{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,23]],"date-time":"2026-08-23T14:25:20Z","timestamp":1787495120548,"version":"build-2736575974"},"publisher-location":"New York, NY","reference-count":81,"publisher":"Springer US","isbn-type":[{"value":"9781071642894","type":"print"},{"value":"9781071642900","type":"electronic"}],"license":[{"start":{"date-parts":[[2024,12,20]],"date-time":"2024-12-20T00:00:00Z","timestamp":1734652800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2024,12,20]],"date-time":"2024-12-20T00:00:00Z","timestamp":1734652800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025]]},"DOI":"10.1007\/978-1-0716-4290-0_18","type":"book-chapter","created":{"date-parts":[[2024,12,19]],"date-time":"2024-12-19T14:30:20Z","timestamp":1734618620000},"page":"403-426","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["A Practical Guideline for MicroRNA Sequencing Data Analysis in Chronic Lymphocytic Leukemia"],"prefix":"10.1007","author":[{"given":"Tuulikki","family":"Suomela","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liang","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julio","family":"Vera","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heiko","family":"Bruns","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Lai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,12,20]]},"reference":[{"key":"18_CR1","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1186\/s40164-020-00170-6","volume":"9","author":"Y Dong","year":"2020","unstructured":"Dong Y, Shi O, Zeng Q et al (2020) Leukemia incidence trends at the global, regional, and national level between 1990 and 2017. Exp Hematol Oncol 9:14. https:\/\/doi.org\/10.1186\/s40164-020-00170-6","journal-title":"Exp Hematol Oncol"},{"key":"18_CR2","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1038\/s41408-021-00556-7","volume":"11","author":"H Kaj\u00fcter","year":"2021","unstructured":"Kaj\u00fcter H, Wellmann I, Khil L et al (2021) Survival of patients with chronic lymphocytic leukemia before and after the introduction of chemoimmunotherapy in Germany. Blood Cancer J 11:174. https:\/\/doi.org\/10.1038\/s41408-021-00556-7","journal-title":"Blood Cancer J"},{"key":"18_CR3","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1186\/s13045-016-0257-2","volume":"9","author":"D Pulte","year":"2016","unstructured":"Pulte D, Castro FA, Jansen L et al (2016) Trends in survival of chronic lymphocytic leukemia patients in Germany and the USA in the first decade of the twenty-first century. J Hematol Oncol 9:28. https:\/\/doi.org\/10.1186\/s13045-016-0257-2","journal-title":"J Hematol Oncol"},{"key":"18_CR4","doi-asserted-by":"publisher","first-page":"810","DOI":"10.1002\/eji.200838676","volume":"39","author":"M Trakala","year":"2009","unstructured":"Trakala M, Arias CF, Garc\u00eda MI et al (2009) Regulation of macrophage activation and septic shock susceptibility via p21(WAF1\/CIP1). Eur J Immunol 39:810\u2013819. https:\/\/doi.org\/10.1002\/eji.200838676","journal-title":"Eur J Immunol"},{"key":"18_CR5","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1080\/17474086.2019.1575130","volume":"12","author":"A Condoluci","year":"2019","unstructured":"Condoluci A, Rossi D (2019) Genetic mutations in chronic lymphocytic leukemia: impact on clinical treatment. Expert Rev Hematol 12:89\u201398. https:\/\/doi.org\/10.1080\/17474086.2019.1575130","journal-title":"Expert Rev Hematol"},{"key":"18_CR6","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1053\/j.seminoncol.2016.02.002","volume":"43","author":"NA Amin","year":"2016","unstructured":"Amin NA, Malek SN (2016) Gene mutations in chronic lymphocytic leukemia. Semin Oncol 43:215\u2013221. https:\/\/doi.org\/10.1053\/j.seminoncol.2016.02.002","journal-title":"Semin Oncol"},{"key":"18_CR7","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1016\/j.clml.2023.01.009","volume":"23","author":"B Fakhri","year":"2023","unstructured":"Fakhri B, Danilov A (2023) SOHO state of the art updates and next questions: new targetable pathways in chronic lymphocytic leukemia. Clin Lymphoma Myeloma Leuk 23:232\u2013237. https:\/\/doi.org\/10.1016\/j.clml.2023.01.009","journal-title":"Clin Lymphoma Myeloma