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

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Items 3,201–3,300 of 4,071

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   Kian A. Caplan, Ke Chen, Martin Wienisch, Yongqi Wang, Ruoyang Chai, In-Hye Kang, Cindy Szyin Chen, Ricardo C.H. del Rosario, Fenna M. Krienen, Fan Wang et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
7. nAPOGEE: A machine-learning platform for clinically actionable pathogenicity assessment of all mitochondrial noncoding variants
   Salvatore Daniele Bianco, Agnese Giovannetti, Marta Adinolfi, Francesco Petrizzelli, Andrea Villani, Manuel Mangoni, Tommaso Biagini, Niccolò Liorni, Alessandro Napoli, Vincent Procaccio et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
8. The distribution of fitness effects of new mutations in regulatory regions of the D. melanogaster genome
   Austin Daigle, Jacob Marsh, Andrew Kay, Parul Johri · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
9. Molecular Dynamics of Brodmann Area 22 in Development and Autism
   Varun Suresh, Emilie M. Wigdor, Yuhan Hao, Rachel Leonard, Joseph Asfouri, Micheal Griffiths, Clements Evans, Guohua Yuan, Narjes Rohani, Jakob Weiss et al. · 2026 · SSRN Electronic Journal
10. Population Genomics on the Fly: Recent Advances in Drosophila
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11. Reinterpreting sheep muscle strand‐specific RNA sequencing data showing extensive 3′UTR extensions
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12. Human ERG oncoprotein represses a Drosophila LIM domain binding protein–coding gene Chip
    Mahima Bharti, A. K. Bajpai, Umanshi Rautela, Nishat Manzar, Bushra Ateeq, Pradip Sinha · 2023 · Proceedings of the National Academy of Sciences
13. Whole exome sequencing of well-differentiated liposarcoma and dedifferentiated liposarcoma in older woman: a case report
    Zidan Zhao, Xiaoyan Chen, Jie Xu, Yuntao Shi, Tsz Kin Mak, Mingyu Huo, Changhua Zhang · 2023 · Frontiers in Medicine
14. Defining the single base importance of human mRNAs and lncRNAs
    Rui Fan, Xiangwen Ji, Jianwei Li, Qinghua Cui, Chunmei Cui · 2023 · Briefings in Bioinformatics
15. DrivR-Base: a feature extraction toolkit for variant effect prediction model construction
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    Troy Alexander von Beck, Meera B. Patel, Niraj Patel, Joshy Jacob · 2024 · Frontiers in Genetics
17. Evolutionary innovations in germline biology of placental mammals identified by transcriptomics of first-wave spermatogenesis in opossum
    Kira Lynn Marshall, Daniel J Stadtmauer, Jamie D. Maziarz, Günter P. Wagner, Bluma J. Lesch · 2024 · Developmental Cell
18. Identifying deleterious noncoding variation through gain and loss of CTCF binding activity
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19. Review of programs for assessing the pathogenicity of genetic variants
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20. Hiding in plain sight: advances in discovery and functional description of plant sORF-encoded peptides
    Alyssa Kearly, Andrew D. L. Nelson · 2025 · Journal of Experimental Botany
21. CompasSeq: epitranscriptome-wide percentage assessment of metabolite-capped RNA at the transcript resolution
    Yuanbo Liu, Dean Li, Xueting Wang, Kongyan Niu, Jun Yuan Bai, Lefeng Qu, Nan Liu · 2025 · Nature Communications
22. Positional distribution of transcription factor binding sites in the human genome
    Chun-Ping Yu, Zhi Thong Soh, Maloyjo Joyraj Bhattacharjee, Wen‐Hsiung Li · 2025 · PLoS ONE
23. Molecular characterization of lumpy skin disease virus in the cattle population of District Lower Chitral, Khyber Pakhtunkhwa, Pakistan
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24. RNase III cleavage sites spread across splice junctions enforce sequential snoRNA processing
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25. Super‐Enhancer‐Mediated DLX5 Activation Defines Regulatory Mechanisms in Human Embryonic Stem Cell‐Derived Osteoblasts
    S. Fujita, Shoichiro Tani, Hiroyuki Okada, Taku Saito, Sakae Tanaka, Shinsuke Ohba, Ung‐il Chung, Hironori Hojo · 2025 · Development Growth & Differentiation
26. Genetic innovations underlying the evolution of root nodule symbiosis in Leguminosae
