Frontiers in Systems Biology | Data and Model Integration

Original Research

Published on 08 Dec 2025

BioMedKG: multimodal contrastive representation learning in augmented BioMedical knowledge graphs

in Data and Model Integration

Tien Dang
Viet Thanh Duy Nguyen
Minh Tuan Le
Truong-Son Hy

Frontiers in Systems Biology

doi 10.3389/fsysb.2025.1651930

745 views

Original Research

Published on 27 Oct 2025

The role of neutrophil-to-lymphocyte ratio in the prognosis of chronic kidney disease: insights from the NHANES cohort study

in Data and Model Integration

Ying Liu
Ru Wang
Jinguo Yuan
Jin Zhao

Frontiers in Systems Biology

doi 10.3389/fsysb.2025.1656683

937 views

Correction

Published on 23 Oct 2025

Correction: A guide to bayesian networks software for structure and parameter learning, with a focus on causal discovery tools

in Data and Model Integration

Francesco Canonaco
Joverlyn Gaudillo
Nicole Astrologo
Fabio Stella
Enzo Acerbi

Frontiers in Systems Biology

doi 10.3389/fsysb.2025.1717030

810 views

Original Research

Published on 29 Sep 2025

GETgene-AI: a framework for prioritizing actionable cancer drug targets

in Data and Model Integration

Adrian Gu
Jake Y. Chen

Frontiers in Systems Biology

doi 10.3389/fsysb.2025.1649758

2,855 views

Mini Review

Published on 25 Aug 2025

A guide to bayesian networks software for structure and parameter learning, with a focus on causal discovery tools

in Data and Model Integration

Francesco Canonaco
Joverlyn Gaudillo
Nicole Astrologo
Fabio Stella
Enzo Acerbi

Frontiers in Systems Biology

doi 10.3389/fsysb.2025.1631901

3,314 views
1 citation

Methods

Published on 03 Jul 2025

Learning Gaussian graphical models from correlated data

in Data and Model Integration

Zeyuan Song
Sophia Gunn
Stefano Monti
Gina M. Peloso
Ching-Ti Liu
Kathryn Lunetta
Paola Sebastiani

Frontiers in Systems Biology

doi 10.3389/fsysb.2025.1589079

1,706 views

Original Research

Published on 03 Jan 2025

Improvement in the prediction power of an astrocyte genome-scale metabolic model using multi-omic data

in Data and Model Integration

Andrea Angarita-Rodríguez
Nicolás Mendoza-Mejía
Janneth González
Jason Papin
Andrés Felipe Aristizábal
Andrés Pinzón

Frontiers in Systems Biology

doi 10.3389/fsysb.2024.1500710

2,973 views

Original Research

Published on 15 Oct 2024

Intertwined roles for GDF-15, HMGB1, and MIG/CXCL9 in Pediatric Acute Liver Failure

in Data and Model Integration

Ruben Zamora
Jinling Yin
Derek Barclay
James E. Squires
Yoram Vodovotz

Frontiers in Systems Biology

doi 10.3389/fsysb.2024.1470000

2,008 views
2 citations

Methods

Published on 03 Oct 2024

Spectral expansion methods for prediction uncertainty quantification in systems biology

in Data and Model Integration

Anna Deneer
Jaap Molenaar
Christian Fleck

Frontiers in Systems Biology

doi 10.3389/fsysb.2024.1419809

1,847 views
2 citations

Original Research

Published on 02 Sep 2024

Accessible Type 2 diabetes medication through stable expression of Exendin-4 in Saccharomyces cerevisiae

in Data and Model Integration

Gia Balius
Kiana Imani
Zoë Petroff
Elizabeth Beer
Thiago Brasileiro Feitosa
Nathan Mccall
Lauren Paule
Neo Yixuan Peng
Joanne Shen
Vidhata Singh

Frontiers in Systems Biology

doi 10.3389/fsysb.2024.1283371

4,164 views
1 citation

Review

Published on 02 Aug 2024

The rise of scientific machine learning: a perspective on combining mechanistic modelling with machine learning for systems biology

in Data and Model Integration

Ben Noordijk
Monica L. Garcia Gomez
Kirsten H. W. J. ten Tusscher
Dick de Ridder
Aalt D. J. van Dijk
Robert W. Smith

