265 Works

Subtyping of common complex diseases and disorders by integrating heterogeneous data. Identifying clusters among women with lower urinary tract symptoms in the LURN study

Victor Andreev, Victor P. Andreev, Margaret E. Helmuth, Abigail R. Smith, Robert M. Merion, Claire C. Yang, Anne P. Cameron, J. Eric Jelovsek, Cindy L. Amundsen, Brian T. Helfand, Catherine S. Bradley, John O. L. DeLancey, James W. Griffith, Alexander P. Glaser, Brenda W. Gillespie, J. Quentin Clemens, H. Henry Lai, Margaret Helmuth & Gang Liu
We present a methodology for subtyping of persons with a common clinical symptom complex by integrating heterogeneous continuous and categorical data. We illustrate it by clustering women with lower urinary tract symptoms (LUTS), who represent a heterogeneous cohort with overlapping symptoms and multifactorial etiology. Data collected in the Symptoms of Lower Urinary Tract Dysfunction Research Network (LURN), a multi-center observational study, included self-reported urinary and non-urinary symptoms, bladder diaries, and physical examination data for 545...

Complementary genomic and epigenomic adaptation to environmental heterogeneity

Yangchun Gao, Yiyong Chen, Shiguo Li, Xuena Huang, Juntao Hu, Dan G. Bock, Hugh J. MacIsaac & Aibin Zhan
While adaptation is commonly thought to result from selection on DNA sequence-based variation, recent studies have highlighted an analogous epigenetic component as well. However, the relative roles of these mechanisms in facilitating population persistence under environmental heterogeneity remain unclear. To address the underlying genetic and epigenetic mechanisms and their relationship during environmental adaptation, we screened the genomes and epigenomes of nine global populations of a predominately sessile marine invasive tunicate, Botryllus schlosseri. We detected clear...

Additional file 2 of Neomorphic DNA-binding enables tumor-specific therapeutic gene expression in fusion-addicted childhood sarcoma

Tilman L. B. Hölting, Florencia Cidre-Aranaz, Dana Matzek, Bastian Popper, Severin J. Jacobi, Cornelius M. Funk, Florian H. Geyer, Jing Li, Ignazio Piseddu, Bruno L. Cadilha, Stephan Ledderose, Jennifer Zwilling, Shunya Ohmura, David Anz, Annette Künkele, Frederick Klauschen, Thomas G. P. Grünewald & Maximilian M. L. Knott
Additional file 2: Additional Tables 1-5.

Additional file 7 of Combining QTL mapping and RNA-Seq Unravels candidate genes for Alfalfa (Medicago sativa L.) leaf development

Xueqian Jiang, Xijiang Yang, Fan Zhang, Tianhui Yang, Changfu Yang, Fei He, Ting Gao, Chuan Wang, Qingchuan Yang, Zhen Wang & Junmei Kang
Additional file 7: Table S5. The information of the seven candidates.

sj-xlsx-4-tct-10.1177_15330338221124658 - Supplemental material for In Vitro and in Vivo Study of the Effect of Osteogenic Pulsed Electromagnetic Fields on Breast and Lung Cancer Cells

Mike Y. Chen, Jing Li, Nianli Zhang, Erik I. Waldorff, James T. Ryaby, Philip Fedor, Yongsheng Jia & Yujun Wang
Supplemental material, sj-xlsx-4-tct-10.1177_15330338221124658 for In Vitro and in Vivo Study of the Effect of Osteogenic Pulsed Electromagnetic Fields on Breast and Lung Cancer Cells by Mike Y. Chen, Jing Li, Nianli Zhang and Erik I. Waldorff, James T. Ryaby, Philip Fedor, Yongsheng Jia, Yujun Wang in Technology in Cancer Research & Treatment

Additional file 6 of Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen & Jianlong Xu
Additional file 6: Table S3. Summary of 639 main-effect QTL affecting 12 traits identified in the combined population across three environments by inclusive composite interval mapping.

Additional file 6 of Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen & Jianlong Xu
Additional file 6: Table S3. Summary of 639 main-effect QTL affecting 12 traits identified in the combined population across three environments by inclusive composite interval mapping.

Additional file 8 of Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen & Jianlong Xu
Additional file 8: Table S5. Classification of 2,736 epistatic QTL pairs into 13 types according to their gene actions identified in the Q9311/WSSM combined population.