Leuk"},{"key":"18_CR8","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1186\/s13045-021-01054-w","volume":"14","author":"K Patel","year":"2021","unstructured":"Patel K, Pagel JM (2021) Current and future treatment strategies in chronic lymphocytic leukemia. J Hematol Oncol 14:69. https:\/\/doi.org\/10.1186\/s13045-021-01054-w","journal-title":"J Hematol Oncol"},{"key":"18_CR9","doi-asserted-by":"publisher","first-page":"816","DOI":"10.1038\/s41576-023-00611-y","volume":"24","author":"R Shang","year":"2023","unstructured":"Shang R, Lee S, Senavirathne G, Lai EC (2023) microRNAs in action: biogenesis, function and regulation. Nat Rev Genet 24:816\u2013833. https:\/\/doi.org\/10.1038\/s41576-023-00611-y","journal-title":"Nat Rev Genet"},{"key":"18_CR10","doi-asserted-by":"publisher","first-page":"1310","DOI":"10.1007\/978-1-4419-9863-7_1121","volume-title":"Encyclopedia of systems biology","author":"X Lai","year":"2013","unstructured":"Lai X, Vera J (2013) MicroRNA clusters. In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H (eds) Encyclopedia of systems biology. Springer, New York, pp 1310\u20131314. https:\/\/doi.org\/10.1007\/978-1-4419-9863-7_1121"},{"key":"18_CR11","doi-asserted-by":"publisher","first-page":"6066","DOI":"10.3390\/ijms25116066","volume":"25","author":"M Billi","year":"2024","unstructured":"Billi M, De Marinis E, Gentile M et al (2024) Nuclear miRNAs: gene regulation activities. Int J Mol Sci 25:6066. https:\/\/doi.org\/10.3390\/ijms25116066","journal-title":"Int J Mol Sci"},{"key":"18_CR12","doi-asserted-by":"publisher","first-page":"613","DOI":"10.1016\/j.tig.2022.02.006","volume":"38","author":"C Diener","year":"2022","unstructured":"Diener C, Keller A, Meese E (2022) Emerging concepts of miRNA therapeutics: from cells to clinic. Trends Genet 38:613\u2013626. https:\/\/doi.org\/10.1016\/j.tig.2022.02.006","journal-title":"Trends Genet"},{"key":"18_CR13","doi-asserted-by":"publisher","first-page":"7753","DOI":"10.1093\/nar\/gkz638","volume":"47","author":"X Lai","year":"2019","unstructured":"Lai X, Eberhardt M, Schmitz U, Vera J (2019) Systems biology-based investigation of cooperating microRNAs as monotherapy or adjuvant therapy in cancer. Nucleic Acids Res 47:7753\u20137766. https:\/\/doi.org\/10.1093\/nar\/gkz638","journal-title":"Nucleic Acids Res"},{"key":"18_CR14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-3-031-08356-3_1","volume":"1385","author":"X Lai","year":"2022","unstructured":"Lai X, Schmitz U, Vera J (2022) The role of microRNAs in cancer biology and therapy from a systems biology perspective. Adv Exp Med Biol 1385:1\u201322. https:\/\/doi.org\/10.1007\/978-3-031-08356-3_1","journal-title":"Adv Exp Med Biol"},{"key":"18_CR15","doi-asserted-by":"publisher","DOI":"10.1155\/2013\/703849","volume":"2013","author":"X Lai","year":"2013","unstructured":"Lai X, Bhattacharya A, Schmitz U et al (2013) A systems\u2019 biology approach to study microRNA-mediated gene regulatory networks. Biomed Res Int 2013:703849. https:\/\/doi.org\/10.1155\/2013\/703849","journal-title":"Biomed Res Int"},{"key":"18_CR16","doi-asserted-by":"publisher","first-page":"509","DOI":"10.3390\/cancers14030509","volume":"14","author":"V Balatti","year":"2022","unstructured":"Balatti V, Croce CM (2022) Small non-coding RNAs in leukemia. Cancers (Basel) 14:509. https:\/\/doi.org\/10.3390\/cancers14030509","journal-title":"Cancers (Basel)"},{"key":"18_CR17","doi-asserted-by":"publisher","DOI":"10.1016\/j.prp.2023.154363","volume":"243","author":"AS Doghish","year":"2023","unstructured":"Doghish AS, Abulsoud AI, Elshaer SS et al (2023) miRNAs as cornerstones in chronic lymphocytic leukemia pathogenesis and therapeutic resistance \u2013 an emphasis on the interaction of signaling pathways. Pathol Res Pract 243:154363. https:\/\/doi.org\/10.1016\/j.prp.2023.154363","journal-title":"Pathol Res Pract"},{"key":"18_CR18","doi-asserted-by":"publisher","unstructured":"Sajjadi-Dokht M, Mohamad TAM, Rahman HS et al (2022) MicroRNAs and JAK\/STAT3 signaling: A new promising therapeutic axis in blood cancers. Genes Dis 9:849\u2013867. https:\/\/doi.org\/10.1016\/j.gendis.2021.10.009","DOI":"10.1016\/j.gendis.2021.10.009"},{"key":"18_CR19","doi-asserted-by":"publisher","first-page":"13944","DOI":"10.1073\/pnas.0506654102","volume":"102","author":"A