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Hashemi Gheinani, Ali; Kim, Jina; You, Sungyong; Adam, Rosalyn M (2024). Bioinformatics in urology - molecular characterization of pathophysiology and response to treatment. Nature Reviews. Urology, 21(4), pp. 214-242. Nature Publishing Group 10.1038/s41585-023-00805-3
Bigger-Allen, Alexander; Hashemi Gheinani, Ali; Adam, Rosalyn M (2024). Investigation of the impact of bromodomain inhibition on cytoskeleton stability and contraction. Cell communication and signaling, 22(1) BioMed Central 10.1186/s12964-024-01553-6
Akshay, Akshay; Hashemi Gheinani, Ali; Besic, Mustafa; Braga, Sophie; Uldry, Anne-Christine; Heller, Manfred; Rehrauer, Hubert; Fournier, Catharine Aquino; Burkhard, Fiona C; Monastyrskaya, Katia (2024). De-obstruction of bladder outlet in humans reverses organ remodelling by normalizing the expression of key transcription factors. BMC urology, 24(33) BMC 10.1186/s12894-024-01417-8
Akshay, Akshay; Besic, Mustafa; Kuhn, Annette; Burkhard, Fiona C; Bigger-Allen, Alex; Adam, Rosalyn M; Monastyrskaya, Katia; Hashemi Gheinani, Ali (2024). Machine Learning-Based Classification of Transcriptome Signatures of Non-Ulcerative Bladder Pain Syndrome. International journal of molecular sciences, 25(3) MDPI 10.3390/ijms25031568
Akshay, Akshay; Katoch, Mitali; Shekarchizadeh, Navid; Abedi, Masoud; Sharma, Ankush; Burkhard, Fiona C; Adam, Rosalyn M; Monastyrskaya, Katia; Hashemi Gheinani, Ali (2024). Machine Learning Made Easy (MLme): a comprehensive toolkit for machine learning-driven data analysis. GigaScience, 13, pp. 1-9. Oxford University Press 10.1093/gigascience/giad111
Kashani, Elham; Schnidrig, Désirée; Hashemi Gheinani, Ali; Ninck, Martina Selina; Zens, Philipp; Maragkou, Theoni; Baumgartner, Ulrich; Schucht, Philippe; Rätsch, Gunnar; Rubin, Mark A; Berezowska, Sabina; Ng, Charlotte K Y; Vassella, Erik (2023). Integrated longitudinal analysis of adult grade 4 diffuse gliomas with long-term relapse interval revealed upregulation of TGF-β signaling in recurrent tumors. Neuro-Oncology, 25(4), pp. 662-673. Oxford University Press 10.1093/neuonc/noac220
von Siebenthal, Michelle; Akshay, Akshay; Besic, Mustafa; Schneider, Marc P; Hashemi Gheinani, Ali; Burkhard, Fiona C; Monastyrskaya, Katia (2023). Molecular Characterization of Non-Neurogenic and Neurogenic Lower Urinary Tract Dysfunction (LUTD) in SCI-Induced and Partial Bladder Outlet Obstruction Mouse Models. International journal of molecular sciences, 24(3) MDPI 10.3390/ijms24032451
Akshay, Akshay; Katoch, Mitali; Abedi, Masoud; Shekarchizadeh, Navid; Besic, Mustafa; Burkhard, Fiona C; Bigger-Allen, Alex; Adam, Rosalyn M; Monastyrskaya, Katia; Hashemi Gheinani, Ali (2022). SpheroScan: a user-friendly deep learning tool for spheroid image analysis. GigaScience, 12 Oxford University Press 10.1093/gigascience/giad082
