Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases

Authors: Kumbhari, Adarsh, Cheng, Thomas N.H., Ananthakrishnan, Ashwin N., Kochar, Bharati, Burke, Kristin E., Shannon, Kevin, Lau, Helena, Xavier, Ramnik J., Smillie, Christopher S.

Source: In Cell Host & Microbe 10 July 2024 32(7):1147-1162

Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states

Authors: Ma, Peijun, Amemiya, Haley M., He, Lorrie L., Gandhi, Shivam J., Nicol, Robert, Bhattacharyya, Roby P., Smillie, Christopher S., Hung, Deborah T.

Source: In Cell 16 February 2023 186(4):877-891

An Integrated Taxonomy for Monogenic Inflammatory Bowel Disease

Authors: Bolton, Chrissy, Smillie, Christopher S., Pandey, Sumeet, Elmentaite, Rasa, Wei, Gabrielle, Argmann, Carmen, Aschenbrenner, Dominik, James, Kylie R., McGovern, Dermot P.B., Macchi, Marina, Cho, Judy, Shouval, Dror S., Kammermeier, Jochen, Koletzko, Sibylle, Bagalopal, Krithika, Capitani, Melania, Cavounidis, Athena, Pires, Elisabete, Weidinger, Carl, McCullagh, James, Arkwright, Peter D., Haller, Wolfram, Siegmund, Britta, Peters, Lauren, Jostins, Luke, Travis, Simon P.L., Anderson, Carl A., Snapper, Scott, Klein, Christoph, Schadt, Eric, Zilbauer, Matthias, Xavier, Ramnik, Teichmann, Sarah, Muise, Aleixo M., Regev, Aviv, Uhlig, Holm H.

Source: Gastroenterology. 162(3):859-876

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100156073033.0x000001&indx=1&recIds=ETOCvdc_100156073033.0x000001

Spatially organized multicellular immune hubs in human colorectal cancer

Authors: Pelka, Karin, Hofree, Matan, Chen, Jonathan H., Sarkizova, Siranush, Pirl, Joshua D., Jorgji, Vjola, Bejnood, Alborz, Dionne, Danielle, Ge, William H., Xu, Katherine H., Chao, Sherry X., Zollinger, Daniel R., Lieb, David J., Reeves, Jason W., Fuhrman, Christopher A., Hoang, Margaret L., Delorey, Toni, Nguyen, Lan T., Waldman, Julia, Klapholz, Max, Wakiro, Isaac, Cohen, Ofir, Albers, Julian, Smillie, Christopher S., Cuoco, Michael S., Wu, Jingyi, Su, Mei-ju, Yeung, Jason, Vijaykumar, Brinda, Magnuson, Angela M., Asinovski, Natasha, Moll, Tabea, Goder-Reiser, Max N., Applebaum, Anise S., Brais, Lauren K., DelloStritto, Laura K., Denning, Sarah L., Phillips, Susannah T., Hill, Emma K., Meehan, Julia K., Frederick, Dennie T., Sharova, Tatyana, Kanodia, Abhay, Todres, Ellen Z., Jané-Valbuena, Judit, Biton, Moshe, Izar, Benjamin, Lambden, Conner D., Clancy, Thomas E., Bleday, Ronald, Melnitchouk, Nelya, Irani, Jennifer, Kunitake, Hiroko, Berger, David L., Srivastava, Amitabh, Hornick, Jason L., Ogino, Shuji, Rotem, Asaf, Vigneau, Sébastien, Johnson, Bruce E., Corcoran, Ryan B., Sharpe, Arlene H., Kuchroo, Vijay K., Ng, Kimmie, Giannakis, Marios, Nieman, Linda T., Boland, Genevieve M., Aguirre, Andrew J., Anderson, Ana C., Rozenblatt-Rosen, Orit, Regev, Aviv, Hacohen, Nir

Source: In Cell 2 September 2021 184(18):4734-4752

Longitudinal proteomic analysis of severe COVID-19 reveals survival-associated signatures, tissue-specific cell death, and cell-cell interactions

Authors: Filbin, Michael R., Mehta, Arnav, Schneider, Alexis M., Kays, Kyle R., Guess, Jamey R., Gentili, Matteo, Fenyves, Bánk G., Charland, Nicole C., Gonye, Anna L.K., Gushterova, Irena, Khanna, Hargun K., LaSalle, Thomas J., Lavin-Parsons, Kendall M., Lilley, Brendan M., Lodenstein, Carl L., Manakongtreecheep, Kasidet, Margolin, Justin D., McKaig, Brenna N., Rojas-Lopez, Maricarmen, Russo, Brian C., Sharma, Nihaarika, Tantivit, Jessica, Thomas, Molly F., Gerszten, Robert E., Heimberg, Graham S., Hoover, Paul J., Lieb, David J., Lin, Brian, Ngo, Debby, Pelka, Karin, Reyes, Miguel, Smillie, Christopher S., Waghray, Avinash, Wood, Thomas E., Zajac, Amanda S., Jennings, Lori L., Grundberg, Ida, Bhattacharyya, Roby P., Parry, Blair Alden, Villani, Alexandra-Chloé, Sade-Feldman, Moshe, Hacohen, Nir, Goldberg, Marcia B.

