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2. Discovery of bioactive microbial gene products in inflammatory bowel disease

Author

Zhang, Yancong, Bhosle, Amrisha, Bae, Sena, McIver, Lauren J., Pishchany, Gleb, Accorsi, Emma K., Thompson, Kelsey N., Arze, Cesar, Wang, Ya, Subramanian, Ayshwarya, Kearney, Sean M., Pawluk, April, Plichta, Damian R., Rahnavard, Ali, Shafquat, Afrah, Xavier, Ramnik J., Vlamakis, Hera, Garrett, Wendy S., Krueger, Andy, Huttenhower, Curtis, and Franzosa, Eric A.

Published
2022
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3. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.

Author

Lloyd-Price, Jason, Arze, Cesar, Ananthakrishnan, Ashwin N, Schirmer, Melanie, Avila-Pacheco, Julian, Poon, Tiffany W, Andrews, Elizabeth, Ajami, Nadim J, Bonham, Kevin S, Brislawn, Colin J, Casero, David, Courtney, Holly, Gonzalez, Antonio, Graeber, Thomas G, Hall, A Brantley, Lake, Kathleen, Landers, Carol J, Mallick, Himel, Plichta, Damian R, Prasad, Mahadev, Rahnavard, Gholamali, Sauk, Jenny, Shungin, Dmitry, Vázquez-Baeza, Yoshiki, White, Richard A, IBDMDB Investigators, Braun, Jonathan, Denson, Lee A, Jansson, Janet K, Knight, Rob, Kugathasan, Subra, McGovern, Dermot PB, Petrosino, Joseph F, Stappenbeck, Thaddeus S, Winter, Harland S, Clish, Clary B, Franzosa, Eric A, Vlamakis, Hera, Xavier, Ramnik J, and Huttenhower, Curtis

Subjects
IBDMDB Investigators, Animals, Humans, Viruses, Fungi, Inflammatory Bowel Diseases, Phylogeny, Species Specificity, Health, Transcriptome, Gastrointestinal Microbiome, General Science & Technology
Abstract

Inflammatory bowel diseases, which include Crohn's disease and ulcerative colitis, affect several million individuals worldwide. Crohn's disease and ulcerative colitis are complex diseases that are heterogeneous at the clinical, immunological, molecular, genetic, and microbial levels. Individual contributing factors have been the focus of extensive research. As part of the Integrative Human Microbiome Project (HMP2 or iHMP), we followed 132 subjects for one year each to generate integrated longitudinal molecular profiles of host and microbial activity during disease (up to 24 time points each; in total 2,965 stool, biopsy, and blood specimens). Here we present the results, which provide a comprehensive view of functional dysbiosis in the gut microbiome during inflammatory bowel disease activity. We demonstrate a characteristic increase in facultative anaerobes at the expense of obligate anaerobes, as well as molecular disruptions in microbial transcription (for example, among clostridia), metabolite pools (acylcarnitines, bile acids, and short-chain fatty acids), and levels of antibodies in host serum. Periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts. Finally, integrative analysis identified microbial, biochemical, and host factors central to this dysregulation. The study's infrastructure resources, results, and data, which are available through the Inflammatory Bowel Disease Multi'omics Database ( http://ibdmdb.org ), provide the most comprehensive description to date of host and microbial activities in inflammatory bowel diseases.