Akshay, Akshay; Abedi, Masoud; Shekarchizadeh, Navid; Burkhard, Fiona C; Katoch, Mitali; Bigger-Allen, Alex; Adam, Rosalyn M; Monastyrskaya, Katia; Hashemi Gheinani, Ali (2022). MLcps: machine learning cumulative performance score for classification problems. GigaScience, 12 Oxford University Press 10.1093/gigascience/giad108
Hashemi Gheinani, Ali; Akshay, Akshay; Besic, Mustafa; Kuhn, Annette; Keller, Irene; Bruggmann, Rémy; Rehrauer, Hubert; Adam, Rosalyn M; Burkhard, Fiona C.; Monastyrskaya, Katia (2021). Integrated mRNA-miRNA transcriptome analysis of bladder biopsies from patients with bladder pain syndrome identifies signaling alterations contributing to the disease pathogenesis. BMC urology, 21(1), p. 172. BMC 10.1186/s12894-021-00934-0
von Siebenthal, Michelle; Besic, Mustafa; Hashemi Gheinani, Ali; Akshay, Akshay; Lizun-Platoni, Salomé; Kunz, Nadine; Burkhard, Fiona C.; Monastyrskaya, Katia (2021). Urinary miRNA profiles discriminate between obstruction-induced bladder dysfunction and healthy controls. Scientific reports, 11(1), p. 10204. Springer Nature 10.1038/s41598-021-89535-3
Koeck, Ivonne; Hashemi Gheinani, Ali; Baumgartner, Ulrich; Vassella, Erik; Bruggmann, Rémy; Burkhard, Fiona C.; Monastyrskaya, Katia (2018). Tumor Necrosis Factor-α Initiates miRNA-mRNA Signaling Cascades in Obstruction-Induced Bladder Dysfunction. The American journal of pathology, 188(8), pp. 1847-1864. Elsevier 10.1016/j.ajpath.2018.05.008
Hashemi Gheinani, Ali; Vögeli, Mike; Baumgartner, Ulrich; Vassella, Erik; Draeger, Annette; Burkhard, Fiona C.; Monastyrskaya-Stäuber, Katia (2018). Improved isolation strategies to increase the yield and purity of human urinary exosomes for biomarker discovery. Scientific Reports, 8(1), p. 3945. Nature Publishing Group 10.1038/s41598-018-22142-x
Baumgartner, Ulrich; Berger, Fabienne; Hashemi Gheinani, Ali; Burgener, Sabrina Sofia; Monastyrskaya-Stäuber, Katia; Vassella, Erik (2018). miR-19b enhances proliferation and apoptosis resistance via the EGFR signaling pathway by targeting PP2A and BIM in non-small cell lung cancer. Molecular cancer, 17(1), p. 44. BioMed Central 10.1186/s12943-018-0781-5
Hashemi Gheinani, Ali; Köck, Ivonne; Vasquez, Evalynn; Baumgartner, Ulrich; Bigger-Allen, Alexander; Sack, Bryan S; Burkhard, Fiona C.; Adam, Rosalyn M; Monastyrskaya, Katia (2018). Concordant miRNA and mRNA expression profiles in humans and mice with bladder outlet obstruction. American journal of clinical and experimental urology, 6(6), pp. 219-233. e-Century Publishing
Vasquez, Evalynn; Cristofaro, Vivian; Lukianov, Stefan; Burkhard, Fiona C.; Hashemi Gheinani, Ali; Monastyrskaya-Stäuber, Katia; Bielenberg, Diane R; Sullivan, Maryrose P; Adam, Rosalyn M (2017). Deletion of neuropilin 2 enhances detrusor contractility following bladder outlet obstruction. JCI insight, 2(3), e90617. JCI Insight 10.1172/jci.insight.90617
Hashemi Gheinani, Ali; Kiss, Bernhard; Moltzahn, Felix Roman; Keller, Irene; Bruggmann, Rémy; Rehrauer, Hubert; Fournier, Catharine Aquino; Burkhard, Fiona C.; Monastyrskaya-Stäuber, Katia (2017). Characterization of miRNA-regulated networks, hubs of signaling, and biomarkers in obstruction-induced bladder dysfunction. JCI insight, 2(2), e89560. JCI Insight 10.1172/jci.insight.89560
