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51. Supplementary Figure 1 from A Pooled Analysis of Smoking and Colorectal Cancer: Timing of Exposure and Interactions with Environmental Factors

Author: Gong, Jian, primary, Hutter, Carolyn, primary, Baron, John A., primary, Berndt, Sonja, primary, Caan, Bette, primary, Campbell, Peter T., primary, Casey, Graham, primary, Chan, Andrew T., primary, Cotterchio, Michelle, primary, Fuchs, Charles S., primary, Gallinger, Steven, primary, Giovannucci, Edward, primary, Harrison, Tabitha, primary, Hayes, Richard, primary, Hsu, Li, primary, Jiao, Shuo, primary, Lin, Yi, primary, Lindor, Noralane M., primary, Newcomb, Polly, primary, Pflugeisen, Bethann, primary, Phipps, Amanda I., primary, Rohan, Thomas, primary, Schoen, Robert, primary, Seminara, Daniela, primary, Slattery, Martha L., primary, Stelling, Deanna, primary, Thomas, Fridtjof, primary, Warnick, Greg, primary, White, Emily, primary, Potter, John, primary, and Peters, Ulrike, primary
Published: 2023
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52. Supplementary Material 1 from A Pooled Analysis of Smoking and Colorectal Cancer: Timing of Exposure and Interactions with Environmental Factors

Author: Gong, Jian, primary, Hutter, Carolyn, primary, Baron, John A., primary, Berndt, Sonja, primary, Caan, Bette, primary, Campbell, Peter T., primary, Casey, Graham, primary, Chan, Andrew T., primary, Cotterchio, Michelle, primary, Fuchs, Charles S., primary, Gallinger, Steven, primary, Giovannucci, Edward, primary, Harrison, Tabitha, primary, Hayes, Richard, primary, Hsu, Li, primary, Jiao, Shuo, primary, Lin, Yi, primary, Lindor, Noralane M., primary, Newcomb, Polly, primary, Pflugeisen, Bethann, primary, Phipps, Amanda I., primary, Rohan, Thomas, primary, Schoen, Robert, primary, Seminara, Daniela, primary, Slattery, Martha L., primary, Stelling, Deanna, primary, Thomas, Fridtjof, primary, Warnick, Greg, primary, White, Emily, primary, Potter, John, primary, and Peters, Ulrike, primary
Published: 2023
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53. Data from Gene–Environment Interaction Involving Recently Identified Colorectal Cancer Susceptibility Loci

Author: Kantor, Elizabeth D., primary, Hutter, Carolyn M., primary, Minnier, Jessica, primary, Berndt, Sonja I., primary, Brenner, Hermann, primary, Caan, Bette J., primary, Campbell, Peter T., primary, Carlson, Christopher S., primary, Casey, Graham, primary, Chan, Andrew T., primary, Chang-Claude, Jenny, primary, Chanock, Stephen J., primary, Cotterchio, Michelle, primary, Du, Mengmeng, primary, Duggan, David, primary, Fuchs, Charles S., primary, Giovannucci, Edward L., primary, Gong, Jian, primary, Harrison, Tabitha A., primary, Hayes, Richard B., primary, Henderson, Brian E., primary, Hoffmeister, Michael, primary, Hopper, John L., primary, Jenkins, Mark A., primary, Jiao, Shuo, primary, Kolonel, Laurence N., primary, Le Marchand, Loic, primary, Lemire, Mathieu, primary, Ma, Jing, primary, Newcomb, Polly A., primary, Ochs-Balcom, Heather M., primary, Pflugeisen, Bethann M., primary, Potter, John D., primary, Rudolph, Anja, primary, Schoen, Robert E., primary, Seminara, Daniela, primary, Slattery, Martha L., primary, Stelling, Deanna L., primary, Thomas, Fridtjof, primary, Thornquist, Mark, primary, Ulrich, Cornelia M., primary, Warnick, Greg S., primary, Zanke, Brent W., primary, Peters, Ulrike, primary, Hsu, Li, primary, and White, Emily, primary
Published: 2023
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54. Data from Characterization of Gene–Environment Interactions for Colorectal Cancer Susceptibility Loci

Author: Hutter, Carolyn M., primary, Chang-Claude, Jenny, primary, Slattery, Martha L., primary, Pflugeisen, Bethann M., primary, Lin, Yi, primary, Duggan, David, primary, Nan, Hongmei, primary, Lemire, Mathieu, primary, Rangrej, Jagadish, primary, Figueiredo, Jane C., primary, Jiao, Shuo, primary, Harrison, Tabitha A., primary, Liu, Yan, primary, Chen, Lin S., primary, Stelling, Deanna L., primary, Warnick, Greg S., primary, Hoffmeister, Michael, primary, Küry, Sébastien, primary, Fuchs, Charles S., primary, Giovannucci, Edward, primary, Hazra, Aditi, primary, Kraft, Peter, primary, Hunter, David J., primary, Gallinger, Steven, primary, Zanke, Brent W., primary, Brenner, Hermann, primary, Frank, Bernd, primary, Ma, Jing, primary, Ulrich, Cornelia M., primary, White, Emily, primary, Newcomb, Polly A., primary, Kooperberg, Charles, primary, LaCroix, Andrea Z., primary, Prentice, Ross L., primary, Jackson, Rebecca D., primary, Schoen, Robert E., primary, Chanock, Stephen J., primary, Berndt, Sonja I., primary, Hayes, Richard B., primary, Caan, Bette J., primary, Potter, John D., primary, Hsu, Li, primary, Bézieau, Stéphane, primary, Chan, Andrew T., primary, Hudson, Thomas J., primary, and Peters, Ulrike, primary
Published: 2023
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55. Supplementary Table 4 from Characterization of Gene–Environment Interactions for Colorectal Cancer Susceptibility Loci

