Related papers: Classification Framework and Structure-Activity-Re…
Emergent behavior in complex systems arises from nonlinear interactions among components, yet the intricate nature of self-organization often obscures the underlying causal relationships, long regarded as the "holy grail" of complexity…
Drug synergy prediction is a critical task in the development of effective combination therapies for complex diseases, including cancer. Although existing methods have shown promising results, they often operate as black-box predictors that…
Peptide-drug conjugates (PDCs) represent a promising therapeutic avenue for human diseases, particularly in cancer treatment. Systematic elucidation of structure-activity relationships (SARs) and accurate prediction of the activity of PDCs…
Drug combination therapy is a well-established strategy for disease treatment with better effectiveness and less safety degradation. However, identifying novel drug combinations through wet-lab experiments is resource intensive due to the…
The study of granular crystals, metamaterials that consist of closely packed arrays of particles that interact elastically, is a vibrant area of research that combines ideas from disciplines such as materials science, nonlinear dynamics,…
Computational drug discovery strategies can be broadly placed in two categories: ligand-based methods which identify novel molecules by similarity with known ligands, and structure-based methods which predict molecules with high-affinity to…
Discoveries of endogenous human stem cell-associated retroviruses (SCARs) revealed consistent activation of specific endogenous retroviral elements in human preimplantation embryos and documented the essential role of the sustained…
The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and micro-clusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell…
Higher-order tensor decompositions have hardly been used in muscle activity analysis despite multichannel electromyography (EMG) datasets naturally occurring as multi-way structures. Here, we seek to demonstrate and discuss the potential of…
T-cells play a key role in adaptive immunity by mounting specific responses against diverse pathogens. An effective binding between T-cell receptors (TCRs) and pathogen-derived peptides presented on Major Histocompatibility Complexes (MHCs)…
Structure-based drug design involves finding ligand molecules that exhibit structural and chemical complementarity to protein pockets. Deep generative methods have shown promise in proposing novel molecules from scratch (de-novo design),…
Disordered systems like liquids, gels, glasses, or granular materials are not only ubiquitous in daily life and in industrial applications but they are also crucial for the mechanical stability of cells or the transport of chemical and…
Understanding causal relationships in multivariate time series is essential for predicting and controlling dynamic systems in fields like economics, neuroscience, and climate science. However, existing causal discovery methods often assume…
Network science is already making an impact on the study of complex systems and offers a promising variety of tools to understand their formation and evolution (1-4) in many disparate fields from large communication networks (5,6),…
Many diseases display heterogeneity in clinical features and their progression, indicative of the existence of disease subtypes. Extracting patterns of disease variable progression for subtypes has tremendous application in medicine, for…
Periodic structures are a type of metamaterial in which the physical properties depend not only on the details of the unit cell but also on how unit cells are arranged and interact with each other. In conventional engineering structures,…
For a set of mulitple sequences, their patterns,Longest Common Subsequences (LCS) and Shortest Common Supersequences (SCS) represent different aspects of these sequences profile, and they can all be used for biological sequence comparisons…
Spectral graph theory-based methods represent an important class of tools for studying the structure of networks. Spectral methods are based on a first-order Markov chain derived from a random walk on the graph and thus they cannot take…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
With the propagation of sensor devices applied in smart home, activity recognition has ignited huge interest and most existing works assume that there is only one habitant. While in reality, there are generally multiple residents at home,…