46 results on '"Jian, Ruiqi"'
Search Results
2. Structure and topography of the synaptic V-ATPase–synaptophysin complex
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Wang, Chuchu, Jiang, Wenhong, Leitz, Jeremy, Yang, Kailu, Esquivies, Luis, Wang, Xing, Shen, Xiaotao, Held, Richard G., Adams, Daniel J., Basta, Tamara, Hampton, Lucas, Jian, Ruiqi, Jiang, Lihua, Stowell, Michael H. B., Baumeister, Wolfgang, Guo, Qiang, and Brunger, Axel T.
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- 2024
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3. Integrative multi-omics profiling in human decedents receiving pig heart xenografts
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Schmauch, Eloi, Piening, Brian, Mohebnasab, Maedeh, Xia, Bo, Zhu, Chenchen, Stern, Jeffrey, Zhang, Weimin, Dowdell, Alexa K., Kim, Jacqueline I., Andrijevic, David, Khalil, Karen, Jaffe, Ian S., Loza, Bao-Li, Gragert, Loren, Camellato, Brendan R., Oliveira, Michelli F., O’Brien, Darragh P., Chen, Han M., Weldon, Elaina, Gao, Hui, Gandla, Divya, Chang, Andrew, Bhatt, Riyana, Gao, Sarah, Lin, Xiangping, Reddy, Kriyana P., Kagermazova, Larisa, Habara, Alawi H., Widawsky, Sophie, Liang, Feng-Xia, Sall, Joseph, Loupy, Alexandre, Heguy, Adriana, Taylor, Sarah E. B., Zhu, Yinan, Michael, Basil, Jiang, Lihua, Jian, Ruiqi, Chong, Anita S., Fairchild, Robert L., Linna-Kuosmanen, Suvi, Kaikkonen, Minna U., Tatapudi, Vasishta, Lorber, Marc, Ayares, David, Mangiola, Massimo, Narula, Navneet, Moazami, Nader, Pass, Harvey, Herati, Ramin S., Griesemer, Adam, Kellis, Manolis, Snyder, Michael P., Montgomery, Robert A., Boeke, Jef D., and Keating, Brendan J.
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- 2024
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4. Chimpanzee and pig-tailed macaque iPSCs: Improved culture and generation of primate cross-species embryos
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Roodgar, Morteza, Suchy, Fabian P, Nguyen, Lan H, Bajpai, Vivek K, Sinha, Rahul, Vilches-Moure, Jose G, Van Bortle, Kevin, Bhadury, Joydeep, Metwally, Ahmed, Jiang, Lihua, Jian, Ruiqi, Chiang, Rosaria, Oikonomopoulos, Angelos, Wu, Joseph C, Weissman, Irving L, Mankowski, Joseph L, Holmes, Susan, Loh, Kyle M, Nakauchi, Hiromitsu, VandeVoort, Catherine A, and Snyder, Michael P
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Biological Sciences ,Stem Cell Research ,Stem Cell Research - Induced Pluripotent Stem Cell ,Biotechnology ,Stem Cell Research - Nonembryonic - Non-Human ,Animals ,Induced Pluripotent Stem Cells ,Macaca mulatta ,Macaca nemestrina ,Pan troglodytes ,Proteomics ,CP: Developmental biology ,Nonhuman primates ,blastocyst ,BCL2 ,chimpanzee ,cross-species embryos ,iPSCs ,interspecies chimera ,pig-tailed macaque ,Biochemistry and Cell Biology ,Medical Physiology ,Biological sciences - Abstract
As our closest living relatives, non-human primates uniquely enable explorations of human health, disease, development, and evolution. Considerable effort has thus been devoted to generating induced pluripotent stem cells (iPSCs) from multiple non-human primate species. Here, we establish improved culture methods for chimpanzee (Pan troglodytes) and pig-tailed macaque (Macaca nemestrina) iPSCs. Such iPSCs spontaneously differentiate in conventional culture conditions, but can be readily propagated by inhibiting endogenous WNT signaling. As a unique functional test of these iPSCs, we injected them into the pre-implantation embryos of another non-human species, rhesus macaques (Macaca mulatta). Ectopic expression of gene BCL2 enhances the survival and proliferation of chimpanzee and pig-tailed macaque iPSCs within the pre-implantation embryo, although the identity and long-term contribution of the transplanted cells warrants further investigation. In summary, we disclose transcriptomic and proteomic data, cell lines, and cell culture resources that may be broadly enabling for non-human primate iPSCs research.
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- 2022
5. Neuron Navigator 1 (Nav1) regulates the response to cocaine in mice
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Bagley, Jared R., Tan, Yalun, Zhu, Wan, Cheng, Zhuanfen, Takeda, Saori, Fang, Zhouqing, Arslan, Ahmed, Wang, Meiyue, Guan, Yuan, Jiang, Lihua, Jian, Ruiqi, Gu, Feng, Parada, Isabel, Prince, David, Jentsch, J. David, and Peltz, Gary
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- 2023
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6. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease
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Zhou, Xin, Shen, Xiaotao, Johnson, Jethro S., Spakowicz, Daniel J., Agnello, Melissa, Zhou, Wenyu, Avina, Monica, Honkala, Alexander, Chleilat, Faye, Chen, Shirley Jingyi, Cha, Kexin, Leopold, Shana, Zhu, Chenchen, Chen, Lei, Lyu, Lin, Hornburg, Daniel, Wu, Si, Zhang, Xinyue, Jiang, Chao, Jiang, Liuyiqi, Jiang, Lihua, Jian, Ruiqi, Brooks, Andrew W., Wang, Meng, Contrepois, Kévin, Gao, Peng, Rose, Sophia Miryam Schüssler-Fiorenza, Tran, Thi Dong Binh, Nguyen, Hoan, Celli, Alessandra, Hong, Bo-Young, Bautista, Eddy J., Dorsett, Yair, Kavathas, Paula B., Zhou, Yanjiao, Sodergren, Erica, Weinstock, George M., and Snyder, Michael P.
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- 2024
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7. Transcriptome variation in human tissues revealed by long-read sequencing
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Glinos, Dafni A., Garborcauskas, Garrett, Hoffman, Paul, Ehsan, Nava, Jiang, Lihua, Gokden, Alper, Dai, Xiaoguang, Aguet, François, Brown, Kathleen L., Garimella, Kiran, Bowers, Tera, Costello, Maura, Ardlie, Kristin, Jian, Ruiqi, Tucker, Nathan R., Ellinor, Patrick T., Harrington, Eoghan D., Tang, Hua, Snyder, Michael, Juul, Sissel, Mohammadi, Pejman, MacArthur, Daniel G., Lappalainen, Tuuli, and Cummings, Beryl B.
