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

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Items 4,001–4,072 of 4,072

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5. Exploring the oasis of plant genomes: From genetic variations to function and beyond
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6. Vision-Based Genomic Model for Copy Number Variant Pathogenicity Prediction
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7. Sequence-Based Prioritization of Promoter Regulatory Variants in Colorectal Cancer Using a DNA Foundation Model
   Sripal Vajinepalli, Aashna Saraf, Sayane Shome · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
8. Intron 13 retention expands the ADAR1 isoform repertoire to rewire PKR signaling and promote tumorigenesis
   Bryan Y.L. Ng, Jesslyn Zhou, Sze Jing Tang, Yuhua Lim, Vincent Tano, Jovi Jian An Lim, Xi Ren, Ömer An, Jinghe Xie, Jian Han et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
9. Functional annotation of non-coding variants identifies a novel enhancer with activity in neural crest cell–derived lineages
   Vartika Bisht, Neil Slaven, Miriam Smits, Ludo Pagie, Tijn van Balen, Jihed Chouaref, Wilhelmina S. Kerstjens‐Frederikse, Cleo C. van Diemen, Jeroen Korving, Harry Begthel et al. · 2026 · Research Square
10. Limited Selection on Neanderthal DNA in 30,780 Recently Admixed Genomes with African-like Ancestry
    Aaron Pfennig, Joseph Lachance · 2026 · Molecular Biology and Evolution
11. Pervasive cryptic selection in the human noncoding genome
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12. Pan-cancer discovery of driver mutations in long noncoding RNAs reveals widespread functional rewiring of RNA regulatory elements
    Sunandini Ramnarayanan, Roofiya Koya, Marta Soszynska-Jozwiak, Marta Szabat, Jack Roban, Sarang Bhutada, Bhavya Dhaka, Tilman Schaefer, Ai Ming Tham, Hugo Guillen-Ramirez et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
13. The origin and evolution of dorsal determination mechanisms in vertebrate paired appendages
    M. Brent Hawkins, Sofía Zdral, Silvia Naranjo, Miguel Juliá, Manuel Sánchez‐Martín, Jacob M. Daane, Nicolás Cumplido, Dávid Jandzík, Daniel M. Medeiros, Sarah K. McMenamin et al. · 2026 · Current Biology
14. Organisational principles of long non-coding RNAs revealed by exon deletion
    Sarang Bhutada, Hugo Guillen-Ramirez, Tina Uroda, Ines Jover Bravo, Michela Coan, Antonio Hermoso, Artem Baranovskii, Annalisa Marsico, Rory Johnson · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
15. DirectASRM: uncovering allele-specific post-transcriptional RNA modifications through direct RNA sequencing
    Jiayin Dai, Yu Zhang, Jiayi Li, Jiongming Ma, Kunqi Chen, Jia Meng, Daniel John Rigden, Zhen Wei, Shaofeng Lin, Qingru Xu · 2026 · Bioinformatics
16. Implementation of a medical genomics program for rare diseases in Uruguay
    Camila Simoes, María Fernanda Domínguez, Soledad Rodriguez, Mariana Moraes, María Paula Frade, Mariana Brandes, Martín Graña, Lucía Sosa, Santiago Fontenla, Alejandra Tapié et al. · 2026 · Orphanet Journal of Rare Diseases
17. mRNA-Scaffolded Cytoplasmic Compartments
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18. GRHL and PGR control WNT4 expression via 3D looping of conserved and species-specific enhancers
    Yorick Bernardus Cornelis van de Grift, Marleen T. Aarts, Katrin E. Wiese, Nika Heijmans, Ingeborg B. Hooijkaas, Colin E.J. Pritchard, Linda Henneman, Paul Krimpenfort, Antonius L. van Boxtel, Renée van Amerongen · 2026 · Cell Reports
19. Computational reconstruction of hierarchical cis-regulatory networks reveals synergistic transcription control and disease-associated rewiring