Published
2019

6. Comprehensive profiling of antibody responses to the human anellome using programmable phage display

Author

Venkataraman, Thiagarajan, primary, Swaminathan, Harish, additional, Arze, Cesar A., additional, Jacobo, Sarah M., additional, Bhattacharyya, Agamoni, additional, David, Tyler, additional, Nawandar, Dhananjay M., additional, Delagrave, Simon, additional, Mani, Vinidhra, additional, Yozwiak, Nathan L., additional, and Larman, H. Benjamin, additional

Published
2022
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7. Independent Emergence of Artemisinin Resistance Mutations Among Plasmodium falciparum in Southeast Asia

Author

Takala-Harrison, Shannon, Jacob, Christopher G., Arze, Cesar, Cummings, Michael P., Silva, Joana C., Dondorp, Arjen M., Fukuda, Mark M., Hien, Tran Tinh, Mayxay, Mayfong, Noedl, Harald, Nosten, Francois, Kyaw, Myat P., Nhien, Nguyen Thanh Thuy, Imwong, Mallika, Bethell, Delia, Se, Youry, Lon, Chanthap, Tyner, Stuart D., Saunders, David L., Ariey, Frederic, Mercereau-Puijalon, Odile, Menard, Didier, Newton, Paul N., Khanthavong, Maniphone, Hongvanthong, Bouasy, Starzengruber, Peter, Fuehrer, Hans-Peter, Swoboda, Paul, Khan, Wasif A., Phyo, Aung Pyae, Nyunt, Myaing M., Nyunt, Myat H., Brown, Tyler S., Adams, Matthew, Pepin, Christopher S., Bailey, Jason, Tan, John C., Ferdig, Michael T., Clark, Taane G., Miotto, Olivo, MacInnis, Bronwyn, Kwiatkowski, Dominic P., White, Nicholas J., Ringwald, Pascal, and Plowe, Christopher V.

Published
2015

8. Anellovirus Structure Reveals a Mechanism for Immune Evasion

Author

Liou, Shu-hao, primary, Cohen, Noah, additional, Zhang, Yue, additional, Acharekar, Nidhi Mukund, additional, Rodgers, Hillary, additional, Islam, Saadman, additional, Zeheb, Lynn, additional, Pitts, Jared, additional, Arze, Cesar, additional, Swaminathan, Harish, additional, Yozwiak, Nathan, additional, Ong, Tuyen, additional, Hajjar, Roger J., additional, Chang, Yong, additional, Swanson, Kurt A., additional, and Delagrave, Simon, additional

Published
2022
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9. Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia

Author

Takala-Harrison, Shannon, Clark, Taane G., Jacob, Christopher G., Cummings, Michael P., Miotto, Olivo, Dondorp, Arjen M., Fukuda, Mark M., Nosten, Francois, Noedl, Harald, Imwong, Mallika, Bethell, Delia, Se, Youry, Lon, Chanthap, Tyner, Stuart D., Saunders, David L., Socheat, Duong, Ariey, Frederic, Phyo, Aung Pyae, Starzengruber, Peter, Fuehrer, Hans-Peter, Swoboda, Paul, Stepniewska, Kasia, Flegg, Jennifer, Arze, Cesar, Cerqueira, Gustavo C., Silva, Joana C., Ricklefs, Stacy M., Porcella, Stephen F., Stephens, Robert M., Adams, Matthew, Kenefic, Leo J., Campino, Susana, Auburn, Sarah, Maclnnis, Bronwyn, Kwiatkowski, Dominic P., Su, Xin-zhuan, White, Nicholas J., Ringwald, Pascal, and Plowe, Christopher V.

Published
2013

10. Human anelloviruses produced by recombinant expression of synthetic genomes

Author

Nawandar, Dhananjay M., primary, Trivedi, Maitri, additional, Bounoutas, George, additional, Lebo, Kevin, additional, Prince, Cato, additional, Scano, Colin, additional, Agarwal, Nidhi, additional, Ozturk, Erin, additional, Yu, Jason, additional, Arze, Cesar A., additional, Bhattacharyya, Agamoni, additional, Verma, Dinesh, additional, Thakker, Parmi, additional, Cabral, Joseph, additional, Liou, Shu-Hao, additional, Swanson, Kurt, additional, Swaminathan, Harish, additional, Diaz, Fernando, additional, Mackey, Ashley, additional, Chang, Yong, additional, Ong, Tuyen, additional, Yozwiak, Nathan L., additional, Hajjar, Roger J., additional, and Delagrave, Simon, additional

