Iman Tavassoly

Iman Tavassoly
Virginia Tech and Icahn School of Medicine at Mount Sinai

MD, PhD

About

64
Publications
45,567
Reads
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4,729
Citations
Introduction
Iman Tavassoly (MD, PhD) is a physician-scientist. His research interests include Systems Biology, Computational Biology, Systems Pharmacology, Genomics, Cancer Biology and Precision Medicine and Oncology.
Additional affiliations
October 2013 - August 2020
Icahn School of Medicine at Mount Sinai
Position
  • PostDoc Position
Description
  • Precision Oncology, Personalized Medicine, Systems Pharmacology of Cancer, Mathematical Oncology, Cancer Biology, Metabolic Reprogramming in Cancer
Education
August 2009 - August 2013
Virginia Polytechnic Institute and State University
Field of study
  • Genetics, Bioinformatics and Computational Biology (Systems Biology)
September 1999 - January 2007
Mazandaran University of Medical Sciences
Field of study
  • Clinical Medicine

Publications

Publications (64)
Article
Full-text available
Autophagy is a conserved biological stress response in mammalian cells that is responsible for clearing damaged proteins and organelles from the cytoplasm and recycling their contents via the lysosomal pathway. In cases of mild stress, autophagy acts as a survival mechanism, while in cases of severe stress cells may switch to programmed cell death....
Article
Full-text available
Cancers of the breast and other tissues arise from aberrant decision-making by cells regarding their survival or death, proliferation or quiescence, damage repair or bypass. These decisions are made by molecular signalling networks that process information from outside and from within the breast cancer cell and initiate responses that determine the...
Chapter
Full-text available
n this chapter we present an experimental quantitative framework for measuring kinetic parameters such as autophagy flux, time course of autophagic response, and stress/response dynamics in single cancer cells including endocrine-resistant breast cancer cells. Some primary data are presented in this chapter.
Book
Full-text available
This interdisciplinary thesis introduces a systems biology approach to study the cell fate decision mediated by autophagy. A mathematical model of interaction between Autophagy and Apoptosis in mammalian cells is proposed. In this dynamic model autophagy acts as a gradual response to stress (Rheostat) that delays the initiation of bistable switch o...
Article
Full-text available
In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring au...
Article
Background: While detection of circulating tumor DNA (ctDNA) is associated with poor cancer prognosis, the clinical utility for guiding treatment decisions is unresolved. Patients with minimal residual disease (MRD) often have less than one genome equivalent of ctDNA per 10 mL blood. Consequently, it is stochastic whether a 10 mL sample contains ct...
Article
Background: Neoadjuvant chemotherapy (NAC) followed by radical cystectomy (CX), is gold standard treatment in localized muscle-invasive bladder cancer (MIBC). About 45% of patients with MIBC develop metastatic relapse within 2 years after CX. The response rate to chemotherapy and immune checkpoint inhibitors (ICI) is relatively low, and biomarker t...
Article
Background: Early detection of recurrence and monitoring of MRD post-surgery is critical for clinical decision-making to tailor adjuvant therapy. In early-stage NSCLC, circulating tumor DNA (ctDNA) detection is especially challenging, requiring highly sensitive and specific assays. Therefore, we used a WGS approach (MRDetect) for ultra-sensitive ct...
Article
Introduction: Liquid biopsy offers a noninvasive approach to monitor cancer burden during therapy and surveillance period. However, in pediatric brain cancers, liquid biopsy methods from the blood have been unsuccessful due to a low tumor burden and low number of mutations in coding regions. We hypothesized that a whole genome sequencing (WGS)-deri...
Article
e13582 Background: Minimal residual disease (MRD) monitoring using liquid biopsy for solid tumors requires a highly sensitive and specific assay that can overcome the limitation of low abundance cfDNA in a standard blood draw. We developed a whole-genome sequencing (WGS)-based assay to detect the presence of circulating tumor DNA (ctDNA) in plasma....
Article
Supplementary Material for: Decoding clinical biomarker space of COVID-19: Exploring matrix factorization-based feature selection methods
Article
One of the most critical challenges in managing complex diseases like COVID-19 is to establish an intelligent triage system that can optimize the clinical decision-making at the time of a global pandemic. The clinical presentation and patients’ characteristics are usually utilized to identify those patients who need more critical care. However, the...
Article
The extraction of predictive features from the complex high-dimensional multi-omic data is necessary for decoding and overcoming the therapeutic responses in systems pharmacology. Developing computational methods to reduce high-dimensional space of features in in vitro, in vivo and clinical data is essential to discover the evolution and mechanisms...
