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ziwZh)mBVP>Enruvrid#{`=h;Yo`F!SQ+Ta6Xh94W>(%4^iQ%D=V=IgUeZRF_;Q~QFOfnAMRHbENKj-eB0m>grTXhN>rNce5K6SphEP>;{zD7YSq zU<@b!K{A9bW!LV5)Bpeg diff --git a/_cite/cite.py b/_cite/cite.py index 77affec..de6493d 100644 --- a/_cite/cite.py +++ b/_cite/cite.py @@ -28,7 +28,7 @@ sources = [] # in-order list of plugins to run -plugins = ["google-scholar", "pubmed", "orcid", "sources"] +plugins = ["google-scholar", "pubmed", "sources"] # loop through plugins for plugin in plugins: diff --git a/_data/citations.yaml b/_data/citations.yaml index 388fd75..64fa2e4 100644 --- a/_data/citations.yaml +++ b/_data/citations.yaml @@ -10,9 +10,6 @@ publisher: Nature Methods date: '2024-01-08' link: https://doi.org/gtcxf4 - orcid: 0000-0003-3454-7357 - plugin: sources.py - file: sources.yaml _title: A fast, scalable and versatile tool for analysis of single-cell omics data image: https://media.springernature.com/w440/springer-static/cover-hires/journal/41592/20/12 group: featured @@ -22,64 +19,8 @@ - type: source text: Code link: https://github.com/kaizhang/SnapATAC2 -- id: doi:10.1101/2024.01.23.576835 - title: Sensory Input, Sex, and Function Shape Hypothalamic Cell Type Development - authors: - - Harris S Kaplan - - Brandon L Logeman - - Kai Zhang - - Celine Santiago - - Noor Sohail - - Serhiy Naumenko - - Shannan J Ho Sui - - David D Ginty - - Bing Ren - - Catherine Dulac - publisher: Cold Spring Harbor Laboratory - date: '2024-01-23' - link: https://doi.org/gtfnrg - orcid: 0000-0003-3454-7357 - plugin: orcid.py - file: orcid.yaml -- id: doi:10.1073/pnas.2210991120 - title: Integrated analysis of single-cell chromatin state and transcriptome identified - common vulnerability despite glioblastoma heterogeneity - authors: - - Ramya Raviram - - Anugraha Raman - - Sebastian Preissl - - Jiangfang Ning - - Shaoping Wu - - Tomoyuki Koga - - Kai Zhang - - Cameron W. Brennan - - Chenxu Zhu - - Jens Luebeck - - Kinsey Van Deynze - - Jee Yun Han - - Xiaomeng Hou - - Zhen Ye - - Anna K. Mischel - - Yang Eric Li - - Rongxin Fang - - Tomas Baback - - Joshua Mugford - - Claudia Z. Han - - Christopher K. Glass - - Cathy L. Barr - - Paul S. Mischel - - Vineet Bafna - - Laure Escoubet - - Bing Ren - - Clark C. Chen - publisher: Proceedings of the National Academy of Sciences - date: '2023-05-08' - link: https://doi.org/gr8ck8 - orcid: 0000-0003-3454-7357 plugin: sources.py file: sources.yaml - _title: Integrated analysis of single-cell chromatin state and transcriptome identified - common vulnerability despite glioblastoma heterogeneity - id: doi:10.1016/j.cell.2021.10.024 title: A single-cell atlas of chromatin accessibility in the human genome authors: @@ -98,9 +39,6 @@ publisher: Cell date: '2021-11-01' link: https://doi.org/gnh2vb - orcid: 0000-0003-3454-7357 - plugin: sources.py - file: sources.yaml _title: A single-cell atlas of chromatin accessibility in the human genome image: https://ars.els-cdn.com/content/image/1-s2.0-S0092867420X00250-cov200h.gif group: featured @@ -113,108 +51,8 @@ - type: data text: Data link: https://data.mendeley.com/datasets/yv4fzv6cnm -- id: doi:10.1038/s41586-021-03604-1 - title: An atlas of gene regulatory elements in adult mouse cerebrum - authors: - - Yang Eric Li - - Sebastian Preissl - - Xiaomeng Hou - - Ziyang Zhang - - Kai Zhang - - Yunjiang Qiu - - Olivier B. Poirion - - Bin Li - - Joshua Chiou - - Hanqing Liu - - Antonio Pinto-Duarte - - Naoki Kubo - - Xiaoyu Yang - - Rongxin Fang - - Xinxin Wang - - Jee Yun Han - - Jacinta Lucero - - Yiming Yan - - Michael Miller - - Samantha Kuan - - David Gorkin - - Kyle J. Gaulton - - Yin Shen - - Michael Nunn - - Eran A. Mukamel - - M. Margarita Behrens - - Joseph R. Ecker - - Bing Ren - publisher: Nature - date: '2021-10-06' - link: https://doi.org/gm2vjc - orcid: 0000-0003-3454-7357 - plugin: sources.py - file: sources.yaml -- id: doi:10.1126/sciadv.abf1444 - title: "Cardiac cell type\u2013specific gene regulatory programs and disease risk\ - \ association" - authors: - - James D. Hocker - - Olivier B. Poirion - - Fugui Zhu - - Justin Buchanan - - Kai Zhang - - Joshua Chiou - - Tsui-Min Wang - - Qingquan Zhang - - Xiaomeng Hou - - Yang E. Li - - Yanxiao Zhang - - Elie N. Farah - - Allen Wang - - Andrew D. McCulloch - - Kyle J. Gaulton - - Bing Ren - - Neil C. Chi - - Sebastian Preissl - publisher: Science Advances - date: '2021-05-14' - link: https://doi.org/gr2jfv - orcid: 0000-0003-3454-7357 - plugin: sources.py - file: sources.yaml -- id: doi:10.1534/genetics.120.303597 - title: 'Motto: Representing Motifs in Consensus Sequences with Minimum Information - Loss' - authors: - - Mengchi Wang - - David Wang - - Kai Zhang - - Vu Ngo - - Shicai Fan - - Wei Wang - publisher: Genetics - date: '2020-10-01' - link: https://doi.org/gr2jfw - orcid: 0000-0003-3454-7357 plugin: sources.py file: sources.yaml -- id: doi:10.1101/573352 - title: Identification of DNA motifs that regulate DNA methylation - authors: - - Mengchi Wang - - Kai Zhang - - Vu Ngo - - Chengyu Liu - - Shicai Fan - - John W Whitaker - - Yue Chen - - Rizi Ai - - Zhao Chen - - Jun Wang - - Lina Zheng - - Wei Wang - publisher: Cold Spring Harbor Laboratory - date: '2019-03-11' - link: https://doi.org/gkv4z6 - orcid: 0000-0003-3454-7357 - plugin: orcid.py - file: orcid.yaml - id: doi:10.1126/sciadv.aav3262 title: 'Taiji: System-level identification of key transcription factors reveals transcriptional waves in mouse embryonic development' @@ -226,62 +64,25 @@ publisher: Science Advances date: '2019-03-01' link: https://doi.org/gpxx3z - orcid: 0000-0003-3454-7357 - plugin: sources.py - file: sources.yaml _title: 'Taiji: System-level identification of key transcription factors reveals transcriptional waves in mouse embryonic development' image: https://www.science.org/cms/asset/7757979b-746e-490b-b3a4-c75f5f7c27d5/sciadv.2019.5.issue-3.largecover.jpg group: featured -- id: doi:10.1038/s41525-019-0077-8 - title: Integrative analysis with expanded DNA methylation data reveals common key - regulators and pathways in cancers - authors: - - Shicai Fan - - Jianxiong Tang - - Nan Li - - Ying Zhao - - Rizi Ai - - Kai Zhang - - Mengchi Wang - - Wei Du - - Wei Wang - publisher: npj Genomic Medicine - date: '2019-02-01' - link: https://doi.org/gr2jf2 - orcid: 0000-0003-3454-7357 plugin: sources.py file: sources.yaml -- id: doi:10.1534/g3.118.200401 - title: Bayesian Networks Predict Neuronal Transdifferentiation +- id: doi:10.1038/ncomms12249 + title: Systematic identification of protein combinations mediating chromatin looping authors: - - Richard I Ainsworth - - Rizi Ai - - Bo Ding - - Nan Li - Kai Zhang + - Nan Li + - Richard