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39 results on '"Butler, Daniel J."'

1. The Space Omics and Medical Atlas (SOMA) and international astronaut biobank

Author

Overbey, Eliah G., Kim, JangKeun, Tierney, Braden T., Park, Jiwoon, Houerbi, Nadia, Lucaci, Alexander G., Garcia Medina, Sebastian, Damle, Namita, Najjar, Deena, Grigorev, Kirill, Afshin, Evan E., Ryon, Krista A., Sienkiewicz, Karolina, Patras, Laura, Klotz, Remi, Ortiz, Veronica, MacKay, Matthew, Schweickart, Annalise, Chin, Christopher R., Sierra, Maria A., Valenzuela, Matias F., Dantas, Ezequiel, Nelson, Theodore M., Cekanaviciute, Egle, Deards, Gabriel, Foox, Jonathan, Narayanan, S. Anand, Schmidt, Caleb M., Schmidt, Michael A., Schmidt, Julian C., Mullane, Sean, Tigchelaar, Seth Stravers, Levitte, Steven, Westover, Craig, Bhattacharya, Chandrima, Lucotti, Serena, Wain Hirschberg, Jeremy, Proszynski, Jacqueline, Burke, Marissa, Kleinman, Ashley S., Butler, Daniel J., Loy, Conor, Mzava, Omary, Lenz, Joan, Paul, Doru, Mozsary, Christopher, Sanders, Lauren M., Taylor, Lynn E., Patel, Chintan O., Khan, Sharib A., Suhail Mohamad, Mir, Byhaqui, Syed Gufran Ahmad, Aslam, Burhan, Gajadhar, Aaron S., Williamson, Lucy, Tandel, Purvi, Yang, Qiu, Chu, Jessica, Benz, Ryan W., Siddiqui, Asim, Hornburg, Daniel, Blease, Kelly, Moreno, Juan, Boddicker, Andrew, Zhao, Junhua, Lajoie, Bryan, Scott, Ryan T., Gilbert, Rachel R., Lai Polo, San-huei, Altomare, Andrew, Kruglyak, Semyon, Levy, Shawn, Ariyapala, Ishara, Beer, Joanne, Zhang, Bingqing, Hudson, Briana M., Rininger, Aric, Church, Sarah E., Beheshti, Afshin, Church, George M., Smith, Scott M., Crucian, Brian E., Zwart, Sara R., Matei, Irina, Lyden, David C., Garrett-Bakelman, Francine, Krumsiek, Jan, Chen, Qiuying, Miller, Dawson, Shuga, Joe, Williams, Stephen, Nemec, Corey, Trudel, Guy, Pelchat, Martin, Laneuville, Odette, De Vlaminck, Iwijn, Gross, Steven, Bolton, Kelly L., Bailey, Susan M., Granstein, Richard, Furman, David, Melnick, Ari M., Costes, Sylvain V., Shirah, Bader, Yu, Min, Menon, Anil S., Mateus, Jaime, Meydan, Cem, and Mason, Christopher E.

Published
2024
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2. Epsilon toxin-producing Clostridium perfringens colonize the MS gut and epsilon toxin overcomes immune privilege

Author

Ma, Yinghua, Sannino, David, Linden, Jennifer R, Haigh, Sylvia, Zhao, Baohua, Grigg, John B, Zumbo, Paul, Dündar, Friederike, Butler, Daniel J, Profaci, Caterina P, Telesford, Kiel M, Winokur, Paige N, Rumah, Kareem R, Gauthier, Susan A, Fischetti, Vincent A, McClane, Bruce A, Uzal, Francisco A, Zexter, Lily, Mazzucco, Michael, Rudick, Richard, Danko, David, Balmuth, Evan, Nealon, Nancy, Perumal, Jai, Kaunzner, Ulrike W, Brito, Ilana L, Chen, Zhengming, Xiang, Jenny Z, Betel, Doron, Daneman, Richard, Sonnenberg, Gregory F, Mason, Christopher E, and Vartanian, Timothy

Subjects
Multiple Sclerosis, Neurosciences, Brain Disorders, Neurodegenerative, Autoimmune Disease, 2.1 Biological and endogenous factors, Aetiology, Neurological, Animals, Humans, Clostridium perfringens, Gastrointestinal Microbiome, Immune Privilege, Lymphocytes, Encephalomyelitis, Autoimmune, Experimental, Autoimmunity, Demyelinating disorders, Microbiology, Multiple sclerosis, Toxins/drugs/xenobiotics, Medical and Health Sciences, Immunology
Abstract

Multiple sclerosis (MS) is a complex disease of the CNS thought to require an environmental trigger. Gut dysbiosis is common in MS, but specific causative species are unknown. To address this knowledge gap, we used sensitive and quantitative PCR detection to show that people with MS were more likely to harbor and show a greater abundance of epsilon toxin-producing (ETX-producing) strains of C. perfringens within their gut microbiomes compared with individuals who are healthy controls (HCs). Isolates derived from patients with MS produced functional ETX and had a genetic architecture typical of highly conjugative plasmids. In the active immunization model of experimental autoimmune encephalomyelitis (EAE), where pertussis toxin (PTX) is used to overcome CNS immune privilege, ETX can substitute for PTX. In contrast to PTX-induced EAE, where inflammatory demyelination is largely restricted to the spinal cord, ETX-induced EAE caused demyelination in the corpus callosum, thalamus, cerebellum, brainstem, and spinal cord, more akin to the neuroanatomical lesion distribution seen in MS. CNS endothelial cell transcriptional profiles revealed ETX-induced genes that are known to play a role in overcoming CNS immune privilege. Together, these findings suggest that ETX-producing C. perfringens strains are biologically plausible pathogens in MS that trigger inflammatory demyelination in the context of circulating myelin autoreactive lymphocytes.

Published
2023

4. A global metagenomic map of urban microbiomes and antimicrobial resistance.

Author

Danko, David, Bezdan, Daniela, Afshin, Evan E, Ahsanuddin, Sofia, Bhattacharya, Chandrima, Butler, Daniel J, Chng, Kern Rei, Donnellan, Daisy, Hecht, Jochen, Jackson, Katelyn, Kuchin, Katerina, Karasikov, Mikhail, Lyons, Abigail, Mak, Lauren, Meleshko, Dmitry, Mustafa, Harun, Mutai, Beth, Neches, Russell Y, Ng, Amanda, Nikolayeva, Olga, Nikolayeva, Tatyana, Png, Eileen, Ryon, Krista A, Sanchez, Jorge L, Shaaban, Heba, Sierra, Maria A, Thomas, Dominique, Young, Ben, Abudayyeh, Omar O, Alicea, Josue, Bhattacharyya, Malay, Blekhman, Ran, Castro-Nallar, Eduardo, Cañas, Ana M, Chatziefthimiou, Aspassia D, Crawford, Robert W, De Filippis, Francesca, Deng, Youping, Desnues, Christelle, Dias-Neto, Emmanuel, Dybwad, Marius, Elhaik, Eran, Ercolini, Danilo, Frolova, Alina, Gankin, Dennis, Gootenberg, Jonathan S, Graf, Alexandra B, Green, David C, Hajirasouliha, Iman, Hastings, Jaden JA, Hernandez, Mark, Iraola, Gregorio, Jang, Soojin, Kahles, Andre, Kelly, Frank J, Knights, Kaymisha, Kyrpides, Nikos C, Łabaj, Paweł P, Lee, Patrick KH, Leung, Marcus HY, Ljungdahl, Per O, Mason-Buck, Gabriella, McGrath, Ken, Meydan, Cem, Mongodin, Emmanuel F, Moraes, Milton Ozorio, Nagarajan, Niranjan, Nieto-Caballero, Marina, Noushmehr, Houtan, Oliveira, Manuela, Ossowski, Stephan, Osuolale, Olayinka O, Özcan, Orhan, Paez-Espino, David, Rascovan, Nicolás, Richard, Hugues, Rätsch, Gunnar, Schriml, Lynn M, Semmler, Torsten, Sezerman, Osman U, Shi, Leming, Shi, Tieliu, Siam, Rania, Song, Le Huu, Suzuki, Haruo, Court, Denise Syndercombe, Tighe, Scott W, Tong, Xinzhao, Udekwu, Klas I, Ugalde, Juan A, Valentine, Brandon, Vassilev, Dimitar I, Vayndorf, Elena M, Velavan, Thirumalaisamy P, Wu, Jun, Zambrano, María M, Zhu, Jifeng, Zhu, Sibo, Mason, Christopher E, and International MetaSUB Consortium

Subjects
International MetaSUB Consortium, AMR, BGC, NGS, antimicrobial resistance, built Environment, de novo assembly, global health, metagenome, microbiome, shotgun sequencing, Antimicrobial Resistance, Biotechnology, Human Genome, Genetics, Infection, Developmental Biology, Biological Sciences, Medical and Health Sciences
Abstract

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.

