Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease

Authors: 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., Snyder, Michael P.

Source: In Cell Host & Microbe 10 April 2024 32(4):506-526

Microbial glutamate metabolism predicts intravenous cocaine self-administration in diversity outbred mice

Authors: Binh Tran, Thi Dong, Nguyen, Hoan, Sodergren, Erica, Addiction, Center for Systems Neurogenetics of, Dickson, Price E., Wright, Susan N., Philip, Vivek M., Weinstock, George M., Chesler, Elissa J., Zhou, Yanjiao, Bubier, Jason A.

Source: In Neuropharmacology 15 March 2023 226

Association of gut microbiota and environment in children with AD, comparison of three cohorts of children

Authors: Jungles, Kylie, Tran, Thi Dong Binh, Botha, Maresa, Rasmussen, Heather E., Teixeira‐Reis, Victoria, Sodergren, Erica, Gray, Claudia, Lunjani, Nonhlanhla, Hlela, Carol, Basera, Wisdom, Hobane, Lelani, Watkins, Alexandra, Engen, Phillip, Mankahla, Avumile, Gaunt, Ben, Facey‐Thomas, Heidi, Landay, Alan, Weinstock, George M., Keshavarzian, Ali, Levin, Michael E., Mahdavinia, Mahboobeh

Source: Clinical & experimental allergy. 52(3):447-450

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Cluster analysis of genome-wide expression differences in disease-unaffected ileal mucosa in inflammatory bowel diseases

Authors: Zhang, Tianyi, DeSimone, Robert A., Chen, Hongyan, Hamm, Christina M, Yuan, Jeffrey, Gong, Qing Qing, Hunt, Steven R., Dassopoulos, Themistocles, Newberry, Rodney D., Frank, Daniel N., Robertson, Charles E., Pace, Norman R., Sodergren, Erica, Weinstock, George, Jiao, Xiangmin, Zhu, Wei, Li, Ellen

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Microbiome Signatures Associated With Steatohepatitis and Moderate to Severe Fibrosis in Children With Nonalcoholic Fatty Liver Disease

Authors: Schwimmer, Jeffrey B., Johnson, Jethro S., Angeles, Jorge E., Behling, Cynthia, Belt, Patricia H., Borecki, Ingrid, Bross, Craig, Durelle, Janis, Goyal, Nidhi P., Hamilton, Gavin, Holtz, Mary L., Lavine, Joel E., Mitreva, Makedonka, Newton, Kimberly P., Pan, Amy, Simpson, Pippa M., Sirlin, Claude B., Sodergren, Erica, Tyagi, Rahul, Yates, Katherine P., Weinstock, George M., Salzman, Nita H.

Source: In Gastroenterology October 2019 157(4):1109-1122

Symbiotic organs shaped by distinct modes of genome evolution in cephalopods

Authors: Belcaid, Mahdi, Casaburi, Giorgio, McAnulty, Sarah J., Schmidbaur, Hannah, Suria, Andrea M., Moriano-Gutierrez, Silvia, Pankey, M. Sabrina, Oakley, Todd H., Kremer, Natacha, Koch, Eric J., Collins, Andrew J., Nguyen, Hoan, Lek, Sai, Goncharenko-Foster, Irina, Minx, Patrick, Sodergren, Erica, Weinstock, George, Rokhsar, Daniel S., McFall-Ngai, Margaret, Simakov, Oleg, Foster, Jamie S., Nyholm, Spencer V.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2019 Feb . 116(8), 3030-3035.

Access URL: https://www.jstor.org/stable/26671946

Diet during Pregnancy and Infancy and the Infant Intestinal Microbiome

Authors: Savage, Jessica H., Lee-Sarwar, Kathleen A., Sordillo, Joanne E., Lange, Nancy E., Zhou, Yanjiao, O'Connor, George T., Sandel, Megan, Bacharier, Leonard B., Zeiger, Robert, Sodergren, Erica, Weinstock, George M., Gold, Diane R., Weiss, Scott T., Litonjua, Augusto A.

