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

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

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

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

Britten, R. J., & Davidson, E. H. (1969) · Science · doi:10.1126/science.165.3891.349 · Cited by 2,078

Additive and mostly adaptive plastic responses of gene expression to multiple stress in Tribolium castaneum

Koch, E. L., & Guillaume, F. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1008768 · Cited by 45

Plastic and Evolutionary Gene Expression Responses Are Correlated in European Grayling (Thymallus thymallus) Subpopulations Adapted to Different Thermal Environments

Mäkinen, H., Papakostas, S., Vøllestad, L. A., Leder, E. H., & Primmer, C. R. (2015) · Journal of Heredity · doi:10.1093/jhered/esv069 · Cited by 47

Gain of An Auto-regulatory Site Led to Divergence of the Arabidopsis APETALA1 and CAULIFLOWER Duplicate Genes in the Time, Space and Level of Expression and Regulation of One Paralog by the Other

Ye, L., Wang, B., Zhang, W., Shan, H., & Kong, H. (2016) · PLANT PHYSIOLOGY · doi:10.1104/pp.16.00320 · Cited by 49

Determination of dosage compensation and comparison of gene expression in a triploid hybrid fish

Ren, L., Tang, C., Li, W., Cui, J., Tan, X.-J., Xiong, Y.-F., Chen, J., Wang, J., Xiao, J., Zhou, Y., et al. (2017) · BMC Genomics · doi:10.1186/s12864-016-3424-5 · Cited by 44

Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species

Mateos, J. L., Tilmes, V., Madrigal, P., Severing, E. I., Richter, R., Rijkenberg, C. W. M., Krajewski, P., & Coupland, G. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1618075114 · Cited by 44

Post-translational buffering leads to convergent protein expression levels between primates

Wang, S. H., Hsiao, C. J., Khan, Z., & Pritchard, J. K. (2018) · Genome biology · doi:10.1186/s13059-018-1451-z · Cited by 42

Nonrandom RNAseq gene expression associated with RNAlater and flash freezing storage methods

Passow, C. N., Kono, T. J. Y., Stahl, B. A., Jaggard, J. B., Keene, A. C., & McGaugh, S. E. (2018) · Molecular Ecology Resources · doi:10.1111/1755-0998.12965 · Cited by 43

Phylotranscriptomics of the Pentapetalae Reveals Frequent Regulatory Variation in Plant Local Responses to the Fungal Pathogen Sclerotinia sclerotiorum

Sucher, J., Mbengué, M., Axel, D., Barascud, M., Didelon, M., Barbacci, A., & Raffaele, S. (2020) · The Plant Cell · doi:10.1105/tpc.19.00806 · Cited by 41

Gene Regulatory Enhancers with Evolutionarily Conserved Activity Are More Pleiotropic than Those with Species-Specific Activity

Fish, A. E., Chen, L., & Capra, J. A. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx194 · Cited by 39

Evolution of mouse circadian enhancers from transposable elements

Judd, J., Sanderson, H., & Feschotte, C. (2021) · Genome biology · doi:10.1186/s13059-021-02409-9 · Cited by 40

Cis-Regulatory Divergence in Gene Expression between Two Thermally Divergent Yeast Species

Li, X., & Fay, J. C. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx072 · Cited by 41

Revisiting the expression of BDNF and its receptors in mammalian development

Esvald, E., Tuvikene, J., Kiir, C. S., Avarlaid, A., Tamberg, L., Sirp, A., Shubina, A., Cabrera-Cabrera, F., Pihlak, A., Koppel, I., et al. (2023) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2023.1182499 · Cited by 43

The ethical dimension in published animal research in critical care: the public face of science

Bara, M., & Joffe, A. R. (2014) · Critical Care · doi:10.1186/cc13694 · Cited by 40

Baseline mRNA expression differs widely between common laboratory strains of zebrafish

Holden, L. A., & Brown, K. H. (2018) · Scientific Reports · doi:10.1038/s41598-018-23129-4 · Cited by 44

Gene expression variability in human and chimpanzee populations share common determinants

Fair, B. J., Blake, L. E., Sarkar, A., Pavlovic, B. J., Cuevas, C., & Gilad, Y. (2020) · eLife · doi:10.7554/elife.59929 · Cited by 38