Published
2021

5. A global metagenomic map of urban microbiomes and antimicrobial resistance

Author

Abdullah, Natasha, Abraao, Marcos, Adel, Ait-hamlat, Afaq, Muhammad, Al-Quaddoomi, Faisal S., Alam, Ireen, Albuquerque, Gabriela E., Alexiev, Alex, Ali, Kalyn, Alvarado-Arnez, Lucia E., Aly, Sarh, Amachee, Jennifer, Amorim, Maria G., Ampadu, Majelia, Amran, Muhammad Al-Fath, An, Nala, Andrew, Watson, Andrianjakarivony, Harilanto, Angelov, Michael, Antelo, Verónica, Aquino, Catharine, Aranguren, Álvaro, Araujo, Luiza F., Vasquez Arevalo, Hitler Francois, Arevalo, Jenny, Arnan, Carme, Alvarado Arnez, Lucia Elena, Arredondo, Fernanda, Arthur, Matthew, Asenjo, Freddy, Aung, Thomas Saw, Auvinet, Juliette, Aventin, Nuria, Ayaz, Sadaf, Baburyan, Silva, Bakere, Abd-Manaaf, Bakhl, Katrin, Bartelli, Thais F., Batdelger, Erdenetsetseg, Baudon, François, Becher, Kevin, Bello, Carla, Benchouaia, Médine, Benisty, Hannah, Benoiston, Anne-Sophie, Benson, Joseph, Benítez, Diego, Bernardes, Juliana, Bertrand, Denis, Beurmann, Silvia, Bitard-Feildel, Tristan, Bittner, Lucie, Black, Christina, Blanc, Guillaume, Blyther, Brittany, Bode, Toni, Boeri, Julia, Boldgiv, Bazartseren, Bolzli, Kevin, Bordigoni, Alexia, Borrelli, Ciro, Bouchard, Sonia, Bouly, Jean-Pierre, Boyd, Alicia, Branco, Gabriela P., Breschi, Alessandra, Brindefalk, Björn, Brion, Christian, Briones, Alan, Buczansla, Paulina, Burke, Catherine M., Burrell, Aszia, Butova, Alina, Buttar, Irvind, Bynoe, Jalia, Bönigk, Sven, Bøifot, Kari O., Caballero, Hiram, Cai, Xiao Wen, Calderon, Dayana, Cantillo, Angela, Carbajo, Miguel, Carbone, Alessandra, Cardenas, Anais, Carrillo, Katerine, Casalot, Laurie, Castro, Sofia, Castro, Ana V., Castro, Astred, Castro, Ana Valeria B., Cawthorne, Simone, Cedillo, Jonathan, Chaker, Salama, Chalangal, Jasna, Chan, Allison, Chasapi, Anastasia I., Chatziefthimiou, Starr, Chaudhuri, Sreya Ray, Chavan, Akash Keluth, Chavez, Francisco, Chem, Gregory, Chen, Xiaoqing, Chen, Michelle, Chen, Jenn-Wei, Chernomoretz, Ariel, Chettouh, Allaeddine, Cheung, Daisy, Chicas, Diana, Chiu, Shirley, Choudhry, Hira, Chrispin, Carl, Ciaramella, Kianna, Cifuentes, Erika, Cohen, Jake, Coil, David A., Collin, Sylvie, Conger, Colleen, Conte, Romain, Corsi, Flavia, Cossio, Cecilia N., Costa, Ana F., Cuebas, Delisia, D’Alessandro, Bruno, Dahlhausen, Katherine E., Darling, Aaron E., Das, Pujita, Davenport, Lucinda B., David, Laurent, Davidson, Natalie R., Dayama, Gargi, Delmas, Stéphane, Deng, Chris K., Dequeker, Chloé, Desert, Alexandre, Devi, Monika, Dezem, Felipe S., Dias, Clara N., Donahoe, Timothy Ryan, Dorado, Sonia, Dorsey, LaShonda, Dotsenko, Valeriia, Du, Steven, Dutan, Alexandra, Eady, Naya, Eisen, Jonathan A., Elaskandrany, Miar, Epping, Lennard, Escalera-Antezana, Juan P., Ettinger, Cassie L., Faiz, Iqra, Fan, Luice, Farhat, Nadine, Faure, Emile, Fauzi, Fazlina, Feigin, Charlie, Felice, Skye, Ferreira, Laís Pereira, Figueroa, Gabriel, Fleiss, Aubin, Flores, Denisse, Velasco Flores, Jhovana L., Fonseca, Marcos A.S., Foox, Jonathan, Forero, Juan Carlos, Francis, Aaishah, French, Kelly, Fresia, Pablo, Friedman, Jacob, Fuentes, Jaime J., Galipon, Josephine, Garcia, Mathilde, Garcia, Laura, García, Catalina, Geiger, Annie, Gerner, Samuel M., Ghose, Sonia L., Giang, Dao Phuong, Giménez, Matías, Giovannelli, Donato, Githae, Dedan, Gkotzis, Spyridon, Godoy, Liliana, Goldman, Samantha, Gonnet, Gaston H., Gonzalez, Juana, Gonzalez, Andrea, Gonzalez-Poblete, Camila, Gray, Andrew, Gregory, Tranette, Greselle, Charlotte, Guasco, Sophie, Guerra, Juan, Gurianova, Nika, Haehr, Wolfgang, Halary, Sebastien, Hartkopf, Felix, Hastings, Jaden J.A., Hawkins-Zafarnia, Arya, Hazrin-Chong, Nur Hazlin, Helfrich, Eric, Hell, Eva, Henry, Tamera, Hernandez, Samuel, Hernandez, Pilar Lopez, Hess-Homeier, David, Hittle, Lauren E., Hoan, Nghiem Xuan, Holik, Aliaksei, Homma, Chiaki, Hoxie, Irene, Huber, Michael, Humphries, Elizabeth, Hyland, Stephanie, Hässig, Andrea, Häusler, Roland, Hüsser, Nathalie, Petit, Robert A., III, Iderzorig, Badamnyambuu, Igarashi, Mizuki, Iqbal, Shaikh B., Ishikawa, Shino, Ishizuka, Sakura, Islam, Sharah, Islam, Riham, Ito, Kohei, Ito, Sota, Ito, Takayuki, Ivankovic, Tomislav, Iwashiro, Tomoki, Jackson, Sarah, Jacobs, JoAnn, James, Marisano, Jaubert, Marianne, Jerier, Marie-Laure, Jiminez, Esmeralda, Jinfessa, Ayantu, De Jong, Ymke, Joo, Hyun Woo, Jospin, Guilllaume, Kajita, Takema, Ahmad Kassim, Affifah Saadah, Kato, Nao, Kaur, Amrit, Kaur, Inderjit, de Souza Gomes Kehdy, Fernanda, Khadka, Vedbar S., Khan, Shaira, Khavari, Mahshid, Ki, Michelle, Kim, Gina, Kim, Hyung Jun, Kim, Sangwan, King, Ryan J., Knights, Kaymisha, KoLoMonaco, Giuseppe, Koag, Ellen, Kobko-Litskevitch, Nadezhda, Korshevniuk, Maryna, Kozhar, Michael, Krebs, Jonas, Kubota, Nanami, Kuklin, Andrii, Kumar, Sheelta S., Kwong, Rachel, Kwong, Lawrence, Lafontaine, Ingrid, Lago, Juliana, Lai, Tsoi Ying, Laine, Elodie, Laiola, Manolo, Lakhneko, Olha, Lamba, Isha, de Lamotte, Gerardo, Lannes, Romain, De Lazzari, Eleonora, Leahy, Madeline, Lee, Hyunjung, Lee, Yunmi, Lee, Lucy, Lemaire, Vincent, Leong, Emily, Leung, Marcus H.Y., Lewandowska, Dagmara, Li, Chenhao, Liang, Weijun, Lin, Moses, Lisboa, Priscilla, Litskevitch, Anna, Liu, Eric Minwei, Liu, Tracy, Livia, Mayra Arauco, Lo, Yui Him, Losim, Sonia, Loubens, Manon, Lu, Jennifer, Lykhenko, Olexandr, Lysakova, Simona, Mahmoud, Salah, Majid, Sara Abdul, Makogon, Natalka, Maldonado, Denisse, Mallari, Krizzy, Malta, Tathiane M., Mamun, Maliha, Manoir, Dimitri, Marchandon, German, Marciniak, Natalia, Marinovic, Sonia, Marques, Brunna, Mathews, Nicole, Matsuzaki, Yuri, Matthys, Vincent, May, Madelyn, McComb, Elias, Meagher, Annabelle, Melamed, Adiell, Menary, Wayne, Mendez, Katterinne N., Mendez, Ambar, Mendy, Irène Mauricette, Meng, Irene, Menon, Ajay, Menor, Mark, Meoded, Roy, Merino, Nancy, Meydan, Cem, Miah, Karishma, Mignotte, Mathilde, Miketic, Tanja, Miranda, Wilson, Mitsios, Athena, Miura, Ryusei, Miyake, Kunihiko, Moccia, Maria