BERMUDA: a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes von Wang, Tongxin, Johnson, Travis S, Shao, Wei, Lu, Zixiao, Helm, Bryan R, Zhang, Jie, Huang, Kun

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SALMON: Survival Analysis Learning With Multi-Omics Neural Networks on Breast Cancer von Huang, Zhi, Zhan, Xiaohui, Xiang, Shunian, Johnson, Travis S, Helm, Bryan, Yu, Christina Y, Zhang, Jie, Salama, Paul, Rizkalla, Maher, Han, Zhi, Huang, Kun

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A protocol to evaluate RNA sequencing normalization methods von Abrams, Zachary B, Johnson, Travis S, Huang, Kun, Payne, Philip R O, Coombes, Kevin

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Disease-associated astrocytes and microglia markers are upregulated in mice fed high fat diet von Lin, Li, Basu, Rashmita, Chatterjee, Debolina, Templin, Andrew T., Flak, Jonathan N., Johnson, Travis S.

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Deep learning-based cancer survival prognosis from RNA-seq data: approaches and evaluations von Huang, Zhi, Johnson, Travis S, Han, Zhi, Helm, Bryan, Cao, Sha, Zhang, Chi, Salama, Paul, Rizkalla, Maher, Yu, Christina Y, Cheng, Jun, Xiang, Shunian, Zhan, Xiaohui, Zhang, Jie, Huang, Kun

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1q amplification and PHF19 expressing high-risk cells are associated with relapsed/refractory multiple myeloma von Johnson, Travis S., Sudha, Parvathi, Liu, Enze, Becker, Nathan, Robertson, Sylvia, Blaney, Patrick, Morgan, Gareth, Chopra, Vivek S., Dos Santos, Cedric, Nixon, Michael, Huang, Kun, Suvannasankha, Attaya, Zaid, Mohammad Abu, Abonour, Rafat, Walker, Brian A.

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Gradient boosting reveals spatially diverse cholesterol gene signatures in colon cancer von Yang, Xiuxiu, Chatterjee, Debolina, Couetil, Justin L, Liu, Ziyu, Ardon, Valerie D, Chen, Chao, Zhang, Jie, Huang, Kun, Johnson, Travis S

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Pseudogene-gene functional networks are prognostic of patient survival in breast cancer von Smerekanych, Sasha, Johnson, Travis S, Huang, Kun, Zhang, Yan

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Combinatorial analyses reveal cellular composition changes have different impacts on transcriptomic changes of cell type specific genes in Alzheimer’s Disease von Johnson, Travis S., Xiang, Shunian, Dong, Tianhan, Huang, Zhi, Cheng, Michael, Wang, Tianfu, Yang, Kai, Ni, Dong, Huang, Kun, Zhang, Jie

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Diagnostic Evidence GAuge of Single cells (DEGAS): a flexible deep transfer learning framework for prioritizing cells in relation to disease von Johnson, Travis S, Yu, Christina Y, Huang, Zhi, Xu, Siwen, Wang, Tongxin, Dong, Chuanpeng, Shao, Wei, Zaid, Mohammad Abu, Huang, Xiaoqing, Wang, Yijie, Bartlett, Christopher, Zhang, Yan, Walker, Brian A, Liu, Yunlong, Huang, Kun, Zhang, Jie

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Optimal transport- and kernel-based early detection of mild cognitive impairment patients based on magnetic resonance and positron emission tomography images von Liu, Ziyu, Johnson, Travis S, Shao, Wei, Zhang, Min, Zhang, Jie, Huang, Kun

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302 Diagnostic Evidence Gauge of Spatial Transcriptomics (DEGAS-ST): Using transfer learning to map clinical data to spatial transcriptomics in prostate cancer von Couetil, Justin, Liu, Ziyu, Alomari, Ahmed K., Zhang, Jie, Huang, Kun, Johnson, Travis S.

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Ventromedial hypothalamic nucleus subset stimulates tissue thermogenesis via preoptic area outputs von Basu, Rashmita, Elmendorf, Andrew J., Lorentz, Betty, Mahler, Connor A., Lazzaro, Olivia, App, Britany, Zhou, Shudi, Yamamoto, Yura, Suber, Mya, Wann, Jamie C., Roh, Hyun Cheol, Sheets, Patrick L., Johnson, Travis S., Flak, Jonathan N.

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239-LB: Single-Cell Analysis Identified Inhibitory Neurons Associated with High-Fat Diet in the Bed Nucleus of the Stria Terminalis von YANG, XIUXIU, FLAK, JONATHAN, JOHNSON, TRAVIS S.

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Gene Co-expression Network and Copy Number Variation Analyses Identify Transcription Factors Associated With Multiple Myeloma Progression von Yu, Christina Y, Xiang, Shunian, Huang, Zhi, Johnson, Travis S, Zhan, Xiaohui, Han, Zhi, Abu Zaid, Mohammad, Huang, Kun

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LAmbDA: label ambiguous domain adaptation dataset integration reduces batch effects and improves subtype detection von Johnson, Travis S, Wang, Tongxin, Huang, Zhi, Yu, Christina Y, Wu, Yi, Han, Yatong, Zhang, Yan, Huang, Kun, Zhang, Jie

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SPCS: a spatial and pattern combined smoothing method for spatial transcriptomic expression von Liu, Yusong, Wang, Tongxin, Duggan, Ben, Sharpnack, Michael, Huang, Kun, Zhang, Jie, Ye, Xiufen, Johnson, Travis S

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TSAFinder: exhaustive tumor-specific antigen detection with RNAseq von Sharpnack, Michael F, Johnson, Travis S, Chalkley, Robert, Han, Zhi, Carbone, David, Huang, Kun, He, Kai

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Predicting Alzheimer's disease subtypes and understanding their molecular characteristics in living patients with transcriptomic trajectory profiling von Huang, Xiaoqing, Jannu, Asha Jacob, Song, Ziyan, Jury‐Garfe, Nur, Lasagna‐Reeves, Cristian A., Johnson, Travis S., Huang, Kun, Zhang, Jie

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Enhanced microglial dynamics and a paucity of tau seeding in the amyloid plaque microenvironment contribute to cognitive resilience in Alzheimer’s disease von Jury-Garfe, Nur, Redding-Ochoa, Javier, You, Yanwen, Martínez, Pablo, Karahan, Hande, Chimal-Juárez, Enrique, Johnson, Travis S., Zhang, Jie, Resnick, Susan, Kim, Jungsu, Troncoso, Juan C., Lasagna-Reeves, Cristian A.

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