Genome-wide analysis of noncoding regulatory mutations in cancer

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Items 101–200 of 486

1. TERT promoter mutations are a major indicator of recurrence and death due to papillary thyroid carcinomas
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2. Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes
   Eric Minwei Liu, Alexander Martinez‐Fundichely, Bianca Jay Diaz, Boaz E. Aronson, Tawny N. Cuykendall, Matthew J. MacKay, Priyanka Dhingra, Elissa W.P. Wong, Ping Chi, Effie Apostolou et al. · 2019 · Cell Systems
3. Cistrome Partitioning Reveals Convergence of Somatic Mutations and Risk Variants on Master Transcription Regulators in Primary Prostate Tumors
   Parisa Mazrooei, Ken J. Kron, Yanyun Zhu, Stanley Zhou, Giacomo Grillo, Tahmid Mehdi, Musaddeque Ahmed, Tesa Severson, Paul Guilhamon, Nicholas Sinnott Armstrong et al. · 2019 · Cancer Cell
4. Familial Melanoma and Susceptibility Genes: A Review of the Most Common Clinical and Dermoscopic Phenotypic Aspect, Associated Malignancies and Practical Tips for Management
   Lamberto Zocchi, Alberto Lontano, Martina Merli, Emi Dika, Eduardo Nagore, Pietro Quaglino, Susana Puig, Simone Ribero · 2021 · Journal of Clinical Medicine
5. FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map
   Tom Aharon Hait, David Amar, Ron Shamir A, Ran Elkon · 2018 · Genome biology
6. Emerging roles of long non-coding RNAs in breast cancer biology and management
   Ivano Amelio, Francesca Bernassola, Eleonora Candi · 2020 · Seminars in Cancer Biology
7. Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival
   Henrik Hornshøj, Morten Muhlig Nielsen, Nasa Sinnott-Armstrong, Michał Świtnicki, Malene Juul, Tobias Lynge Madsen, Richard C. Sallari, M Kellis, Torben Falck Orntoft, Asger Hobolth et al. · 2018 · npj Genomic Medicine
8. Promoter capture Hi-C-based identification of recurrent noncoding mutations in colorectal cancer
   Giulia Orlando, Philip Law, Alex J. Cornish, Sara E. Dobbins, Daniel Chubb, Peter Broderick, Kevin Litchfield, Fadi Hariri, Tomi Pastinen, Cameron S. Osborne et al. · 2018 · Nature Genetics
9. Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma
   Swati Venkat, Arwen A. Tisdale, Johann RE Schwarz, Abdulrahman A. Alahmari, H. Carlo Maurer, Kenneth P. Olive, Kevin Hasegawa Eng, Michael E. Feigin · 2020 · Genome Research
10. Genome-wide enhancer annotations differ significantly in genomic distribution, evolution, and function
    Mary Lauren Benton, Sai Charan Talipineni, Dennis Kostka, John A. Capra · 2019 · BMC Genomics
11. Frequent DPH3 promoter mutations in skin cancers
    Evgeniya Denisova, Barbara Heidenreich, Eduardo Nagore, P. Sivaramakrishna Rachakonda, Md. Ismail Hosen, Ivana Akrap, Víctor Traves, Zaida García‐Casado, José Antonio López‐Guerrero, Celia Requena et al. · 2015 · Oncotarget
12. DBTSS/DBKERO for integrated analysis of transcriptional regulation
    A. Suzuki, S. Kawano, Toutai Mitsuyama, M. Suyama, Y. Kanai, K. Shirahige, H. Sasaki, K. Tokunaga, K. Tsuchihara, S. Sugano et al. · 2017 · Nucleic Acids Res.
