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
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  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
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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
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  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
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  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
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  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
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  5. Reproducible processing of TCGA regulatory networks
    Viola Fanfani, Katherine H. Shutta, Panagiotis Mandros, and 7 more authors
    GigaScience, 2025
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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
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  2. Bayesian inference of sample-specific coexpression networks
    Enakshi Saha, Viola Fanfani, Panagiotis Mandros, and 6 more authors
    Genome Research, 2024
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  3. Spatial Cellular Networks from omics data with SpaCeNet
    Stefan Schrod, Niklas Lück, Robert Lohmayer, and 11 more authors
    Genome Research, 2024
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  4. Higher-order correction of persistent batch effects in correlation networks
    Soel Micheletti, Daniel Schlauch, John Quackenbush, and 1 more author
    Bioinformatics, 2024
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  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
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  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
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  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
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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
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  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
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  3. Application of Traditional Vaccine Development Strategies to SARS-CoV-2
    Halie M. Rando, Ronan Lordan, Alexandra Lee, and 58 more authors
    mSystems, 2023
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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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
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  2. Predicting genotype-specific gene regulatory networks
    Deborah Weighill, Marouen Ben Guebila, Kimberly Glass, and 2 more authors
    Genome Research, 2022
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  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
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  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
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  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
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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
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  2. Crowdsourced mapping of unexplored target space of kinase inhibitors
    Anna Cichońska, Balaguru Ravikumar, Robert J. Allaway, and 97 more authors
    Nature Communications, 2021
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  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
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  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
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  5. Gene Targeting in Disease Networks
    Deborah Weighill, Marouen Ben Guebila, Kimberly Glass, and 3 more authors
    Frontiers in Genetics, 2021
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  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
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  7. Dynamic flux balance analysis of whole-body metabolism for type 1 diabetes
    Marouen Ben Guebila and Ines Thiele
    Nature Computational Science, 2021
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  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
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  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
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  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
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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
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  2. Predicting gastrointestinal drug effects using contextualized metabolic models
    Marouen Ben Guebila and Ines Thiele
    PLoS Computational Biology, 2019
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  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
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  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
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  5. ACHR.cu: GPU-accelerated sampling of metabolic networks
    Marouen Ben Guebila
    The Journal of Open Source Software, 2019
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2018

  1. Dynamic load balancing enables large-scale flux variability analysis
    Marouen Ben Guebila
    bioRxiv (Cold Spring Harbor Laboratory), 2018
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  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
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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
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  2. Toward a closed-loop subcutaneous delivery of L-DOPA
    Marouen Ben Guebila and Johan Thunberg
    arXiv (Cornell University), 2016
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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
2018
2015