Source: In Cell Reports Medicine 18 May 2021 2(5)

The Human and Mouse Enteric Nervous System at Single-Cell Resolution

Authors: Drokhlyansky, Eugene, Smillie, Christopher S., Van Wittenberghe, Nicholas, Ericsson, Maria, Griffin, Gabriel K., Eraslan, Gokcen, Dionne, Danielle, Cuoco, Michael S., Goder-Reiser, Max N., Sharova, Tatyana, Kuksenko, Olena, Aguirre, Andrew J., Boland, Genevieve M., Graham, Daniel, Rozenblatt-Rosen, Orit, Xavier, Ramnik J., Regev, Aviv

Source: In Cell 17 September 2020 182(6):1606-1622

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

Authors: Smillie, Christopher S., Biton, Moshe, Ordovas-Montanes, Jose, Sullivan, Keri M., Burgin, Grace, Graham, Daniel B., Herbst, Rebecca H., Rogel, Noga, Slyper, Michal, Waldman, Julia, Sud, Malika, Andrews, Elizabeth, Velonias, Gabriella, Haber, Adam L., Jagadeesh, Karthik, Vickovic, Sanja, Yao, Junmei, Stevens, Christine, Dionne, Danielle, Nguyen, Lan T., Villani, Alexandra-Chloé, Hofree, Matan, Creasey, Elizabeth A., Huang, Hailiang, Rozenblatt-Rosen, Orit, Garber, John J., Khalili, Hamed, Desch, A. Nicole, Daly, Mark J., Ananthakrishnan, Ashwin N., Shalek, Alex K., Xavier, Ramnik J., Regev, Aviv

Source: In Cell 25 July 2019 178(3):714-730

Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation

Authors: Smillie, Christopher S., Sauk, Jenny, Gevers, Dirk, Friedman, Jonathan, Sung, Jaeyun, Youngster, Ilan, Hohmann, Elizabeth L., Staley, Christopher, Khoruts, Alexander, Sadowsky, Michael J., Allegretti, Jessica R., Smith, Mark B., Xavier, Ramnik J., Alm, Eric J.

Source: In Cell Host & Microbe 14 February 2018 23(2):229-240

Unraveling the diversity and functions of tissue-resident plasma cells

Authors: Tellier, Julie, Tarasova, Ilariya, Nie, Junli, Smillie, Christopher S., Fedele, Pasquale L., Cao, Wang H. J., Groom, Joanna R., Belz, Gabrielle T., Bhattacharya, Deepta, Smyth, Gordon K., Nutt, Stephen L.

Source: Nature Immunology; February 2024, Vol. 25 Issue: 2 p330-342, 13p

Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases

Authors: Weeks, Elle M., Ulirsch, Jacob C., Cheng, Nathan Y., Trippe, Brian L., Fine, Rebecca S., Miao, Jenkai, Patwardhan, Tejal A., Kanai, Masahiro, Nasser, Joseph, Fulco, Charles P., Tashman, Katherine C., Aguet, Francois, Li, Taibo, Ordovas-Montanes, Jose, Smillie, Christopher S., Biton, Moshe, Shalek, Alex K., Ananthakrishnan, Ashwin N., Xavier, Ramnik J., Regev, Aviv, Gupta, Rajat M., Lage, Kasper, Ardlie, Kristin G., Hirschhorn, Joel N., Lander, Eric S., Engreitz, Jesse M., Finucane, Hilary K.

Source: Nature Genetics; August 2023, Vol. 55 Issue: 8 p1267-1276, 10p

Genome and sequence determinants governing the expression of horizontally acquired DNA in bacteria.

Authors: Gomes, Antonio L. C., Johns, Nathan I., Yang, Anthony, Velez-Cortes, Florencia, Smillie, Christopher S., Smith, Mark B., Alm, Eric J., Wang, Harris H.

Source: ISME Journal: Multidisciplinary Journal of Microbial Ecology; Sep2020, Vol. 14 Issue 9, p2347-2357, 11p

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Longitudinal proteomic analysis of plasma from patients with severe COVID-19 reveal patient survival-associated signatures, tissue-specific cell death, and cell-cell interactions

Authors: Filbin, Michael R., Mehta, Arnav, Schneider, Alexis M., Kays, Kyle R., Guess, Jamey R., Gentili, Matteo, Fenyves, Bánk G., Charland, Nicole C., Gonye, Anna L.K., Gushterova, Irena, Khanna, Hargun K., LaSalle, Thomas J., Lavin-Parsons, Kendall M., Lilley, Brendan M., Lodenstein, Carl L., Manakongtreecheep, Kasidet, Margolin, Justin D., McKaig, Brenna N., Rojas-Lopez, Maricarmen, Russo, Brian C., Sharma, Nihaarika, Tantivit, Jessica, Thomas, Molly F., Gerszten, Robert E., Heimberg, Graham S., Hoover, Paul J., Lieb, David J., Lin, Brian, Ngo, Debby, Pelka, Karin, Reyes, Miguel, Smillie, Christopher S., Waghray, Avinash, Wood, Thomas E., Zajac, Amanda S., Jennings, Lori L., Grundberg, Ida, Bhattacharyya, Roby P., Parry, Blair Alden, Villani, Alexandra-Chloé, Sade-Feldman, Moshe, Hacohen, Nir, Goldberg, Marcia B.

Source: Cell Reports Medicine; 20210101, Issue: Preprints