Genome-wide analysis of noncoding regulatory mutations in cancer

Weinhold, Nils, Jacobsen, Anders, Schultz, Nikolaus, Sander, Chris, Lee, William·2014·Nature Genetics

Cited by (486)

Items 401–486 of 486

  1. A Pan-Cancer Analysis of the Oncogenic Role of WD Repeat Domain 74 in Multiple Tumors
    Xiaoxuan Wu, Peng Song, Shun Wang, Zhirong Qian, Jianming Ying, Shugeng Gao, Wenbin Li · 2022 · Frontiers in Genetics
  2. Discovery of a non-canonical GRHL1 binding site using deep convolutional and recurrent neural networks
    Sebastian Proft, Janna Leiz, Udo Heinemann, Dominik Seelow, Kai Martin Schmidt-Ott, Maria Rutkiewicz · 2023 · BMC Genomics
  3. The Search for Cancer Drivers
    Alessandro Laganà · 2024 · Lecture notes in computer science
  4. Highlights from the Literature
    Jason T. Huse, Roger Abounader, Benjamin W. Purow, Monika E. Hegi, Riccardo Soffietti, Kenneth Aldape · 2016 · Neuro-Oncology
  5. The Zebrafish as Model for Deciphering the Regulatory Architecture of Vertebrate Genomes
    Sepand Rastegar, Uwe Strähle · 2016 · Advances in genetics
  6. Bioinformatics and Computational Biology in Toxicology: Gateways for Precision Medicine
    Kenneth S. Ramos, M. Martin, Irma N. Ramos, Grzegorz A. Rempała · 2016 · Elsevier eBooks
  7. Epigenetics, Enhancers, and Cancer
    James J. Morrow, Peter C. Scacheri · 2016 · Energy balance and cancer
  8. Exploration of regression models for cancer noncoding mutation recurrence
    Tanjin Xu, Stephen A. Ramsey · 2016 · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)
  9. SDHD promoter mutations are rare events in cutaneous melanomas but SDHD protein expression is downregulated in advanced cutaneous melanoma
    Helena Pópulo, Rui Batısta, Cristina Sampaio, Joana Pardal, José Manuel Lopes, Paula Soares · 2017 · PLoS ONE
  10. A non-coding cancer mutation disrupting an HNF4α binding motif affects an enhancer regulating genes associated to the progression of liver cancer
    Marco Cavalli, Klev Diamanti, Gang Pan, Michał J. Dąbrowski, Jan Komorowski, Claes Wadelius · 2021 · Experimental Oncology
  11. An update on clinical applications of iPSCs from a genomic point of view
    Masahito Yoshihara, Yasuhiro Murakawa · 2022 · Elsevier eBooks
  12. Molecular Pathology and Genomics of Melanoma
    Klaus Griewank, Rajmohan Murali, Thomas Wiesner · 2018 · Springer eBooks
  13. cis ‐Regulatory Driver Mutations in Cancer Genomes
    Rebecca C. Poulos, Jason W.H. Wong · 2017 · Encyclopedia of Life Sciences
  14. A catalog of cis -regulatory mutations in 12 major cancer types
    Zhongshan Cheng, Michael Vermeulen, Micheal Rollins-Green, Brian DeVeale, Tomas Babak · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  15. Transcription Factor-Centric Approach to Identify Non-recurring Putative Regulatory Drivers in Cancer
    Jingkang Zhao, Vincentius Martin, Raluca Gordân · 2022 · Lecture notes in computer science
  16. Short Inverted Repeats as Mutational Hotspots and Putative Drivers of Genome Instability in Osteosarcoma
    Minghua Li, Chun Liang · 2025 · Genes
  17. Targeted long-read methylation analysis using hybridization capture suitable for clinical specimens
    Keisuke Kunigo, Satoi Nagasawa, Keiko Kajiya, Yoshitaka Sakamoto, Suzuko Zaha, Yuta Kuze, Akinori Kanai, Kotaro Nomura, Masahiro Tsuboi, Genichiro Ishii et al. · 2025 · Cell Reports Methods
  18. MODCAN: driver gene identification based on multi-omics features and differential co-association networks for tumor subtypes
    Ponian Li, GUODONG XIAO, Haihui Wang, Chunrui Xu, Yusen Zhang · 2026 · BMC Bioinformatics
  19. Long-Read Amplicon Sequencing for the Detection of TERT Promoter Variant Clonal Hematopoiesis in Patients with Telomere Biology Disorders