Author: Hutter, Carolyn M., primary, Chang-Claude, Jenny, primary, Slattery, Martha L., primary, Pflugeisen, Bethann M., primary, Lin, Yi, primary, Duggan, David, primary, Nan, Hongmei, primary, Lemire, Mathieu, primary, Rangrej, Jagadish, primary, Figueiredo, Jane C., primary, Jiao, Shuo, primary, Harrison, Tabitha A., primary, Liu, Yan, primary, Chen, Lin S., primary, Stelling, Deanna L., primary, Warnick, Greg S., primary, Hoffmeister, Michael, primary, Küry, Sébastien, primary, Fuchs, Charles S., primary, Giovannucci, Edward, primary, Hazra, Aditi, primary, Kraft, Peter, primary, Hunter, David J., primary, Gallinger, Steven, primary, Zanke, Brent W., primary, Brenner, Hermann, primary, Frank, Bernd, primary, Ma, Jing, primary, Ulrich, Cornelia M., primary, White, Emily, primary, Newcomb, Polly A., primary, Kooperberg, Charles, primary, LaCroix, Andrea Z., primary, Prentice, Ross L., primary, Jackson, Rebecca D., primary, Schoen, Robert E., primary, Chanock, Stephen J., primary, Berndt, Sonja I., primary, Hayes, Richard B., primary, Caan, Bette J., primary, Potter, John D., primary, Hsu, Li, primary, Bézieau, Stéphane, primary, Chan, Andrew T., primary, Hudson, Thomas J., primary, and Peters, Ulrike, primary
Published: 2023
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56. Supplementary Table 6 from Characterization of Gene–Environment Interactions for Colorectal Cancer Susceptibility Loci

Author: Hutter, Carolyn M., primary, Chang-Claude, Jenny, primary, Slattery, Martha L., primary, Pflugeisen, Bethann M., primary, Lin, Yi, primary, Duggan, David, primary, Nan, Hongmei, primary, Lemire, Mathieu, primary, Rangrej, Jagadish, primary, Figueiredo, Jane C., primary, Jiao, Shuo, primary, Harrison, Tabitha A., primary, Liu, Yan, primary, Chen, Lin S., primary, Stelling, Deanna L., primary, Warnick, Greg S., primary, Hoffmeister, Michael, primary, Küry, Sébastien, primary, Fuchs, Charles S., primary, Giovannucci, Edward, primary, Hazra, Aditi, primary, Kraft, Peter, primary, Hunter, David J., primary, Gallinger, Steven, primary, Zanke, Brent W., primary, Brenner, Hermann, primary, Frank, Bernd, primary, Ma, Jing, primary, Ulrich, Cornelia M., primary, White, Emily, primary, Newcomb, Polly A., primary, Kooperberg, Charles, primary, LaCroix, Andrea Z., primary, Prentice, Ross L., primary, Jackson, Rebecca D., primary, Schoen, Robert E., primary, Chanock, Stephen J., primary, Berndt, Sonja I., primary, Hayes, Richard B., primary, Caan, Bette J., primary, Potter, John D., primary, Hsu, Li, primary, Bézieau, Stéphane, primary, Chan, Andrew T., primary, Hudson, Thomas J., primary, and Peters, Ulrike, primary
Published: 2023
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57. Supplementary Table 3 from Characterization of Gene–Environment Interactions for Colorectal Cancer Susceptibility Loci

Author: Hutter, Carolyn M., primary, Chang-Claude, Jenny, primary, Slattery, Martha L., primary, Pflugeisen, Bethann M., primary, Lin, Yi, primary, Duggan, David, primary, Nan, Hongmei, primary, Lemire, Mathieu, primary, Rangrej, Jagadish, primary, Figueiredo, Jane C., primary, Jiao, Shuo, primary, Harrison, Tabitha A., primary, Liu, Yan, primary, Chen, Lin S., primary, Stelling, Deanna L., primary, Warnick, Greg S., primary, Hoffmeister, Michael, primary, Küry, Sébastien, primary, Fuchs, Charles S., primary, Giovannucci, Edward, primary, Hazra, Aditi, primary, Kraft, Peter, primary, Hunter, David J., primary, Gallinger, Steven, primary, Zanke, Brent W., primary, Brenner, Hermann, primary, Frank, Bernd, primary, Ma, Jing, primary, Ulrich, Cornelia M., primary, White, Emily, primary, Newcomb, Polly A., primary, Kooperberg, Charles, primary, LaCroix, Andrea Z., primary, Prentice, Ross L., primary, Jackson, Rebecca D., primary, Schoen, Robert E., primary, Chanock, Stephen J., primary, Berndt, Sonja I., primary, Hayes, Richard B., primary, Caan, Bette J., primary, Potter, John D., primary, Hsu, Li, primary, Bézieau, Stéphane, primary, Chan, Andrew T., primary, Hudson, Thomas J., primary, and Peters, Ulrike, primary
Published: 2023
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58. Supplementary Table 2 from Characterization of Gene–Environment Interactions for Colorectal Cancer Susceptibility Loci

