2025 Hyper Recent •CC0 1.0 Universal

This work is dedicated to the public domain. No rights reserved.

Access Preprint From Server
June 2nd, 2025
Version: 1
Westlake University
systems biology
biorxiv

BioLogical: a universal analysis framework for biosystem logical dynamic

Yao, Y.Open in Google Scholar•Liu, D.Open in Google Scholar•Zhang, Z.Open in Google Scholar•Zhao, C.Open in Google Scholar•Pei, D.Open in Google Scholar

Complex biosystems exhibit ordered, functional, self-organized features. However, a universal framework for exploring their logical paradigms and dynamic characteristics remains lacking. Here we describe BioLogical, a user-friendly R package, designed for analyzing properties of biosystems. We demonstrate its versatile capacities of deciphering multi-valued logical paradigms, calculating order parameters, and simulating system dynamic, even multi-valued Quine-McCluskey and logical satisfiability analysis. The open-source software is available at https://github.com/YuxiangYao/BioLogical.

Similar Papers

biorxiv
Wed Jun 04 2025
Disentangling the cost of gene expression
Gene expression is essential for biological functions but also incurs a fitness cost, measured by the relative reduction in growth rate. However, the limiting factors generating the fitness cost remain elusive due to the complexity of cell growth. In this work, we disentangle the fitness cost into components generated by different limiting resources based on a resource competition model. We derive...
Yan, Y.
•
Lin, J.
biorxiv
Tue Jun 03 2025
Critical assessment of the ability of Boolean threshold models to describe gene regulatory network dynamics.
The inference of gene regulatory networks (GRNs) from high-throughput data constitutes a fundamental and challenging task in systems biology. Boolean networks are a popular modeling framework to understand the dynamic nature of GRNs. In the absence of reliable methods to infer the regulatory logic of Boolean GRN models, researchers frequently assume threshold logic as a default. Using the largest ...
Kadelka, C.
•
Hari, K.
biorxiv
Tue Jun 03 2025
Recurrent Emergence of Boundary Cell Types During Evolution of Floral Bullseye Patterns
Petal patterns contribute to the reproductive success of flowering plants by attracting pollinators and protecting reproductive organs from environmental factors. While some transcription factors (TFs) controlling pigment production and cuticle elaboration have been identified, little is known about the upstream developmental processes that first establish the petal regions where these regulators ...
Oud, S.
•
Zurowski, M. M.
•
van der Jagt, P. L.
•
Yeo, M. T. S.
...•
Vroomans, R. M. A.
biorxiv
Tue Jun 03 2025
A Solid-Phase Extraction Capture (SPEC) workflow in nanoliter volumes for fast, robust and ultrasensitive proteomics
Despite great progress, sample preparation remains an area for improvement in proteomics, particularly for low-input samples where conventional protocols lead to losses and incomplete digestion. We present Solid-Phase Extraction Capture (SPEC), a modular workflow that confines protein processing to nanoliter-scale volumes within C18 or ion-exchange tips. SPEC enables highly efficient proteolysis d...
Heymann, T.
•
Oliinyk, D.
•
Henneberg, L.
•
Rodriguez, E.
...•
Mann, M.
biorxiv
Tue Jun 03 2025
Dissecting crosstalk induced by cell-cell communication using single-cell transcriptomic data
During cell-cell communication (CCC), pathways activated by different ligand-receptor pairs may have crosstalk with each other. While multiple methods have been developed to infer CCC networks and their downstream response using single-cell RNA-seq data (scRNA-seq), the potential crosstalk between pathways connecting CCC with its downstream targets has been ignored. Here we introduce a machine lea...
Hou, J.
•
Zhao, W.
•
Nie, Q.
biorxiv
Tue Jun 03 2025
Multi-Omic Profiling Identifies Conserved Metabolic Pathways Critical for SARS-CoV-2 Variants Infection
The rapid evolution of SARS-CoV-2 has led to the emergence of numerous variants with en-hanced transmissibility and immune evasion. Despite widespread vaccination, infections persist, and the mechanisms by which SARS-CoV-2 reprograms host metabolism remain in-completely understood. Here, we investigated whether virus-induced lipid remodeling is con-served across variants and whether changes in lip...
Farley, S. E.
•
Kyle, J. E.
•
Jahn, H.
•
Bramer, L.
...•
Tafesse, F.
biorxiv
Mon Jun 02 2025
Inference and prediction for random walk models in biology
Parameter inference is a critical step in the process of interpreting biological data using mathematical models. Inference provides a means of deriving quantitative, mechanistic insights from sparse, noisy data. While methods for parameter inference, parameter identifiability, and model prediction are well-developed for deterministic continuum models, working with biological applications often req...
Simpson, M. J.
•
Plank, M. J.
biorxiv
Mon Jun 02 2025
Informed Data-Independent Acquisition Enables Targeted Quantification of Key Regulatory Proteins in Cell Fate Decision at Single-Cell Resolution
Cellular differentiation processes are largely orchestrated by variation in transcription factor (TF) abundance. Since these proteins are usually expressed at extremely low levels, studying TF-driven cellular processes using single-cell proteomics by mass spectrometry (scp-MS) has been challenging. Here we present informed DIA (iDIA), an acquisition method tailored towards low-input and scp-MS. iD...
Woessmann, J.
•
Petrosius, V.
•
Schovsbo, S.
•
Arrey, T. N.
...•
Schoof, E. M.
biorxiv
Sun Jun 01 2025
EXOSC3 S1-domain variants implicated in PCH1b alter RNA exosome cap subunit abundance and thermal stability disrupting rRNA processing and targeting of AU-rich mRNA
Missense variants in EXOSC3, an RNA exosome subunit, have been identified in patients with PCH1b. We investigated three missense variants in the S1 domain of EXOSC3, including one variant of uncertain significance (VUS) and two pathogenic variants (hence S1 variants). EXOSC3 S1 variant cell lines were generated using CRISPR-Cas9 resulting in widespread proteome changes including decreases in some ...
Runnebohm, A. M.
•
Wijeratne, H. S.
•
Barron, M. P.
•
Smith-Kinnaman, W. R.
...•
Mosley, A. L.