{"title":"Inferring absolute counts from proportions by constraining multivariate normal distributions.","authors":"Jeffrey Hage, Devin Koestler, Brock Christensen","doi":"10.1038/s41540-026-00737-9","DOIUrl":"10.1038/s41540-026-00737-9","url":null,"abstract":"<p><p>Biological measurements often result in proportional data, which are derived from underlying biological counts. Proportion data are lacking a dimension of information as compared to counts, restricting available analysis methods and separating the data from the biology. We demonstrate a mathematical technique that estimates absolute counts corresponding to proportion data, which we refer to as Mahalanobis Count Inference (MCI). MCI uses information from a population-representative multivariate normal (MVN) distribution of component counts and ultimately outputs an estimated count and a confidence interval per observation proportion vector. We apply MCI to the imputation of white blood cell (WBC) counts, and of total mRNA within single cells. The method performs very well on total mRNA recapitulation (log-space Pearson's R = 0.81), and well enough on WBC counts to outperform proportions at multiple classification tasks. MCI offers a general approach to count inference that is applicable to multiple biological omics.</p>","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13396772/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147932108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"tugMedi: simulator of cancer-cell evolution for personalized medicine based on the genomic data of patients.","authors":"Iurii Nagornov, Eisaku Furukawa, Momoko Nagai, Shigehiro Yagishita, Tatsuhiro Shibata, Mamoru Kato","doi":"10.1038/s41540-026-00736-w","DOIUrl":"10.1038/s41540-026-00736-w","url":null,"abstract":"<p><p>Cancer comprehensive genomic profiling tests are increasingly used, but drug response rates to matched therapies remain limited, indicating a gap between genomic data and clinical benefit. However, existing cancer evolution simulations focus mainly on basic biology and rarely provide patient‑specific predictions for therapy response. We present tugMedi, a cancer‑cell evolution simulator designed for cancer genome medicine. Integrating patient‑specific genomic data from next‑generation sequencing and radiological imaging, tugMedi reconstructs tumor features and growth, enabling real‑time predictions of clonal dynamics under drug interventions. It explicitly models copy number alterations and SNVs on parental chromosomes with recessive/dominant modes, capturing intra‑tumor heterogeneity and loss‑of‑heterozygosity to yield precise variant allele frequencies and tumor purity estimates. Synthetic tests confirmed recovery of ground‑truth tumor parameters and trajectories. For TCGA samples, tugMedi provided ensemble forecasts of drug response, tumor shrinkage, and recurrence times under specific drug conditions, demonstrating the feasibility of simulation‑driven genome medicine using patient‑derived virtual tumors.</p>","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13402625/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147932153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Adrian Ratwatte, Samitha Somathilaka, Ngoc Dan Thanh Cao, Xu Li, Sasitharan Balasubramaniam
{"title":"Bacterial gene regulatory neural network as a biocomputing library of mathematical solvers.","authors":"Adrian Ratwatte, Samitha Somathilaka, Ngoc Dan Thanh Cao, Xu Li, Sasitharan Balasubramaniam","doi":"10.1038/s41540-026-00733-z","DOIUrl":"10.1038/s41540-026-00733-z","url":null,"abstract":"<p><p>Current biocomputing approaches predominantly rely on engineered circuits with fixed logic, offering limited stability and reliability under diverse environmental conditions. Here, we use the gene regulatory neural network (GRNN) framework introduced in our previous work to transform bacterial gene expression dynamics into a biocomputing library of mathematical solvers. We introduce a sub-GRNN search algorithm as a general computational framework for identifying functional subnetworks within native transcriptional networks by evaluating gene expression patterns across chemically encoded input conditions. Mathematical calculation and classification tasks, including identifying Fibonacci numbers, prime numbers, multiplication, and Collatz step counts, are used as case studies to validate the proposed framework. The identified problem-specific sub-GRNNs are then assessed using gene-wise and collective perturbation, as well as Lyapunov-based stability analysis, to evaluate robustness and reliability. Our results demonstrate that native transcriptional machinery can be harnessed to perform diverse mathematical calculation and classification tasks, while maintaining computing stability and reliability.</p>","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13389163/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147932081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Patrick M Jensen, Jan Lellmann, Christian Sperling, Frieder Meier, Marius Distler, Daniela E Aust, Herbert Thiele, Pia Hönscheid