Author: Hutter, Carolyn M., primary, Chang-Claude, Jenny, primary, Slattery, Martha L., primary, Pflugeisen, Bethann M., primary, Lin, Yi, primary, Duggan, David, primary, Nan, Hongmei, primary, Lemire, Mathieu, primary, Rangrej, Jagadish, primary, Figueiredo, Jane C., primary, Jiao, Shuo, primary, Harrison, Tabitha A., primary, Liu, Yan, primary, Chen, Lin S., primary, Stelling, Deanna L., primary, Warnick, Greg S., primary, Hoffmeister, Michael, primary, Küry, Sébastien, primary, Fuchs, Charles S., primary, Giovannucci, Edward, primary, Hazra, Aditi, primary, Kraft, Peter, primary, Hunter, David J., primary, Gallinger, Steven, primary, Zanke, Brent W., primary, Brenner, Hermann, primary, Frank, Bernd, primary, Ma, Jing, primary, Ulrich, Cornelia M., primary, White, Emily, primary, Newcomb, Polly A., primary, Kooperberg, Charles, primary, LaCroix, Andrea Z., primary, Prentice, Ross L., primary, Jackson, Rebecca D., primary, Schoen, Robert E., primary, Chanock, Stephen J., primary, Berndt, Sonja I., primary, Hayes, Richard B., primary, Caan, Bette J., primary, Potter, John D., primary, Hsu, Li, primary, Bézieau, Stéphane, primary, Chan, Andrew T., primary, Hudson, Thomas J., primary, and Peters, Ulrike, primary
Published: 2023
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59. Supplementary Table 5 from Characterization of Gene–Environment Interactions for Colorectal Cancer Susceptibility Loci

Author: Hutter, Carolyn M., primary, Chang-Claude, Jenny, primary, Slattery, Martha L., primary, Pflugeisen, Bethann M., primary, Lin, Yi, primary, Duggan, David, primary, Nan, Hongmei, primary, Lemire, Mathieu, primary, Rangrej, Jagadish, primary, Figueiredo, Jane C., primary, Jiao, Shuo, primary, Harrison, Tabitha A., primary, Liu, Yan, primary, Chen, Lin S., primary, Stelling, Deanna L., primary, Warnick, Greg S., primary, Hoffmeister, Michael, primary, Küry, Sébastien, primary, Fuchs, Charles S., primary, Giovannucci, Edward, primary, Hazra, Aditi, primary, Kraft, Peter, primary, Hunter, David J., primary, Gallinger, Steven, primary, Zanke, Brent W., primary, Brenner, Hermann, primary, Frank, Bernd, primary, Ma, Jing, primary, Ulrich, Cornelia M., primary, White, Emily, primary, Newcomb, Polly A., primary, Kooperberg, Charles, primary, LaCroix, Andrea Z., primary, Prentice, Ross L., primary, Jackson, Rebecca D., primary, Schoen, Robert E., primary, Chanock, Stephen J., primary, Berndt, Sonja I., primary, Hayes, Richard B., primary, Caan, Bette J., primary, Potter, John D., primary, Hsu, Li, primary, Bézieau, Stéphane, primary, Chan, Andrew T., primary, Hudson, Thomas J., primary, and Peters, Ulrike, primary
Published: 2023
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60. Supplementary Table 1 from Characterization of Gene–Environment Interactions for Colorectal Cancer Susceptibility Loci

Author: Hutter, Carolyn M., primary, Chang-Claude, Jenny, primary, Slattery, Martha L., primary, Pflugeisen, Bethann M., primary, Lin, Yi, primary, Duggan, David, primary, Nan, Hongmei, primary, Lemire, Mathieu, primary, Rangrej, Jagadish, primary, Figueiredo, Jane C., primary, Jiao, Shuo, primary, Harrison, Tabitha A., primary, Liu, Yan, primary, Chen, Lin S., primary, Stelling, Deanna L., primary, Warnick, Greg S., primary, Hoffmeister, Michael, primary, Küry, Sébastien, primary, Fuchs, Charles S., primary, Giovannucci, Edward, primary, Hazra, Aditi, primary, Kraft, Peter, primary, Hunter, David J., primary, Gallinger, Steven, primary, Zanke, Brent W., primary, Brenner, Hermann, primary, Frank, Bernd, primary, Ma, Jing, primary, Ulrich, Cornelia M., primary, White, Emily, primary, Newcomb, Polly A., primary, Kooperberg, Charles, primary, LaCroix, Andrea Z., primary, Prentice, Ross L., primary, Jackson, Rebecca D., primary, Schoen, Robert E., primary, Chanock, Stephen J., primary, Berndt, Sonja I., primary, Hayes, Richard B., primary, Caan, Bette J., primary, Potter, John D., primary, Hsu, Li, primary, Bézieau, Stéphane, primary, Chan, Andrew T., primary, Hudson, Thomas J., primary, and Peters, Ulrike, primary
Published: 2023
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61. Supplementary Figure 1 from Characterization of Gene–Environment Interactions for Colorectal Cancer Susceptibility Loci

Author: Hutter, Carolyn M., primary, Chang-Claude, Jenny, primary, Slattery, Martha L., primary, Pflugeisen, Bethann M., primary, Lin, Yi, primary, Duggan, David, primary, Nan, Hongmei, primary, Lemire, Mathieu, primary, Rangrej, Jagadish, primary, Figueiredo, Jane C., primary, Jiao, Shuo, primary, Harrison, Tabitha A., primary, Liu, Yan, primary, Chen, Lin S., primary, Stelling, Deanna L., primary, Warnick, Greg S., primary, Hoffmeister, Michael, primary, Küry, Sébastien, primary, Fuchs, Charles S., primary, Giovannucci, Edward, primary, Hazra, Aditi, primary, Kraft, Peter, primary, Hunter, David J., primary, Gallinger, Steven, primary, Zanke, Brent W., primary, Brenner, Hermann, primary, Frank, Bernd, primary, Ma, Jing, primary, Ulrich, Cornelia M., primary, White, Emily, primary, Newcomb, Polly A., primary, Kooperberg, Charles, primary, LaCroix, Andrea Z., primary, Prentice, Ross L., primary, Jackson, Rebecca D., primary, Schoen, Robert E., primary, Chanock, Stephen J., primary, Berndt, Sonja I., primary, Hayes, Richard B., primary, Caan, Bette J., primary, Potter, John D., primary, Hsu, Li, primary, Bézieau, Stéphane, primary, Chan, Andrew T., primary, Hudson, Thomas J., primary, and Peters, Ulrike, primary
Published: 2023
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62. Supplementary Table 7 from Characterization of Gene–Environment Interactions for Colorectal Cancer Susceptibility Loci