    Xunuo Zhu, Xuheng Zhou, Yufang Zhang, Guoxin Cai, Weidong Zhao, Binbin Zhou, Jingqi Zhou, Zefang Tang, Jie Liu, Qingqing Zhu et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
20. Synonymous Codons as Potential Contributors to Chromatin Stability and Gene Body Methylation in Plants
    Bevin Nishanth J, Suji Somasundaram · 2026 · Journal of Molecular Evolution
21. Genome-wide rotational and translational phasing of nucleosomes with human transcription factors
    Haining Chen, Jordan Krebs, Olivia W. Lang, Jiayi Hu, Devin C Mellini, Judith W. Hyle, Chunliang Li, William Lai, B. Franklin Pugh · 2026 · Molecular Cell
22. Novel DMD Frameshift Variant (p.Leu2017Profs*5) in Spectrin‐Like Repeat 16 Expands the Mutational Spectrum of DMD
    Y Y Lin, G. W. Gant Luxton, Hwei‐Jen Lee, Yu-Yang Lu, Hung-Chi Yang, Kuo‐Sheng Hung, Ming-Tsong Lai, Chih-Fen Hu · 2026 · Molecular Genetics & Genomic Medicine
23. cis-Regulatory Elements in Crops: From Natural Variation to Precision Engineering
    Alessandra Boccaccini, Benedetta Pizziconi, Michela Molinari, Sara Cimini, Laura De Gara · 2026 · Agronomy
24. Recent advances in the detection and functional analysis of circRNAs with short-read RNA sequencing-based methods
    Grace Lindner, Si-Mei Xu, Kristina Santucci, Yulan Gao, Michael Janitz · 2026 · Molecular Biology Reports
25. SUMOylation of HSF1 orchestrates transcriptional and splicing programs during the proteotoxic stress response
    Stefan P Müller, Upayan Patra, Svenja Kuska, Thorsten Mosler, Timur Makarov, Urbi Mukhopadhyay, Christian Münch, Ulrich Bernd Keller, Michaela Müller-McNicoll, Matthias Wirth · 2026 · Research Square
26. A genome-wide functional analysis of conserved intronic regions reveals essential roles for speckle-associated retained introns.
    Shaghayegh Farhangmehr, Ulrich Braunschweig, Mingkun Wu, Syed Nabeel-Shah, Kevin R. Brown, Jacob L. Fine, Jason Moffat, B. Blencowe · 2026 · Cell Reports
27. CNEwrap: a scalable toolkit with a novel algorithm for large-scale genome-wide accelerated conserved non-coding elements detection
    Ruihan Li, Wei Wu, Chaochao Yan, Jia‐Tang Li · 2026 · Nucleic Acids Research
28. Comprehensive landscape of potential CTCF-binding sites across the complete telomere-to-telomere human genome
    Eleftherios Bochalis, Ilias Georgakopoulos‐Soares · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
29. Investigating the role of CpG islands and DNA methylation at 3′UTRs in cancer
    Claire Wilson, Aditi Kanhere · 2026 · Life Science Alliance
30. MetaSplice: pathogenicity prediction and ACMG/AMP evidence for intronic variants outside the canonical splice sites
    Xiaoming Liu · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
31. Beyond Invariable Sites: Using Evolutionary Stasis to Map Multilayered Constraints on the Evolution of Viral and Mammalian Genomes
    Sergei L. Kosakovsky Pond, Hannah Verdonk, Steven Weaver, Gallean Brown, Danielle Callan, Anton Nekrutenko, Darren Patrick Martin · 2026 · Genome Biology and Evolution
32. Chromatin topology and distal elements underlie divergent cell-type-specific regulation of 9p21 locus cell cycle genes
    Elena Torlai Triglia, Tyler E. Miller, Neva C. Durand, Kyung Lock Kim, Salvador Casaní-Galdón, Joshua D’Antonio, Nauman Javed, Alessandro Paz Hernandez, Ayush Raman, Anna J. Cruz et al. · 2026 · Cell Genomics
33. Unveiling New Insights: Reinterpreting DES Mutation, p. Arg383His , Through a Study of an Iranian Family With Isolated Hypertrophic Cardiomyopathy, Implication for Phenotype–Genotype Correlation Analysis
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34. Expanding the ocular and genetic spectrum of FLVCR1-associated disease in a Chinese cohort
    Xing Wei, Wuyi Li, Yunyu Zhou, Yamei Li, Yue Liu, Ruifang Sui · 2026 · Documenta Ophthalmologica
