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

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Items 1,601–1,700 of 4,071

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3. Deep conservation of cis -regulatory elements in metazoans
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4. Ancient Pbx-Hox signatures define hundreds of vertebrate developmental enhancers
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6. Tissue Expression Pattern of PMK-2 p38 MAPK Is Established by the miR-58 Family in C. elegans
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7. Clinical Implications of Human Population Differences in Genome-Wide Rates of Functional Genotypes
   Ali Torkamani, Phillip Pham, Ondrej Libiger, Vikas Bansal, Guangfa Zhang, Ashley A. Scott‐Van Zeeland, Ryan Tewhey, Eric J. Topol, Nicholas J. Schork · 2012 · Frontiers in Genetics
8. Upf1/Upf2 Regulation of 3′ Untranslated Region Splice Variants of AUF1 Links Nonsense-Mediated and A+U-Rich Element-Mediated mRNA Decay
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9. Sequence signatures extracted from proximal promoters can be used to predict distal enhancers
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10. The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data
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11. Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome
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12. Self-supervised learning on millions of pre-mRNA sequences improves sequence-based RNA splicing prediction
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14. Missense Pathogenic variants in KIF4A Affect Dental Morphogenesis Resulting in X-linked Taurodontism, Microdontia and Dens-Invaginatus
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15. Cistrome Data Browser and Toolkit: analyzing human and mouse genomic data using compendia of ChIP‐seq and chromatin accessibility data
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16. Computational approaches and challenges in the analysis of circRNA data
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17. Rare variation in non-coding regions with evolutionary signatures contributes to autism spectrum disorder risk
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18. Phylogenomic analyses of all species of swordtail fishes (genus Xiphophorus) show that hybridization preceded speciation
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19. Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns
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20. UTR dinucleotide simple sequence repeat evolution exhibits recurring patterns including regulatory sequence motif replacements
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22. When needles look like hay: How to find tissue-specific enhancers in model organism genomes
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23. Predicting tissue specific transcription factor binding sites
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24. Conserved noncoding elements and the evolution of animal body plans
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25. Mammalian TBX1 Preferentially Binds and Regulates Downstream Targets Via a Tandem T-site Repeat
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26. Transcription Factors Are Targeted by Differentially Expressed miRNAs in Primates
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27. Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb
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28. An inferred fitness consequence map of the rice genome
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29. DNA steganography: hiding undetectable secret messages within the single nucleotide polymorphisms of a genome and detecting mutation-induced errors
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30. Unified inference of missense variant effects and gene constraints in the human genome
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31. Signatures of host–pathogen evolutionary conflict reveal MISTR—A conserved MItochondrial STress Response network
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32. Evolution of Conserved Noncoding Sequences in Arabidopsis thaliana
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33. Cancer LncRNA Census 2 (CLC2): an enhanced resource reveals clinical features of cancer lncRNAs
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34. Genome of Peştera Muierii skull shows high diversity and low mutational load in pre-glacial Europe
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35. Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish
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36. Non‐coding regulatory elements: Potential roles in disease and the case of epilepsy
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37. Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development
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38. Classification of non-coding variants with high pathogenic impact
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39. Single-cell chromatin accessibility identifies enhancer networks driving gene expression during spinal cord development in mouse
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40. Splicing of internal large exons is defined by novel cis -acting sequence elements
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41. Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs
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42. Genome-wide polycomb target gene prediction in Drosophila melanogaster
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43. A 3′ untranslated region variant in FMR1 eliminates neuronal activity-dependent translation of FMRP by disrupting binding of the RNA-binding protein HuR
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44. miR-92a Corrects CD34+ Cell Dysfunction in Diabetes by Modulating Core Circadian Genes Involved in Progenitor Differentiation
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45. Selective Sweeps across Twenty Millions Years of Primate Evolution
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46. Recessive Spondylocarpotarsal Synostosis Syndrome Due to Compound Heterozygosity for Variants in MYH3
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47. Identification of genetic variants affecting vitamin D receptor binding and associations with autoimmune disease
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48. Recapitulation-like developmental transitions of chromatin accessibility in vertebrates