I. Ainsworth - Wei Wang - publisher: G3 Genes|Genomes|Genetics - date: '2018-07-01' - link: https://doi.org/gr2jfz - orcid: 0000-0003-3454-7357 - plugin: sources.py - file: sources.yaml -- id: doi:10.1093/database/bay017 - title: 'Finding relevant biomedical datasets: the UC San Diego solution for the - bioCADDIE Retrieval Challenge' - authors: - - Wei Wei - - Zhanglong Ji - - Yupeng He - - Kai Zhang - - Yuanchi Ha - - Qi Li - - Lucila Ohno-Machado - publisher: Database - date: '2018-01-01' - link: https://doi.org/gr2jfx - orcid: 0000-0003-3454-7357 + publisher: Nature Communications + date: '2016-07-27' + link: https://doi.org/f8wq2r + _title: Systematic identification of protein combinations mediating chromatin looping + image: https://upload.wikimedia.org/wikipedia/en/b/bf/Nature_Communications_-_Journal_Cover.jpg + group: featured plugin: sources.py file: sources.yaml - id: doi:10.1038/ni.3706 @@ -303,104 +104,10 @@ publisher: Nature Immunology date: '2017-03-13' link: https://doi.org/f9twpc - orcid: 0000-0003-3454-7357 - plugin: sources.py - file: sources.yaml _title: Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation image: https://media.springernature.com/w200/springer-static/cover-hires/journal/41590/18/3 group: featured -- id: doi:10.1038/nature24993 - title: Runx3 programs CD8+ T cell residency in non-lymphoid tissues and tumours - authors: - - J. Justin Milner - - Clara Toma - - Bingfei Yu - - Kai Zhang - - Kyla Omilusik - - Anthony T. Phan - - Dapeng Wang - - Adam J. Getzler - - Toan Nguyen - - Shane Crotty - - Wei Wang - - Matthew E. Pipkin - - Ananda W. Goldrath - publisher: Nature - date: '2017-12-06' - link: https://doi.org/gcm4xz - orcid: 0000-0003-3454-7357 - plugin: sources.py - file: sources.yaml -- id: doi:10.1038/ncomms12249 - title: Systematic identification of protein combinations mediating chromatin looping - authors: - - Kai Zhang - - Nan Li - - Richard I. Ainsworth - - Wei Wang - publisher: Nature Communications - date: '2016-07-27' - link: https://doi.org/f8wq2r - orcid: 0000-0003-3454-7357 - plugin: sources.py - file: sources.yaml - _title: Systematic identification of protein combinations mediating chromatin looping - image: https://upload.wikimedia.org/wikipedia/en/b/bf/Nature_Communications_-_Journal_Cover.jpg - group: featured -- id: doi:10.1038/ncomms10812 - title: Constructing 3D interaction maps from 1D epigenomes - authors: - - Yun Zhu - - Zhao Chen - - Kai Zhang - - Mengchi Wang - - David Medovoy - - John W. Whitaker - - Bo Ding - - Nan Li - - Lina Zheng - - Wei Wang - publisher: Nature Communications - date: '2016-03-10' - link: https://doi.org/f8c9h9 - orcid: 0000-0003-3454-7357 - plugin: sources.py - file: sources.yaml -- id: doi:10.1016/j.ymeth.2010.04.005 - title: Isolation and functional characterization of P-TEFb-associated factors that - control general and HIV-1 transcriptional elongation - authors: - - Ruichuan Chen - - Min Liu - - Kai Zhang - - Qiang Zhou - publisher: Methods - date: '2011-01-01' - link: https://doi.org/bzkd5q - orcid: 0000-0003-3454-7357 - plugin: sources.py - file: sources.yaml -- id: doi:10.1093/nar/gkr698 - title: Signal-induced Brd4 release from chromatin is essential for its role transition - from chromatin targeting to transcriptional regulation - authors: - - Nanping Ai - - Xiangming Hu - - Feng Ding - - Bingfei