Tongli Zhang
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View article: Advancing drug development with “Fit-for-Purpose” modeling informed approaches
Advancing drug development with “Fit-for-Purpose” modeling informed approaches Open
Model-informed Drug Development (MIDD) is an essential framework for advancing drug development and supporting regulatory decision-making. The current review presents a strategic blueprint to closely align MIDD tools with key questions of …
View article: Practical Perspectives on Enhancing Predictive Modeling for Drug Development
Practical Perspectives on Enhancing Predictive Modeling for Drug Development Open
Purpose of Review The ability to predict drug efficacy and toxicity holds transformative potential for drug development, offering the promise of reducing late-stage failures and accelerating the delivery of effective therapies to patients …
View article: A curated collection of transcriptome datasets to study the transcriptional response in blood and nasal samples following viral respiratory inoculation and vaccination
A curated collection of transcriptome datasets to study the transcriptional response in blood and nasal samples following viral respiratory inoculation and vaccination Open
Background Our understanding of the human immune system’s response to viral respiratory tract infections (VRTIs) and vaccines, including the molecular mechanisms and correlates of protection, remains incomplete. Extensive transcriptomic da…
View article: Applying neural ordinary differential equations for analysis of hormone dynamics in Trier Social Stress Tests
Applying neural ordinary differential equations for analysis of hormone dynamics in Trier Social Stress Tests Open
Introduction: This study explores using Neural Ordinary Differential Equations (NODEs) to analyze hormone dynamics in the hypothalamicpituitary-adrenal (HPA) axis during Trier Social Stress Tests (TSST) to classify patients with Major Depr…
View article: VeVaPy, a Python Platform for Efficient Verification and Validation of Systems Biology Models with Demonstrations Using Hypothalamic-Pituitary-Adrenal Axis Models
VeVaPy, a Python Platform for Efficient Verification and Validation of Systems Biology Models with Demonstrations Using Hypothalamic-Pituitary-Adrenal Axis Models Open
In order for mathematical models to make credible contributions, it is essential for them to be verified and validated. Currently, verification and validation (V&V) of these models does not meet the expectations of the system biology and s…
View article: SWAP, SWITCH, and STABILIZE: Mechanisms of Kinetochore–Microtubule Error Correction
SWAP, SWITCH, and STABILIZE: Mechanisms of Kinetochore–Microtubule Error Correction Open
For correct chromosome segregation in mitosis, eukaryotic cells must establish chromosome biorientation where sister kinetochores attach to microtubules extending from opposite spindle poles. To establish biorientation, any aberrant kineto…
View article: Perspectives on training quantitative systems pharmacologists
Perspectives on training quantitative systems pharmacologists Open
The rapidly evolving field of Quantitative Systems Pharmacology (QSP) calls for updated education curriculums and programs. QSP scientists need a wide variety of quantitative and soft skills, including "mechanistic modeling" skills, "data …
View article: Two heads are better than one: current landscape of integrating QSP and machine learning
Two heads are better than one: current landscape of integrating QSP and machine learning Open
View article: Understanding virtual patients efficiently and rigorously by combining machine learning with dynamical modelling
Understanding virtual patients efficiently and rigorously by combining machine learning with dynamical modelling Open
Individual biological organisms are characterized by daunting heterogeneity, which precludes describing or understanding populations of ‘patients’ with a single mathematical model. Recently, the field of quantitative systems pharmacology (…
View article: Synthesis of Chiral 5-Aryl-2-oxazolidinones via an Ir-BiphPHOX Catalyzed Enantioselective Hydrogenation
Synthesis of Chiral 5-Aryl-2-oxazolidinones via an Ir-BiphPHOX Catalyzed Enantioselective Hydrogenation Open
申杰峰 a 刘德龙 * ,a 张万斌 * ,a,b ( a 上海交通大学药学院 上海市手性药物分子工程重点实验室 上海 200240) ( b 上海交通大学化学化工学院 教育部变革性分子前沿科学中心 上海 200240) 摘要 利用轴手性 Ir-BiphPHOX 催化剂, 首次实现了 5-芳基噁唑-2-酮的不对称催化氢化反应, 高收率、高选择性地合 成了一系列手性 5-芳基噁唑烷-2-酮类化合物.该反应对多种官能团具有良好的相容性, 所得产物经简单转化可得到多 种手性氨基醇…
View article: Comment on "Approximation algorithms for quadratic programming"
Comment on "Approximation algorithms for quadratic programming" Open
The radius of the outer Dikin ellipsoid of the intersection of $m$ ellipsoids due to Fu et al. (J. Comb. Optim., 2, 29-50, 1998) is corrected from $m$ to $\sqrt{m^2+m}$. The approximation bound for the general convex quadratic constrained …
View article: A Modeling and Machine Learning Pipeline to Rationally Design Treatments to Restore Neuroendocrine Disorders in Heterogeneous Individuals
A Modeling and Machine Learning Pipeline to Rationally Design Treatments to Restore Neuroendocrine Disorders in Heterogeneous Individuals Open
Heterogeneity among individual patients presents a fundamental challenge to effective treatment, since a treatment protocol working for a portion of the population often fails in others. We hypothesize that a computational pipeline integra…
View article: Extracting Insights From Temporal Data by Integrating Dynamic Modeling and Machine Learning
Extracting Insights From Temporal Data by Integrating Dynamic Modeling and Machine Learning Open
Biological processes are dynamic. As a result, temporal analyses are necessary to fully understand the complex interactions that occurs within these systems. One example of a multifaceted biological process is restitution: the initial step…
View article: Designing combination therapies with modeling chaperoned machine learning
Designing combination therapies with modeling chaperoned machine learning Open
Chemotherapy resistance is a major challenge to the effective treatment of cancer. Thus, a systematic pipeline for the efficient identification of effective combination treatments could bring huge biomedical benefit. In order to facilitate…
View article: Correction to: A quantitative systems pharmacology (QSP) model for Pneumocystis treatment in mice
Correction to: A quantitative systems pharmacology (QSP) model for Pneumocystis treatment in mice Open
It was highlighted that the original article [1] contained errors in the figures and their legends and by extension the in-text figure citations. This Corrections article shows the correct figures and correct figure legends.