D., Mohan, Natasha, Mohsin, Mohammed, Moitra, Karobi, Moldes, Mauricio, Molina, Laura, Molinet, Jennifer, Molomjamts, Orgil-Erdene, Moniruzzaman, Eftar, Moon, Sookwon, de Oliveira Moraes, Isabelle, Moreno, Mario, Mosella, Maritza S., Moser, Josef W., Mozsary, Christopher, Muehlbauer, Amanda L., Muner, Oasima, Munia, Muntaha, Munim, Naimah, Muscat, Maureen, Mustac, Tatjana, Muñoz, Cristina, Nadalin, Francesca, Naeem, Areeg, Nagy-Szakal, Dorottya, Nakagawa, Mayuko, Narce, Ashanti, Nasu, Masaki, Navarrete, Irene González, Naveed, Hiba, Nazario, Bryan, Nedunuri, Narasimha Rao, Neff, Thomas, Nesimi, Aida, Ng, Wan Chiew, Ng, Synti, Nguyen, Gloria, Ngwa, Elsy, Nicolas, Agier, Nicolas, Pierre, Nika, Abdollahi, Noorzi, Hosna, Nosrati, Avigdor, Noushmehr, Houtan, Nunes, Diana N., O’Brien, Kathryn, O’Hara, Niamh B., Oken, Gabriella, Olawoyin, Rantimi A., Oliete, Javier Quilez, Olmeda, Kiara, Oluwadare, Tolulope, Oluwadare, Itunu A., Ordioni, Nils, Orpilla, Jenessa, Orrego, Jacqueline, Ortega, Melissa, Osma, Princess, Osuolale, Israel O., Osuolale, Oluwatosin M., Ota, Mitsuki, Oteri, Francesco, Oto, Yuya, Ounit, Rachid, Ouzounis, Christos A., Pakrashi, Subhamitra, Paras, Rachel, Pardo-Este, Coral, Park, Young-Ja, Pastuszek, Paulina, Patel, Suraj, Pathmanathan, Jananan, Patrignani, Andrea, Perez, Manuel, Peros, Ante, Persaud, Sabrina, Peters, Anisia, Phillips, Adam, Pineda, Lisbeth, Pizzi, Melissa P., Plaku, Alma, Plaku, Alketa, Pompa-Hogan, Brianna, Portilla, María Gabriela, Posada, Leonardo, Priestman, Max, Prithiviraj, Bharath, Priya, Sambhawa, Pugdeethosal, Phanthira, Pugh, Catherine E., Pulatov, Benjamin, Pupiec, Angelika, Pyrshev, Kyrylo, Qing, Tao, Rahiel, Saher, Rahmatulloev, Savlatjon, Rajendran, Kannan, Ramcharan, Aneisa, Ramirez-Rojas, Adan, Rana, Shahryar, Ratnanandan, Prashanthi, Read, Timothy D., Rehrauer, Hubert, Richer, Renee, Rivera, Alexis, Rivera, Michelle, Robertiello, Alessandro, Robinson, Courtney, Rodríguez, Paula, Rojas, Nayra Aguilar, Roldán, Paul, Rosario, Anyelic, Roth, Sandra, Ruiz, Maria, Boja Ruiz, Stephen Eduard, Russell, Kaitlan, Rybak, Mariia, Sabedot, Thais S., Sabina, Mahfuza, Saito, Ikuto, Saito, Yoshitaka, Malca Salas, Gustavo Adolfo, Salazar, Cecilia, San, Kaung Myat, Sanchez, Jorge, Sanchir, Khaliun, Sankar, Ryan, de Souza Santos, Paulo Thiago, Saravi, Zulena, Sasaki, Kai, Sato, Yuma, Sato, Masaki, Sato, Seisuke, Sato, Ryo, Sato, Kaisei, Sayara, Nowshin, Schaaf, Steffen, Schacher, Oli, Schinke, Anna-Lena M., Schlapbach, Ralph, Schori, Christian, Schriml, Jason R., Segato, Felipe, Sepulveda, Felipe, Serpa, Marianna S., De Sessions, Paola F., Severyn, Juan C., Shaaban, Heba, Shakil, Maheen, Shalaby, Sarah, Shari, Aliyah, Shim, Hyenah, Shirahata, Hikaru, Shiwa, Yuh, Siam, Rania, Da Silva, Ophélie, Silva, Jordana M., Simon, Gwenola, Singh, Shaleni K., Sluzek, Kasia, Smith, Rebecca, So, Eunice, Andreu Somavilla, Núria, Sonohara, Yuya, Rufino de Sousa, Nuno, Souza, Camila, Sperry, Jason, Sprinsky, Nicolas, Stark, Stefan G., La Storia, Antonietta, Suganuma, Kiyoshi, Suliman, Hamood, Sullivan, Jill, Supie, Arif Asyraf Md, Suzuki, Chisato, Takagi, Sora, Takahara, Fumie, Takahashi, Naoya, Takahashi, Kou, Takeda, Tomoki, Takenaka, Isabella K., Tanaka, Soma, Tang, Anyi, Man Tang, Yuk, Tarcitano, Emilio, Tassinari, Andrea, Taye, Mahdi, Terrero, Alexis, Thambiraja, Eunice, Thiébaut, Antonin, Thomas, Sade, Thomas, Andrew M., Togashi, Yuto, Togashi, Takumi, Tomaselli, Anna, Tomita, Masaru, Tomita, Itsuki, Tong, Xinzhao, Toth, Oliver, Toussaint, Nora C., Tran, Jennifer M., Truong, Catalina, Tsonev, Stefan I., Tsuda, Kazutoshi, Tsurumaki, Takafumi, Tuz, Michelle, Tymoshenko, Yelyzaveta, Urgiles, Carmen, Usui, Mariko, Vacant, Sophie, Valentine, Brandon, Vann, Laura E., Velter, Fabienne, Ventorino, Valeria, Vera-Wolf, Patricia, Vicedomini, Riccardo, Suarez-Villamil, Michael A., Vincent, Sierra, Vivancos-Koopman, Renee, Wan, Andrew, Wang, Cindy, Warashina, Tomoro, Watanabe, Ayuki, Weekes, Samuel, Werner, Johannes, Westfall, David, Wieler, Lothar H., Williams, Michelle, Wolf, Silver A., Wong, Brian, Wong, Yan Ling, Wong, Tyler, Wright, Rasheena, Wunderlin, Tina, Yamanaka, Ryota, Yang, Jingcheng, Yano, Hirokazu, Yeh, George C., Yemets, Olena, Yeskova, Tetiana, Yoshikawa, Shusei, Zafar, Laraib, Zhang, Yang, Zhang, Shu, Zhang, Amy, Zheng, Yuanting, Zubenko, Stas, Danko, David, Bezdan, Daniela, Afshin, Evan E., Ahsanuddin, Sofia, Bhattacharya, Chandrima, Butler, Daniel J., Chng, Kern Rei, Donnellan, Daisy, Hecht, Jochen, Jackson, Katelyn, Kuchin, Katerina, Karasikov, Mikhail, Lyons, Abigail, Mak, Lauren, Meleshko, Dmitry, Mustafa, Harun, Mutai, Beth, Neches, Russell Y., Ng, Amanda, Nikolayeva, Olga, Nikolayeva, Tatyana, Png, Eileen, Ryon, Krista A., Sanchez, Jorge L., Sierra, Maria A., Thomas, Dominique, Young, Ben, Abudayyeh, Omar O., Alicea, Josue, Bhattacharyya, Malay, Blekhman, Ran, Castro-Nallar, Eduardo, Cañas, Ana M., Chatziefthimiou, Aspassia D., Crawford, Robert W., De Filippis, Francesca, Deng, Youping, Desnues, Christelle, Dias-Neto, Emmanuel, Dybwad, Marius, Elhaik, Eran, Ercolini, Danilo, Frolova, Alina, Gankin, Dennis, Gootenberg, Jonathan S., Graf, Alexandra B., Green, David C., Hajirasouliha, Iman, Hernandez, Mark, Iraola, Gregorio, Jang, Soojin, Kahles, Andre, Kelly, Frank J., Kyrpides, Nikos C., Łabaj, Paweł P., Lee, Patrick K.H., Ljungdahl, Per O., Mason-Buck, Gabriella, McGrath, Ken, Mongodin, Emmanuel F., Moraes, Milton Ozorio, Nagarajan, Niranjan, Nieto-Caballero, Marina, Oliveira, Manuela, Ossowski, Stephan, Osuolale, Olayinka O., Özcan, Orhan, Paez-Espino, David, Rascovan, Nicolás, Richard, Hugues, Rätsch, Gunnar, Schriml, Lynn M., Semmler, Torsten, Sezerman, Osman U., Shi, Leming, Shi, Tieliu, Song, Le Huu, Suzuki, Haruo, Court, Denise Syndercombe, Tighe, Scott W., Udekwu, Klas I., Ugalde, Juan A., Vassilev, Dimitar I., Vayndorf, Elena M., Velavan, Thirumalaisamy P., Wu, Jun, Zambrano, María M., Zhu, Jifeng, Zhu, Sibo, and Mason, Christopher E.

