Regulatory divergence in Drosophila revealed by mRNA-seq

McManus, C. Joel, Coolon, Joseph D., Duff, Michael O., Eipper-Mains, Jodi, Graveley, Brenton R., Wittkopp, Patricia J.·2010·Genome Research

Cited by (386)

Items 301–386 of 386

  1. Genomic analysis of allele-specific expression in the mouse liver
    Ashutosh K. Pandey, Robert W. Williams · 2015 · bioRxiv (Cold Spring Harbor Laboratory)
  2. Rampant hybrid misexpression in craniofacial tissues within a recent adaptive radiation of Cyprinodon pupfishes
    J. A. McGirr, C. Martin · 2018 · bioRxiv
  3. Multi-locus interactions and the build-up of reproductive isolation
    Ina Satokangas, Simon H. Martin, Heikki Helanterä, Jari Saramäki, Jonna Kulmuni · 2020 · arXiv (Cornell University)
  4. The regulatory architecture of gene expression variation in Caenorhabditis elegans revealed by multi-strain allele-specific analysis
    Avery Davis Bell, Francisco Valencia, Annalise B. Paaby · 2025 · Genetics
  5. De novo assembly, annotation and gene expression profiles of gonads of Cytorace-3, a hybrid lineage of Drosophila nasuta nasuta and D. n. albomicans
    Koushik Ponnanna, Stafny Dsouza, Nallur B. Ramachandra · 2021 · Genomics & Informatics
  6. Heterogeneous Genomic Divergence Landscape in Two Commercially Important European Scallop Species
    David L. J. Vendrami, Joseph Ivan Hoffman, Craig Stephen Wilding · 2022 · Genes
  7. Pervasive tissue-, genetic background-, and allele-specific gene expression effects in Drosophila melanogaster
    Amanda Glaser‐Schmitt, Marion Lemoine, Martin Kaltenpoth, John Parsch · 2024 · PLoS Genetics
  8. Unraveling the genetic mechanisms of maize ear diameter heterosis
    Liangfa Wang, Juan Li, Baiyu Yuan, Huiyu Zhang, Yuan Yu Lin, Jiong Wan, Jiawen Zhao, Qiyue Wang, Xiaolong Ju, Xiaoyang Chen et al. · 2024 · New Crops
  9. Gene-by-environment Interactions and Adaptive Body Size Variation in Mice From the Americas
    Katya L. Mack, Nico P Landino, Mariia Tertyshnaia, Tiffany C Longo, Sebastian A Vera, Lilia Crew, Kristi McDonald, Megan Phifer‐Rixey · 2025 · Molecular Biology and Evolution
  10. Optimization Techniques For Next-Generation Sequencing Data Analysis
    Adrian Caciula · 2022
  11. Genome Mapping and Genomics in Drosophila
    Boris Adryan, Steven R. H. Russell · 2012 · Springer eBooks
  12. Transcriptome-Wide Analyses Identify Dominant as the Predominantly Non-Conservative Alternative Splicing Inheritance Patterns in F1 Chickens
    Xin Qi, Hongchang Gu, Lujiang Qu · 2021 · Frontiers in Genetics
  13. Evolution of X‐Linked Male‐Biased Genes in Drosophila
    Danielle K. Herrig, Ana Llopart · 2014 · Encyclopedia of Life Sciences
  14. RNA sequencing for the study of gene expression regulation
    Ângela Gonçalves · 2012 · Apollo (University of Cambridge)
  15. CompMap: an allele-specific expression read-counter based on competitive mapping
    Santiago Sanchez Ramirez, Asher D. Cutter · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  16. Cis -regulatory divergence underpins the evolution of C 3 -C 4 intermediate photosynthesis in Moricandia
    Meng-Ying Lin, Urte Schlüter, Benjamin Stich, Andreas P.M. Weber · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  17. Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
