| Understanding tissue-specific gene regulation AR Sonawane, J Platig, M Fagny, CY Chen, JN Paulson, ... Cell reports 21 (4), 1077-1088, 2017 | 410 | 2017 |
| Sex differences in gene expression and regulatory networks across 29 human tissues CM Lopes-Ramos, CY Chen, ML Kuijjer, JN Paulson, AR Sonawane, ... Cell reports 31 (12), 2020 | 271 | 2020 |
| Genome-wide sex and gender differences in cancer CM Lopes-Ramos, J Quackenbush, DL DeMeo Frontiers in oncology 10, 597788, 2020 | 121 | 2020 |
| miRIAD—integrating microRNA inter- and intragenic data LC Hinske, GS Franca, HAM Torres, DT Ohara, CM Lopes-Ramos, J Heyn, ... Database 2014, bau099, 2014 | 111 | 2014 |
| 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, ... Cancer Research 78 (19), 5538-5547, 2018 | 106 | 2018 |
| Exploring regulation in tissues with eQTL networks M Fagny, JN Paulson, ML Kuijjer, AR Sonawane, CY Chen, ... Proceedings of the National Academy of Sciences 114 (37), E7841-E7850, 2017 | 98 | 2017 |
| Overexpression of miR-21-5p as a predictive marker for complete tumor regression to neoadjuvant chemoradiotherapy in rectal cancer patients CM Lopes-Ramos, A Habr-Gama, BS Quevedo, NM Felício, F Bettoni, ... BMC medical genomics 7, 1-14, 2014 | 88 | 2014 |
| GRAND: a database of gene regulatory network models across human conditions M Ben Guebila, CM Lopes-Ramos, D Weighill, AR Sonawane, R Burkholz, ... Nucleic Acids Research 50 (D1), D610-D621, 2022 | 64 | 2022 |
| Regulatory network changes between cell lines and their tissues of origin CM Lopes-Ramos, JN Paulson, CY Chen, ML Kuijjer, M Fagny, J Platig, ... BMC genomics 18, 1-13, 2017 | 62 | 2017 |
| Comprehensive evaluation of the effectiveness of gene expression signatures to predict complete response to neoadjuvant chemoradiotherapy and guide surgical intervention in … C Lopes-Ramos, FC Koyama, A Habr-Gama, ACM Salim, F Bettoni, ... Cancer genetics 208 (6), 319-326, 2015 | 58 | 2015 |
| Enoxacin extends lifespan of C. elegans by inhibiting miR-34-5p and promoting mitohormesis S Pinto, VN Sato, EA De-Souza, RC Ferraz, H Camara, APF Pinca, ... Redox biology 18, 84-92, 2018 | 57 | 2018 |
| White and grey matter abnormalities in patients with SPG11 mutations MC França, CL Yasuda, FRS Pereira, A D'Abreu, CM Lopes-Ramos, ... Journal of Neurology, Neurosurgery & Psychiatry 83 (8), 828-833, 2012 | 56 | 2012 |
| Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data JN Paulson, CY Chen, CM Lopes-Ramos, ML Kuijjer, J Platig, ... BMC bioinformatics 18, 1-10, 2017 | 55 | 2017 |
| Enoxacin induces oxidative metabolism and mitigates obesity by regulating adipose tissue miRNA expression AL Rocha, TI de Lima, GP de Souza, RO Corrêa, DL Ferrucci, ... Science advances 6 (49), eabc6250, 2020 | 29 | 2020 |
| Sexual dimorphism in gene expression and regulatory networks across human tissues CY Chen, C Lopes-Ramos, ML Kuijjer, JN Paulson, AR Sonawane, ... BioRxiv, 082289, 2016 | 27 | 2016 |
| E2F1 somatic mutation within miRNA target site impairs gene regulation in colorectal cancer CM Lopes-Ramos, BP Barros, FC Koyama, PA Carpinetti, J Pezuk, ... PLoS One 12 (7), e0181153, 2017 | 25 | 2017 |
| Gene regulatory network inference as relaxed graph matching D Weighill, MB Guebila, C Lopes-Ramos, K Glass, J Quackenbush, ... Proceedings of the AAAI Conference on Artificial Intelligence 35 (11), 10263 …, 2021 | 22 | 2021 |
| Effect of Akt activation and experimental pharmacological inhibition on responses to neoadjuvant chemoradiotherapy in rectal cancer FC Koyama, CM Lopes Ramos, F Ledesma, VAF Alves, JM Fernandes, ... Journal of British Surgery 105 (2), e192-e203, 2018 | 22 | 2018 |
| Regulatory network of PD1 signaling is associated with prognosis in glioblastoma multiforme CM Lopes-Ramos, T Belova, TH Brunner, M Ben Guebila, D Osorio, ... Cancer research 81 (21), 5401-5412, 2021 | 18 | 2021 |
| The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks M Ben Guebila, T Wang, CM Lopes-Ramos, V Fanfani, D Weighill, ... Genome Biology 24 (1), 45, 2023 | 17 | 2023 |
John QuackenbushHarvard T.H. Chan School of Public Health, Channing Division of Network Medicine, and Dana-FarberVerified email at hsph.harvard.edu