Published
2021
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6. Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions

Author

Gong, Binsheng, Li, Dan, Kusko, Rebecca, Novoradovskaya, Natalia, Zhang, Yifan, Wang, Shangzi, Pabón-Peña, Carlos, Zhang, Zhihong, Lai, Kevin, Cai, Wanshi, LoCoco, Jennifer S., Lader, Eric, Richmond, Todd A., Mittal, Vinay K., Liu, Liang-Chun, Johann, Jr, Donald J., Willey, James C., Bushel, Pierre R., Yu, Ying, Xu, Chang, Chen, Guangchun, Burgess, Daniel, Cawley, Simon, Giorda, Kristina, Haseley, Nathan, Qiu, Fujun, Wilkins, Katherine, Arib, Hanane, Attwooll, Claire, Babson, Kevin, Bao, Longlong, Bao, Wenjun, Lucas, Anne Bergstrom, Best, Hunter, Bhandari, Ambica, Bisgin, Halil, Blackburn, James, Blomquist, Thomas M., Boardman, Lisa, Burgher, Blake, Butler, Daniel J., Chang, Chia-Jung, Chaubey, Alka, Chen, Tao, Chierici, Marco, Chin, Christopher R., Close, Devin, Conroy, Jeffrey, Cooley Coleman, Jessica, Craig, Daniel J., Crawford, Erin, del Pozo, Angela, Deveson, Ira W., Duncan, Daniel, Eterovic, Agda Karina, Fan, Xiaohui, Foox, Jonathan, Furlanello, Cesare, Ghosal, Abhisek, Glenn, Sean, Guan, Meijian, Haag, Christine, Hang, Xinyi, Happe, Scott, Hennigan, Brittany, Hipp, Jennifer, Hong, Huixiao, Horvath, Kyle, Hu, Jianhong, Hung, Li-Yuan, Jarosz, Mirna, Kerkhof, Jennifer, Kipp, Benjamin, Kreil, David Philip, Łabaj, Paweł, Lapunzina, Pablo, Li, Peng, Li, Quan-Zhen, Li, Weihua, Li, Zhiguang, Liang, Yu, Liu, Shaoqing, Liu, Zhichao, Ma, Charles, Marella, Narasimha, Martín-Arenas, Rubén, Megherbi, Dalila B., Meng, Qingchang, Mieczkowski, Piotr A., Morrison, Tom, Muzny, Donna, Ning, Baitang, Parsons, Barbara L., Paweletz, Cloud P., Pirooznia, Mehdi, Qu, Wubin, Raymond, Amelia, Rindler, Paul, Ringler, Rebecca, Sadikovic, Bekim, Scherer, Andreas, Schulze, Egbert, Sebra, Robert, Shaknovich, Rita, Shi, Qiang, Shi, Tieliu, Silla-Castro, Juan Carlos, Smith, Melissa, López, Mario Solís, Song, Ping, Stetson, Daniel, Strahl, Maya, Stuart, Alan, Supplee, Julianna, Szankasi, Philippe, Tan, Haowen, Tang, Lin-ya, Tao, Yonghui, Thakkar, Shraddha, Thierry-Mieg, Danielle, Thierry-Mieg, Jean, Thodima, Venkat J., Thomas, David, Tichý, Boris, Tom, Nikola, Garcia, Elena Vallespin, Verma, Suman, Walker, Kimbley, Wang, Charles, Wang, Junwen, Wang, Yexun, Wen, Zhining, Wirta, Valtteri, Wu, Leihong, Xiao, Chunlin, Xiao, Wenzhong, Xu, Shibei, Yang, Mary, Ying, Jianming, Yip, Shun H., Zhang, Guangliang, Zhang, Sa, Zhao, Meiru, Zheng, Yuanting, Zhou, Xiaoyan, Mason, Christopher E., Mercer, Timothy, Tong, Weida, Shi, Leming, Jones, Wendell, and Xu, Joshua

Published
2021
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8. A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

