| Title | Authors | Publication | Year | Type | Cite |
|---|---|---|---|---|---|
| scGPT: Towards Building a Foundation Model for Single-Cell Multi-omics Using Generative AI | Haotian Cui, Chloe Wang, Hassaan Maan, Bo Wang | Nature Method | 2024 | Journal | bib |
| Decentralised, collaborative, and privacy-preserving machine learning for multi-hospital data | C Fang, A Dziedzic, L Zhang, L Oliva, A Verma, F Razak, N Papernot, Bo Wang | Lancet eBioMedicine | 2024 | Journal | bib |
| Segment Anything in Medical Images | Jun Ma, Yuting He, Feifei Li, Lin Han, Chenyu You, Bo Wang | Nature Communications | 2024 | Journal | bib |
| DeepVelo: Deep Learning extends RNA velocity to multi-lineage systems with cell-specific kinetics | Haotian Cui, Hassaan Maan, Maria C Vladoiu, Jiao Zhang, Michael D Taylor, Bo Wang. | Genome Biology | 2024 | Genome Biology | bib |
| Graph-Mamba: Towards Long-Range Graph Sequence Modeling with Selective State Spaces | Chloe Wang, Oleksii Tsepa, Jun Ma, Bo Wang | arXiv | 2024 | Preprint | bib |
| U-Mamba: Enhancing Long-range Dependency for Biomedical Image Segmentation | Jun Ma, Feifei Li, Bo Wang | arXiv | 2024 | Preprint | bib |
| Integrate Any Omics: Towards genome-wide data integration for patient stratification | Shihao Ma, Andy GX Zeng, Benjamin Haibe-Kains, Anna Goldenberg, John E Dick, Bo Wang | arXiv | 2024 | Preprint | bib |
| Clinical Camel: An Open-Source Expert-Level Medical Language Model with Dialogue-Based Knowledge Encoding | Augustin Toma, Patrick R. Lawler, Jimmy Ba, Rahul G. Krishnan, Barry B. Rubin, Bo Wang | arXiv | 2023 | Preprint | bib |
| AGILE Platform: A Deep Learning-Powered Approach to Accelerate LNP Development for mRNA Delivery | Yue Xu, Shihao Ma, Haotian Cui, Jingan Chen, Shufen Xu, Kevin Wang, Andrew Varley, Rick Xing Ze Lu, Bo Wang, Bowen Li | bioRxiv | 2023 | Preprint | bib |
| CongFu: Conditional Graph Fusion for Drug Synergy Prediction | ROleksii Tsepa, Bohdan Naida, Bo Wang | arXiv | 2023 | Preprint | bib |
| Spatially Resolved Gene Expression Prediction from H&E Histology Images via Bi-modal Contrastive Learning | Ronald Xie, Kuan Pang, Gary D. Bader, Bo Wang | arXiv | 2023 | Preprint | bib |
| BIONIC: discovering new biology through deep learning-based network integration | Forster, D. T. et al | Nature Methods briefing | 2022 | Journal | bib |
| BIONIC: Biological Network Integration using Convolutions | Forster D, Li S, Yashiroda Y, Yoshimura M, Li Z, Isuhuaylas L, Itto-Nakama K, Yamanaka D, Ohya Y, Osada H, Wang B*, Bader G*, Boone C*. | Nature Methods | 2022 | Journal | bib |
| The differential impacts of dataset imbalance in single-cell data integration | Hassaan Maan, Lin Zhang, Chengxin Yu, Michael Geuenich, Kieran R Campbell, Bo Wang | bioRxiv | 2022 | Preprint | bib |
| Standardized Radiographic Evaluation of Human Donor Lungs During Ex Vivo Lung Perfusion Predicts Lung Injury and Lung Transplant Outcomes | BT Chao, MC McInnis, AT Sage, J Yeung, M Cypel, M Liu, B Wang, S Keshavjee | The Journal of Heart and Lung Transplantation | 2022 | Journal | bib |
| Transcriptional and functional motifs defining renal function revealed by single-nucleus RNA sequencing | Jun Xu, Yifang Liu, Hongjie Li, Alexander J Tarashansky, Colin H Kalicki, Ruei-Jiun Hung, Yanhui Hu, Aram Comjean, Sai Saroja Kolluru, Bo Wang, Stephen R Quake, Liqun Luo, Andrew P McMahon, Julian AT Dow, Norbert Perrimon | Proceedings of the National Academy of Sciences | 2022 | Journal | bib |
| Use of Wearable Technology and Deep Learning to Improve the Diagnosis of Brugada Syndrome | Liao, S., Bokhari, M., Chakraborty, P., Suszko, A., Jones, G., Spears, D., Gollob, M., Zhang, Z., Wang B* and Chauhan, V.S | JACC: Clinical Electrophysiology | 2022 | Journal | bib |
