Comparative studies of gene expression and the evolution of gene regulation

RNA-Seq: a revolutionary tool for transcriptomics

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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

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

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

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 2,925

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

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

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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

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

Gene Regulation for Higher Cells: A Theory

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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

Natural selection and random genetic drift in phenotypic evolution

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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

The evolutionary significance of cis-regulatory mutations

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

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

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

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 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

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

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 985

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 886

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 861

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

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 807

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

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

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 776

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 775

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

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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

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

The Raw and the Stolen

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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

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 635

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

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 593

Variation in Transcription Factor Binding Among Humans

Kasowski, M. M., Grubert, F., Heffelfinger, C., Hariharan, M., Asabere, A., Waszak, S. M., Habegger, L., Rozowsky, J. S., Shi, M., Urban, A. E., et al. (2010) · Science · doi:10.1126/science.1183621 · Cited by 580

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 579

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

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 552

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

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

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

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 447

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 436

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 434

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

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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 433

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 422

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

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

PHENOTYPIC EVOLUTION BY NEUTRAL MUTATION

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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

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 394

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 393

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

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 367

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 357

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

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 344

Evolution of primate gene expression

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

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

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 284

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 270

From DNA sequence to transcriptional behaviour: a quantitative approach

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

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 235

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

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

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

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 223

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

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 218

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 216

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

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 203

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

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 197

From genome to epigenome

Murrell, A., Rakyan, V. K., & Beck, S. (2005) · Human Molecular Genetics · doi:10.1093/hmg/ddi110 · Cited by 192

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

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 162

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

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 161

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

Frequent Gain and Loss of Functional Transcription Factor Binding Sites

Doniger, S. W., & Fay, J. C. (2005) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030099 · Cited by 152

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 149

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 147

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 140

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 135

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

Sequence features that drive human promoter function and tissue specificityPreprint

Landolin, J. M., Johnson, D. S., Trinklein, N. D., Aldred, S. F., Medina, C., Shulha, H. P., Weng, Z., & Myers, R. (2010) · Genome Research · doi:10.1101/gr.100370.109 · Cited by 113

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 111

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

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 106

The molecular elements that underlie developmental evolution

Alonso, C. R., & Wilkins, A. S. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1676 · Cited by 100

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 99

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

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

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

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

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

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

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 77

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 77

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

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