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- 2022
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8. Systematic Identification of Host Cell Regulators of Legionella pneumophila Pathogenesis Using a Genome-wide CRISPR Screen
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Jeng, Edwin E, Bhadkamkar, Varun, Ibe, Nnejiuwa U, Gause, Haley, Jiang, Lihua, Chan, Joanne, Jian, Ruiqi, Jimenez-Morales, David, Stevenson, Erica, Krogan, Nevan J, Swaney, Danielle L, Snyder, Michael P, Mukherjee, Shaeri, and Bassik, Michael C
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Biochemistry and Cell Biology ,Biological Sciences ,Pneumonia & Influenza ,Lung ,Infectious Diseases ,Pneumonia ,Aetiology ,2.1 Biological and endogenous factors ,Infection ,Animals ,Bacterial Proteins ,Cell Line ,Clustered Regularly Interspaced Short Palindromic Repeats ,Endoplasmic Reticulum ,Guanine Nucleotide Exchange Factors ,HEK293 Cells ,HeLa Cells ,Humans ,Legionella pneumophila ,Legionnaires' Disease ,Macrophages ,Membrane Proteins ,Mice ,Phagocytosis ,Proteins ,RAW 264.7 Cells ,U937 Cells ,Vacuoles ,Virulence Factors ,rab GTP-Binding Proteins ,Hela Cells ,C1ORF43 ,CRISPR screen ,RAB10 ,host-pathogen interaction ,intracellular bacteria ,pathogen ,phagocytosis ,Microbiology ,Medical Microbiology ,Immunology ,Biochemistry and cell biology ,Medical microbiology - Abstract
During infection, Legionella pneumophila translocates over 300 effector proteins into the host cytosol, allowing the pathogen to establish an endoplasmic reticulum (ER)-like Legionella-containing vacuole (LCV) that supports bacterial replication. Here, we perform a genome-wide CRISPR-Cas9 screen and secondary targeted screens in U937 human monocyte/macrophage-like cells to systematically identify host factors that regulate killing by L. pneumophila. The screens reveal known host factors hijacked by L. pneumophila, as well as genes spanning diverse trafficking and signaling pathways previously not linked to L. pneumophila pathogenesis. We further characterize C1orf43 and KIAA1109 as regulators of phagocytosis and show that RAB10 and its chaperone RABIF are required for optimal L. pneumophila replication and ER recruitment to the LCV. Finally, we show that Rab10 protein is recruited to the LCV and ubiquitinated by the effectors SidC/SdcA. Collectively, our results provide a wealth of previously undescribed insights into L. pneumophila pathogenesis and mammalian cell function.
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- 2019
9. A genome-wide atlas of co-essential modules assigns function to uncharacterized genes
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Wainberg, Michael, Kamber, Roarke A., Balsubramani, Akshay, Meyers, Robin M., Sinnott-Armstrong, Nasa, Hornburg, Daniel, Jiang, Lihua, Chan, Joanne, Jian, Ruiqi, Gu, Mingxin, Shcherbina, Anna, Dubreuil, Michael M., Spees, Kaitlyn, Meuleman, Wouter, Snyder, Michael P., Bassik, Michael C., and Kundaje, Anshul
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- 2021
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10. Synergic catalysis by a CuO-like phase and Cu0 for anaerobic dehydrogenation of 2,3-butanediol
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Yuan, Enxian, Ni, Ping, Zhuang, Wanli, Jian, Ruiqi, and Jian, Panming
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- 2020
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11. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease
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Zhou, Xin, primary, Shen, Xiaotao, additional, Johnson, Jethro, additional, Spakowicz, Daniel, additional, Agnello, Melissa, additional, Zhou, Wenyu, additional, Avina, Monica, additional, Honkala, Alexander, additional, Chleilat, Faye, additional, Chen, Shirley Jingyi, additional, Cha, Kexin, additional, Leopold, Shana, additional, Zhu, Chenchen, additional, Chen, Lei, additional, Lyu, Lin, additional, Hornburg, Daniel, additional, Wu, Si, additional, Zhang, Xinyue, additional, Jiang, Chao, additional, Jiang, Liuyiqi, additional, jiang, lihua, additional, Jian, Ruiqi, additional, Brooks, Andrew W, additional, Wang, Meng, additional, Contrepois, Kevin, additional, Gao, Peng, additional, Schussler-Fiorenza Rose, Sophia Miryam, additional, Tran, Thi Dong Binh, additional, Nguyen, Hoan, additional, Celli, Alessandra, additional, Hong, Bo-Young, additional, Bautista, Eddy J, additional, Dorsett, Yair, additional, Kavathas, Paula, additional, zhou, yanjiao, additional, Sodergren, Erica, additional, Weinstock, George M, additional, and Snyder, Michael P, additional
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- 2024
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12. Achieving high-performance for catalytic epoxidation of styrene with uniform magnetically separable CoFe2O4 nanoparticles
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Liu, Jiangyong, Meng, Ru, Li, Jinxing, Jian, Panming, Wang, Lixia, and Jian, Ruiqi
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- 2019
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13. Selective synthesis of triacetin from glycerol catalyzed by HZSM-5/MCM-41 micro/mesoporous molecular sieve
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Liu, Jiangyong, Wang, Zihao, Sun, Yunlin, Jian, Ruiqi, Jian, Panming, and Wang, Dan
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- 2019
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14. Amorphous TiO2–SiO2 composites as selective heterogeneous catalysts for the oxidation of styrene to 1, 2-epoxyethylbenzene
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Liu, Jiangyong, Zhang, Yayun, Wang, Zihao, Deng, Yonghang, Jian, Panming, Wang, Lixia, and Jian, Ruiqi
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- 2019
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15. Integrative Multi-omic Profiling of Two Human Decedents Receiving Pig Heart Xenografts Reveals Strong Perturbations in Early Immune-Cell and Cellular Metabolism Responses
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Schmauch, Eloi, primary, Piening, Brian, additional, Xia, Bo, additional, Zhu, Chenchen, additional, Stern, Jeffrey, additional, Zhang, Weimin, additional, Dowdell, Alexa, additional, Loza, Bao-Li, additional, Mohebnasab, Maede, additional, Gragert, Loren, additional, Khalil, Karen, additional, Camellato, Brendan, additional, de Oliveira, Michelli Faria, additional, O’Brien, Darragh, additional, Weldon, Elaina, additional, Lin, Xiangping, additional, Gao, Hui, additional, Kagermazova, Larisa, additional, Kim, Jacqueline, additional, Loupy, Alexandre, additional, Heguy, Adriana, additional, Taylor, Sarah, additional, Zhu, Florrie, additional, Gao, Sarah, additional, Gandla, Divya, additional, Reddy, Kriyana, additional, Chang, Andrew, additional, Michael, Basil, additional, Jiang, Lihua, additional, Jian, Ruiqi, additional, Narula, Navneet, additional, Linna-Kuosmanen, Suvi, additional, Kaikkonen-Määttä, Minna, additional, Lorber, Marc, additional, Kellis, Manolis, additional, Tatapudi, Vasishta, additional, Ayares, David, additional, Griesemer, Adam, additional, Mangiola, Massimo, additional, Pass, Harvey, additional, Snyder, Michael P., additional, Montgomery, Robert A., additional, Boeke, Jef D., additional, and Keating, Brendan J., additional