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49. Cross-species de novo identification of cis-regulatory modules with GibbsModule: Application to gene regulation in embryonic stem cells
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50. Widespread cis-regulatory convergence between the extinct Tasmanian tiger and gray wolf
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51. Computational prediction of human deep intronic variation
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52. GAMES identifies and annotates mutations in next-generation sequencing projects
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53. Resequencing of the auxiliary GABAB receptor subunit gene KCTD12 in chronic tinnitus
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54. Faster than Neutral Evolution of Constrained Sequences: The Complex Interplay of Mutational Biases and Weak Selection
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55. Non-polyadenylated transcription in embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation
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56. Genomic approaches to studying human-specific developmental traits
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57. Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals
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58. Pan-Cancer Analysis Reveals the Functional Importance of Protein Lysine Modification in Cancer Development
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59. Accurate annotation of accessible chromatin in mouse and human primordial germ cells
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60. Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics, and epigenetics data
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61. Systematic discovery of conservation states for single-nucleotide annotation of the human genome
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62. Challenges in funding and developing genomic software: roots and remedies
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63. Genome-wide analysis and functional annotation of chromatin-enriched noncoding RNAs in rice during somatic cell regeneration
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64. A systematic benchmark of machine learning methods for protein–RNA interaction prediction
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65. Molecular genetic studies ofDMT1on 12q in French‐Canadian restless legs syndrome patients and families
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66. Array-Based FMR1 Sequencing and Deletion Analysis in Patients with a Fragile X Syndrome–Like Phenotype
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69. Stochastic models of sequence evolution including insertion—deletion events
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70. NRE: a tool for exploring neutral loci in the human genome
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71. Gene Isoform Specificity through Enhancer-Associated Antisense Transcription
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72. Scan Statistics With Weighted Observations
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74. Depression and anxiety in children with CFS/ME: cause or effect?
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75. Purifying Selection on Exonic Splice Enhancers in Intronless Genes
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76. LncRNA and mRNA expression profiles of glioblastoma multiforme (GBM) reveal the potential roles of lncRNAs in GBM pathogenesis
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77. X Chromosome Evolution in Cetartiodactyla
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78. On-Line Viterbi Algorithm for Analysis of Long Biological Sequences
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79. Conserved distances between vertebrate highly conserved elements
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80. GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction
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81. Functional differences between TSHR alleles associate with variation in spawning season in Atlantic herring
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82. Multiple overlapping binding sites determine transcription factor occupancy
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83. Sebnif: An Integrated Bioinformatics Pipeline for the Identification of Novel Large Intergenic Noncoding RNAs (lincRNAs) - Application in Human Skeletal Muscle Cells
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84. Reptiles and Mammals Have Differentially Retained Long Conserved Noncoding Sequences from the Amniote Ancestor
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85. Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebrates
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88. Chemosensory adaptations of the mountain fly Drosophila nigrosparsa (Insecta: Diptera) through genomics’ and structural biology’s lenses
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89. Identification of long non-coding transcripts with feature selection: a comparative study
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90. A pan‐cancer atlas of cancer hallmark‐associated candidate driver lnc RNA s
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91. Impact of Mutation Rate and Selection at Linked Sites on DNA Variation across the Genomes of Humans and Other Homininae
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92. InMeRF: prediction of pathogenicity of missense variants by individual modeling for each amino acid substitution
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95. A systematic evaluation of bioinformatics tools for identification of long noncoding RNAs
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96. Chromosome‐level assembly of southern catfish (silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles
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97. Comprehensive multi-omics integration identifies differentially active enhancers during human brain development with clinical relevance
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98. CRAG: de novo characterization of cell-free DNA fragmentation hotspots in plasma whole-genome sequencing
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99. The expansion of agriculture has shaped the recent evolutionary history of a specialized squash pollinator
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100. Scrutinizing the FTO locus: compelling evidence for a complex, long-range regulatory context
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