    R Kirchner, Miguel Pereira, Madilynn Peterson, Mark E. Berres, Jane E. Churpek · 2026 · Journal of Molecular Diagnostics
  20. Nucleotide-resolution mapping of regulatory elements via allelic readout of tiled base editing
    Basheer Becerra, Sandra Wittibschlager, Zain M. Patel, Ana P. Kutschat, Justin Delano, Eric Che, Anzhelika Tauber, Ting Wu, M M Starrs, Christina S. Horstmann et al. · 2026 · Nature Communications
  21. Genomic-guided precision oncology in canine cancer: from comparative genomics to liquid biopsy and molecular monitoring
    Minjeong Kang, Jaemin Kim, Jinho Park, DoHyeon Yu · 2026 · Journal of Veterinary Science
  22. Genetic Variations of Long Noncoding RNAs in Cancer
    Nadya Dimitrova · 2017 · Elsevier eBooks
  23. Melanomics: Comprehensive Molecular Analysis of Normal and Neoplastic Melanocytes
    Xuan Tien Steven Nguyen, Ian R. Watson · 2018 · Springer eBooks
  24. Dysregulation of Cis-Regulatory Elements in Cancer
    Jayne A. Barbour, Jason W.H. Wong · 2019 · Springer eBooks
  25. Mitochondrial dysfunction induced by variation in the non-coding genome – A proposed workflow to improve diagnostics
    Dorine Jeanne Mariëtte du Mee, Mads Bak, Elsebet Østergaard, Lene Juel Rasmussen · 2020 · Mitochondrion
  26. Molecular Pathology and Genomics of Melanoma
    Klaus Griewank, Rajmohan Murali, Thomas Wiesner · 2020 · Springer eBooks
  27. Mutation hotspots in cis-regulatory regions in cancer
    Rebecca C. Poulos, Jason W.H. Wong · 2016 · Oncoscience
  28. BreakCA, a method to discover indels using ChIP-seq and ATAC-seq reads, finds recurrent indels in regulatory regions of neuroblastoma genomes
    Arko Sen, Sélène T. Tyndale, Yi Fu, Galina A. Erikson, Graham McVicker · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  29. Detection of fusion transcripts and their genomic breakpoints from RNA sequencing data
    Youri Hoogstrate, Malgorzata A. Komor, René Böttcher, Job van Riet, Harmen J.G. van de Werken, Stef van Lieshout, Ralf Hoffmann, Evert van den Broek, Anne S. Bolijn, Natasja F. J. Dits et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  30. Differential expression of key CmPn members distinguishes histological and immune subtypes of hepatic cancers
    Johnathan Abou‐Fadel, Victoria A. Reid, Alexander Le, Jun Zhang · 2022
  31. A New R Package for Categorizing Coding and Non-Coding Genes
    Masroor Bayati, Narges Rezaie, Mehrab Hamidi, Maedeh Sadat Tahaei, Hamid Reza Rabiee · 2023 · Preprints.org
  32. Telomerase reactivation induces progression of mouse Braf V600E -driven thyroid cancers without telomere lengthening
    Iñigo Landa, Caitlin E.M. Thornton, Bin Xu, Jacob Haase, Gnana Prakasam Krishnamoorthy, Jingzhu Hao, Jeffrey A. Knauf, Zachary T. Herbert, Marı́a A. Blasco, Ronald A. Ghossein et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  33. Novel hepatocellular carcinomas (HCC) Subtype-Specific Biomarkers
    Jacob Croft, Odalys Quintanar, Liyuan Gao, Victor S. Sheng, Jun Zhang · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  34. The promoter mutation paucity as part of the dark matter of the cancer genome
    Nicholas Allen Baclig Abad, Irina Glas, Chen Hong, Annika Small, Yoann Pageaud, Ana Rita R. Maia, Dieter Weichenhan, Christoph Plass, Barbara Hutter, Benedikt Brors et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  35. Prioritising Functional Noncoding Variants via eRNA Post-transcriptional Interaction Maps in Human Samples
    Natalia Benova, Rene Kuklinkova, Jessica L. Haigh, James R. Boyne, Chinedu Anthony Anene · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  36. Elementary: breast cancer culprits leave their signatures on the double helix
    Delphine Mérino, Bhupinder Pal, Anthony T. Papenfuss · 2016 · Cell Death and Differentiation