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- 2023
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16. Abstract 3497: The polyclonal path to malignant transformation in familial adenomatous polyposis
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Schenck, Ryan O., primary, Khan, Aziz, additional, Horning, Aaron, additional, Esplin, Edward D., additional, Monte, Emma, additional, Wu, Si, additional, Hanson, Casey, additional, Bararpour, Nasim, additional, Neves, Stephanie, additional, Jiang, Lihua, additional, Contrepois, Kévin, additional, Lee, Hayan, additional, Guha, Tuhin K., additional, Hu, Zheng, additional, Laquindanum, Rozelle, additional, Mills, Meredith A., additional, Chaib, Hassan, additional, Chiu, Roxanne, additional, Jian, Ruiqi, additional, Chan, Jeannie, additional, Ellenberger, Mathew, additional, Becker, Winston R., additional, Bahmani, Bahareh, additional, Michael, Basil, additional, Shen, Jeanne, additional, Lancaster, Samuel, additional, Ladabaum, Uri, additional, Kundaje, Anshul, additional, Longacre, Teri A., additional, Greenleaf, William J., additional, Ford, James M., additional, Snyder, Michael P., additional, and Curtis, Christina, additional
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- 2023
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17. Density functional theory study of selective aerobic oxidation of cyclohexane: the roles of acetic acid and cobalt ion
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Yuan, Enxian, Liu, Hanzhong, Tao, Yunwen, Xie, Ju, Jian, Ruiqi, Jian, Panming, and Liu, Jiangyong
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- 2019
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18. The impact of rare variation on gene expression across tissues
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Li, Xin, Kim, Yungil, Tsang, Emily K., Davis, Joe R., Damani, Farhan N., Chiang, Colby, Hess, Gaelen T., Zappala, Zachary, Strober, Benjamin J., Scott, Alexandra J., Li, Amy, Ganna, Andrea, Bassik, Michael C., Merker, Jason D., Aguet, Franois, Ardlie, Kristin G., Cummings, Beryl B., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Karczewski, Konrad J., Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segr, Ayellet V., Trowbridge, Casandra A., Tukiainen, Taru, Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Castel, Stephane E., Chen, Lin S., Conrad, Donald F., Cox, Nancy J., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D.H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Sul, Jae Hoon, Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Billy Li, Jin, Li, Qin, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Zhang, Rui, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, and Zhu, Jingchun
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Disease susceptibility -- Genetic aspects ,Genetic variation -- Observations ,Gene expression -- Observations ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): Xin Li [1]; Yungil Kim [2]; Emily K. Tsang [1, 3]; Joe R. Davis [1, 4]; Farhan N. Damani [2]; Colby Chiang [5]; Gaelen T. Hess [4]; Zachary Zappala [...]
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- 2017
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19. Dynamic landscape and regulation of RNA editing in mammals
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Tan, Meng How, Li, Qin, Shanmugam, Raghuvaran, Piskol, Robert, Kohler, Jennefer, Young, Amy N., Liu, Kaiwen Ivy, Zhang, Rui, Ramaswami, Gokul, Ariyoshi, Kentaro, Gupte, Ankita, Keegan, Liam P., George, Cyril X., Ramu, Avinash, Huang, Ni, Pollina, Elizabeth A., Leeman, Dena S., Rustighi, Alessandra, Goh, Y. P. Sharon, Aguet, Franois, Ardlie, Kristin G., Cummings, Beryl B., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Karczewski, Konrad J., Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segr, Ayellet V., Trowbridge, Casandra A., Tukiainen, Taru, Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Castel, Stephane E., Chen, Lin S., Chiang, Colby, Conrad, Donald F., Cox, Nancy J., Damani, Farhan N., Davis, Joe R., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D. H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J., Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Strober, Benjamin J., Sul, Jae Hoon, Tsang, Emily K., Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zappala, Zachary, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Li, Jin Billy, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, Zhu, Jingchun, Chawla, Ajay, Del Sal, Giannino, Peltz, Gary, Brunet, Anne, Samuel, Charles E., OConnell, Mary A., Walkley, Carl R., and Nishikura, Kazuko
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Genetic research ,Mammals -- Genetic aspects ,RNA processing -- Research ,Genetic regulation ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): Meng How Tan (corresponding author) [1, 2, 3]; Qin Li [1]; Raghuvaran Shanmugam [2, 3]; Robert Piskol [1]; Jennefer Kohler [1]; Amy N. Young [1]; Kaiwen Ivy Liu [3]; [...]
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- 2017
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20. Landscape of X chromosome inactivation across human tissues
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Tukiainen, Taru, Villani, Alexandra-Chlo, Yen, Angela, Rivas, Manuel A., Marshall, Jamie L., Satija, Rahul, Aguirre, Matt, Gauthier, Laura, Fleharty, Mark, Kirby, Andrew, Cummings, Beryl B., Castel, Stephane E., Karczewski, Konrad J., Aguet, Franois, Byrnes, Andrea, Ardlie, Kristin G., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segr, Ayellet V., Trowbridge, Casandra A., Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Chen, Lin S., Chiang, Colby, Conrad, Donald F., Cox, Nancy J., Damani, Farhan N., Davis, Joe R., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D. H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J., Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Strober, Benjamin J., Sul, Jae Hoon, Tsang, Emily K., Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zappala, Zachary, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Li, Jin Billy, Li, Qin, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Zhang, Rui, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, Zhu, Jingchun, Regev, Aviv, and Hacohen, Nir
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Chromosomes -- Physiological aspects ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): Taru Tukiainen (corresponding author) [1, 2]; Alexandra-Chlo Villani [2, 3]; Angela Yen [2, 4]; Manuel A. Rivas [1, 2, 5]; Jamie L. Marshall [1, 2]; Rahul Satija [2, 6, [...]
