Feature selection revisited in the single-cell era von Yang, Pengyi, Huang, Hao, Liu, Chunlei

Volltext

Evaluating spatially variable gene detection methods for spatial transcriptomics data von Chen, Carissa, Kim, Hani Jieun, Yang, Pengyi

Volltext

Benchmarking clustering algorithms on estimating the number of cell types from single-cell RNA-sequencing data von Yu, Lijia, Cao, Yue, Yang, Jean Y H, Yang, Pengyi

Volltext

A benchmark study of simulation methods for single-cell RNA sequencing data von Cao, Yue, Yang, Pengyi, Yang, Jean Yee Hwa

Volltext

scClassify: sample size estimation and multiscale classification of cells using single and multiple reference von Lin, Yingxin, Cao, Yue, Kim, Hani Jieun, Salim, Agus, Speed, Terence P, Lin, David M, Yang, Pengyi, Yang, Jean Yee Hwa

Volltext

scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets von Lin, Yingxin, Ghazanfar, Shila, Wang, Kevin Y. X., Gagnon-Bartsch, Johann A., Lo, Kitty K., Su, Xianbin, Han, Ze-Guang, Ormerod, John T., Speed, Terence P., Yang, Pengyi, Yang, Jean Yee Hwa

Volltext

Evaluation of deep learning-based feature selection for single-cell RNA sequencing data analysis von Huang, Hao, Liu, Chunlei, Wagle, Manoj M, Yang, Pengyi

Volltext

Single‐Cell Transcriptome Profiling Reveals Multicellular Ecosystem of Nucleus Pulposus during Degeneration Progression von Tu, Ji, Li, Wentian, Yang, Sidong, Yang, Pengyi, Yan, Qi, Wang, Shenyu, Lai, Kaitao, Bai, Xupeng, Wu, Cenhao, Ding, Wenyuan, Cooper‐White, Justin, Diwan, Ashish, Yang, Cao, Yang, Huilin, Zou, Jun

Volltext

Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis von Geddes, Thomas A, Kim, Taiyun, Nan, Lihao, Burchfield, James G, Yang, Jean Y H, Tao, Dacheng, Yang, Pengyi

Volltext

DNMT1 is essential for mammary and cancer stem cell maintenance and tumorigenesis von Pathania, Rajneesh, Ramachandran, Sabarish, Elangovan, Selvakumar, Padia, Ravi, Yang, Pengyi, Cinghu, Senthilkumar, Veeranan-Karmegam, Rajalakshmi, Arjunan, Pachiappan, Gnana-Prakasam, Jaya P., Sadanand, Fulzele, Pei, Lirong, Chang, Chang-Sheng, Choi, Jeong-Hyeon, Shi, Huidong, Manicassamy, Santhakumar, Prasad, Puttur D, Sharma, Suash, Ganapathy, Vadivel, Jothi, Raja, Thangaraju, Muthusamy

Volltext

Histone-Fold Domain Protein NF-Y Promotes Chromatin Accessibility for Cell Type-Specific Master Transcription Factors von Oldfield, Andrew J., Yang, Pengyi, Conway, Amanda E., Cinghu, Senthilkumar, Freudenberg, Johannes M., Yellaboina, Sailu, Jothi, Raja

Volltext

PhosR enables processing and functional analysis of phosphoproteomic data von Kim, Hani Jieun, Kim, Taiyun, Hoffman, Nolan J., Xiao, Di, James, David E., Humphrey, Sean J., Yang, Pengyi

Volltext

Intragenic Enhancers Attenuate Host Gene Expression von Cinghu, Senthilkumar, Yang, Pengyi, Kosak, Justin P., Conway, Amanda E., Kumar, Dhirendra, Oldfield, Andrew J., Adelman, Karen, Jothi, Raja

Volltext

Global redox proteome and phosphoproteome analysis reveals redox switch in Akt von Su, Zhiduan, Burchfield, James G., Yang, Pengyi, Humphrey, Sean J., Yang, Guang, Francis, Deanne, Yasmin, Sabina, Shin, Sung-Young, Norris, Dougall M., Kearney, Alison L., Astore, Miro A., Scavuzzo, Jonathan, Fisher-Wellman, Kelsey H., Wang, Qiao-Ping, Parker, Benjamin L., Neely, G. Gregory, Vafaee, Fatemeh, Chiu, Joyce, Yeo, Reichelle, Hogg, Philip J., Fazakerley, Daniel J., Nguyen, Lan K., Kuyucak, Serdar, James, David E.

Volltext

NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region von Oldfield, Andrew J., Henriques, Telmo, Kumar, Dhirendra, Burkholder, Adam B., Cinghu, Senthilkumar, Paulet, Damien, Bennett, Brian D., Yang, Pengyi, Scruggs, Benjamin S., Lavender, Christopher A., Rivals, Eric, Adelman, Karen, Jothi, Raja

Volltext

scReClassify: post hoc cell type classification of single-cell rNA-seq data von Kim, Taiyun, Lo, Kitty, Geddes, Thomas A, Kim, Hani Jieun, Yang, Jean Yee Hwa, Yang, Pengyi

Volltext

scDC: single cell differential composition analysis von Cao, Yue, Lin, Yingxin, Ormerod, John T, Yang, Pengyi, Yang, Jean Y H, Lo, Kitty K

Volltext

A hierarchical approach to removal of unwanted variation for large-scale metabolomics data von Kim, Taiyun, Tang, Owen, Vernon, Stephen T., Kott, Katharine A., Koay, Yen Chin, Park, John, James, David E., Grieve, Stuart M., Speed, Terence P., Yang, Pengyi, Figtree, Gemma A., O’Sullivan, John F., Yang, Jean Yee Hwa

Volltext

Multi-omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency von Yang, Pengyi, Humphrey, Sean J., Cinghu, Senthilkumar, Pathania, Rajneesh, Oldfield, Andrew J., Kumar, Dhirendra, Perera, Dinuka, Yang, Jean Y.H., James, David E., Mann, Matthias, Jothi, Raja

Volltext

A multi-filter enhanced genetic ensemble system for gene selection and sample classification of microarray data von Yang, Pengyi, Zhou, Bing B, Zhang, Zili, Zomaya, Albert Y

Volltext