.00603 · Cited by 78 · see citing works

Phylogenetic Analysis of Gene Expression

Dunn, C. W., Luo, X., & Wu, Z. (2013) · Integrative and Comparative Biology · doi:10.1093/icb/ict068 · Cited by 78 · see citing works

Sex-Specific Selection Drives the Evolution of Alternative Splicing in Birds

Rogers, T. F., Droguett, D. H. P., & Wright, A. E. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa242 · Cited by 77 · see citing works

What to compare and how: Comparative transcriptomics for Evo‐Devo

Roux, J., Rosikiewicz, M., & Robinson‐Rechavi, M. (2015) · Journal of Experimental Zoology Part B Molecular and Developmental Evolution · doi:10.1002/jez.b.22618 · Cited by 77 · see citing works

Gene Expression and Diet Breadth in Plant-Feeding Insects: Summarizing Trends

Birnbaum, S. S. L., & Abbot, P. (2019) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2019.10.014 · Cited by 76 · see citing works

The logic of gene regulatory networks in early vertebrate forebrain patterning

Beccari, L. L., Marco-Ferreres, R., & Bovolenta, P. (2012) · Mechanisms of Development · doi:10.1016/j.mod.2012.10.004 · Cited by 71 · 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

Selection against admixture and gene regulatory divergence in a long-term primate field study

Vilgalys, T., Fogel, A. S., Anderson, J. A., Mututua, R. S., Warutere, J. K., Siodi, I., Kim, S. Y., Voyles, T. N., Robinson, J. A., Wall, J., et al. (2021) · bioRxiv · doi:10.1126/science.abm4917 · Cited by 70 · see citing works

Evolutionary history of a complex adaptation: Tetrodotoxin resistance in salamanders

Hanifin, C. T., & Gilly, W. F. (2014) · Evolution · doi:10.1111/evo.12552 · Cited by 72 · see citing works

Nature's fat-burning machine: brown adipose tissue in a hibernating mammal

Ballinger, M. A., & Andrews, M. T. (2018) · Journal of Experimental Biology · doi:10.1242/jeb.162586 · Cited by 72 · see citing works

Evolution of Gene Regulation in Humans

Reilly, S. K., & Noonan, J. P. (2016) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090314-045935 · Cited by 67 · see citing works

Genome-wide analyses reveal the role of noncoding variation in complex traits during rice domestication

Zheng, X., Chen, J., Pang, H., Liu, S., Gao, Q., Wang, J. R., Qiao, W., Wang, H., Liu, J., Olsen, K. M., et al. (2019) · Science Advances · doi:10.1126/sciadv.aax3619 · Cited by 70 · see citing works

Divergence in gene expression within and between two closely related flycatcher species

Uebbing, S., Künstner, A., Mäkinen, H., Backström, N., Bolívar, P., Burri, R., Dutoit, L., Mugal, C. F., Nater, A., Aken, B. L., et al. (2016) · Molecular Ecology · doi:10.1111/mec.13596 · Cited by 66 · see citing works

Evolution of Cold Acclimation and Its Role in Niche Transition in the Temperate Grass Subfamily Pooideae

Schubert, M., Grønvold, L., Sandve, S. R., Hvidsten, T. R., & Fjellheim, S. (2019) · PLANT PHYSIOLOGY · doi:10.1104/pp.18.01448 · Cited by 66 · see citing works

A molecular and cellular perspective on human brain evolution and tempo

Lindhout, F. W., Krienen, F. M., Pollard, K. S., & Lancaster, M. A. (2024) · Nature · doi:10.1038/s41586-024-07521-x · Cited by 70 · see citing works

A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues

Pavlovic, B. J., Blake, L. E., Roux, J., Chavarria, C. I., & Gilad, Y. (2018) · Scientific Reports · doi:10.1038/s41598-018-33478-9 · Cited by 64 · see citing works