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- 2017
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21. Neuron Navigator 1Regulates Learning, Memory, and the Response to Multiple Potentially Addictive Drugs
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Bagley, Jared R., primary, Tan, Yalun, additional, Zhu, Wan, additional, Cheng, Zhuanfen, additional, Takeda, Saori, additional, Fang, Zhouqing, additional, Arslan, Ahmed, additional, Wang, Meiyue, additional, Guan, Yuan, additional, Jiang, Lihua, additional, Jian, Ruiqi, additional, Gu, Feng, additional, Parada, Isabel, additional, Prince, David, additional, Jentsch, J. David, additional, and Peltz, Gary, additional
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- 2022
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22. Genetic effects on gene expression across human tissues
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Aguet, François, Ardlie, Kristin G., Cummings, Beryl B., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Karczewski, Konrad J., Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segrè, Ayellet V., Trowbridge, Casandra A., Tukiainen, Taru, Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Castel, Stephane E., Chen, Lin S., Chiang, Colby, Conrad, Donald F., Cox, Nancy J., Damani, Farhan N., Davis, Joe R., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frésard, Laure, Gamazon, Eric R., Garrido-Martín, Diego, Gewirtz, Ariel D.H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Im, Hae Kyung, Jo, Brian, Kang, Eun Yong, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muñoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J., Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Strober, Benjamin J., Sul, Jae Hoon, Tsang, Emily K., Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zappala, Zachary, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Li, Jin Billy, Li, Qin, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Zhang, Rui, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, Roger A., Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, James W., Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, Zhu, Jingchun, Brown, Andrew A., Nguyen, Duyen Y., Sullivan, Timothy J., Addington, Anjene, Koester, Susan, Lockhart, Nicole C., Roe, Bryan, Valley, Dana, Gewirtz, Ariel D. H., He, Amy Z., Quon, Gerald, Ripke, Stephan, Shimko, Tyler C., Teran, Nicole A., Zhang, Hailei, Bustamante, Carlos D., and Guigó, Roderic
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- 2017
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23. Multi-omic Analysis of Familial Adenomatous Polyposis Reveals Molecular Pathways and Polyclonal Spreading Associated with Early Tumorigenesis
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Snyder, Michael, primary, Horning, Aaron, additional, Esplin, Edward, additional, Wu, Si, additional, Hanson, Casey, additional, Bararpour, Nasim, additional, Nevins, Stephanie, additional, Jiang, Lihua, additional, Contrepoi, Kevin, additional, Lee, Hayan, additional, Guha, Tuhin, additional, Hu, Zheng, additional, Laquindanum, Rozelle, additional, Mills, Meredith, additional, Chaib, Hassan, additional, Chiu, Roxanne, additional, Jian, Ruiqi, additional, Chan, Joanne, additional, Ellenberger, Mathew, additional, Khan, Aziz, additional, Michael, Basil, additional, Bahmani, Bahareh, additional, Esplin, Glen, additional, Shen, Jeanne, additional, Lancaster, Samuel, additional, Ladabaum, Uri, additional, Kundaje, Anshul, additional, Longacre, Teri, additional, Greenleaf, William, additional, Curtis, Christina, additional, Ford, James, additional, and Becker, Winston, additional
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- 2021
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24. Intriguing hierarchical Co@NC microflowers in situ assembled by nanoneedles: Towards enhanced reduction of nitroaromatic compounds via interfacial synergistic catalysis
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Liu, Jiangyong, primary, Li, Jinxing, additional, Jian, Panming, additional, and Jian, Ruiqi, additional
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- 2021
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25. CeO2 Nanoparticle-Decorated Co3O4 Microspheres for Selective Oxidation of Ethylbenzene with Molecular Oxygen under Solvent- and Additive-Free Conditions
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Liu, Jiangyong, primary, Meng, Ru, additional, Jian, Panming, additional, and Jian, Ruiqi, additional
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- 2020
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26. RobNorm: model-based robust normalization method for labeled quantitative mass spectrometry proteomics data
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Wang, Meng, primary, Jiang, Lihua, additional, Jian, Ruiqi, additional, Chan, Joanne Y, additional, Liu, Qing, additional, Snyder, Michael P, additional, and Tang, Hua, additional
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- 2020
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27. A Quantitative Proteome Map of the Human Body
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Jiang, Lihua, primary, Wang, Meng, additional, Lin, Shin, additional, Jian, Ruiqi, additional, Li, Xiao, additional, Chan, Joanne, additional, Dong, Guanlan, additional, Fang, Huaying, additional, Robinson, Aaron E., additional, Snyder, Michael P., additional, Aguet, François, additional, Anand, Shankara, additional, Ardlie, Kristin G., additional, Gabriel, Stacey, additional, Getz, Gad, additional, Graubert, Aaron, additional, Hadley, Kane, additional, Handsaker, Robert E., additional, Huang, Katherine H., additional, Kashin, Seva, additional, MacArthur, Daniel G., additional, Meier, Samuel R., additional, Nedzel, Jared L., additional, Nguyen, Duyen Y., additional, Segrè, Ayellet V., additional, Todres, Ellen, additional, Balliu, Brunilda, additional, Barbeira, Alvaro N., additional, Battle, Alexis, additional, Bonazzola, Rodrigo, additional, Brown, Andrew, additional, Brown, Christopher D., additional, Castel, Stephane E., additional, Conrad, Don, additional, Cotter, Daniel J., additional, Cox, Nancy, additional, Das, Sayantan, additional, de Goede, Olivia M., additional, Dermitzakis, Emmanouil T., additional, Engelhardt, Barbara E., additional, Eskin, Eleazar, additional, Eulalio, Tiffany Y., additional, Ferraro, Nicole M., additional, Flynn, Elise, additional, Fresard, Laure, additional, Gamazon, Eric R., additional, Garrido-Martín, Diego, additional, Gay, Nicole R., additional, Guigó, Roderic, additional, Hamel, Andrew R., additional, He, Yuan, additional, Hoffman, Paul J., additional, Hormozdiari, Farhad, additional, Hou, Lei, additional, Im, Hae