Preprint
Full-text available
The extraction of predictive features from the complex high-dimensional multi-omic data is necessary for decoding and overcoming the therapeutic responses in systems pharmacology. Developing computational methods to reduce high-dimensional space of features in in vitro, in vivo and clinical data is essential to discover the evolution and mechanisms...
Article
BACKGROUND Plasma circulating tumor DNA (ctDNA) is rarely detectable by traditional methods in patients with GBM. As a result, unlike in lung and other cancers, serial next generation sequencing of ctDNA for monitoring GBM tumor burden has been challenging. In light of the low tumor fraction (TF) of DNA fragments in GBM patient plasma and the urgen...
Article
Full-text available
COVID-19 affects multiple organs. Clinical data from the Mount Sinai Health System shows that substantial numbers of COVID-19 patients without prior heart disease develop cardiac dysfunction. How COVID-19 patients develop cardiac disease is not known. We integrated cell biological and physiological analyses of human cardiomyocytes differentiated fr...
Article
Full-text available
The delivery of hydrophobic therapeutic agents to tumors is a challenge in the treatment of cancers. Here, we review recent advances in coiled-coil protein origami and discuss a proposed programmable protein origami structure, switchable by a protein kinase A/phosphatase switch, as an example of functionalization for designing future protein nanoro...
Preprint
Full-text available
One of the most important challenges in managing complex diseases like COVID-19 is to establish an intelligent triage system which can optimize the clinical decision-making at the time of a global pandemic. The clinical presentation and patients characteristics are usually utilized to identify those patients who need more critical care. However, th...
Article
Full-text available
Cells are the basic units of all living matter which harness the flow of energy to drive the processes of life. While the biochemical networks involved in energy transduction are well-characterized, the energetic costs and constraints for specific cellular processes remain largely unknown. In particular, what are the energy budgets of cells? What a...
Article
Full-text available
Cells are the basic units of all living matter which harness the flow of energy to drive the processes of life. While the biochemical networks involved in energy transduction are well-characterized, the energetic costs and constraints for specific cellular processes remain largely unknown. In particular, what are the energy budgets of cells? What a...
Conference Paper
Full-text available
Background: Bladder cancer (BC) is the 9th most commonly diagnosed cancer worldwide and each year responsible for 165,000 deaths. Neoadjuvant combination chemotherapy, followed by radical cystectomy, is used for the management of localized muscle-invasive bladder cancer. One of the critical challenges in this therapeutic regimen is monitoring the t...
Article
Full-text available
Recent findings showed that preformed fibrils (PFFs) of misfolded proteins, including α-synuclein (α-syn) and amyloid-β (Aβ), activate EGFR in cell cultures and animal models of amyloid propagation. Comparing these supramolecular structures to normal EGFR ligands such as EGF and HB-EGF suggests that these PFFs might trigger the formation of high or...
Preprint
Full-text available
COVID-19 affects multiple organs. Clinical data from the Mount Sinai Health System shows that substantial numbers of COVID-19 patients without prior heart disease develop cardiac dysfunction. How COVID-19 patients develop cardiac disease is not known. We integrate cell biological and physiological analyses of human cardiomyocytes differentiated fro...
Article
Full-text available
Postinfection complications of coronavirus disease 2019 (COVID-19) are still unknown, and one of the long-term concerns in infected people are brain pathologies. The question is that severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection may be an environmental factor in accelerating the sporadic neurodegeneration in the infected po...
Article
Full-text available
Heparan Sulfate Proteoglycans (HSPGs) are cell surface receptors that are involved in the cellular uptake of pathological amyloid proteins and viruses, including the novel coronavirus; Severe Acute Respiratory Syndrome CoronaVirus-2 (SARS-CoV-2). Heparin and heparan sulfate antagonize the binding of these pathogens to HSPGs and stop their cellular...
Article
Full-text available
Several reports have been published recently demonstrating a beneficial effect of epidermal growth factor receptor (EGFR) inhibitors in improving pathological and behavioral conditions in neurodegenerative diseases (NDDs) such as Alzheimer’s disease (AD) and Amyotrophic Lateral Sclerosis (ALS) as well as the brain and spinal cord injuries (SCI). De...