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27. Comparative genomics sheds light on mammalian and avian gene regulation and phenotypic evolution
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28. Genomic prediction using mCADD scores as prior information in a mouse population
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29. Using Untargeted Mass Spectrometry-Based Proteomics to Identify Putative Microprotein Biomarkers from Patient Tampons
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30. Leveraging protein language models to identify complex trait associations with previously inaccessible classes of functional rare variants
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31. Modeling the Evolution of Ultraconserved Elements by Indels
    Priscila do Nascimento Biller · 2025 · Molecular Biology and Evolution
32. Clinical and Genetic Profiles of 11 Chinese Patients With Angelman Syndrome
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33. Actin network heterogeneity tunes activator–inhibitor dynamics at the cell cortex
    Ondrej Maxian, Aaron R. Dinner, Edwin Munro · 2025 · Proceedings of the National Academy of Sciences
34. Integrating machine learning and functional genomics to study cross-species gene regulatory evolution
    Erin N. Gilbertson, Steven K. Reilly · 2025 · Current Opinion in Genetics & Development
35. Cis-regulatory co-option of a transposon family reinforces cell identity across the immune system
    Jason D. Chobirko, Cedric Feschotte, Andrew Grimson · 2026 · The EMBO Journal
36. Small open reading frame-encoded peptides (SEPs) as hidden treasures: a review
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37. Differentiation in the human urothelia is defined by distinct alternative polyadenylation
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38. Master of none: GPRC6A gene loss is more widespread than previously known
    Saumya Gupta, Ajinkya Bharatraj Patil, Aswin S Soman, Nagarjun Vijay · 2026 · Genetica
39. Comparative Single‐Cell Transcriptomic Atlas Reveals the Genetic Regulation of Reproductive Traits
    Bingru Zhao, Hanpeng Luo, Dailu Guan, Xuefeng Fu, Feng Wang, G Zhang, Shanglai Li, Hua Yang, Yanli Zhang · 2026 · Advanced Science
40. The functional landscape of alternative splicing in hematopoietic lineage commitment
    Xiao Hu, Jinrui Wang, Li Chen, Qin Yang, Manuel Tardáguila, Bin Mao, 牛胜辉, Zijie Xu, GuiHua Wang, Dan Zhang et al. · 2026 · Nature Communications
41. PATHOS: Predicting variant pathogenicity by combining protein language models and biological features
    Ragousandirane Radjasandirane, Gabriel Cretin, Julien Diharce, Alexandre G. de Brevern, Jean‐Christophe Gelly · 2026 · Artificial Intelligence in the Life Sciences
42. Multilayer Timing of Cardiac Circadian Regulation Informs Prevention and Treatment of Cardiovascular Disease
    Lanxiao Zhu, Bin Qian, Xin Zhang, Linlin Hu · 2026 · Vascular Health and Risk Management
43. The elusive genomic signature of tadpole shrimps’ ancient morphology
    Giobbe Forni, Filippo Nicolini, Jacopo Martelossi, Castrense Savojardo, Simona Corneti, Federico Marrone, Andrea Luchetti · 2026 · Biology Letters
44. A Genetic Landscape of Euploid Miscarriages From Couples With Recurrent Pregnancy Loss Through Whole Exome Sequencing
    Fanjuan Kong, Zhaochu Yin, Haiyan Zhou, Zhiyu Liu, Wanqin Xie · 2026 · Molecular Genetics & Genomic Medicine
45. Doxorubicin-induced apoptosis and mitochondrial fission are promoted by LncRNA TGFB2-AS1 through BMP7/Smad signaling
    Hailan Gao, Kai Lan, Hui Gong · 2026 · Toxicology and Applied Pharmacology
46. A novel homozygous MICOS13 frameshift mutation causing mitochondrial hepatoencephalopathy and mtDNA depletion: clinical characterization and dynamic structural simulation
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47. Novel HEXB variant and first evidence of urinary Gb4 isoforms in Sandhoff disease: Biochemical and bioinformatic characterization in two Moroccan families
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48. GraphyloVar: predicting the impact of non-coding variants using a multi-species sequence model
    Dongjoon Lim, Mathieu Blanchette · 2026 · Bioinformatics
49. dsRNAscan maps human dsRNAome, revealing conservation, intermolecular dsRNA, and correlates of ADAR dependency