    Olga M. Sigalova, Mattia Forneris, Frosina Stojanovska, Bingqing Zhao, Rebecca R. Viales, Adam H. Rabinowitz, Fayrouz Hammal, Benoît Ballester, Judith B. Zaugg, Eileen E. M. Furlong · 2025 · Genome Research
  18. Genome-wide identification and analysis of recurring patterns of epigenetic variation across individuals
    Jennifer Zou, Emily Maciejewski, Jason Ernst · 2025 · Communications Biology
  19. A Balanced Inversion Polymorphism Exhibits a Dominance Reversal at the Gene Expression Level that Depends on Developmental Context
    Esra Durmaz Mitchell, Envel Kerdaffrec, P. Schmidt, T. Flatt, Sebastian Kittelmann · 2025 · Molecular biology and evolution
  20. Regionally specific and highly pleiotropic loci together mediate skeletal evolution in tropical and temperate house mice
    Sylvia M. Durkin, Kathleen G. Ferris, Mallory A. Ballinger, Ke Bi, Gabriela P. Heyer, Michael W. Nachman · 2026 · Genetics
  21. Gene expression is stable despite widespread cis and trans regulatory divergence in Saccharomyces yeasts
    Danithza S. Rojas, Gregory I. Lang · 2026 · Genetics
  22. Workshop: Inference of allele specific expression levels from RNA-Seq data
    Sahar Al Seesi, Ion Măndoiu · 2012 · IEEE International Conference on Computational Advances in Bio and Medical Sciences
  23. ЭКСПРЕССИЯ ГЕНОВ ИММУНИТЕТА И АДАПТАЦИИ И СОСТАВ МИКРОБИОМА У РОДИТЕЛЬСКОГО ПОГОЛОВЬЯ КУР И ПЕТУХОВ (Gallus gallus L.) ЛИНИЙ СМ5 И СМ9 КРОССА СМЕНА 9
    ООО «БИОТРОФ+», Г.Ю. ЛАПТЕВ · 2023 · Sel skokhozyaistvennaya Biologiya
  24. Non-Additive and Asymmetric Allelic Expression of p38 mapk in Hybrid Tilapia (Oreochromis niloticus ♀ × O. aureus ♂)
    Zihui Liu, Binglin Chen, Zhiying Zou, Dayu Li, Jinglin Zhu, Jie Yu, Wei Xiao, Hong Yang · 2024 · Animals
  25. Transcriptome analysis reveals genetic regulation of growth diversity in F2 intergeneric hybrids of Megalobrama amblycephala and Culter alburnus
    Mengxue Luo, Yakui Tai, Mengdan Li, Yiyan Zeng, Chang Wu, Ling Liu, Hong Zhang, Ren Li, Shaojun Liu · 2024 · Aquaculture
  26. Recent allopolyploidization and transcriptomic asymmetry in the mangrove shrub Acanthus tetraploideus
    Wuxia Guo, Achyut Kumar Banerjee, Hui Feng, Wei Lun Ng, Haidan Wu, Weixi Li, Yang Yuan, Yelin Huang · 2025 · BMC Genomics
  27. Yeast Hybrids and Polyploids as Models in Evolutionary Studies
    Avraham A. Levy, Itay Tirosh, Sharon Reikhav, Yasmin Bloch, Naama Barkai · 2013
  28. Transcriptome assembly and quantification from Ion Torrent RNA-Seq data
    Serghei Mangul, Sahar Al Seesi, Ion Măndoiu, Adrian Caciula, Alex Zelikovsky, Dumitru Brinza · 2013 · IEEE International Conference on Computational Advances in Bio and Medical Sciences
  29. A bioinformatic analysis of genetic factors affecting primary root growth in Zea mays
    Ann Meyer · 2015 · The Atrium (University of Guelph)
  30. cis dominantly explains regulatory divergence between two indica rice genotypes; drought further enhances regulatory differences
    Nelzo C. Ereful, Antonio C. Laurena, Li-Yu Daisy Liu, Shu‐Min Kao, Eric Tsai, Michael J. Thomson, Andy Greenland, Wayne Powell, Ian Mackay, Hei Leung · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  31. Patterns of regulatory divergence and gene expression in hybrids are associated with molecular evolution in species undergoing gene flow
    Fernando Dı́az, Jason B. Wolf, Reinaldo de Brito · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  32. Abundant trans -driven variation in detoxification gene expression in the extreme generalist herbivore Tetranychus urticae