  37. Prevalencia, en carcinomas papilares de tiroides metastásicos, de mutaciones somáticas activan tes en la región promotora de TERT
    Dirigido Por Dra, Ginesa García‐Rostán · 2016 · University of Valladolid Documentary Repository (University of Valladolid)
  38. Convergence of regulatory mutations into oncogenic pathways across multiple tumor types
    Karthik Murugadoss · 2017 · DSpace@MIT (Massachusetts Institute of Technology)
  39. Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
    Yu‐Hua Lo, Monica C. Pillon, Robin Evans Stanley · 2018 · Journal of Visualized Experiments
  40. In search of non-coding driver mutations by deep sequencing of regulatory elements in colorectal cancer
    Rebecca C. Poulos, Dilmi Perera, Deborah Packham, Anushi Shah, Caroline Janitz, John E. Pimanda, Nicholas John Hawkins, Robyn Lynne Ward, Luke B. Hesson, Jason W.H. Wong · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  41. Detecting Protein Variants within Mass Spectrometry Datasets
    Javier A. Alfaro · 2018 · TSpace (University of Toronto)
  42. Large-scale study of rna processing alterations in multiple cancers
    Babita Singh · 2017 · LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas)
  43. Integrated Genomic and Epigenomic Analyses of Atypical Teratoid Rhabdoid Tumour
    Jonathon Torchia · 2016 · TSpace (University of Toronto)
  44. Algorithms for deciphering cancer genomes: from differential mutation to differential allele specific expression
    Pawel F. Przytycki · 2018
  45. Dynamics and Topology of Human Transcribed Cis -regulatory Elements
    Shigeki Hirabayashi, Shruti Bhagat, Yu Matsuki, Yujiro Takegami, Takuya Uehata, Ai Kanemaru, Masayoshi Itoh, Kotaro Shirakawa, Akifumi Takaori‐Kondo, Osamu Takeuchi et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  46. Coding and noncoding somatic mutations in basal cell carcinoma
    Maria Giovanna Maturo, Sivaramakrishna P. Rachakonda, Barbara Heidenreich, Cristina Pellegrini, Nalini Srinivas, Celia Requena, Carlos Serra-Guillén, B. Llombart, Onofre Sanmartín, Carlos Guillén et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  47. Interrogating telomerase activity and telomere function through in-flask template evolution
    Margaret Pruitt · 2017 · KU ScholarWorks (The University of Kansas)
  48. Convergent mutations in tissue-specific regulatory regions reveal novel cancer drivers
    Nasa Sinnott-Armstrong, José Antonio Seoane, Richard C. Sallari, Jonathan K. Pritchard, Christina N. Curtis, Michael P. Snyder · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  49. Predicting Active Enhancers From Chromatin Accessibility and RNA-seq Datasets
    Francis Nguyen · 2019 · TSpace (University of Toronto)
  50. Ennet: construction of potential cancer-driving networks based on somatic enhancer mutations only
    Ya Cui, Yiwei Niu, Xueyi Teng, Dan Wang, Huaxia Luo, Peng Zhang, Wei Wu, Shunmin He, Jianjun Luo, Runsheng Chen · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  51. Investigating the Genetic Influences of the Germline and Somatic Genomes in Three Subtypes of Lung Cancer
    Timothy O’Brien · 2017
  52. Establishment, Characterisation And Mirna Transcriptome Profiling Of Spheroid-Enriched Cells With Breast Cancer Stem Cell Properties
    Lily Boo · 2020
  53. Role of Noncoding Single Nucleotide Variants on Transcription Factors’ activity in Cancer
    Parisa Mazrooei · 2019 · TSpace (University of Toronto)
  54. Role of Epigenetics in Colorectal Cancer
    Beiping Miao, Sonal Gupta, Manisha Mathur, Prashanth Suravajhala, Obul Reddy Bandapalli · 2021 · Springer eBooks
  55. Mutational Hotspot Detection in LGL Leukemia
    Nikki Aaron, Prabhjot K Singh, Siddharth Surapaneni, Joseph Wysocki · 2021 · Systems and Information Engineering Design Symposium