Additional file 1 of Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen & Jianlong Xu
Additional file 1: Table S1. Phenotypic performance and heterosis of traits in Q9311B/WSSM RILs and backcross F1s (Q9311A × RIL).

sj-xlsx-4-tct-10.1177_15330338221124658 - Supplemental material for In Vitro and in Vivo Study of the Effect of Osteogenic Pulsed Electromagnetic Fields on Breast and Lung Cancer Cells

Mike Y. Chen, Jing Li, Nianli Zhang, Erik I. Waldorff, James T. Ryaby, Philip Fedor, Yongsheng Jia & Yujun Wang
Supplemental material, sj-xlsx-4-tct-10.1177_15330338221124658 for In Vitro and in Vivo Study of the Effect of Osteogenic Pulsed Electromagnetic Fields on Breast and Lung Cancer Cells by Mike Y. Chen, Jing Li, Nianli Zhang and Erik I. Waldorff, James T. Ryaby, Philip Fedor, Yongsheng Jia, Yujun Wang in Technology in Cancer Research & Treatment

Additional file 4 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen & Yanyi Huang
Additional file 4: Table S3.qPCR results of gDNA after DNase treatment. (recording data values of Additional file 1: Fig. S6B).

Additional file 5 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen & Yanyi Huang
Additional file 5: Table S4.Normalized abundance of marker genes in each GC cell type. (recording data values of Additional file 1: Fig. S7D).

R code of RSPB-2022-1850 from Tree-ring evidence of ecological stress memory

Yumei Mu, Lixin Lyu, Yan Li & Ouya Fang
R code used to do linear mixed model and plot Figure 2 in our parper

Additional file 1 of Genome-wide identification of key enzyme-encoding genes and the catalytic roles of two 2-oxoglutarate-dependent dioxygenase involved in flavonoid biosynthesis in Cannabis sativa L.

Xuewen Zhu, Yaolei Mi, Xiangxiao Meng, Yiming Zhang, Weiqiang Chen, Xue Cao, Huihua Wan, Wei Yang, Jun Li, Sifan Wang, Zhichao Xu, Atia Tul Wahab, Shilin Chen & Wei Sun
Additional file 1: Table S1. Physical characteristics of the major enzyme-encoding genes of flavonoid metabolic pathway in C. sativa.

Additional file 1 of Gene Identification, expression analysis and molecular docking of ATP sulfurylase in the selenization pathway of Cardamine hupingshanensis

Zhijing Xiao, Yanke Lu, Yi Zou, Chi Zhang, Li Ding, Kai Luo, Qiaoyu Tang & Yifeng Zhou
Supplementary Figure S1: Multiple sequence alignment of all the ChATPS proteins; Supplementary Table S1: Physicochemical properties of ATPS proteins in C. hupingshanensis. Supplementary Table S2: The gene coding sequences and protein sequences of ChATPS. Supplementary Table S3: Secondary structure analysis of the nine proteins. Supplementary Table S4: Primers used in qRT-PCR analysis for ChATPS. Table S5: The binding energy of each ligand to each protein at the catalytic site (unit: kcal mol-1). Table S6: At...

Additional file 1 of Neoplastic cell enrichment of tumor tissues using coring and laser microdissection for proteomic and genomic analyses of pancreatic ductal adenocarcinoma

Qing Kay Li, Yingwei Hu, Lijun Chen, Michael Schnaubelt, Daniel Cui Zhou, Yize Li, Rita Jui-Hsien Lu, Mathangi Thiagarajan, Galen Hostetter, Chelsea J. Newton, Scott D. Jewell, Gil Omenn, Ana I. Robles, Mehdi Mesri, Oliver F. Bathe, Bing Zhang, Li Ding, Ralph H. Hruban, Daniel W. Chan & Hui Zhang
Additional file 1: Table S1. Clinical information of study cases. Table S2. Expression of proteins from the PDAC tumors and NATs

Additional file 10 of Genome-wide identification and characterization of lncRNAs in sunflower endosperm

Shuai Yu, Zhichao Zhang, Jing Li, Yanbin Zhu, Yanzhe Yin, Xiaoyu Zhang, Yuxin Dai, Ao Zhang, Cong Li, Yanshu Zhu, Jinjuan Fan, Yanye Ruan & Xiaomei Dong
Additional file 10: Table S5. The summary of lncRNAs exhibiting allele-specific expression in cultivated sunflower lines for edible fruit and oil identified in 12 DAP sunflower endosperm.