    Andre H. Kurlovs, Berdien De Beer, Meiyuan Ji, Marilou Vandenhole, Tim De Meyer, René Feyereisen, Richard M. Clark, Thomas Van Leeuwen · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  33. Tissue-specific and cis -regulatory changes underlie parallel, adaptive gene expression evolution in house mice
    Sylvia M. Durkin, Mallory A. Ballinger, Michael W. Nachman · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  34. The role of heterochronic gene expression and regulatory architecture in early developmental divergence
    Nathan D. Harry, Christina Zakas · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  35. The role of heterochronic gene expression and regulatory architecture in early developmental divergence
    Nathan D. Harry, Christina Zakas · 2024 · eLife
  36. Molecular Heterosis in the Abaca ( Musa textilis Née) BC 2 Hybrid, Bandala
    Nelzo C. Ereful, Roneil Christian S. Alonday, Antonio G. Lalusin · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  37. Predominantly genetic determination and stable transmission of DNA methylation in an avian hybrid zone
    Fritjof Lammers, Valentina Peona, Madeline A. Chase, Dave Lutgen, Marta Burri, Reto Burri · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  38. Genetic & Molecular Analysis Of Hybrid Incompatibility In Drosophila.
    Arundhati Maheshwari · 2012 · eCommons (Cornell University)
  39. Gene Expression Divergence Between Zebra Finch (Taeniopygia Guttata) Subspecies And Gene Regulation In Hybrids
    John H. Davidson · 2015 · ProQuest Demo Repository
  40. The Genetic Landscape of Transcriptional Networks in a Combined Haploid/Diploid Plant System
    J. Verta, C. Landry, J. MacKay · 2014 · bioRxiv
  41. Evolution of Gene Regulation during Transcription and
    Zhe Wang, Xuepeng Sun, Huifeng Jiang, Hongye Li, Zhenglong Gu · 2015
  42. Characterization of the Iberian pig genome and transcriptome using high throughput sequencing
    Anna Esteve‐Codina · 2012 · LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas)
  43. Identification of the molecular changes underlying head morphology variation in closely related Drosophila species
    Montserrat Torres-Oliva · 2016
  44. Dysfunctional Gene Regulation of the Meiotic Program in an Interspecific Yeast Hybrid
    Devjanee Swain-Lenz · 2013 · Open Scholarship Institutional Repository (Washington University in St. Louis)
  45. Functional Analysis of Genomic Variation and Impact on Molecular and Higher Order Phenotypes
    Ashutosh K. Pandey · 2015
  46. The specific problems of the experimental design in the high-throughput sequencing studies of transcriptome
    Petr N. Menshanov, Н. Н. Дыгало · 2017 · Russian Journal of Genetics Applied Research
  47. Measuring Gene Expression With Next Generation Sequencing Technology
    Michele Busby · 2012
  48. Genetics of gene expression in conifers
    Jukka‐Pekka Verta · 2014 · Corpus Université Laval (Université Laval)
  49. Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast
    C. Joel McManus, Gemma E. May, Pieter Spealman, Alan Shteyman · 2013 · arXiv (Cornell University)
  50. New gene formation in hybrid Drosophila
    Rebekah L. Rogers, Cathy C. Moore, Nicholas B. Stewart · 2021 · arXiv (Cornell University)