Kyung, additional, Jo, Brian, additional, Kasela, Silva, additional, Kellis, Manolis, additional, Kim-Hellmuth, Sarah, additional, Kwong, Alan, additional, Lappalainen, Tuuli, additional, Li, Xin, additional, Liang, Yanyu, additional, Mangul, Serghei, additional, Mohammadi, Pejman, additional, Montgomery, Stephen B., additional, Muñoz-Aguirre, Manuel, additional, Nachun, Daniel C., additional, Nobel, Andrew B., additional, Oliva, Meritxell, additional, Park, YoSon, additional, Park, Yongjin, additional, Parsana, Princy, additional, Reverter, Ferran, additional, Rouhana, John M., additional, Sabatti, Chiara, additional, Saha, Ashis, additional, Skol, Andrew D., additional, Stephens, Matthew, additional, Stranger, Barbara E., additional, Strober, Benjamin J., additional, Teran, Nicole A., additional, Viñuela, Ana, additional, Wang, Gao, additional, Wen, Xiaoquan, additional, Wright, Fred, additional, Wucher, Valentin, additional, Zou, Yuxin, additional, Ferreira, Pedro G., additional, Li, Gen, additional, Melé, Marta, additional, Yeger-Lotem, Esti, additional, Barcus, Mary E., additional, Bradbury, Debra, additional, Krubit, Tanya, additional, McLean, Jeffrey A., additional, Qi, Liqun, additional, Robinson, Karna, additional, Roche, Nancy V., additional, Smith, Anna M., additional, Sobin, Leslie, additional, Tabor, David E., additional, Undale, Anita, additional, Bridge, Jason, additional, Brigham, Lori E., additional, Foster, Barbara A., additional, Gillard, Bryan M., additional, Hasz, Richard, additional, Hunter, Marcus, additional, Johns, Christopher, additional, Johnson, Mark, additional, Karasik, Ellen, additional, Kopen, Gene, additional, Leinweber, William F., additional, McDonald, Alisa, additional, Moser, Michael T., additional, Myer, Kevin, additional, Ramsey, Kimberley D., additional, Roe, Brian, additional, Shad, Saboor, additional, Thomas, Jeffrey A., additional, Walters, Gary, additional, Washington, Michael, additional, Wheeler, Joseph, additional, Jewell, Scott D., additional, Rohrer, Daniel C., additional, Valley, Dana R., additional, Davis, David A., additional, Mash, Deborah C., additional, Branton, Philip A., additional, Barker, Laura K., additional, Gardiner, Heather M., additional, Mosavel, Maghboeba, additional, Siminoff, Laura A., additional, Flicek, Paul, additional, Haeussler, Maximilian, additional, Juettemann, Thomas, additional, Kent, W. James, additional, Lee, Christopher M., additional, Powell, Conner C., additional, Rosenbloom, Kate R., additional, Ruffier, Magali, additional, Sheppard, Dan, additional, Taylor, Kieron, additional, Trevanion, Stephen J., additional, Zerbino, Daniel R., additional, Abell, Nathan S., additional, Akey, Joshua, additional, Chen, Lin, additional, Demanelis, Kathryn, additional, Doherty, Jennifer A., additional, Feinberg, Andrew P., additional, Hansen, Kasper D., additional, Hickey, Peter F., additional, Jasmine, Farzana, additional, Kaul, Rajinder, additional, Kibriya, Muhammad G., additional, Li, Jin Billy, additional, Li, Qin, additional, Linder, Sandra E., additional, Pierce, Brandon L., additional, Rizzardi, Lindsay F., additional, Smith, Kevin S., additional, Stamatoyannopoulos, John, additional, Tang, Hua, additional, Carithers, Latarsha J., additional, Guan, Ping, additional, Koester, Susan E., additional, Little, A. Roger, additional, Moore, Helen M., additional, Nierras, Concepcion R., additional, Rao, Abhi K., additional, Vaught, Jimmie B., additional, and Volpi, Simona, additional
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- 2020
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28. Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding
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Roodgar, Morteza, primary, Babveyh, Afshin, primary, Nguyen, Lan H, primary, Zhou, Wenyu, primary, Sinha, Rahul, primary, Lee, Hayan, primary, Hanks, John B, primary, Avula, Mohan, primary, Jiang, Lihua, primary, Jian, Ruiqi, primary, Lee, Hoyong, primary, Song, Giltae, primary, Chaib, Hassan, primary, Weissman, Irv L, primary, Batzoglou, Serafim, primary, Holmes, Susan, primary, Smith, David G, primary, Mankowski, Joseph L, primary, Prost, Stefan, primary, and Snyder, Michael P, primary
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- 2020
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29. Tissue Sample Preparation for LC-MS Analysis v1
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Chan, Joanne, primary, Jian, Ruiqi, additional, and jiang, lihua, additional
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- 2020
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30. LC-MS3 Proteomics Data Acquisition v1
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Jian, Ruiqi, primary, Chan, Joanne, additional, and jiang, lihua, additional
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- 2020
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31. RobNorm: Model-Based Robust Normalization for High-Throughput Proteomics from Mass Spectrometry Platform
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Wang, Meng, Jiang, Lihua, Jian, Ruiqi, Chen, Joanne, Snyder, Michael P., and Tang, Hua
- Abstract
Motivation In the analysis of proteomics data from mass spectrometry (MS), normalization is an important preprocessing step to correct sample-level variation and make abundance measurements for each specific protein comparable across different samples. Under heterogeneous samples such as in the Phase I study of the Enhancing Genotype-Tissue Expression (eGTEx) project (Jiang, et al., 2019), the samples coming from 32 different tissues, and without prior housekeeping protein information or spike-ins, how to robustly correct the bias but keep tissue internal variations becomes a challenging question. Majority of previous normalization methods cannot guarantee a robust and tissue adaptive correction. This motivates us to develop a data-driven robust normalization method in MS platform to adapt tissue sample heterogeneities. Methods To robustly estimate the sample effect, we take use of the density power weight to down weigh the outliers and extend the one-dimensional robust fitting in (Windham, 1995) and (Fujisawa and Eguchi, 2008) to our structured data. We construct our robust criterion and build the algorithm to get our robust normalization (RobNorm). Results We focus our comparison to the PQN a widely used normalization method in MS. In the simulation studies and real data application, we conclude that our robust normalization method to estimate the sample effect performs better than PQN especially when the regulation magnitude and proportion are large and strong. We also discuss some limitations in our method. Contact huatang@stanford.edu
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- 2019
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32. Systematic Identification of Host Cell Regulators of Legionella pneumophila Pathogenesis Using a Genome-wide CRISPR Screen.
