User profiles for Z. Safikhani

Zhaleh Safikhani

Post doctoral fellow
Verified email at utoronto.ca
Cited by 1365

[HTML][HTML] Machine learning approaches to drug response prediction: challenges and recent progress

G Adam, L Rampášek, Z Safikhani, P Smirnov… - NPJ precision …, 2020 - nature.com
Cancer is a leading cause of death worldwide. Identifying the best treatment using computational
models to personalize drug response prediction holds great promise to improve patient’…

PharmacoGx: an R package for analysis of large pharmacogenomic datasets

P Smirnov, Z Safikhani, N El-Hachem, D Wang… - …, 2016 - academic.oup.com
Pharmacogenomics holds great promise for the development of biomarkers of drug response
and the design of new therapeutic options, which are key challenges in precision medicine…

Public data and open source tools for multi-assay genomic investigation of disease

…, A Re, N El-Hachem, Z Safikhani… - Briefings in …, 2016 - academic.oup.com
Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA
profiling, proteomics and other assays, has the potential to provide a systems level …

PharmacoDB: an integrative database for mining in vitro anticancer drug screening studies

…, GA Adam, W Ba-Alawi, Z Safikhani… - Nucleic acids …, 2018 - academic.oup.com
Recent cancer pharmacogenomic studies profiled large panels of cell lines against hundreds
of approved drugs and experimental chemical compounds. The overarching goal of these …

[HTML][HTML] Revisiting inconsistency in large pharmacogenomic studies

Z Safikhani, P Smirnov, M Freeman, N El-Hachem… - …, 2016 - ncbi.nlm.nih.gov
In 2013, we published a comparative analysis of mutation and gene expression profiles and
drug sensitivity measurements for 15 drugs characterized in the 471 cancer cell lines …

Consensus on molecular subtypes of high-grade serous ovarian carcinoma

…, L Kannan, L Geistlinger, V Kofia, Z Safikhani… - Clinical Cancer …, 2018 - AACR
… Zhaleh SafikhaniZ. Safikhani was supported by The Cancer Research Society (Canada).
G. Parmigiani was supported by The National Cancer Institute 5P30CA006516-53. …

Disruption of the anaphase-promoting complex confers resistance to TTK inhibitors in triple-negative breast cancer

…, AS Mer, P Smirnov, Z Safikhani… - Proceedings of the …, 2018 - National Acad Sciences
TTK protein kinase (TTK), also known as Monopolar spindle 1 (MPS1), is a key regulator of
the spindle assembly checkpoint (SAC), which functions to maintain genomic integrity. TTK …

[HTML][HTML] Gene isoforms as expression-based biomarkers predictive of drug response in vitro

Z Safikhani, P Smirnov, KL Thu, J Silvester… - Nature …, 2017 - nature.com
Next-generation sequencing technologies have recently been used in pharmacogenomic
studies to characterize large panels of cancer cell lines at the genomic and transcriptomic …

Integrative cancer pharmacogenomics to infer large-scale drug taxonomy

N El-Hachem, DMA Gendoo, LS Ghoraie, Z Safikhani… - Cancer research, 2017 - AACR
… We relied on the Z-score and area under the curve (AUC d ) metrics from drug dose–response
curves of the NCI60 and CTRPv2, respectively. Drug similarity was defined as the …

[PDF][PDF] Assessment of genetic drift in large pharmacogenomic studies

…, D Tkachuk, C Ho, N El-Hachem, Z Safikhani… - Cell systems, 2020 - cell.com
… for each segmented region and used this value to draw a z-score threshold of ±4 to classify
a region … Finally, we used a z-score threshold of ±2 to classify a region as significantly drifted. …