  51. Nonadditive gene expression is correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow ( Salix spp.)
    Craig H. Carlson, Yongwook Choi, Agnes Pui-Yee Chan, Christopher D. Town, Lawrence B. Smart · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  52. Genome-Wide Regulatory Interactions in the Early Stages of Drosophila Speciation
    Alwyn C. Go · 2020
  53. RNA-Seq Analysis Reveals Expression Regulatory Divergence of W-Linked Genes between Two Contrasting Chicken Breeds
    Hongchang Gu, Liang Wang, Xueze Lv, Weifang Yang, Yu Chen, Kaiyang Li, Jianwei Zhang, Yaxiong Jia, Zhonghua Ning, Lujiang Qu · 2022 · Animals
  54. A lotus by any other color: Gene regulation divergence in lotus petal development
    Amy Lanctot · 2022 · PLANT PHYSIOLOGY
  55. The role of heterochronic gene expression and regulatory architecture in early developmental divergence
    Nathan D. Harry, Christina Zakas · 2024 · eLife
  56. Additional file 2 of Gene expression variation explains maize seed germination heterosis
    Jiong Wan, Qiyue Wang, Jiawen Zhao, Xuehai Zhang, Zhanyong Guo, Desheng Hu, Shujun Meng, Yuan Yu Lin, Xiaoqian Qiu, Liqin Mu et al. · 2022 · Figshare
  57. Additional file 6 of Gene expression variation explains maize seed germination heterosis
    Jiong Wan, Qiyue Wang, Jiawen Zhao, Xuehai Zhang, Zhanyong Guo, Desheng Hu, Shujun Meng, Yuan Yu Lin, Xiaoqian Qiu, Liqin Mu et al. · 2022 · Figshare
  58. Additional file 3 of Gene expression variation explains maize seed germination heterosis
    Jiong Wan, Qiyue Wang, Jiawen Zhao, Xuehai Zhang, Zhanyong Guo, Hu, Desheng, Shujun Meng, Yuan Yu Lin, Xiaoqian Qiu, Liqin Mu et al. · 2022 · Figshare
  59. Additional file 4 of Gene expression variation explains maize seed germination heterosis
    Jiong Wan, Qiyue Wang, Jiawen Zhao, Xuehai Zhang, Zhanyong Guo, Desheng Hu, Shujun Meng, Yuan Yu Lin, Xiaoqian Qiu, Liqin Mu et al. · 2022 · Figshare
  60. Additional file 5 of Gene expression variation explains maize seed germination heterosis
    Jiong Wan, Qiyue Wang, Jiawen Zhao, Xuehai Zhang, Zhanyong Guo, Desheng Hu, Shujun Meng, Yuan Yu Lin, Xiaoqian Qiu, Liqin Mu et al. · 2022 · Figshare
  61. Contextualising transcription factor binding during embryogenesis using natural sequence variation
    Olga M. Sigalova, Mattia Forneris, Frosina Stojanovska, Bingqing Zhao, Rebecca R. Viales, Adam H. Rabinowitz, Fayrouz Hammal, Benoît Ballester, Judith B. Zaugg, Eileen E. M. Furlong · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  62. Ecophysiological transition mediated by hybridization in a hybrid pine species complex
    Zhi-Chao Li, Chaoqun Xu, Wei Zhao, Shuai Nie, Yu-Tao Bao, Hui Liu, Zhen Xing, Jian‐Feng Mao, Xiaoru Wang · 2025 · Acta Botanica Yunnanica
  63. RNA-sequencing Analysis of Hybrid Females Reveals a Dominance of Expression of Alleles From Outcrossing Species Over Those From Selfing Species
    Yanwen Shao, Yiwen Zhang, Xiaoliang Ren, Vincy Wing Sze Ho, Yu Fang Bi, Zhongying Zhao, Runsheng Li · 2025 · Genome Biology and Evolution
