Author Archives: Kermit Murray

BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" SingleCellGGM enables gene expression program identification from single-cell transcriptomes and facilitates universal cell label transfer Gene co-expression analysis of single-cell transcriptomes that aims to define functional relationships between genes is challenging due to excessive dropout values. Here, we developed …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Extended fractional-polynomial generalizations of diffusion and Fisher-KPP equations on directed networks: Modeling neurodegenerative progression In a variety of practical applications, there is a need to investigate diffusion or reaction-diffusion processes on complex structures, including brain networks, that can be …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Mathematically mapping the network of cells in the tumor microenvironment Cell-cell interaction networks are pivotal in cancer development and treatment response. These networks can be inferred from data, however this process often combines data from multiple patients, and/or creates …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Low dimensionality of phenotypic space as an emergent property of coordinated teams in biological regulatory networks Cell-fate decisions are driven by complex regulatory networks. Despite their complexity, these networks often exhibit low-dimensional dynamics and allow only a limited number …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Systematic identification of structure-specific protein-protein interactions Protein-protein interactions (PPIs) mediate numerous essential functions and regulatory events in living organisms. The physical interactome of a protein can be abnormally altered in response to external and internal cues, thus modulating cell …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Structure primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference The modeling of gene regulatory networks (GRNs) is limited due to a lack of direct measurements of regulatory features …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Consensus tissue domain detection in spatial -omics data using MILWRM Spatially resolved molecular assays provide high dimensional genetic, transcriptomic, proteomic, and epigenetic information in situ and at various resolutions. Pairing these data across modalities with histological features enables powerful …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" The attractor landscape of duplicated networks We study the effect that network duplication has on the topology of the state space of dynamical Boolean networks with thresholds. We show that the problem of finding the attractor dynamics is just …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Single cell ATAC sequencing identifies sleepy macrophages during reciprocity of cytokines in L.major infection Hallmark for macrophages is their ability to possess plasticity which enables them to respond to changing microenvironment. Leishmania takes use of the phenotypic plasticity of …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Computational modeling of DLBCL predicts response to BH3-mimetics. In healthy cells, pro- and anti-apoptotic BCL2 family and BH3-only proteins are expressed in a delicate equilibrium. In contrast, this homeostasis is frequently perturbed in cancer cells due to the overexpression …

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