Published
2022
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11. Correction: Corrigendum: Allelic variation contributes to bacterial host specificity

Author

Yue, Min, Han, Xiangan, De Masi, Leon, Zhu, Chunhong, Ma, Xun, Zhang, Junjie, Wu, Renwei, Schmieder, Robert, Kaushik, Radhey S., Fraser, George P., Zhao, Shaohua, McDermott, Patrick F., Weill, François-Xavier, Mainil, Jacques G., Arze, Cesar, Fricke, W. Florian, Edwards, Robert A., Brisson, Dustin, Zhang, Nancy R., Rankin, Shelley C., and Schifferli, Dieter M.

Published
2017
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13. Global genome analysis reveals a vast and dynamic anellovirus landscape within the human virome

Author

Arze, Cesar A., primary, Springer, Simeon, additional, Dudas, Gytis, additional, Patel, Sneha, additional, Bhattacharyya, Agamoni, additional, Swaminathan, Harish, additional, Brugnara, Carlo, additional, Delagrave, Simon, additional, Ong, Tuyen, additional, Kahvejian, Avak, additional, Echelard, Yann, additional, Weinstein, Erica G., additional, Hajjar, Roger J., additional, Andersen, Kristian G., additional, and Yozwiak, Nathan L., additional

Published
2021
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14. A framework for human microbiome research

Author

Methé, Barbara A., Nelson, Karen E., Pop, Mihai, Creasy, Heather H., Giglio, Michelle G., Huttenhower, Curtis, Gevers, Dirk, Petrosino, Joseph F., Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Earl, Ashlee M., FitzGerald, Michael G., Fulton, Robert S., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Martin, John C., Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Young, Sarah K., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Anderson, Scott, Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Bonazzi, Vivien R., Brooks, Paul, Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Chu, Ken, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Dewhirst, Floyd E., Deych, Elena, Ding, Yan, Dooling, David J., Dugan, Shannon P., Dunne, Michael W., Jr, Durkin, Scott A., Edgar, Robert C., Erlich, Rachel L., Farmer, Candace N., Farrell, Ruth M., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry, Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goldberg, Jonathan M., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haas, Brian J., Hamilton, Holli A., Harris, Emily L., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huang, Katherine H., Huse, Susan M., Izard, Jacques, Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, Kinder-Haake, Susan, King, Nicholas B., Knight, Rob, Knights, Dan, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lee, Sandra L., Lemon, Katherine P., Lennon, Niall, Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Liu, Bo, Liu, Yue, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, Dwayne R., Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavrommatis, Konstantinos, McCorrison, Jamison M., McDonald, Daniel, McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Miller, Jason R., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Pearson, Matthew, Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Sankar, Pamela, Sathirapongsasuti, Fah J., Schloss, Jeffery A., Schloss, Patrick D., Schmidt, Thomas M., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Smillie, Chris S., Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Sykes, Sean M., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Lu, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., White, James R., Wilczek-Boney, Katarzyna, Wu, Yuan Qing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Liang, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhang, Lan, Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Zucker, Jeremy D., Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Weinstock, George M., Wilson, Richard K., and White, Owen

Published
2012
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15. Structure, function and diversity of the healthy human microbiome