  64. CompMap: an allele-specific expression read counter based on competitive mapping
    Santiago Sanchez Ramirez, Asher D. Cutter · 2025 · PubMed Central
  65. A next generation of studies: Heterosis and inbreeding depression
    Shreyartha Mukherjee · 2014
  66. Functional Evolutionary Genomics: Yeast as a Model System.
    Wenfeng Qian · 2012 · Deep Blue (University of Michigan)
  67. Additional file 1 of Gene expression variation explains maize seed germination heterosis
    Jiong Wan, Wang, Qiyue, Jiawen Zhao, Zhang, Xuehai, Zhanyong Guo, Hu, Desheng, Meng, Shujun, Lin, Yuan, Qiu, Xiaoqian, Liqin Mu et al. · 2022 · Figshare
  68. Additional file 7 of Gene expression variation explains maize seed germination heterosis
    Jiong Wan, Wang, Qiyue, Jiawen Zhao, Zhang, Xuehai, Zhanyong Guo, Hu, Desheng, Meng, Shujun, Lin, Yuan, Qiu, Xiaoqian, Liqin Mu et al. · 2022 · Figshare
  69. Expression heterosis in the abaca (Musa textilis Née) BC2 hybrid, Dioscoro 1
    Nelzo C. Ereful, Roneil Christian S. Alonday, Antonio G. Lalusin · 2026 · BMC Genomics
  70. Non-Additive Transcriptional Regulation Underpins Additive Survival Trait In Populations Of Drosophila Selected For Increased Post Infection Survival
    Tsering Choton, Nidhi Krishna Shrivastava, Harisankar Durga, Aindrila Das, Nagaraj Guru Prasad · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  71. Male sterility in Drosophila hybrids revealed by a multi-generational transcriptomic analysis of genes and transposable elements in testes
    Alejandra Bodelόn, Vicente Chillida, Daniel Siqueira de Oliveira, Cristina P Vieira, Maria Pilar García Guerreiro · 2026 · BMC Biology
  72. Polyploïdie et adaptation des plantes : caractérisation et variation de l'expression des gènes homoélogues chez le caféier Coffea arabica
    Marie-Christine Gavalda · 2015
  73. Étude de l’adaptation du mil à la variation climatique : analyse phénotypique, d’association génotype / phénotype et de sélection
    Ousseini Issaka Salia · 2016 · theses.fr (ABES)
  74. Deregulation of genes and transposable elements and hybrid incompatibility among Drosophila mojavensis subspecies and D. arizonae
    Cecília Ártico Banho · 2020
  75. Computational analysis and modelling of regulatory networks controlling embryonic development
    Swann Floc’hlay · 2020 · theses.fr (ABES)
  76. Dynamique des éléments transposables chez Drosophila suzukii
    Vincent Mérel · 2021 · theses.fr (ABES)
  77. Evolution of the eye in Astyanax mexicanus : contribution of maternal and early developmental regulations
    Julien Leclercq · 2022 · theses.fr (ABES)
  78. Species-wide exploration of the complexity, expressivity, and missing heritability of traits
    Andreas Tsouris · 2023
  79. Restoration of ancestral transcriptional plasticity contributes to plastic heterosis in fatty liver of hybrid ducks
    Ming-Min Xu, Yinhua Huang, Ya‐Ping Zhang, Min‐Sheng Peng · 2026 · Communications Biology
  80. Unlocking open-access genomic and transcriptomic data: the first bioinformatic exploitation of tunisian durum wheat landraces Chili and Mahmoudi
    Maroua Gdoura-Ben Amor, Nour El Houda Mathlouthi, Imen Belguith, Rania Derouich · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  81. Modes of natural selection on maternal and zygotic gene expression in Drosophila melanogaster embryos
    Thomas S. O’Leary, Brent L. Lockwood · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  82. Non-additive transcriptional regulation underpins an additive survival trait in populations of Drosophila selected for increased post infection survival
    Tsering Choton, Nidhi Krishna Shrivastava, Harisankar Durga, Aindrila Das, Nagaraj Guru Prasad · 2026 · BMC Ecology and Evolution
  83. Molecular evolution in light of regulatory-coding epistasis
    Pavithra Venkataraman, Christian R. Landry · 2026 · EMBO Reports
  84. A maternal effect shapes early-life adaptive body size variation in house mice
    Sylvia M. Durkin, Christina Gao, Michael W. Nachman · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  85. Pervasive and context-dependent homeologous expression remodeling in intersubspecific diploid F1 hybrids and segmental allotetraploids of rice
    Li Guo, Ting Luo, Xinshi Xu, Xu Han, Jiahao Li, Taotao Lian, Bingqi Zhang, Tiantian Zhu, Xiuyun Lin, Xiufang Ou et al. · 2026 · PLANT PHYSIOLOGY
  86. Algorithms for Transcriptome Quantification and Reconstruction from RNA-Seq Data
    Serghei Mangul · 2022 · Digital Archive @ GSU