Additional file 11 of Genome-wide identification and characterization of lncRNAs in sunflower endosperm

Shuai Yu, Zhichao Zhang, Jing Li, Yanbin Zhu, Yanzhe Yin, Xiaoyu Zhang, Yuxin Dai, Ao Zhang, Cong Li, Yanshu Zhu, Jinjuan Fan, Yanye Ruan & Xiaomei Dong
Additional file 11: Table S6. GO Gene Ontology analysis of co-expressed protein-coding genes with lncRNAs of allelic bias toward cultivated lines for edible fruit.

Additional file 12 of Genome-wide identification and characterization of lncRNAs in sunflower endosperm

Shuai Yu, Zhichao Zhang, Jing Li, Yanbin Zhu, Yanzhe Yin, Xiaoyu Zhang, Yuxin Dai, Ao Zhang, Cong Li, Yanshu Zhu, Jinjuan Fan, Yanye Ruan & Xiaomei Dong
Additional file 12: Table S7. GO Gene Ontology analysis of co-expressed protein-coding genes with lncRNAs of allelic bias toward cultivated lines for oil.

Additional file 2 of Genome-wide identification and characterization of lncRNAs in sunflower endosperm

Shuai Yu, Zhichao Zhang, Jing Li, Yanbin Zhu, Yanzhe Yin, Xiaoyu Zhang, Yuxin Dai, Ao Zhang, Cong Li, Yanshu Zhu, Jinjuan Fan, Yanye Ruan & Xiaomei Dong
Additional file 2: Table S2. The genomic information of lncRNAs in sunflower endosperm at 12DAP.

Additional file 3 of Genome-wide identification and characterization of lncRNAs in sunflower endosperm

Shuai Yu, Zhichao Zhang, Jing Li, Yanbin Zhu, Yanzhe Yin, Xiaoyu Zhang, Yuxin Dai, Ao Zhang, Cong Li, Yanshu Zhu, Jinjuan Fan, Yanye Ruan & Xiaomei Dong
Additional file 3: Table S3. GO Gene Ontology analysis of co-expressed protein-coding genes with all candidate lncRNAs.

Additional file 4 of A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology

Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng … & Barry Smith
Additional file 4: Supplemental Table 3. Protein Ontology representation of SARS-CoV-2 proteins. Comparative information in RefSeq and UniProtKB is also provided.

Additional file 1 of Community composition and trophic mode diversity of fungi associated with fruiting body of medicinal Sanghuangporus vaninii

Yanjun Ma, Weiqian Gao, Fan Zhang, Xuetai Zhu, Weibao Kong, Shiquan Niu, Kun Gao & Hongqin Yang
Supplementary material 1: Table S1. Taxonomic classification of OTUs detected from Sanghuangporus vaninii fruiting body with total ITS rDNA read numbers. Table S2. The fungal OTUs associated with S. vaninii fruiting body were annotated into trophic modes. Table S3. Trophic modes annotation of associated fungi at genus level. Table S4. Trophic modes and their guilds annotation of fungi associated with S. vaninii fruiting body.

Contrast the distribution, transformation, and degradation of dissolved and particulate organic matter in the South Yellow Sea, the East China Sea, and its adjacent Kuroshio Current

Chongxiao Ji, Gui-Peng Yang, Yan Chen, Yan Li & Lin Zhang
The detailed information of sampling stations, the carbon, nitrogen, and amino acids levels in DOM and POM, as well as other parameters including temperature, salinity, nutrients, chlorophyll-a, and biological parameters (heterotrophic bacteria, Synechococcus, and picoeukaryotes) are dispalyed in this dataset.

Contrast the distribution, transformation, and degradation of dissolved and particulate organic matter in the South Yellow Sea, the East China Sea, and its adjacent Kuroshio Current

Chongxiao Ji, Gui-Peng Yang, Yan Chen, Yan Li & Lin Zhang
The detailed information of sampling stations, the carbon, nitrogen, and amino acids levels in DOM and POM, as well as other parameters including temperature, salinity, nutrients, chlorophyll-a, and biological parameters (heterotrophic bacteria, Synechococcus, and picoeukaryotes) are dispalyed in this dataset.

Registration Year

  • 2022
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Resource Types

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    265

Affiliations

  • Washington University in St. Louis
    265
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    179
  • Sichuan University
    160
  • Shanghai Jiao Tong University
    160
  • Zhejiang University
    157
  • Fudan University
    156
  • Sun Yat-sen University
    139
  • Capital Medical University
    125
  • Xuzhou Medical College
    122
  • University of Chinese Academy of Sciences
    113