publications

publications by categories in reversed chronological order. generated by jekyll-scholar.

My publications

2026

  1. Sex differences in gene regulation and its impact on cancer incidence
    Camila Lopes-Ramos, Rebekka Burkholz, Marouen Ben Guebila, and 6 more authors
    iScience, 2026
    DOI HTML
  2. Gene regulatory network analysis identifies dysregulation of hypoxia pathways as contributing to glioblastoma treatment resistance in females
    Tomisin Adebari, Viola Fanfani, Marouen Ben Guebila, and 7 more authors
    Biology of Sex Differences, 2026
    DOI HTML

2025

  1. Aging-associated alterations in gene regulatory networks associate with risk, prognosis and response to therapy in lung adenocarcinoma
    Enakshi Saha, Marouen Ben Guebila, Viola Fanfani, and 4 more authors
    npj Aging, 2025
    DOI HTML
  2. Multi-omics protein signaling networks identify sex-specific therapeutic candidates in lung adenocarcinoma
    Chen Chen, Enakshi Saha, Jonas Fischer, and 8 more authors
    Biology of Sex Differences, 2025
    DOI HTML
  3. BLOBFISH: Bipartite Limited Subnetworks from Multiple Observations using Breadth-First Search with Constrained Hops
    Tara Eicher, Marouen Ben Guebila, and John Quackenbush
    bioRxiv (Cold Spring Harbor Laboratory), 2025
    DOI HTML
  4. Identifying Sex Differences in Lung Adenocarcinoma Using Multi-Omics Integrative Protein Signaling Networks
    Chen Chen, Enakshi Saha, Jonas Fischer, and 8 more authors
    bioRxiv (Cold Spring Harbor Laboratory), 2025
    DOI HTML
  5. Reproducible processing of TCGA regulatory networks
    Viola Fanfani, Katherine H. Shutta, Panagiotis Mandros, and 7 more authors
    GigaScience, 2025
    DOI HTML

2024

  1. Gene regulatory networks reveal sex difference in lung adenocarcinoma
    Enakshi Saha, Marouen Ben Guebila, Viola Fanfani, and 6 more authors
    Biology of Sex Differences, 2024
    DOI HTML
  2. Bayesian inference of sample-specific coexpression networks
    Enakshi Saha, Viola Fanfani, Panagiotis Mandros, and 6 more authors
    Genome Research, 2024
    DOI HTML
  3. Spatial Cellular Networks from omics data with SpaCeNet
    Stefan Schrod, Niklas Lück, Robert Lohmayer, and 11 more authors
    Genome Research, 2024
    DOI HTML
  4. Higher-order correction of persistent batch effects in correlation networks
    Soel Micheletti, Daniel Schlauch, John Quackenbush, and 1 more author
    Bioinformatics, 2024
    DOI HTML
  5. Selective loss of Y chromosomes in lung adenocarcinoma modulates the tumor immune environment through cancer/testis antigens
    Jonas Fischer, Katherine H. Shutta, Chen Chen, and 12 more authors
    bioRxiv (Cold Spring Harbor Laboratory), 2024
    DOI HTML
  6. SpaCeNet: Spatial Cellular Networks from Omics Data
    Stefan Schrod, Niklas Lück, Robert Lohmayer, and 10 more authors
    In Lecture notes in computer science, 2024
    DOI HTML
  7. Aging-associated Alterations in the Gene Regulatory Network Landscape Associate with Risk, Prognosis and Response to Therapy in Lung Adenocarcinoma
    Enakshi Saha, Marouen Ben Guebila, Viola Fanfani, and 4 more authors
    bioRxiv (Cold Spring Harbor Laboratory), 2024
    DOI HTML

