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

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Items 801–900 of 4,072

1. Disruption of an Evolutionarily Novel Synaptic Expression Pattern in Autism
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2. A genome-wide survey for SNPs altering microRNA seed sites identifies functional candidates in GWAS
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3. Decoding disease: from genomes to networks to phenotypes
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4. Adaptive Evolution of Conserved Noncoding Elements in Mammals
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5. Gene-specific patterns of expression variation across organs and species
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8. Therapeutic adenine base editing of human hematopoietic stem cells
   Jiaoyang Liao, Shuanghong Chen, Shenlin Hsiao, Yanhong Jiang, Yang Yang, Yuanjin Zhang, Xin Wang, Yongrong Lai, Daniel E. Bauer, Yuxuan Wu · 2023 · Nature Communications
9. Two Novel Mutations in theBCKDK(Branched-Chain Keto-Acid Dehydrogenase Kinase) Gene Are Responsible for a Neurobehavioral Deficit in Two Pediatric Unrelated Patients
   Àngels García‐Cazorla, Alfonso Oyarzábal, Joana Fort, Concepción López Robles, Esperanza Castejón, Pedro Ruiz‐Sala, Susanna Bodoy, Begoña Merinero, Anna López Sala, Joaquı́n Dopazo et al. · 2014 · Human Mutation
10. VaRank: a simple and powerful tool for ranking genetic variants
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11. Searching for Sympatric Speciation in the Genomic Era
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12. Exploring the function of genetic variants in the non-coding genomic regions: approaches for identifying human regulatory variants affecting gene expression
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13. Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution
    Juliana G. Roscito, Katrin Sameith, Genı́s Parra, Björn E. Langer, Andreas Petzold, Claudia Moebius, Marc Bickle, Miguel Tréfaut Rodrigues, Michael Hiller · 2018 · Nature Communications
14. glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data
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15. Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression
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16. Absence of canonical marks of active chromatin in developmentally regulated genes
    Sílvia Pérez-Lluch, Enrique Blanco, Hagen Tilgner, João Curado, Marina Ruiz‐Romero, Montserrat Corominas, Roderic Guigó · 2015 · Nature Genetics
17. The Ground State and Evolution of Promoter Region Directionality
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18. Nature of epigenetic aging from a single-cell perspective
    Andrei E. Tarkhov, Thomas Lindstrom-Vautrin, Sirui Zhang, Kejun Ying, Mahdi Moqri, Bohan Zhang, Alexander Tyshkovskiy, Orr Levy, Vadim N. Gladyshev · 2024 · Nature Aging
19. Regulation of SHOOT MERISTEMLESS genes via an upstream-conserved noncoding sequence coordinates leaf development
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20. MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences
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21. Identification of Widespread Ultra-Edited Human RNAs
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22. Quantification and discovery of sequence determinants of protein‐per‐mRNA amount in 29 human tissues
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23. The expanding transcriptome: the genome as the ‘Book of Sand’
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24. Epigenetics and T helper 1 differentiation
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25. The UCSC Archaeal Genome Browser: 2012 update
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26. Bayesian estimation of gene constraint from an evolutionary model with gene features
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27. Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes
    Princess S. Gilbert, Jonathan Chang, Calvin Pan, Eric M. Sobel, Janet S. Sinsheimer, Brant C. Faircloth, Michael E. Alfaro · 2015 · Molecular Phylogenetics and Evolution
28. GenomeGraphs: integrated genomic data visualization with R
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29. Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals
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30. Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes
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31. Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex
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32. Application of Computational Biology and Artificial Intelligence Technologies in Cancer Precision Drug Discovery
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33. Genetic Architecture of Gene Expression in European and African Americans: An eQTL Mapping Study in GENOA
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34. Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells
    Ioannis Sarropoulos, Mari Sepp, Robert Frömel, Kevin Leiss, Nils Trost, Evgeny V. Leushkin, Konstantin Okonechnikov, Piyush K. Joshi, Peter Giere, Lena M. Kutscher et al. · 2021 · Science
35. Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression
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36. The mystery of extreme non-coding conservation
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37. PhenCode: connecting ENCODE data with mutations and phenotype
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38. Analysis of Sequence Conservation at Nucleotide Resolution
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39. The Origins, Evolution, and Functional Potential of Alternative Splicing in Vertebrates
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40. Cooperative gene regulation by microRNA pairs and their identification using a computational workflow
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41. Genome-wide identification of conserved regulatory function in diverged sequences
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42. Genomic approaches for understanding the genetics of complex disease
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43. A Comprehensive Nuclear Receptor Network for Breast Cancer Cells
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44. A sequence-based, deep learning model accurately predicts RNA splicing branchpoints
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45. Tissue-specific usage of transposable element-derived promoters in mouse development
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46. Chromosome-wide linkage disequilibrium caused by an inversion polymorphism in the white-throated sparrow (Zonotrichia albicollis)
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47. Inference of Natural Selection from Interspersed Genomic Elements Based on Polymorphism and Divergence
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48. Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses
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49. Small RNA expression and strain specificity in the rat
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50. Understanding the development of human bladder cancer by using a whole-organ genomic mapping strategy
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51. Cell Type-Specific Epigenomic Analysis Reveals a Uniquely Closed Chromatin Architecture in Mouse Rod Photoreceptors
