Changes in microbiome diversity following beta-lactam antibiotic treatment are associated with therapeutic versus subtherapeutic antibiotic exposure in cystic fibrosis

por Hahn, Andrea, Fanous, Hani, Jensen, Caroline, Chaney, Hollis, Sami, Iman, Perez, Geovanny F., Koumbourlis, Anastassios C., Louie, Stan, Bost, James E., van den Anker, John N., Freishtat, Robert J., Zemanick, Edith T., Crandall, Keith A.
Publicado 2019

Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression

por Bendall, Matthew L., de Mulder, Miguel, Iñiguez, Luis Pedro, Lecanda-Sánchez, Aarón, Pérez-Losada, Marcos, Ostrowski, Mario A., Jones, R. Brad, Mulder, Lubbertus C. F., Reyes-Terán, Gustavo, Crandall, Keith A., Ormsby, Christopher E., Nixon, Douglas F.
Publicado 2019

Insights into HIV-1 Transmission Dynamics Using Routinely Collected Data in the Mid-Atlantic United States

por Kassaye, Seble G., Grossman, Zehava, Vengurlekar, Priyanka, Chai, William, Wallace, Megan, Rhee, Soo-Yon, Meyer, William A., Kaufman, Harvey W., Castel, Amanda, Jordan, Jeanne, Crandall, Keith A., Kang, Alisa, Kumar, Princy, Katzenstein, David A., Shafer, Robert W., Maldarelli, Frank
Publicado 2022

Fish-T1K (Transcriptomes of 1,000 Fishes) Project: large-scale transcriptome data for fish evolution studies

por Sun, Ying, Huang, Yu, Li, Xiaofeng, Baldwin, Carole C., Zhou, Zhuocheng, Yan, Zhixiang, Crandall, Keith A., Zhang, Yong, Zhao, Xiaomeng, Wang, Min, Wong, Alex, Fang, Chao, Zhang, Xinhui, Huang, Hai, Lopez, Jose V., Kilfoyle, Kirk, Zhang, Yong, Ortí, Guillermo, Venkatesh, Byrappa, Shi, Qiong
Publicado 2016

Association of Early Aspirin Use With In-Hospital Mortality in Patients With Moderate COVID-19

por Chow, Jonathan H., Rahnavard, Ali, Gomberg-Maitland, Mardi, Chatterjee, Ranojoy, Patodi, Pranay, Yamane, David P., Levine, Andrea R., Davison, Danielle, Hawkins, Katrina, Jackson, Amanda M., Quintana, Megan T., Lankford, Allison S., Keneally, Ryan J., Al-Mashat, Mustafa, Fisher, Daniel, Williams, Jeffrey, Berger, Jeffrey S., Mazzeffi, Michael A., Crandall, Keith A.
Publicado 2022

Unlocking capacities of viral genomics for the COVID-19 pandemic response

por Knyazev, Sergey, Chhugani, Karishma, Sarwal, Varuni, Ayyala, Ram, Singh, Harman, Karthikeyan, Smruthi, Deshpande, Dhrithi, Comarova, Zoia, Lu, Angela, Porozov, Yuri, Wu, Aiping, Abedalthagafi, Malak S., Nagaraj, Shivashankar H., Smith, Adam L., Skums, Pavel, Ladner, Jason, Lam, Tommy Tsan-Yuk, Wu, Nicholas C., Zelikovsky, Alex, Knight, Rob, Crandall, Keith A., Mangul, Serghei
Publicado 2021

COVID-19 Disease Severity among People with HIV Infection or Solid Organ Transplant in the United States: A Nationally-representative, Multicenter, Observational Cohort Study

por Sun, Jing, Patel, Rena C., Zheng, Qulu, Madhira, Vithal, Olex, Amy L., Islam, Jessica Y., French, Evan, Chiang, Teresa Po-Yu, Akselrod, Hana, Moffitt, Richard, Alexander, G. Caleb, Andersen, Kathleen M., Vinson, Amanda J., Brown, Todd T., Chute, Christopher G., Crandall, Keith A., Franceschini, Nora, Mannon, Roslyn B., Kirk, Gregory D.
Publicado 2021

Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms

por Speiser, Daniel I, Pankey, M Sabrina, Zaharoff, Alexander K, Battelle, Barbara A, Bracken-Grissom, Heather D, Breinholt, Jesse W, Bybee, Seth M, Cronin, Thomas W, Garm, Anders, Lindgren, Annie R, Patel, Nipam H, Porter, Megan L, Protas, Meredith E, Rivera, Ajna S, Serb, Jeanne M, Zigler, Kirk S, Crandall, Keith A, Oakley, Todd H
Publicado 2014

