| The glutathione peroxidase Gpx4 prevents lipid peroxidation and ferroptosis to sustain Treg cell activation and suppression of antitumor immunity C Xu, S Sun, T Johnson, R Qi, S Zhang, J Zhang, K Yang Cell reports 35 (11), 2021 | 221 | 2021 |
| SALMON: survival analysis learning with multi-omics neural networks on breast cancer Z Huang, X Zhan, S Xiang, TS Johnson, B Helm, CY Yu, J Zhang, ... Frontiers in genetics 10, 166, 2019 | 187 | 2019 |
| BERMUDA: a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes T Wang, TS Johnson, W Shao, Z Lu, BR Helm, J Zhang, K Huang Genome biology 20, 1-15, 2019 | 111 | 2019 |
| A protocol to evaluate RNA sequencing normalization methods ZB Abrams, TS Johnson, K Huang, PRO Payne, K Coombes BMC bioinformatics 20, 1-7, 2019 | 92 | 2019 |
| Deep learning-based cancer survival prognosis from RNA-seq data: approaches and evaluations Z Huang, TS Johnson, Z Han, B Helm, S Cao, C Zhang, P Salama, ... BMC medical genomics 13, 1-12, 2020 | 72 | 2020 |
| LAmbDA: label ambiguous domain adaptation dataset integration reduces batch effects and improves subtype detection TS Johnson, T Wang, Z Huang, CY Yu, Y Wu, Y Han, Y Zhang, K Huang, ... Bioinformatics 35 (22), 4696-4706, 2019 | 39 | 2019 |
| PseudoFuN: Deriving functional potentials of pseudogenes from integrative relationships with genes and microRNAs across 32 cancers TS Johnson, S Li, E Franz, Z Huang, S Dan Li, MJ Campbell, K Huang, ... Gigascience 8 (5), giz046, 2019 | 18 | 2019 |
| Topological methods for visualization and analysis of high dimensional single-cell RNA sequencing data T Wang, T Johnson, J Zhang, K Huang BIOCOMPUTING 2019: Proceedings of the Pacific Symposium, 350-361, 2018 | 18 | 2018 |
| Diagnostic Evidence GAuge of Single cells (DEGAS): a flexible deep transfer learning framework for prioritizing cells in relation to disease TS Johnson, CY Yu, Z Huang, S Xu, T Wang, C Dong, W Shao, MA Zaid, ... Genome medicine 14 (1), 11, 2022 | 15 | 2022 |
| Combinatorial analyses reveal cellular composition changes have different impacts on transcriptomic changes of cell type specific genes in Alzheimer’s Disease TS Johnson, S Xiang, T Dong, Z Huang, M Cheng, T Wang, K Yang, D Ni, ... Scientific Reports 11 (1), 353, 2021 | 14 | 2021 |
| Spatial cell type composition in normal and Alzheimers human brains is revealed using integrated mouse and human single cell RNA sequencing TS Johnson, S Xiang, BR Helm, ZB Abrams, P Neidecker, R Machiraju, ... Scientific reports 10 (1), 18014, 2020 | 14 | 2020 |
| Clinical and molecular correlates of tumor mutation burden in non-small cell lung cancer MF Sharpnack, JH Cho, TS Johnson, GA Otterson, PG Shields, K Huang, ... Lung Cancer 146, 36-41, 2020 | 14 | 2020 |
| ParsVNN: parsimony visible neural networks for uncovering cancer-specific and drug-sensitive genes and pathways X Huang, K Huang, T Johnson, M Radovich, J Zhang, J Ma, Y Wang NAR genomics and bioinformatics 3 (4), lqab097, 2021 | 13 | 2021 |
| Pseudogene-gene functional networks are prognostic of patient survival in breast cancer S Smerekanych, TS Johnson, K Huang, Y Zhang BMC medical genomics 13, 1-13, 2020 | 13 | 2020 |
| Lack of human cytomegalovirus expression in single cells from glioblastoma tumors and cell lines TS Johnson, ZB Abrams, X Mo, Y Zhang, K Huang Journal of neurovirology 23, 671-678, 2017 | 13 | 2017 |
| Functional virtual flow cytometry: a visual analytic approach for characterizing single-cell gene expression patterns Z Han, T Johnson, J Zhang, X Zhang, K Huang BioMed research international 2017, 2017 | 12 | 2017 |
| Network analysis of pseudogene-gene relationships: from pseudogene evolution to their functional potentials TS Johnson, S Li, JR Kho, K Huang, Y Zhang PACIFIC SYMPOSIUM ON BIOCOMPUTING 2018: Proceedings of the Pacific Symposium …, 2018 | 10 | 2018 |
| Gene co-expression network and copy number variation analyses identify transcription factors associated with multiple myeloma progression CY Yu, S Xiang, Z Huang, TS Johnson, X Zhan, Z Han, M Abu Zaid, ... Frontiers in genetics 10, 468, 2019 | 9 | 2019 |
| Opportunities for patient matching algorithms to improve patient care in oncology T Johnson, D Liebner, JL Chen JCO Clinical Cancer Informatics 1, 2017 | 9 | 2017 |
| SPCS: a spatial and pattern combined smoothing method for spatial transcriptomic expression Y Liu, T Wang, B Duggan, M Sharpnack, K Huang, J Zhang, X Ye, ... Briefings in Bioinformatics 23 (3), bbac116, 2022 | 7 | 2022 |