Cimmino","year":"2005","unstructured":"Cimmino A, Calin GA, Fabbri M et al (2005) miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc Natl Acad Sci USA 102:13944\u201313949. https:\/\/doi.org\/10.1073\/pnas.0506654102","journal-title":"Proc Natl Acad Sci USA"},{"key":"18_CR20","doi-asserted-by":"publisher","first-page":"2589","DOI":"10.1182\/blood-2009-05-224071","volume":"114","author":"T Zenz","year":"2009","unstructured":"Zenz T, H\u00e4be S, Denzel T et al (2009) Detailed analysis of p53 pathway defects in fludarabine-refractory chronic lymphocytic leukemia (CLL): dissecting the contribution of 17p deletion, TP53 mutation, p53-p21 dysfunction, and miR34a in a prospective clinical trial. Blood 114:2589\u20132597. https:\/\/doi.org\/10.1182\/blood-2009-05-224071","journal-title":"Blood"},{"key":"18_CR21","doi-asserted-by":"publisher","first-page":"3872","DOI":"10.1182\/blood-2009-06-229211","volume":"114","author":"R Visone","year":"2009","unstructured":"Visone R, Rassenti LZ, Veronese A et al (2009) Karyotype-specific microRNA signature in chronic lymphocytic leukemia. Blood 114:3872\u20133879. https:\/\/doi.org\/10.1182\/blood-2009-06-229211","journal-title":"Blood"},{"key":"18_CR22","doi-asserted-by":"publisher","first-page":"1106","DOI":"10.1182\/blood-2014-12-618025","volume":"126","author":"J Paggetti","year":"2015","unstructured":"Paggetti J, Haderk F, Seiffert M et al (2015) Exosomes released by chronic lymphocytic leukemia cells induce the transition of stromal cells into cancer-associated fibroblasts. Blood 126:1106\u20131117. https:\/\/doi.org\/10.1182\/blood-2014-12-618025","journal-title":"Blood"},{"key":"18_CR23","doi-asserted-by":"publisher","first-page":"2179","DOI":"10.1182\/blood-2018-04-845115","volume":"132","author":"V Balatti","year":"2018","unstructured":"Balatti V, Tomasello L, Rassenti LZ et al (2018) miR-125a and miR-34a expression predicts Richter syndrome in chronic lymphocytic leukemia patients. Blood 132:2179\u20132182. https:\/\/doi.org\/10.1182\/blood-2018-04-845115","journal-title":"Blood"},{"key":"18_CR24","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1038\/nrd.2016.246","volume":"16","author":"R Rupaimoole","year":"2017","unstructured":"Rupaimoole R, Slack FJ (2017) MicroRNA therapeutics: towards a new era for the management of cancer and other diseases. Nat Rev Drug Discov 16:203. https:\/\/doi.org\/10.1038\/nrd.2016.246","journal-title":"Nat Rev Drug Discov"},{"key":"18_CR25","doi-asserted-by":"publisher","first-page":"759","DOI":"10.1038\/nrd4278","volume":"13","author":"U Sahin","year":"2014","unstructured":"Sahin U, Karik\u00f3 K, T\u00fcreci \u00d6 (2014) mRNA-based therapeutics--developing a new class of drugs. Nat Rev Drug Discov 13:759\u2013780. https:\/\/doi.org\/10.1038\/nrd4278","journal-title":"Nat Rev Drug Discov"},{"key":"18_CR26","doi-asserted-by":"publisher","DOI":"10.1016\/j.ocarto.2020.100131","volume":"3","author":"P Potla","year":"2021","unstructured":"Potla P, Ali SA, Kapoor M (2021) A bioinformatics approach to microRNA-sequencing analysis. Osteoarthr Cartil Open 3:100131. https:\/\/doi.org\/10.1016\/j.ocarto.2020.100131","journal-title":"Osteoarthr Cartil Open"},{"key":"18_CR27","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1038\/s41408-019-0272-y","volume":"10","author":"G Kaur","year":"2020","unstructured":"Kaur G, Ruhela V, Rani L et al (2020) RNA-Seq profiling of deregulated miRs in CLL and their impact on clinical outcome. Blood Cancer J 10:6. https:\/\/doi.org\/10.1038\/s41408-019-0272-y","journal-title":"Blood Cancer J"},{"key":"18_CR28","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1186\/s13059-018-1588-9","volume":"19","author":"W Kang","year":"2018","unstructured":"Kang W, Eldfjell Y, Fromm B et al (2018) miRTrace reveals the organismal origins of microRNA sequencing data. Genome Biol 19:213. https:\/\/doi.org\/10.1186\/s13059-018-1588-9","journal-title":"Genome Biol"},{"key":"18_CR29","doi-asserted-by":"publisher","first-page":"10","DOI":"10.14806\/ej.17.1.200","volume":"17","author":"M Martin","year":"2011","unstructured":"Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17:10\u201312. https:\/\/doi.org\/10.14806\/ej.17.1.200","journal-title":"EMBnet