Abdel-Hafiz HA, Schafer JM, Chen X, Xiao T, Gauntner TD, Li Z, Theodorescu D (2023) Y chromosome loss in cancer drives growth by evasion of adaptive immunity. Nature 619:624–631. https://doi.org/10.1038/s41586-023-06234-x
Article CAS PubMed PubMed Central Google Scholar
Alfred Witjes J, Lebret T, Compérat EM, Cowan NC, De Santis M, Bruins HM, Hernández V, Espinós EL, Dunn J, Rouanne M, Neuzillet Y, Veskimäe E, van der Heijden AG, Gakis G, Ribal MJ (2017) Updated 2016 EAU Guidelines on Muscle-invasive and Metastatic Bladder Cancer. Eur Urol 71:462–475. https://doi.org/10.1016/j.eururo.2016.06.020
Article CAS PubMed Google Scholar
Butler A, Hoffman P, Smibert P, Papalexi E, Satija R (2018) Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol 36:411–420. https://doi.org/10.1038/nbt.4096
Article CAS PubMed PubMed Central Google Scholar
Advanced Bladder Cancer (ABC) Meta-analysis Collaboration (2005) Neoadjuvant chemotherapy in invasive bladder cancer: update of a systematic review and meta-analysis of individual patient data advanced bladder cancer (ABC) meta-analysis collaboration. Eur Urol 48:202–205. https://doi.org/10.1016/j.eururo.2005.04.006 discussion 205–206
Che D, Liu Q, Rasheed K, Tao X (2011) Decision tree and ensemble learning algorithms with their applications in bioinformatics. Adv Exp Med Biol 696:191–199. https://doi.org/10.1007/978-1-4419-7046-6_19
Article CAS PubMed Google Scholar
Chen S-H, Chang J-Y (2019) New Insights into Mechanisms of Cisplatin Resistance: From Tumor Cell to Microenvironment. Int J Mol Sci 20:4136. https://doi.org/10.3390/ijms20174136
Article CAS PubMed PubMed Central Google Scholar
Choi W, Porten S, Kim S, Willis D, Plimack ER, Hoffman-Censits J, Roth B, Cheng T, Tran M, Lee I-L, Melquist J, Bondaruk J, Majewski T, Zhang S, Pretzsch S, Baggerly K, Siefker-Radtke A, Czerniak B, Dinney CPN, McConkey DJ (2014) Identification of distinct basal and luminal subtypes of muscle-invasive bladder cancer with different sensitivities to frontline chemotherapy. Cancer Cell 25:152–165. https://doi.org/10.1016/j.ccr.2014.01.009
Article CAS PubMed PubMed Central Google Scholar
Fu Y, Zhao J, Wang Y (2025) LASSO regression and Boruta algorithm to explore the relationship between neutrophil percentage to albumin ratio and asthma: results from the NHANES 2001 to 2018. Clin Exp Med 25:149. https://doi.org/10.1007/s10238-025-01701-3
Article PubMed PubMed Central Google Scholar
Gulati GS, Sikandar SS, Wesche DJ, Manjunath A, Bharadwaj A, Berger MJ, Ilagan F, Kuo AH, Hsieh RW, Cai S, Zabala M, Scheeren FA, Lobo NA, Qian D, Yu FB, Dirbas FM, Clarke MF, Newman AM (2020) Single-cell transcriptional diversity is a hallmark of developmental potential. Science 367:405–411. https://doi.org/10.1126/science.aax0249
Article CAS PubMed PubMed Central Google Scholar
Hänzelmann S, Castelo R, Guinney J (2013) BMC Bioinformatics 14:7. https://doi.org/10.1186/1471-2105-14-7. GSVA: gene set variation analysis for microarray and RNA-seq data
Hu J, Szymczak S (2023) A review on longitudinal data analysis with random forest. Brief Bioinform 24:bbad002. https://doi.org/10.1093/bib/bbad002
Article PubMed PubMed Central Google Scholar
Hua C, Zhang G, Yu W, Zhou J, Ru L, Xue G, Zheng L, Wang M, Wang Y, Yu D, Wang Q, Liu J, Wang R, Deng W, Tang R, Guo W (2025) CROT overactivation within peroxisomes confers chemoresistance to non-small cell lung cancer by targeting fatty acid oxidation-Nrf2-ferroptosis resistance axis. Pharmacol Res 220:107911. https://doi.org/10.1016/j.phrs.2025.107911
Article CAS PubMed Google Scholar
Hubert T, Impe KV, Vandekerckhove J, Gettemans J (2009) The actin-capping protein CapG localizes to microtubule-dependent organelles during the cell cycle. Biochem Biophys Res Commun 380:166–170. https://doi.org/10.1016/j.bbrc.2009.01.064
Article CAS PubMed Google Scholar
Iyer G, Hanrahan AJ, Milowsky MI, Al-Ahmadie H, Scott SN, Janakiraman M, Pirun M, Sander C, Socci ND, Ostrovnaya I, Viale A, Heguy A, Peng L, Chan TA, Bochner B, Bajorin DF, Berger MF, Taylor BS, Solit DB (2012) Genome Sequencing Identifies a Basis for Everolimus Sensitivity. Science 338:221–221. https://doi.org/10.1126/science.1226344
