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Yi-Ting Guo, Qin-Qin Li, Chun-Sheng Liang

Vishal Rana, Jianhao Peng, Chao Pan, Hanbaek Lyu, Albert Cheng, Minji Kim, Olgica Milenkovic

Hongsong Feng, Sean Cottrell, Yuta Hozumi, Guo-Wei Wei

Yisong Wang, Mingzhi Wang

Kivilcim Ozturk, Rebecca Panwala, Jeanna Sheen, Kyle Ford, Nathan Jayne, Andrew Portell, Dong-Er Zhang, Stephan Hutter, Torsten Haferlach, Trey Ideker, Prashant Mali, Hannah Carter

Bing He, Yao Xiao, Haodong Liang, Qianhui Huang, Yuheng Du, Yijun Li, David Garmire, Duxin Sun, Lana X. Garmire

Neeraj Kumar, Daniel Skubleny, Michael Parkes, Ruchika Verma, Sacha Davis, Luke Kumar, Amira Aissiou, Russell Greiner

Diksha Pandey, Perumal P. Onkara

Yifan Zhou, Kaixuan Luo, Lifan Liang, Mengjie Chen, Xin He

Han Zhang, Xinghua Lu, Binfeng Lu, Lujia Chen

Jeanette A. I. Johnson, Ashley P. Tsang, Jacob T. Mitchell, David L. Zhou, Julia Bowden, Emily Davis-Marcisak, Thomas Sherman, Ted Liefeld, Melanie Loth, Loyal A. Goff, Jacquelyn W. Zimmerman, Ben Kinny-Köster, Elizabeth M. Jaffee, Pablo Tamayo, Jill P. Mesirov, Michael Reich, Elana J. Fertig, Genevieve L. Stein-O’Brien

Ron Zeira, Max Land, Alexander Strzalkowski, Benjamin J. Raphael

Ya-Li Zhu, Sha-Sha Yuan, Jin-Xing Liu

Weming Wu, Xiaoke Ma

Shengfeng Gan, Huan Deng, Yang Qiu, Mohammed Alshahrani, Shichao Liu

Haiyue Wang, Xiaoke Ma

Cui-Na Jiao, Jin-Xing Liu, Juan Wang, Junliang Shang, Chun-Hou Zheng

Angelica Alejandra Serrano-Rubio, Guillermo B. Morales-Luna, Amilcar Meneses-Viveros

Mikio Shiga, Shigeto Seno, Makoto Onizuka, Hideo Matsuda

Emily F. Davis-Marcisak, Atul Deshpande, Genevieve L. Stein-O’Brien, Won J. Ho, Daniel Laheru, Elizabeth M. Jaffee, Elana J. Fertig, Luciane T. Kagohara

Ya‐Li Zhu, Xiao‐Ning Zhang, Chuan‐Yuan Wang, Jin‐Xing Liu, Xiang‐Zhen Kong

Fangyuan Chen, Kai Ding, Nolan Priedigkeit, Ashuvinee Elangovan, Kevin M. Levine, Neil Carleton, Laura Savariau, Jennifer M. Atkinson, Steffi Oesterreich, Adrian V. Lee

Qianhui Huang, Yu Liu, Yuheng Du, Lana X. Garmire

Dongyuan Song, Kexin Li, Zachary Hemminger, Roy Wollman, Jingyi Jessica Li

Moritz Hess, Maren Hackenberg, Harald Binder

Valentine Svensson, Adam Gayoso, Nir Yosef, Lior Pachter

Wenming Wu, Xiaoke Ma

Kevin Y Yang, Manching Ku, Kathy O Lui

Arkaitz Ibarra, Jiali Zhuang, Yue Zhao, Neeraj S. Salathia, Vera Huang, Alexander D. Acosta, Jonathan Aballi, Shusuke Toden, Amy P. Karns, Intan Purnajo, Julianna R. Parks, Lucy Guo, James Mason, Darren Sigal, Tina S. Nova, Stephen R. Quake, Michael Nerenberg

Ruiqing Zheng, Zhenlan Liang, Xiang Chen, Yu Tian, Chen Cao, Min Li

Lifan Liang, Kunju Zhu, Songjian Lu

Thomas D. Sherman, Tiger Gao, Elana J. Fertig

Xiangtao Li, Ka-Chun Wong

Xiangtao Li, Shixiong Zhang, Ka-Chun Wong

Cédric Arisdakessian, Olivier Poirion, Breck Yunits, Xun Zhu, Lana X. Garmire

Xiangtao Li, Ka-Chun Wong

Min Jung, Daniel Wells, Jannette Rusch, Suhaira Ahmad, Jonathan Marchini, Simon R Myers, Donald F Conrad