J"},{"key":"18_CR30","doi-asserted-by":"publisher","first-page":"D155","DOI":"10.1093\/nar\/gky1141","volume":"47","author":"A Kozomara","year":"2019","unstructured":"Kozomara A, Birgaoanu M, Griffiths-Jones S (2019) miRBase: from microRNA sequences to function. Nucleic Acids Res 47:D155\u2013D162. https:\/\/doi.org\/10.1093\/nar\/gky1141","journal-title":"Nucleic Acids Res"},{"key":"18_CR31","doi-asserted-by":"publisher","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","volume":"10","author":"B Langmead","year":"2009","unstructured":"Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25. https:\/\/doi.org\/10.1186\/gb-2009-10-3-r25","journal-title":"Genome Biol"},{"key":"18_CR32","doi-asserted-by":"publisher","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","volume":"10","author":"P Danecek","year":"2021","unstructured":"Danecek P, Bonfield JK, Liddle J et al (2021) Twelve years of SAMtools and BCFtools. Gigascience 10:giab008. https:\/\/doi.org\/10.1093\/gigascience\/giab008","journal-title":"Gigascience"},{"key":"18_CR33","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","volume":"26","author":"MD Robinson","year":"2010","unstructured":"Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139\u2013140. https:\/\/doi.org\/10.1093\/bioinformatics\/btp616","journal-title":"Bioinformatics"},{"key":"18_CR34","doi-asserted-by":"publisher","first-page":"776","DOI":"10.1093\/bib\/bbx008","volume":"19","author":"C Evans","year":"2018","unstructured":"Evans C, Hardin J, Stoebel DM (2018) Selecting between-sample RNA-seq normalization methods from the perspective of their assumptions. Brief Bioinform 19:776\u2013792. https:\/\/doi.org\/10.1093\/bib\/bbx008","journal-title":"Brief Bioinform"},{"key":"18_CR35","doi-asserted-by":"publisher","first-page":"3470","DOI":"10.1016\/j.csbj.2021.05.040","volume":"19","author":"A Stupnikov","year":"2021","unstructured":"Stupnikov A, McInerney CE, Savage KI et al (2021) Robustness of differential gene expression analysis of RNA-seq. Comput Struct Biotechnol J 19:3470\u20133481. https:\/\/doi.org\/10.1016\/j.csbj.2021.05.040","journal-title":"Comput Struct Biotechnol J"},{"key":"18_CR36","doi-asserted-by":"publisher","first-page":"D304","DOI":"10.1093\/nar\/gkad1071","volume":"52","author":"G Skoufos","year":"2024","unstructured":"Skoufos G, Kakoulidis P, Tastsoglou S et al (2024) TarBase-v9.0 extends experimentally supported miRNA-gene interactions to cell-types and virally encoded miRNAs. Nucleic Acids Res 52:D304\u2013D310. https:\/\/doi.org\/10.1093\/nar\/gkad1071","journal-title":"Nucleic Acids Res"},{"key":"18_CR37","doi-asserted-by":"publisher","first-page":"W148","DOI":"10.1093\/nar\/gkad283","volume":"51","author":"S Tastsoglou","year":"2023","unstructured":"Tastsoglou S, Alexiou A, Karagkouni D et al (2023) DIANA-microT 2023: including predicted targets of virally encoded miRNAs. Nucleic Acids Res 51:W148\u2013W153. https:\/\/doi.org\/10.1093\/nar\/gkad283","journal-title":"Nucleic Acids Res"},{"key":"18_CR38","doi-asserted-by":"publisher","first-page":"1622","DOI":"10.1182\/blood.V112.11.1622.1622","volume":"112","author":"M Shehata","year":"2008","unstructured":"Shehata M, Demirtas D, Tauber S et al (2008) Identification of genes associated with resistance and response in vivo to therapy with rituximab, fludarabine and cyclophosphamide in patients with chronic lymphocytic leukemia. Blood 112:1622. https:\/\/doi.org\/10.1182\/blood.V112.11.1622.1622","journal-title":"Blood"},{"key":"18_CR39","doi-asserted-by":"publisher","first-page":"11673","DOI":"10.1093\/nar\/gks901","volume":"40","author":"CE Vejnar","year":"2012","unstructured":"Vejnar CE, Zdobnov EM (2012) MiRmap: comprehensive prediction of microRNA target repression strength. Nucleic Acids Res 40:11673\u201311683. https:\/\/doi.org\/10.1093\/nar\/gks901","journal-title":"Nucleic Acids Res"},{"key":"18_CR40","doi-asserted-by":"publisher","first-page":"654","DOI":"10.3389\/fgene.2020.00654","volume":"11","author":"F Maleki","year":"2020","unstructured":"Maleki F, Ovens K, Hogan DJ, Kusalik AJ (2020) Gene set analysis: challenges, opportunities, and future research. Front Genet 11:654. https:\/\/doi.org\/10.3389\/fgene.2020.00654","journal-title":"Front