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ArticlesPeer ReviewedFull Text
Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data
Author / Creator:Sun, Duanchen ; Guan, Xiangnan ; Moran, Amy E. ; Wu, Ling-Yun ; Qian, David Z. ; Schedin, Pepper ; Dai, Mu-Shui ; Danilov, Alexey V. ; Alumkal, Joshi J. ; Adey, Andrew C. ; Spellman, Paul T. ; Xia, Zheng
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2022-04, Vol.40 (4), p.527-538
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ArticlesPeer ReviewedFull Text
Postpartum breast cancer has a distinct molecular profile that predicts poor outcomes
Author / Creator:Jindal, Sonali ; Pennock, Nathan D. ; Sun, Duanchen ; Horton, Wesley ; Ozaki, Michelle K. ; Narasimhan, Jayasri ; Bartlett, Alexandra Q. ; Weinmann, Sheila ; Goss, Paul E. ; Borges, Virginia F. ; Xia, Zheng ; Schedin, Pepper
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2021-11, Vol.12 (1), p.6341-6341, Article 6341
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ArticlesPeer ReviewedFull Text
Highly scalable generation of DNA methylation profiles in single cells
Author / Creator:Mulqueen, Ryan M ; Pokholok, Dmitry ; Norberg, Steven J ; Torkenczy, Kristof A ; Fields, Andrew J ; Sun, Duanchen ; Sinnamon, John R ; Shendure, Jay ; Trapnell, Cole ; O'Roak, Brian J ; Xia, Zheng ; Steemers, Frank J ; Adey, Andrew C
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2018-06, Vol.36 (5), p.428-431
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ArticlesPeer ReviewedFull Text
BET bromodomain inhibition blocks the function of a critical AR-independent master regulator network in lethal prostate cancer
Author / Creator:Coleman, Daniel J. ; Gao, Lina ; King, Carly J. ; Schwartzman, Jacob ; Urrutia, Joshua ; Sehrawat, Archana ; Tayou, Junior ; Balter, Ariel ; Burchard, Julja ; Chiotti, Kami E. ; Derrick, Daniel S. ; Sun, Duanchen ; Xia, Zheng ; Heiser, Laura M. ; Alumkal, Joshi J.
Publisher:London: Nature Publishing Group UK
Journal title:Oncogene, 2019-07, Vol.38 (28), p.5658-5669
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ArticlesPeer ReviewedFull Text
CDK9 inhibition induces epigenetic reprogramming revealing strategies to circumvent resistance in lymphoma
Author / Creator:Thieme, Elana ; Bruss, Nur ; Sun, Duanchen ; Dominguez, Edward C ; Coleman, Daniel ; Liu, Tingting ; Roleder, Carly ; Martinez, Melissa ; Garcia-Mansfield, Krystine ; Ball, Brian ; Pirrotte, Patrick ; Wang, Lili ; Xia, Zheng ; Danilov, Alexey V
Publisher:England: BioMed Central Ltd
Journal title:Molecular cancer, 2023-03, Vol.22 (1), p.64-64, Article 64
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ArticlesPeer ReviewedFull Text
RNA-seq from archival FFPE breast cancer samples: molecular pathway fidelity and novel discovery
Author / Creator:Pennock, Nathan D ; Jindal, Sonali ; Horton, Wesley ; Sun, Duanchen ; Narasimhan, Jayasri ; Carbone, Lucia ; Fei, Suzanne S ; Searles, Robert ; Harrington, Christina A ; Burchard, Julja ; Weinmann, Sheila ; Schedin, Pepper ; Xia, Zheng
Publisher:England: BioMed Central Ltd
Journal title:BMC medical genomics, 2019-12, Vol.12 (1), p.195-195, Article 195
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ArticlesPeer ReviewedFull Text
Incorporating network diffusion and peak location information for better single-cell ATAC-seq data analysis
Author / Creator:Yu, Jiating ; Leng, Jiacheng ; Hou, Zhichao ; Sun, Duanchen ; Wu, Ling-Yun
Publisher:England: Oxford University Press
Journal title:Briefings in bioinformatics, 2024-01, Vol.25 (2)
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ArticlesPeer ReviewedFull Text
Transcriptional profiling identifies an androgen receptor activity-low, stemness program associated with enzalutamide resistance
Author / Creator:Alumkal, Joshi J. ; Sun, Duanchen ; Lu, Eric ; Beer, Tomasz M. ; Thomas, George V. ; Latour, Emile ; Aggarwal, Rahul ; Cetnar, Jeremy ; Ryan, Charles J. ; Tabatabaei, Shaadi ; Bailey, Shawna ; Turina, Claire B. ; Quigley, David A. ; Guan, Xiangnan ; Foye, Adam ; Youngren, Jack F. ; Urrutia, Joshua ; Huang, Jiaoti ; Weinstein, Alana S. ; Friedl, Verena ; Rettig, Matthew ; Reiter, Robert E. ; Spratt, Daniel E. ; Gleave, Martin ; Evans, Christopher P. ; Stuart, Joshua M. ; Chen, Yiyi ; Feng, Felix Y. ; Small, Eric J. ; Witte, Owen N. ; Xia, Zheng