Preprint
Full-text available
Over the last decades, several features of obesity have been identified at behavioral, physiological, endocrine and genomic levels, and they have revealed the complexity of the disease; obesity results from a combination of genetic predisposition, endocrine disorders, and dysregulation of both food intake and energy expenditure. This complexity mak...
Article
Mechanistic target of rapamycin (mTOR) is a critical protein in the regulation of cell fate decision making, especially in cancer cells. mTOR acts as a signal integrator and is one of the main elements of interactions among the pivotal cellular processes such as cell death, autophagy, metabolic reprogramming, cell growth, and cell cycle. The tempor...
Chapter
Full-text available
The emergence of mobile device technologies has made digital medicine and health enter a new era. Mobile devices and smart gadgets can be used as tools for collecting and analyzing data related to health and help improving patient care. They also are applicable for educational purposes and designing preventive medicine platforms in which patients c...
Article
Full-text available
Background: Pancreatic cystic lesions are often challenging entities for diagnosis and management. EUS-FNA diagnostic accuracy is limited by paucicellularity of cytology specimens and sampling errors. Needle-based confocal laser endomicroscopy (nCLE) provides real-time imaging of the microscopic structure of the cystic lesion and could result in a...
Article
Signal integration has a crucial role in the cell fate decision and dysregulation of the cellular signaling pathways is a primary characteristic of cancer. As a signal integrator, mTOR shows a complex dynamical behavior which determines the cell fate at different cellular processes levels, including cell cycle progression, cell survival, cell death...
Conference Paper
Full-text available
Immunotherapy by immune checkpoint blockade has had a promising impact on the treatment of Non-Small Cell Lung Cancer (NSCLC). Although single and combination therapy with checkpoint inhibitors such as PDL-1 inhibitors have been proved to be effective in making the survival of patients with NSCLC longer, but there is always a population of patients...
Article
Full-text available
The ability to predict responsiveness to drugs in individual patients is limited. We hypothesized that integrating molecular information from databases would yield predictions that could be experimentally tested to develop transcriptomic signatures for specific drugs. We analyzed lung adenocarcinoma patient data from The Cancer Genome Atlas (TCGA)...
Preprint
Full-text available
Signal integration in the mTOR pathway plays a vital role in cell fate decision making in cancer cells. As a signal integrator, mTOR shows a complex dynamical behavior which determines the cell fate at different cellular processes levels including cell cycle progression, cell survival, cell death, metabolic reprogramming, and aging. The dynamics of...
Preprint
Full-text available
Renal cell carcinoma (RCC) is one of the ten most common and lethal cancers in the United States. Tumor heterogeneity and development of resistance to treatment suggest that patient-specific evolutionary therapies may hold the key to better patients prognosis. Mathematical models are a powerful tool to help develop such strategies; however, they de...
Data
Autophagy is a conserved biological stress response in mammalian cells that is responsible for clearing damaged proteins and organelles from the cytoplasm and recycling their contents via the lysosomal pathway. In cases of mild stress, autophagy acts as a survival mechanism, while in cases of severe stress cells may switch to programmed cell death....
Article
Full-text available
Systems biology is an integrative discipline connecting the molecular components within a single biological scale and also among different scales (e.g. cells, tissues and organ systems) to physiological functions and organismal phenotypes through quantitative reasoning, computational models and high-throughput experimental technologies. Systems bio...
Preprint
Full-text available
The ability to predict responsiveness to drugs in individual patients is limited. We hypothesized that integrating molecular information from databases would yield predictions that could be experimentally tested to develop genomic signatures for sensitivity or resistance to specific drugs. We analyzed TCGA data for lung adenocarcinoma (LUAD) patien...
Article
Full-text available
Genomic alterations are important characteristics of therapeutic responses and therapeutic-resistance phenotype in cancer. These genomic alterations are complex and are determinants of aberrations in signaling pathways and their dynamics. A genomic signature includes a set of genomic alterations like gene expressions, mutations, copy number variati...
Conference Paper
Dynamic models of pathological phenomena in diseases such as cancer are very useful tools to understand the pathogenesis of disease progression and development. These models study physiological and pathological phenomenon at cell and tissue level focusing not only on components within cells and tissues but also on the evolution of diseases in time...