Author

Jones, Wendell, Gong, Binsheng, Novoradovskaya, Natalia, Li, Dan, Kusko, Rebecca, Richmond, Todd A., Johann, Jr, Donald J., Bisgin, Halil, Sahraeian, Sayed Mohammad Ebrahim, Bushel, Pierre R., Pirooznia, Mehdi, Wilkins, Katherine, Chierici, Marco, Bao, Wenjun, Basehore, Lee Scott, Lucas, Anne Bergstrom, Burgess, Daniel, Butler, Daniel J., Cawley, Simon, Chang, Chia-Jung, Chen, Guangchun, Chen, Tao, Chen, Yun-Ching, Craig, Daniel J., del Pozo, Angela, Foox, Jonathan, Francescatto, Margherita, Fu, Yutao, Furlanello, Cesare, Giorda, Kristina, Grist, Kira P., Guan, Meijian, Hao, Yingyi, Happe, Scott, Hariani, Gunjan, Haseley, Nathan, Jasper, Jeff, Jurman, Giuseppe, Kreil, David Philip, Łabaj, Paweł, Lai, Kevin, Li, Jianying, Li, Quan-Zhen, Li, Yulong, Li, Zhiguang, Liu, Zhichao, López, Mario Solís, Miclaus, Kelci, Miller, Raymond, Mittal, Vinay K., Mohiyuddin, Marghoob, Pabón-Peña, Carlos, Parsons, Barbara L., Qiu, Fujun, Scherer, Andreas, Shi, Tieliu, Stiegelmeyer, Suzy, Suo, Chen, Tom, Nikola, Wang, Dong, Wen, Zhining, Wu, Leihong, Xiao, Wenzhong, Xu, Chang, Yu, Ying, Zhang, Jiyang, Zhang, Yifan, Zhang, Zhihong, Zheng, Yuanting, Mason, Christopher E., Willey, James C., Tong, Weida, Shi, Leming, and Xu, Joshua

Published
2021
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9. Abstract A16: Multi-omic analyses in genetically engineered mice reveal distinct and opposite effects of leukemogenic Idh and Tet2 mutations in hematopoietic stem and progenitor cells

Author

Fortin, Jerome, primary, Chiang, Ming-Feng, additional, Meydan, Cem, additional, Foox, Jonathan, additional, Ramachandran, Parameswaran, additional, Leca, Julie, additional, Lemonnier, Francois, additional, Li, Wanda Y., additional, Gams, Miki S., additional, Sakamoto, Takashi, additional, Chu, Mandy, additional, Tobin, Chantal, additional, Laugesen, Eric, additional, Robinson, Troy M., additional, You-Ten, Annick, additional, Butler, Daniel J., additional, Berger, Thorsten, additional, Minden, Mark D., additional, Levine, Ross L., additional, Guidos, Cynthia J., additional, Melnick, Ari M., additional, Mason, Christopher E., additional, and Mak, Tak W., additional

Published
2023
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10. Lessons and Insights from Creating a Synthetic Optical Flow Benchmark

Author

Wulff, Jonas, Butler, Daniel J., Stanley, Garrett B., Black, Michael J., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Fusiello, Andrea, editor, Murino, Vittorio, editor, and Cucchiara, Rita, editor

Published
2012
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11. A Naturalistic Open Source Movie for Optical Flow Evaluation

Author

Butler, Daniel J., Wulff, Jonas, Stanley, Garrett B., Black, Michael J., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Fitzgibbon, Andrew, editor, Lazebnik, Svetlana, editor, Perona, Pietro, editor, Sato, Yoichi, editor, and Schmid, Cordelia, editor

Published
2012
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12. Distinct and opposite effects of leukemogenic Idh and Tet2 mutations in hematopoietic stem and progenitor cells

Author

Fortin, Jerome, primary, Chiang, Ming-Feng, additional, Meydan, Cem, additional, Foox, Jonathan, additional, Ramachandran, Parameswaran, additional, Leca, Julie, additional, Lemonnier, François, additional, Li, Wanda Y., additional, Gams, Miki S., additional, Sakamoto, Takashi, additional, Chu, Mandy, additional, Tobin, Chantal, additional, Laugesen, Eric, additional, Robinson, Troy M., additional, You-Ten, Annick, additional, Butler, Daniel J., additional, Berger, Thorsten, additional, Minden, Mark D., additional, Levine, Ross L., additional, Guidos, Cynthia J., additional, Melnick, Ari M., additional, Mason, Christopher E., additional, and Mak, Tak W., additional

Published
2023
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14. System-wide transcriptome damage and tissue identity loss in COVID-19 patients

Author

Park, Jiwoon, primary, Foox, Jonathan, additional, Hether, Tyler, additional, Danko, David C., additional, Warren, Sarah, additional, Kim, Youngmi, additional, Reeves, Jason, additional, Butler, Daniel J., additional, Mozsary, Christopher, additional, Rosiene, Joel, additional, Shaiber, Alon, additional, Afshin, Evan E., additional, MacKay, Matthew, additional, Rendeiro, André F., additional, Bram, Yaron, additional, Chandar, Vasuretha, additional, Geiger, Heather, additional, Craney, Arryn, additional, Velu, Priya, additional, Melnick, Ari M., additional, Hajirasouliha, Iman, additional, Beheshti, Afshin, additional, Taylor, Deanne, additional, Saravia-Butler, Amanda, additional, Singh, Urminder, additional, Wurtele, Eve Syrkin, additional, Schisler, Jonathan, additional, Fennessey, Samantha, additional, Corvelo, André, additional, Zody, Michael C., additional, Germer, Soren, additional, Salvatore, Steven, additional, Levy, Shawn, additional, Wu, Shixiu, additional, Tatonetti, Nicholas P., additional, Shapira, Sagi, additional, Salvatore, Mirella, additional, Westblade, Lars F., additional, Cushing, Melissa, additional, Rennert, Hanna, additional, Kriegel, Alison J., additional, Elemento, Olivier, additional, Imielinski, Marcin, additional, Rice, Charles M., additional, Borczuk, Alain C., additional, Meydan, Cem, additional, Schwartz, Robert E., additional, and Mason, Christopher E., additional

Published
2022
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15. Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications

Author

Moore, Keith J. M., primary, Cahill, Jeremy, additional, Aidelberg, Guy, additional, Aronoff, Rachel, additional, Bektaş, Ali, additional, Bezdan, Daniela, additional, Butler, Daniel J., additional, Chittur, Sridar V., additional, Codyre, Martin, additional, Federici, Fernan, additional, Tanner, Nathan A., additional, Tighe, Scott W., additional, True, Randy, additional, Ware, Sarah B., additional, Wyllie, Anne L., additional, Afshin, Evan E., additional, Bendesky, Andres, additional, Chang, Connie B., additional, Dela Rosa, Richard, additional, Elhaik, Eran, additional, Erickson, David, additional, Goldsborough, Andrew S., additional, Grills, George, additional, Hadasch, Kathrin, additional, Hayden, Andrew, additional, Her, Seong-Young, additional, Karl, Julie A., additional, Kim, Chang Hee, additional, Kriegel, Alison J., additional, Kunstman, Thomas, additional, Landau, Zeph, additional, Land, Kevin, additional, Langhorst, Bradley W., additional, Lindner, Ariel B., additional, Mayer, Benjamin E., additional, McLaughlin, Lee A., additional, McLaughlin, Matthew T., additional, Molloy, Jenny, additional, Mozsary, Christopher, additional, Nadler, Jerry L., additional, D'Silva, Melinee, additional, Ng, David, additional, O'Connor, David H., additional, Ongerth, Jerry E., additional, Osuolale, Olayinka, additional, Pinharanda, Ana, additional, Plenker, Dennis, additional, Ranjan, Ravi, additional, Rosbash, Michael, additional, Rotem, Assaf, additional, Segarra, Jacob, additional, Schürer, Stephan, additional, Sherrill-Mix, Scott, additional, Solo-Gabriele, Helena, additional, To, Shaina, additional, Vogt, Merly C., additional, Yu, Albert D., additional, and Mason, Christopher E., additional

Published
2021
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16. Additional file 9 of A comprehensive metagenomics framework to characterize organisms relevant for planetary protection

Author

Danko, David C., Sierra, Maria A., Benardini, James N., Guan, Lisa, Wood, Jason M., Nitin Singh, Seuylemezian, Arman, Butler, Daniel J., Ryon, Krista, Kuchin, Katerina, Meleshko, Dmitry, Bhattacharya, Chandrima, Kasthuri J. Venkateswaran, and Mason, Christopher E.

Abstract

Additional file 8: Figure S7. Prevalence of species in different categories. Heatmap showing the prevalence (fraction of samples where a taxon is detected) of different taxa across categories. Too many taxa are present to individually name taxa.