Genevieve L. Stein-O’Brien, Brian S. Clark, Thomas Sherman, Cristina Zibetti, Qiwen Hu, Rachel Sealfon, Sheng Liu, Jiang Qian, Carlo Colantuoni, Seth Blackshaw, Loyal A. Goff, Elana J. Fertig

Xun Zhu, Lana X. Garmire

Jun Woo, Boris J. Winterhoff, Timothy K. Starr, Constantin Aliferis, Jinhua Wang

Runmin Wei, Alastair B. Ross, MingMing Su, Jingye Wang, Seu‐Ping Guiraud, Colleen Fogarty Draper, Maurice Beaumont, Wei Jia, Francois‐Pierre Martin

Shuai Wang, Peng Wu, Manqi Zhou, Tsung-Hui Chang, Song Wu

Genevieve L. Stein-O’Brien, Raman Arora, Aedin C. Culhane, Alexander V. Favorov, Lana X. Garmire, Casey S. Greene, Loyal A. Goff, Yifeng Li, Aloune Ngom, Michael F. Ochs, Yanxun Xu, Elana J. Fertig

Chung-Chau Hon, Jay W Shin, Piero Carninci, Michael J T Stubbington

Donghyung Lee, Anthony Cheng, Nathan Lawlor, Mohan Bolisetty, Duygu Ucar

Genevieve Stein-O’Brien, Luciane T. Kagohara, Sijia Li, Manjusha Thakar, Ruchira Ranaweera, Hiroyuki Ozawa, Haixia Cheng, Michael Considine, Sandra Schmitz, Alexander V. Favorov, Ludmila V. Danilova, Joseph A. Califano, Evgeny Izumchenko, Daria A. Gaykalova, Christine H. Chung, Elana J. Fertig

Mitsuhiro Eto, Wataru Hirota, Shigeto Seno, Hideo Matsuda

Dong Seong Cho, Jason D. Doles

Michael A. Ortega, Olivier Poirion, Xun Zhu, Sijia Huang, Thomas K. Wolfgruber, Robert Sebra, Lana X. Garmire