  56. MYC overexpression in cancer increases chromatin interactions at superenhancers and c-Myc binding sites
    Yi Xiang See · 2021
  57. Rôle de la succinate déshydrogénase dans le cancer
    Sophie Moog, Judith Favier · 2022 · médecine/sciences
  58. Melanomics: Comprehensive Molecular Analysis of Normal and Neoplastic Melanocytes
    Xuan Tien Steven Nguyen, Ian R. Watson · 2019 · Springer eBooks
  59. Faculty Opinions recommendation of Telomeres in cancer: tumour suppression and genome instability.
    Sharon A. Savage · 2018 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  60. In vitro Germ Cell Induction From Fertile and Infertile Research Participants
    Erica C. Pandolfi, Fei‐Man Hsu, Mark Duhon, Yi Zheng, Sierra Goldsmith, Jianping Fu, Sherman J. Silber, Amander T. Clark · 2022 · SSRN Electronic Journal
  61. Widespread perturbation of ETS factor binding sites in cancer
    Sebastian Carrasco Pro, Heather Hook, D Bray, Daniel Berenzy, Devlin C. Moyer, M Yin, Adam Thomas Labadorf, Ryan Tewhey, Trevor Siggers, Juan I. Fuxman Bass · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  62. Telomerase Reverse Transcriptase in Humans: From Biology to Cancer Immunity
    Magalie Dosset, Andrea Castro, Xian Su, Hannah K. Carter, Maurizio Zanetti · 2022 · Interdisciplinary cancer research
  63. Data from Somatic Mutations Enriched in Cis-Regulatory Elements Affect Genes Involved in Embryonic Development and Immune System Response in Neuroblastoma
    Vito Alessandro Lasorsa, Annalaura Montella, Sueva Cantalupo, Matilde Tirelli, Carmen de Torres, Sanja Aveic, Gian Paolo Tonini, Achille Iolascon, Mario Capasso · 2023
  64. Data from Transcription Factors Involved in Tumorigenesis Are Over-Represented in Mutated Active DNA-Binding Sites in Neuroblastoma
    Mario Capasso, Vito Alessandro Lasorsa, Flora Cimmino, Marianna Avitabile, Sueva Cantalupo, Annalaura Montella, Biagio De Angelis, Martina Morini, Carmen de Torres, Aurora Castellano et al. · 2023
  65. Data from Somatic Mutations Enriched in Cis-Regulatory Elements Affect Genes Involved in Embryonic Development and Immune System Response in Neuroblastoma
    Vito Alessandro Lasorsa, Annalaura Montella, Sueva Cantalupo, Matilde Tirelli, Carmen de Torres, Sanja Aveic, Gian Paolo Tonini, Achille Iolascon, Mario Capasso · 2023
  66. Chromosome 10
    Saurav Panicker, Satish Ramalingam · 2023 · BENTHAM SCIENCE PUBLISHERS eBooks
  67. Heterogeneity and genomic evolution of metastatic prostate cancer
    Sijia Wu, Zhennan Lu, Yanfei Wang, Xiaobo Zhou, Liyu Huang · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  68. Towards a comprehensive regulatory map of Mammalian Genomes
    Tássia Mangetti Gonçalves, Casey L. Stewart, Samantha D Baxley, Jason Xu, Daofeng Li, Harrison W. Gabel, Ting Wang, Oshri Avraham, Guoyan Zhao · 2023 · Research Square
  69. Additional file 2 of NIMBus: a negative binomial regression based Integrative Method for mutation Burden Analysis
    Zhang, Jing, Jason J. Liu, Patrick D. McGillivray, Caroline Yi, Lucas Lochovsky, Donghoon Lee, Mark Gerstein · 2020 · Figshare