Genet"},{"key":"18_CR41","doi-asserted-by":"publisher","first-page":"300","DOI":"10.1016\/j.bbcan.2016.10.002","volume":"1866","author":"O Menyh\u00e1rt","year":"2016","unstructured":"Menyh\u00e1rt O, Harami-Papp H, Sukumar S et al (2016) Guidelines for the selection of functional assays to evaluate the hallmarks of cancer. Biochim Biophys Acta 1866:300\u2013319. https:\/\/doi.org\/10.1016\/j.bbcan.2016.10.002","journal-title":"Biochim Biophys Acta"},{"key":"18_CR42","doi-asserted-by":"publisher","first-page":"D20","DOI":"10.1093\/nar\/gkab1112","volume":"50","author":"EW Sayers","year":"2022","unstructured":"Sayers EW, Bolton EE, Brister JR et al (2022) Database resources of the national center for biotechnology information. Nucleic Acids Res 50:D20\u2013D26. https:\/\/doi.org\/10.1093\/nar\/gkab1112","journal-title":"Nucleic Acids Res"},{"key":"18_CR43","doi-asserted-by":"publisher","unstructured":"Wijesooriya K, Jadaan SA, Perera KL et al (2021) Guidelines for reliable and reproducible functional enrichment analysis. bioRxiv:1\u201321. https:\/\/doi.org\/10.1101\/2021.09.06.459114","DOI":"10.1101\/2021.09.06.459114"},{"key":"18_CR44","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.43","volume":"1","author":"Z Gu","year":"2022","unstructured":"Gu Z (2022) Complex heatmap visualization. iMeta 1:e43. https:\/\/doi.org\/10.1002\/imt2.43","journal-title":"iMeta"},{"key":"18_CR45","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A, Ozier O et al (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498\u20132504. https:\/\/doi.org\/10.1101\/gr.1239303","journal-title":"Genome Res"},{"key":"18_CR46","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1016\/j.cell.2011.02.013","volume":"144","author":"D Hanahan","year":"2011","unstructured":"Hanahan D, Weinberg RA (2011) Hallmarks of cancer: the next generation. Cell 144:646\u2013674. https:\/\/doi.org\/10.1016\/j.cell.2011.02.013","journal-title":"Cell"},{"key":"18_CR47","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1159\/000334577","volume":"81","author":"JC Wang","year":"2011","unstructured":"Wang JC, Kafeel MI, Avezbakiyev B et al (2011) Histone deacetylase in chronic lymphocytic leukemia. Oncology 81:325\u2013329. https:\/\/doi.org\/10.1159\/000334577","journal-title":"Oncology"},{"key":"18_CR48","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1007\/978-1-61779-833-7_6","volume":"880","author":"X Lai","year":"2012","unstructured":"Lai X, Wolkenhauer O, Vera J (2012) Modeling miRNA regulation in cancer signaling systems: miR-34a regulation of the p53\/Sirt1 signaling module. Methods Mol Biol 880:87\u2013108. https:\/\/doi.org\/10.1007\/978-1-61779-833-7_6","journal-title":"Methods Mol Biol"},{"key":"18_CR49","doi-asserted-by":"publisher","first-page":"300","DOI":"10.1080\/15384047.2016.1139246","volume":"17","author":"S Bhalla","year":"2016","unstructured":"Bhalla S, Gordon LI (2016) Functional characterization of NAD dependent de-acetylases SIRT1 and SIRT2 in B-Cell Chronic Lymphocytic Leukemia (CLL). Cancer Biol Ther 17:300\u2013309. https:\/\/doi.org\/10.1080\/15384047.2016.1139246","journal-title":"Cancer Biol Ther"},{"key":"18_CR50","doi-asserted-by":"publisher","first-page":"3158","DOI":"10.1182\/blood.V84.9.3158.3158","volume":"84","author":"T Watanabe","year":"1994","unstructured":"Watanabe T, Hotta T, Ichikawa A et al (1994) The MDM2 oncogene overexpression in chronic lymphocytic leukemia and low-grade lymphoma of B-cell origin. Blood 84:3158\u20133165","journal-title":"Blood"},{"key":"18_CR51","doi-asserted-by":"publisher","first-page":"1880","DOI":"10.3324\/haematol.2010.025734","volume":"95","author":"D Winkler","year":"2010","unstructured":"Winkler D, Schneider C, Zucknick M et al (2010) Protein expression analysis of chronic lymphocytic leukemia defines the effect of genetic aberrations and uncovers a correlation of CDK4, P27 and P53 with hierarchical risk. Haematologica 95:1880\u20131888. https:\/\/doi.org\/10.3324\/haematol.2010.025734","journal-title":"Haematologica"},{"key":"18_CR52","doi-asserted-by":"publisher","first-page":"1469","DOI":"10.1056\/NEJMp078126","volume":"357","author":"J Gearhart","year":"2007","unstructured":"Gearhart J, Pashos EE, Prasad MK (2007) Pluripotency