View article: Constitutive STAT5 activation regulates Paneth and Paneth-like cells to control <i>Clostridium difficile</i> colitis
Constitutive STAT5 activation regulates Paneth and Paneth-like cells to control <i>Clostridium difficile</i> colitis Open
Clostridium difficile impairs Paneth cells, driving intestinal inflammation that exaggerates colitis. Besides secreting bactericidal products to restrain C. difficile , Paneth cells act as guardians that constitute a niche for intestinal e…
View article: Trefoil factor 2 activation of CXCR4 requires calcium mobilization to drive epithelial repair in gastric organoids
Trefoil factor 2 activation of CXCR4 requires calcium mobilization to drive epithelial repair in gastric organoids Open
Key points Determining the signalling cascade of epithelial repair, using murine gastric organoids, allows definition of regulatory processes intrinsic to epithelial cells, at the same time as validating and dissecting the signalling casca…
View article: Unraveling the Control of Cell Cycle Periods during Intestinal Stem Cell Differentiation
Unraveling the Control of Cell Cycle Periods during Intestinal Stem Cell Differentiation Open
View article: Cell injury triggers actin polymerization to initiate epithelial restitution
Cell injury triggers actin polymerization to initiate epithelial restitution Open
The role of the actin cytoskeleton in the sequence of physiological epithelial repair in the intact epithelium has yet to be elucidated. Here, we explore the role of actin in gastric repair in vivo and in vitro gastric organoids (gastroids…
View article: A quantitative systems pharmacology (QSP) model for Pneumocystis treatment in mice
A quantitative systems pharmacology (QSP) model for Pneumocystis treatment in mice Open
View article: Multiscale positive feedbacks contribute to unidirectional gastric disease progression induced by helicobacter pylori infection
Multiscale positive feedbacks contribute to unidirectional gastric disease progression induced by helicobacter pylori infection Open
View article: A dynamical framework for complex fractional killing
A dynamical framework for complex fractional killing Open
View article: A mathematical model of a recombinant humanized anti-cocaine monoclonal antibody's effects on cocaine pharmacokinetics in mice
A mathematical model of a recombinant humanized anti-cocaine monoclonal antibody's effects on cocaine pharmacokinetics in mice Open
View article: Solving a class of generalized fractional programming problems using the feasibility of linear programs
Solving a class of generalized fractional programming problems using the feasibility of linear programs Open
View article: Intercellular Coupling of the Cell Cycle and Circadian Clock in Adult Stem Cell Culture
Intercellular Coupling of the Cell Cycle and Circadian Clock in Adult Stem Cell Culture Open
View article: Time to move on: Modeling transcription dynamics during an embryonic transition away from maternal control
Time to move on: Modeling transcription dynamics during an embryonic transition away from maternal control Open
In a recent study, we investigated the regulation of hunchback (hb) transcription dynamics in Drosophila embryos. Our results suggest that shutdown of hb transcription at early nuclear cycle (nc) 14 is an event associated with the global c…
View article: A Dynamical Framework for the All-or-None G1/S Transition
A Dynamical Framework for the All-or-None G1/S Transition Open
View article: Intrinsic Age-Dependent Changes and Cell-Cell Contacts Regulate Nephron Progenitor Lifespan
Intrinsic Age-Dependent Changes and Cell-Cell Contacts Regulate Nephron Progenitor Lifespan Open
View article: Erratum: Kinetochore–microtubule error correction is driven by differentially regulated interaction modes
Erratum: Kinetochore–microtubule error correction is driven by differentially regulated interaction modes Open
View article: Kinetochore–microtubule error correction is driven by differentially regulated interaction modes
Kinetochore–microtubule error correction is driven by differentially regulated interaction modes Open