Yu Zhang

Yu Zhang
Wyss Institute at Harvard University

Doctor of Philosophy

About

22
Publications
3,162
Reads
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247
Citations
Introduction
At the Wyss Institute and Broad Institute of MIT and Harvard, my research focuses on using Artificial Intelligence in drug discovery. My PhD studies in Biomedical Engineering at Johns Hopkins University School of Medicine focused on applying computational systems biology and quantitative systems pharmacology (QSP) modeling to understand and target cellular signaling pathways involved in angiogenesis and microvasculature-related diseases.
Education
September 2013 - December 2016
Johns Hopkins University
Field of study
  • Biomedical Engineering, Applied Mathematics and Statistics

Publications

Publications (22)
Article
Full-text available
Purpose: Quantitative understanding of the transport of therapeutic macromolecules following intraocular injections is critical for the design of efficient strategies in treating eye diseases, such as neovascular (wet) age-related macular degeneration (AMD) and macular edema (ME). Antiangiogenic treatments, such as neutralizing antibodies against...
Article
Full-text available
The angiopoietin-Tie signaling pathway is an important vascular signaling pathway involved in angiogenesis, vascular stability, and quiescence. Dysregulation in the pathway is linked to the impairments in vascular function associated with many diseases, including cancer, ocular diseases, systemic inflammation, and cardiovascular diseases. The prese...
Article
Angiogenesis is a critical step in tumor growth, development, and invasion. Nascent tumor cells secrete vascular endothelial growth factor (VEGF) that significantly remodels the tumor microenvironment through interaction with multiple receptors on vascular endothelial cells, including type 2 VEGF receptor (VEGFR2). The complex pathways initiated by...
Article
Full-text available
Recently, immunotherapies for antitumoral response have adopted conditionally activated molecules with the objective of reducing systemic toxicity. Amongst these are conditionally activated antibodies, such as PROBODY® activatable therapeutics (Pb-Tx), engineered to be proteolytically activated by proteases found locally in the tumor microenvironme...
Article
Full-text available
Red blood cell (RBC) aging manifests through progressive changes in cell morphology, rigidity, and expression of membrane proteins. To maintain the quality of circulating blood, splenic macrophages detect the biochemical signals and biophysical changes of RBCs and selectively clear them through erythrophagocytosis. In sickle cell disease (SCD), RBC...
Article
Full-text available
Conditionally activated molecules, such as Probody therapeutics (PbTx), have recently been investigated to improve antitumoral response while reducing systemic toxicity. PbTx are engineered to be proteolytically activated by proteases that are preferentially active locally in the tumor microenvironment (TME). Here, we perform an exploratory study u...
Article
Full-text available
Although immune checkpoint blockade therapies have shown evidence of clinical effectiveness in many types of cancer, the outcome of clinical trials shows that very few patients with colorectal cancer benefit from treatments with checkpoint inhibitors. Bispecific T cell engagers (TCEs) are gaining popularity because they can improve patients’ immuno...
Article
The Angiopoietin-Tie (Ang-Tie) pathway is a key signaling pathway regulating vascular stability and permeability, and it significantly intersects and crosstalk with the vascular endothelial growth factor (VEGF) signaling pathway, a major signaling pathway regulating angiogenesis and vascular permeability. Disrupted Ang-Tie and VEGF signaling is lin...
Article
Full-text available
In peripheral arterial disease (PAD), the degree of endogenous capacity to modulate revascularization of limb muscle is central to the management of leg ischemia. To characterize the multiscale and multicellular nature of revascularization in PAD, we have developed the first computational systems biology model that mechanistically incorporates intr...
Chapter
Angiogenesis is an important biological process involved in development, growth, reproduction, and wound healing. Dysregulation of angiogenesis is linked to many diseases, including cancer, ocular diseases, and cardiovascular diseases. Angiogenesis is a highly regulated process that involves a plethora of cells and cellular signaling events, includ...
Article
Full-text available
Angiogenesis is a highly regulated multiscale process that involves a plethora of cells, their cellular signal transduction, activation, proliferation, differentiation, as well as their intercellular communication. The coordinated execution and integration of such complex signaling programs is critical for physiological angiogenesis to take place i...
Article
Full-text available
The Ang–Tie signaling pathway is an important vascular signaling pathway regulating vascular growth and stability. Dysregulation in the pathway is associated with vascular dysfunction and numerous diseases that involve abnormal vascular permeability and endothelial cell inflammation. The understanding of the molecular mechanisms of the Ang–Tie path...
Article
Full-text available
Mathematical modeling can be used to predict the efficacy of drug therapies in liver cancer for individual patients. A team lead by Mohammad Jafarnejad at Johns Hopkins University developed a mathematical model of cellular signaling in liver cells that can predict drug interactions affecting the growth pathways in liver cells found to be responsibl...
Article
Full-text available
The angiopoietin-Tie signaling pathway is an important vascular signaling pathway involved in angiogenesis, vascular stability, and quiescence. Dysregulation in the pathway is linked to the impairments in vascular function associated with many diseases, including cancer, ocular diseases, systemic inflammation, and cardiovascular diseases. The prese...
Article
Full-text available
MicroRNAs (miRs) are endogenous non-coding RNA molecules that play important roles in human health and disease by regulating gene expression and cellular processes. In recent years, with the increasing scientific knowledge and new discovery of miRs and their gene targets, as well as the plentiful experimental evidence that shows dysregulation of mi...
Article
Full-text available
The matricellular protein thrombospondin-1 (TSP1) is a potent inhibitor of angiogenesis. Specifically, TSP1 has been experimentally shown to inhibit signaling downstream of vascular endothelial growth factor (VEGF). The molecular mechanism of this inhibition is not entirely clear. We developed a detailed computational model of VEGF signaling to Akt...

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