Single-cell dissection of aggression in honeybee colonies

Traniello, I. M., Bukhari, S. A., Dibaeinia, P., Serrano, G., Avalos, A., Cash-Ahmed, A. C., Sankey, A. L., Hernáez, M., Sinha, S., Zhao, S. D., et al. (2023) · Nature Ecology & Evolution · doi:10.1038/s41559-023-02090-0 · Cited by 42

Genetic and genomic analysis for cocoon yield traits in silkworm

Fang, S., Zhou, Q., Yu, Q., & Zhang, Z. (2020) · Scientific Reports · doi:10.1038/s41598-020-62507-9 · Cited by 38

Inferring Evolutionary Histories of Pathway Regulation from Transcriptional Profiling Data

Schraiber, J. G., Mostovoy, Y., Hsu, T. Y., & Brem, R. B. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003255 · Cited by 40

The Role of microRNAs in the Repeated Parallel Diversification of Lineages of Midas Cichlid Fish from Nicaragua

Franchini, P., Xiong, P., Fruciano, C., & Meyer, A. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evw097 · Cited by 38

Population Genomics of Marine Zooplankton

Bucklin, A., Castellano, K. R., Smolina, I., Choquet, M., Questel, J. M., Hoarau, G. G., & O'Neill, R. J. W. (2018) · Population genomics · doi:10.1007/13836_2017_9 · Cited by 40

An enhanced developmental staging table for the painted turtle,Chrysemys picta(Testudines: Emydidae)

Cordero, G. A., & Janzen, F. J. (2013) · Journal of Morphology · doi:10.1002/jmor.20226 · Cited by 37

Genomic insights into selection for heterozygous alleles and woody traits in Populus tomentosa

Li, P., Xiao, L., Du, Q., Quan, M., Song, Y., He, Y., Huang, W., Xie, J., Lv, C., Wang, D., et al. (2023) · Plant Biotechnology Journal · doi:10.1111/pbi.14108 · Cited by 36

Modular organization of the white spruce ( P icea glauca) transcriptome reveals functional organization and evolutionary signatures

Raherison, E., Giguère, I., Caron, S., Lamara, M., & MacKay, J. J. (2015) · New Phytologist · doi:10.1111/nph.13343 · Cited by 37

Comparative ecological transcriptomics and the contribution of gene expression to the evolutionary potential of a threatened fish

Brauer, C. J., Unmack, P. J., & Beheregaray, L. B. (2017) · Molecular Ecology · doi:10.1111/mec.14432 · Cited by 36

A comparative study of endoderm differentiation in humans and chimpanzees

Blake, L. E., Thomas, S. M., Blischak, J., Hsiao, C. J., Chavarria, C. I., Myrthil, M., Gilad, Y., & Pavlovic, B. J. (2018) · Genome biology · doi:10.1186/s13059-018-1490-5 · Cited by 34

Evolutionary shifts in gene expression decoupled from gene duplication across functionally distinct spider silk glands

Clarke, T. H., Garb, J. E., Haney, R. A., Chaw, R. C., Hayashi, C. Y., & Ayoub, N. A. (2017) · Scientific Reports · doi:10.1038/s41598-017-07388-1 · Cited by 37

Gene Age Predicts the Strength of Purifying Selection Acting on Gene Expression Variation in Humans

Popadin, K. Y., Gutiérrez‐Arcelus, M., Lappalainen, T., Buil, A., Steinberg, J., Nikolaev, S. I., Lukowski, S. W., Bazykin, G. A., Seplyarskiy, V. B., Ioannidis, P., et al. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.11.003 · Cited by 37

Ecological population genomics in the marine environment

Crawford, D. L., & Oleksiak, M. F. (2016) · Briefings in Functional Genomics · doi:10.1093/bfgp/elw008 · Cited by 35

Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs

Guðbrandsson, J., Franzdóttir, S. R., Kristjánsson, B. K., Ahi, E. P., Maier, V. H., Kapralova, K. H., Snorrason, S. S., Jónsson, Z. O., & Pálsson, A. (2018) · PeerJ · doi:10.7717/peerj.4345 · Cited by 37