{"title":"Interpreting MALDI imaging data for rare types of ampullary cancer using machine learning.","authors":"Patrick M Jensen, Jan Lellmann, Christian Sperling, Frieder Meier, Marius Distler, Daniela E Aust, Herbert Thiele, Pia Hönscheid","doi":"10.1038/s41540-026-00705-3","DOIUrl":"10.1038/s41540-026-00705-3","url":null,"abstract":"<p><p>Rare tumor diseases are difficult to diagnose and there is a lack of routine diagnostic procedures. Approaches must be found that allow comprehensive identification and evaluation of prognostic relevant target proteins or transcripts. Analyzing rare ampullary cancer, respectively, to their prognosis and predictive factors by machine learning (ML) based matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) imaging is a first step towards providing new solutions for diagnostics of those cancer samples. In this study, we investigated a cohort of ampullary adenocarcinomas, including intestinal, pancreatic and cases of unknown subtypes, to identify differences in the proteome. Human formalin-fixed paraffin-embedded (FFPE) tissues were pathologically assessed, immunohistological stained, MALDI Imaging detected, and ML-related analyzed. We enable MALDI imaging as a diagnostic complement for immunohistochemical analysis and provide a MALDI Imaging neural network for broad application in tumor diagnostics. Moreover, using tools from ML model explainability, we determined a small subset of influential m/z-values from the trained models. The transformation of locally established ML networks dependent on one proteomic application source to other similar application sources (without peak picking or other pre-processing) is the basis for future rare cancer patient data collection.</p>","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13388676/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147932127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Insuck Baek, Seunghyun Lim, Lalit M Kandpal, Chansong Hwang, Moon S Kim, Sunchung Park, Louis K Prom, Lyndel W Meinhardt, Clint Magill, Ezekiel Ahn
{"title":"Decoupling the chemical and physical origins of the seed spectral manifold in sorghum.","authors":"Insuck Baek, Seunghyun Lim, Lalit M Kandpal, Chansong Hwang, Moon S Kim, Sunchung Park, Louis K Prom, Lyndel W Meinhardt, Clint Magill, Ezekiel Ahn","doi":"10.1038/s41540-026-00728-w","DOIUrl":"10.1038/s41540-026-00728-w","url":null,"abstract":"<p><p>Biological structures interact with light as complex manifolds, yet genomic studies often reduce these phenotypes to scalar traits. Here we resolve the sorghum seed spectral manifold into separable axes corresponding primarily to pigment-associated and structure-associated optical variation. Path analysis indicates that near-infrared (NIR) reflectance is associated primarily with an indirect path through seed mass, supporting partial decoupling from pigmentation-related variation. We identify a chromosome 6 region associated with NIR reflectance and spectral entropy, consistent with a contribution to the physical-structural axis of the seed optical phenotype. Furthermore, in silico perturbation analyses suggest that major axes of seed optics are structured and can be predictably shifted within the observed phenotypic manifold. By linking spectral variation to morphology and genetic association, this work provides a framework for interpreting seed optical phenotypes beyond simple color categories and for studying how light-matter interactions are shaped by plant structure and chemistry.</p>","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13381802/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147875164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"CT-TADB predicts TAD boundaries without Hi-C by integrating DNA sequences and epigenomic features.","authors":"Tong Chen, Shuaibin Wang, Yuyu Jin, Yuan Yuan, Zhen Liang, Yin Shen","doi":"10.1038/s41540-026-00734-y","DOIUrl":"10.1038/s41540-026-00734-y","url":null,"abstract":"<p><p>Topologically associating domains (TADs) are fundamental units of three-dimensional genome organization, and their boundaries play important roles in gene regulation and genomic stability. However, accurate computational prediction of TAD boundaries remains challenging because of the complex interplay between DNA sequence and epigenomic regulatory signals. Here we present CT-TADB, a hybrid CNN-Transformer framework that integrates