13. Telomere Length Dynamics and the Evolution of Cancer Genome Architecture
    Kez Cleal, Kevin Norris, Duncan M. Baird · 2018 · International Journal of Molecular Sciences
14. Multiplexed functional genomic analysis of 5’ untranslated region mutations across the spectrum of prostate cancer
    Yiting Lim, Sonali Arora, Samantha L. Schuster, Lukas Corey, Matthew Fitzgibbon, Cynthia L. Wladyka, Xiaoying Wu, Ilsa M. Coleman, Jeffrey J. Delrow, Eva Corey et al. · 2021 · Nature Communications
15. Noncoding mutations target cis-regulatory elements of the FOXA1 plexus in prostate cancer
    Stanley Zhou, James R. Hawley, Fraser Soares, Giacomo Grillo, Mona Teng, Seyed Ali Madani Tonekaboni, Junjie Tony Hua, Ken J. Kron, Parisa Mazrooei, Musaddeque Ahmed et al. · 2020 · Nature Communications
16. Control of Cellular Aging, Tissue Function, and Cancer by p53 Downstream of Telomeres
    Caitlin M. Roake, Steven E. Artandi · 2017 · Cold Spring Harbor Perspectives in Medicine
17. Germline TERT promoter mutations are rare in familial melanoma
    Mark Harland, Mia Petljak, Carla Daniela Robles‐Espinoza, Zhihao Ding, Nelleke A. Gruis, Remco van Doorn, Karen A. Pooley, Alison M. Dunning, Lauren G. Aoude, Karin Wadt et al. · 2015 · Familial Cancer
18. Implications of TERT promoter mutations and telomerase activity in urothelial carcinogenesis
    Çagatay Güneş, Felix Wezel, Jennifer Southgate, Christian Bolenz · 2018 · Nature Reviews Urology
19. Emerging Roles of RNA 3′-end Cleavage and Polyadenylation in Pathogenesis, Diagnosis and Therapy of Human Disorders
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20. Discovery of regulatory noncoding variants in individual cancer genomes by using cis-X
    Liu, Yu, Li, Chunliang, Shen, Shuhong, Chen, Xiaolong, Szlachta, Karol, Edmonson, Michael N., Shao, Ying, Ma, Xiaotu, Hyle, Judith, Wright, Shaela et al. · 2020 · Nature Genetics
21. Rethinking pheochromocytomas and paragangliomas from a genomic perspective
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22. Telomeres and telomerase in head and neck squamous cell carcinoma: from pathogenesis to clinical implications
    Paolo Boscolo‐Rizzo, Maria Cristina Da Mosto, Enrica Rampazzo, Silvia Giunco, Annarosa Del Mistro, Anna Menegaldo, Lorena Baboçi, Monica Mantovani, Giancarlo Tirelli, Anita De Rossi · 2016 · Cancer and Metastasis Reviews
23. A study of the mutational landscape of pediatric-type follicular lymphoma and pediatric nodal marginal zone lymphoma
    Michael G. Ozawa, Aparna Bhaduri, Karen M. Chisholm, Steven Andrew Baker, Lisa Ma, James L. Zehnder, Sandra Luna‐Fineman, Michael Paul Link, Jason D. Merker, Daniel A. Arber et al. · 2016 · Modern Pathology
24. Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma
    Michael E. Feigin, Tyler H. Garvin, Peter J. Bailey, Nicola Waddell, David Kuang-Fu Chang, David R. Kelley, Shimin Shuai, Steve Gallinger, John D. McPherson, Sean Michael Grimmond et al. · 2017 · Nature Genetics
25. Epigenetic landscape influences the liver cancer genome architecture
    Hama, Natsuko, Totoki, Yasushi, Miura, Fumihito, Tatsuno, Kenji, Saito-Adachi, Mihoko, Nakamura, Hiromi, Arai, Yasuhito, Hosoda, Fumie, Urushidate, Tomoko, Ohashi, Shoko et al. · 2018 · Nature Communications
26. Mutations in the small nuclear RNA gene RNU2-2 cause a severe neurodevelopmental disorder with prominent epilepsy
    Daniel Greene, Koenraad De Wispelaere, Jonathan Gill Lees, Marta Codina‐Solà, Brynjar Ö. Jensson, Emma Hales, Andrea Katrinecz, Esther Nieto Molina, Sónia Pascoal, Rolph Pfundt et al. · 2025 · Nature Genetics
