Seyed Ali Madani Tonekaboni
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View article: Biased Deep Learning Methods in Detection of COVID-19 Using CT Images: A Challenge Mounted by Subject-Wise-Split ISFCT Dataset
Biased Deep Learning Methods in Detection of COVID-19 Using CT Images: A Challenge Mounted by Subject-Wise-Split ISFCT Dataset Open
Accurate detection of respiratory system damage including COVID-19 is considered one of the crucial applications of deep learning (DL) models using CT images. However, the main shortcoming of the published works has been unreliable reporte…
View article: Chronic hypoxia favours adoption to a castration-resistant cell state in prostate cancer
Chronic hypoxia favours adoption to a castration-resistant cell state in prostate cancer Open
Predicting and treating recurrence in intermediate-risk prostate cancer patients remains a challenge despite having identified genomic instability [1] and hypoxia [2, 3] as risk factors. This underlies challenges in assigning the functiona…
View article: Data from Epigenetic Switch–Induced Viral Mimicry Evasion in Chemotherapy-Resistant Breast Cancer
Data from Epigenetic Switch–Induced Viral Mimicry Evasion in Chemotherapy-Resistant Breast Cancer Open
Tumor progression upon treatment arises from preexisting resistant cancer cells and/or adaptation of persister cancer cells committing to an expansion phase. Here, we show that evasion from viral mimicry response allows the growth of taxan…
View article: Supplementary Data from Epigenetic Switch–Induced Viral Mimicry Evasion in Chemotherapy-Resistant Breast Cancer
Supplementary Data from Epigenetic Switch–Induced Viral Mimicry Evasion in Chemotherapy-Resistant Breast Cancer Open
Supplementary data, figures and table
View article: Data from Epigenetic Switch–Induced Viral Mimicry Evasion in Chemotherapy-Resistant Breast Cancer
Data from Epigenetic Switch–Induced Viral Mimicry Evasion in Chemotherapy-Resistant Breast Cancer Open
Tumor progression upon treatment arises from preexisting resistant cancer cells and/or adaptation of persister cancer cells committing to an expansion phase. Here, we show that evasion from viral mimicry response allows the growth of taxan…
View article: Supplementary Data from Epigenetic Switch–Induced Viral Mimicry Evasion in Chemotherapy-Resistant Breast Cancer
Supplementary Data from Epigenetic Switch–Induced Viral Mimicry Evasion in Chemotherapy-Resistant Breast Cancer Open
Supplementary data, figures and table
View article: NodeCoder: a graph-based machine learning platform to predict active sites of modeled protein structures
NodeCoder: a graph-based machine learning platform to predict active sites of modeled protein structures Open
While accurate protein structure predictions are now available for nearly every observed protein sequence, predicted structures lack much of the functional context offered by experimental structure determination. We address this gap with N…
View article: Multiscale interactome analysis coupled with off‑target drug predictions reveals drug repurposing candidates for human coronavirus disease
Multiscale interactome analysis coupled with off‑target drug predictions reveals drug repurposing candidates for human coronavirus disease Open
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 infection with the human coronavirus SARS-CoV-2, while other related human coro…
View article: Multiscale interactome analysis coupled with off‑target drug predictions reveals drug repurposing candidates for human coronavirus disease
Multiscale interactome analysis coupled with off‑target drug predictions reveals drug repurposing candidates for human coronavirus disease Open
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 infection with the human coronavirus SARS-CoV-2, while other related human coro…
View article: Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease
Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease Open
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 infection with the human coronavirus SARS-CoV-2, while other related human corona…
View article: Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease
Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease Open
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 infection with the human coronavirus SARS-CoV-2, while other related human corona…
View article: A primary hierarchically organized patient-derived model enables in depth interrogation of stemness driven by the coding and non-coding genome
A primary hierarchically organized patient-derived model enables in depth interrogation of stemness driven by the coding and non-coding genome Open
View article: A primary patient-derived model for investigating functional heterogeneity within the human Leukemic Stem Cell Compartment
A primary patient-derived model for investigating functional heterogeneity within the human Leukemic Stem Cell Compartment Open
The ability of leukemic stem cells (LSC) to evade therapy and fuel leukemic progression causing relapse impedes therapeutic success in acute myeloid leukemia (AML). The LSC pool within a patient sample is not homogenous but comprises disti…
View article: Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease
Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease Open
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 infection with the human coronavirus SARS-CoV-2, while other related human corona…
View article: Proteome‐Scale Drug‐Target Interaction Predictions: Approaches and Applications
Proteome‐Scale Drug‐Target Interaction Predictions: Approaches and Applications Open
Drug‐Target interaction predictions are an important cornerstone of computer‐aided drug discovery. While predictive methods around individual targets have a long history, the application of proteome‐scale models is relatively recent. In th…
View article: Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease
Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease Open
The COVID-19 pandemic has led to an urgent need for the identification of new antiviral drug therapies that can be rapidly deployed to treat patients with this disease. COVID-19 is caused by infection with the human coronavirus SARS-CoV-2.…
View article: Transposable Elements Shape Stemness in Normal and Leukemic Hematopoiesis
Transposable Elements Shape Stemness in Normal and Leukemic Hematopoiesis Open
Despite most acute myeloid leukemia (AML) patients achieving complete remission after induction chemotherapy, two-thirds will relapse with fatal disease within five years. AML is organized as a cellular hierarchy sustained by leukemia stem…
View article: Biological and therapeutic implications of a unique subtype of NPM1 mutated AML
Biological and therapeutic implications of a unique subtype of NPM1 mutated AML Open
In acute myeloid leukemia (AML), molecular heterogeneity across patients constitutes a major challenge for prognosis and therapy. AML with NPM1 mutation is a distinct genetic entity in the revised World Health Organization classification. …
View article: Large organized chromatin lysine domains help distinguish primitive from differentiated cell populations
Large organized chromatin lysine domains help distinguish primitive from differentiated cell populations Open
View article: Single-cell chromatin accessibility profiling of glioblastoma identifies an invasive cancer stem cell population associated with lower survival
Single-cell chromatin accessibility profiling of glioblastoma identifies an invasive cancer stem cell population associated with lower survival Open
Chromatin accessibility discriminates stem from mature cell populations, enabling the identification of primitive stem-like cells in primary tumors, such as glioblastoma (GBM) where self-renewing cells driving cancer progression and recurr…
View article: Author response: Single-cell chromatin accessibility profiling of glioblastoma identifies an invasive cancer stem cell population associated with lower survival
Author response: Single-cell chromatin accessibility profiling of glioblastoma identifies an invasive cancer stem cell population associated with lower survival Open
View article: Learning across label confidence distributions using Filtered Transfer Learning
Learning across label confidence distributions using Filtered Transfer Learning Open
Performance of neural network models relies on the availability of large datasets with minimal levels of uncertainty. Transfer Learning (TL) models have been proposed to resolve the issue of small dataset size by letting the model train on…
View article: Pathway-Based Drug Response Prediction Using Similarity Identification in Gene Expression
Pathway-Based Drug Response Prediction Using Similarity Identification in Gene Expression Open
Lapatinib and trastuzumab (Herceptin) are targeted therapies designed for patients with HER2+ breast tumors. Although these therapies improved survival rates of patients with this tumor type, not all the patients harboring HER2 amplificati…
View article: GLUT1 inhibition blocks growth of RB1-positive triple negative breast cancer
GLUT1 inhibition blocks growth of RB1-positive triple negative breast cancer Open
View article: Epigenetic Switch–Induced Viral Mimicry Evasion in Chemotherapy-Resistant Breast Cancer
Epigenetic Switch–Induced Viral Mimicry Evasion in Chemotherapy-Resistant Breast Cancer Open
Tumor progression upon treatment arises from preexisting resistant cancer cells and/or adaptation of persister cancer cells committing to an expansion phase. Here, we show that evasion from viral mimicry response allows the growth of taxan…
View article: Learning across label confidence distributions using Filtered Transfer\n Learning
Learning across label confidence distributions using Filtered Transfer\n Learning Open
Performance of neural network models relies on the availability of large\ndatasets with minimal levels of uncertainty. Transfer Learning (TL) models have\nbeen proposed to resolve the issue of small dataset size by letting the model\ntrain…
View article: SYNERGxDB: an integrative pharmacogenomic portal to identify synergistic drug combinations for precision oncology
SYNERGxDB: an integrative pharmacogenomic portal to identify synergistic drug combinations for precision oncology Open
Drug-combination data portals have recently been introduced to mine huge amounts of pharmacological data with the aim of improving current chemotherapy strategies. However, these portals have only been investigated for isolated datasets, a…
View article: Noncoding mutations target cis-regulatory elements of the FOXA1 plexus in prostate cancer
Noncoding mutations target cis-regulatory elements of the FOXA1 plexus in prostate cancer Open
Prostate cancer is the second most commonly diagnosed malignancy among men worldwide. Recurrently mutated in primary and metastatic prostate tumors, FOXA1 encodes a pioneer transcription factor involved in disease onset and progression thr…
View article: Identifying clusters of <i>cis</i>-regulatory elements underpinning TAD structures and lineage-specific regulatory networks
Identifying clusters of <i>cis</i>-regulatory elements underpinning TAD structures and lineage-specific regulatory networks Open
Cellular identity relies on cell-type–specific gene expression controlled at the transcriptional level by cis -regulatory elements (CREs). CREs are unevenly distributed across the genome, giving rise to individual CREs and clusters of CREs…
View article: GLUT1 inhibition blocks growth of RB1-positive Triple Negative Breast Cancer
GLUT1 inhibition blocks growth of RB1-positive Triple Negative Breast Cancer Open
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 therapeutics and companion biomarkers are urgently needed. Recognizing the elev…