Conference Paper
Full-text available
Lung cancers are among the most common invasive cancers worldwide and annually lead to high mortality and morbidity. Genomic alterations have been known to control the evolution of hallmarks of cancer in a dynamic way. These molecular alterations combined with epigenomic and post-genomic modifications contribute to formation of these neoplasms. Mul...
Article
Full-text available
Using a gelatin microbial transglutaminase (gelatin-mTG) cell culture platform tuned to exhibit stiffness spanning that of healthy and diseased glomeruli, we demonstrate that kidney podocytes show marked stiffness sensitivity. Podocyte-specific markers that are critical in the formation of the renal filtration barrier are found to be regulated in a...
Chapter
Full-text available
The Matlab code for solving ODEs used for modeling autophagy and apoptosis pathways is presented in this chapter.
Chapter
In this chapter autophagy and cell death pathways in cancer are reviewed and their roles in physiology and pathophysiology are discussed. Network organization of these pathways are explained and a signalling network linking autophagy to programmed cell death is proposed.
Chapter
Full-text available
In this chapter systems biology of cell death pathways and autophagy in cancer is discussed and based on current knowledge of signalling networks, dynamic model and quantitative data, the future directions in systems biology of autophagy and cell death pathways in cancer are explained.
Chapter
Full-text available
In this chapter, we have proposed a theoretical framework for analysis of dynamics of interplay of autophagy and apoptosis in mammalian cells including cancer cells. Because quantitative experimental data on time course of interplay of autophagy and apoptosis is very limited, we have used the observations of interaction of autophagy and apoptosis i...
Book
Full-text available
This interdisciplinary thesis introduces a systems biology approach to study the cell fate decision mediated by autophagy. A mathematical model of interaction between Autophagy and Apoptosis in mammalian cells is proposed. In this dynamic model autophagy acts as a gradual response to stress (Rheostat) that delays the initiation of bistable switch o...
Article
Full-text available
Autophagy is a conserved biological stress response in mammalian cells that is responsible for clearing damaged proteins and organelles from the cytoplasm and recycling their contents via the lysosomal pathway. In cases where the stress is not too severe, autophagy acts as a survival mechanism. In cases of severe stress, may lead to programmed cell...
Article
Full-text available
Understanding the origins of resistance to anti-oestrogen drugs is of critical importance to many breast cancer patients. Recent experiments show that knockdown of GRP78, a key gene in the unfolded protein response (UPR), can re-sensitize resistant cells to anti-oestrogens, and overexpression of GRP78 in sensitive cells can cause them to become res...
Article
Full-text available
How breast cancer cells respond to the stress of endocrine therapies determines whether they will acquire a resistant phenotype or execute a cell-death pathway. After a survival signal is successfully executed, a cell must decide whether it should replicate. How these cell-fate decisions are regulated is unclear, but evidence suggests that the sign...
Article
Full-text available
Lack of understanding of endocrine resistance remains one of the major challenges for breast cancer researchers, clinicians, and patients. Current reductionist approaches to understanding the molecular signaling driving resistance have offered mostly incremental progress over the past 10 years. As the field of systems biology has begun to mature, t...
Conference Paper
Full-text available
Chaos Game Representation (CGR) is an iterative mapping method which can convert a nucleotide sequence into a unique and scale-independent image. In CGR image of a DNA sequence both global and local patterns are displayed. These images allow us to investigate hidden self-similar patterns in genomic sequences. In this paper the fractal properties of...
Conference Paper
Full-text available
Chaos game representation (CGR) has been proposed as a method to convert genomic sequences to scale-independent and unique images. Many useful properties and applications have been indicated for these images. In this paper, a new procedure for three- dimensional visualization of genomic sequences is introduced based on Chaos Game Representation alg...

Questions

Question (1)
Question
I am looking for some mouse models to test efficacy of some immunotherapy agents on NSCLC PDX tumor models.

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Projects

Projects (6)
Project
A Systems Biology Atlas for Obesity Parthenogenesis and Treatment.
Project
CGR images of biological sequences and Ergodic Theory.