27. Genomic Instability of iPSCs and Challenges in Their Clinical Applications
    Masahito Yoshihara, Akiko Oguchi, Yasuhiro Murakawa · 2019 · Advances in experimental medicine and biology
28. Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies
    Kailong Li, Yuannyu Zhang, Xin Liu, Yuxuan Liu, Zhimin Gu, Hui Cao, Kathryn E. Dickerson, Mingyi Chen, Weina Chen, Zhen Shao et al. · 2020 · Cancer Discovery
29. Reconciling Non-Genetic Plasticity with Somatic Evolution in Cancer
    Sui Huang · 2021 · Trends in cancer
30. Personal Mutanomes Meet Modern Oncology Drug Discovery and Precision Health
    Feixiong Cheng, Han Liang, Atul Janardhan Butte, Charis Eng, Ruth Nussinov · 2018 · Pharmacological Reviews
31. An interaction proteomics survey of transcription factor binding at recurrent TERT promoter mutations
    Matthew M. Makowski, Esther Willems, Jun Fang, Jiyeon Choi, Tongwu Zhang, Pascal W.T.C. Jansen, Kevin M. Brown, Michiel Vermeulen · 2015 · PROTEOMICS
32. High-throughput characterization of the role of non-B DNA motifs on promoter function
    Ilias Georgakopoulos‐Soares, Jesús Victorino, Guillermo E. Parada, Vikram Agarwal, Jingjing Zhao, Hei Yuen Wong, Mubarak Ishaq Umar, Orry Elor, Allan Muhwezi, Joon‐Yong An et al. · 2022 · Cell Genomics
33. Molecular characterisation of cutaneous melanoma: creating a framework for targeted and immune therapies
    Shivshankari Rajkumar, Ian R. Watson · 2016 · British Journal of Cancer
34. Non-coding genetic variation in cancer
    Tawny N. Cuykendall, Mark A. Rubin, Ekta Khurana · 2017 · Current Opinion in Systems Biology
35. Long noncoding RNAs: Undeciphered cellular codes encrypting keys of colorectal cancer pathogenesis
    Tae‐Wan Kim, Carlo Maria Croce · 2018 · Cancer Letters
36. Circulating Cell-Free DNA in Hepatocellular Carcinoma: Current Insights and Outlook
    C. Ng, G. D. Di Costanzo, L. Terracciano, S. Piscuoglio · 2018 · Frontiers in Medicine
37. Functional CRISPR screen identifies AP1-associated enhancer regulating FOXF1 to modulate oncogene-induced senescence
    Ruiqi Han, Li Li, Alejandro Pineiro Ugalde, A Tal, Zohar Manber, Eric Pintó Barberà, Veronica Della Chiara, Ran Elkon, Reuven Agami · 2018 · Genome biology
38. RNA processing as an alternative route to attack glioblastoma
    Fabiana Marcelino Meliso, Christopher G. Hubert, Pedro A. F. Galante, Luiz O. F. Penalva · 2017 · Human Genetics
39. The number of key carcinogenic events can be predicted from cancer incidence
    Aleksey V. Belikov · 2017 · Scientific Reports
40. Quantitative Whole Genome Sequencing of Circulating Tumor Cells Enables Personalized Combination Therapy of Metastatic Cancer
    Natali Gulbahce, Mark Jesus M. Magbanua, Robert G. Chin, Misha R. Agarwal, Xuhao Luo, Jia Liu, Daniel M. Hayden, Qing Mao, Serban Ciotlos, Zhenyu Li et al. · 2017 · Cancer Research
41. Mutational processes contributing to the development of multiple myeloma
    Phuc H. Hoang, Alex J. Cornish, Sara E. Dobbins, Martin Kaiser, Richard S. Houlston · 2019 · Blood Cancer Journal
42. Disruption of Transcriptional Coactivator Sub1 Leads to Genome-Wide Re-distribution of Clustered Mutations Induced by APOBEC in Active Yeast Genes
    Artem G. Lada, Sergei F. Kliver, Alok Dhar, Dmitrii E. Polev, Alexey Masharsky, Igor B. Rogozin, Youri I. Pavlov · 2015 · PLoS Genetics
43. Deregulated Regulators: Disease-Causing cis Variants in Transcription Factor Genes
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44. The migration ability of stem cells can explain the existence of cancer of unknown primary site. Rethinking metastasis.