Frontiers in Systems Biology

doi 10.3389/fsysb.2024.1407994

11,326 views
25 citations

Perspective

Published on 24 Jul 2024

Transporter annotations are holding up progress in metabolic modeling

in Data and Model Integration

John Casey
Brian Bennion
Patrik D’haeseleer
Jeffrey Kimbrel
Gianna Marschmann
Ali Navid

Frontiers in Systems Biology

doi 10.3389/fsysb.2024.1394084

3,631 views
10 citations

Original Research

Published on 30 May 2024

Surface-displayed silicatein-α enzyme in bioengineered E. coli enables biocementation and silica mineralization

in Data and Model Integration

Toriana N. Vigil
Nikolas K. Schwendeman
Melanie L. M. Grogger
Victoria L. Morrison
Margaret C. Warner
Nathaniel B. Bone
Morgan T. Vance
David C. Morris
Kristi McElmurry
Bryan W. Berger

Frontiers in Systems Biology

doi 10.3389/fsysb.2024.1377188

3,755 views

Technology and Code

Published on 18 Apr 2024

Context-aware knowledge selection and reliable model recommendation with ACCORDION

in Data and Model Integration

Yasmine Ahmed
Cheryl A. Telmer
Gaoxiang Zhou
Natasa Miskov-Zivanov

Frontiers in Systems Biology

doi 10.3389/fsysb.2024.1308292

2,209 views
8 citations

Original Research

Published on 09 Apr 2024

Forecasting SARS-CoV-2 spike protein evolution from small data by deep learning and regression

in Data and Model Integration

Samuel King
Xinyi E. Chen
Sarah W. S. Ng
Kimia Rostin
Samuel V. Hahn
Tylo Roberts
Janella C. Schwab
Parneet Sekhon
Madina Kagieva
Taylor Reilly

Frontiers in Systems Biology

doi 10.3389/fsysb.2024.1284668

11,477 views
4 citations

Original Research

Published on 27 Mar 2024

In silico biomarker analysis of the adverse effects of perfluorooctane sulfonate (PFOS) exposure on the metabolic physiology of embryo-larval zebrafish

in Data and Model Integration

Rayna M. Nolen
Lene H. Petersen
Karl Kaiser
Antonietta Quigg
David Hala

Frontiers in Systems Biology

doi 10.3389/fsysb.2024.1367562

2,877 views
1 citation

Mini Review

Published on 13 Mar 2024

Computational insights in cell physiology

in Data and Model Integration

Geneviève Dupont
Didier Gonze

Frontiers in Systems Biology

doi 10.3389/fsysb.2024.1335885

1,814 views

Perspective

Published on 08 Mar 2024

Integrating inverse reinforcement learning into data-driven mechanistic computational models: a novel paradigm to decode cancer cell heterogeneity

in Data and Model Integration

Patrick C. Kinnunen
Kenneth K. Y. Ho
Siddhartha Srivastava
Chengyang Huang
Wanggang Shen
Krishna Garikipati
Gary D. Luker
Nikola Banovic
Xun Huan
Jennifer J. Linderman

Frontiers in Systems Biology

doi 10.3389/fsysb.2024.1333760

3,013 views
1 citation

Perspective

Published on 27 Feb 2024

BioModels’ Model of the Year 2023

in Data and Model Integration

Rahuman S. Malik Sheriff
Hiroki Asari
Henning Hermjakob
Wolfgang Huber
Thomas Quail
Silvia D. M. Santos
Amber M. Smith
Virginie Uhlmann

Frontiers in Systems Biology

doi 10.3389/fsysb.2024.1363884

3,782 views

Original Research

Published on 15 Feb 2024

Computational inference of chemokine-mediated roles for the vagus nerve in modulating intra- and inter-tissue inflammation

in Data and Model Integration

Ashti M. Shah
Ruben Zamora
Derek Barclay
Jinling Yin
Fayten El-Dehaibi
Meghan Addorisio
Tea Tsaava
Aisling Tynan
Kevin Tracey
Sangeeta S. Chavan

