定量方法
Motivation: Over the past decade, network-based approaches have proven useful in identifying disease modules within the human interactome, often providing insights into key mechanisms and guiding the quest for therapeutic targets. This is…
Pretraining molecular representation models without labels is fundamental to various applications. Conventional methods mainly process 2D molecular graphs and focus solely on 2D tasks, making their pretrained models incapable of…
Intercellular signaling has an important role in organism development, but not all communication occurs using the same mechanism. Here, we analyze the energy efficiency of intercellular signaling by two canonical mechanisms: diffusion of…
Acute myocardial infarction (AMI) is one of the most severe manifestation of coronary artery disease. ST-segment elevation myocardial infarction (STEMI) is the most serious type of AMI. We proposed to develop a machine learning algorithm…
Cryo-electron microscopy (cryo-EM) is unique among tools in structural biology in its ability to image large, dynamic protein complexes. Key to this ability is image processing algorithms for heterogeneous cryo-EM reconstruction, including…
Face masks have been widely used as a protective measure against COVID-19. However, pre-pandemic empirical studies have produced mixed statistical results on the effectiveness of masks against respiratory viruses. The implications of the…
A fibration of graphs is an homomorphism that is a local isomorphism of in-neighbourhoods, much in the same way a covering projection is a local isomorphism of neighbourhoods. Recently, it has been shown that graph fibrations are useful…
The generation of conformers has been a long-standing interest to structural chemists and biologists alike. A subset of proteins known as intrinsically disordered proteins (IDPs) fail to exhibit a fixed structure and, therefore, must also…
Resolving the structural variability of proteins is often key to understanding the structure-function relationship of those macromolecular machines. Single particle analysis using Cryogenic electron microscopy (CryoEM), combined with…
Cancer claims millions of lives yearly worldwide. While many therapies have been made available in recent years, by in large cancer remains unsolved. Exploiting computational predictive models to study and treat cancer holds great promise…
Drug discovery is vitally important for protecting human against disease. Target-based screening is one of the most popular methods to develop new drugs in the past several decades. This method efficiently screens candidate drugs inhibiting…
The ability to design and optimize biological sequences with specific functionalities would unlock enormous value in technology and healthcare. In recent years, machine learning-guided sequence design has progressed this goal significantly,…
Cell spheroids are in vitro multicellular model systems that mimic the crowded micro-environment of biological tissues. Their mechanical characterization can provide valuable insights in how single-cell mechanics and cell-cell interactions…
Signed networks, i.e., networks with positive and negative edges, commonly arise in various domains from social media to epidemiology. Modeling signed networks has many practical applications, including the creation of synthetic data sets…
Avian botulism is a paralytic bacterial disease in birds often leading to high fatality. In-vitro diagnostic techniques such as Mouse Bioassay, ELISA, PCR are usually non-preventive, post-mortem in nature, and require invasive sample…
Spontaneous mouse behavior is composed from repeatedly-used modules of movement (e.g., rearing, running, grooming) that are flexibly placed into sequences whose content evolves over time. By identifying behavioral modules and the order in…
It is shown that various symptoms could remain in the stage of post-acute sequelae of SARS-CoV-2 infection (PASC), otherwise known as Long COVID. A number of COVID patients suffer from heterogeneous symptoms, which severely impact recovery…
Survival risk prediction using gene expression data is important in making treatment decisions in cancer. Standard neural network (NN) survival analysis models are black boxes with lack of interpretability. More interpretable visible neural…
The massive amount of genomic data appearing for SARS-CoV-2 since the beginning of the COVID-19 pandemic has challenged traditional methods for studying its dynamics. As a result, new methods such as Pangolin, which can scale to the…
Summary: The Systems Biology Markup Language (SBML) is an extensible standard format for exchanging biochemical models. One of the extensions for SBML is the SBML Layout and Render package. This allows modelers to describe a biochemical…