Author: Hutter, Carolyn M., primary, Chang-Claude, Jenny, primary, Slattery, Martha L., primary, Pflugeisen, Bethann M., primary, Lin, Yi, primary, Duggan, David, primary, Nan, Hongmei, primary, Lemire, Mathieu, primary, Rangrej, Jagadish, primary, Figueiredo, Jane C., primary, Jiao, Shuo, primary, Harrison, Tabitha A., primary, Liu, Yan, primary, Chen, Lin S., primary, Stelling, Deanna L., primary, Warnick, Greg S., primary, Hoffmeister, Michael, primary, Küry, Sébastien, primary, Fuchs, Charles S., primary, Giovannucci, Edward, primary, Hazra, Aditi, primary, Kraft, Peter, primary, Hunter, David J., primary, Gallinger, Steven, primary, Zanke, Brent W., primary, Brenner, Hermann, primary, Frank, Bernd, primary, Ma, Jing, primary, Ulrich, Cornelia M., primary, White, Emily, primary, Newcomb, Polly A., primary, Kooperberg, Charles, primary, LaCroix, Andrea Z., primary, Prentice, Ross L., primary, Jackson, Rebecca D., primary, Schoen, Robert E., primary, Chanock, Stephen J., primary, Berndt, Sonja I., primary, Hayes, Richard B., primary, Caan, Bette J., primary, Potter, John D., primary, Hsu, Li, primary, Bézieau, Stéphane, primary, Chan, Andrew T., primary, Hudson, Thomas J., primary, and Peters, Ulrike, primary
Published: 2023
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63. The climate‐driven distribution and response to global change of soil‐borne pathogens in agroecosystems

Author: Peng, Ziheng, primary, Liu, Yu, additional, Qi, Jiejun, additional, Gao, Hang, additional, Li, Xiaomeng, additional, Tian, Qi, additional, Qian, Xun, additional, Wei, Gehong, additional, and Jiao, Shuo, additional
Published: 2023
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64. Investigating the genetic relationship between Alzheimer’s disease and cancer using GWAS summary statistics

Author: Feng, Yen-Chen Anne, Cho, Kelly, Lindstrom, Sara, Kraft, Peter, Cormack, Jean, Liang, Liming, Driver, Jane A., Blalock, Kendra, Campbell, Peter T., Casey, Graham, Conti, David V., Edlund, Christopher K., Figueiredo, Jane, James Gauderman, W., Gong, Jian, Green, Roger C., Gruber, Stephen B., Harju, John F., Harrison, Tabitha A., Jacobs, Eric J., Jenkins, Mark A., Jiao, Shuo, Li, Li, Lin, Yi, Manion, Frank J., Moreno, Victor, Mukherjee, Bhramar, Peters, Ulrike, Raskin, Leon, Schumacher, Fredrick R., Seminara, Daniela, Severi, Gianluca, Stenzel, Stephanie L., Thomas, Duncan C., Hopper, John L., Southey, Melissa C., Makalic, Enes, Schmidt, Daniel F., Fletcher, Olivia, Peto, Julian, Gibson, Lorna, dos Santos Silva, Isabel, Hunter, David J., Lindström, Sara, Kraft, Peter, Ahsan, Habib, Whittemore, Alice, Waisfisz, Quinten, Meijers-Heijboer, Hanne, Adank, Muriel, van der Luijt, Rob B., Uitterlinden, Andre G., Hofman, Albert, Meindl, Alfons, Schmutzler, Rita K., Müller-Myhsok, Bertram, Lichtner, Peter, Nevanlinna, Heli, Muranen, Taru A., Aittomäki, Kristiina, Blomqvist, Carl, Chang-Claude, Jenny, Hein, Rebecca, Dahmen, Norbert, Beckman, Lars, Crisponi, Laura, Hall, Per, Czene, Kamila, Irwanto, Astrid, Liu, Jianjun, Easton, Douglas F., Turnbull, Clare, Rahman, Nazneen, Kote-Jarai, Zsofia, Muir, Kenneth, Giles, Graham, Severi, Gianluca, Neal, David, Donovan, Jenny L., Hamdy, Freddie C., Wiklund, Fredrik, Gronberg, Henrik, Haiman, Christopher, Schumacher, Fred, Travis, Ruth, Riboli, Elio, Kraft, Peter, Hunter, David, Gapstur, Susan, Berndt, Sonja, Chanock, Stephen, Han, Younghun, Su, Li, Wei, Yongyue, Hung, Rayjean J., Brhane, Yonathan, McLaughlin, John, Brennan, Paul, McKay, James D., Bickeböller, Heike, Rosenberger, Albert, Houlston, Richard S., Caporaso, Neil, Landi, Maria Teresa, Heinrich, Joachim, Risch, Angela, Wu, Xifeng, Ye, Yuanqing, Christiani, David C., Amos, Christopher I., IGAP Consortium, Colorectal Transdisciplinary Study (CORECT), Discovery, Biology, and Risk of Inherited Variants in Breast Cancer (DRIVE), Elucidating Loci Involved in Prostate Cancer Susceptibility (ELLIPSE), and Transdisciplinary Research in Cancer of the Lung (TRICL)
Published: 2017
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65. Additional file 1 of Plant domestication shapes rhizosphere microbiome assembly and metabolic functions