Hashemi Gheinani, Ali; Burkhard, Fiona C.; Rehrauer, Hubert; Aquino Fournier, Catharine; Monastyrskaya-Stäuber, Katia (2015). MicroRNA miR-199a-5p regulates smooth muscle cell proliferation and morphology by targeting Wnt2 signaling pathway. Journal of biological chemistry, 290(11), pp. 7067-7086. American Society for Biochemistry and Molecular Biology 10.1074/jbc.M114.618694
Monastyrskaya, Katia; Sánchez-Freire, Verónica; Hashemi Gheinani, Ali; Klumpp, David J; Babiychuk, Eduard B; Draeger, Annette; Burkhard, Fiona C (2013). miR-199a-5p regulates urothelial permeability and may play a role in bladder pain syndrome. American journal of pathology, 182(2), pp. 431-48. New York, N.Y.: Elsevier 10.1016/j.ajpath.2012.10.020
Hashemi Gheinani, Ali; Burkhard, Fiona C.; Monastyrskaya, Katia (2013). Deciphering microRNA code in pain and inflammation: lessons from bladder pain syndrome. Cellular and molecular life sciences, 70(20), pp. 3773-3789. Springer Basel 10.1007/s00018-013-1275-7
Schneider, Marc; Küffer, Michelle; Besic, Mustafa; Hashemi Gheinani, Ali; Vassella, Erik; Burkhard, Fiona C.; Monastyrskaya-Stäuber, Katia (5 May 2019). Towards non-invasive diagnosis of benign prostatic obstruction using urinary miRNAs. The journal of urology, 201(4S), e893-e894. American Urological Association 10.1097/01.JU.0000556840.49371.d1
Hashemi Gheinani, Ali; Burkhard, F.; Rehrauer, H.; Aquino Fournier, C.; Rémi, B.; Monastyrskaya, K. (15 March 2019). Molecular characterization of bladder pain syndrome identifies functional mRNA-microRNA regulatory modules. European Urology Supplements, 18(1), e718-e718. Elsevier 10.1016/S1569-9056(19)30527-5
Hashemi Gheinani, Ali; Sack, Bryan S; Bigger-Allen, Alex; Thaker, Hatim; Atta, Hussein; Lambrinos, George; Costa, Kyle; Doyle, Claire; Gharaee-Kermani, Mehrnaz; Patalano, Susan; Piper, Mary; Cotellessa, Justin F; Vitko, Dijana; Li, Haiying; Prabhakaran, Manubhai Kadayil; Cristofaro, Vivian; Froehlich, John; Lee, Richard S; Yang, Wei; Sullivan, Maryrose P; ... (10 December 2023). Integrated omics analysis unveils a DNA damage response to neurogenic injury. (bioRxiv). Cold Spring Harbor Laboratory 10.1101/2023.12.10.571015
Akshay, Akshay; Katoch, Mitali; Shekarchizadeh, Navid; Abedi, Masoud; Sharma, Ankush; Burkhard, Fiona C.; Adam, Rosalyn M; Monastyrskaya, Katia; Hashemi Gheinani, Ali (4 July 2023). Machine Learning Made Easy (MLme): A Comprehensive Toolkit for Machine Learning-Driven Data Analysis. (bioRxiv). Cold Spring Harbor Laboratory 10.1101/2023.07.04.546825
Akshay, Akshay; Katoch, Mitali; Abedi, Masoud; Besic, Mustafa; Shekarchizadeh, Navid; Burkhard, Fiona C.; Bigger-Allen, Alex; Adam, Rosalyn M; Monastyrskaya, Katia; Hashemi Gheinani, Ali (28 June 2023). SpheroScan: A User-Friendly Deep Learning Tool for Spheroid Image Analysis. (bioRxiv). Cold Spring Harbor Laboratory 10.1101/2023.06.28.533479