Baseline human gut microbiota profile in healthy people and standard reporting template

por King, Charles H., Desai, Hiral, Sylvetsky, Allison C., LoTempio, Jonathan, Ayanyan, Shant, Carrie, Jill, Crandall, Keith A., Fochtman, Brian C., Gasparyan, Lusine, Gulzar, Naila, Howell, Paul, Issa, Najy, Krampis, Konstantinos, Mishra, Lopa, Morizono, Hiroki, Pisegna, Joseph R., Rao, Shuyun, Ren, Yao, Simonyan, Vahan, Smith, Krista, VedBrat, Sharanjit, Yao, Michael D., Mazumder, Raja
Publicado 2019

SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiome with inclusion of pathobionts

por Hoque, M. Nazmul, Sarkar, Md. Murshed Hasan, Rahman, M. Shaminur, Akter, Shahina, Banu, Tanjina Akhtar, Goswami, Barna, Jahan, Iffat, Hossain, M. Saddam, Shamsuzzaman, A. K. Mohammad, Nafisa, Tasnim, Molla, M. Maruf Ahmed, Yeasmin, Mahmuda, Ghosh, Asish Kumar, Osman, Eshrar, Alam, S. K. Saiful, Uzzaman, Mohammad Samir, Habib, Md Ahashan, Mahmud, Abu Sayeed Mohammad, Crandall, Keith A., Islam, Tofazzal, Khan, Md. Salim
Publicado 2021

Why sequence all eukaryotes?

por Blaxter, Mark, Archibald, John M., Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Di Palma, Federica, Durbin, Richard, Edwards, Scott V., Graves, Jennifer A. M., Hackett, Kevin J., Hall, Neil, Jarvis, Erich D., Johnson, Rebecca N., Karlsson, Elinor K., Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K. N., Lindblad-Toh, Kerstin, Lopez, Jose V., Moran, Nancy A., Robinson, Gene E., Ryder, Oliver A., Shapiro, Beth, Soltis, Pamela S., Warnow, Tandy, Zhang, Guojie, Lewin, Harris A.
Publicado 2022

The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View

por Xavier, Joao B., Young, Vincent B., Skufca, Joseph, Ginty, Fiona, Testerman, Traci, Pearson, Alexander T., Macklin, Paul, Mitchell, Amir, Shmulevich, Ilya, Xie, Lei, Caporaso, J. Gregory, Crandall, Keith A., Simone, Nicole L., Godoy-Vitorino, Filipa, Griffin, Timothy J., Whiteson, Katrine L., Gustafson, Heather H., Slade, Daniel J., Schmidt, Thomas M., Walther-Antonio, Marina R.S., Korem, Tal, Webb-Robertson, Bobbie-Jo M., Styczynski, Mark P., Johnson, W. Evan, Jobin, Christian, Ridlon, Jason M., Koh, Andrew Y., Yu, Michael, Kelly, Libusha, Wargo, Jennifer A.
Publicado 2020

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

por Mavian, Carla, Pond, Sergei Kosakovsky, Marini, Simone, Magalis, Brittany Rife, Vandamme, Anne-Mieke, Dellicour, Simon, Scarpino, Samuel V., Houldcroft, Charlotte, Villabona-Arenas, Julian, Paisie, Taylor K., Trovão, Nídia S., Boucher, Christina, Zhang, Yun, Scheuermann, Richard H., Gascuel, Olivier, Lam, Tommy Tsan-Yuk, Suchard, Marc A., Abecasis, Ana, Wilkinson, Eduan, de Oliveira, Tulio, Bento, Ana I., Schmidt, Heiko A., Martin, Darren, Hadfield, James, Faria, Nuno, Grubaugh, Nathan D., Neher, Richard A., Baele, Guy, Lemey, Philippe, Stadler, Tanja, Albert, Jan, Crandall, Keith A., Leitner, Thomas, Stamatakis, Alexandros, Prosperi, Mattia, Salemi, Marco
Publicado 2020

