| Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants K Varala, A Marshall-Colón, J Cirrone, MD Brooks, AV Pasquino, S Léran, ... Proceedings of the National Academy of Sciences 115 (25), 6494-6499, 2018 | 188 | 2018 |
| Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions MD Brooks, J Cirrone, AV Pasquino, JM Alvarez, J Swift, S Mittal, ... Nature Communications 10 (1), 1-13, 2019 | 143 | 2019 |
| Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization P Roszak, J Heo, B Blob, K Toyokura, Y Sugiyama, MA de Luis Balaguer, ... Science 374 (6575), eaba5531, 2021 | 84 | 2021 |
| ConnecTF: A platform to integrate transcription factor–gene interactions and validate regulatory networks MD Brooks, CL Juang, MS Katari, JM Alvarez, A Pasquino, HJ Shih, ... Plant Physiology 185 (1), 49-66, 2021 | 41 | 2021 |
| OutPredict: multiple datasets can improve prediction of expression and inference of causality J Cirrone, MD Brooks, R Bonneau, GM Coruzzi, DE Shasha Nature Scientific Reports 10 (1), 1-9, 2020 | 20 | 2020 |
| Analysis of phloem trajectory links tissue maturation to cell specialization P Roszak, J Heo, B Blob, K Toyokura, MA de Luis Balaguer, WWY Lau, ... BioRxiv, 2021.01. 18.427084, 2021 | 15 | 2021 |
| SuperNoder: a tool to discover over-represented modular structures in networks D Dessì, J Cirrone, DR Recupero, D Shasha BMC Bioinformatics 19 (1), 1-12, 2018 | 13 | 2018 |
| CASS: Cross Architectural Self-Supervision for Medical Image Analysis P Singh, E Sizikova, J Cirrone NeurIPS - Neural Information Processing Systems Workshop: Self-Supervised …, 2022 | 9 | 2022 |
| A Data-Efficient Deep Learning Framework for Segmentation and Classification of Histopathology Images P Singh, J Cirrone Springer Nature, Lecture Notes in Computer Science, Medical Computer Vision …, 2022 | 8 | 2022 |
| Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions. Nat Commun 10: 1569 MD Brooks, J Cirrone, AV Pasquino, JM Alvarez, J Swift, S Mittal, ... | 5 | 2019 |
| Enhancing Medical Image Segmentation: Optimizing Cross-Entropy Weights and Post-Processing with Autoencoders P Singh, L Chen, M Chen, J Pan, R Chukkapalli, S Chaudhari, J Cirrone International Conference on Computer Vision Proceedings, 2023 | 3 | 2023 |
| Efficient Representation Learning for Healthcare with Cross-Architectural Self-Supervision P Singh, J Cirrone Proceedings of Machine Learning Research - PMLR Machine Learning for Healthcare, 2023 | 2 | 2023 |
| Prediction of drug effectiveness in rheumatoid arthritis patients based on machine learning algorithms S Chen, N Gupta, WB Galbraith, V Shah, J Cirrone ACM, Association for Computing Machinery, International Conference on …, 2022 | 2 | 2022 |
| Shifting to machine supervision: annotation-efficient semi and self-supervised learning for automatic medical image segmentation and classification P Singh, R Chukkapalli, S Chaudhari, L Chen, M Chen, J Pan, C Smuda, ... Nature Scientific Reports - Nature Publishing Group - https://www.nature.com …, 2024 | 1 | 2024 |
| Free Form Medical Visual Question Answering in Radiology A Narayanan, R Musthyala, R Sankar, A Nistala, P Singh, J Cirrone https://arxiv.org/pdf/2401.13081.pdf, 2024 | 1 | 2024 |
| ConnecTF: A platform to build gene networks by integrating transcription factor-target gene interactions MD Brooks, CL Juang, MS Katari, JM Alvarez, A Pasquino, HJ Shih, ... bioRxiv, 2020 | 1 | 2020 |
| Exploring Intrinsic Properties of Medical Images for Self-Supervised Binary Semantic Segmentation P Singh, J Cirrone arXiv preprint arXiv:2402.02367, 2024 | | 2024 |
| Cross-Architectural Positive Pairs improve the effectiveness of Self-Supervised Learning P Singh, J Cirrone arXiv preprint arXiv:2301.12025, 2023 | | 2023 |
| Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization. Science 374, eaba5531 P Roszak, JO Heo, B Blob, K Toyokura, Y Sugiyama, ... | | 2021 |
| Author Correction: OutPredict: multiple datasets can improve prediction of expression and inference of causality J Cirrone, MD Brooks, R Bonneau, GM Coruzzi, DE Shasha Nature Scientific Reports 10 (1), 1-1, 2020 | | 2020 |
