BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomes Background: The multiome is an integrated assembly of distinct classes of molecules and molecular properties, or omes, measured in the same biospecimen. Freezing and formalin-fixed paraffin-embedding …
Tag Archives: BioRxiv
Ensemble and Iterative Engineering for Maximized Bioconversion to the Blue Pigment, Indigoidine from Non-Canonical Sustainable Carbon Sources
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Ensemble and Iterative Engineering for Maximized Bioconversion to the Blue Pigment, Indigoidine from Non-Canonical Sustainable Carbon Sources While many heterologous molecules can be produced at trace concentrations via microbial bioconversion processes, maximizing their titers, rates, and yields from lignin-derived …
Integrative proteomics and transcriptomics of human T-cells reveals temporal metabolic reprogramming following TCR-induced activation
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Integrative proteomics and transcriptomics of human T-cells reveals temporal metabolic reprogramming following TCR-induced activation T-cells are critical components of the adaptive immune system. Upon activation, they acquire effector functions through a complex interplay between mRNA transcripts and proteins, the …
Exploring the noncanonical translatome using massively integrated coexpression analysis
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Exploring the noncanonical translatome using massively integrated coexpression analysis Cells transcribe and translate thousands of noncanonical open reading frames (nORFs) whose impacts on cellular phenotypes are unknown. Here, we investigated nORF transcription, evolution, and potential cellular roles using a …
Identifying drug effects in a cardiac model of electrophysiology using kernel-based parameter estimation methods
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Identifying drug effects in a cardiac model of electrophysiology using kernel-based parameter estimation methods Computational models of cardiac electrophysiology hold great potential in the drug discovery process to bridge the gap between in vitro and in vivo preclinical trials. …
Guide-specific loss of efficiency and off-target reduction with Cas9 variants
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Guide-specific loss of efficiency and off-target reduction with Cas9 variants High-fidelity Cas9 variants have been developed to reduce the off-target effects of CRISPR systems at a cost of efficiency loss. To systematically evaluate the efficiency and off-target tolerance of …
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Comparative analysis between RNA-seq and single-molecule RNA FISH indicates that the pyrimidine nucleobase idoxuridine (IdU) globally amplifies transcriptional noise
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Comparative analysis between RNA-seq and single-molecule RNA FISH indicates that the pyrimidine nucleobase idoxuridine (IdU) globally amplifies transcriptional noise Stochastic fluctuations (noise) in transcription generate substantial cell-to-cell variability, but the physiological roles of noise have remained difficult to determine …
Leveraging gene correlations in single cell transcriptomic data
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Leveraging gene correlations in single cell transcriptomic data Many approaches have been developed to overcome technical noise in single cell (and single nucleus) RNA-sequencing (scRNAseq). As researchers dig deeper into data–looking for rare cell types, subtleties of cell states, …
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MolClustPy: A Python Package to Characterize Multivalent Biomolecular Clusters
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" MolClustPy: A Python Package to Characterize Multivalent Biomolecular Clusters SUMMARY: Low-affinity interactions among multivalent biomolecules may lead to the formation of molecular complexes that undergo phase transitions to become extra-large clusters. Characterizing the physical properties of these clusters is …
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Leukemia core transcriptional circuitry is a sparsely interconnected hierarchy stabilized by incoherent feed-forward loops
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Leukemia core transcriptional circuitry is a sparsely interconnected hierarchy stabilized by incoherent feed-forward loops Lineage-defining transcription factors form densely interconnected circuits in chromatin occupancy assays, but the functional significance of these networks remains underexplored. We reconstructed the functional topology …
A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion T cells play a key role in a variety of immune responses, including infection and cancer. Upon stimulation, naive CD8+ T cells proliferate and differentiate …
Distilling identifiable and interpretable dynamic models from biological data
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Distilling identifiable and interpretable dynamic models from biological data Mechanistic dynamical models allow us to study the behavior of complex biological systems. They can provide an objective and quantitative understanding that would be difficult to achieve through other means. …
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TimeTeller: a tool to probe the circadian clock as a multigene dynamical system
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" TimeTeller: a tool to probe the circadian clock as a multigene dynamical system Recent studies have established that the circadian clock influences onset, progression and therapeutic outcomes in a number of diseases including cancer and heart diseases. Therefore, there …
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In silico agent-based modeling approach to characterize multiple in vitro tuberculosis infection models
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" In silico agent-based modeling approach to characterize multiple in vitro tuberculosis infection models In vitro models of Mycobacterium tuberculosis (Mtb) infection are a valuable tool to examine host-pathogen interactions and screen drugs. With the development of more complex in …
Cardiopulmonary structural, functional and immune-alterations in a Down syndrome mouse model and upon modulation of EGCG
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Cardiopulmonary structural, functional and immune-alterations in a Down syndrome mouse model and upon modulation of EGCG In individuals with Down syndrome (DS), cardiovascular and pulmonary diseases are the most common health problem and result in increased mortality and morbidity. …
OptEnvelope: a target point guided method for growth-coupled production using knockouts
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" OptEnvelope: a target point guided method for growth-coupled production using knockouts Finding the best knockout strategy for coupling biomass growth and production of a target metabolite using a metabolic model is a challenge in biotechnology. In this research, a …
A systematic search for RNA structural switches across the human transcriptome
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" A systematic search for RNA structural switches across the human transcriptome RNA structural switches are key regulators of gene expression in bacteria, yet their characterization in Metazoa remains limited. Here we present SwitchSeeker, a comprehensive computational and experimental approach …
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A Consensus Model of Glucose-Stimulated Insulin Secretion in the Pancreatic beta-Cell
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" A Consensus Model of Glucose-Stimulated Insulin Secretion in the Pancreatic beta-Cell The pancreas plays a critical role in maintaining glucose homeostasis through the secretion of hormones from the islets of Langerhans. Glucose-stimulated insulin secretion (GSIS) by the pancreatic beta-cell …
Multidimensional proteomics identifies molecular trajectories of cellular aging and rejuvenation
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Multidimensional proteomics identifies molecular trajectories of cellular aging and rejuvenation The declining capacity of cells to maintain a functional proteome is a major driver of cellular dysfunction and decreased fitness in aging. Here we assess the impact of aging …
Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors Colorectal cancer exhibits dynamic cellular and genetic heterogeneity during progression from precursor lesions toward malignancy. Leveraging spatial molecular information to construct a phylogeographic map of tumor evolution can …