| Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs J Listgarten, M Weinstein, BP Kleinstiver, AA Sousa, JK Joung, J Crawford, ... Nature biomedical engineering 2 (1), 38-47, 2018 | 273 | 2018 |
| Assessment of network module identification across complex diseases S Choobdar, ME Ahsen, J Crawford, M Tomasoni, T Fang, D Lamparter, ... Nature methods 16 (9), 843-852, 2019 | 266* | 2019 |
| Incorporating biological structure into machine learning models in biomedicine J Crawford, CS Greene Current opinion in biotechnology 63, 126-134, 2020 | 31 | 2020 |
| MONET: a toolbox integrating top-performing methods for network modularization M Tomasoni, S Gomez, J Crawford, W Zhang, S Choobdar, D Marbach, ... Bioinformatics 36 (12), 3920-3921, 2020 | 18 | 2020 |
| Widespread redundancy in-omics profiles of cancer mutation states J Crawford, BC Christensen, M Chikina, CS Greene Genome Biology 23 (1), 137, 2022 | 7* | 2022 |
| Detangling PPI networks to uncover functionally meaningful clusters S Hall-Swan, J Crawford, R Newman, LJ Cowen Proceedings of the 8th ACM International Conference on Bioinformatics …, 2017 | 6* | 2017 |
| Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs. Nat Biomed Eng 2: 38–47 J Listgarten, M Weinstein, BP Kleinstiver, AA Sousa, JK Joung, J Crawford, ... | 5 | 2018 |
| CAJAL enables analysis and integration of single-cell morphological data using metric geometry KW Govek, P Nicodemus, Y Lin, J Crawford, AB Saturnino, H Cui, K Zoga, ... Nature Communications 14 (1), 3672, 2023 | 3 | 2023 |
| SOPHIE: generative neural networks separate common and specific transcriptional responses AJ Lee, DL Mould, J Crawford, D Hu, RK Powers, G Doing, JC Costello, ... Genomics, Proteomics and Bioinformatics 20 (5), 912-927, 2022 | 3* | 2022 |
| Graph biased feature selection of genes is better than random for many genes J Crawford, CS Greene Biorxiv, 2020.01. 17.910703, 2020 | 3 | 2020 |
| The effect of non-linear signal in classification problems using gene expression BJ Heil, J Crawford, CS Greene PLOS Computational Biology 19 (3), e1010984, 2023 | 1* | 2023 |
| Excessive salivation as a hidden comorbidity of basal ganglia germ cell tumor K Kobayashi, M Suehiro, T Maihara, I Usami, T Heike Journal of Pediatric Neurology 17 (05), 187-190, 2019 | 1 | 2019 |
| Retraction Note: detangling PPI networks to uncover functionally meaningful clusters S Hall-Swan, J Crawford, R Newman, LJ Cowen BMC Systems Biology 12 (1), 113-113, 2018 | 1 | 2018 |
| Optimizer’s dilemma: optimization strongly influences model selection in transcriptomic prediction J Crawford, M Chikina, CS Greene Bioinformatics Advances 4 (1), vbae004, 2024 | | 2024 |
| wenda_gpu: fast domain adaptation for genomic data AA Hippen, J Crawford, JR Gardner, CS Greene Bioinformatics 38 (22), 5129-5130, 2022 | | 2022 |
| Efficient domain adaptation for cancer mutation prediction AA Hippen, J Crawford, JR Gardner, CS Greene Cancer Research 82 (12_Supplement), 1222-1222, 2022 | | 2022 |
| Multi-modal analysis and integration of single-cell morphological data KW Govek, J Crawford, AB Saturnino, K Zoga, MP Hart, PG Camara | | 2022 |
| Supplementary Information-MONET M Tomasoni, S Gómez, J Crawford, W Zhang | | |