  70. Olovnikov, telomeres and telomerase. is it possible to prolong a healthy life?
    Y. E. Yegorov · 2023 · Biochemistry (Moscow)
  71. Bioinformatics and Genetic Correlation Studies of Functional Gene Partners of Tp53 Gene Associated With Hepatocellular Carcinoma and Liver Cirrhosis Among Patients in Ucth, Calabar
    Godwin Michael Ubi, Blessing B Ekpenyong, Iyam O. Edodi, Bassey Ekeng Effiom, Nseabasi A. Etangetuk, Ivon A. Ettah, N. E. Edu, Mary E. Kooffreh, Chinyere A. Osondu, Imaobong Sunday Essien · 2024 · Research Square
  72. Genome-wide analysis of somatic non-coding mutation patterns and mitochondrial heteroplasmy in type B1 and B2 thymomas
    Kohei Fujikura, Isabel Correa, Susanne Heck, Juliet Elizabeth King, Emma McLean, Andrea Billè, Daisuke Nonaka · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  73. A sequence context-based approach for classifying tumor structural variants without paired normal samples
    Wolu Chukwu, Siyun Lee, Alexander Crane, Shu Zhang, Sophie Webster, Oumayma Dakhama, Ipsa Mittra, Carlos Rauert, Marcin B. Imielinski, Rameen Beroukhim et al. · 2025 · Cell Reports Methods
  74. A Novel Weighted Network Control Model for Identifying Coding and Non-coding Drivers in Cancer
    Bolin Chen, Jianjun Zhang, Weihua Meng, Youpeng Hu, Yuhang Li, Xinyue Hu, Z. J. Xu, Zhengyu Wang, Xingyu Liao, Xingyi Li · 2025 · Lecture notes in computer science
  75. Mitigation of multi-scale biases in cell-type deconvolution for spatially resolved transcriptomics using HarmoDecon
    Zirui Wang, Ke Xu, Yang Liu, Yu Xu, Lu Zhang · 2025 · Bioinformatics
  76. Additional file 1 of NIMBus: a negative binomial regression based Integrative Method for mutation Burden Analysis
    Zhang, Jing, Jason J. Liu, Patrick D. McGillivray, Caroline Yi, Lucas Lochovsky, Lee, Donghoon, Mark Gerstein · 2020 · Figshare
  77. Additional file 1 of Model selection and robust inference of mutational signatures using Negative Binomial non-negative matrix factorization
    Marta Pelizzola, Ragnhild Laursen, Asger Hobolth · 2024 · Figshare
  78. Additional file 1 of Discovery of a non-canonical GRHL1 binding site using deep convolutional and recurrent neural networks
    Sebastian Proft, Janna Leiz, Udo Heinemann, Dominik Seelow, Schmidt-Ott, Kai M., Rutkiewicz, Maria · 2023 · Figshare
  79. Additional file 1 of 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, Ahituv, Nadav, Hemberg, Martin · 2022 · Figshare
  80. Additional file 1 of MutEnricher: a flexible toolset for somatic mutation enrichment analysis of tumor whole genomes
    Anthony R. Soltis, Dalgard, Clifton L., Pollard, Harvey B., Wilkerson, Matthew D. · 2020 · Figshare
  81. Additional file 2 of Discovery of a non-canonical GRHL1 binding site using deep convolutional and recurrent neural networks
    Sebastian Proft, Janna Leiz, Udo Heinemann, Dominik Seelow, Schmidt-Ott, Kai M., Rutkiewicz, Maria · 2024 · MDC Repository (Max-Delbrueck-Center for Molecular Medicine)
  82. Rôle des protéines de liaison à l'ARN hnRNP H et hnRNP F dans les régulations traductionnelles dans les glioblastomes
    Morgane Le Bras · 2018
  83. Maintenance des télomères dans la carcinogenèse hépatique : fonction et transfert vers la clinique
    Massih Ningarhari · 2022 · theses.fr (ABES)
  84. Impact of cell volume on the evolutionary strategies of eukaryotic cells
    Akanksha Jain · 2024
  85. Preliminary examination of noncoding mutations of esophageal squamous cell carcinoma in African Americans
    Hayriye Verda Erkizan, Robert G. Wadleigh · 2026 · Frontiers in Genetics
  86. Analysis of PLEKHS1 promoter mutation in preoperative thyroid nodule samples
    Sarah Azad, Timothy E. Graham, Shiri Levy, Evana Valenzuela Scheker, David N. Bimston, Andrea Ferenczi, Yang Chen, Mohammed Alshalalfa, Yangyang Hao, Joshua Paul Klopper et al. · 2026 · Cancer Cytopathology