Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks

Cited by (146)

Items 101–146 of 146

1. Predicting chromatin interactions between open chromatin regions from DNA sequences
   Fan Cao, Ying Zhang, Yan Ping Loh, Yichao Cai, Melissa J. Fullwood · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
2. NSD2-epigenomic reprogramming and maintenance of plasma cell phenotype in t(4;14) myeloma
   Andrea Gunnell, Scott T. Kimber, Richard S. Houlston, Martin Kaiser · 2025 · Oncotarget
3. Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells
   Azusa Tanaka, Yasuhiro Ishitsuka, Hiroki Ohta, Akihiro Fujimoto, Jun‐ichirou Yasunaga, Masao Matsuoka · 2020 · PLoS Computational Biology
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   Valeriya Malysheva, Marco Antonio Mendoza-Parra, Matthias Blum, Mikhail Spivakov, Hinrich Gronemeyer · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
5. scFFPE-ATAC enables high-throughput single cell chromatin accessibility profiling in formalin-fixed paraffin-embedded samples
   Ram Prakash Yadav, Pengwei Xing, Miao Zhao, Peter Hollander, Carina Strell, Minglu Xie, Maede Salehi, Emma Torell, Tobias Sjöblom, Gunilla Enblad et al. · 2025 · Nature Communications
6. Biological, prognostic, and therapeutic impact of the epigenome in CLL
   Alba Maiqués-Díaz, José Ignacio Martín-Subero · 2023 · Seminars in Hematology
7. ALTRE: workflow for defining ALTered regulatory elements using chromatin accessibility data
   Elizabeth Baskin, Rick Farouni, Ewy A. Mathé · 2017 · Bioinformatics
8. The Etiology of Cancer
   David M. Vail, Douglas H. Thamm, Julias M. Liptak · 2019 · Elsevier eBooks
9. Epigenetic Variation Taking Center Stage in Immunological Research
   Simone Ecker, Stephan Beck · 2017 · Epigenomics
10. Fosl2 facilitates chromatin accessibility to determine developmental events during follicular maturation
    Hongyong Zhang, Zechen Li, Yanmei Zhu, Wencong Lyu, Wenlu Wei, Haochen Wang, Shuangjie Tian, Wei Yue, Jiajing Zhong, Qing‐Yuan Sun et al. · 2025 · Nature Communications
11. Integrative systems medicine approaches to identify molecular targets in lymphoid malignancies
    Raffaele Frazzi, Charles Auffray, Angela Ferrari, Perla Filippini, Sergio Rutella, Alfredo Cesario · 2016 · Journal of Translational Medicine
12. CAME: identification of chromatin accessibility from nucleosome occupancy and methylome sequencing
    Yongjun Piao, Seong Keon Lee, Eun-Joon Lee, Keith D. Robertson, Huidong Shi, Keun Ho Ryu, Jeong-Hyeon Choi · 2016 · Bioinformatics
13. ALTRE: workflow for defining ALTered Regulatory Elements using chromatin accessibility data
    Elizabeth Baskin, Rick Farouni, Ewy A. Mathé · 2016 · Bioinformatics
14. BROCKMAN: Deciphering variance in epigenomic regulators by k -mer factorization
    Carl G. de Boer, Aviv Regev · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
15. Insights into Leukemia from Single-Cell Genomics
    Nurefsan E. Sariipek, Peter van Galen · 2024 · Annual Review of Cancer Biology
16. Core binding factor leukemia hijacks T-cell prone PU.1 antisense promoter
    E. van der Kouwe, Gerwin Heller, A. Czibere, L.H. Castilla, R. Delwel, A. Di Ruscio, A.K. Ebralidze, M. Forte, L. Kazianka, C. Kornauth et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
17. Integrated Multi-omics Analyses of NFKB1 patients B cells points towards an up regulation of NF-κB network inhibitors
    Nadezhda Camacho-Ordóñez, Neftali Jose Ramirez, Sara Posadas‐Cantera, Andrés Caballero-Oteyza, Manfred Fliegauf, Fangwen Zhao, Maria Guarini, Victoria Gernedl, Mateo Pecoroaro, Klaus Warnatz et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
18. Combining signal and sequence to detect RNA polymerase initiation in ATAC-seq data
    Ignacio J. Tripodi, Murad Chowdhury, Margaret Gruca, Robin D. Dowell · 2020 · PLoS ONE
