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

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6. Oncogenic effects of germline variants in lysosomal storage disease genes
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10. Diverse ancestry whole-genome sequencing association study identifies TBX5 and PTK7 as susceptibility genes for posterior urethral valves
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11. The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order
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12. Genetic Incompatibilities and Evolutionary Rescue by Wild Relatives Shaped Grain Amaranth Domestication
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15. Human gene regulatory evolution is driven by the divergence of regulatory element function in both cis and trans
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16. Lineage-specific evolution of the vertebrate Otopetringene family revealed by comparative genomic analyses
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17. Computational Identification of Active Enhancers in Model Organisms
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18. Genomic Selection Identifies Vertebrate Transcription Factor Fezf2 Binding Sites and Target Genes
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19. Novel Data Fusion Method and Exploration of Multiple Information Sources for Transcription Factor Target Gene Prediction
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20. Lineage-Specific Conserved Noncoding Sequences of Plant Genomes: Their Possible Role in Nucleosome Positioning
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21. Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters
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22. MGA repository: a curated data resource for ChIP-seq and other genome annotated data
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23. Combined annotation‐dependent depletion score for BRCA1/2 variants in patients with breast and/or ovarian cancer
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24. Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements
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25. Genome urbanization: clusters of topologically co-regulated genes delineate functional compartments in the genome of Saccharomyces cerevisiae
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26. The Roles of Long Non-coding RNA in Osteoporosis
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27. Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral
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28. Immunohistochemistry and Mutation Analysis of SDHx Genes in Carotid Paragangliomas
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29. Mutation Frequency in Main Susceptibility Genes Among Patients With Head and Neck Paragangliomas
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30. SnoRNA copy regulation affects family size, genomic location and family abundance levels
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31. The Normal Structure and Regulation of Human Globin Gene Clusters
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32. Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology
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33. A High Resolution Genome-Wide Scan of HNF4α Recognition Sites Infers a Regulatory Gene Network in Colon Cancer
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34. WordCluster: detecting clusters of DNA words and genomic elements
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35. Detection of lineage-specific evolutionary changes among primate species
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36. Smooth Muscle Expression of Lipoma Preferred Partner Is Mediated by an Alternative Intronic Promoter That Is Regulated by Serum Response Factor/Myocardin
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37. A systematic, large-scale comparison of transcription factor binding site models
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38. A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery
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39. Allele frequency selection and no age-related increase in human oocyte mitochondrial mutations
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40. Comparative analysis of sequence features involved in the recognition of tandem splice sites
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41. Functional 5′ UTR motif discovery with LESMoN: Local Enrichment of Sequence Motifs in biological Networks
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42. Genome sequencing data analysis for rare disease gene discovery
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43. Revealing the novel complexity of plant long non-coding RNA by strand-specific and whole transcriptome sequencing for evolutionarily representative plant species
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44. Pervasive translation of small open reading frames in plant long non-coding RNAs
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45. High-throughput functional dissection of noncoding SNPs with biased allelic enhancer activity for insulin resistance-relevant phenotypes
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46. Genome-wide Cas9-mediated screening of essential non-coding regulatory elements via libraries of paired single-guide RNAs
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47. Interactions between immune cell types facilitate the evolution of immune traits
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48. Approaches to identify genetic variants that influence the risk for onset of fragile X-associated primary ovarian insufficiency (FXPOI): a preliminary study
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49. Prioritizing Genetic Variants for Causality on the Basis of Preferential Linkage Disequilibrium
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50. NcDNAlign: Plausible multiple alignments of non-protein-coding genomic sequences
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51. An ensemble SVM model for the accurate prediction of non-canonical MicroRNA targets
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52. Identification of a FOXA-dependent enhancer of human alcohol dehydrogenase 4 (ADH4)
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53. Assessing the fraction of short-distance tandem splice sites under purifying selection
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54. A Population Genetic Hidden Markov Model for Detecting Genomic Regions Under Selection
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55. The recently identified modifier of murine metastable epialleles, Rearranged L-Myc Fusion, is involved in maintaining epigenetic marks at CpG island shores and enhancers
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56. Identification of lung cancer histology-specific variants applying Bayesian framework variant prioritization approaches within the TRICL and ILCCO consortia