Author: Yue, Hong, Yue, Wenjie, Jiao, Shuo, Kim, Hyun, Lee, Yong-Hwan, Wei, Gehong, Song, Weining, and Shu, Duntao
Abstract: Additional file 1: Fig. S1. Alpha diversity included Shannon index, Simpson index, ACE index, and Chao index for bacteria and fungi communities in different accession of domesticated and wild wheats. Errors bars represent standard errors (n= 5). Different lowcase letters above the bars indicate significant differences (P< 0.05), based on Kruskal-Wallis test. Fig. S2. The Bray-Curtis dissimilarity of bacteria and fungi communities in domesticated and wild wheats. DB1~DB3 and WB1-WB3 indicates that samples are affiliated with bulk soil in the domesticated and wild wheats, respectively. DT1~DT3 and WT1-WT3 indicates that samples are affiliated with rhizosphere soil in the domesticated and wild wheats, respectively. The dots represent the values of Bray-Curtis dissimilarity between replicates in the any of groups. The details on the D1-D3 and W1-W3 groups are available in Table S2. Fig. S3. Constrained Analysis of Principal Coordinates analysis (CAP) ordination constraned to domestication status (left panel), habitat type (middle panel), and genome group (right panel) based on Bray-Curtis metric of bacteria and fungi communities. Variance of community dissimilarity among five treatment were draw from ANOVA-like permutation analysis. Fig. S4. Principal coordinate analysis ordinations (PCoA) for bacteria and fungi communities in domesticated and wild wheats. Fig. S5. Distribution of dominant phyla and genus in the bacteria and fungi communities in domesticated and wild wheats. Fig. S6. Amplicon sequences variants (ASVs) form bulk soils responsible for the community differences in the wild wheats and domesticated wheats that are calculated by a differential abundance test and random forest classification. (A) and (B) The volcano plot illustrating the enrichment and depletion patterns of rhizosphere bacterial and fungal microbiomes in the three wild wheats compared with three domesticated wheat accessions. DI, depleted index; DSI, dissimilarity index. (C) and (D) Joyplots showing the relative abundance profiles of top 20 ASVs in bacterial and fungal communities that are revealed by a Random forest (RF) classifier. The top ASVs on the genus level are listed along the y-axis represent their importance in contributing to the accuracy of domesticated and wild wheats prediction by calculating their mean decrease accuracy in the RF model. Fig. S7. Microbial interkingdom association networks and node-level topological features for bulk soils. (A) and (B) Interkingdom co-occurrence networks in the domesticated and wild wheats. Only compositionality-robust (p > 0.7) and statistically significant (q < 0.01) correlations were shown. The size of each node indicates the relative abundance of each ASV. The color of each node represents the bacteria or fungi taxa. Blue solid lines represent co-presence associations and red line represent mutual exclusive correlations. The thickness of each link line is proportional to the correlation coefficients of the connections. The keystone taxa and dominant modules for each networks were also shown. (C) and (D) Box graphs illustrating the node-level topological features of each networks, including betweenness and degree. Comparison of these two features demonstrating the high degree and low betweenness for the keystone taxa. Bar diagrams showing the proportion of inter-and intra-kingdom edges of positive or negative correlations in the rhizosphere network. The significance of differences between domesticated and wild wheats were determined by Kruskal-Wallis test. Fig. S8. Network modularity profiles of rhizosphere soil and bulk soil microbial communities in the domesticated and wild wheats. The eight bar plots in the left and middle columns represents microbial taxa on the class level in the module I and module II. The four bar plots in the right columns indicates the proportion of ASVs that affiliated with bacteria and fungi communities in the module I and module II. Fig. S9. The volcano plot illustrating the enrichment and depletion patterns of KO functional categories and KO pathway in the wild wheats compared with domesticated wheat accessions. The KOs were colored by their categorization as “wild-enriched”, “domesticated-enriched”, and “non-differential” according to their values of Log2(count per million) and Log2(fold change). Fig. S10. (A) Nonmetric multidimensional scaling (NMDS) ordination of KEGG Orthology, CAZyome, and COG based on Bray-Curtis distances. The significance of differences between domesticated and wild wheats were determined by Kruskal-Wallis test. (B) Heat map illustrating the relative abundance (Z-score) of functional genes (based on KO) affiliated with carbon cycling in different accession of wheats. Fig. S11. Heat map illustrating the relative abundance (Z-score) of functional genes (based on KO) affiliated with nitrogen (A) and phosphorus (B) cycling in different accession of wheats. Fig. S12. (A-H) Random forest (RF) mean predictor importance of KO functional categories as drivers for the plant phenotypes, including (A) plant height (PH), (B) chlorophyll content (CC), (C) ear length (EL), (D) subsegment length (SSL), (E) Tiller, (F) thousand grain weight (TGW), (G) seed length (SL), and (H) seed width (SW), respectively. The accuracy importance measure was calculated for each tree and averaged over the forest (2000 trees). Percentage increase in the mean squared error (MSE) of variables were applied to evaluate the importance of these predictors, and higher MSE% values represent more important predictors. Significance levels of each predictor are as follows: *P< 0.05, **P< 0.01, and ***P< 0.001. Fig. S13. Partial least squares discriminant analysis (PLS-DA) and orthogonal partial least squares discriminant analysis (OPLS-DA) for root exudates that extracted from roots of wild and domesticated wheats. Fig. S14. (A) The average relative abundance of enriched root exudates in the wild and domesticated wheats. (B) The fold changes of enriched metabolites in domesticated and wild wheats. The error bars represent standard errors of sample replicates and asterisks (*) indicate metabolic categories that are significantly more predominant in wild or domesticated wheats (P value
Published: 2023
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66. Additional file 3 of Plant domestication shapes rhizosphere microbiome assembly and metabolic functions

Author: Yue, Hong, Yue, Wenjie, Jiao, Shuo, Kim, Hyun, Lee, Yong-Hwan, Wei, Gehong, Song, Weining, and Shu, Duntao
Abstract: Additional file 3: Method S1. Experiment design and field site management. Method S2. Samples collection, DNA extraction, PCR amplification and amplicon sequencing. Method S3. Shotgun metagenomics sequencing. Method S4. Root exudate collection and LC-MS analysis. Method S5. Microbiota inoculation experiment. Method S6. Statistical analyses.
Published: 2023
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67. Author Correction: Bacterial and fungal gut communities of Agrilus mali at different developmental stages and fed different diets