DNA sequence with histone modification and CTCF binding signals to predict TAD boundaries without requiring Hi-C data. Trained on six human cell lines, CT-TADB achieved AUC values of 0.932-0.950, demonstrating competitive or superior performance relative to existing multi-modal methods. The model maintained stable performance on strictly independent and dataset-specific boundary subsets, and exhibited robust cross-cell-type transferability and cross-species generalization between human and mouse (AUC > 0.80 for human-to-mouse transfer). Feature attribution analysis identified CTCF as the dominant boundary-associated factor, supported by active chromatin marks, and quantitative attention analysis revealed significant long-range CTCF-mediated dependencies (p < 0.001). CT-TADB further identified a clinically validated PITX2-associated TAD boundary linked to cardiac arrhythmia and captured condition-specific boundary dynamics. By leveraging routinely available epigenomic data, CT-TADB provides a practical and complementary framework for investigating chromatin architecture across diverse biological contexts.</p>","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13376763/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147864167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Flux sampling and graph neural networks for improved gene essentiality prediction in mammalian genome-scale metabolic models.","authors":"Kieren Sharma, Lucia Marucci, Zahraa S Abdallah","doi":"10.1038/s41540-026-00738-8","DOIUrl":"10.1038/s41540-026-00738-8","url":null,"abstract":"<p><p>Gene essentiality, the requirement of a gene for survival or proliferation, is central to understanding cellular processes and identifying drug targets. Experimental determination requires large growth screens that are time-consuming and expensive, motivating in silico approaches. Existing methods predominantly use flux balance analysis (FBA), a constraint-based optimisation framework that requires a predefined cellular objective function. This can introduce observer bias, because the objective often reflects the researcher's assumptions rather than the cell's biological goals. Here, we present FluxGAT, a graph neural network (GNN) that predicts gene essentiality from graphical representations of flux sampling data. Flux sampling removes the need for an explicit objective and instead characterises feasible steady-state fluxes. FluxGAT combines this information with metabolic network topology to learn flux-informed node representations and classify reactions as essential or non-essential. We apply FluxGAT to the iCHO2291 genome-scale model of Chinese hamster ovary cells and Mouse1, a generic mouse model with independent essentiality labels. In both systems, FluxGAT improves sensitivity over FBA while maintaining high precision and specificity, and recovers more experimentally essential genes, especially where FBA predicts very few essentials. These results show that flux-informed GNNs can provide more general gene essentiality predictions across mammalian genome-scale models without hand-crafted objective functions.</p>","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13369363/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147856769","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Philipp Henning, Julia Schultz, Simone Baltrusch, Adelinde M Uhrmacher
{"title":"A rule-based simulation model illuminates the role of asymmetric mitochondrial fission on beta-cell health.","authors":"Philipp Henning, Julia Schultz, Simone Baltrusch, Adelinde M Uhrmacher","doi":"10.1038/s41540-026-00732-0","DOIUrl":"10.1038/s41540-026-00732-0","url":null,"abstract":"<p><p>Mitochondrial dynamics play a critical role in the development of aging-related diseases such as type 2 diabetes mellitus. To investigate how mitochondrial dynamics influence cellular behavior in pancreatic beta-cells, we developed a rule-based, multi-level simulation model of insulin secretion. The pancreatic beta-cell model encompasses metabolic pathways (glycolysis and oxidative phosphorylation), compartmental processes (mitochondrial fusion and fission), and cellular processes (insulin secretion), allowing for the investigation of their interplay. The rule-based simulation model captures the high plasticity of these organelles and integrates and builds upon insights from various experimental studies and previous simulation models. Its rule-based specification facilitates the exploration of new hypotheses, the integration of new knowledge and data, and the successive extension of the model. The results of our simulation experiments underscore the importance of peripheral, sorted mitochondrial fission in maintaining mitochondrial health. Downregulation of the fission-associated anchor proteins Fis1 and MFF impacts mitochondrial structure and function differently, highlighting their distinct roles in maintaining mitochondrial health and cellular biogenesis, respectively. With respect to insulin secretion, Drp1 suppression shows that beta-cells become unresponsive to glucose, whereas Fis1 downregulation only attenuates the cellular response. The simulation model and simulation results corroborate experimental findings and contribute to a deeper understanding of the mechanisms involved in mitochondrial dynamics of pancreatic beta-cells and their relation to metabolic dysregulation in type 2 diabetes mellitus.