Transcriptional and epigenetic adaptation of maize chromosomes in Oat-Maize addition lines

Dong, Z., Yu, J., Li, H., Huang, W., Xu, L., Zhao, Y., Zhang, T., Xu, W., Jiang, J., Su, Z., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky209 · Cited by 35

Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum

Dennis, A. B., Ballesteros, G., Robin, S., Schrader, L., Bast, J., Berghöfer, J., Beukeboom, L. W., Belghazi, M., Bretaudeau, A., Buellesbach, J., et al. (2020) · BMC Genomics · doi:10.1186/s12864-020-6764-0 · Cited by 38

Towards integration of population and comparative genomics in forest trees

Ingvarsson, P. K., Hvidsten, T. R., & Street, N. R. (2016) · New Phytologist · doi:10.1111/nph.14153 · Cited by 34

Regulatory Divergence in Wound-Responsive Gene Expression between Domesticated and Wild Tomato

Liu, M., Sugimoto, K., Uygun, S., Panchy, N. L., Campbell, M. S., Yandell, M. D., Howe, G. A., & Shiu, S. (2018) · The Plant Cell · doi:10.1105/tpc.18.00194 · Cited by 34

Gene expression divergence between malaria vector sibling species Anopheles gambiae and An. coluzzii from rural and urban Yaoundé Cameroon

Cassone, B. J., Kamdem, C., Cheng, C., Tan, J. C., Hahn, M. W., Costantini, C., & Besansky, N. J. (2014) · Molecular Ecology · doi:10.1111/mec.12733 · Cited by 46

Host plant diet affects growth and induces altered gene expression and microbiome composition in the wood white (Leptidea sinapis) butterfly

Näsvall, K., Wiklund, C., Mrazek, V., Künstner, A., Talla, V., Busch, H. S., Vila, R., & Backström, N. (2020) · Molecular Ecology · doi:10.1111/mec.15745 · Cited by 32

Accelerated evolution of developmentally biased genes in the tetraphenic ant Cardiocondyla obscurior

Schrader, L., Helanterä, H., & Oettler, J. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw240 · Cited by 32

The Molecular Basis of Freshwater Adaptation in Prawns: Insights from Comparative Transcriptomics of Three Macrobrachium Species

Rahi, M. L., Mather, P. B., Ezaz, T., & Hurwood, D. A. (2019) · Genome Biology and Evolution · doi:10.1093/gbe/evz045 · Cited by 34

Drift and Directional Selection Are the Evolutionary Forces Driving Gene Expression Divergence in Eye and Brain Tissue of Heliconius Butterflies

Catalán, A., Briscoe, A. D., & Höhna, S. (2019) · Genetics · doi:10.1534/genetics.119.302493 · Cited by 32

Bivalve Molluscs as Model Systems for Studying Mitochondrial Biology

Ghiselli, F., Iannello, M., Piccinini, G., & Milani, L. (2021) · Integrative and Comparative Biology · doi:10.1093/icb/icab057 · Cited by 31

Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila

Ullastres, A., Merenciano, M., & González, J. (2021) · Genome biology · doi:10.1186/s13059-021-02471-3 · Cited by 38

Dynamic Transcriptomic Profiles between Tomato and a Wild Relative Reflect Distinct Developmental Architectures

Chitwood, D. H., Maloof, J., & Sinha, N. R. (2013) · PLANT PHYSIOLOGY · doi:10.1104/pp.112.213546 · Cited by 31

XSAnno: a framework for building ortholog models in cross-species transcriptome comparisons

Zhu, Y., Li, M., Sousa, A. M. M., & Šestan, N. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-343 · Cited by 31

Transcriptional regulatory network reveals key transcription factors for regulating agronomic traits in soybean

Wu, J., Wang, M.-M., Guan, Y.-J., Guo, W., Zhang, C., Wei, Y., Zhao, Z., Ma, H., Wang, L., Jiang, X., et al. (2024) · Genome biology · doi:10.1186/s13059-024-03454-w · Cited by 30

Genomic approaches to studying human-specific developmental traits

Franchini, L. F., & Pollard, K. S. (2015) · Development · doi:10.1242/dev.120048 · Cited by 29

