Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

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Items 1,101–1,200 of 4,071

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3. Repeated mutation of a developmental enhancer contributed to human thermoregulatory evolution
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7. Species-aware DNA language models capture regulatory elements and their evolution
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8. Mutations in gamma adducin are associated with inherited cerebral palsy
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13. Branch Point Selection in RNA Splicing Using Deep Learning
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14. Alternative splicing coupled mRNA decay shapes the temperature‐dependent transcriptome
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15. Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation
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16. XRate: a fast prototyping, training and annotation tool for phylo-grammars
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17. Inference of Transcriptional Networks in Arabidopsis through Conserved Noncoding Sequence Analysis
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18. WW-Domain-Containing Oxidoreductase Is Associated with Low Plasma HDL-C Levels
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19. The Vast, Conserved Mammalian lincRNome
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20. Otx2 ChIP-seq Reveals Unique and Redundant Functions in the Mature Mouse Retina
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21. Comparative Genomic Analysis of the Streptococcus dysgalactiae Species Group: Gene Content, Molecular Adaptation, and Promoter Evolution
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22. “Reverse genomics” predicts function of human conserved noncoding elements
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23. Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves
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24. Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay
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25. The G protein-coupled receptor GPR34 – The past 20 years of a grownup
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26. Deep cis-regulatory homology of the butterfly wing pattern ground plan
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27. IFRD1 Is a Candidate Gene for SMNA on Chromosome 7q22-q23
    Zoran Brkanac, David H. Spencer, Jay Shendure, Peggy D. Robertson, Mark M. Matsushita, Tiffany H. Vu, Thomas D. Bird, Maynard V. Olson, Wendy H. Raskind · 2009 · The American Journal of Human Genetics
28. Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes
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29. Species-Specific Strategies Underlying Conserved Functions of Metabolic Transcription Factors
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30. New GJA8 variants and phenotypes highlight its critical role in a broad spectrum of eye anomalies
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31. Approximation to the Distribution of Fitness Effects across Functional Categories in Human Segregating Polymorphisms
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32. Reconsidering proteomic diversity with functional investigation of small ORFs and alternative ORFs
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33. SNP@Promoter: a database of human SNPs (Single Nucleotide Polymorphisms) within the putative promoter regions
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34. The tedious task of finding homologous noncoding RNA genes
    Peter Menzel, Jan Gorodkin, Peter Florian Stadler · 2009 · RNA
35. Deep congenic analysis identifies many strong, context-dependent QTLs, one of which, Slc35b4 , regulates obesity and glucose homeostasis
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36. A framework to score the effects of structural variants in health and disease
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37. Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer
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38. ConsRM: collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome
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39. Transcriptional Enhancers in Protein-Coding Exons of Vertebrate Developmental Genes
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40. A Mammalian Conserved Element Derived from SINE Displays Enhancer Properties Recapitulating Satb2 Expression in Early-Born Callosal Projection Neurons
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41. Fetal haemoglobin response to hydroxycarbamide treatment and sar1a promoter polymorphisms in sickle cell anaemia
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42. GluA2 mRNA distribution and regulation by miR-124 in hippocampal neurons
    Victoria M. Ho, Liane O. Dallalzadeh, Nestoras Karathanasis, Mehmet F. Keleş, Sitaram Vangala, Tristan Grogan, Panayiota Poirazi, Kelsey C. Martin · 2014 · Molecular and Cellular Neuroscience
43. Somatic, germline and sex hierarchy regulated gene expression during Drosophila metamorphosis
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44. Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach
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45. Comparative population genomics: power and principles for the inference of functionality
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46. Transposable elements as genetic accelerators of evolution: contribution to genome size, gene regulatory network rewiring and morphological innovation
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47. The Evolution of Human Cancer Gene Duplications across Mammals
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48. Developmental and temporal characteristics of clonal sperm mosaicism
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49. Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins
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50. Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function
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51. mRNA transport, translation, and decay in adult mammalian central nervous system axons
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52. The Foundational Data Initiative for Parkinson Disease: Enabling efficient translation from genetic maps to mechanism
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53. Genome-wide prediction of pathogenic gain- and loss-of-function variants from ensemble learning of a diverse feature set
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54. Using epigenomics data to predict gene expression in lung cancer