Published
2021
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17. Additional file 7 of A comprehensive metagenomics framework to characterize organisms relevant for planetary protection

Author

Danko, David C., Sierra, Maria A., Benardini, James N., Guan, Lisa, Wood, Jason M., Nitin Singh, Seuylemezian, Arman, Butler, Daniel J., Ryon, Krista, Kuchin, Katerina, Meleshko, Dmitry, Bhattacharya, Chandrima, Kasthuri J. Venkateswaran, and Mason, Christopher E.

Abstract

Additional file 6: Figure S5. Rarefaction Analysis. The number of unique species detected in multiple samples of the same type. A) Sample sets appear to reach a maximum suggesting that the majority of species have been fully categorized in each category and ISO level. B) number of species detected when individual samples are rarefied to a maximum read count

Published
2021
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18. Additional file of A comprehensive metagenomics framework to characterize organisms relevant for planetary protection

Author

Danko, David C., Sierra, Maria A., Benardini, James N., Guan, Lisa, Wood, Jason M., Nitin Singh, Seuylemezian, Arman, Butler, Daniel J., Ryon, Krista, Kuchin, Katerina, Meleshko, Dmitry, Bhattacharya, Chandrima, Kasthuri J. Venkateswaran, and Mason, Christopher E.

Abstract

Additional file of A comprehensive metagenomics framework to characterize organisms relevant for planetary protection

Published
2021
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19. Additional file 2 of A comprehensive metagenomics framework to characterize organisms relevant for planetary protection

Author

Danko, David C., Sierra, Maria A., Benardini, James N., Guan, Lisa, Wood, Jason M., Nitin Singh, Seuylemezian, Arman, Butler, Daniel J., Ryon, Krista, Kuchin, Katerina, Meleshko, Dmitry, Bhattacharya, Chandrima, Kasthuri J. Venkateswaran, and Mason, Christopher E.

Abstract

Additional file 1: Table S1. Sample Sets and Categories for JPL Planetary Protection Testing

Published
2021
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20. Additional file 5 of A comprehensive metagenomics framework to characterize organisms relevant for planetary protection

Author

Danko, David C., Sierra, Maria A., Benardini, James N., Guan, Lisa, Wood, Jason M., Nitin Singh, Seuylemezian, Arman, Butler, Daniel J., Ryon, Krista, Kuchin, Katerina, Meleshko, Dmitry, Bhattacharya, Chandrima, Kasthuri J. Venkateswaran, and Mason, Christopher E.

Abstract

Additional file 4: Figure S3. Comparison of QC Metrics in cases to controls. We detected 24 species across all control samples after initial filtering. Environmental metagenomic samples are qualitatively similar to samples of laboratory contamination so filtering based on controls is non-trivial. We compared the number of unique marker k-mers found for each taxa in each case sample to the maximum number found in one control (A) and, analogously, the total number of reads (B). We took all taxonomic assignments with a read ratio greater than 2 and a k-mer ratio greater than 5 (C). If a taxonomic assignment met both criteria in at least two samples, it was permitted (red taxa on bottom right) otherwise the taxa was filtered from all assignments (blue taxa on bottom right).

Published
2021
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21. Systemic Tissue and Cellular Disruption from SARS-CoV-2 Infection revealed in COVID-19 Autopsies and Spatial Omics Tissue Maps

Author

Park, Jiwoon, primary, Foox, Jonathan, additional, Hether, Tyler, additional, Danko, David, additional, Warren, Sarah, additional, Kim, Youngmi, additional, Reeves, Jason, additional, Butler, Daniel J., additional, Mozsary, Christopher, additional, Rosiene, Joel, additional, Shaiber, Alon, additional, Afshinnekoo, Ebrahim, additional, MacKay, Matthew, additional, Bram, Yaron, additional, Chandar, Vasuretha, additional, Geiger, Heather, additional, Craney, Arryn, additional, Velu, Priya, additional, Melnick, Ari M., additional, Hajirasouliha, Iman, additional, Beheshti, Afshin, additional, Taylor, Deanne, additional, Saravia-Butler, Amanda, additional, Singh, Urminder, additional, Wurtele, Eve Syrkin, additional, Schisler, Jonathan, additional, Fennessey, Samantha, additional, Corvelo, André, additional, Zody, Michael C., additional, Germer, Soren, additional, Salvatore, Steven, additional, Levy, Shawn, additional, Wu, Shixiu, additional, Tatonetti, Nicholas, additional, Shapira, Sagi, additional, Salvatore, Mirella, additional, Loda, Massimo, additional, Westblade, Lars F., additional, Cushing, Melissa, additional, Rennert, Hanna, additional, Kriegel, Alison J., additional, Elemento, Olivier, additional, Imielinski, Marcin, additional, Borczuk, Alain C., additional, Meydan, Cem, additional, Schwartz, Robert E., additional, and Mason, Christopher E., additional

Published
2021
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25. Genetic and Immunological Evidence for Microbial Transfer Between the International Space Station and an Astronaut

Author

Danko, David C., primary, Singh, Nitin, additional, Butler, Daniel J., additional, Mozsary, Christopher, additional, Jiang, Peng, additional, Keshavarzian, Ali, additional, Maienschein-Cline, Mark, additional, Chlipala, George, additional, Afshinnekoo, Ebrahim, additional, Bezdan, Daniela, additional, Garrett-Bakelman, Francine, additional, Green, Stefan J., additional, Turek, Fred W., additional, Vitaterna, Martha Hotz, additional, Venkateswaran, Kasthuri, additional, and Mason, Christopher E., additional

Published
2020
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26. Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions

Author

Butler, Daniel J., primary, Mozsary, Christopher, additional, Meydan, Cem, additional, Danko, David, additional, Foox, Jonathan, additional, Rosiene, Joel, additional, Shaiber, Alon, additional, Afshinnekoo, Ebrahim, additional, MacKay, Matthew, additional, Sedlazeck, Fritz J., additional, Ivanov, Nikolay A., additional, Sierra, Maria, additional, Pohle, Diana, additional, Zietz, Michael, additional, Gisladottir, Undina, additional, Ramlall, Vijendra, additional, Westover, Craig D., additional, Ryon, Krista, additional, Young, Benjamin, additional, Bhattacharya, Chandrima, additional, Ruggiero, Phyllis, additional, Langhorst, Bradley W., additional, Tanner, Nathan, additional, Gawrys, Justyna, additional, Meleshko, Dmitry, additional, Xu, Dong, additional, Steel, Peter A. D., additional, Shemesh, Amos J., additional, Xiang, Jenny, additional, Thierry-Mieg, Jean, additional, Thierry-Mieg, Danielle, additional, Schwartz, Robert E., additional, Iftner, Angelika, additional, Bezdan, Daniela, additional, Sipley, John, additional, Cong, Lin, additional, Craney, Arryn, additional, Velu, Priya, additional, Melnick, Ari M., additional, Hajirasouliha, Iman, additional, Horner, Stacy M., additional, Iftner, Thomas, additional, Salvatore, Mirella, additional, Loda, Massimo, additional, Westblade, Lars F., additional, Cushing, Melissa, additional, Levy, Shawn, additional, Wu, Shixiu, additional, Tatonetti, Nicholas, additional, Imielinski, Marcin, additional, Rennert, Hanna, additional, and Mason, Christopher E., additional

Published
2020
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27. Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Author