Estimating Phylogenies from Shape and Similar Multidimensional Data: Why It Is Not Reliable

Varón‐González, C., Whelan, S., & Klingenberg, C. P. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa003 · Cited by 30

Widespread and Adaptive Alterations in Genome-Wide Gene Expression Associated with Ecological Divergence of TwoOryzaSpecies

Guo, J., Liu, R., Huang, L., Zheng, X., Liu, P., Du, Y.-S., Cai, Z., Zhou, L., Wei, X.-H., Zhang, F., et al. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv196 · Cited by 31

Building the differences: a case for the ground tissue patterning in plants

Ruocco, G. D., Mambro, R. D., & Ioio, R. D. (2018) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2018.1746 · Cited by 31

Complexities of gene expression patterns in natural populations of an extremophile fish ( Poecilia mexicana , Poeciliidae)

Passow, C. N., Brown, A. P. C., Arias‐Rodríguez, L., Yee, M., Sockell, A., Schartl, M., Warren, W. C., Bustamante, C. D., Kelley, J. L., & Tobler, M. (2017) · Molecular Ecology · doi:10.1111/mec.14198 · Cited by 29

Evolutionary shifts dramatically reorganized the human hippocampal complex

Schilder, B. M., Petry, H. M., & Hof, P. R. (2019) · The Journal of Comparative Neurology · doi:10.1002/cne.24822 · Cited by 31

Ecological Speciation Promoted by Divergent Regulation of Functional Genes Within African Cichlid Fishes

Carruthers, M., Edgley, D. E., Saxon, A. D., Gabagambi, N. P., Shechonge, A., Miska, E. A., Durbin, R. M., Bridle, J. R., Turner, G. F., & Genner, M. J. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac251 · Cited by 30

Restoring ancestral phenotypes is a general pattern in gene expression evolution during adaptation to new environments in Tribolium castaneum

Koch, E. L., & Guillaume, F. (2020) · Molecular Ecology · doi:10.1111/mec.15607 · Cited by 29

The zinc-finger bearing xenogeneic silencer MucR in α-proteobacteria balances adaptation and regulatory integrity

Jiao, J., Zhang, B., Li, M., Zhang, Z., & Tian, C. F. (2021) · The ISME Journal · doi:10.1038/s41396-021-01118-2 · Cited by 28

MAP4K4 controlled transcription factor POUM1 regulates PxABCG1 expression influencing Cry1Ac resistance in Plutella xylostella (L.)

Xu, L., Qin, J., Fu, W., Wang, S., Wu, Q., Zhou, X. J., Crickmore, N., Guo, Z., & Zhang, Y. (2022) · Pesticide Biochemistry and Physiology · doi:10.1016/j.pestbp.2022.105053 · Cited by 28

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 26

A necroptosis‐related gene signature for predicting prognosis, immune landscape, and drug sensitivity in hepatocellular carcinoma

Chen, J., Wang, H., Zhou, L., Liu, Z., Chen, H., & Tan, X. (2022) · Cancer Medicine · doi:10.1002/cam4.4812 · Cited by 28

The methodological quality of animal research in critical care: the public face of science

Bara, M., & Joffe, A. R. (2014) · Annals of Intensive Care · doi:10.1186/s13613-014-0026-8 · Cited by 29

Impact of salinity changes on growth, oxygen consumption and expression pattern of selected candidate genes in the orange mud crab ( Scylla olivacea )

Rahi, M. L., Ferdusy, T., Ahmed, S. W., Khan, M. N., Aziz, D., & Salin, K. R. (2020) · Aquaculture Research · doi:10.1111/are.14772 · Cited by 27

Microbial control of host gene regulation and the evolution of host–microbiome interactions in primates

Grieneisen, L., Muehlbauer, A. L., & Blekhman, R. (2020) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2019.0598 · Cited by 25

Comparative transcriptomics of limb regeneration: Identification of conserved expression changes among three species of Ambystoma

Dwaraka, V. B., Smith, J. J., Woodcock, M. R., & Voss, S. R. (2018) · Genomics · doi:10.1016/j.ygeno.2018.07.017 · Cited by 27