redux--advances in stem-cell research. N Engl J Med 357:1469\u20131472. https:\/\/doi.org\/10.1056\/NEJMp078126","journal-title":"N Engl J Med"},{"key":"18_CR53","doi-asserted-by":"publisher","first-page":"4694","DOI":"10.18632\/oncotarget.2100","volume":"5","author":"JM Caraballo","year":"2014","unstructured":"Caraballo JM, Acosta JC, Cort\u00e9s MA et al (2014) High p27 protein levels in chronic lymphocytic leukemia are associated to low Myc and Skp2 expression, confer resistance to apoptosis and antagonize Myc effects on cell cycle. Oncotarget 5:4694\u20134708. https:\/\/doi.org\/10.18632\/oncotarget.2100","journal-title":"Oncotarget"},{"key":"18_CR54","doi-asserted-by":"publisher","first-page":"60","DOI":"10.32471\/exp-oncology.2312-8852.vol-42-no-1.14214","volume":"42","author":"N Bilous","year":"2020","unstructured":"Bilous N, Abramenko I, Chumak A et al (2020) MYC copy number and mRNA expression in chronic lymphocytic leukemia patients exposed to ionizing radiation due to the Chornobyl NPP accident. Exp Oncol 42:60\u201365. https:\/\/doi.org\/10.32471\/exp-oncology.2312-8852.vol-42-no-1.14214","journal-title":"Exp Oncol"},{"key":"18_CR55","doi-asserted-by":"publisher","first-page":"2931","DOI":"10.1182\/blood-2016-04-712562","volume":"128","author":"B Cui","year":"2016","unstructured":"Cui B, Ghia EM, Chen L et al (2016) High-level ROR1 associates with accelerated disease progression in chronic lymphocytic leukemia. Blood 128:2931\u20132940. https:\/\/doi.org\/10.1182\/blood-2016-04-712562","journal-title":"Blood"},{"key":"18_CR56","doi-asserted-by":"publisher","first-page":"101042831769455","DOI":"10.1177\/1010428317694551","volume":"39","author":"M Witkowska","year":"2017","unstructured":"Witkowska M, Majchrzak A, Cebula-Obrzut B et al (2017) The distribution and potential prognostic value of SMAD protein expression in chronic lymphocytic leukemia. Tumour Biol 39:1010428317694551. https:\/\/doi.org\/10.1177\/1010428317694551","journal-title":"Tumour Biol"},{"key":"18_CR57","doi-asserted-by":"publisher","first-page":"244","DOI":"10.15252\/embr.201744311","volume":"19","author":"P Brauns-Schubert","year":"2018","unstructured":"Brauns-Schubert P, Schubert F, Wissler M et al (2018) CDK9-mediated phosphorylation controls the interaction of TIP60 with the transcriptional machinery. EMBO Rep 19:244\u2013256. https:\/\/doi.org\/10.15252\/embr.201744311","journal-title":"EMBO Rep"},{"key":"18_CR58","doi-asserted-by":"publisher","first-page":"194","DOI":"10.1038\/38304","volume":"389","author":"TE Spencer","year":"1997","unstructured":"Spencer TE, Jenster G, Burcin MM et al (1997) Steroid receptor coactivator-1 is a histone acetyltransferase. Nature 389:194\u2013198. https:\/\/doi.org\/10.1038\/38304","journal-title":"Nature"},{"key":"18_CR59","doi-asserted-by":"publisher","first-page":"jcs260723","DOI":"10.1242\/jcs.260723","volume":"136","author":"BW Walters","year":"2023","unstructured":"Walters BW, Tan TJ, Tan CT et al (2023) Divergent functions of histone acetyltransferases KAT2A and KAT2B in keratinocyte self-renewal and differentiation. J Cell Sci 136:jcs260723. https:\/\/doi.org\/10.1242\/jcs.260723","journal-title":"J Cell Sci"},{"key":"18_CR60","doi-asserted-by":"publisher","first-page":"3274","DOI":"10.18632\/oncotarget.13712","volume":"8","author":"V Griggio","year":"2017","unstructured":"Griggio V, Mandili G, Vitale C et al (2017) Humoral immune responses toward tumor-derived antigens in previously untreated patients with chronic lymphocytic leukemia. Oncotarget 8:3274\u20133288. https:\/\/doi.org\/10.18632\/oncotarget.13712","journal-title":"Oncotarget"},{"key":"18_CR61","doi-asserted-by":"publisher","first-page":"5793","DOI":"10.1182\/blood-2023-185189","volume":"142","author":"J Gu","year":"2023","unstructured":"Gu J, Mavis C, Wang JC et al (2023) Novel drug to target HK2 overcomes therapeutic resistance in preclinical B-cell lymphoma models. Blood 142:5793. https:\/\/doi.org\/10.1182\/blood-2023-185189","journal-title":"Blood"},{"key":"18_CR62","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1016\/j.trecan.2016.02.005","volume":"2","author":"V Balatti","year":"2016","unstructured":"Balatti V, Acunzo M, Pekarky Y, Croce CM (2016) Novel mechanisms of regulation