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Ibe, Nnejiuwa, Ibe, Nnejiuwa, Gause, Haley, Jiang, Lihua, Chan, Joanne, Jian, Ruiqi, Jimenez-Morales, David, Stevenson, Erica, Jeng, Edwin, Swaney, Danielle, Krogan, Nevan, Mukherjee, Shaeri, Bassik, Michael, Snyder, Michael, Bhadkamkar, Varun, Ibe, Nnejiuwa, Ibe, Nnejiuwa, Gause, Haley, Jiang, Lihua, Chan, Joanne, Jian, Ruiqi, Jimenez-Morales, David, Stevenson, Erica, Jeng, Edwin, Swaney, Danielle, Krogan, Nevan, Mukherjee, Shaeri, Bassik, Michael, Snyder, Michael, and Bhadkamkar, Varun
- Abstract
During infection, Legionella pneumophila translocates over 300 effector proteins into the host cytosol, allowing the pathogen to establish an endoplasmic reticulum (ER)-like Legionella-containing vacuole (LCV) that supports bacterial replication. Here, we perform a genome-wide CRISPR-Cas9 screen and secondary targeted screens in U937 human monocyte/macrophage-like cells to systematically identify host factors that regulate killing by L. pneumophila. The screens reveal known host factors hijacked by L. pneumophila, as well as genes spanning diverse trafficking and signaling pathways previously not linked to L. pneumophila pathogenesis. We further characterize C1orf43 and KIAA1109 as regulators of phagocytosis and show that RAB10 and its chaperone RABIF are required for optimal L. pneumophila replication and ER recruitment to the LCV. Finally, we show that Rab10 protein is recruited to the LCV and ubiquitinated by the effectors SidC/SdcA. Collectively, our results provide a wealth of previously undescribed insights into L. pneumophila pathogenesis and mammalian cell function.
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- 2019
33. NiCo2O4 nanoneedle-assembled hierarchical microflowers for highly selective oxidation of styrene
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Liu, Jiangyong, Chen, Tingting, Yan, Xiaodong, Wang, Zihao, Jian, Ruiqi, Jian, Panming, and Yuan, Enxian
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- 2018
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34. A genome-wide almanac of co-essential modules assigns function to uncharacterized genes
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Wainberg, Michael, primary, Kamber, Roarke A., additional, Balsubramani, Akshay, additional, Meyers, Robin M., additional, Sinnott-Armstrong, Nasa, additional, Hornburg, Daniel, additional, Jiang, Lihua, additional, Chan, Joanne, additional, Jian, Ruiqi, additional, Gu, Mingxin, additional, Shcherbina, Anna, additional, Dubreuil, Michael M., additional, Spees, Kaitlyn, additional, Snyder, Michael P., additional, Kundaje, Anshul, additional, and Bassik, Michael C., additional
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- 2019
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35. RobNorm: Model-Based Robust Normalization Method for Labeled Quantitative Mass Spectrometry Proteomics Data
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Wang, Meng, primary, Jiang, Lihua, additional, Jian, Ruiqi, additional, Chan, Joanne Y., additional, Liu, Qing, additional, Snyder, Michael P., additional, and Tang, Hua, additional
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- 2019
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36. RobNorm: model-based robust normalization method for labeled quantitative mass spectrometry proteomics data.
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Wang, Meng, Jiang, Lihua, Jian, Ruiqi, Chan, Joanne Y, Liu, Qing, Snyder, Michael P, and Tang, Hua
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PROTEOMICS ,PROTEIN expression ,QUANTITATIVE research ,MASS spectrometry ,DATA analysis ,ELECTRONIC data processing - Abstract
Motivation Data normalization is an important step in processing proteomics data generated in mass spectrometry experiments, which aims to reduce sample-level variation and facilitate comparisons of samples. Previously published methods for normalization primarily depend on the assumption that the distribution of protein expression is similar across all samples. However, this assumption fails when the protein expression data is generated from heterogenous samples, such as from various tissue types. This led us to develop a novel data-driven method for improved normalization to correct the systematic bias meanwhile maintaining underlying biological heterogeneity. Results To robustly correct the systematic bias, we used the density-power-weight method to down-weigh outliers and extended the one-dimensional robust fitting method described in the previous work to our structured data. We then constructed a robustness criterion and developed a new normalization algorithm, called RobNorm. In simulation studies and analysis of real data from the genotype-tissue expression project, we compared and evaluated the performance of RobNorm against other normalization methods. We found that the RobNorm approach exhibits the greatest reduction in systematic bias while maintaining across-tissue variation, especially for datasets from highly heterogeneous samples. Availabilityand implementation https://github.com/mwgrassgreen/RobNorm. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]
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- 2021
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37. Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease The eGTEx Project
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Stranger, Barbara E., Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana, Davis, David A., Mash, Deborah C., Gould, Sarah E., Guan, Ping, Koester, Susan, Little, A. Roger, Martin, Casey, Moore, Helen M., Rao, Abhi, Struewing, Jeffery P., Volpi, Simona, Hansen, Kasper D., Hickey, Peter F., Rizzardi, Lindsay F., Hou, Lei, Liu, Yaping, Molinie, Benoit, Park, Yongjin, Rinaldi, Nicola, Wang, Li B., Van Wittenberghe, Nicholas, Claussnitzer, Melina, Gelfand, Ellen T., Li, Qin, Linder, Sandra, Smith, Kevin S., Tsang, Emily K., Demanelis, Kathryn, Doherty, Jennifer A., Jasmine, Farzana, Kibriya, Muhammad G., Jiang, Lihua, Lin, Shin, Wang, Meng, Jian, Ruiqi, Li, Xiao, Chan, Joanne, Bates, Daniel, Diegel, Morgan, Halow, Jessica, Haugen, Eric, Johnson, Audra, Kaul, Rajinder, Lee, Kristen, Maurano, Matthew T., Nelson, Jemma, Neri, Fidencio J., Sandstrom, Richard, Fernando, Marian S., Linke, Caroline, Oliva, Meritxell, Skol, Andrew, Wu, Fan, Akey, Joshua M., Feinberg, Andrew P., Li, Jin Billy, Pierce, Brandon L., Stamatoyannopoulos, John A., Tang, Hua, Ardlie, Kristin G., Kellis, Manolis, Snyder, Michael P., and Montgomery, Stephen B.
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Article - Abstract
Genetic variants have been associated with a myriad of molecular phenotypes that provide new insight into the range of mechanisms underlying genetic traits and diseases. Identifying any particular genetic variant’s cascade of effects, from molecule to individual, requires assaying multiple layers of molecular complexity. We introduce the Enhancing GTEx (eGTEx) project that extends the GTEx project to combine gene expression with additional intermediate molecular measurements on the same tissues to provide a resource for studying how genetic differences cascade through molecular phenotypes to impact human health.
