| TREM2 sustains macrophage-hepatocyte metabolic coordination in nonalcoholic fatty liver disease and sepsis J Hou, J Zhang, P Cui, Y Zhou, C Liu, X Wu, Y Ji, S Wang, B Cheng, H Ye, ... The Journal of clinical investigation 131 (4), 2021 | 134 | 2021 |
| Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment Y Zhou, J Xu, Y Hou, JB Leverenz, A Kallianpur, R Mehra, Y Liu, H Yu, ... Alzheimer's research & therapy 13 (1), 110, 2021 | 123 | 2021 |
| Multimodal single-cell/nucleus RNA sequencing data analysis uncovers molecular networks between disease-associated microglia and astrocytes with implications for drug … J Xu, P Zhang, Y Huang, Y Zhou, Y Hou, LM Bekris, J Lathia, CW Chiang, ... Genome research 31 (10), 1900-1912, 2021 | 60 | 2021 |
| Artificial intelligence framework identifies candidate targets for drug repurposing in Alzheimer’s disease J Fang, P Zhang, Q Wang, CW Chiang, Y Zhou, Y Hou, J Xu, R Chen, ... Alzheimer's Research & Therapy 14, 1-23, 2022 | 50 | 2022 |
| Synergy from gene expression and network mining (SynGeNet) method predicts synergistic drug combinations for diverse melanoma genomic subtypes KE Regan-Fendt, J Xu, M DiVincenzo, MC Duggan, R Shakya, R Na, ... NPJ systems biology and applications 5 (1), 6, 2019 | 50 | 2019 |
| Graph embedding and Gaussian mixture variational autoencoder network for end-to-end analysis of single-cell RNA sequencing data J Xu, J Xu, Y Meng, C Lu, L Cai, X Zeng, R Nussinov, F Cheng Cell Reports Methods 3 (1), 2023 | 37 | 2023 |
| Interpretable deep learning translation of GWAS and multi-omics findings to identify pathobiology and drug repurposing in Alzheimer’s disease J Xu, C Mao, Y Hou, Y Luo, JL Binder, Y Zhou, LM Bekris, J Shin, M Hu, ... Cell reports 41 (9), 111717, 2022 | 27 | 2022 |
| Core signaling pathways in ovarian cancer stem cell revealed by integrative analysis of multi-marker genomics data T Zhang, J Xu, S Deng, F Zhou, J Li, L Zhang, L Li, QE Wang, F Li PLoS One 13 (5), e0196351, 2018 | 25 | 2018 |
| The effect of LKB1 activity on the sensitivity to PI3K/mTOR inhibition in non-small cell lung cancer T Shukuya, T Yamada, MJ Koenig, J Xu, T Okimoto, F Li, JM Amann, ... Journal of Thoracic Oncology, 2019 | 19 | 2019 |
| The Alzheimer's Cell Atlas (TACA): A single‐cell molecular map for translational therapeutics accelerator in Alzheimer's disease Y Zhou, J Xu, Y Hou, L Bekris, JB Leverenz, AA Pieper, J Cummings, ... Alzheimer's & Dementia: Translational Research & Clinical Interventions 8 (1 …, 2022 | 15 | 2022 |
| Pik3c3 deficiency in myeloid cells imparts partial resistance to experimental autoimmune encephalomyelitis associated with reduced IL-1β production G Yang, W Song, J Xu, JL Postoak, F Cheng, J Martinez, J Zhang, L Wu, ... Cellular & molecular immunology 18 (8), 2024-2039, 2021 | 12 | 2021 |
| Diffusion mapping of drug targets on disease signaling network elements reveals drug combination strategies J Xu, K Regan-Fendt, S Deng, WE Carson III, PRO Payne, F Li PACIFIC SYMPOSIUM ON BIOCOMPUTING 2018: Proceedings of the Pacific Symposium …, 2018 | 12 | 2018 |
| Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer’s disease C Gupta, J Xu, T Jin, S Khullar, X Liu, S Alatkar, F Cheng, D Wang PLoS Computational Biology 18 (7), e1010287, 2022 | 11 | 2022 |
| Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment. Alzheimers Res Ther. 2021; 13 (1 … Y Zhou, J Xu, Y Hou, JB Leverenz, A Kallianpur, R Mehra, Y Liu, H Yu, ... Mol Immunol 127, 124-35, 2020 | 7 | 2020 |
| Comprehensively modeling heterogeneous symptom progression for Parkinson's disease subtyping. C Su, Y Hou, J Xu, M Brendel, JRMA Maasch, Z Bai, Y Zhu, C Henchcliffe, ... AMIA, 2022 | 4* | 2022 |
| Altered gene expression in excitatory neurons is associated with Alzheimer's disease and its higher incidence in women AX Garcia, J Xu, F Cheng, E Ruppin, AA Schäffer Alzheimer's & Dementia: Translational Research & Clinical Interventions 9 (1 …, 2023 | 2 | 2023 |
| Comprehensive characterization of multi-omic landscapes between gut-microbiota metabolites and the G-protein-coupled receptors in Alzheimer’s disease Y Qiu, Y Hou, Y Zhou, J Xu, M Bykova, JB Leverenz, AA Pieper, ... bioRxiv, 2022.09. 20.508759, 2022 | 2 | 2022 |
| A Signaling Network based Computational Model to Uncover Loop as the Novel Molecular Mechanisms for Medulloblastoma J Xu, F Li bioRxiv, 2019 | 1 | 2019 |
| Systematic characterization of multi-omics landscape between gut microbial metabolites and GPCRome in Alzheimer’s disease Y Qiu, Y Hou, D Gohel, Y Zhou, J Xu, M Bykova, Y Yang, JB Leverenz, ... Cell Reports 43 (5), 2024 | | 2024 |
| Network medicine informed multi-omics integration identifies drug targets and repurposable medicines for Amyotrophic Lateral Sclerosis F Cheng, M Yu, J Xu, R Dutta, B Trapp, A Pieper | | 2024 |
