Search Results - "Madani Tonekaboni, Seyed Ali"

Noncoding mutations target cis-regulatory elements of the FOXA1 plexus in prostate cancer by Zhou, Stanley, Hawley, James R., Soares, Fraser, Grillo, Giacomo, Teng, Mona, Madani Tonekaboni, Seyed Ali, Hua, Junjie Tony, Kron, Ken J., Mazrooei, Parisa, Ahmed, Musaddeque, Arlidge, Christopher, Yun, Hwa Young, Livingstone, Julie, Huang, Vincent, Yamaguchi, Takafumi N., Espiritu, Shadrielle M. G., Zhu, Yanyun, Severson, Tesa M., Murison, Alex, Cameron, Sarina, Zwart, Wilbert, van der Kwast, Theodorus, Pugh, Trevor J., Fraser, Michael, Boutros, Paul C., Bristow, Robert G., He, Housheng Hansen, Lupien, Mathieu

“…Prostate cancer is the second most commonly diagnosed malignancy among men worldwide. Recurrently mutated in primary and metastatic prostate tumors, FOXA1…”
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Single-cell chromatin accessibility profiling of glioblastoma identifies an invasive cancer stem cell population associated with lower survival by Guilhamon, Paul, Chesnelong, Charles, Kushida, Michelle M, Nikolic, Ana, Singhal, Divya, MacLeod, Graham, Madani Tonekaboni, Seyed Ali, Cavalli, Florence Mg, Arlidge, Christopher, Rajakulendran, Nishani, Rastegar, Naghmeh, Hao, Xiaoguang, Hassam, Rozina, Smith, Laura J, Whetstone, Heather, Coutinho, Fiona J, Nadorp, Bettina, Ellestad, Katrina I, Luchman, H Artee, Chan, Jennifer Ai-Wen, Shoichet, Molly S, Taylor, Michael D, Haibe-Kains, Benjamin, Weiss, Samuel, Angers, Stephane, Gallo, Marco, Dirks, Peter B, Lupien, Mathieu

“…Chromatin accessibility discriminates stem from mature cell populations, enabling the identification of primitive stem-like cells in primary tumors, such as…”
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Biological and therapeutic implications of a unique subtype of NPM1 mutated AML by Mer, Arvind Singh, Heath, Emily M., Madani Tonekaboni, Seyed Ali, Dogan-Artun, Nergiz, Nair, Sisira Kadambat, Murison, Alex, Garcia-Prat, Laura, Shlush, Liran, Hurren, Rose, Voisin, Veronique, Bader, Gary D., Nislow, Corey, Rantalainen, Mattias, Lehmann, Soren, Gower, Mark, Guidos, Cynthia J., Lupien, Mathieu, Dick, John E., Minden, Mark D., Schimmer, Aaron D., Haibe-Kains, Benjamin

“…In acute myeloid leukemia (AML), molecular heterogeneity across patients constitutes a major challenge for prognosis and therapy. AML with NPM1 mutation is a…”
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SYNERGxDB: an integrative pharmacogenomic portal to identify synergistic drug combinations for precision oncology by Seo, Heewon, Tkachuk, Denis, Ho, Chantal, Mammoliti, Anthony, Rezaie, Aria, Madani Tonekaboni, Seyed Ali, Haibe-Kains, Benjamin

“…Abstract Drug-combination data portals have recently been introduced to mine huge amounts of pharmacological data with the aim of improving current…”
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GLUT1 inhibition blocks growth of RB1-positive triple negative breast cancer by Wu, Qin, ba-alawi, Wail, Deblois, Genevieve, Cruickshank, Jennifer, Duan, Shili, Lima-Fernandes, Evelyne, Haight, Jillian, Tonekaboni, Seyed Ali Madani, Fortier, Anne-Marie, Kuasne, Hellen, McKee, Trevor D., Mahmoud, Hassan, Kushida, Michelle, Cameron, Sarina, Dogan-Artun, Nergiz, Chen, WenJun, Nie, Yan, Zhang, Lan Xin, Vellanki, Ravi N., Zhou, Stanley, Prinos, Panagiotis, Wouters, Bradly G., Dirks, Peter B., Done, Susan J., Park, Morag, Cescon, David W., Haibe-Kains, Benjamin, Lupien, Mathieu, Arrowsmith, Cheryl H.

“…Triple negative breast cancer (TNBC) is a deadly form of breast cancer due to the development of resistance to chemotherapy affecting over 30% of patients. New…”
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Predictive approaches for drug combination discovery in cancer by Madani Tonekaboni, Seyed Ali, Soltan Ghoraie, Laleh, Manem, Venkata Satya Kumar, Haibe-Kains, Benjamin

“…Abstract Drug combinations have been proposed as a promising therapeutic strategy to overcome drug resistance and improve efficacy of monotherapy regimens in…”
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Large organized chromatin lysine domains help distinguish primitive from differentiated cell populations by Madani Tonekaboni, Seyed Ali, Haibe-Kains, Benjamin, Lupien, Mathieu

“…The human genome is partitioned into a collection of genomic features, inclusive of genes, transposable elements, lamina interacting regions, early replicating…”
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Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease by Sugiyama, Michael G., Cui, Haotian, Redka, Dar’ya S., Karimzadeh, Mehran, Rujas, Edurne, Maan, Hassaan, Hayat, Sikander, Cheung, Kyle, Misra, Rahul, McPhee, Joseph B., Viirre, Russell D., Haller, Andrew, Botelho, Roberto J., Karshafian, Raffi, Sabatinos, Sarah A., Fairn, Gregory D., Madani Tonekaboni, Seyed Ali, Windemuth, Andreas, Julien, Jean-Philippe, Shahani, Vijay, MacKinnon, Stephen S., Wang, Bo, Antonescu, Costin N.