of miRNAs in CLL. Trends Cancer 2:134\u2013143. https:\/\/doi.org\/10.1016\/j.trecan.2016.02.005","journal-title":"Trends Cancer"},{"key":"18_CR63","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/s13045-015-0112-x","volume":"8","author":"V Balatti","year":"2015","unstructured":"Balatti V, Pekarky Y, Croce CM (2015) Role of microRNA in chronic lymphocytic leukemia onset and progression. J Hematol Oncol 8:12. https:\/\/doi.org\/10.1186\/s13045-015-0112-x","journal-title":"J Hematol Oncol"},{"key":"18_CR64","doi-asserted-by":"publisher","first-page":"1314","DOI":"10.1038\/s12276-023-01050-9","volume":"55","author":"T Kim","year":"2023","unstructured":"Kim T, Croce CM (2023) MicroRNA: trends in clinical trials of cancer diagnosis and therapy strategies. Exp Mol Med 55:1314\u20131321. https:\/\/doi.org\/10.1038\/s12276-023-01050-9","journal-title":"Exp Mol Med"},{"key":"18_CR65","doi-asserted-by":"publisher","first-page":"8818","DOI":"10.1093\/nar\/gks657","volume":"40","author":"X Lai","year":"2012","unstructured":"Lai X, Schmitz U, Gupta SK et al (2012) Computational analysis of target hub gene repression regulated by multiple and cooperative miRNAs. Nucleic Acids Res 40:8818\u20138834. https:\/\/doi.org\/10.1093\/nar\/gks657","journal-title":"Nucleic Acids Res"},{"key":"18_CR66","doi-asserted-by":"publisher","first-page":"1106","DOI":"10.7150\/thno.19904","volume":"8","author":"X Lai","year":"2018","unstructured":"Lai X, Gupta SK, Schmitz U et al (2018) MiR-205-5p and miR-342-3p cooperate in the repression of the E2F1 transcription factor in the context of anticancer chemotherapy resistance. Theranostics 8:1106\u20131120. https:\/\/doi.org\/10.7150\/thno.19904","journal-title":"Theranostics"},{"key":"18_CR67","doi-asserted-by":"publisher","first-page":"7539","DOI":"10.1093\/nar\/gku465","volume":"42","author":"U Schmitz","year":"2014","unstructured":"Schmitz U, Lai X, Winter F et al (2014) Cooperative gene regulation by microRNA pairs and their identification using a computational workflow. Nucleic Acids Res 42:7539\u20137552. https:\/\/doi.org\/10.1093\/nar\/gku465","journal-title":"Nucleic Acids Res"},{"key":"18_CR68","doi-asserted-by":"publisher","first-page":"1412","DOI":"10.7150\/thno.53092","volume":"11","author":"X Lai","year":"2021","unstructured":"Lai X, Dreyer FS, Cantone M et al (2021) Network- and systems-based re-engineering of dendritic cells with non-coding RNAs for cancer immunotherapy. Theranostics 11:1412\u20131428. https:\/\/doi.org\/10.7150\/thno.53092","journal-title":"Theranostics"},{"key":"18_CR69","doi-asserted-by":"publisher","first-page":"467","DOI":"10.3390\/biology12030467","volume":"12","author":"SS Shinde","year":"2023","unstructured":"Shinde SS, Ahmed S, Malik JA et al (2023) Therapeutic delivery of tumor suppressor miRNAs for breast cancer treatment. Biology (Basel) 12:467. https:\/\/doi.org\/10.3390\/biology12030467","journal-title":"Biology (Basel)"},{"key":"18_CR70","doi-asserted-by":"publisher","first-page":"1208547","DOI":"10.3389\/fbioe.2023.1208547","volume":"11","author":"LA Bravo-V\u00e1zquez","year":"2023","unstructured":"Bravo-V\u00e1zquez LA, M\u00e9ndez-Garc\u00eda A, Rodr\u00edguez AL et al (2023) Applications of nanotechnologies for miRNA-based cancer therapeutics: current advances and future perspectives. Front Bioeng Biotechnol 11:1208547. https:\/\/doi.org\/10.3389\/fbioe.2023.1208547","journal-title":"Front Bioeng Biotechnol"},{"key":"18_CR71","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1186\/s12864-018-4726-6","volume":"19","author":"A Yeri","year":"2018","unstructured":"Yeri A, Courtright A, Danielson K et al (2018) Evaluation of commercially available small RNASeq library preparation kits using low input RNA. BMC Genomics 19:331. https:\/\/doi.org\/10.1186\/s12864-018-4726-6","journal-title":"BMC Genomics"},{"key":"18_CR72","doi-asserted-by":"publisher","first-page":"1898","DOI":"10.3390\/jcm13071898","volume":"13","author":"M Polak","year":"2024","unstructured":"Polak M, Wieczorek J, Botor M et al (2024) Principles and limitations of miRNA purification and analysis in whole blood collected during ablation procedure from patients with atrial fibrillation. J Clin Med 13:1898. https:\/\/doi.org\/10.3390\/jcm13071898","journal-title":"J