Rolling-Circle Transposons Catalyze Genomic Innovation in a Mammalian Lineage

Thomas, J., Phillips, C. D., Baker, R. J., & Pritham, E. J. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu204 · Cited by 67 · see citing works

Genome-Wide Analysis Reveals Diverged Patterns of Codon Bias, Gene Expression, and Rates of Sequence Evolution in Picea Gene Families

Torre, A. R. D. L., Lin, Y., de Peer, Y. V., & Ingvarsson, P. K. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv044 · Cited by 66 · see citing works

Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS

Lin, H.-Y., Liu, Q., Li, X., Yang, J., Liu, S., Huang, Y., Scanlon, M. J., Nettleton, D. S., & Schnable, P. S. (2017) · Genome biology · doi:10.1186/s13059-017-1328-6 · Cited by 65 · see citing works

Data Mining in Healthcare: Applying Strategic Intelligence Techniques to Depict 25 Years of Research Development

Kolling, M. L., Furstenau, L. B., Sott, M. K., Rabaioli, B., Ulmi, P. H., Bragazzi, N. L., & Tedesco, L. P. (2021) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph18063099 · Cited by 65 · see citing works

Evolution of transcript modification by N6-methyladenosine in primatesPreprint

Ma, L., Zhao, B. S., Chen, K., Thomas, A. F., Tuteja, J. H., He, X., He, C., & White, K. P. (2017) · Genome Research · doi:10.1101/gr.212563.116 · Cited by 65 · see citing works

Contrasting Modes and Tempos of Venom Expression Evolution in Two Snake Species

Margres, M. J., McGivern, J. J., Seavy, M. A., Wray, K. P., Facente, J., & Rokyta, D. R. (2014) · Genetics · doi:10.1534/genetics.114.172437 · Cited by 64 · see citing works

Association mapping desiccation resistance within chromosomal inversions in the African malaria vectorAnopheles gambiae

Ayala, D., Zhang, S. V., Chateau, M., Fouet, C., Morlais, I., Costantini, C., Hahn, M. W., & Besansky, N. J. (2018) · Molecular Ecology · doi:10.1111/mec.14880 · Cited by 63 · see citing works

Rapid evolutionary changes in gene expression in response to climate fluctuations

Hamann, E., Pauli, C. S., Joly‐Lopez, Z., Groen, S. C., Rest, J. S., Kane, N. C., Purugganan, M. D., & Franks, S. J. (2020) · Molecular Ecology · doi:10.1111/mec.15583 · 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

Bat pluripotent stem cells reveal unusual entanglement between host and viruses

Déjosez, M., Marín, A., Hughes, G. M., Morales, A. E., Godoy-Parejo, C., Gray, J. L., Qin, Y., Singh, A. A., Xu, H., Javier Juste, B., et al. (2023) · Cell · doi:10.1016/j.cell.2023.01.011 · Cited by 62 · see citing works

Expression of the β‐glucosidase genePgβglu‐1underpins natural resistance of white spruce against spruce budworm

Magerøy, M. H., Parent, G. J., Germanos, G., Giguère, I., Delvas, N., Maaroufi, H., Bauce, É., Bohlmann, J., & MacKay, J. J. (2014) · The Plant Journal · doi:10.1111/tpj.12699 · Cited by 61 · see citing works

Leveraging massively parallel reporter assays for evolutionary questions

Romero, I. G., & Lea, A. J. (2023) · Genome biology · doi:10.1186/s13059-023-02856-6 · Cited by 62 · see citing works

Closing the genotype–phenotype gap: Emerging technologies for evolutionary genetics in ecological model vertebrate systems

Kratochwil, C. F., & Meyer, A. (2014) · BioEssays · doi:10.1002/bies.201400142 · Cited by 56 · see citing works

Evolution of dosage compensation under sexual selection differs between X and Z chromosomes

Mullon, C., Wright, A. E., Reuter, M., Pomiankowski, A., & Mank, J. E. (2015) · Nature Communications · doi:10.1038/ncomms8720 · Cited by 58 · see citing works