| Comparison of machine learning and the regression-based EHMRG model for predicting early mortality in acute heart failure | David E Austin, Douglas S Lee, Chloe X Wang, Shihao Ma, Xuesong Wang, Joan Porter, Bo Wang | International Journal of Cardiology | 2022 | Journal | bib |
| A Graph Neural Network Approach to Molecule Carcinogenicity Prediction | Fradkin, P., Young, A., Atanackovic, L., Frey, B., Lee, L. J., & Wang B* | Bioinformatics | 2022 | Journal | bib |
| Machine Learning Approaches to the Human Metabolome in Sepsis Identify Metabolic Links with Survival | 5. Kosyakovsky, L., Somerset, E., Rogers, A.J., Sklar, M., Mayers, J.R., Toma, A., Szekely, Y., Soussi, S., Wang B., Fan, C., Baron, R., Lawler, P | Intensive Care Medicine Experimental | 2022 | Journal | bib |
| A biomarker assay to risk-stratify patients with symptoms of respiratory tract infection | Shahid Husain, Andrew T Sage, Lorenzo Del Sorbo, Marcelo Cypel, Tereza Martinu, Stephen C Juvet, Andrea Mariscal, Julie Wright, Bonnie T Chao, Alaa A Shamandy, S Hossein Mousavi, Jin Ma, Bo Wang, Jerome Valero, Mingyao Liu, Megan Landes, Sharaniyaa Balachandran, Kimberley Hudson, Michelle Ngai, Marialessia Capuano, Maria Gelardi, Enrico Lupia, Daniel R Marinowic, Frederico O Friedrich, Carine RR Schmitz, Leticya SM Dos Santos, Florencia M Barbe-Tuana, Marcus H Jones, Kevin C Kain, Tony Mazzulli, Sam Sabbah, Shaf Keshavjee | European Respiratory Journal | 2022 | Journal | bib |
| Colony stimulating factor-1 producing endothelial cells and mesenchymal stromal cells maintain monocytes within a perivascular bone marrow niche | Takuo Emoto, Jessie Lu, Tharini Sivasubramaniyam, Hassaan Maan, Aniqa B Khan, Amina A Abow, Stephanie A Schroer, Sharon J Hyduk, Marwan G Althagafi, Trevor D McKee, Fred Fu, Shiva Shabro, Antigona Ulndreaj, Felix Chiu, Elvira Paneda, Shaun Pacheco, Tao Wang, Angela Li, Jean X Jiang, Peter Libby, Mansoor Husain, Bo Wang, Barry B Rubin, Myron I Cybulsky, Clinton S Robbins. | Cell Immunity | 2022 | Journal | bib |
| A sequence-to-sequence approach for document-level relation extraction | John Giorgi, Gary D Bader, Bo Wang. | arXiv | 2022 | Preprint | bib |
| One Cell At a Time (OCAT): a unified framework to integrate and analyze single-cell RNA-seq data | Chloe X. Wang, Lin Zhang, Bo Wang. | Genome Biology | 2022 | Journal | bib |
| InsighTx: A Machine-Learning Model That Accurately Predicts Transplant Outcomes During Ex Vivo Lung Perfusion. | AT Sage, AA Shamandy, SH Mousavi, BT Chao, O Nitski, X Zhou, L Del Sorbo, JC Yeung, M Liu, M Cypel, Bo Wang, S Keshavjee | The Journal of Heart and Lung Transplantation | 2022 | Journal | bib |
| Artificial intelligence for the echocardiographic assessment of valvular heart disease. | Rashmi Nedadur, Bo Wang, Wendy Tsang. | Heart | 2022 | Journal | bib |
| Machine learning as a new frontier in mitral valve surgical strategy. | Rashmi Nedadur, Bo Wang, Wendy Tsang. | Journal of Cardiac Surgery | 2022 | Journal | bib |
| Factors associated with SARS-CoV-2 test positivity in long-term care homes: A population-based cohort analysis using machine learning | Douglas S Lee, Chloe X Wang, Finlay A McAlister, Shihao Ma, Anna Chu, Paula A Rochon, Padma Kaul, Peter C Austin, Xuesong Wang, Sunil V Kalmady, Jacob A Udell, Michael J Schull, Barry B Rubin, Bo Wang. | The Lancet Regional Health – Americas | 2022 | Journal | bib |
| Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease | Michael Sugiyama, Haotian Cui, S Redka Dar'ya, Mehran Karimzadeh, Edurne Rujas, Hasaan Maan, Sikander Hayat, Kyle Cheung, Rahul Misra, Joseph B McPhee, Russell D Viirre, Andrew Haller, Roberto Botelho, Raffi Karshafian, Sarah A Sabatinos, Gregory D Fairn, Seyed Ali Madani Tonekaboni, Andreas Windemuth, Jean-Philippe Julien, Vijay Shahani, Stephen S MacKinnon, Bo Wang, Costin N Antonescu。 | Nature Scientific Reports | 2021 | Journal | bib |
| Predictors of mortality among long-term care residents with SARS-CoV-2 infection | Douglas S Lee, Shihao Ma, Anna Chu, Chloe X Wang, Xuesong Wang, Peter C Austin, Finlay A McAlister, Sunil V Kalmady, Moira K Kapral, Padma Kaul, Dennis T Ko, Paula A Rochon, Michael J Schull, Barry B Rubin, Bo Wang. | Journal of the American Geriatrics Society | 2021 | Journal | bib |
| Long-term mortality risk stratification of liver transplant recipients: real-time application of deep learning algorithms on longitudinal data | Osvald Nitski, Amirhossein Azhie, Fakhar Ali Qazi-Arisar, Xueqi Wang, Shihao Ma, Leslie Lilly, Kymberly D Watt, Josh Levitsky, Sumeet K Asrani, Douglas S Lee, Barry B Rubin, Mamatha Bhat, Bo Wang. | The Lancet Digital Health | 2021 | Journal | bib |
| The cardiac surgeon's guide to artificial intelligence | Rashmi Nedadur, Bo Wang, Bobby Yanagawa | Current Opinion in Cardiology | 2021 | Journal | bib |
| A MACHINE LEARNING MODEL FOR CHARACTERIZATION OF MIXED AORTIC VALVE DISEASE PATIENTS | Rashmi Nedadur, Zeinab Navidi Ghaziani, Maala Sooriyakanthan, Natalie Ho, Geraldine Ong, Howard Leong-Poi, Bo Wang, Wendy Tsang | Journal of the American College of Cardiology | 2021 | Journal | bib |
| simATAC: a single-cell ATAC-seq simulation framework | Zeinab Navidi, Lin Zhang, Bo Wang. | Genome Biology | 2021 | Journal | bib |
| Deep Learning Classification of Unipolar Electrograms in Human Atrial Fibrillation: Application in Focal Source Mapping. | Shun Liao, Don Ragot, Sachin Nayyar, Adrian Suszko, Zhaolei Zhang, Bo Wang, Vijay S Chauhan. | Frontiers in Physiology | 2021 | Journal | bib |
| Machine Learning to Improve Left Ventricular Scar Quantification in Hypertrophic Cardiomyopathy Patients. | Zeinab N Ghaziani, Jesse Sun, Raymond H Chan, Harry Rakowski, Martin S Maron, Ethan J Rowin, Bo Wang, Wendy Tsang | Circulation | 2020 | Journal | bib |
| Declutr: Deep contrastive learning for unsupervised textual representations. | John M Giorgi, Osvald Nitski, Gary D Bader, Bo Wang. | arXiv | 2020 | Preprint | bib |
| Genotyping SARS-CoV-2 through an interactive web application. | Hassaan Maan, Hamza Mbareche, Amogelang R Raphenya, Arinjay Banerjee, Jalees A Nasir, Robert A Kozak, Natalie Knox, Samira Mubareka, Andrew G McArthur, Bo Wang. | The Lancet Digital Health | 2020 | Journal | bib |
| CDF-Net: Cross-Domain Fusion Network for Accelerated MRI Reconstruction. | Osvald Nitski, Sayan Nag, Chris McIntosh, Bo Wang. | Medical Image Computing and Computer Assisted Intervention (MICCAI) | 2020 | Conference | bib |
| SAUNet: Shape Attentive U-Net for Interpretable Medical Image Segmentation. | Jesse Sun, Fatemeh Darbeha, Mark Zaidi, Bo Wang. | Medical Image Computing and Computer Assisted Intervention (MICCAI) | 2020 | Conference | bib |
| Learning Global and Local Consistent Representations for Unsupervised Image Retrieval via Deep Graph Diffusion Networks. | Zhiyong Dou, Haotian Cui, Bo Wang. | arXiv | 2020 | Preprint | bib |
| End-to-end Named Entity Recognition and Relation Extraction using Pre-trained Language Models. | John Giorgi, Xindi Wang, Nicola Sahar, Won Young Shin, Gary D. Bader, Bo Wang. | arXiv | 2019 | Preprint | bib |
| Deep Differentiable Random Forests for Age Estimation. | Wei Shen, Yilu Guo, Yan Wang, Kai Zhao, Bo Wang, Alan Yuille. | IEEE Trans. Pattern Analysis and Machine Intelligence (TPAMI) | 2019 | Journal | bib |