2023

  1. The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks
    Marouen Ben Guebila, Tian Wang, Camila M. Lopes‐Ramos, and 22 more authors
    Genome biology, 2023
    DOI HTML
  2. The Coming of Age of Nucleic Acid Vaccines during COVID-19
    Halie M. Rando, Ronan Lordan, Likhitha Kolla, and 58 more authors
    mSystems, 2023
    DOI HTML
  3. Application of Traditional Vaccine Development Strategies to SARS-CoV-2
    Halie M. Rando, Ronan Lordan, Alexandra Lee, and 58 more authors
    mSystems, 2023
    DOI HTML
  4. A state-of-the-art database enables a macro perspective on tumor microenvironment
    Krisha Mehta, Talha Ahmad Khan, and Marouen Ben Guebila
    HAL (Le Centre pour la Communication Scientifique Directe), 2023
    DOI HTML
  5. Figure SF2 from Regulatory Network of PD1 Signaling Is Associated with Prognosis in Glioblastoma Multiforme
    Camila M. Lopes‐Ramos, Tatiana Belova, Tess H. Brunner, and 4 more authors
    Preprint, 2023
    DOI HTML
  6. Table ST1 from Regulatory Network of PD1 Signaling Is Associated with Prognosis in Glioblastoma Multiforme
    Camila M. Lopes‐Ramos, Tatiana Belova, Tess H. Brunner, and 4 more authors
    Preprint, 2023
    DOI HTML
  7. Data from Regulatory Network of PD1 Signaling Is Associated with Prognosis in Glioblastoma Multiforme
    Camila M. Lopes‐Ramos, Tatiana Belova, Tess H. Brunner, and 4 more authors
    Preprint, 2023
    DOI HTML
  8. Figure SF4 from Regulatory Network of PD1 Signaling Is Associated with Prognosis in Glioblastoma Multiforme
    Camila M. Lopes‐Ramos, Tatiana Belova, Tess H. Brunner, and 4 more authors
    Preprint, 2023
    DOI HTML
  9. Figure SF3 from Regulatory Network of PD1 Signaling Is Associated with Prognosis in Glioblastoma Multiforme
    Camila M. Lopes‐Ramos, Tatiana Belova, Tess H. Brunner, and 4 more authors
    Preprint, 2023
    DOI HTML
  10. Figure SF5 from Regulatory Network of PD1 Signaling Is Associated with Prognosis in Glioblastoma Multiforme
    Camila M. Lopes‐Ramos, Tatiana Belova, Tess H. Brunner, and 4 more authors
    Preprint, 2023
    DOI HTML
  11. Figure SF1 from Regulatory Network of PD1 Signaling Is Associated with Prognosis in Glioblastoma Multiforme
    Camila M. Lopes‐Ramos, Tatiana Belova, Tess H. Brunner, and 4 more authors
    Preprint, 2023
    DOI HTML
  12. Referee report. For: scANANSE gene regulatory network and motif analysis of single-cell clusters [version 1; peer review: 1 approved, 1 approved with reservations]
    Marouen Ben Guebila
    Faculty of 1000 Research Ltd, 2023
    DOI HTML
  13. Referee report. For: scANANSE gene regulatory network and motif analysis of single-cell clusters [version 2; peer review: 2 approved]
    Marouen Ben Guebila
    Faculty of 1000 Research Ltd, 2023
    DOI HTML

2022

  1. DRAGON: Determining Regulatory Associations using Graphical models on multi-Omic Networks
    Katherine H. Shutta, Deborah Weighill, Rebekka Burkholz, and 5 more authors
    Nucleic Acids Research, 2022
    DOI HTML
  2. Predicting genotype-specific gene regulatory networks
    Deborah Weighill, Marouen Ben Guebila, Kimberly Glass, and 2 more authors
    Genome Research, 2022
    DOI HTML
  3. An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks
    Marouen Ben Guebila, Deborah Weighill, Camila M. Lopes‐Ramos, and 11 more authors
    Nature Methods, 2022
    DOI HTML
  4. gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit
    Marouen Ben Guebila, Daniel Morgan, Kimberly Glass, and 3 more authors
    NAR Genomics and Bioinformatics, 2022
    DOI HTML
  5. The Network Zoo: a multilingual package for the inference and analysis of biological networks
    Marouen Ben Guebila, Tian Wang, Camila M. Lopes‐Ramos, and 21 more authors
    bioRxiv (Cold Spring Harbor Laboratory), 2022
    DOI HTML