</p>","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":"12 1","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13144372/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147841001","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hong Liu, Xuanfeng Li, Ning Sun, Jingjing Tian, Ming Xu, Chitin Hon
{"title":"Spatiotemporal instability of influenza seasonality during viral co-circulation.","authors":"Hong Liu, Xuanfeng Li, Ning Sun, Jingjing Tian, Ming Xu, Chitin Hon","doi":"10.1038/s41540-026-00729-9","DOIUrl":"10.1038/s41540-026-00729-9","url":null,"abstract":"<p><p>Co-circulation of multiple influenza subtypes poses a major challenge to global public health. However, its specific impact on non-stationary epidemic sequences and coupling relationships with environmental drivers remains poorly understood. By integrating STL, Adaptive Fourier Decomposition, Continuous Wavelet Transform, and Wavelet Coherence, we analyzed 323 weekly influenza surveillance time series from China (2011-2025). The study identifies a fundamental regime shift during co-circulation periods, transitioning from ordered single-dominant transmission to a chaotic state. This instability is characterized by significant dominant periodicity dispersion, amplified seasonality shifts, and high-intensity anomalies in residual components, with overall seasonal strength dropping by 28%. Crucially, we uncover a marked north-south mechanistic divergence: northern regions exhibited \"Environmental Locking,\" remaining strongly constrained by climates during co-circulation; conversely, southern regions demonstrated \"Environmental Decoupling\" (H3N2 phase consistency with soil moisture plummeted from R=0.45 to 0.07), where viral ecological competition overshadowed environmental drivers. Influenza co-circulation acts as a systemic perturbation reshaping transmission dynamics. Our findings highlight the necessity for context-adaptive strategies: northern regions can maintain reliance on meteorological warnings, while southern regions must dynamically shift focus toward real-time virological surveillance during co-circulation to capture rapid ecological shifts.</p>","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13346841/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genetic basis of temporal variation in phenology in a woody perennial plant.","authors":"Yang Liu","doi":"10.1038/s41540-026-00691-6","DOIUrl":"10.1038/s41540-026-00691-6","url":null,"abstract":"<p><p>The form of phenotypic plasticity in traits that are repeatedly and potentially reversibly expressed multiple times throughout an individual's lifetime is labile plasticity. Yet, little is known about selection on, and genetic variation and inheritance in, such plasticity. Herein I embedded dynamic growth phenology traits into empirical understanding of the variability, inheritance, and predictability of their labile plasticity using a Populus common-garden experiment. I found no single nucleotide polymorphisms (SNPs) peak associated at P < 1e<sup>-4</sup> with labile plasticity in phenological traits, overlapping in its two populations and no such plasticity-associated SNPs identified across study traits in single populations. Higher plasticity and more plasticity SNPs were identified in the population from climatically harsher conditions. While 6% of phenology peak-associated SNPs underwent adaptive selection, 95% of the identified plasticity SNPs were also peak associated with a given phenology, but none of them were found under selection. Plasticity SNP-containing genes highlighted environmental responsiveness functions for phenology plasticity. Projections for labile plasticity in phenology consistently showed that plasticity or trait peak-associated SNPs generated a higher predictive accuracy than non-associative counterparts. Altogether, the study elucidates the idiosyncratic characteristics of labile plasticity in growth phenology and deepens our understanding of its genetic modulation and evolution.</p>","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13347011/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}