Batch-Corrected Distance Mitigates Temporal and Spatial Variability for Clustering and Visualization of Single-Cell Gene Expression Data

por Liang, Shaoheng, Dou, Jinzhuang, Iqbal, Ramiz, Chen, Ken
Publicado 2023

Latent periodic process inference from single-cell RNA-seq data

por Liang, Shaoheng, Wang, Fang, Han, Jincheng, Chen, Ken
Publicado 2020

Stratified Test Alleviates Batch Effects in Single-Cell Data

por Liang, Shaoheng, Liang, Qingnan, Chen, Rui, Chen, Ken
Publicado 2020

Batch-Corrected Distance Mitigates Temporal and Spatial Variability for Clustering and Visualization of Single-Cell Gene Expression Data

por Liang, Shaoheng, Dou, Jinzhuang, Iqbal, Ramiz, Chen, Ken
Publicado 2020

SCMarker: Ab initio marker selection for single cell transcriptome profiling

por Wang, Fang, Liang, Shaoheng, Kumar, Tapsi, Navin, Nicholas, Chen, Ken
Publicado 2019

Sensei: how many samples to tell a change in cell type abundance?

por Liang, Shaoheng, Willis, Jason, Dou, Jinzhuang, Mohanty, Vakul, Huang, Yuefan, Vilar, Eduardo, Chen, Ken
Publicado 2022

An interpretable ML model to characterize patient-specific HLA-I antigen presentation

por Liang, Shaoheng, Jiang, Xianli, Chiu, Yulun, Xu, Haodong, Kim, Kun Hee, Lizee, Gregory, Chen, Ken
Publicado 2023

Extended live-cell barcoding approach for multiplexed mass cytometry

por Muftuoglu, Muharrem, Li, Li, Liang, Shaoheng, Mak, Duncan, Lin, Angelique J., Fang, Junxiang, Burks, Jared K., Chen, Ken, Andreeff, Michael
Publicado 2021

In-depth analysis of SARS-CoV-2–specific T cells reveals diverse differentiation hierarchies in vaccinated individuals

por Li, Li, Muftuoglu, Muharrem, Liang, Shaoheng, Basyal, Mahesh, LV, Jiangxing, Akdogan, Mehmet Emin, Chen, Ken, Andreeff, Michael, Flowers, Christopher R., Parmar, Simrit
Publicado 2022

MEDALT: single-cell copy number lineage tracing enabling gene discovery

por Wang, Fang, Wang, Qihan, Mohanty, Vakul, Liang, Shaoheng, Dou, Jinzhuang, Han, Jincheng, Minussi, Darlan Conterno, Gao, Ruli, Ding, Li, Navin, Nicholas, Chen, Ken
Publicado 2021

Integrated multi-omics analyses identify key anti-viral host factors and pathways controlling SARS-CoV-2 infection

por Hou, Jiakai, Wei, Yanjun, Zou, Jing, Jaffery, Roshni, Liang, Shaoheng, Zheng, Caishang, Chen, Ken, Shi, Pei-Yong, Chen, Yiwen, Xie, Xuping, Peng, Weiyi
Publicado 2022

Single-nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling

por Liang, Qingnan, Dharmat, Rachayata, Owen, Leah, Shakoor, Akbar, Li, Yumei, Kim, Sangbae, Vitale, Albert, Kim, Ivana, Morgan, Denise, Liang, Shaoheng, Wu, Nathaniel, Chen, Ken, DeAngelis, Margaret M., Chen, Rui
Publicado 2019

Bi-order multimodal integration of single-cell data

por Dou, Jinzhuang, Liang, Shaoheng, Mohanty, Vakul, Miao, Qi, Huang, Yuefan, Liang, Qingnan, Cheng, Xuesen, Kim, Sangbae, Choi, Jongsu, Li, Yumei, Li, Li, Daher, May, Basar, Rafet, Rezvani, Katayoun, Chen, Rui, Chen, Ken
Publicado 2022

Single-cell CRISPR immune screens reveal immunological roles of tumor intrinsic factors

por Hou, Jiakai, Liang, Shaoheng, Xu, Chunyu, Wei, Yanjun, Wang, Yunfei, Tan, Yukun, Sahni, Nidhi, McGrail, Daniel J, Bernatchez, Chantale, Davies, Michael, Li, Yumei, Chen, Rui, Yi, S Stephen, Chen, Yiwen, Yee, Cassian, Chen, Ken, Peng, Weiyi
Publicado 2022

Occult polyclonality of preclinical pancreatic cancer models drives in vitro evolution

por Monberg, Maria E., Geiger, Heather, Lee, Jaewon J., Sharma, Roshan, Semaan, Alexander, Bernard, Vincent, Wong, Justin, Wang, Fang, Liang, Shaoheng, Swartzlander, Daniel B., Stephens, Bret M., Katz, Matthew H. G., Chen, Ken, Robine, Nicolas, Guerrero, Paola A., Maitra, Anirban
Publicado 2022

Single-cell chromatin accessibility profiling of acute myeloid leukemia reveals heterogeneous lineage composition upon therapy-resistance

por Fan, Huihui, Wang, Feng, Zeng, Andy, Murison, Alex, Tomczak, Katarzyna, Hao, Dapeng, Jelloul, Fatima Zahra, Wang, Bofei, Barrodia, Praveen, Liang, Shaoheng, Chen, Ken, Wang, Linghua, Zhao, Zhongming, Rai, Kunal, Jain, Abhinav K., Dick, John, Daver, Naval, Futreal, Andy, Abbas, Hussein A.
Publicado 2023

Decoupling Lineage-Associated Genes in Acute Myeloid Leukemia Reveals Inflammatory and Metabolic Signatures Associated With Outcomes

por Abbas, Hussein A., Mohanty, Vakul, Wang, Ruiping, Huang, Yuefan, Liang, Shaoheng, Wang, Feng, Zhang, Jianhua, Qiu, Yihua, Hu, Chenyue W., Qutub, Amina A., Dail, Monique, Bolen, Christopher R., Daver, Naval, Konopleva, Marina, Futreal, Andrew, Chen, Ken, Wang, Linghua, Kornblau, Steven M.
Publicado 2021

Loss of metabolic fitness drives tumor resistance after CAR-NK cell therapy and can be overcome by cytokine engineering

por Li, Li, Mohanty, Vakul, Dou, Jinzhuang, Huang, Yuefan, Banerjee, Pinaki P., Miao, Qi, Lohr, Jens G., Vijaykumar, Tushara, Frede, Julia, Knoechel, Birgit, Muniz-Feliciano, Luis, Laskowski, Tamara J., Liang, Shaoheng, Moyes, Judy S., Nandivada, Vandana, Basar, Rafet, Kaplan, Mecit, Daher, May, Liu, Enli, Li, Ye, Acharya, Sunil, Lin, Paul, Shanley, Mayra, Rafei, Hind, Marin, David, Mielke, Stephan, Champlin, Richard E., Shpall, Elizabeth J., Chen, Ken, Rezvani, Katayoun
Publicado 2023