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57. Exome Sequencing Analysis: A Guide to Disease Variant Detection
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58. Solving the master equation for Indels
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59. Natural selection beyond genes: Identification and analyses of evolutionarily conserved elements in the genome of the collared flycatcher (Ficedula albicollis)
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60. Long non-coding RNAs involved in the regulatory network during porcine pre-implantation embryonic development and iPSC induction
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61. The RNA exosome shapes the expression of key protein-coding genes
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62. Identification of Edible Short- and Long-Horned Grasshoppers and Their Host Plants in East Africa
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63. Overcoming constraints on the detection of recessive selection in human genes from population frequency data
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64. African Suid Genomes Provide Insights into the Local Adaptation to Diverse African Environments
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65. Differential regulation of splicing, localization and stability of mammalian ARD1235 and ARD1225 isoforms
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66. Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans
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67. Loss‐of‐Function Mutations in MC4R Are Very Rare in the Greek Severely Obese Adult Population
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68. An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes
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69. The PRC2-binding long non-coding RNAs in human and mouse genomes are associated with predictive sequence features
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70. Ancient human miRNAs are more likely to have broad functions and disease associations than young miRNAs
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71. Disrupting the three-dimensional regulatory topology of the Pitx1 locus results in overtly normal development
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72. Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements
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73. Genome-wide quantification of the effects of DNA methylation on human gene regulation
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74. The impact of purifying and background selection on the inference of population history: problems and prospects
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75. Variant Effect Prediction in the Age of Machine Learning
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76. Predicting variant deleteriousness in non-human species: applying the CADD approach in mouse
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77. Genotype–phenotype correlation of 33 patients with maple syrup urine disease
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78. Genetic-variant hotspots and hotspot clusters in the human genome facilitating adaptation while increasing instability
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79. Multi-Omic Analysis in a Metabolic Syndrome Porcine Model Implicates Arachidonic Acid Metabolism Disorder as a Risk Factor for Atherosclerosis
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80. Evaluating the relevance of sequence conservation in the prediction of pathogenic missense variants
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81. Phylogenomic analysis of the Neotropical fish subfamily Characinae using ultraconserved elements (Teleostei: Characidae)
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82. Developmental regulation of conserved non-coding element evolution provides insights into limb loss in squamates
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83. Whole genome analyses reveal weak signatures of population structure and environmentally associated local adaptation in an important North American pollinator, the bumble bee Bombus vosnesenskii
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84. Stimulating Wnt signaling reveals context-dependent genetic effects on gene regulation in primary human neural progenitors
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85. Paucity and preferential suppression of transgenes in late replication domains of the D. melanogaster genome
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86. Evolutionary Dynamics of the Ty3/Gypsy LTR Retrotransposons in the Genome of Anopheles gambiae
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87. Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression
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88. Segmenting the human genome based on states of neutral genetic divergence
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89. CpG Islands Undermethylation in Human Genomic Regions under Selective Pressure
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90. Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae
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91. Natural re-colonization and admixture of wolves (Canis lupus) in the US Pacific Northwest: challenges for the protection and management of rare and endangered taxa
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92. Analysis of Genetic Variation Indicates DNA Shape Involvement in Purifying Selection
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93. An Evolutionary Mechanism for the Generation of Competing RNA Structures Associated with Mutually Exclusive Exons
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94. Ice ages and butterflyfishes: Phylogenomics elucidates the ecological and evolutionary history of reef fishes in an endemism hotspot
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95. Non-neutral evolution of H3.3-encoding genes occurs without alterations in protein sequence
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96. Genome-wide analysis of differentially expressed mRNAs, lncRNAs, and circRNAs in chicken bursae of Fabricius during infection with very virulent infectious bursal disease virus
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97. Whole Genome Sequencing Prioritizes CHEK2, EWSR1, and TIAM1 as Possible Predisposition Genes for Familial Non-Medullary Thyroid Cancer
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98. Evolution of host use in fungivorous ciid beetles (Coleoptera: Ciidae): Molecular phylogeny focusing on Japanese taxa
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99. Detection and characterization of small insertion and deletion genetic variants in modern layer chicken genomes
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100. Discovering sequences with potential regulatory characteristics
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