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Tumors bearing Ras mutations are notoriously difficult to treat. Drug combinations targeting the Ras protein or its pathway have also not met with success. Pathway drug cocktails, which are combinations aiming at parallel pathways, appear…
A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…
Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…
Determining which proteins interact together is crucial to a systems-level understanding of the cell. Recently, algorithms based on Direct Coupling Analysis (DCA) pairwise maximum-entropy models have allowed to identify interaction partners…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
Link prediction is a popular research area with important applications in a variety of disciplines, including biology, social science, security, and medicine. The fundamental requirement of link prediction is the accurate and effective…
Protein-protein interactions (PPIs) are crucial in regulating numerous cellular functions, including signal transduction, transportation, and immune defense. As the accuracy of multi-chain protein complex structure prediction improves, the…
Accurate identification of protein binding sites is crucial for understanding biomolecular interaction mechanisms and for the rational design of drug targets. Traditional predictive methods often struggle to balance prediction accuracy with…
We introduce a new family of graphical models that consists of graphs with possibly directed, undirected and bidirected edges but without directed cycles. We show that these models are suitable for representing causal models with additive…
Faced with data-driven policies, individuals will manipulate their features to obtain favorable decisions. While earlier works cast these manipulations as undesirable gaming, recent works have adopted a more nuanced causal framing in which…
Gene regulatory networks play a crucial role in controlling an organism's biological processes, which is why there is significant interest in developing computational methods that are able to extract their structure from high-throughput…
Link prediction is central to unraveling social network evolution and node relationships, as well as understanding the characteristic mechanisms of complex networks. Currently, research on link prediction for complex dynamic networks…
A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…
Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…
Link and sign prediction in complex networks bring great help to decision-making and recommender systems, such as in predicting potential relationships or relative status levels. Many previous studies focused on designing the special…
Modeling biological networks serves as both a major goal and an effective tool of systems biology in studying mechanisms that orchestrate the activities of gene products in cells. Biological networks are context specific and dynamic in…
A cell routinely responds to one of many competing environmental cues. A fundamental question is whether the cell follows the cue prioritized by its internal signaling network or the cue that carries the most external information. We…
Identifying control strategies for biological networks is paramount for practical applications that involve reprogramming a cell's fate, such as disease therapeutics and stem cell reprogramming. Here we develop a novel network control…
A blood cell lineage consists of several consecutive developmental stages from the pluri- or multipotent stem cell to a state of terminal differentiation. Despite their importance for human biology, the regulatory pathways and gene networks…
The study of cellular signalling pathways and their deregulation in disease states, such as cancer, is a large and extremely complex task. Indeed, these systems involve many parts and processes but are studied piecewise and their…