Author: Zhang, Zhengqing, Jiao, Shuo, Li, Xiaohui, and Li, Menglou
Published: 2019
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68. Environmental filtering drives distinct continental atlases of soil archaea between dryland and wetland agricultural ecosystems

Author: Jiao, Shuo, Xu, Yiqin, Zhang, Jie, and Lu, Yahai
Published: 2019
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69. Bacterial and fungal gut communities of Agrilus mali at different developmental stages and fed different diets

Author: Zhang, Zhengqing, Jiao, Shuo, Li, Xiaohui, and Li, Menglou
Published: 2018
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70. Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems

Author: Jiao, Shuo, Chen, Weimin, Wang, Jieli, Du, Nini, Li, Qiaoping, and Wei, Gehong
Published: 2018
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71. Core phylotypes enhance the resistance of soil microbiome to environmental changes to maintain multifunctionality in agricultural ecosystems

Author: Jiao, Shuo, primary, Qi, Jiejun, additional, Jin, Chujie, additional, Liu, Yu, additional, Wang, Yang, additional, Pan, Haibo, additional, Chen, Shi, additional, Liang, Chunling, additional, Peng, Ziheng, additional, Chen, Beibei, additional, Qian, Xun, additional, and Wei, Gehong, additional
Published: 2022
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72. Afforestation can lower microbial diversity and functionality in deep soil layers in a semiarid region

Author: Kong, Weibo, primary, Wei, Xiaorong, additional, Wu, Yonghong, additional, Shao, Mingan, additional, Zhang, Qian, additional, Sadowsky, Michael J., additional, Ishii, Satoshi, additional, Reich, Peter B., additional, Wei, Gehong, additional, Jiao, Shuo, additional, Qiu, Liping, additional, and Liu, Liling, additional
Published: 2022
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73. Evidence for saponin diversity–mycobiome links and conservatism of plant–fungi interaction patterns across Holarctic disjunct Panax species

Author: Zhang, Guozhuang, primary, Wei, Fugang, additional, Chen, Zhongjian, additional, Wang, Yong, additional, Jiao, Shuo, additional, Yang, JiaYing, additional, Chen, Yongzhong, additional, Liu, Congsheng, additional, Huang, Zhixin, additional, Dong, Linlin, additional, and Chen, Shilin, additional
Published: 2022
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74. Rare Species-Driven Diversity–Ecosystem Multifunctionality Relationships are Promoted by Stochastic Community Assembly

Author: Zhang, Zhengqing, primary, Lu, Yahai, additional, Wei, Gehong, additional, and Jiao, Shuo, additional
Published: 2022
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75. Agricultural Management Drive Bacterial Community Assembly in Different Compartments of Soybean Soil-Plant Continuum

Author: Chen, Shi, primary, Wang, Lulu, additional, Gao, Jiamin, additional, Zhao, Yiwen, additional, Wang, Yang, additional, Qi, Jiejun, additional, Peng, Ziheng, additional, Chen, Beibei, additional, Pan, Haibo, additional, Wang, Zhifeng, additional, Gao, Hang, additional, Jiao, Shuo, additional, and Wei, Gehong, additional
Published: 2022
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76. Bacterial and fungal community assembly in relation to soil nutrients and plant growth across different ecoregions of shrubland in Shaanxi, northwestern China

Author: Cao, Ying, primary, Chai, Yongfu, additional, Jiao, Shuo, additional, Li, Xinyi, additional, Wang, Xubo, additional, Zhang, Yani, additional, and Yue, Ming, additional
Published: 2022
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77. Temporal Dynamics of Rhizosphere Communities Across the Life Cycle of Panax notoginseng

Author: Wei, Guangfei, primary, Li, Mengzhi, additional, Zhang, Guozhuang, additional, Chen, Zhongjian, additional, Wei, Fugang, additional, Jiao, Shuo, additional, Qian, Jun, additional, Wang, Yong, additional, Wei, Jianhe, additional, Wang, Yitao, additional, Meng, Xiangxiao, additional, Fitzgerald, Martin, additional, Yu, Yuqi, additional, Dong, Linlin, additional, and Chen, Shilin, additional
Published: 2022
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78. Spatiotemporal Dynamics of Bacterial Taxonomic and Functional Profiles in Estuarine Intertidal Soils of China Coastal Zone

Author: Zhang, Zongxiao, primary, Han, Ping, additional, Zheng, Yanling, additional, Jiao, Shuo, additional, Dong, Hongpo, additional, Liang, Xia, additional, Gao, Dengzhou, additional, Niu, Yuhui, additional, Yin, Guoyu, additional, Liu, Min, additional, and Hou, Lijun, additional
Published: 2022
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79. Linking soil fungi to bacterial community assembly in arid ecosystems

Author: Jiao, Shuo, primary, Chu, Haiyan, additional, Zhang, Baogang, additional, Wei, Xiaorong, additional, Chen, Weimin, additional, and Wei, Gehong, additional
Published: 2022
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80. Aridity Threshold Induces Abrupt Change of Soil Abundant and Rare Bacterial Biogeography in Dryland Ecosystems

Author: Pan, Haibo, primary, Gao, Hang, additional, Peng, Ziheng, additional, Chen, Beibei, additional, Chen, Shi, additional, Liu, Yu, additional, Gu, Jie, additional, Wei, Xiaorong, additional, Chen, Weimin, additional, Wei, Gehong, additional, and Jiao, Shuo, additional
Published: 2022
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81. Common and rare von Willebrand factor (VWF) coding variants, VWF levels, and factor VIII levels in African Americans: the NHLBI Exome Sequencing Project