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52. Genetic architecture of autism spectrum disorder: Lessons from large-scale genomic studies
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53. Evolution and comparative analysis of the MHC Class III inflammatory region
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54. ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs
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55. Evaluation of the RET regulatory landscape reveals the biological relevance of a HSCR-implicated enhancer
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56. MicroRNA-like off-target transcript regulation by siRNAs is species specific
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57. HmtVar: a new resource for human mitochondrial variations and pathogenicity data
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58. Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes
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59. Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci
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60. SIRT7 mediates L1 elements transcriptional repression and their association with the nuclear lamina
    Vazquez, Berta N, Thackray, Joshua K, Simonet, Nicolas G, Chahar, Sanjay, Kane-Goldsmith, Noriko, Newkirk, Simon J, Lee, Suman, Xing, Jinchuan, Verzi, Michael P, An, Wenfeng et al. · 2019 · Nucleic Acids Research
61. Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish
    Hiller, Michael, Agarwal, Saatvik, Notwell, James H., Parikh, Ravi, Guturu, Harendra, Wenger, Aaron M., Bejerano, Gill · 2013 · Nucleic Acids Research
62. Lost in translation: returning germline genetic results in genome-scale cancer research
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63. <i>Cis</i> -regulatory elements explain most of the mRNA stability variation across genes in yeast
    Cheng, Jun, Maier, Kerstin C., Avsec, Žiga, Rus, Petra, Gagneur, Julien · 2017 · RNA
64. An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome
    Michael Ferlaino, Mark F. Rogers, Hashem A. Shihab, Matthew E. Mort, D.N. Cooper, Tom R. Gaunt, Colin Campbell · 2017 · BMC Bioinformatics
65. Neomorphic PDGFRA extracellular domain driver mutations are resistant to PDGFRA targeted therapies
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66. Intrinsic transcriptomic sex differences in human endothelial cells at birth and in adults are associated with coronary artery disease targets
    Robin J. G. Hartman, Daniek Kapteijn, Saskia Haitjema, Mireille N. Bekker, Michal Mokrý, Gerard Pasterkamp, Mete Civelek, Hester M. den Ruijter · 2020 · Scientific Reports
67. Evolutionary conservation and divergence of the human brain transcriptome
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68. Ultraconserved enhancer function does not require perfect sequence conservation
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69. A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes
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70. Evolutionary footprints of nucleosome positions in yeast
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71. Enriching the Analysis of Genomewide Association Studies with Hierarchical Modeling
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72. Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay
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73. The conservation landscape of the human ribosomal RNA gene repeats
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74. Genotype-phenotype correlations in MYCN-related Feingold syndrome
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75. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models
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76. Challenges of SNP genotyping and genetic variation: its future role in diagnosis and treatment of cancer
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77. Long nuclear-retained non-coding RNAs and allele-specific higher-order chromatin organization at imprinted snoRNA gene arrays
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78. Phylogenomic analysis of trichomycterid catfishes (Teleostei: Siluriformes) inferred from ultraconserved elements
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79. Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data
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80. A regulatory toolbox of MiniPromoters to drive selective expression in the brain
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81. Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs
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82. Genomic Features and Regulatory Roles of Intermediate-Sized Non-Coding RNAs in Arabidopsis
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83. Utilizing the Dog Genome in the Search for Novel Candidate Genes Involved in Glioma Development—Genome Wide Association Mapping followed by Targeted Massive Parallel Sequencing Identifies a Strongly Associated Locus
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84. Single nucleus multi-omics regulatory landscape of the murine pituitary
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85. Genome interpretation using in silico predictors of variant impact
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86. Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes
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87. Epigenetic inheritance of DNA methylation limits activation-induced expression of FOXP3 in conventional human CD25-CD4+ T cells
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88. The interplay between DNA methylation and sequence divergence in recent human evolution
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89. Extensive Cooperation of Immune Master Regulators IRF3 and NFκB in RNA Pol II Recruitment and Pause Release in Human Innate Antiviral Transcription
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90. Making Sense of the Epigenome Using Data Integration Approaches
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91. New insights into the pathogenicity of non-synonymous variants through multi-level analysis
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92. RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication
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93. Visualization of genomic data with the Hilbert curve
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94. Epigenetic modifications are associated with inter-species gene expression variation in primates
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95. EpiExplorer: live exploration and global analysis of large epigenomic datasets
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96. microRNA-185 modulates low density lipoprotein receptor expression as a key posttranscriptional regulator.
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97. The functional and evolutionary impacts of human-specific deletions in conserved elements
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98. Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction
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99. Expression of the leukemia oncogene Lmo2 is controlled by an array of tissue-specific elements dispersed over 100 kb and bound by Tal1/Lmo2, Ets, and Gata factors
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100. Natural Selection in Gene-Dense Regions Shapes the Genomic Pattern of Polymorphism in Wild and Domesticated Rice
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