| To Embed or Not: Network Embedding as a Paradigm in Computational Biology. | Walter Nelson, Marinka Zitnik, Bo Wang, Jure Leskovec, Anna Goldenberg, Roded Sharan. | Frontiers in Genetics | 2019 | Journal | bib |
| Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities. | M Zitnik, F Nguyen, B Wang, J Leskovec, A Goldenberg, MM Hoffman. | Information Fusion | 2019 | Journal | bib |
| Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival. | D Ramazzotti, A Lal, B Wang, S Batzoglou, A Sidow. | Nature Communications | 2018 | Journal | bib |
| Network Enhancement: a general method to denoise weighted biological networks. | Bo Wang, Armin Pourshafeie, Marinka Zitnik, Junjie Zhu, Carlos D Bustamante, Serafim Batzoglou, Jure Leskovec. | Nature Communications | 2018 | Journal | bib |
| SIMLR: A Tool for Large‐Scale Genomic Analyses by Multi‐Kernel Learning. | Bo Wang, Daniele Ramazzotti, Luca De Sano, Junjie Zhu, Emma Pierson, Serafim Batzoglou. | Proteomics | 2018 | Journal | bib |
| Vicus: Exploiting local structures to improve network-based analysis of biological data. | Bo Wang, Lin Huang, Yuke Zhu, Anshul Kundaje, Serafim Batzoglou, Anna Goldenberg. | PLoS Computational Biology | 2017 | Journal | bib |
| Microbial typing by machine learned DNA melt signatures. | Nadya Andini, Bo Wang Pornpat Athamanolap. et al. | Scientific Reports | 2017 | Journal | bib |
| Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning. | Bo Wang, Junjie Zhu, Emma Pierson, Serafim Batzoglou. | Nature Methods | 2017 | Journal | bib |
| Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. | Solveig K Sieberts, Fan Zhu, [...] Bo Wang. et al. | Nature Communications | 2016 | Journal | bib |
| Reveel: large-scale population genotyping using low-coverage sequencing data. | Lin Huang, Bo Wang, Ruitang Chen, Sivan Bercovici, Serafim Batzoglou. | Bioinformatics | 2015 | Journal | bib |
| Similarity network fusion for aggregating data types on a genomic scale. | Bo Wang, Aziz M Mezlini, Feyyaz Demir, Marc Fiume, Zhuowen Tu, Michael Brudno, Benjamin Haibe-Kains, Anna Goldenberg. | Nature Methods | 2014 | Journal | bib |
| Parameter Estimation for ODEs Using a Cross-Entropy Approach. | Bo Wang, Wayne Enright. | SIAM Journal on Scientific Computing (SISC) | 2013 | Journal | bib |
| Identifying cancer specific functionally relevant miRNAs from gene expression and miRNA-to-gene networks using regularized regression. | Aziz M Mezlini, Bo Wang, Amit Deshwar, Quaid Morris, Anna Goldenberg. | PloS One | 2013 | Journal | bib |
| Face identification using reference-based features with message passing model. | Wei Shen, Bo Wang, Yueming Wang, Xiang Bai, Longin Jan Latecki. | Neurocomputing | 2013 | Journal | bib |
| Co-transduction for shape retrieval. | Xiang Bai, Bo Wang, Cong Yao, Wenyu Liu, Zhuowen Tu. | IEEE Transactions on Image Processing (TIP) | 2011 | Journal | bib |
| Effective Improved Graph Transduction. | Jun Chen, Yu Zhou, Yajun Gao, Bo Wang, Lin-bo Luo, Wenyu Liu. | JSW | 2011 | Journal | bib |
| Diversity Transfer Network for Few-Shot Learning. | Mengting Chen, Yuxin Fang, Xinggang Wang, Heng Luo, Yifeng Geng, Xinyu Zhang, Chang Huang, Wenyu Liu, Bo Wang. | AAAI Conference on Artificial Intelligence (AAAI) | 2020 | Conference | bib |
| Moment Matching for Multi-Source Domain Adaptation. | Xingchao Peng, Qinxun Bai, Xide Xia, Zijun Huang, Kate Saenko, Bo Wang. | International Conference on Computer Vision (ICCV) | 2019 | Conference | bib |