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- 2017
38. Genetic effects on gene expression across human tissues
- Author
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Haugen, Eric, He, Yuan, Chen, Lin S., Dermitzakis, Emmanouil T., Branton, Philip A., Nobel, Andrew B., Park, YoSon, McLean, Jeffrey A., Neri, Fidencio J., Tabor, David E., Saha, Ashis, Sobin, Leslie, Doherty, Jennifer A., Rosenbloom, Kate R., Quan, Jie, Strober, Benjamin J., Liu, Yaping, Valley, Dana, Basha, Omer, Barshir, Ruth, Trowbridge, Casandra A., Segrè, Ayellet V., Skol, Andrew, Karasik, Ellen, Bridge, Jason, Kent, W. James, Chiang, Colby, Damani, Farhan N., Karczewski, Konrad J., Barcus, Mary E., Oliva, Meritxell, Papasaikas, Panagiotis, Nelson, Jemma, Linke, Caroline, Paten, Benedict, Gelfand, Ellen T., Zhu, Jingchun, Wright, Fred A., Smith, Kevin S., Halow, Jessica, Kim-Hellmuth, Sarah, Salvatore, Michael, Hunter, Steven, Noble, Michael S., Goldman, Mary, Nguyen, Duyen Y., Singh, Shilpi, Rohrer, Daniel C., Cox, Nancy J., Hickey, Peter F., Battle, Alexis, Claussnitzer, Melina, Molinie, Benoit, Aguet, François, Balliu, Brunilda, Thomas, Jeffrey A., Hormozdiari, Farhad, Hou, Lei, Kaul, Rajinder, Peterson, Christine B., Lin, Jessica, Barker, Laura K., Brown, Christopher D., Guan, Ping, Lee, Kristen, Gloudemans, Michael J., Ripke, Stephan, Moser, Michael T., Muñoz-Aguirre, Manuel, Haeussler, Maximilian, Vatanian, Negin, Gewirtz, Ariel D.H., Castel, Stephane E., Monlong, Jean, Scott, Alexandra J., Stamatoyannopoulos, John, Ruffier, Magali, Zappala, Zachary, Li, Xiao, Ferreira, Pedro G., Nierras, Concepcion R., Yeger-Lotem, Esti, Wen, Xiaoquan, Struewing, Jeffery P., Delaneau, Olivier, Tukiainen, Taru, Tomaszewski, Maria M., Jo, Brian, Park, Yongjin, Martin, Casey, Bogu, Gireesh K., Pierce, Brandon L., Zhou, Yi-Hui, Eskin, Eleazar, Reverter, Ferran, Guigó, Roderic, Teran, Nicole A., Lek, Monkol, Leinweber, William F., Ardlie, Kristin G., Kopen, Gene, Ongen, Halit, Lonsdale, John T., Hall, Ira M., Bustamante, Carlos D., Quon, Gerald, Han, Buhm, Mohammadi, Pejman, Nicolae, Dan L., Kellis, Manolis, Vivian, John, Robinson, Karna L., Davis, David A., Washington, Michael, Montroy, Robert G., Craft, Brian, Wang, Gao, Garrido-Martín, Diego, Taylor, Kieron, Linder, Sandra, Hadley, Kane, Addington, Anjene M., Davis, Joe R., Siminoff, Laura A., Miklos, Mark, Tsang, Emily K., Diegel, Morgan, Mash, Deborah C., McDowell, Ian C., Lockhart, Nicole C., Payne, Anthony J., Abell, Nathan S., Cummings, Beryl B., Wheeler, Joseph, Matose, Takunda, Demanelis, Kathryn, Gliner, Genna, Stephens, Matthew, McDonald, Alisa, Rao, Abhi, Foster, Barbara A., Frésard, Laure, Brown, Andrew A., Zhang, Rui, Rinaldi, Nicola J., Gillard, Bryan M., Zerbino, Daniel R., Sabatti, Chiara, Moore, Helen M., Hasz, Richard, Brigham, Lori E., Zaugg, Judith B., Jian, Ruiqi, Conrad, Donald F., Snyder, Michael P., Im, Hae Kyung, Wu, Fan, MacArthur, Daniel G., Liu, Boxiang, Gamazon, Eric R., Jiang, Lihua, Sammeth, Michael, Johns, Christopher, Maurano, Matthew T., Hansen, Kasper D., Kang, Eun Yong, Myer, Kevin, Tang, Hua, Johnson, Mark, Fernando, Marian S., Smith, Anna M., Urbut, Sarah, Gould, Sarah E., Van Wittenberghe, Nicholas, Lee, Christopher M., Engelhardt, Barbara E., Panousis, Nikolaos, Palowitch, John J., Kibriya, Muhammad G., Sheppard, Dan, McCarthy, Mark I., Ndungu, Anne W., Valentino, Kimberly M., Sodaei, Reza, Sandstrom, Richard, Parsana, Princy, Kim, Yungil, Kumar, Rachna, Chan, Joanne, Little, A. Roger, Shimko, Tyler C., Volpi, Simona, Li, Qin, Akey, Joshua M., Walters, Gary, Roe, Bryan, Undale, Anita H., Van De Bunt, Martijn, Getz, Gad, Li, Jin Billy, Mangul, Serghei, Feinberg, Andrew P., Sul, Jae Hoon, Rizzardi, Lindsay F., Nguyen, Duyen T., Stranger, Barbara E., Um, Ki Sung, Flicek, Paul, Trevanion, Stephen J., Vaught, Jimmie B., Lockart, Nicole C., Nedzel, Jared L., Handsaker, Robert E., Hunter, Marcus, Xi, Hualin S., Bates, Daniel, Howald, Cedric, Roche, Nancy V., Koester, Susan, Huang, Katherine H., Sullivan, Timothy J., Wang, Meng, Shabalin, Andrey A., Shad, Saboor, Hariharan, Pushpa, He, Amy Z., Qi, Liqun, Lappalainen, Tuuli, Li, Xin, Carithers, Latarsha J., Mestichelli, Bernadette, Kashin, Seva, Li, Gen, Jasmine, Farzana, Juettemann, Thomas, Montgomery, Stephen B., Zhang, Hailei, Traino, Heather M., Mosavel, Maghboeba, Koester, Susan E., Lin, Shin, Jewell, Scott D., Johnson, Audra, and Wang, Li
- Abstract
Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease.
- Published
- 2017
- Full Text
- View/download PDF
39. CeO2 Nanoparticle-Decorated Co3O4 Microspheres for Selective Oxidation of Ethylbenzene with Molecular Oxygen under Solvent- and Additive-Free Conditions.