Author: Johnsen, Jill M., Auer, Paul L., Morrison, Alanna C., Jiao, Shuo, Wei, Peng, Haessler, Jeffrey, Fox, Keolu, McGee, Sean R., Smith, Joshua D., Carlson, Christopher S., Smith, Nicholas, Boerwinkle, Eric, Kooperberg, Charles, Nickerson, Deborah A., Rich, Stephen S., Green, David, Peters, Ulrike, Cushman, Mary, and Reiner, Alex P.
Published: 2013
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82. Chronic treatment with baicalin prevents the chronic mild stress-induced depressive-like behavior: Involving the inhibition of cyclooxygenase-2 in rat brain

Author: Li, Yu-Cheng, Shen, Ji-Duo, Li, Jing, Wang, Rui, Jiao, Shuo, and Yi, Li-Tao
Published: 2013
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83. Composition of Mycorrhiza-Associated Trees Mediates Community Assembly of Soil Fungi But Not of Bacteria

Author: Xing, Hua, primary, Jiao, Shuo, additional, Wu, Xian, additional, Zhang, Minhua, additional, Dong, Shu, additional, He, Fangliang, additional, and Liu, Yu, additional
Published: 2022
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84. Neighboring Plant Community Attributes Drive Rhizobiome Assemblages of a Focal Plant in a Kobresia Meadow

Author: Zhang, Baogang, primary, Jiao, Shuo, additional, Zhu, Gaodi, additional, Chen, Huai, additional, Cai, Yanjiang, additional, and Chang, Scott X., additional
Published: 2022
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85. Set-Based Gene × Environment Interaction Tests for Complex Diseases with Application to Genome-Wide Association and Sequencing Studies

Author: Jiao, Shuo, primary
Published: 2016
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86. Spatiotemporal Dynamics of Bacterial Taxonomic and Functional Profiles in Estuarine Intertidal Soils of China Coastal Zone

Author: Zhang, Zongxiao, primary, Han, Ping, additional, Zheng, Yanling, additional, Jiao, Shuo, additional, Dong, Hongpo, additional, Liang, Xia, additional, Gao, Dengzhou, additional, Niu, Yuhui, additional, Yin, Guoyu, additional, Liu, Min, additional, and Hou, Lijun, additional
Published: 2021
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87. Core microbiota drive functional stability of soil microbiome in reforestation ecosystems

Author: Jiao, Shuo, primary, Chen, Weimin, additional, and Wei, Gehong, additional
Published: 2021
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88. Trophic interrelationships drive the biogeography of protistan community in agricultural ecosystems

Author: Chen, Beibei, primary, Xiong, Wu, additional, Qi, Jiejun, additional, Pan, Haibo, additional, Chen, Shi, additional, Peng, Ziheng, additional, Gao, Hang, additional, Zhang, Limei, additional, Jiang, Yuji, additional, Wei, Gehong, additional, and Jiao, Shuo, additional
Published: 2021
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89. Responses of soil bacterial community structure and function to dry–wet cycles more stable in paddy than in dryland agricultural ecosystems

Author: Qi, Jiejun, primary, Chen, Beibei, additional, Gao, Jiamin, additional, Peng, Ziheng, additional, Jiao, Shuo, additional, Wei, Gehong, additional, and Kivlin, Stephanie, additional
Published: 2021
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90. Regulation of root secondary metabolites by partial root‐associated microbiotas under the shaping of licorice ecotypic differentiation in northwest China

Author: Liu, Yang, primary, Wang, Hao, additional, Peng, Ziheng, additional, Li, Da, additional, Chen, Weimin, additional, Jiao, Shuo, additional, and Wei, Gehong, additional
Published: 2021
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91. Soil multitrophic network complexity enhances the link between biodiversity and multifunctionality in agricultural systems

Author: Jiao, Shuo, primary, Lu, Yahai, additional, and Wei, Gehong, additional
Published: 2021
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92. Homogeneous selection shapes rare biosphere in rhizosphere of medicinal plant

Author: Zhang, Guozhuang, primary, Wei, Guangfei, additional, Wei, Fugang, additional, Chen, Zhongjian, additional, He, Mingjun, additional, Jiao, Shuo, additional, Wang, Yong, additional, Yu, Yuqi, additional, Dong, Linlin, additional, and Chen, Shilin, additional
Published: 2021
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93. Adaptation of Soil Fungal Community Structure and Assembly to Long- Versus Short-Term Nitrogen Addition in a Tropical Forest

Author: He, Jinhong, primary, Jiao, Shuo, additional, Tan, Xiangping, additional, Wei, Hui, additional, Ma, Xiaomin, additional, Nie, Yanxia, additional, Liu, Juxiu, additional, Lu, Xiankai, additional, Mo, Jiangming, additional, and Shen, Weijun, additional
Published: 2021
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94. Dispersal Limitation Plays Stronger Role in the Community Assembly of Fungi Relative to Bacteria in Rhizosphere Across the Arable Area of Medicinal Plant

Author: Zhang, Guozhuang, primary, Wei, Guangfei, additional, Wei, Fugang, additional, Chen, Zhongjian, additional, He, Mingjun, additional, Jiao, Shuo, additional, Wang, Yong, additional, Dong, Linlin, additional, and Chen, Shilin, additional
Published: 2021
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95. Stochastic community assembly decreases soil fungal richness in arid ecosystems

Author: Jiao, Shuo, primary, Zhang, Baogang, additional, Zhang, Guozhuang, additional, Chen, Weimin, additional, and Wei, Gehong, additional
Published: 2021
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96. Thermodynamics shapes the biogeography of propionate‐oxidizing syntrophs in paddy field soils

