miRIAD - integrating microRNA inter- and intragenic data. - Ludwig Christian G. Hinske; Gustavo S. França; Hugo A. M. Torres; Daniel T. Ohara; Camila Miranda Lopes-Ramos; Jens Heyn; Luiz F. L. Reis; Lucila Ohno-Machado; Simone Kreth; Pedro A. F. Galante (Database J. Biol. Databases Curation, 2014)

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. - Joseph N. Paulson; Cho-Yi Chen; Camila Miranda Lopes-Ramos; Marieke L. Kuijjer; John Platig; Abhijeet R. Sonawane; Maud Fagny; Kimberly Glass; John Quackenbush (BMC Bioinform., 2017)

Gene Regulatory Network Inference as Relaxed Graph Matching. - Deborah A. Weighill; Marouen Ben Guebila; Camila Miranda Lopes-Ramos; Kimberly Glass; John Quackenbush; John Platig; Rebekka Burkholz (AAAI, 2021)

GRAND: a database of gene regulatory network models across human conditions. - Marouen Ben Guebila; Camila Miranda Lopes-Ramos; Deborah A. Weighill; Abhijeet Rajendra Sonawane; Rebekka Burkholz; Behrouz Shamsaei; John Platig; Kimberly Glass; Marieke L. Kuijjer; John Quackenbush (Nucleic Acids Res., 2022)

Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data. - Ping-Han Hsieh; Camila Miranda Lopes-Ramos; Manuela Zucknick; Geir Kjetil Sandve; Kimberly Glass; Marieke L. Kuijjer (Bioinform., 2023)

BONOBO: Bayesian Optimized Sample-Specific Networks Obtained by Omics Data. - Enakshi Saha; Viola Fanfani; Panagiotis Mandros; Marouen Ben Guebila; Jonas Fischer; Katherine H. Shutta; Kimberly Glass; Dawn L. DeMeo; Camila Miranda Lopes-Ramos; John Quackenbush (RECOMB, 2024)