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2020-06, Vol.117 (22), p.12315-12323
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ArticlesPeer ReviewedFull Text
CEA: Combination-based gene set functional enrichment analysis
Author / Creator:Sun, Duanchen ; Liu, Yinliang ; Zhang, Xiang-Sun ; Wu, Ling-Yun
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2018-08, Vol.8 (1), p.13085-13, Article 13085
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ArticlesPeer ReviewedFull Text
Discovering cooperative biomarkers for heterogeneous complex disease diagnoses
Author / Creator:Sun, Duanchen ; Ren, Xianwen ; Ari, Eszter ; Korcsmaros, Tamas ; Csermely, Peter ; Wu, Ling-Yun
Publisher:England: Oxford University Press
Journal title:Briefings in bioinformatics, 2019-01, Vol.20 (1), p.89-101
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ArticlesPeer ReviewedFull Text
NetGen: a novel network-based probabilistic generative model for gene set functional enrichment analysis
Author / Creator:Sun, Duanchen ; Liu, Yinliang ; Zhang, Xiang-Sun ; Wu, Ling-Yun
Publisher:England: BioMed Central Ltd
Journal title:BMC systems biology, 2017-09, Vol.11 (Suppl 4), p.75-75, Article 75
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ArticlesFull Text
Single-Cell ATAC-seq analysis via Network Refinement with peaks location information
Author / Creator:Yu, Jiating ; Sun, Duanchen ; Hou, Zhichao ; Ling-Yun, Wu
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2022-11
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ArticlesFull Text
Scalable and efficient single-cell DNA methylation sequencing by combinatorial indexing
Author / Creator:Mulqueen, Ryan M ; Pokholok, Dmitry ; Norberg, Steve ; Fields, Andrew J ; Sun, Duanchen ; Torkenczy, Kristof A ; Shendure, Jay ; Cole Trapnell ; O'roak, Brian J ; Zheng, Xia ; Steemers, Frank J ; Adey, Andrew C
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2017-06
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Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data

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Postpartum breast cancer has a distinct molecular profile that predicts poor outcomes

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Highly scalable generation of DNA methylation profiles in single cells

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BET bromodomain inhibition blocks the function of a critical AR-independent master regulator network in lethal prostate cancer

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CDK9 inhibition induces epigenetic reprogramming revealing strategies to circumvent resistance in lymphoma

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RNA-seq from archival FFPE breast cancer samples: molecular pathway fidelity and novel discovery

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Incorporating network diffusion and peak location information for better single-cell ATAC-seq data analysis

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Transcriptional profiling identifies an androgen receptor activity-low, stemness program associated with enzalutamide resistance

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CEA: Combination-based gene set functional enrichment analysis

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Discovering cooperative biomarkers for heterogeneous complex disease diagnoses

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NetGen: a novel network-based probabilistic generative model for gene set functional enrichment analysis

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Single-Cell ATAC-seq analysis via Network Refinement with peaks location information

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Scalable and efficient single-cell DNA methylation sequencing by combinatorial indexing

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