Gene regulatory network analysis identifies dysregulation of hypoxia pathways as contributing to glioblastoma treatment resistance in females

Tomisin Adebari, Viola Fanfani, Marouen Ben Guebila, Derrick DeConti, Katherine Hoff Shutta, Camila M Lopes-Ramos, Lauren Hsu, Dawn L DeMeo, John Quackenbush, Tara Eicher

Biology of Sex Differences, vol. 17, BioMed Central, 2026, p. 134

Sex differences in gene regulation and its impact on cancer incidence

Camila M Lopes-Ramos, Rebekka Burkholz, Marouen Ben Guebila, Viola Fanfani, Enakshi Saha, Katherine H Shutta, Kimberly Glass, John Quackenbush, Dawn L DeMeo

Iscience, vol. 29, Elsevier, 2026

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, Katherine H Shutta, Dawn L DeMeo, John Quackenbush, Camila M Lopes-Ramos

npj Aging, vol. 11, Nature Publishing Group UK London, 2025, p. 61

Multi-omics protein signaling networks identify sex-specific therapeutic candidates in lung adenocarcinoma

Chen Chen, Enakshi Saha, Jonas Fischer, Marouen Ben Guebila, Viola Fanfani, Katherine H Shutta, Megha Padi, Kimberly Glass, Dawn L DeMeo, Camila M Lopes-Ramos, others

Biology of sex Differences, vol. 16, BioMed Central London, 2025, p. 71

Reproducible processing of TCGA regulatory networks

Viola Fanfani, Katherine H Shutta, Panagiotis Mandros, Jonas Fischer, Enakshi Saha, Soel Micheletti, Chen Chen, Marouen Ben Guebila, Camila M Lopes-Ramos, John Quackenbush

GigaScience, vol. 14, Oxford University Press, 2025, pp. giaf126

Sex-biased regulation of extracellular matrix genes in chronic obstructive pulmonary disease

Camila M Lopes-Ramos, Katherine H Shutta, Min Hyung Ryu, Yichen Huang, Enakshi Saha, John Ziniti, Robert Chase, Brian D Hobbs, Jeong H Yun, Peter Castaldi, others

American Journal of Respiratory Cell and Molecular Biology, vol. 72, Oxford University Press, 2025, pp. 72--81

Bayesian inference of sample-specific coexpression networks

Enakshi Saha, Viola Fanfani, Panagiotis Mandros, Marouen Ben Guebila, Jonas Fischer, Katherine H Shutta, Dawn L DeMeo, Camila M Lopes-Ramos, John Quackenbush

Genome research, vol. 34, Cold Spring Harbor Laboratory Press, 2024, pp. 1397--1410

Gene regulatory networks reveal sex difference in lung adenocarcinoma

Enakshi Saha, Marouen Ben Guebila, Viola Fanfani, Jonas Fischer, Katherine H Shutta, Panagiotis Mandros, Dawn L DeMeo, John Quackenbush, Camila M Lopes-Ramos

Biology of sex differences, vol. 15, BioMed Central London, 2024, p. 62

The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks

Marouen Ben Guebila, Tian Wang, Camila M Lopes-Ramos, Viola Fanfani, Des Weighill, Rebekka Burkholz, Daniel Schlauch, Joseph N Paulson, Michael Altenbuchinger, Katherine H Shutta, others

Genome Biology, vol. 24, BioMed Central London, 2023, p. 45

GRAND: a database of gene regulatory network models across human conditions

Marouen Ben Guebila, Camila M Lopes-Ramos, Deborah Weighill, Abhijeet Rajendra Sonawane, Rebekka Burkholz, Behrouz Shamsaei, John Platig, Kimberly Glass, Marieke L Kuijjer, John Quackenbush

Nucleic acids research, vol. 50, Oxford University Press, 2022, pp. D610--D621

Regulatory network of PD1 signaling is associated with prognosis in glioblastoma multiforme

Camila M Lopes-Ramos, Tatiana Belova, Tess H Brunner, Marouen Ben Guebila, Daniel Osorio, John Quackenbush, Marieke L Kuijjer

Cancer research, vol. 81, American Association for Cancer Research, 2021, pp. 5401--5412

Genome-wide sex and gender differences in cancer

Camila M Lopes-Ramos, John Quackenbush, Dawn L DeMeo

Frontiers in oncology, vol. 10, Frontiers, 2020, p. 597788

Sex differences in gene expression and regulatory networks across 29 human tissues

Camila M Lopes-Ramos, Cho-Yi Chen, Marieke L Kuijjer, Joseph N Paulson, Abhijeet R Sonawane, Maud Fagny, John Platig, Kimberly Glass, John Quackenbush, Dawn L DeMeo

Cell reports, vol. 31, Elsevier, 2020

Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism

CM Lopes-Ramos, ML Kuijjer, S Ogino, CS Fuchs, DL DeMeo, K Glass, J Quackenbush

Cancer Research, vol. 78, doi: 10.1158/0008-5472.CAN-18-0454, 2018, pp. 5538--5547

E2F1 somatic mutation within miRNA target site impairs gene regulation in colorectal cancer

Camila M Lopes-Ramos, Bruna P Barros, Fernanda C Koyama, Paola A Carpinetti, Julia Pezuk, Nayara TS Doimo, Angelita Habr-Gama, Rodrigo O Perez, Raphael B Parmigiani

PLoS One, vol. 12, Public Library of Science San Francisco, CA USA, 2017, pp. e0181153

Regulatory network changes between cell lines and their tissues of origin

Camila M Lopes-Ramos, Joseph N Paulson, Cho-Yi Chen, Marieke L Kuijjer, Maud Fagny, John Platig, Abhijeet R Sonawane, Dawn L DeMeo, John Quackenbush, Kimberly Glass

BMC genomics, vol. 18, BioMed Central London, 2017, p. 723

Comprehensive evaluation of the effectiveness of gene expression signatures to predict complete response to neoadjuvant chemoradiotherapy and guide surgical intervention in rectal cancer

Camila Lopes-Ramos, Fernanda C Koyama, Angelita Habr-Gama, Anna Christina M Salim, Fabiana Bettoni, Paula F Asprino, Gustavo S Franca, Joaquim Gama-Rodrigues, Raphael B Parmigiani, Rodrigo O Perez, others

Cancer genetics, vol. 208, Elsevier, 2015, pp. 319--326

Overexpression of miR-21-5p as a predictive marker for complete tumor regression to neoadjuvant chemoradiotherapy in rectal cancer patients

Camila Miranda Lopes-Ramos, Angelita Habr-Gama, Bruna de Souza Quevedo, Natalia Mariana Felicio, Fabiana Bettoni, Fernanda Christtanini Koyama, Paula Fontes Asprino, Pedro Alexandre Galante, Joaquim Gama-Rodrigues, Anamaria Aranha Camargo, others

BMC medical genomics, vol. 7, BioMed Central London, 2014, p. 68