Article CAS PubMed PubMed Central Google Scholar
Jin S, Guerrero-Juarez CF, Zhang L, Chang I, Ramos R, Kuan C-H, Myung P, Plikus MV, Nie Q (2021) Inference and analysis of cell-cell communication using CellChat. Nat Commun 12:1088. https://doi.org/10.1038/s41467-021-21246-9
Article CAS PubMed PubMed Central Google Scholar
Jovic D, Liang X, Zeng H, Lin L, Xu F, Luo Y (2022) Single-cell RNA sequencing technologies and applications: A brief overview. Clin Transl Med 12:e694. https://doi.org/10.1002/ctm2.694
Article CAS PubMed PubMed Central Google Scholar
Kamat AM, Hahn NM, Efstathiou JA, Lerner SP, Malmström PU, Choi W, Guo CC, Lotan Y, Kassouf W (2016) Bladder cancer. Lancet (London England) 388. https://doi.org/10.1016/S0140-6736(16)30512-8
Kawahara I, Yoshino H, Fukumoto W, Arima J, Saito S, Li G, Fukuda I, Mitsuke A, Sakaguchi T, Inoguchi S, Matsushita R, Nakagawa M, Tatarano S, Yamada Y, Enokida H (2024) Targeting metabolic reprogramming to overcome drug resistance in advanced bladder cancer: insights from gemcitabine- and cisplatin-resistant models. Mol Oncol 18:2196–2211. https://doi.org/10.1002/1878-0261.13684
Article CAS PubMed PubMed Central Google Scholar
Ke X, Li K, Jiang A, Zhang Y, Wang Q, Li Z, Zhang J, Hajd A, Shi W, Kahlert U, Lin A, Zhang P, Luo P (2025) Cloud-Based GWAS Platform: An Innovative Solution for Efficient Acquisition and Analysis of Genomic Data. Med Res 1:397–411. https://doi.org/10.1002/mdr2.70040
Kim PH, Cha EK, Sfakianos JP, Iyer G, Zabor EC, Scott SN, Ostrovnaya I, Ramirez R, Sun A, Shah R, Yee AM, Reuter VE, Bajorin DF, Rosenberg JE, Schultz N, Berger MF, Al-Ahmadie HA, Solit DB, Bochner BH (2015) Genomic predictors of survival in patients with high-grade urothelial carcinoma of the bladder. Eur Urol 67:198–201. https://doi.org/10.1016/j.eururo.2014.06.050
Korsunsky I, Millard N, Fan J, Slowikowski K, Zhang F, Wei K, Baglaenko Y, Brenner M, Loh P-R, Raychaudhuri S (2019) Fast, sensitive and accurate integration of single-cell data with Harmony. Nat Methods 16:1289–1296. https://doi.org/10.1038/s41592-019-0619-0
Article CAS PubMed PubMed Central Google Scholar
Lai H, Cheng X, Liu Q, Luo W, Liu M, Zhang M, Miao J, Ji Z, Lin GN, Song W, Zhang L, Bo J, Yang G, Wang J, Gao W-Q (2021) Single-cell RNA sequencing reveals the epithelial cell heterogeneity and invasive subpopulation in human bladder cancer. Int J Cancer 149:2099–2115. https://doi.org/10.1002/ijc.33794
Article CAS PubMed Google Scholar
Li F, Zheng Z, Chen W, Li D, Zhang H, Zhu Y, Mo Q, Zhao X, Fan Q, Deng F, Han C, Tan W (2023) Regulation of cisplatin resistance in bladder cancer by epigenetic mechanisms. Drug Resist Updat 68. https://doi.org/10.1016/j.drup.2023.100938
Li C, Hao R, Li C, Liu L, Ding Z (2025) Integration of single-cell and bulk RNA sequencing data using machine learning identifies oxidative stress-related genes LUM and PCOLCE2 as potential biomarkers for heart failure. Int J Biol Macromol 300:140793. https://doi.org/10.1016/j.ijbiomac.2025.140793
Article CAS PubMed Google Scholar
Lopez-Beltran A, Cookson MS, Guercio BJ, Cheng L (2024) Advances in diagnosis and treatment of bladder cancer, BMJ 384. https://doi.org/10.1136/bmj-2023-076743
Luo Y, Tao T, Tao R, Huang G, Wu S (2022) Single-Cell Transcriptome Comparison of Bladder Cancer Reveals Its Ecosystem. Front Oncol 12:818147. https://doi.org/10.3389/fonc.2022.818147
Article CAS PubMed PubMed Central Google Scholar
McConkey DJ, Choi W, Shen Y, Lee I-L, Porten S, Matin SF, Kamat AM, Corn P, Millikan RE, Dinney C, Czerniak B, Siefker-Radtke AO (2016) A Prognostic Gene Expression Signature in the Molecular Classification of Chemotherapy-naïve Urothelial Cancer is Predictive of Clinical Outcomes from Neoadjuvant Chemotherapy: A Phase 2 Trial of Dose-dense Methotrexate, Vinblastine, Doxorubicin, and Cisplatin with Bevacizumab in Urothelial Cancer. Eur Urol 69:855–862. https://doi.org/10.1016/j.eururo.2015.08.034
Article CAS PubMed Google Scholar
Morabito S, Reese F, Rahimzadeh N, Miyoshi E, Swarup V (2023) hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data. Cell Rep Methods 3:100498. https://doi.org/10.1016/j.crmeth.2023.100498
Comments (0)