Source: In The Journal of Pediatrics December 2018 203:47-54

Integrative Personal Omics Profiles during Periods of Weight Gain and Loss

Authors: Piening, Brian D., Zhou, Wenyu, Contrepois, Kévin, Röst, Hannes, Gu Urban, Gucci Jijuan, Mishra, Tejaswini, Hanson, Blake M., Bautista, Eddy J., Leopold, Shana, Yeh, Christine Y., Spakowicz, Daniel, Banerjee, Imon, Chen, Cynthia, Kukurba, Kimberly, Perelman, Dalia, Craig, Colleen, Colbert, Elizabeth, Salins, Denis, Rego, Shannon, Lee, Sunjae, Zhang, Cheng, Wheeler, Jessica, Sailani, M. Reza, Liang, Liang, Abbott, Charles, Gerstein, Mark, Mardinoglu, Adil, Smith, Ulf, Rubin, Daniel L., Pitteri, Sharon, Sodergren, Erica, McLaughlin, Tracey L., Weinstock, George M., Snyder, Michael P.

Source: In Cell Systems 28 February 2018 6(2):157-170

A longitudinal big data approach for precision health

Authors: Schüssler-Fiorenza Rose, Sophia, Contrepois, Kévin, Moneghetti, Kegan, Zhou, Wenyu, Mishra, Tejaswini, Mataraso, Samson, Dagan-Rosenfeld, Orit, Ganz, Ariel, Dunn, Jessilyn, Hornburg, Daniel, Rego, Shannon, Perelman, Dalia, Ahadi, Sara, Sailani, M., Zhou, Yanjiao, Leopold, Shana, Chen, Jieming, Ashland, Melanie, Christle, Jeffrey, Avina, Monika, Limcaoco, Patricia, Ruiz, Camilo, Tan, Marilyn, Butte, Atul, Weinstock, George, Slavich, George, Sodergren, Erica, McLaughlin, Tracey, Haddad, Francois, Snyder, Michael

Source: Nature medicine. 25(5):792-804

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Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

Authors: Johnson, Jethro, Spakowicz, Daniel, Hong, Bo-Young, Petersen, Lauren, Demkowicz, Patrick, Chen, Lei, Leopold, Shana, Hanson, Blake, Agresta, Hanako, Gerstein, Mark, Sodergren, Erica, Weinstock, George

Source: Nature communications. 10(1):1-11

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Longitudinal multi-omics of host–microbe dynamics in prediabetes

Authors: Zhou, Wenyu, Sailani, M., Contrepois, Kévin, Zhou, Yanjiao, Ahadi, Sara, Leopold, Shana, Zhang, Martin, Rao, Varsha, Avina, Monika, Mishra, Tejaswini, Johnson, Jethro, Lee-McMullen, Brittany, Chen, Songjie, Metwally, Ahmed, Tran, Thi Dong Binh, Nguyen, Hoan, Zhou, Xin, Albright, Brandon, Hong, Bo-Young, Petersen, Lauren, Bautista, Eddy, Hanson, Blake, Chen, Lei, Spakowicz, Daniel, Bahmani, Amir, Salins, Denis, Leopold, Benjamin, Ashland, Melanie, Dagan-Rosenfeld, Orit, Rego, Shannon, Limcaoco, Patricia, Colbert, Elizabeth, Allister, Candice, Perelman, Dalia, Craig, Colleen, Wei, Eric, Chaib, Hassan, Hornburg, Daniel, Dunn, Jessilyn, Liang, Liang, Rose, Sophia, Kukurba, Kim, Piening, Brian, Rost, Hannes, Tse, David, McLaughlin, Tracey, Sodergren, Erica, Weinstock, George, Snyder, Michael

Source: Nature. 569(7758):663-671

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An Analysis of the Epidemic of Klebsiella pneumoniae Carbapenemase-Producing K. pneumoniae : Convergence of Two Evolutionary Mechanisms Creates the “Perfect Storm”

Authors: Rojas, Laura J., Weinstock, George M., De La Cadena, Elsa, Diaz, Lorena, Rios, Rafael, Hanson, Blake M., Brown, Joseph S., Vats, Purva, Phillips, Daniel S., Nguyen, Hoan, Hujer, Kristine M., Correa, Adriana, Adams, Mark D., Perez, Federico, Sodergren, Erica, Narechania, Apurva, Planet, Paul J., Villegas, Maria V., Bonomo, Robert. A., Arias, Cesar A.

Source: The Journal of Infectious Diseases, 2018 Jan 01. 217(1), 82-92.

Access URL: https://www.jstor.org/stable/26494557

Comparison of the Genome of the Oral Pathogen Treponema denticola with Other Spirochete Genomes

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Source: Proceedings of the National Academy of Sciences of the United States of America, 2004 Apr . 101(15), 5646-5651.