35. MUGO: Differentiable Combinatorial Optimization for Causal Variant Discovery in the Non-coding Genome
    Simon Dongbo Sun, Junhao Liu, Xu Pengcheng, Yaqi Hu, Martin Jinye Zhang, Jing Zhang · 2026 · ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD)
36. DeNovoSeer:a deep learning framework for pathogenicity prediction of De novo mutations
    Rong Qiu, Xiyu Rao, Hong Feng Jiang, Jinchen Li, Guihu Zhao · 2026 · Briefings in Bioinformatics
37. Two Unrelated Families With Noncoding Duplications Upstream of MSX2 Refine the Critical Regulatory Region Likely Involved in Cranial Bone Development and a Cleidocranial Dysplasia‐Like Phenotype
    Mamiko Yamada, Mark Cleghorn, Krishnamurthy Prabhakara, Tegan French, David Francis, Kenjiro Kosaki, Tiong Yang Tan · 2026 · Human Mutation
38. Pervasive noise in human pre-mRNA splice site selection
    Eraj Shafiq Khokhar, Kaitlyn Brokaw, Zachary J. Kartje, Ye Liu, Valeria C. Sanabria, Nida Javeed, Ayush Kumar, Ezequiel Calvo-Roitberg, Jonathan K. Watts, Athma A. Pai · 2026 · Molecular Cell
39. AWTI-Net Enables Accurate and Interpretable Functional Assessment of Disease-Associated LncRNA Mutations
    Haipeng Zhu, D. Z. Li, Zehang Jiang, Mingle Yang, Guoying Wang, Wenliang Zhang · 2026 · Interdisciplinary Sciences Computational Life Sciences
40. aiDIVA – hybrid AI for rare disease diagnostics using evidence-based, machine learning and language models
    Dominic Boceck, Lucia Laugwitz, Marc Sturm, Daniela Bezdan, Axel Gschwind, Tobias B. Haack, Stephan Ossowski · 2026 · npj Genomic Medicine
41. Gene-level complexity explains genome-wide variation in the distribution of fitness effects
    Buŗcin Yıldırım, Jennifer James · 2026 · Molecular Biology and Evolution
42. Two distributed enhancers of Sox17 additively regulate the developmental fate of bipotential ventral pancreato-biliary progenitor cells
    Ryan R. Finnel, Jessica R.B. Musselman, Margaret E. McFadden, Isabella M. Silvestri, Jennifer Skelton, Leesa L. Sampson, Anna B. Osipovich, Christopher V.E. Wright, Mark A. Magnuson · 2026 · Development
43. Functional Prediction of Epitranscriptome
    Yuxin Zhang, Bowen Song, Kunqi Chen · 2026 · Methods in molecular biology
44. Identification of accelerated regions associated with extended post-reproductive lifespan in toothed whales
    Nelli A. Arakelyan, Andrey Dmitrievich Manakhov, Gelena V. Izotova, Maria N. Abramova, Evgeny I. Rogaev · 2026 · Frontiers in Ecology and Evolution
45. Mutation rate heterogeneity biases variant effect prediction and reveals genuine mutational robustness
    Hossameldin Loay, Prathitha Kar, Evan Koch, Vladimir B. Seplyarskiy, Donate Weghorn · 2026 · The American Journal of Human Genetics
46. Functional convergence of regulatory regions provides vital insights into mammalian gliding adaptation
    Xin Hao Du, Huizhong Fan, Yibo Hu, Xin Huang, Fuwen Wei · 2026 · Science China Life Sciences
47. PHACTn enables training-free, context-independent inference of nucleotide variant tolerance across the genome
    Ceren Yıldırım, Nurdan Kuru, Ogün Adebalı · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
48. Enhancer Tuning by Sequence-Specific Repressors
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49. Hox/Meis-dependent gene-regulatory transition underlies cardiopharyngeal neural crest diversification
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50. Measurement reliability bounds functional benchmarks and relocates where variant effect prediction fails
    Ningyi Zhang · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
51. The functional diversification of somatosensory neuron repertoires across Mammalia