Oocyte Developmental Competence: Insights from Cross-Species Differential Gene Expression and Human Oocyte-Specific Functional Gene Networks

Biase, F. H. (2017) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2016.0177 · Cited by 26

Evolution of DNA Methylation in Papio Baboons

Vilgalys, T. P., Rogers, J., Jolly, C. J., Analysis, B. G., Mukherjee, S., & Tung, J. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy227 · Cited by 30

Transcriptomic divergence between upland and lowland ecotypes contributes to rice adaptation to a drought‐prone agroecosystem

Luo, Z., Xiong, J., Xia, H., Ma, X., Gao, M., Wang, L., Liu, G., Yu, X., & Luo, L. (2020) · Evolutionary Applications · doi:10.1111/eva.13054 · Cited by 26

Bridging organ transcriptomics for advancing multiple organ toxicity assessment with a generative AI approach

Li, T., Chen, X., & Tong, W. (2024) · npj Digital Medicine · doi:10.1038/s41746-024-01317-z · Cited by 26

Plasticity of Promoter-Core Sequences Allows Bacteria to Compensate for the Loss of a Key Global Regulatory Gene

Lamrabet, O., PLUMBRIDGE, J. A., Martin, M., Lenski, R. E., Schneider, D., & Hindré, T. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz042 · Cited by 23

Temperature induced changes in physiological traits and expression of selected candidate genes in black tiger shrimp (Penaeus monodon) larvae

Rahi, M. L., Mahmud, S., Dilruba, K. J., Sabbir, W., Aziz, D., & Hurwood, D. A. (2021) · Aquaculture Reports · doi:10.1016/j.aqrep.2021.100620 · Cited by 25

microRNA expression variation as a potential molecular mechanism contributing to adaptation to hydrogen sulphide

Kelley, J. L., Desvignes, T., McGowan, K. L., Perez, M. A., Arias‐Rodríguez, L., Brown, A. P. C., Culumber, Z. W., & Tobler, M. (2020) · Journal of Evolutionary Biology · doi:10.1111/jeb.13727 · Cited by 25

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

Sperm competition shapes gene expression and sequence evolution in the ocellated wrasse

Dean, R., Wright, A. E., Marsh‐Rollo, S. E., Nugent, B. M., Alonzo, S. H., & Mank, J. E. (2016) · Molecular Ecology · doi:10.1111/mec.13919 · Cited by 24

The strength and form of natural selection on transcript abundance in the wild

Ahmad, F., Debes, P. V., Nousiainen, I., Kahar, S., Pukk, L., Gross, R., Ozerov, M. Y., & Vasemägi, A. (2020) · Molecular Ecology · doi:10.1111/mec.15743 · Cited by 27

Are long‐lived trees poised for evolutionary change? Single locus effects in the evolution of gene expression networks in spruce

Verta, J., Landry, C. R., & MacKay, J. J. (2013) · Molecular Ecology · doi:10.1111/mec.12189 · Cited by 23

Genetic diversity and gene expression diversity shape the adaptive pattern of the aquatic plant Batrachium bungei along an altitudinal gradient on the Qinghai–Tibet plateau

Yu, X., Chen, F., Chen, Z., Wei, P., Song, X., Liu, C., Liu, T., Li, X., & Liu, X. (2022) · Plant Molecular Biology · doi:10.1007/s11103-022-01326-0 · Cited by 23

Comparative gene expression between two yeast species

Guan, Y., Dunham, M. J., Troyanskaya, O. G., & Caudy, A. A. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-33 · Cited by 23

Tracing the Evolution of Lineage-Specific Transcription Factor Binding Sites in a Birth-Death Framework

Yokoyama, K. D., Zhang, Y., & Ma, J. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003771 · Cited by 23

Population transcriptomics in Daphnia: The role of thermal selection

Herrmann, M., Ravindran, S. P., Schwenk, K., & Cordellier, M. (2017) · Molecular Ecology · doi:10.1111/mec.14450 · Cited by 22

Evolutionary divergence of 3’ UTRs in cichlid fishes

Xiong, P., Hulsey, C. D., Meyer, A., & Franchini, P. (2018) · BMC Genomics · doi:10.1186/s12864-018-4821-8 · Cited by 22