19. Bioinformatics of epigenetic data generated from next-generation sequencing
    Chiao-Yu Lyra Sheu, Yu‐Chun Huang, Pei-Yu Lin, Guan-Jun Lin, Pao‐Yang Chen · 2023 · Elsevier eBooks
20. ATAC-seq signal processing and recurrent neural networks can identify RNA polymerase activity
    Ignacio J. Tripodi, Murad Chowdhury, Robin D. Dowell · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
21. Nucleosome repositioning in chronic lymphocytic leukaemia
    Kristan V. Piroeva, Charlotte McDonald, Charalampos Xanthopoulos, Chelsea Fox, Christopher T. Clarkson, Jan‐Philipp Mallm, Yevhen Vainshtein, Luminiţa Ruje, Lara C. Klett, Stephan Stilgenbauer et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
22. A Functional Polymorphism in Accessible Chromatin Region Confers Risk of Non-Small Cell Lung Cancer in Chinese Population
    Jieyi Long, Tingting Long, Ying Li, Peihong Yuan, Ke Liu, Jiaoyuan Li, Liming Cheng · 2021 · Frontiers in Oncology
23. Non-canonical transcriptional regulation of the poor prognostic factor UGT2B17 in chronic lymphocytic leukemic and normal B cells
    Michèle Rouleau, Lyne Villeneuve, Eric Pierre Allain, Jules McCabe-Leroux, Sophie Tremblay, Flora Nguyen Van Long, Ashwini Uchil, Charles Joly-Beauparlant, Arnaud Droit, Chantal Guillemette · 2024 · BMC Cancer
24. Continuous β− particle exposure: A study of DNA damage in ex vivo peripheral blood mononuclear cells irradiation with Radioiodine
    Laura Mazzitelli-Fuentes, Lara Negrin, Virginia Venier, Hadar Romano, Lucia Pereira, Jerónimo Leberle, Maria Soledad Ausas, Ananya Choudhury, Luisa Vanesa Biolatti · 2025 · Clinical and Translational Radiation Oncology
25. PACells identifies phenotype-associated cell states from single-cell chromatin accessibility profiles
    Jiao Hua, Qiongyu Sheng, Shutong Xiao, Zhou Yang, Jing Qi, Shuilin Jin · 2026 · The American Journal of Human Genetics
26. Chromosomal abnormalities in bone marrow cells in relapse of chronic lymphocytic leukemia
    Svitlana V. Andreieva, Kateryna V. Korets, O. G. Alkhimova · 2017 · The Nucleus
27. Ibrutinibrezisztencia krónikus limfocitás leukémiában
    Dóra Aczél, Zoltán Mátrai, Richárd Kiss, Alexandra Balogh, Sarolta Illés, Csaba Bödör, Donát Alpár · 2019 · Hematológia–Transzfuziológia
28. Analysis of Data on Fludarabine, Cyclophosphamide, and Rituximab Chemoimmunotherapy for Chronic Lymphocytic Leukemia Shows High Patient Heterogeneity and the Need for More Consideration of Individualized Treatment
    Xiaoli Xu, Ying Zhao, Haiyan Ye, Yonglei Qi, Wenning Xu, Yiwen Ling, Shaojiang Yang · 2022 · Computational and Mathematical Methods in Medicine · Retracted
29. Over-accessible chromatin links myeloma initiating genetic events to oncogenic transcriptomes and aberrant transcription factor regulatory networks
    Jaime Alvarez-Benayas, Alexia Katsarou, Nikolaos Trasanidis, Aristeidis Chaidos, Philippa C. May, Kanagaraju Ponnusamy, Xiaolin Xiao, Marco Bua, Maria Luiza B. Sousa Atta, Irene A.G. Roberts et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
30. Combinatorial drug-microenvironment interaction mapping reveals cell-extrinsic drug resistance mechanisms and clinically relevant patient subgroups in CLL
    Peter‐Martin Bruch, Holly A. R. Giles, Carolin Kolb, Sophie A. Herbst, Tina Becirovic, Tobias Roider, Junyan Lu, Sebastian Scheinost, Lena Wagner, Jennifer Hüellein et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
31. The Genomic and Epigenomic Landscape of Chronic Lymphocytic Leukemia
    Jonathan C. Strefford, Renata J. Walewska, David Graham Oscier · 2017 · Springer eBooks
32. Identification of a primitive intestinal transcription factor network shared between oesophageal adenocarcinoma and its pre-cancerous precursor state
    Connor Rogerson, Edward Britton, Sarah Withey, Neil A. Hanley, Yeng Shiong Ang, Andrew D Sharrocks · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