2024	The rise of nonnegative matrix factorization: Algorithms and applications Information Systems Yi-Ting Guo, Qin-Qin Li, Chun-Sheng Liang
2024	Interpretable online network dictionary learning for inferring long-range chromatin interactions PLOS Computational Biology Vishal Rana, Jianhao Peng, Chao Pan, Hanbaek Lyu, Albert Cheng, Minji Kim, Olgica Milenkovic
2024	Multiscale differential geometry learning of networks with applications to single-cell RNA sequencing data Computers in Biology and Medicine Hongsong Feng, Sean Cottrell, Yuta Hozumi, Guo-Wei Wei
2024	Robust scRNA-seq Cell Types Identification by Self-Guided Deep Clustering Network IEEE Access Yisong Wang, Mingzhi Wang
2024	Interface-guided phenotyping of coding variants in the transcription factor RUNX1 Cell Reports Kivilcim Ozturk, Rebecca Panwala, Jeanna Sheen, Kyle Ford, Nathan Jayne, Andrew Portell, Dong-Er Zhang, Stephan Hutter, Torsten Haferlach, Trey Ideker, Prashant Mali, Hannah Carter
2023	ASGARD is A Single-cell Guided Pipeline to Aid Repurposing of Drugs Nature Communications Bing He, Yao Xiao, Haodong Liang, Qianhui Huang, Yuheng Du, Yijun Li, David Garmire, Duxin Sun, Lana X. Garmire
2023	Learning Individual Survival Models from PanCancer Whole Transcriptome Data Clinical Cancer Research Neeraj Kumar, Daniel Skubleny, Michael Parkes, Ruchika Verma, Sacha Davis, Luke Kumar, Amira Aissiou, Russell Greiner
2023	Improved downstream functional analysis of single-cell RNA-sequence data using DGAN Scientific Reports Diksha Pandey, Perumal P. Onkara
2023	A new Bayesian factor analysis method improves detection of genes and biological processes affected by perturbations in single-cell CRISPR screening Nature Methods Yifan Zhou, Kaixuan Luo, Lifan Liang, Mengjie Chen, Xin He
2023	scGEM: Unveiling the Nested Tree-Structured Gene Co-Expressing Modules in Single Cell Transcriptome Data Cancers Han Zhang, Xinghua Lu, Binfeng Lu, Lujia Chen
2023	Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS Nature Protocols Jeanette A. I. Johnson, Ashley P. Tsang, Jacob T. Mitchell, David L. Zhou, Julia Bowden, Emily Davis-Marcisak, Thomas Sherman, Ted Liefeld, Melanie Loth, Loyal A. Goff, Jacquelyn W. Zimmerman, Ben Kinny-Köster, Elizabeth M. Jaffee, Pablo Tamayo, Jill P. Mesirov, Michael Reich, Elana J. Fertig, Genevieve L. Stein-O’Brien
2022	Alignment and integration of spatial transcriptomics data Nature Methods Ron Zeira, Max Land, Alexander Strzalkowski, Benjamin J. Raphael
2022	Similarity and Dissimilarity Regularized Nonnegative Matrix Factorization for Single-Cell RNA-seq Analysis Interdisciplinary Sciences: Computational Life Sciences Ya-Li Zhu, Sha-Sha Yuan, Jin-Xing Liu
2022	Network-based Structural Learning Nonnegative Matrix Factorization Algorithm for Clustering of scRNA-seq Data IEEE/ACM Transactions on Computational Biology and Bioinformatics Weming Wu, Xiaoke Ma
2022	DSAE-Impute: Learning Discriminative Stacked Autoencoders for Imputing Single-cell RNA-seq Data Current Bioinformatics Shengfeng Gan, Huan Deng, Yang Qiu, Mohammed Alshahrani, Shichao Liu
2022	Learning discriminative and structural samples for rare cell types with deep generative model Briefings in Bioinformatics Haiyue Wang, Xiaoke Ma
2022	Visualization and Analysis of Single Cell RNA-Seq Data by Maximizing Correntropy Based Non-Negative Low Rank Representation IEEE Journal of Biomedical and Health Informatics Cui-Na Jiao, Jin-Xing Liu, Juan Wang, Junliang Shang, Chun-Hou Zheng
2021	Gene Expression Analysis through Parallel Non-Negative Matrix Factorization Computation Angelica Alejandra Serrano-Rubio, Guillermo B. Morales-Luna, Amilcar Meneses-Viveros
2021	The triumphs and limitations of computational methods for scRNA-seq Nature Methods Peter V. Kharchenko
2021	SC-JNMF: single-cell clustering integrating multiple quantification methods based on joint non-negative matrix factorization PeerJ Mikio Shiga, Shigeto Seno, Makoto Onizuka, Hideo Matsuda
2021	From bench to bedside: Single-cell analysis for cancer immunotherapy Cancer Cell Emily F. Davis-Marcisak, Atul Deshpande, Genevieve L. Stein-O’Brien, Won J. Ho, Daniel Laheru, Elizabeth M. Jaffee, Elana J. Fertig, Luciane T. Kagohara
2021	Adaptive total variation constraint hypergraph regularized NMF for single‐cell RNA‐seq data analysis Quantitative Biology Ya‐Li Zhu, Xiao‐Ning Zhang, Chuan‐Yuan Wang, Jin‐Xing Liu, Xiang‐Zhen Kong
2021	Single-Cell Transcriptomic Heterogeneity in Invasive Ductal and Lobular Breast Cancer Cells Cancer Research Fangyuan Chen, Kai Ding, Nolan Priedigkeit, Ashuvinee Elangovan, Kevin M. Levine, Neil Carleton, Laura Savariau, Jennifer M. Atkinson, Steffi Oesterreich, Adrian V. Lee
2021	Evaluation of Cell Type Annotation R Packages on Single-Cell RNA-Seq Data Genomics, Proteomics & Bioinformatics Qianhui Huang, Yu Liu, Yuheng Du, Lana X. Garmire
2021	scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling Bioinformatics Dongyuan Song, Kexin Li, Zachary Hemminger, Roy Wollman, Jingyi Jessica Li