Chng, Kern Rei, Li, Chenhao, Bertrand, Denis, Ng, Amanda Hui Qi, Kwah, Junmei Samantha, Low, Hwee Meng, Tong, Chengxuan, Natrajan, Maanasa, Zhang, Michael Hongjie, Xu, Licheng, Ko, Karrie Kwan Ki, Ho, Eliza Xin Pei, Av-Shalom, Tamar, Teo, Jeanette Woon Pei, Khor, Chiea Chuen, Chen, Swaine L., Mason, Christopher E., Ng, Oon Tek, Marimuthu, Kalisvar, Ang, Brenda, Nagarajan, Niranjan, Danko, David, Bezdan, Daniela, Afshinnekoo, Ebrahim, Ahsanuddin, Sofia, Bhattacharya, Chandrima, Butler, Daniel J., De Filippis, Francesca, Hecht, Jochen, Kahles, Andre, Karasikov, Mikhail, Kyrpides, Nikos C., Leung, Marcus H. Y., Meleshko, Dmitry, Mustafa, Harun, Mutai, Beth, Neches, Russell Y., Ng, Amanda, Nieto-Caballero, Marina, Nikolayeva, Olga, Nikolayeva, Tatyana, Png, Eileen, Sanchez, Jorge L., Shaaban, Heba, Sierra, Maria A., Tong, Xinzhao, Young, Ben, Alicea, Josue, Bhattacharyya, Malay, Blekhman, Ran, Castro-Nallar, Eduardo, Canas, Ana M., Chatziefthimiou, Aspassia D., Crawford, Robert W., Deng, Youping, Desnues, Christelle, Dias-Neto, Emmanuel, Donnellan, Daisy, Dybwad, Marius, Elhaik, Eran, Ercolini, Danilo, Frolova, Alina, Graf, Alexandra B., Green, David C., Hajirasouliha, Iman, Hernandez, Mark, Iraola, Gregorio, Jang, Soojin, Jones, Angela, Kelly, Frank J., Knights, Kaymisha, Labaj, Pawel P., Lee, Patrick K. H., Shawn, Levy, Ljungdahl, Per, Lyons, Abigail, Mason-Buck, Gabriella, McGrath, Ken, Mongodin, Emmanuel F., Moraes, Milton Ozorio, Noushmehr, Houtan, Oliveira, Manuela, Ossowski, Stephan, Osuolale, Olayinka O., Ozcan, Orhan, Paez-Espino, David, Rascovan, Nicolas, Richard, Hugues, Raetsch, Gunnar, Schriml, Lynn M., Semmler, Torsten, Sezerman, Osman U., Shi, Leming, Song, Le Huu, Suzuki, Haruo, Court, Denise Syndercombe, Thomas, Dominique, Tighe, Scott W., Udekwu, Klas, Ugalde, Juan A., Valentine, Brandon, Vassilev, Dimitar, Vayndorf, Elena, Velavan, Thirumalaisamy P., Zambrano, Maria M., Zhu, Jifeng, Zhu, Sibo, Chng, Kern Rei, Li, Chenhao, Bertrand, Denis, Ng, Amanda Hui Qi, Kwah, Junmei Samantha, Low, Hwee Meng, Tong, Chengxuan, Natrajan, Maanasa, Zhang, Michael Hongjie, Xu, Licheng, Ko, Karrie Kwan Ki, Ho, Eliza Xin Pei, Av-Shalom, Tamar, Teo, Jeanette Woon Pei, Khor, Chiea Chuen, Chen, Swaine L., Mason, Christopher E., Ng, Oon Tek, Marimuthu, Kalisvar, Ang, Brenda, Nagarajan, Niranjan, Danko, David, Bezdan, Daniela, Afshinnekoo, Ebrahim, Ahsanuddin, Sofia, Bhattacharya, Chandrima, Butler, Daniel J., De Filippis, Francesca, Hecht, Jochen, Kahles, Andre, Karasikov, Mikhail, Kyrpides, Nikos C., Leung, Marcus H. Y., Meleshko, Dmitry, Mustafa, Harun, Mutai, Beth, Neches, Russell Y., Ng, Amanda, Nieto-Caballero, Marina, Nikolayeva, Olga, Nikolayeva, Tatyana, Png, Eileen, Sanchez, Jorge L., Shaaban, Heba, Sierra, Maria A., Tong, Xinzhao, Young, Ben, Alicea, Josue, Bhattacharyya, Malay, Blekhman, Ran, Castro-Nallar, Eduardo, Canas, Ana M., Chatziefthimiou, Aspassia D., Crawford, Robert W., Deng, Youping, Desnues, Christelle, Dias-Neto, Emmanuel, Donnellan, Daisy, Dybwad, Marius, Elhaik, Eran, Ercolini, Danilo, Frolova, Alina, Graf, Alexandra B., Green, David C., Hajirasouliha, Iman, Hernandez, Mark, Iraola, Gregorio, Jang, Soojin, Jones, Angela, Kelly, Frank J., Knights, Kaymisha, Labaj, Pawel P., Lee, Patrick K. H., Shawn, Levy, Ljungdahl, Per, Lyons, Abigail, Mason-Buck, Gabriella, McGrath, Ken, Mongodin, Emmanuel F., Moraes, Milton Ozorio, Noushmehr, Houtan, Oliveira, Manuela, Ossowski, Stephan, Osuolale, Olayinka O., Ozcan, Orhan, Paez-Espino, David, Rascovan, Nicolas, Richard, Hugues, Raetsch, Gunnar, Schriml, Lynn M., Semmler, Torsten, Sezerman, Osman U., Shi, Leming, Song, Le Huu, Suzuki, Haruo, Court, Denise Syndercombe, Thomas, Dominique, Tighe, Scott W., Udekwu, Klas, Ugalde, Juan A., Valentine, Brandon, Vassilev, Dimitar, Vayndorf, Elena, Velavan, Thirumalaisamy P., Zambrano, Maria M., Zhu, Jifeng, and Zhu, Sibo

Abstract

Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections. Spatiotemporal characterization of microbial diversity and antibiotic resistance in a tertiary-care hospital reveals broad distribution and persistence of antibiotic-resistant organisms that could cause opportunistic infections in a healthcare setting.

Published
2020
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31. 3D Wikipedia.

Author

Russell, Bryan C., Martin-Brualla, Ricardo, Butler, Daniel J., Seitz, Steven M., and Zettlemoyer, Luke

Subjects
THREE-dimensional imaging, TOURIST attractions, VISUALIZATION, NATURAL language processing, RENDERING (Computer graphics)
Abstract

We introduce an approach for analyzing Wikipedia and other text, together with online photos, to produce annotated 3D models of famous tourist sites. The approach is completely automated, and leverages online text and photo co-occurrences via Google Image Search. It enables a number of new interactions, which we demonstrate in a new 3D visualization tool. Text can be selected to move the camera to the corresponding objects, 3D bounding boxes provide anchors back to the text describing them, and the overall narrative of the text provides a temporal guide for automatically flying through the scene to visualize the world as you read about it. We show compelling results on several major tourist sites. [ABSTRACT FROM AUTHOR]

Published
2017
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32. 3D Wikipedia

Author

Russell, Bryan C., primary, Martin-Brualla, Ricardo, additional, Butler, Daniel J., additional, Seitz, Steven M., additional, and Zettlemoyer, Luke, additional

Published
2013
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33. The Privacy-Utility Tradeoff for Remotely Teleoperated Robots.

Author

Butler, Daniel J., Huang, Justin, Roesner, Franziska, and Cakmak, Maya

Subjects
ROBOT control systems, REMOTE control, USER interfaces, COMPUTER security, HUMAN-robot interaction, IMAGE analysis
Abstract

Though teleoperated robots have become common for more extreme tasks such as bomb diffusion, search-and-rescue, and space exploration, they are not commonly used in human-populated environments for more ordinary tasks such as house cleaning or cooking. This presents near-term opportunities for teleoperated robots in the home. However, a teleoperator's remote presence in a consumer's home presents serious security and privacy risks, and the concerns of end-users about these risks may hinder the adoption of such in-home robots. In this paper, we define and explore the privacy-utility tradeoff for remotely teleoperated robots: as we reduce the quantity or fidelity of visual information received by the teleoperator to preserve the end-user's privacy, we must balance this against the teleoperator's need for sufficient information to successfully carry out tasks. We explore this tradeoff with two surveys that provide a frame-work for understanding the privacy attitudes of end-users, and with a user study that empirically examines the effect of different filters of visual information on the ability of a teleoperator to carry out a task. Our findings include that respondents do desire privacy protective measures from tele-operators, that respondents prefer certain visual filters from a privacy perspective, and that, for the studied task, we can identify a filter that balances privacy with utility. We make recommendations for in-home teleoperation based on these findings. [ABSTRACT FROM AUTHOR]

Published
2015
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34. Additional file 4 of A comprehensive metagenomics framework to characterize organisms relevant for planetary protection

Author

Danko, David C., Sierra, Maria A., Benardini, James N., Guan, Lisa, Wood, Jason M., Nitin Singh, Seuylemezian, Arman, Butler, Daniel J., Ryon, Krista, Kuchin, Katerina, Meleshko, Dmitry, Bhattacharya, Chandrima, Kasthuri J. Venkateswaran, and Mason, Christopher E.