    Ryan J. Andrews, Brenda Bass · 2026 · Molecular Cell
50. Two parallel neural ectoderm progenitors contribute to the developing brain
    Rayyan Trebonias Jokhai, Carolyn E. Dundes, Hadia S. Ahsan, Rachel S. Kang, Rachel E.A. Salomon, Arjun Rajan, Yoon Seok Kim, Liam James Stanton, Christine L. Xu, Stephanie Do et al. · 2026 · Nature Neuroscience
51. Emerging Technologies to Study Long Non-coding RNAs
    Fereshteh Jahaniani, Varsha Rao, Stephanie A. Nevins, Damek V. Spacek, Neal Bharadwaj, Jason Reuter, Michael P. Snyder · 2013 · Springer eBooks
52. Handling Permutation in Sequence Comparison: Genome-Wide Enhancer Prediction in Vertebrates by a Novel Non-Linear Alignment Scoring Principle
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53. eXtasy simplified-towards opening the black box
    D. Popović, A. Sifrim, Y. Moreau, B. De Moor · 2013 · IEEE International Conference on Bioinformatics and Biomedicine
54. VAS: a convenient web portal for efficient integration of genomic features with millions of genetic variants
    Eric Dun Ho, Qin Cao, Sau Dan Lee, Kevin Yuk-Lap Yip · 2014 · BMC Genomics
55. Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites
    Mathieu Blanchette · 2012 · BMC Bioinformatics
56. High-resolution mapping of transcription factor binding sites on native chromatin
    Sivakanthan Kasinathan, Steven Henikoff · 2013 · Epigenetics & Chromatin
57. Functional Genomics Analysis of Big Data Identifies Novel Peroxisome Proliferator–Activated Receptor γ Target Single Nucleotide Polymorphisms Showing Association With Cardiometabolic Outcomes
    Kris Richardson, Gavin R. Schnitzler, Chao‐Qiang Lai, José María Ordovás · 2015 · Circulation Cardiovascular Genetics
58. Sequential data selection for predicting the pathogenic effects of sequence variation
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59. Research progress of conserved non-coding elements in metazoan
    Jun Feng, Guang Li, Yiquan Wang · 2013 · Hereditas (Beijing)
60. Conserved non-coding elements in human genome
    Jing Tian, Zhihu Zhao, Huipeng Chen · 2009 · Hereditas (Beijing)
61. Statistical techniques for biological motif discovery
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62. Improving Prediction Accuracy of Microarray Cancer Data with Non-negative Matrix Factorization and Its Variant
    Nakul Patel, Kalpdrum Passi, Chakresh Kumar Jain · 2020 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
63. Amplicon genome fishing (AGF): a rapid and efficient method for sequencing target cis-regulatory regions in nonmodel organisms
    HanMei Gu, Peng Zhang, Manhao Xu, Dan Liang · 2021 · Zeitschrift für Induktive Abstammungs- und Vererbungslehre
64. ACES: Analysis of Conservation with an Extensive list of Species
    Evin M. Padhi, Jeffrey K. Ng, Elvisa Mehinovic, Eleanor I. Sams, Tychele N. Turner · 2021 · Bioinformatics
65. Predicting deleterious missense genetic variants via integrative supervised nonnegative matrix tri-factorization
    Asieh Amousoltani Arani, Mohammadreza Sehhati, Mohammad Amin Tabatabaiefar · 2021 · Scientific Reports
66. Eukaryote Genomes
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67. Whole-Genome Cartography of Estrogen Receptorα Binding Sites
    Chin‐Yo Lin, Vinsensius Berlian Vega, Jane S. Thomsen, Tao Zhang, Say Li Kong, Ming Xie, Kuo‐Ping Chiu, Leonard Lipovich, Daniel Barnett, Fabio Stossi et al. · 2005 · PLoS Genetics
68. miR-6087 Might Regulate Cell Cycle–Related mRNAs During Cardiomyogenesis of hESCs
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69. A comprehensive knowledgebase of known and predicted human genetic variants associated with COVID-19 susceptibility and severity
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70. Evaluating the mouse neural precursor line, SN4741, as a suitable proxy for midbrain dopaminergic neurons
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71. Three linked variants have opposing regulatory effects on isovaleryl-CoA dehydrogenase gene expression
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72. The rapidly evolving X-linked MIR-506 family fine-tunes spermatogenesis to enhance sperm competition
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73. Evolutionary changes of noncoding elements associated with transition of sexual mode in Caenorhabditis nematodes