Author: Jin, Yidan, primary, Jiao, Shuo, additional, Dolfing, Jan, additional, and Lu, Yahai, additional
Published: 2021
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97. Linking phylogenetic niche conservatism to soil archaeal biogeography, community assembly and species coexistence

Author: Jiao, Shuo, primary, Chen, Weimin, additional, and Wei, Gehong, additional
Published: 2021
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98. Genetic variants of adiponectin and risk of colorectal cancer

Author: Song, Mingyang, Gong, Jian, Giovannucci, Edward L., Berndt, Sonja I., Brenner, Hermann, Chang-Claude, Jenny, Curtis, Keith R., Harrison, Tabitha A., Hoffmeister, Michael, Hsu, Li, Jiao, Shuo, Le Marchand, Loic, Potter, John D., Schoen, Robert E., Seminara, Daniela, Slattery, Martha L., White, Emily, Wu, Kana, Ogino, Shuji, Fuchs, Charles S., Hunter, David J., Tworoger, Shelley S., Hu, Frank B., Rimm, Eric, Jensen, Majken, Peters, Ulrike, and Chan, Andrew T.
Published: 2015
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99. Association of Aspirin and NSAID Use With Risk of Colorectal Cancer According to Genetic Variants

Author: Nan, Hongmei, Hutter, Carolyn M., Lin, Yi, Jacobs, Eric J., Ulrich, Cornelia M., White, Emily, Baron, John A., Berndt, Sonja I., Brenner, Hermann, Butterbach, Katja, Caan, Bette J., Campbell, Peter T., Carlson, Christopher S., Casey, Graham, Chang-Claude, Jenny, Chanock, Stephen J., Cotterchio, Michelle, Duggan, David, Figueiredo, Jane C., Fuchs, Charles S., Giovannucci, Edward L., Gong, Jian, Haile, Robert W., Harrison, Tabitha A., Hayes, Richard B., Hoffmeister, Michael, Hopper, John L., Hudson, Thomas J., Jenkins, Mark A., Jiao, Shuo, Lindor, Noralane M., Lemire, Mathieu, Le Marchand, Loic, Newcomb, Polly A., Ogino, Shuji, Pflugeisen, Bethann M., Potter, John D., Qu, Conghui, Rosse, Stephanie A., Rudolph, Anja, Schoen, Robert E., Schumacher, Fredrick R., Seminara, Daniela, Slattery, Martha L., Thibodeau, Stephen N., Thomas, Fridtjof, Thornquist, Mark, Warnick, Greg S., Zanke, Brent W., Gauderman, W. James, Peters, Ulrike, Hsu, Li, and Chan, Andrew T.
Published: 2015
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100. Additional file 2 of Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies

Author: Li, Dong, Haowei Ni, Jiao, Shuo, Yahai Lu, Jizhong Zhou, Sun, Bo, and Liang, Yuting
Abstract: Additional file 1: Figure S1. Sampling and sequencing of methanogens. Abscissa: the number of sequences randomly selected from the sample; ordinate: the species diversity and the number of OTU that can be represented by the random sampling sequence. Each curve in the figure represents a sample, marked with a different color. Figure S2. Linear regression of methanogenic archaea α-diversity and MAT (A) and CH4 emissions (B). Solid lines denote significant relationship with 95% confidence interval (shadow area). Dotted line denotes P > 0.05. Figure S3. The co-occurrence network structure of methanogenic community of 39 plots. Percentage in the top right corner indicates the proportion of 33 key OTUs (Table S4) in total node numbers of each network. Figure S4. Contributions of climatic variables and soil properties to the network topological attributes based on correlation and random forest regression model. Circle size represents the variable importance (that is, proportion of explained variability calculated via forest regression analysis analysis). Colors represent Spearman’s correlation coefficients (node: node number; edge: edge number; modularity: modularity; positive: positive correlations; negative: negative correlations; Avg.C.C: average clustering coefficient; N.D: network diameter; C.P.L: characteristic path length). Figure S5. Spearman’s correlation analysis of network topological attributes and richness. Blue shaded area is a 95% confidence interval. Figure S6. Spearman’s correlation analysis of network topological attributes and CH4 emissions. Dotted lines denote P > 0.05. Solid lines indicate a significant correlation (P < 0.05), with the blue shaded area showing the 95% confidence interval. Figure S7. Relative abundance of OTUs of the five groups of methanogenic archaeal communities. Each column followed by different letters differed significantly at P < 0.05 (ANOVA, Duncan test). (A.endemic: always endemic group; C.endemic: conditionally endemic group; C.common: conditionally common group; A.common: always common group). Figure S8. Relative abundance frequency histogram of 33 keystone OTUs in 429 samples. The blue histogram indicates rare OTUs (average relative abundance < 1% in 429 samples). The red histogram indicates abundant OTUs (average relative abundance > 1% in 429 samples), and the inset represents low-frequency OTUs with average relative abundance < 1%. Figure S9. The relative abundance of keystone taxa (at the family level) changes with temperature. (HL: 1.5°C, CC: 4.5°C, SY:8.3°C, YY: 14.4°C, FQ:13.9°C, LA: 16.1°C, QZ:17.9°C, ZX:17°C, JO:18.8°C, CT:19°C, HY:18°C, QX:21.6°C, HK:23.8°C). Figure S10. The relationship between keystone species and microbial functional genes related to methane generation depicted as colored segments in a CIRCOS plot. Ribbons connecting two segments indicate the interaction between the two. The size of the ribbon is proportional to the number of links. Table S1. Geographic information of 13 sampling regions with 3 plots in each region. Table S2. The topological features of the co-occurrence network in each plot. Table S3. Partial mantel test between network topology attributes and variables. Table S4. Changes of network topology attributes with latitude. Table S5. Information of 33 keystone OTUs involved in common co-occurrence relationship.
Published: 2021
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