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

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

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PAD2: interactive exploration of transcription factor genomic colocalization using ChIP-seq data by Taiyun Kim, Hani Jieun Kim, Andrew J. Oldfield, Pengyi Yang

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Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data by Daniel Kim, Andy Tran, Hani Jieun Kim, Yingxin Lin, Jean Yee Hwa Yang, Pengyi Yang

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Thinking process templates for constructing data stories with SCDNEY [version 2; peer review: 2 approved] by Marni Torkel, Pengyi Yang, Shila Ghazanfar, Nick Robertson, Yingxin Lin, Andy Tran, Hani Kim, Yue Cao, Ellis Patrick, Jean Yang

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

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Comprehensive characterization of fetal and mature retinal cell identity to assess the fidelity of retinal organoids by Hani Jieun Kim, Michelle O’Hara-Wright, Daniel Kim, To Ha Loi, Benjamin Y. Lim, Robyn V. Jamieson, Anai Gonzalez-Cordero, Pengyi Yang

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Trans-omic profiling uncovers molecular controls of early human cerebral organoid formation by Carissa Chen, Scott Lee, Katherine G. Zyner, Milan Fernando, Victoria Nemeruck, Emilie Wong, Lee L. Marshall, Jesse R. Wark, Nader Aryamanesh, Patrick P.L. Tam, Mark E. Graham, Anai Gonzalez-Cordero, Pengyi Yang

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Phosphoproteomics reveals rewiring of the insulin signaling network and multi-nodal defects in insulin resistance by Daniel J. Fazakerley, Julian van Gerwen, Kristen C. Cooke, Xiaowen Duan, Elise J. Needham, Alexis Díaz-Vegas, Søren Madsen, Dougall M. Norris, Amber S. Shun-Shion, James R. Krycer, James G. Burchfield, Pengyi Yang, Mark R. Wade, Joseph T. Brozinick, David E. James, Sean J. Humphrey

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Atlas of multilineage stem cell differentiation reveals TMEM88 as a developmental regulator of blood pressure by Sophie Shen, Tessa Werner, Samuel W. Lukowski, Stacey Andersen, Yuliangzi Sun, Woo Jun Shim, Dalia Mizikovsky, Sakurako Kobayashi, Jennifer Outhwaite, Han Sheng Chiu, Xiaoli Chen, Gavin Chapman, Ella M. M. A. Martin, Di Xia, Duy Pham, Zezhuo Su, Daniel Kim, Pengyi Yang, Men Chee Tan, Enakshi Sinniah, Qiongyi Zhao, Sumedha Negi, Meredith A. Redd, Joseph E. Powell, Sally L. Dunwoodie, Patrick P. L. Tam, Mikael Bodén, Joshua W. K. Ho, Quan Nguyen, Nathan J. Palpant

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