Yu - - Huiping Wang - - Xiaodong Lu - - Kai Zhang - - Yannan Li - - Aidong Han - - Wen Lin - - Runzhong Liu - - Ruichuan Chen - publisher: Nucleic Acids Research - date: '2011-09-02' - link: https://doi.org/dqdbbr - orcid: 0000-0003-3454-7357 plugin: sources.py file: sources.yaml - id: doi:10.1038/s41586-023-06824-9 @@ -498,6 +205,42 @@ link: https://doi.org/gq4f5r plugin: sources.py file: sources.yaml +- id: doi:10.1038/s41586-021-03604-1 + title: An atlas of gene regulatory elements in adult mouse cerebrum + authors: + - Yang Eric Li + - Sebastian Preissl + - Xiaomeng Hou + - Ziyang Zhang + - Kai Zhang + - Yunjiang Qiu + - Olivier B. Poirion + - Bin Li + - Joshua Chiou + - Hanqing Liu + - Antonio Pinto-Duarte + - Naoki Kubo + - Xiaoyu Yang + - Rongxin Fang + - Xinxin Wang + - Jee Yun Han + - Jacinta Lucero + - Yiming Yan + - Michael Miller + - Samantha Kuan + - David Gorkin + - Kyle J. Gaulton + - Yin Shen + - Michael Nunn + - Eran A. Mukamel + - M. Margarita Behrens + - Joseph R. Ecker + - Bing Ren + publisher: Nature + date: '2021-10-06' + link: https://doi.org/gm2vjc + plugin: sources.py + file: sources.yaml - id: doi:10.7554/elife.62522 title: Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes @@ -533,6 +276,33 @@ link: https://doi.org/gjksd9 plugin: sources.py file: sources.yaml +- id: doi:10.1126/sciadv.abf1444 + title: "Cardiac cell type\u2013specific gene regulatory programs and disease risk\ + \ association" + authors: + - James D. Hocker + - Olivier B. Poirion + - Fugui Zhu + - Justin Buchanan + - Kai Zhang + - Joshua Chiou + - Tsui-Min Wang + - Qingquan Zhang + - Xiaomeng Hou + - Yang E. Li + - Yanxiao Zhang + - Elie N. Farah + - Allen Wang + - Andrew D. McCulloch + - Kyle J. Gaulton + - Bing Ren + - Neil C. Chi + - Sebastian Preissl + publisher: Science Advances + date: '2021-05-14' + link: https://doi.org/gr2jfv + plugin: sources.py + file: sources.yaml - id: doi:10.1038/s41467-021-21583-9 title: Comprehensive analysis of single cell ATAC-seq data with SnapATAC authors: @@ -557,6 +327,21 @@ link: https://doi.org/gjd74h plugin: sources.py file: sources.yaml +- id: doi:10.1534/genetics.120.303597 + title: 'Motto: Representing Motifs in Consensus Sequences with Minimum Information + Loss' + authors: + - Mengchi Wang + - David Wang + - Kai Zhang + - Vu Ngo + - Shicai Fan + - Wei Wang + publisher: Genetics + date: '2020-10-01' + link: https://doi.org/gr2jfw + plugin: sources.py + file: sources.yaml - id: doi:10.1093/nar/gkz483 title: Identification of DNA motifs that regulate DNA methylation authors: @@ -577,6 +362,27 @@ link: https://doi.org/ggd6hs plugin: sources.py file: sources.yaml +- id: doi:10.1038/nature24993 + title: Runx3 programs CD8+ T cell residency in non-lymphoid tissues and tumours + authors: + - J. Justin Milner + - Clara Toma + - Bingfei Yu + - Kai Zhang + - Kyla Omilusik + - Anthony T. Phan + - Dapeng Wang + - Adam J. Getzler + - Toan Nguyen + - Shane Crotty + - Wei Wang + - Matthew E. Pipkin + - Ananda W. Goldrath + publisher: Nature + date: '2017-12-06' + link: https://doi.org/gcm4xz + plugin: sources.py + file: sources.yaml - id: doi:10.1073/pnas.1813565116 title: Epigenomic analysis reveals DNA motifs regulating histone modifications in human and mouse @@ -592,3 +398,141 @@ link: https://doi.org/ggfb5z plugin: sources.py file: sources.yaml +- id: doi:10.1093/nar/gkr698 + title: Signal-induced Brd4 release from chromatin is essential for its role transition + from chromatin targeting to transcriptional regulation + authors: + - Nanping Ai + - Xiangming Hu + - Feng Ding + - Bingfei Yu + - Huiping Wang + - Xiaodong Lu + - Kai Zhang + - Yannan Li + - Aidong Han + - Wen Lin + - Runzhong Liu + - Ruichuan Chen + publisher: Nucleic Acids Research + date: '2011-09-02' + link: https://doi.org/dqdbbr + plugin: sources.py + file: sources.yaml +- id: doi:10.1093/database/bay017 + title: 'Finding relevant biomedical datasets: the UC San Diego solution for the + bioCADDIE Retrieval Challenge' + authors: + - Wei Wei + - Zhanglong Ji + - Yupeng He + - Kai Zhang + - Yuanchi Ha + - Qi Li + - Lucila Ohno-Machado + publisher: Database + date: '2018-01-01' + link: https://doi.org/gr2jfx + plugin: sources.py + file: sources.yaml +- id: doi:10.1534/g3.118.200401 + title: Bayesian Networks Predict Neuronal Transdifferentiation + authors: + - Richard I Ainsworth + - Rizi Ai + - Bo Ding + - Nan Li + - Kai Zhang + - Wei Wang + publisher: G3 Genes|Genomes|Genetics + date: '2018-07-01' + link: https://doi.org/gr2jfz + plugin: sources.py + file: sources.yaml +- id: doi:10.1038/ncomms10812 + title: Constructing 3D interaction maps from 1D epigenomes + authors: + - Yun Zhu + - Zhao Chen + - Kai Zhang + - Mengchi Wang + - David Medovoy + - John W. Whitaker + - Bo Ding + - Nan Li + - Lina Zheng + - Wei Wang + publisher: Nature Communications + date: '2016-03-10' + link: https://doi.org/f8c9h9 + plugin: sources.py + file: sources.yaml +- id: doi:10.1038/s41525-019-0077-8 + title: Integrative analysis with expanded DNA methylation data reveals common key + regulators and pathways in cancers + authors: + - Shicai Fan + - Jianxiong Tang + - Nan Li + - Ying Zhao + - Rizi Ai + - Kai Zhang + - Mengchi Wang + - Wei Du + - Wei Wang + publisher: npj Genomic Medicine + date: '2019-02-01' + link: https://doi.org/gr2jf2 + plugin: sources.py + file: sources.yaml +- id: doi:10.1016/j.ymeth.2010.04.005 + title: Isolation and functional characterization of P-TEFb-associated factors that + control general and HIV-1 transcriptional elongation + authors: + - Ruichuan Chen + - Min Liu + - Kai Zhang + - Qiang Zhou + publisher: Methods + date: '2011-01-01' + link: https://doi.org/bzkd5q + plugin: sources.py + file: sources.yaml +- id: doi:10.1073/pnas.2210991120 + title: Integrated analysis of single-cell chromatin state and transcriptome identified + common vulnerability despite glioblastoma heterogeneity + authors: + - Ramya Raviram + - Anugraha Raman + - Sebastian Preissl + - Jiangfang Ning + - Shaoping Wu + - Tomoyuki Koga + - Kai Zhang + - Cameron W. Brennan + - Chenxu Zhu + - Jens Luebeck + - Kinsey Van Deynze + - Jee Yun Han + - Xiaomeng Hou + - Zhen Ye + - Anna K. Mischel + - Yang Eric Li + - Rongxin Fang + - Tomas Baback + - Joshua Mugford + - Claudia Z. Han + - Christopher K. Glass + - Cathy L. Barr + - Paul S. Mischel + - Vineet Bafna + - Laure Escoubet + - Bing Ren + - Clark C. Chen + publisher: Proceedings of the National Academy of Sciences + date: '2023-05-08' + link: https://doi.org/gr8ck8 + _title: Integrated analysis of single-cell chromatin state and transcriptome identified + common vulnerability despite glioblastoma heterogeneity + plugin: sources.py + file: sources.yaml