Clin Med"},{"key":"18_CR73","doi-asserted-by":"publisher","first-page":"466","DOI":"10.1182\/hematology.2019000367","volume":"2019","author":"C Gutierrez","year":"2019","unstructured":"Gutierrez C, Wu CJ (2019) Clonal dynamics in chronic lymphocytic leukemia. Hematology Am Soc Hematol Educ Program 2019:466\u2013475. https:\/\/doi.org\/10.1182\/hematology.2019000367","journal-title":"Hematology Am Soc Hematol Educ Program"},{"key":"18_CR74","doi-asserted-by":"publisher","first-page":"1446","DOI":"10.1182\/blood-2018-09-835389","volume":"133","author":"SH Gohil","year":"2019","unstructured":"Gohil SH, Wu CJ (2019) Dissecting CLL through high-dimensional single-cell technologies. Blood 133:1446\u20131456. https:\/\/doi.org\/10.1182\/blood-2018-09-835389","journal-title":"Blood"},{"key":"18_CR75","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1186\/s13148-018-0587-8","volume":"11","author":"W Si","year":"2019","unstructured":"Si W, Shen J, Zheng H, Fan W (2019) The role and mechanisms of action of microRNAs in cancer drug resistance. Clin Epigenetics 11:25. https:\/\/doi.org\/10.1186\/s13148-018-0587-8","journal-title":"Clin Epigenetics"},{"key":"18_CR76","doi-asserted-by":"publisher","first-page":"4657","DOI":"10.3390\/ijms23094657","volume":"23","author":"Y Sbirkov","year":"2022","unstructured":"Sbirkov Y, Vergov B, Mehterov N, Sarafian V (2022) miRNAs in lymphocytic leukaemias-the miRror of drug resistance. Int J Mol Sci 23:4657. https:\/\/doi.org\/10.3390\/ijms23094657","journal-title":"Int J Mol Sci"},{"key":"18_CR77","doi-asserted-by":"publisher","first-page":"234","DOI":"10.1101\/gr.205146.116","volume":"27","author":"N Pinz\u00f3n","year":"2017","unstructured":"Pinz\u00f3n N, Li B, Martinez L et al (2017) microRNA target prediction programs predict many false positives. Genome Res 27:234\u2013245. https:\/\/doi.org\/10.1101\/gr.205146.116","journal-title":"Genome Res"},{"key":"18_CR78","doi-asserted-by":"publisher","first-page":"1740","DOI":"10.1016\/j.csbj.2024.04.015","volume":"23","author":"S Bader","year":"2024","unstructured":"Bader S, Tuller T (2024) Advanced computational predictive models of miRNA-mRNA interaction efficiency. Comput Struct Biotechnol J 23:1740\u20131754. https:\/\/doi.org\/10.1016\/j.csbj.2024.04.015","journal-title":"Comput Struct Biotechnol J"},{"key":"18_CR79","doi-asserted-by":"publisher","first-page":"1732","DOI":"10.1111\/jphp.13351","volume":"72","author":"V Shah","year":"2020","unstructured":"Shah V, Shah J (2020) Recent trends in targeting miRNAs for cancer therapy. J Pharm Pharmacol 72:1732\u20131749. https:\/\/doi.org\/10.1111\/jphp.13351","journal-title":"J Pharm Pharmacol"},{"key":"18_CR80","doi-asserted-by":"publisher","first-page":"12471","DOI":"10.3390\/ijms241512471","volume":"24","author":"F Autore","year":"2023","unstructured":"Autore F, Ramassone A, Stirparo L et al (2023) Role of microRNAs in chronic lymphocytic leukemia. Int J Mol Sci 24:12471. https:\/\/doi.org\/10.3390\/ijms241512471","journal-title":"Int J Mol Sci"},{"key":"18_CR81","doi-asserted-by":"publisher","unstructured":"Bruns H, B\u00f6ttcher M, Qorraj M, Fabri M, Jitschin S, Dindorf J, Busch L, Jitschin R, Mackensen A, Mougiakakos D (2017) CLL-cell-mediated MDSC induction by exosomal miR-155 transfer is disrupted by vitamin. D Leukemia 31(4):985\u2013988. https:\/\/doi.org\/10.1038\/leu.2016.378","DOI":"10.1038\/leu.2016.378"}],"container-title":["Methods in Molecular Biology","Computational Biology of Non-Coding RNA"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-1-0716-4290-0_18","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,6]],"date-time":"2025-02-06T15:25:17Z","timestamp":1738855517000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-1-0716-4290-0_18"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,12,20]]},"ISBN":["9781071642894","9781071642900"],"references-count":81,"URL":"https:\/\/doi.org\/10.1007\/978-1-0716-4290-0_18","relation":{},"ISSN":["1064-3745","1940-6029"],"issn-type":[{"value":"1064-3745","type":"print"},{"value":"1940-6029","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,12,20]]},"assertion":[{"value":"20 December 2024","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}}]}}