Multiple drivers of decline in the global status of freshwater crayfish (Decapoda: Astacidea)

por Richman, Nadia I., Böhm, Monika, Adams, Susan B., Alvarez, Fernando, Bergey, Elizabeth A., Bunn, John J. S., Burnham, Quinton, Cordeiro, Jay, Coughran, Jason, Crandall, Keith A., Dawkins, Kathryn L., DiStefano, Robert J., Doran, Niall E., Edsman, Lennart, Eversole, Arnold G., Füreder, Leopold, Furse, James M., Gherardi, Francesca, Hamr, Premek, Holdich, David M., Horwitz, Pierre, Johnston, Kerrylyn, Jones, Clive M., Jones, Julia P. G., Jones, Robert L., Jones, Thomas G., Kawai, Tadashi, Lawler, Susan, López-Mejía, Marilu, Miller, Rebecca M., Pedraza-Lara, Carlos, Reynolds, Julian D., Richardson, Alastair M. M., Schultz, Mark B., Schuster, Guenter A., Sibley, Peter J., Souty-Grosset, Catherine, Taylor, Christopher A., Thoma, Roger F., Walls, Jerry, Walsh, Todd S., Collen, Ben
Publicado 2015

Standards recommendations for the Earth BioGenome Project

por Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark L., Marques Bonet, Tomas, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, Lopez, Jose Victor, Myers, Eugene W., Pettersson, Olga Vinnere, Phillippy, Adam M., Poelchau, Monica F., Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Françoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen
Publicado 2022

Synergies between centralized and federated approaches to data quality: a report from the national COVID cohort collaborative

por Pfaff, Emily R, Girvin, Andrew T, Gabriel, Davera L, Kostka, Kristin, Morris, Michele, Palchuk, Matvey B, Lehmann, Harold P, Amor, Benjamin, Bissell, Mark, Bradwell, Katie R, Gold, Sigfried, Hong, Stephanie S, Loomba, Johanna, Manna, Amin, McMurry, Julie A, Niehaus, Emily, Qureshi, Nabeel, Walden, Anita, Zhang, Xiaohan Tanner, Zhu, Richard L, Moffitt, Richard A, Haendel, Melissa A, Chute, Christopher G, Adams, William G, Al-Shukri, Shaymaa, Anzalone, Alfred, Baghal, Ahmad, Bennett, Tellen D, Bernstam, Elmer V, Bernstam, Elmer V, Bissell, Mark M, Bush, Brian, Campion, Thomas R, Castro, Victor, Chang, Jack, Chaudhari, Deepa D, Chen, Wenjin, Chu, San, Cimino, James J, Crandall, Keith A, Crooks, Mark, Davies, Sara J Deakyne, DiPalazzo, John, Dorr, David, Eckrich, Dan, Eltinge, Sarah E, Fort, Daniel G, Golovko, George, Gupta, Snehil, Haendel, Melissa A, Hajagos, Janos G, Hanauer, David A, Harnett, Brett M, Horswell, Ronald, Huang, Nancy, Johnson, Steven G, Kahn, Michael, Khanipov, Kamil, Kieler, Curtis, Luzuriaga, Katherine Ruiz De, Maidlow, Sarah, Martinez, Ashley, Mathew, Jomol, McClay, James C, McMahan, Gabriel, Melancon, Brian, Meystre, Stephane, Miele, Lucio, Morizono, Hiroki, Pablo, Ray, Patel, Lav, Phuong, Jimmy, Popham, Daniel J, Pulgarin, Claudia, Santos, Carlos, Sarkar, Indra Neil, Sazo, Nancy, Setoguchi, Soko, Soby, Selvin, Surampalli, Sirisha, Suver, Christine, Vangala, Uma Maheswara Reddy, Visweswaran, Shyam, von Oehsen, James, Walters, Kellie M, Wiley, Laura, Williams, David A, Zai, Adrian
Publicado 2021

The Earth BioGenome Project 2020: Starting the clock

por Lewin, Harris A., Richards, Stephen, Lieberman Aiden, Erez, Allende, Miguel L., Archibald, John M., Bálint, Miklós, Barker, Katharine B., Baumgartner, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark L., Cai, Jing, Caperello, Nicolette D., Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu-Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., DiPalma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott V., Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Graves, Jennifer Marshall, Greely, Henry T., Grigoriev, Igor V., Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J. M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin-Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K. N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sophie, Mazet, Jonna A. K., Mazzoni, Camila J., Myers, Eugene W., O’Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene E., Roquet, Cristina, Ryder, Oliver A., Sabir, Jamal S. M., Shaffer, H. Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela S., Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne D., Zhang, Guojie
Publicado 2022