- Author
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Liu, Jiangyong, Meng, Ru, Jian, Panming, and Jian, Ruiqi
- Published
- 2020
- Full Text
- View/download PDF
40. Highly selective oxidation of styrene to benzaldehyde over a tailor-made cobalt oxide encapsulated zeolite catalyst
- Author
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Liu, Jiangyong, primary, Wang, Zihao, additional, Jian, Panming, additional, and Jian, Ruiqi, additional
- Published
- 2018
- Full Text
- View/download PDF
41. Silylated Pd/Ti-MCM-41 catalyst for the selective production of propylene oxide from the oxidation of propylene with cumene hydroperoxide
- Author
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Liu, Jiangyong, primary, Fang, Simeng, additional, Jian, Ruiqi, additional, Wu, Faming, additional, and Jian, Panming, additional
- Published
- 2018
- Full Text
- View/download PDF
42. Plasma Biomarkers for Colorectal Cancer Diagnosis Based on Metabolomics
- Author
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Wang, Maoqing, primary, Long, Zhiping, additional, Tian, Jingshen, additional, Chen, Songjie, additional, Sun, Hongru, additional, Jian, Ruiqi, additional, Zhou, Junde, additional, Xue, Weinan, additional, Yin, Huihui, additional, Xi, Chunyang, additional, Zhu, Lin, additional, Li, Shuo, additional, Zhang, Nannan, additional, Xie, Kun, additional, Yu, Yanming, additional, Gong, Chen, additional, Yang, Yihui, additional, Sun, Changhao, additional, Wang, Fan, additional, and Zhao, Yashuang, additional
- Published
- 2018
- Full Text
- View/download PDF
43. Amorphous TiO2–SiO2composites as selective heterogeneous catalysts for the oxidation of styrene to 1, 2-epoxyethylbenzene
- Author
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Liu, Jiangyong, Zhang, Yayun, Wang, Zihao, Deng, Yonghang, Jian, Panming, Wang, Lixia, and Jian, Ruiqi
- Abstract
A series of amorphous TiO2–SiO2composite oxides with different TiO2contents were prepared by a one-step co-precipitation process as catalysts for selective oxidation of styrene to 1, 2-epoxyethylbenzene with aqueous hydrogen peroxide in acetonitrile. The amorphous TiO2–SiO2composites are found to be much more catalytically active than the one with partially crystallized TiO2. The TiO2–SiO2composite with 40 wt% TiO2(TSCO-3) presents the best catalytic performance. Under the optimal reaction conditions, the styrene conversion can reach 61.0% with a high selectivity of 95.4% to 1, 2-epoxyethylbenzene upon 1 h reaction. Moreover, the TSCO-3 catalyst exhibits a good cycling stability. The excellent catalytic performance can be attributed to the numerous exposed active centers and the fast release of the product from the active centers.
- Published
- 2019
- Full Text
- View/download PDF
44. Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics
- Author
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Barbeira, Alvaro N., Dickinson, Scott P., Bonazzola, Rodrigo, Zheng, Jiamao, Wheeler, Heather E., Torres, Jason M., Torstenson, Eric S., Shah, Kaanan P., Garcia, Tzintzuni, Edwards, Todd L., Stahl, Eli A., Huckins, Laura M., Aguet, François, Ardlie, Kristin G., Cummings, Beryl B., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Karczewski, Konrad J., Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segrè, Ayellet V., Trowbridge, Casandra A., Tukiainen, Taru, Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Castel, Stephane E., Chen, Lin S., Chiang, Colby, Conrad, Donald F., Damani, Farhan N., Davis, Joe R., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frésard, Laure, Gamazon, Eric R., Garrido-Martín, Diego, Gewirtz, Ariel D. H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Jo, Brian, Kang, Eun Yong, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muñoz-Aguirre, Manuel, Ndungu, Anne W., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J., Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Strober, Benjamin J., Sul, Jae Hoon, Tsang, Emily K., Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zappala, Zachary, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Li, Jin Billy, Li, Qin, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Zhang, Rui, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, Zhu, Jingchun, Nicolae, Dan L., Cox, Nancy J., and Im, Hae Kyung
- Abstract
Scalable, integrative methods to understand mechanisms that link genetic variants with phenotypes are needed. Here we derive a mathematical expression to compute PrediXcan (a gene mapping approach) results using summary data (S-PrediXcan) and show its accuracy and general robustness to misspecified reference sets. We apply this framework to 44 GTEx tissues and 100+ phenotypes from GWAS and meta-analysis studies, creating a growing public catalog of associations that seeks to capture the effects of gene expression variation on human phenotypes. Replication in an independent cohort is shown. Most of the associations are tissue specific, suggesting context specificity of the trait etiology. Colocalized significant associations in unexpected tissues underscore the need for an agnostic scanning of multiple contexts to improve our ability to detect causal regulatory mechanisms. Monogenic disease genes are enriched among significant associations for related traits, suggesting that smaller alterations of these genes may cause a spectrum of milder phenotypes.
- Published
- 2018
- Full Text
- View/download PDF
45. Amorphous TiO2–SiO2 composites as selective heterogeneous catalysts for the oxidation of styrene to 1, 2-epoxyethylbenzene.
- Author
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Liu, Jiangyong, Zhang, Yayun, Wang, Zihao, Deng, Yonghang, Jian, Panming, Wang, Lixia, and Jian, Ruiqi
- Subjects
- *
HETEROGENEOUS catalysts , *STYRENE , *OXIDATION , *COPRECIPITATION (Chemistry) - Abstract
A series of amorphous TiO2–SiO2 composite oxides with different TiO2 contents were prepared by a one-step co-precipitation process as catalysts for selective oxidation of styrene to 1, 2-epoxyethylbenzene with aqueous hydrogen peroxide in acetonitrile. The amorphous TiO2–SiO2 composites are found to be much more catalytically active than the one with partially crystallized TiO2. The TiO2–SiO2 composite with 40 wt% TiO2 (TSCO-3) presents the best catalytic performance. Under the optimal reaction conditions, the styrene conversion can reach 61.0% with a high selectivity of 95.4% to 1, 2-epoxyethylbenzene upon 1 h reaction. Moreover, the TSCO-3 catalyst exhibits a good cycling stability. The excellent catalytic performance can be attributed to the numerous exposed active centers and the fast release of the product from the active centers. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
46. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease.
- Author
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Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Schüssler-Fiorenza Rose SM, Binh Tran TD, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas P, Zhou Y, Sodergren E, Weinstock GM, and Snyder MP
- Abstract
To understand dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune and clinical markers of microbiomes from four body sites in 86 participants over six years. We found that microbiome stability and individuality are body-site-specific and heavily influenced by the host. The stool and oral microbiome were more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. Also, we identified individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlated across body sites, suggesting systemic coordination influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals showed altered microbial stability and associations between microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease., Study Highlights: The stability of the human microbiome varies among individuals and body sites.Highly individualized microbial genera are more stable over time.At each of the four body sites, systematic interactions between the environment, the host and bacteria can be detected.Individuals with insulin resistance have lower microbiome stability, a more diversified skin microbiome, and significantly altered host-microbiome interactions.
- Published
- 2024
- Full Text
- View/download PDF
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