    S. Andrew Shuster, Jia Yin Xiao, Bruno Gegenhuber, Shamsuddin A. Bhuiyan, Min Dai, Yongting Chen, Michelle M. DeLisle, Preston Sheng, Elizabeth Howell, Michael Brecht et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
52. ELE: Estimating tissue‐specific long noncoding RNA gene essentiality using graph neural networks
    Wan-Ting Shi, Yingdong Liu, Xiujun Gong, Pu-Feng Du · 2026 · Quantitative Biology
53. Exome Sequencing Identifies Novel Variants Causing Hearing Loss in Three Consanguineous Pakistani Families: Insights From Genomics and Bioinformatics Analyses
    Zafar Ali, Najeeb Ullah, Muneeba Bibi, Sania Fawad, Sana Khan, Mansoor Ali, Irum Hassan, Sana Fazal, Fazal Akbar, Shahid Baig et al. · 2026 · Annals of Human Genetics
54. Single-cell multiomics across nine mammals reveals cell-type-specific regulatory conservation in the brain
    Ashlyn G. Anderson, Brianne B. Rogers, Erin A. Barinaga, Jacob M. Loupe, Elisa WaMaina, S. Quinn Johnston, Henry L. Limbo, Elizabeth A. Gardner, Anna J. Moyer, Amanda L. Gross et al. · 2026 · Cell Genomics
55. Untranslated Region-FNex: An Integrative Multimodal Framework for Functional Untranslated Region Variant Prioritization
    Yaning Li, Fang Ge, Lei Pan, Ming Zhang · 2026 · Journal of Chemical Information and Modeling
56. Novel Branch Point Variant in PGAP1 Causing Neurodevelopmental Disorder
    Ida Marie Aakerlund, Maria Barington, Thomas van Overeem Hansen, Jakob Ek, Stense Farholt, Elsebet Østergaard · 2026 · Current Genetic Medicine Reports
57. Familial case of rapid-onset dystonia-parkinsonism (DYT/PARK-ATP1A3, DYT12)
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58. HiFIseek: Gene-specific enrichment of high-impact mutations in associated genomic regions
    Rafael Riudavets Puig, Denise G O'Mahony, Ina Skaara Brorson, Ksenia Sokolova, Vessela Nedelcheva Kristensen, Anthony Mathelier · 2026 · PLoS Computational Biology
59. Strong correlations between mutation rates and selective constraint in the human genome?
    Gustavo Valadares Barroso, Aaron P. Ragsdale · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
60. Expression predictions inform molecular interpretation of Alzheimer’s disease risk loci
    Choi byung hyug, Jaeseung Jeong · 2026 · medRxiv
61. From conservation scores to language models: a feature engineering perspective on machine learning for genetic variant interpretation
    Matteo Bulloni, Martina Vescio, Federico De Mori Bajolin, Linda Pattini · 2026 · Briefings in Bioinformatics
62. Hybrid Framework for Early Genetic Risk Detection in Newborn Screening
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63. FAIRsharing record for: Endogenous G-quadruplex Database
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64. MitImpact 4: a genome-wide resource for the interpretation of coding and non-coding mitochondrial DNA variants
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65. Clinical and Genetic Spectrum of OPN1LW/OPN1MW-Associated Disorders in a Chinese Cohort: Contribution of Long-Read Sequencing
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68. Integrative Statistical Learning with Applications to Predicting Features of Diseases and Health
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69. Organisation of transcriptomes : searching for regulatory DNA elements involved in the correlated expression of genomic neighbours
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70. Latent variable models in statistical genetics
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71. Identification and Characterization of Site-Directed A-to-I RNA Editing Targets
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72. A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants
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