| Deep co-training for semi-supervised image recognition. | Siyuan Qiao, Wei Shen, Zhishuai Zhang, Bo Wang, Alan Yuille. | European Conference on Computer Vision (ECCV) | 2018 | Conference | bib |
| Single-shot object detection with enriched semantics. | Zhishuai Zhang, Siyuan Qiao, Cihang Xie, Wei Shen, Bo Wang, Alan L Yuille. | IEEE Conference on Computer Vision and Pattern Recognition (CVPR) | 2018 | Conference | bib |
| Deep regression forests for age estimation.. | Wei Shen, Yilu Guo, Yan Wang, Kai Zhao, Bo Wang, Alan L Yuille. | IEEE Conference on Computer Vision and Pattern Recognition (CVPR) | 2018 | Conference | bib |
| Gradually updated neural networks for large-scale image recognition. | Siyuan Qiao, Zhishuai Zhang, Wei Shen, Bo Wang, Alan Yuille. | International Conference on Machine Learning (ICML) | 2018 | Conference | bib |
| Unsupervised learning from noisy networks with applications to Hi-C data. | Bo Wang, Junjie Zhu, Armin Pourshafeie, Oana Ursu, Serafim Batzoglou, Anshul Kundaje. | Advances in Neural Information Processing Systems (NIPS) | 2016 | Conference | bib |
| Early Recurrence Improves Edge Detection. | Xun Shi, Bo Wang, John K Tsotsos. | Proceedings of the British Machine Vision Conference (BMVC) | 2013 | Conference | bib |
| Dynamic Label Propagation for Semi-supervised Multi-class Multi-label Classification. . | Bo Wang, Zhuowen Tu, John K Tsotsos. | International Conference on Computer Vision (ICCV) | 2013 | Conference | bib |
| Sparse Subspace Denoising for Image Manifolds. | Bo Wang, Zhuowen Tu. | IEEE Conference on Computer Vision and Pattern Recognition (CVPR) | 2013 | Conference | bib |
| Affinity learning via self-diffusion for image segmentation and clustering. . | Bo Wang, Zhuowen Tu. | IEEE Conference on Computer Vision and Pattern Recognition (CVPR) | 2012 | Conference | bib |
| Unsupervised metric fusion by cross diffusion. | Bo Wang, Jiayan Jiang, Wei Wang, Zhi-Hua Zhou, Zhuowen Tu. | IEEE Conference on Computer Vision and Pattern Recognition (CVPR) | 2012 | Conference | bib |
| Unsupervised metric learning by self-smoothing operator. | Jiayan Jiang, Bo Wang, Zhuowen Tu. | International Conference on Computer Vision (ICCV) | 2011 | Conference | bib |
| Shape classification using tree-unions. | Bo Wang, Wei Shen, Wenyu Liu, Xinge You, Xiang Bai. | International Conference on Pattern Recognition (ICPR) | 2010 | Conference | bib |
| Object recognition using junctions. | Bo Wang, Xiang Bai, Xinggang Wang, Wenyu Liu, Zhuowen Tu. | European Conference on Computer Vision (ECCV) | 2010 | Conference | bib |
| Rapid Shape Retrieval Using Improved Graph Transduction. | Jun Chen, Yu Zhou, Bo Wang, Linbo Luo, Wenyu Liu. | International Conference on Information Engineering and Computer Science | 2009 | Conference | bib |
| Evolutionary game for distributed power allocation over cooperative relay networks. | Jin Hu, Bo Wang, Jiao-long Wei, Shuang-lin Huang. | International Conference on Wireless Communications, Networking and Mobile Computing (WiCOM) | 2009 | Conference | bib |
| Skeleton graph matching based on critical points using path similarity. . | Yao Xu, Bo Wang, Wenyu Liu, Xiang Bai. | Asian Conference on Computer Vision (ACCV) | 2009 | Conference | bib |
| Robust Face Detection via Learning Small Faces on Hard Images. | Zhishuai Zhang, Wei Shen, Siyuan Qiao, Yan Wang, Bo Wang, Alan Yuille. | arXiv | 2018 | Preprint | bib |
| Deep learning for object saliency detection and image segmentation. | Hengyue Pan, Bo Wang, Hui Jiang. | arXiv | 2015 | Preprint | bib |
| Gradient-based Laplacian Feature Selection. | Bo Wang, Anna Goldenberg. | arXiv | 2014 | Preprint | bib |
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