2021

  1. GRAND: a database of gene regulatory network models across human conditions
    Marouen Ben Guebila, Camila M. Lopes‐Ramos, Deborah Weighill, and 7 more authors
    Nucleic Acids Research, 2021
    DOI HTML
  2. Crowdsourced mapping of unexplored target space of kinase inhibitors
    Anna Cichońska, Balaguru Ravikumar, Robert J. Allaway, and 97 more authors
    Nature Communications, 2021
    DOI HTML
  3. Toward a Generalizable Framework of Disturbance Ecology Through Crowdsourced Science
    Emily Graham, Colin Averill, Ben Bond‐Lamberty, and 26 more authors
    Frontiers in Ecology and Evolution, 2021
    DOI HTML
  4. Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure
    Halie M. Rando, Adam L. MacLean, Alexandra Lee, and 31 more authors
    arXiv (Cornell University), 2021
    DOI HTML
  5. Gene Targeting in Disease Networks
    Deborah Weighill, Marouen Ben Guebila, Kimberly Glass, and 3 more authors
    Frontiers in Genetics, 2021
    DOI HTML
  6. Regulatory Network of PD1 Signaling Is Associated with Prognosis in Glioblastoma Multiforme
    Camila M. Lopes‐Ramos, Tatiana Belova, Tess H. Brunner, and 4 more authors
    Cancer Research, 2021
    DOI HTML
  7. Dynamic flux balance analysis of whole-body metabolism for type 1 diabetes
    Marouen Ben Guebila and Ines Thiele
    Nature Computational Science, 2021
    DOI HTML
  8. Gene Regulatory Network Inference as Relaxed Graph Matching
    Deborah Weighill, Marouen Ben Guebila, Camila M. Lopes‐Ramos, and 4 more authors
    Proceedings of the AAAI Conference on Artificial Intelligence, 2021
    DOI HTML
  9. Dynamic flux balance analysis on whole-body metabolism for Type 1 diabetes
    Marouen Ben Guebila and Ines Thiele
    Zenodo (CERN European Organization for Nuclear Research), 2021
    DOI HTML
  10. Identification and Development of Therapeutics for COVID-19
    Halie M. Rando, Nils Wellhausen, Soumita Ghosh, and 20 more authors
    PubMed, 2021

2020

  1. SARS-CoV-2 and COVID-19: An Evolving Review of Diagnostics and Therapeutics
    Halie M. Rando, Casey S. Greene, Michael P. Robson, and 32 more authors
    2020
  2. VFFVA: dynamic load balancing enables large-scale flux variability analysis
    Marouen Ben Guebila
    BMC Bioinformatics, 2020
    DOI HTML

2019

  1. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
    Laurent Heirendt, Sylvain Arreckx, Thomas Pfau, and 52 more authors
    Nature Protocols, 2019
    DOI HTML
  2. Predicting gastrointestinal drug effects using contextualized metabolic models
    Marouen Ben Guebila and Ines Thiele
    PLoS Computational Biology, 2019
    DOI HTML
  3. Global network of computational biology communities: ISCB’s Regional Student Groups breaking barriers
    Sayane Shome, R. Gonzalo Parra, Nazeefa Fatima, and 39 more authors
    F1000Research, 2019
    DOI HTML
  4. Pan-organ model integration of metabolic and regulatory processes in type 1 diabetes
    Marouen Ben Guebila and Ines Thiele
    bioRxiv (Cold Spring Harbor Laboratory), 2019
    DOI HTML
  5. ACHR.cu: GPU-accelerated sampling of metabolic networks
    Marouen Ben Guebila
    The Journal of Open Source Software, 2019
    DOI HTML

2018

  1. Dynamic load balancing enables large-scale flux variability analysis
    Marouen Ben Guebila
    bioRxiv (Cold Spring Harbor Laboratory), 2018
    DOI HTML
  2. Dynamical hybrid modeling of human metabolism
    Marouen Ben Guebila
    2018

2017

  1. Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0
    Laurent Heirendt, Sylvain Arreckx, Thomas Pfau, and 52 more authors
    arXiv (Cornell University), 2017
    DOI HTML

2016

  1. Model-based dietary optimization for late-stage, levodopa-treated, Parkinson’s disease patients
    Marouen Ben Guebila and Ines Thiele
    npj Systems Biology and Applications, 2016
    DOI HTML
  2. Toward a closed-loop subcutaneous delivery of L-DOPA
    Marouen Ben Guebila and Johan Thunberg
    arXiv (Cornell University), 2016
    DOI HTML

Papers of the year

Two of the coolest papers I came across each year — work from the wider community that I keep coming back to, not my own.

2026
2025
2021
2020
2019
2018
2017
2015
2012