33. Molecular Genetics of Chronic Lymphocytic Leukaemia
    Lara E Makewita, Jonathan C. Strefford · 2019 · Encyclopedia of Life Sciences
34. Chromatin Structure Research Methods
    Nikolaos A. Parisis · 2019 · Materials and Methods
35. Faculty Opinions recommendation of Fate mapping of human glioblastoma reveals an invariant stem cell hierarchy.
    John Silke, Delphine Mérino · 2018 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
36. Quantitating and Characterizing the Effects of Epigenetic Targeted Drugs
    Emily Gruber, Alexander Charles Lewis, Lev M. Kats · 2023 · Wiley eBooks
37. The Chronic Lymphocytic Leukemia Epigenome
    Antonio Perez-Castro, Lynne V. Abruzzo, Christopher C. Oakes · 2025 · Hematology/Oncology Clinics of North America
38. Additional file 1 of Chromatin interaction neural network (ChINN): a machine learning-based method for predicting chromatin interactions from DNA sequences
    Cao, Fan, Zhang, Yu, Yichao Cai, Sambhavi Animesh, Zhang, Ying, Semih Can Akıncılar, Yan Ping Loh, Li, Xinya, Chng, Wee Joo, Tergaonkar, Vinay et al. · 2021 · Figshare
39. Additional file 1 of Non-canonical transcriptional regulation of the poor prognostic factor UGT2B17 in chronic lymphocytic leukemic and normal B cells
    Michèle Rouleau, Villeneuve, Lyne, Eric Pierre Allain, Jules McCabe-Leroux, Sophie Tremblay, Flora Nguyen Van Long, Ashwini Uchil, Joly-Beauparlant, Charles, Arnaud Droit, Chantal Guillemette · 2024 · Figshare
40. Additional file 2 of Chromatin interaction neural network (ChINN): a machine learning-based method for predicting chromatin interactions from DNA sequences
    Cao, Fan, Zhang, Yu, Yichao Cai, Sambhavi Animesh, Zhang, Ying, Semih Can Akıncılar, Yan Ping Loh, Li, Xinya, Chng, Wee Joo, Tergaonkar, Vinay et al. · 2021 · Figshare
41. UniChrom: a universal deep learning architecture for cross-scale chromatin interaction prediction
    Shuaibin Wang, Tong Chen, Zhongxin Yang, Xuan Xu, Yin Shen · 2026 · BMC Genomics
42. Epigenetics in leukemia
    Cristina Bagacean · 2018 · theses.fr (ABES)
43. Etude de l'accessibilité chromatinienne des néoplasies lymphoïdes T matures : amélioration de la précision diagnostique et classification par cellule d'origine
    Edith Julia · 2023 · theses.fr (ABES)
44. Resistance pathways and next-generation treatments in chronic lymphocytic leukemia
    Rawane Bellemrrabet, Ezzahra Rachid, Meriem Lahmouad, Youssef Aboussaleh, Waleed Al Abdulmonem, Abdelhakim Bouyahya, Oualid Abboussi, Loubna Amahdar · 2026 · Discover Oncology
45. Repair-associated epigenetic memory: A conceptual framework for persistent chromatin signatures following DNA double-Strand break repair
    Altunbek Burabaev, Assilbek Amirbekovih Burabaev · 2026 · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
46. Epigenetic regulation of humoral immunity: molecular mechanisms, diseases and therapeutic targets
    Shaocun Zhang, Wang Zhi Yu, Xin Min, Yuzhang Wu, Wanli Liu · 2026 · Signal Transduction and Targeted Therapy