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55. Analysis of Human Small Nucleolar RNAs (snoRNA) and the Development of snoRNA Modulator of Gene Expression Vectors
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56. Deciphering the 8q24.21 association for glioma
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57. Effects of genetic variations on microRNA: target interactions
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58. Genetic Gastric Cancer Susceptibility in the International Clinical Cancer Genomics Community Research Network
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59. Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution
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60. Comprehensive analysis of long noncoding RNA (lncRNA)-chromatin interactions reveals lncRNA functions dependent on binding diverse regulatory elements
    Guanxiong Zhang, Yujia Lan, Aimin Xie, Jian Shi, Hongying Zhao, Liwen Xu, Shiwei Zhu, Tao Luo, Tingting Zhao, Yun Xiao et al. · 2019 · Journal of Biological Chemistry
61. Mutations of Intrinsically Disordered Protein Regions Can Drive Cancer but Lack Therapeutic Strategies
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62. Measuring the accuracy of genome-size multiple alignments
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63. Conservation of alternative polyadenylation patterns in mammalian genes
    Takeshi Ara, Fabrice Lopez, William Ritchie, Philippe D. Benech, Daniel Gautheret · 2006 · BMC Genomics
64. High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation
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65. Coexpression patterns define epigenetic regulators associated with neurological dysfunction
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66. Predicting RAD-seq Marker Numbers across the Eukaryotic Tree of Life
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67. High-throughput identification of RNA localization elements in neuronal cells
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68. Transposable element exonization generates a reservoir of evolving and functional protein isoforms
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69. Single Nucleotide Polymorphisms in MicroRNA Binding Sites of Oncogenes: Implications in Cancer and Pharmacogenomics
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70. Probabilistic Inference of Transcription Factor Binding from Multiple Data Sources
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71. Extracting Sequence Features to Predict\nProtein–DNA Interactions: A Comparative Study
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72. High-throughput discovery of post-transcriptional cis-regulatory elements
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73. Single–base pair differences in a shared motif determine differential Rhodopsin expression
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74. DAZL mediates a broad translational program regulating expansion and differentiation of spermatogonial progenitors
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75. Ancient RNA virus epidemics through the lens of recent adaptation in human genomes
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76. Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
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77. Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons
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78. Evolutionary Constraint on Visual and Nonvisual Mammalian Opsins
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79. Three amphioxus reference genomes reveal gene and chromosome evolution of chordates
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80. The Conserved Intronic Cleavage and Polyadenylation Site of CstF-77 Gene Imparts Control of 3′ End Processing Activity through Feedback Autoregulation and by U1 snRNP
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81. Long identical multispecies elements in plant and animal genomes
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82. The Nature of Protein Domain Evolution: Shaping the Interaction Network
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83. Functional dissection of the PROPEP2 and PROPEP3 promoters reveals the importance of WRKY factors in mediating microbe‐associated molecular pattern‐induced expression
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84. The Mathematics of Phylogenomics
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85. Prediction of CpG-island function: CpG clustering vs. sliding-window methods
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86. Exome sequencing identifies rare variants in multiple genes in atrioventricular septal defect
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87. Secondary structure impacts patterns of selection in human lncRNAs
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88. Long Noncoding RNA Identification: Comparing Machine Learning Based Tools for Long Noncoding Transcripts Discrimination
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89. Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re‐Visiting the “Gene‐Battery” Model
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90. Disease-causing mutations in the promoter and enhancer of the ornithine transcarbamylase gene
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91. Trends in the Application of “Omics” to Ecotoxicology and Stress Ecology
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92. Nomadic Enhancers: Tissue-Specific cis-Regulatory Elements of yellow Have Divergent Genomic Positions among Drosophila Species
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93. Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage
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94. Functional variation and evolution of non-coding DNA
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95. Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes
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96. Integrating convolution and self-attention improves language model of human genome for interpreting non-coding regions at base-resolution
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97. Convergent and complementary selection shaped gains and losses of eusociality in sweat bees
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98. Analysis of the P. lividus sea urchin genome highlights contrasting trends of genomic and regulatory evolution in deuterostomes
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99. A long non-coding RNA links calreticulin-mediated immunogenic cell removal to RB1 transcription
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100. Bovine ncRNAs Are Abundant, Primarily Intergenic, Conserved and Associated with Regulatory Genes
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