Access URL: https://www.jstor.org/stable/3371674

Complete Genome Sequence of Treponema pallidum, the Syphilis Spirochete

Authors: Fraser, Claire M., Norris, Steven J., Weinstock, George M., White, Owen, Sutton, Granger G., Dodson, Robert, Gwinn, Michelle, Hickey, Erin K., Clayton, Rebecca, Ketchum, Karen A., Sodergren, Erica, Hardham, John M., McLeod, Michael P., Salzberg, Steven, Peterson, Jeremy, Khalak, Hanif, Richardson, Delwood, Howell, Jerrilyn K., Chidambaram, Monjula, Utterback, Teresa, McDonald, Lisa, Artiach, Patricia, Bowman, Cheryl, Cotton, Matthew D., Fujii, Claire, Garland, Stacey, Hatch, Bonnie, Horst, Kurt, Roberts, Kevin, Sandusky, Mina, Weidman, Janice, Smith, Hamilton O., Venter, J. Craig

Source: Science, 1998 Jul . 281(5375), 375-388.

Access URL: https://www.jstor.org/stable/2896320

A prospective microbiome‐wide association study of food sensitization and food allergy in early childhood

Authors: Savage, Jessica H., Lee‐Sarwar, Kathleen A., Sordillo, Joanne, Bunyavanich, Supinda, Zhou, Yanjiao, O'Connor, George, Sandel, Megan, Bacharier, Leonard B., Zeiger, Robert, Sodergren, Erica, Weinstock, George M., Gold, Diane R., Weiss, Scott T., Litonjua, Augusto A.

Source: Allergy. 73(1):145-152

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Gut bacteria dysbiosis and necrotising enterocolitis in very low birthweight infants: a prospective case-control study

Authors: Warner, Barbara B, Deych, Elena, Zhou, Yanjiao, Hall-Moore, Carla, Weinstock, George M, Sodergren, Erica, Shaikh, Nurmohammad, Hoffmann, Julie A, Linneman, Laura A, Hamvas, Aaron, Khanna, Geetika, Rouggly-Nickless, Lucina C, Ndao, I Malick, Shands, Berkley A, Escobedo, Marilyn, Sullivan, Janice E, Radmacher, Paula G, Shannon, William D, Tarr, Phillip I

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Rapid replacement by non-vaccine pneumococcal serotypes may mitigate the impact of the pneumococcal conjugate vaccine on nasopharyngeal bacterial ecology

Authors: Kwambana-Adams, Brenda, Hanson, Blake, Worwui, Archibald, Agbla, Schadrac, Foster-Nyarko, Ebenezer, Ceesay, Fatima, Ebruke, Chinelo, Egere, Uzochukwu, Zhou, Yanjiao, Ndukum, Maze, Sodergren, Erica, Barer, Michael, Adegbola, Richard, Weinstock, George, Antonio, Martin

Source: Scientific reports. 7(1):1-11

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Community characteristics of the gut microbiomes of competitive cyclists

Authors: Petersen, Lauren, Bautista, Eddy, Nguyen, Hoan, Hanson, Blake, Chen, Lei, Lek, Sai, Sodergren, Erica, Weinstock, George

Source: Microbiome. 5(1):1-13

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100140032747.0x000001&indx=1&recIds=ETOCvdc_100140032747.0x000001

Patterned progression of bacterial populations in the premature infant gut

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Source: Proceedings of the National Academy of Sciences of the United States of America, 2014 Aug . 111(34), 12522-12527.

Access URL: https://www.jstor.org/stable/43043163

Propionibacterium acnes Strain Populations in the Human Skin Microbiome Associated with Acne

Authors: Fitz-Gibbon, Sorel ^{1, 8}, Tomida, Shuta ^{1, 8}, Chiu, Bor-Han ¹, Nguyen, Lin ¹, Du, Christine ^{1, 2}, Liu, Minghsun ³, Elashoff, David ², Erfe, Marie C. ⁴, Loncaric, Anya ², Kim, Jenny ^{2, 5}, Modlin, Robert L. ^{2, 3}, Miller, Jeff F. ³, Sodergren, Erica ⁶, Craft, Noah ⁴, Weinstock, George M. ⁶, Li, Huiying ^{1, 7, *}

Source: In Journal of Investigative Dermatology September 2013 133(9):2152-2160