Frontiers in Systems Biology

doi 10.3389/fsysb.2024.1266279

1,964 views
2 citations

Original Research

Published on 29 Jan 2024

Genome-scale flux balance analysis reveals redox trade-offs in the metabolism of the thermoacidophile Methylacidiphilum fumariolicum under auto-, hetero-and methanotrophic conditions

in Data and Model Integration

Alexis Saldivar
Patricia Ruiz-Ruiz
Sergio Revah
Cristal Zuñiga

Frontiers in Systems Biology

doi 10.3389/fsysb.2024.1291612

5,771 views
6 citations

Editorial

Published on 20 Dec 2023

Editorial: Integrative systems biology and big data for agricultural improvement and understanding

in Data and Model Integration

Liliana Fadul-Pacheco
Antony T. Vincent
Eric R. Paquet

Frontiers in Systems Biology

doi 10.3389/fsysb.2023.1347323

1,307 views

Original Research

Published on 20 Nov 2023

Fine tuning a logical model of cancer cells to predict drug synergies: combining manual curation and automated parameterization

in Data and Model Integration

Åsmund Flobak
John Zobolas
Miguel Vazquez
Tonje S. Steigedal
Liv Thommesen
Asle Grislingås
Barbara Niederdorfer
Evelina Folkesson
Martin Kuiper

Frontiers in Systems Biology

doi 10.3389/fsysb.2023.1252961

3,261 views
6 citations

Original Research

Published on 22 Sep 2023

Multilayered safety framework for living diagnostics in the colon

in Data and Model Integration

Sonia Mecacci
Lucía Torregrosa-Barragán
Enrique Asin-Garcia
Robert W. Smith

Frontiers in Systems Biology

doi 10.3389/fsysb.2023.1240040

4,467 views
2 citations

48 articles

articles

BioMedKG: multimodal contrastive representation learning in augmented BioMedical knowledge graphs

The role of neutrophil-to-lymphocyte ratio in the prognosis of chronic kidney disease: insights from the NHANES cohort study

Correction: A guide to bayesian networks software for structure and parameter learning, with a focus on causal discovery tools

GETgene-AI: a framework for prioritizing actionable cancer drug targets

A guide to bayesian networks software for structure and parameter learning, with a focus on causal discovery tools

Learning Gaussian graphical models from correlated data

Improvement in the prediction power of an astrocyte genome-scale metabolic model using multi-omic data

Intertwined roles for GDF-15, HMGB1, and MIG/CXCL9 in Pediatric Acute Liver Failure

Spectral expansion methods for prediction uncertainty quantification in systems biology

Accessible Type 2 diabetes medication through stable expression of Exendin-4 in Saccharomyces cerevisiae

The rise of scientific machine learning: a perspective on combining mechanistic modelling with machine learning for systems biology

Transporter annotations are holding up progress in metabolic modeling

Surface-displayed silicatein-α enzyme in bioengineered E. coli enables biocementation and silica mineralization

Context-aware knowledge selection and reliable model recommendation with ACCORDION

Forecasting SARS-CoV-2 spike protein evolution from small data by deep learning and regression

In silico biomarker analysis of the adverse effects of perfluorooctane sulfonate (PFOS) exposure on the metabolic physiology of embryo-larval zebrafish

Computational insights in cell physiology

Integrating inverse reinforcement learning into data-driven mechanistic computational models: a novel paradigm to decode cancer cell heterogeneity

BioModels’ Model of the Year 2023

Computational inference of chemokine-mediated roles for the vagus nerve in modulating intra- and inter-tissue inflammation

Genome-scale flux balance analysis reveals redox trade-offs in the metabolism of the thermoacidophile Methylacidiphilum fumariolicum under auto-, hetero-and methanotrophic conditions

Editorial: Integrative systems biology and big data for agricultural improvement and understanding

Fine tuning a logical model of cancer cells to predict drug synergies: combining manual curation and automated parameterization

Multilayered safety framework for living diagnostics in the colon