    Miguel López‐Lázaro · 2015 · Oncoscience
45. Genomic Analysis Revealed New Oncogenic Signatures in TP53-Mutant Hepatocellular Carcinoma
    Venkatesh Kancherla, Samir Abdullazade, Matthias Sebastian Matter, Manuela Lanzafame, Luca Quagliata, Guglielmo Roma, Yujin Hoshida, Luigi Terracciano, Charlotte K.Y. Ng, Salvatore Piscuoglio · 2018 · Frontiers in Genetics
46. OncoBase: a platform for decoding regulatory somatic mutations in human cancers
    Xianfeng Li, Leisheng Shi, Yan Wang, Jianing Zhong, Xiaolu Zhao, Huajing Teng, Xiaohui Shi, Haonan Yang, Shasha Ruan, MingKun Li et al. · 2018 · Nucleic Acids Research
47. Mining TCGA Database for Tumor Microenvironment-Related Genes of Prognostic Value in Hepatocellular Carcinoma
    Zhenfeng Deng, Jilong Wang, Banghao Xu, Zongrui Jin, Guolin Wu, Jingjing Zeng, Minhao Peng, Ya Guo, Wen Zhang · 2019 · BioMed Research International
48. Frequency and geographic distribution of TERT promoter mutations in primary hepatocellular carcinoma
    F. Pezzuto, L. Buonaguro, F. Buonaguro, M. Tornesello · 2017 · Infectious Agents and Cancer
49. Melanoma: Genetic Abnormalities, Tumor Progression, Clonal Evolution and Tumor Initiating Cells
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50. The Application of Long-Read Sequencing to Cancer
    Luca Ermini, Patrick Driguez · 2024 · Cancers
51. A Glutamatergic Network Mediates Lithium Response in Bipolar Disorder as Defined by Epigenome Pathway Analysis
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52. Research into cancer metabolomics: Towards a clinical metamorphosis
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53. Induction of Telomere Dysfunction Prolongs Disease Control of Therapy-Resistant Melanoma
    Gao Zhang, Lawrence Wen Wu, Ilgen Mender, Michal Barzily-Rokni, Marc R. Hammond, Omotayo Ope, Chaoran Cheng, Themistoklis Vasilopoulos, Sergio Randell, Norah Layla Sadek et al. · 2018 · Clinical Cancer Research
54. A Significant Regulatory Mutation Burden at a High-Affinity Position of the CTCF Motif in Gastrointestinal Cancers
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55. Kataegis Expression Signature in Breast Cancer Is Associated with Late Onset, Better Prognosis, and Higher HER2 Levels
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56. Mosaicism in Cutaneous Disorders
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57. CRISPR Screens in Synthetic Lethality and Combinatorial Therapies for Cancer
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58. Risk Stratification Using a Novel Genetic Classifier Including PLEKHS1 Promoter Mutations for Differentiated Thyroid Cancer with Distant Metastasis
    Chan Kwon Jung, Seung‐Hyun Jung, Sora Jeon, Young Mun Jeong, Yourha Kim, Sohee Lee, Ja Seong Bae, Yeun‐Jun Chung · 2020 · Thyroid
59. TPP1 promoter mutations cooperate with TERT promoter mutations to lengthen telomeres in melanoma
    Pattra Chun‐on, Angela M. Hinchie, Holly C. Beale, Agustin A. Gil Silva, Elizabeth A. Rush, Cindy Sander, Carla J. Connelly, Brittani K. N. Seynnaeve, John M. Kirkwood, Olena M. Vaske et al. · 2022 · Science
60. Cancer-associated noncoding mutations affect RNA G-quadruplex-mediated regulation of gene expression
    Mahdi Zeraati, Aaron L. Moye, Jason W. H. Wong, Dilmi Perera, M. Cowley, D. Christ, T. Bryan, M. Dinger · 2017 · Scientific Reports
61. Advances in genomic hepatocellular carcinoma research
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62. Challenges in identifying cancer genes by analysis of exome sequencing data
    Matan Hofree, Hannah K. Carter, Jason F. Kreisberg, Sourav Bandyopadhyay, Paul S. Mischel, Stephen Henry Friend, Trey Ideker · 2016 · Nature Communications
63. Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes
    Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Grace Tiao, Henrik Hornshøj, Julian M. Hess, Randi Istrup Pedersen, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Lynge Madsen et al. · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
64. Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate
    Malene Juul, Johanna Bertl, Qianyun Guo, Morten Muhlig Nielsen, Michał Świtnicki, Henrik Hornshøj, Tobias Lynge Madsen, Asger Hobolth, Jakob Skou Pedersen · 2017 · eLife
65. Transcriptional dysregulation by aberrant enhancer activation and rewiring in cancer
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66. IW-Scoring: an Integrative Weighted Scoring framework for annotating and prioritizing genetic variations in the noncoding genome
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67. RNA-mediated gene regulation is less evolvable than transcriptional regulation
    Joshua L. Payne, Fahad Khalid, Andreas Wagner · 2018 · Proceedings of the National Academy of Sciences
68. Circular synthesized CRISPR/Cas gRNAs for functional interrogations in the coding and noncoding genome
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69. Systematic evaluation of the effects of genetic variants on PIWI-interacting RNA expression across 33 cancer types
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70. A survey of tandem repeat instabilities and associated gene expression changes in 35 colorectal cancers