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74. Predicting genome‐wide tissue‐specific enhancers via combinatorial transcription factor genomic occupancy analysis
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75. Second transplantation after kidney graft loss in primary hyperoxaluria type 2: a pedigree study and mutation analysis
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76. Clinical phenotype and functional influence of GRIN2A variants in epilepsy‐aphasia syndrome
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77. Genome‐Wide Development and Characterization of Microsatellite Markers in the Great Web‐Spinning Sawfly Acantholyda posticalis
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78. A versatile pipeline to identify convergently lost ancestral conserved fragments associated with convergent evolution of vocal learning
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79. Computational analysis of congenital heart disease associated SNPs: unveiling their impact on the gene regulatory system
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80. The combinatorial binding syntax of transcription factors in forebrain-specific enhancers
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81. Divergent accumulation patterns of SNVs and INDELs reveal negative selection in noncancerous cells
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82. A generic pipeline for CADD score generation: chickenCADD and turkeyCADD
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83. Regulation and Function of Non-Exonic Recursive Splicing
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84. Why the DNA self-depurination mechanism operates in HB-β but not in β-globin paralogs HB-δ, HB-ɛ1, HB-γ1 and HB-γ2
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85. baal-nf identifies motif-disrupting variants that decrease transcription factor binding affinity
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86. Coordinated transcriptional networks program organelle expansion and metabolic flows for high endothelial morphology and function
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87. Transcriptional regulation of microRNA genes and the regulatory networks in which they participate
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88. In silico approaches to investigating mechanisms of gene regulation
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89. Estudio genético de la fractura femoral atípica mediante la secuenciación del exoma en tres hermanas afectas y tres pacientes no relacionadas
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90. Evolution of Exons and the Exon–Intron Structure of Long Intergenic Noncoding RNA Genes in Placental Mammals
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91. AnnoLnc: A One-Stop Portal to Systematically Annotate Novel Human Long Noncoding RNAs
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92. Phylogenetic Manifold Regularization: A semi-supervised approach to predict transcription factor binding sites
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93. Ultraconservation of enhancers is not ultranecessary
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94. In-Depth Annotation of the Drosophila Bithorax-Complex Reveals the Presence of Several Alternative ORFs That Could Encode for Motif-Rich Peptides
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95. Computational Methods and Approaches in Pharmacogenomic Research
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96. Prediction of functional microexons by transfer learning
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97. InsuLock: A Weakly Supervised Learning Approach for Accurate Insulator Prediction, and Variant Impact Quantification
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98. Unsupervised clustering analysis of SARS-Cov-2 population structure reveals six major subtypes at early stage across the world
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99. HARs: History, Functions, and Role in the Evolution and Pathogenesis of Human Diseases
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100. Functional characteristics and computational model of abundant hyperactive loci in the human genome
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