Phenotypic integration in the feeding system of the eastern diamondback rattlesnake (Crotalus adamanteus)

Margres, M. J., Wray, K. P., Seavy, M. A., McGivern, J. J., Sanader, D., & Rokyta, D. R. (2015) · Molecular Ecology · doi:10.1111/mec.13240 · Cited by 56 · see citing works

Comparative venom-gland transcriptomics and venom proteomics of four Sidewinder Rattlesnake (Crotalus cerastes) lineages reveal little differential expression despite individual variation

Hofmann, E. P., Rautsaw, R. M., Strickland, J. L., Holding, M. L., Hogan, M., Mason, A. J., Rokyta, D. R., & Parkinson, C. L. (2018) · Scientific Reports · doi:10.1038/s41598-018-33943-5 · Cited by 56 · see citing works

Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modulesPreprint

Roy, S., Wapinski, I. N., Pfiffner, J., French, C. E., Socha, A. L., Konieczka, J. H., Habib, N., Kellis, M., Thompson, D. A., & Regev, A. (2013) · Genome Research · doi:10.1101/gr.146233.112 · Cited by 55 · see citing works

ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa

Netotea, S., Sundell, D., Street, N. R., & Hvidsten, T. R. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-106 · Cited by 54 · see citing works

Predictive analytics of environmental adaptability in multi-omic network models

Angione, C., & Lió, P. (2015) · Scientific Reports · doi:10.1038/srep15147 · Cited by 53 · see citing works

Epigenetic variation in animal populations: Sources, extent, phenotypic implications, and ecological and evolutionary relevance

Vogt, G. (2021) · Journal of Biosciences · doi:10.1007/s12038-021-00138-6 · Cited by 54 · see citing works

Osmoregulation in decapod crustaceans: physiological and genomic perspectives

Rahi, M. L., Moshtaghi, A., Mather, P. B., & Hurwood, D. A. (2018) · Hydrobiologia · doi:10.1007/s10750-018-3690-0 · Cited by 53 · see citing works

The Red Queen's long race: human adaptation to pathogen pressure

Siddle, K. J., & Quintana‐Murci, L. (2014) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2014.07.004 · Cited by 49 · see citing works

Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases

Kumbhari, A., Cheng, T. N. H., Ananthakrishnan, A. N., Kochar, B., Burke, K. E., Shannon, K., Lau, H., Xavier, R. J., & Smillie, C. S. (2024) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2024.05.022 · Cited by 54 · see citing works

Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution

Suresh, H., Crow, M., Jorstad, N. L., Hodge, R. D., Lein, E. S., Dobin, A., Bakken, T. E., & Gillis, J. (2023) · Nature Ecology & Evolution · doi:10.1038/s41559-023-02186-7 · Cited by 55 · see citing works

Genomics of Adaptation to Multiple Concurrent Stresses: Insights from Comparative Transcriptomics of a Cichlid Fish from One of Earth’s Most Extreme Environments, the Hypersaline Soda Lake Magadi in Kenya, East Africa

Kavembe, G. D., Franchini, P., Irisarri, I., Machado‐Schiaffino, G., & Meyer, A. (2015) · Journal of Molecular Evolution · doi:10.1007/s00239-015-9696-6 · Cited by 51 · see citing works

The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi

Trail, F., Wang, Z., Stefanko, K., Cubba, C., & Townsend, J. P. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006867 · Cited by 51 · see citing works

Phenotypic Variation in Mojave Rattlesnake (Crotalus scutulatus) Venom Is Driven by Four Toxin Families

Strickland, J. L., Mason, A. J., Rokyta, D. R., & Parkinson, C. L. (2018) · Toxins · doi:10.3390/toxins10040135 · Cited by 51 · see citing works

Gene expression evolution in pattern-triggered immunity within Arabidopsis thaliana and across Brassicaceae species

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

Population transcriptomics reveals a potentially positive role of expression diversity in adaptation