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71. Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas
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72. Beyond the exome: the role of non-coding somatic mutations in cancer
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73. WDR74 modulates melanoma tumorigenesis and metastasis through the RPL5–MDM2–p53 pathway
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74. Systematic dissection of transcriptional regulatory networks by genome-scale and single-cell CRISPR screens
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75. Regulatory elements in molecular networks
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76. Transcriptional regulators and alterations that drive melanoma initiation and progression
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77. The Sirenic Links between Diabetes, Obesity, and Bladder Cancer
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78. Use of telomerase promoter mutations to mark specific molecular subsets with reciprocal clinical behavior in IDH mutant and IDH wild-type diffuse gliomas
    Cemaliye Boylu Akyerli, Şirin Yüksel, Özge Can, Zeynep Erson-Omay, Yavuz Oktay, Erdal Coşgun, Ege Ülgen, Yiğit Erdemgil, Aydın Sav, Andreas von Deimling et al. · 2017 · Journal of neurosurgery
79. Cell Immortalization: In Vivo Molecular Bases and In Vitro Techniques for Obtention
    de Bardet, Javier Curi, Cardentey, Celeste Ramírez, González, Belkis López, Patrone, Deanira, Mulet, Idania Lores, Siniscalco, Dario, Robinson-Agramonte, María de los Angeles · 2023 · BioTech
80. Integrated Molecular Characterization of the Lethal Pediatric Cancer Pancreatoblastoma
    Tomoya Isobe, Masafumi Seki, Kenichi Yoshida, Masahiro Sekiguchi, Yusuke Shiozawa, Yuichi Shiraishi, Shunsuke Kimura, Misa Yoshida, Yoshikage Inoue, Akira Yokoyama et al. · 2017 · Cancer Research
81. CScape-somatic: distinguishing driver and passenger point mutations in the cancer genome
    Mark F. Rogers, Tom R. Gaunt, Colin Campbell · 2020 · Bioinformatics
82. Comprehensive Characterization of Somatic Mutations Impacting lncRNA Expression for Pan-Cancer
    Yue Gao, Xin Li, Hui Zhi, Yunpeng Zhang, Yanxia Wang, Yanxia Wang, Shipeng Shang, Ying Fang, Weitao Shen, Shangwei Ning et al. · 2019 · Molecular Therapy — Nucleic Acids
83. The Many Faces of Gene Regulation in Cancer: A Computational Oncogenomics Outlook
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84. Chromatin structure–based prediction of recurrent noncoding mutations in cancer
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85. Short inverted repeats contribute to localized mutability in human somatic cells
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86. Discovery of driver non-coding splice-site-creating mutations in cancer
    Song Cao, Daniel Cui Zhou, Clara Oh, Reyka G. Jayasinghe, Yanyan Zhao, Christopher J. Yoon, Matthew A. Wyczalkowski, Matthew H. Bailey, Terrence C. Tsou, Qingsong Gao et al. · 2020 · Nature Communications
87. High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation
    Ilias Georgakopoulos‐Soares, Candace S. Y. Chan, Nadav Ahituv, Martin Hemberg · 2022 · Genome biology
88. A survey on algorithms to characterize transcription factor binding sites
    Manuel Tognon, Rosalba Giugno, Luca Pinello · 2023 · Briefings in Bioinformatics
89. Identification of coding and non-coding mutational hotspots in cancer genomes
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90. Implementing precision cancer medicine in the genomic era
    Hui‐Zi Chen, Russell Bonneville, Sameek Roychowdhury · 2018 · Seminars in Cancer Biology
91. Pan-cancer noncoding genomic analysis identifies functional CDC20 promoter mutation hotspots
    Zaoke He, Tao Wu, Shixiang Wang, Jing Zhang, Xiaoqin Sun, Ziyu Tao, Xiangyu Zhao, Huimin Li, Kai Wu, Xue-Song Liu · 2021 · iScience
92. Human stem cell-based disease modeling: prospects and challenges
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93. Telomerase and CD4 T Cell Immunity in Cancer
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94. Signatures of accelerated somatic evolution in gene promoters in multiple cancer types
    K. S. Smith, Vinod Kumar Yadav, Brent S. Pedersen, Rita Shaknovich, Mark W. Geraci, Katherine S. Pollard, Subhajyoti De · 2015 · Nucleic Acids Research
95. Dissecting the sources of gene expression variation in a pan-cancer analysis identifies novel regulatory mutations
    Anchal Sharma, Chuan Jiang, Subhajyoti De · 2018 · Nucleic Acids Research
96. CBNA: A control theory based method for identifying coding and non-coding cancer drivers
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97. Genomics of chromophobe renal cell carcinoma: implications from a rare tumor for pan-cancer studies
    K. Rathmell, Feng-Ju Chen, C. Creighton · 2015 · Oncoscience
98. Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network
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99. Computational Methods for Characterizing Cancer Mutational Heterogeneity
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100. Advances of DNase-seq for mapping active gene regulatory elements across the genome in animals
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