Construction, comparison and evolution of networks in life sciences and other disciplines

Gysi, D. M., & Nowick, K. (2020) · Journal of The Royal Society Interface · doi:10.1098/rsif.2019.0610 · Cited by 25

Identification of Genes Related to Cold Tolerance and Novel Genetic Markers for Molecular Breeding in Taiwan Tilapia (Oreochromis spp.) via Transcriptome Analysis

Chu, P., Li, J.-X., Hsu, T., Gong, H., Lin, C., Wang, J.-H., & Huang, C. (2021) · Animals · doi:10.3390/ani11123538 · Cited by 22

Accounting for cis-regulatory constraint prioritizes genes likely to affect species-specific traits

Starr, A. L., Gokhman, D., & Fraser, H. B. (2023) · Genome biology · doi:10.1186/s13059-023-02846-8 · Cited by 21

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 22

Great Ape Genomics

Wall, J. D. (2013) · ILAR Journal · doi:10.1093/ilar/ilt048 · Cited by 25

Comparative Transcriptomics in Two Bivalve Species Offers Different Perspectives on the Evolution of Sex-Biased Genes

Ghiselli, F., Iannello, M., Puccio, G., Chang, P. L., Plazzi, F., Nuzhdin, S. V., & Passamonti, M. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy082 · Cited by 23

Intraspecific sequence and gene expression variation contribute little to venom diversity in sidewinder rattlesnakes (Crotalus cerastes)

Rautsaw, R. M., Hofmann, E. P., Margres, M. J., Holding, M. L., Strickland, J. L., Mason, A. J., Rokyta, D. R., & Parkinson, C. L. (2019) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2019.0810 · Cited by 22

High spatial resolution proteomic comparison of the brain in humans and chimpanzees

Bauernfeind, A. L., Reyzer, M. L., Caprioli, R. M., Ely, J. J., Babbitt, C. C., Wray, G. A., Hof, P. R., & Sherwood, C. C. (2015) · The Journal of Comparative Neurology · doi:10.1002/cne.23777 · Cited by 22

Phenotypic variation reveals sites of evolutionary constraint in the androgenic signaling pathway

Schuppe, E. R., & Fuxjager, M. J. (2019) · Hormones and Behavior · doi:10.1016/j.yhbeh.2019.06.002 · Cited by 21

Transcriptome analyses reveal alterations in muscle metabolism, immune responses and reproductive behavior of Japanese mantis shrimp (Oratosquilla oratoria) at different cold temperature

Lou, F., Gao, T., & Han, Z. (2019) · Comparative Biochemistry and Physiology Part D Genomics and Proteomics · doi:10.1016/j.cbd.2019.100615 · Cited by 22

Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F1 hybridsPreprint

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The 3D-Evo Space: Evolution of Gene Expression and Alternative Splicing Regulation

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Adaptation of peroxisome proliferator-activated receptor alpha to hibernation in bats

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Parallel genetics of regulatory sequences using scalable genome editing in vivo

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Yeast Interspecies Comparative Proteomics Reveals Divergence in Expression Profiles and Provides Insights into Proteome Resource Allocation and Evolutionary Roles of Gene Duplication

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Intraspecific and interspecific investigations of skeletal DNA methylation and femur morphology in primates

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Do plasticity in gene expression and physiological responses in Palaemonid prawns facilitate adaptive response to different osmotic challenges?

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The decreased expression of GW2 homologous genes contributed to the increased grain width and thousand‑grain weight in wheat-Dasypyrum villosum 6VS·6DL translocation lines

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Transcription factors, chromatin proteins and the diversification of Hemiptera

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Metal accumulation and expression of genes encoding for metallothionein and copper transporters in a chronically exposed wild population of the fish Hyphessobrycon luetkenii

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Stochastic Modeling of Gene Expression Evolution Uncovers Tissue- and Sex-Specific Properties of Expression Evolution in the Drosophila Genus

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Conserved and species-specific transcription factor co-binding patterns drive divergent gene regulation in human and mouse

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Comparative studies of gene regulatory mechanisms

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Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures

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Using Genomic Tools to Study Regulatory Evolution

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

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