“…The COVID-19 pandemic has highlighted the urgent need for the identification of new antiviral drug therapies for a variety of diseases. COVID-19 is caused by…”
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Tissue specificity of in vitro drug sensitivity by Yao, Fupan, Madani Tonekaboni, Seyed Ali, Safikhani, Zhaleh, Smirnov, Petr, El-Hachem, Nehme, Freeman, Mark, Manem, Venkata Satya Kumar, Haibe-Kains, Benjamin

“…Abstract Objectives We sought to investigate the tissue specificity of drug sensitivities in large-scale pharmacological studies and compare these associations…”
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Biased Deep Learning Methods in Detection of COVID-19 Using CT Images: A Challenge Mounted by Subject-Wise-Split ISFCT Dataset by Parsarad, Shiva, Saeedizadeh, Narges, Soufi, Ghazaleh Jamalipour, Shafieyoon, Shamim, Hekmatnia, Farzaneh, Zarei, Andrew Parviz, Soleimany, Samira, Yousefi, Amir, Nazari, Hengameh, Torabi, Pegah, S. Milani, Abbas, Madani Tonekaboni, Seyed Ali, Rabbani, Hossein, Hekmatnia, Ali, Kafieh, Rahele

“…Accurate detection of respiratory system damage including COVID-19 is considered one of the crucial applications of deep learning (DL) models using CT images…”
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Identifying clusters of cis -regulatory elements underpinning TAD structures and lineage-specific regulatory networks by Madani Tonekaboni, Seyed Ali, Mazrooei, Parisa, Kofia, Victor, Haibe-Kains, Benjamin, Lupien, Mathieu

“…Cellular identity relies on cell-type-specific gene expression controlled at the transcriptional level by -regulatory elements (CREs). CREs are unevenly…”
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Mathematical modelling of phenotypic plasticity and conversion to a stem-cell state under hypoxia by Dhawan, Andrew, Madani Tonekaboni, Seyed Ali, Taube, Joseph H., Hu, Stephen, Sphyris, Nathalie, Mani, Sendurai A., Kohandel, Mohammad

“…Hypoxia, or oxygen deficiency, is known to be associated with breast tumour progression, resistance to conventional therapies and poor clinical prognosis. The…”
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A primary hierarchically organized patient-derived model enables in depth interrogation of stemness driven by the coding and non-coding genome by Boutzen, Héléna, Madani Tonekaboni, Seyed Ali, Chan-Seng-Yue, Michelle, Murison, Alex, Takayama, Naoya, Mbong, Nathan, Wagenblast, Elvin, Orouji, Elias, Arruda, Andrea, Mitchell, Amanda, Notta, Faiyaz, Minden, Mark D., Lupien, Mathieu, Kaufmann, Kerstin B., Dick, John E.

“…Many cancers are organized as cellular hierarchies sustained by cancer stem cells (CSC), whose eradication is crucial for achieving long-term remission…”
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Mathematical modelling of plasticity and phenotype switching in cancer cell populations by Tonekaboni, Seyed Ali Madani, Dhawan, Andrew, Kohandel, Mohammad

“…•We consider a two-compartment model and a hierarchical model to incorporate cellular plasticity of cancer cells.•We use experimental data to estimate the…”
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SIGN: similarity identification in gene expression by Madani Tonekaboni, Seyed Ali, Manem, Venkata Satya Kumar, El-Hachem, Nehme, Haibe-Kains, Benjamin

“…Abstract Motivation High-throughput molecular profiles of human cells have been used in predictive computational approaches for stratification of healthy and…”
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Pathway-Based Drug Response Prediction Using Similarity Identification in Gene Expression by Madani Tonekaboni, Seyed Ali, Beri, Gangesh, Haibe-Kains, Benjamin

“…Lapatinib and trastuzumab (Herceptin) are targeted therapies designed for patients with HER2+ breast tumors. Although these therapies improved survival rates…”
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Chronic hypoxia favours adoption to a castration-resistant cell state in prostate cancer by Cameron, Sarina, Deblois, Genevieve, Hawley, James R., Qamra, Aditi, Zhou, Stanley, Tonekaboni, Seyed Ali Madani, Murison, Alexander, Van Vliet, Romy, Liu, Juan, Locasale, Jason W., Lupien, Mathieu

“…Predicting and treating recurrence in intermediate-risk prostate cancer patients remains a challenge despite having identified genomic instability [ 1 ] and…”
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A homotopy analysis solution to large deformation of beams under static arbitrary distributed load by Maleki, Mohammad, Tonekaboni, Seyed Ali Madani, Abbasbandy, Saeid

“…In this article, homotopy analysis method (HAM) is employed to investigate non-linear large deformation of Euler–Bernoulli beams subjected to an arbitrary…”
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Computational Models for Mapping Transcriptome and Epigenome to Human Phenotypes by Madani Tonekaboni, Seyed Ali

“…Fate and identity of eukaryotic cells are results of the cooperative function of biological features such as transcripts, cis-regulatory elements and…”
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NodeCoder: a graph-based machine learning platform to predict active sites of modeled protein structures by Abdollahi, Nasim, Tonekaboni, Seyed Ali Madani, Huang, Jay, Wang, Bo, MacKinnon, Stephen

“…While accurate protein structure predictions are now available for nearly every observed protein sequence, predicted structures lack much of the functional…”
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