Subjects
15. Life on land
Abstract

Additional file 3: Figure S2. Distribution of QC Metrics. The distributions of various QC metrics for controls and ISO levels. Distributions of QC metrics for non-control samples are largely unaffected by category which suggests good overall quality. A) Distribution of read count. B) Coverage of marker k-mer set for each taxa detected in samples. C) Number of unique marker k-mers for each taxa detected in samples. D) The ratio of unique marker k-mers to read count for each taxa detected in sample. A low ratio (about 1) could indicate a false positive.

35. Additional file 6 of A comprehensive metagenomics framework to characterize organisms relevant for planetary protection

Author

Danko, David C., Sierra, Maria A., Benardini, James N., Guan, Lisa, Wood, Jason M., Nitin Singh, Seuylemezian, Arman, Butler, Daniel J., Ryon, Krista, Kuchin, Katerina, Meleshko, Dmitry, Bhattacharya, Chandrima, Kasthuri J. Venkateswaran, and Mason, Christopher E.

Subjects
15. Life on land
Abstract

Additional file 5: Figure S4. Relationship of QC Values to Taxonomic Assignment. A. Total number of reads per sample, note log scale on y-axis. B. Top-Left) Diversity of marker k-mers compared to diversity of identified taxa measured by Shannon’s entropy, Pearson’s correlation coefficients rho=0.625. Top-Right) Fraction of singleton k-mers compared to diversity of identified taxa, rho=0.499. Bottom-Right) Read count compared to diversity of identified taxa, rho=0.781. Bottom-Left) Read count compared to total number of detected species (rarefied to 1,000 reads), rho=0.886.

36. Additional file 6 of A comprehensive metagenomics framework to characterize organisms relevant for planetary protection

Author

Danko, David C., Sierra, Maria A., Benardini, James N., Guan, Lisa, Wood, Jason M., Nitin Singh, Seuylemezian, Arman, Butler, Daniel J., Ryon, Krista, Kuchin, Katerina, Meleshko, Dmitry, Bhattacharya, Chandrima, Kasthuri J. Venkateswaran, and Mason, Christopher E.

Subjects
15. Life on land
Abstract

Additional file 5: Figure S4. Relationship of QC Values to Taxonomic Assignment. A. Total number of reads per sample, note log scale on y-axis. B. Top-Left) Diversity of marker k-mers compared to diversity of identified taxa measured by Shannon’s entropy, Pearson’s correlation coefficients rho=0.625. Top-Right) Fraction of singleton k-mers compared to diversity of identified taxa, rho=0.499. Bottom-Right) Read count compared to diversity of identified taxa, rho=0.781. Bottom-Left) Read count compared to total number of detected species (rarefied to 1,000 reads), rho=0.886.

37. Additional file 4 of A comprehensive metagenomics framework to characterize organisms relevant for planetary protection

Author

Danko, David C., Sierra, Maria A., Benardini, James N., Guan, Lisa, Wood, Jason M., Nitin Singh, Seuylemezian, Arman, Butler, Daniel J., Ryon, Krista, Kuchin, Katerina, Meleshko, Dmitry, Bhattacharya, Chandrima, Kasthuri J. Venkateswaran, and Mason, Christopher E.

Subjects
15. Life on land
Abstract

Additional file 3: Figure S2. Distribution of QC Metrics. The distributions of various QC metrics for controls and ISO levels. Distributions of QC metrics for non-control samples are largely unaffected by category which suggests good overall quality. A) Distribution of read count. B) Coverage of marker k-mer set for each taxa detected in samples. C) Number of unique marker k-mers for each taxa detected in samples. D) The ratio of unique marker k-mers to read count for each taxa detected in sample. A low ratio (about 1) could indicate a false positive.

38. Systemic Tissue and Cellular Disruption from SARS-CoV-2 Infection revealed in COVID-19 Autopsies and Spatial Omics Tissue Maps.

Author

Park J, Foox J, Hether T, Danko D, Warren S, Kim Y, Reeves J, Butler DJ, Mozsary C, Rosiene J, Shaiber A, Afshinnekoo E, MacKay M, Bram Y, Chandar V, Geiger H, Craney A, Velu P, Melnick AM, Hajirasouliha I, Beheshti A, Taylor D, Saravia-Butler A, Singh U, Wurtele ES, Schisler J, Fennessey S, Corvelo A, Zody MC, Germer S, Salvatore S, Levy S, Wu S, Tatonetti N, Shapira S, Salvatore M, Loda M, Westblade LF, Cushing M, Rennert H, Kriegel AJ, Elemento O, Imielinski M, Borczuk AC, Meydan C, Schwartz RE, and Mason CE

Abstract

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus has infected over 115 million people and caused over 2.5 million deaths worldwide. Yet, the molecular mechanisms underlying the clinical manifestations of COVID-19, as well as what distinguishes them from common seasonal influenza virus and other lung injury states such as Acute Respiratory Distress Syndrome (ARDS), remains poorly understood. To address these challenges, we combined transcriptional profiling of 646 clinical nasopharyngeal swabs and 39 patient autopsy tissues, matched with spatial protein and expression profiling (GeoMx) across 357 tissue sections. These results define both body-wide and tissue-specific (heart, liver, lung, kidney, and lymph nodes) damage wrought by the SARS-CoV-2 infection, evident as a function of varying viral load (high vs. low) during the course of infection and specific, transcriptional dysregulation in splicing isoforms, T cell receptor expression, and cellular expression states. In particular, cardiac and lung tissues revealed the largest degree of splicing isoform switching and cell expression state loss. Overall, these findings reveal a systemic disruption of cellular and transcriptional pathways from COVID-19 across all tissues, which can inform subsequent studies to combat the mortality of COVID-19, as well to better understand the molecular dynamics of lethal SARS-CoV-2 infection and other viruses.

Published
2021
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39. Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions.

Author

Butler DJ, Mozsary C, Meydan C, Danko D, Foox J, Rosiene J, Shaiber A, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Westover CD, Ryon K, Young B, Bhattacharya C, Ruggiero P, Langhorst BW, Tanner N, Gawrys J, Meleshko D, Xu D, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Schwartz RE, Iftner A, Bezdan D, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Hajirasouliha I, Horner SM, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Levy S, Wu S, Tatonetti N, Imielinski M, Rennert H, and Mason CE

Abstract

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused thousands of deaths worldwide, including >18,000 in New York City (NYC) alone. The sudden emergence of this pandemic has highlighted a pressing clinical need for rapid, scalable diagnostics that can detect infection, interrogate strain evolution, and identify novel patient biomarkers. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs, plus a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, bacterial, and viral profiling. We applied both technologies across 857 SARS-CoV-2 clinical specimens and 86 NYC subway samples, providing a broad molecular portrait of the COVID-19 NYC outbreak. Our results define new features of SARS-CoV-2 evolution, nominate a novel, NYC-enriched viral subclade, reveal specific host responses in interferon, ACE, hematological, and olfaction pathways, and examine risks associated with use of ACE inhibitors and angiotensin receptor blockers. Together, these findings have immediate applications to SARS-CoV-2 diagnostics, public health, and new therapeutic targets., Competing Interests: Conflicts of Interest Nathan Tanner and Bradley W. Langhorst are employees at New England Biolabs.

Published
2020
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