2020	Exploring generative deep learning for omics data using log-linear models Bioinformatics Moritz Hess, Maren Hackenberg, Harald Binder
2020	Interpretable factor models of single-cell RNA-seq via variational autoencoders Bioinformatics Valentine Svensson, Adam Gayoso, Nir Yosef, Lior Pachter
2020	Joint learning dimension reduction and clustering of single-cell RNA-sequencing data Bioinformatics Wenming Wu, Xiaoke Ma
2020	Single-cell transcriptomics uncover distinct innate and adaptive cell subsets during tissue homeostasis and regeneration Journal of Leukocyte Biology Kevin Y Yang, Manching Ku, Kathy O Lui
2020	Non-invasive characterization of human bone marrow stimulation and reconstitution by cell-free messenger RNA sequencing Nature Communications Arkaitz Ibarra, Jiali Zhuang, Yue Zhao, Neeraj S. Salathia, Vera Huang, Alexander D. Acosta, Jonathan Aballi, Shusuke Toden, Amy P. Karns, Intan Purnajo, Julianna R. Parks, Lucy Guo, James Mason, Darren Sigal, Tina S. Nova, Stephen R. Quake, Michael Nerenberg
2020	An Adaptive Sparse Subspace Clustering for Cell Type Identification Frontiers in Genetics Ruiqing Zheng, Zhenlan Liang, Xiang Chen, Yu Tian, Chen Cao, Min Li
2020	BEM: Mining Coregulation Patterns in Transcriptomics via Boolean Matrix Factorization Bioinformatics Lifan Liang, Kunju Zhu, Songjian Lu
2020	CoGAPS 3: Bayesian non-negative matrix factorization for single-cell analysis with asynchronous updates and sparse data structures BMC Bioinformatics Thomas D. Sherman, Tiger Gao, Elana J. Fertig
2019	Single-Cell RNA Sequencing Data Interpretation by Evolutionary Multiobjective Clustering IEEE/ACM Transactions on Computational Biology and Bioinformatics Xiangtao Li, Ka-Chun Wong
2019	Single-cell RNA-seq interpretations using evolutionary multiobjective ensemble pruning Bioinformatics Xiangtao Li, Shixiong Zhang, Ka-Chun Wong
2019	DeepImpute: an accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data Genome Biology Cédric Arisdakessian, Olivier Poirion, Breck Yunits, Xun Zhu, Lana X. Garmire
2019	Elucidating Genome-Wide Protein-RNA Interactions Using Differential Evolution IEEE/ACM Transactions on Computational Biology and Bioinformatics Xiangtao Li, Ka-Chun Wong
2019	Unified single-cell analysis of testis gene regulation and pathology in five mouse strains eLife Min Jung, Daniel Wells, Jannette Rusch, Suhaira Ahmad, Jonathan Marchini, Simon R Myers, Donald F Conrad
2019	Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species Cell Systems Genevieve L. Stein-O’Brien, Brian S. Clark, Thomas Sherman, Cristina Zibetti, Qiwen Hu, Rachel Sealfon, Sheng Liu, Jiang Qian, Carlo Colantuoni, Seth Blackshaw, Loyal A. Goff, Elana J. Fertig
2019	Single-Cell Omics Xun Zhu, Lana X. Garmire
2019	De novo prediction of cell-type complexity in single-cell RNA-seq and tumor microenvironments Life Science Alliance Jun Woo, Boris J. Winterhoff, Timothy K. Starr, Constantin Aliferis, Jinhua Wang
2018	Metabotypes Related to Meat and Vegetable Intake Reflect Microbial, Lipid and Amino Acid Metabolism in Healthy People Molecular Nutrition & Food Research Runmin Wei, Alastair B. Ross, MingMing Su, Jingye Wang, Seu‐Ping Guiraud, Colleen Fogarty Draper, Maurice Beaumont, Wei Jia, Francois‐Pierre Martin
2018	2018 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) Shuai Wang, Peng Wu, Manqi Zhou, Tsung-Hui Chang, Song Wu
2018	Enter the Matrix: Factorization Uncovers Knowledge from Omics Trends in Genetics Genevieve L. Stein-O’Brien, Raman Arora, Aedin C. Culhane, Alexander V. Favorov, Lana X. Garmire, Casey S. Greene, Loyal A. Goff, Yifeng Li, Aloune Ngom, Michael F. Ochs, Yanxun Xu, Elana J. Fertig
2018	The Human Cell Atlas: Technical approaches and challenges Briefings in Functional Genomics Chung-Chau Hon, Jay W Shin, Piero Carninci, Michael J T Stubbington
2018	Detection of correlated hidden factors from single cell transcriptomes using Iteratively Adjusted-SVA (IA-SVA) Scientific Reports Donghyung Lee, Anthony Cheng, Nathan Lawlor, Mohan Bolisetty, Duygu Ucar
2018	Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance Genome Medicine Genevieve Stein-O’Brien, Luciane T. Kagohara, Sijia Li, Manjusha Thakar, Ruchira Ranaweera, Hiroyuki Ozawa, Haixia Cheng, Michael Considine, Sandra Schmitz, Alexander V. Favorov, Ludmila V. Danilova, Joseph A. Califano, Evgeny Izumchenko, Daria A. Gaykalova, Christine H. Chung, Elana J. Fertig
2018	2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Mitsuhiro Eto, Wataru Hirota, Shigeto Seno, Hideo Matsuda
2018	Single-cell RNA sequencing for the study of development, physiology and disease Nature Reviews Nephrology S. Steven Potter
2017	Single cell transcriptome analysis of muscle satellite cells reveals widespread transcriptional heterogeneity Gene Dong Seong Cho, Jason D. Doles
2017	Using single‐cell multiple omics approaches to resolve tumor heterogeneity Clinical and Translational Medicine Michael A. Ortega, Olivier Poirion, Xun Zhu, Sijia Huang, Thomas K. Wolfgruber, Robert Sebra, Lana X. Garmire
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