Xu, Q., Xing, S., Zhu, C., Liu, W., Fan, Y., Wang, Q., Song, Z., Yang, W., Luo, F., Shang, F., et al. (2014) · Journal of Integrative Plant Biology · doi:10.1111/jipb.12287 · Cited by 50 · see citing works

Inference and Evolutionary Analysis of Genome-Scale Regulatory Networks in Large Phylogenies

Koch, C., Konieczka, J. H., Delorey, T. M., Lyons, A. M., Socha, A. L., Davis, K., Knaack, S., Thompson, D. A., O’Shea, E. K., Regev, A., et al. (2017) · Cell Systems · doi:10.1016/j.cels.2017.04.010 · Cited by 48 · see citing works

The rise of genomics in snake venom research: recent advances and future perspectives

Rao, W., Kalogeropoulos, K., Allentoft, M. E., Gopalakrishnan, S., Zhao, W., Workman, C. T., Knudsen, C., Jiménez‐Mena, B., Seneci, L., Mousavi‐Derazmahalleh, M., et al. (2022) · GigaScience · doi:10.1093/gigascience/giac024 · Cited by 48 · see citing works

Comparison of the Venom Peptides and Their Expression in Closely Related Conus Species: Insights into Adaptive Post-speciation Evolution of Conus Exogenomes

Barghi, N., Concepción, G. P., Olivera, B. M., & Lluisma, A. O. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv109 · Cited by 48 · see citing works

Comparative transcriptome analysis of the metal hyperaccumulator Noccaea caerulescens

Halimaa, P., Blande, D., Aarts, M. G. M., Tuomainen, M. H., Tervahauta, A. I., & Kärenlampi, S. O. (2014) · Frontiers in Plant Science · doi:10.3389/fpls.2014.00213 · Cited by 47 · see citing works

Denisovan introgression has shaped the immune system of present-day Papuans

Vespasiani, D. M., Jacobs, G. S., Cook, L. E., Brucato, N., Leavesley, M., Kinipi, C., Ricaut, F.-X., Cox, M. P., & Gallego Romero, I. (2022) · PLOS Genetics · doi:10.1371/journal.pgen.1010470 · Cited by 46 · see citing works

A time-resolved multi-omics atlas of transcriptional regulation in response to high-altitude hypoxia across whole-body tissues

Yan, Z., Yang, J. H., Wei, W.-T., Zhou, M., Mo, D.-X., Wan, X., Ma, R., Wu, M.-M., Huang, J.-H., Liu, Y.-J., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-48261-w · Cited by 49 · see citing works

What are we missing about marine invasions? Filling in the gaps with evolutionary genomics

Sherman, C. D. H., Lotterhos, K. E., Richardson, M. F., Tepolt, C. K., Rollins, L. A., Palumbi, S. R., & Miller, A. D. (2016) · Marine Biology · doi:10.1007/s00227-016-2961-4 · Cited by 46 · see citing works

Deep homology in the age of next-generation sequencing

Tschopp, P., & Tabin, C. J. (2016) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0475 · Cited by 46 · see citing works

Learning common and specific patterns from data of multiple interrelated biological scenarios with matrix factorization

Zhang, L., & Zhang, S. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz488 · Cited by 46 · see citing works

Comparative studies of gene regulatory mechanisms

Pai, A. A., & Gilad, Y. (2014) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2014.08.010 · Cited by 15 · 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

Using Genomic Tools to Study Regulatory Evolution

Gilad, Y. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-585-5_14 · Cited by 7 · see citing works

Broadening primate genomics: new insights into the ecology and evolution of primate gene regulation

Anderson, J. A., Vilgalys, T. P., & Tung, J. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.05.009 · Cited by 23 · see citing works

Accelerated Evolution of Context-Dependent Gene Expression in Primate Immune CellsPreprint

Durvasula, A., Longtin, A., Arner, A. M., Köhler, K., Rivas-González, I., Tung, J., Housman, G., & Lea, A. J. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.09.23.753790