Author

Huttenhower, Curtis, Gevers, Dirk, Knight, Rob, Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Creasy, Heather H., Earl, Ashlee M., FitzGerald, Michael G., Fulton, Robert S., Giglio, Michelle G., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Martin, John C., Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Young, Sarah K., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Anderson, Scott, Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Bonazzi, Vivien, Brooks, Paul J., Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S. G., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Chu, Ken, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Dewhirst, Floyd E., Deych, Elena, Ding, Yan, Dooling, David J., Dugan, Shannon P., Dunne, Wm Michael, Durkin, Scott A., Edgar, Robert C., Erlich, Rachel L., Farmer, Candace N., Farrell, Ruth M., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry J., Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goldberg, Jonathan M., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haake, Susan Kinder, Haas, Brian J., Hamilton, Holli A., Harris, Emily L., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huang, Katherine H., Huse, Susan M., Izard, Jacques, Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, King, Nicholas B., Knights, Dan, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lee, Sandra L., Lemon, Katherine P., Lennon, Niall, Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Liu, Bo, Liu, Yue, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, Dwayne R., Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavromatis, Konstantinos, McCorrison, Jamison M., McDonald, Daniel, McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Miller, Jason R., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Pearson, Matthew, Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Pop, Mihai, Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Sankar, Pamela, Sathirapongsasuti, Fah J., Schloss, Jeffery A., Schloss, Patrick D., Schmidt, Thomas M., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Smillie, Christopher S., Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Sykes, Sean M., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Lu, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., White, James R., Wilczek-Boney, Katarzyna, Wu, YuanQing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Liang, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhang, Lan, Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Zucker, Jeremy D., Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Methé, Barbara A., Nelson, Karen E., Petrosino, Joseph F., Weinstock, George M., Wilson, Richard K., and White, Owen

Published
2012
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17. Association Between Sulfur-Metabolizing Bacterial Communities in Stool and Risk of Distal Colorectal Cancer in Men

Author

Nguyen, Long H., primary, Ma, Wenjie, additional, Wang, Dong D., additional, Cao, Yin, additional, Mallick, Himel, additional, Gerbaba, Teklu K., additional, Lloyd-Price, Jason, additional, Abu-Ali, Galeb, additional, Hall, A. Brantley, additional, Sikavi, Daniel, additional, Drew, David A., additional, Mehta, Raaj S., additional, Arze, Cesar, additional, Joshi, Amit D., additional, Yan, Yan, additional, Branck, Tobyn, additional, DuLong, Casey, additional, Ivey, Kerry L., additional, Ogino, Shuji, additional, Rimm, Eric B., additional, Song, Mingyang, additional, Garrett, Wendy S., additional, Izard, Jacques, additional, Huttenhower, Curtis, additional, and Chan, Andrew T., additional

Published
2020
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19. 631 – Dietary Intake, H2S-Producing Microbes, and Risk of Colorectal Cancer

Author

Nguyen, Long H., primary, Song, Mingyang, additional, Cao, Yin, additional, Ma, Wenjie, additional, Lloyd-Price, Jason, additional, Drew, David A., additional, Mehta, Raaj S., additional, Arze, Cesar, additional, Hall, Brantley, additional, Gerbaba, Teklu K., additional, Abu-Ali, Galeb, additional, Mallick, Himel, additional, Rahnavard, Ali, additional, Yan, Yan, additional, Joshi, Amit D., additional, Ivey, Kerry L., additional, Ogino, Shuji, additional, Izard, Jacques, additional, Garrett, Wendy, additional, Rimm, Eric, additional, Huttenhower, Curtis, additional, and Chan, Andrew T., additional

Published
2019
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20. CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing

Author

Arze Cesar, Riley David R, Vangala Mahesh, Galens Kevin, Gussman Aaron, Matalka Malcolm, Angiuoli Samuel V, White James R, White Owen, and Fricke W Florian

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Next-generation sequencing technologies have decentralized sequence acquisition, increasing the demand for new bioinformatics tools that are easy to use, portable across multiple platforms, and scalable for high-throughput applications. Cloud computing platforms provide on-demand access to computing infrastructure over the Internet and can be used in combination with custom built virtual machines to distribute pre-packaged with pre-configured software. Results We describe the Cloud Virtual Resource, CloVR, a new desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing. In a case study, we demonstrate the use of CloVR to automatically process next-generation sequencing data on multiple cloud computing platforms. Conclusion The CloVR VM and associated architecture lowers the barrier of entry for utilizing complex analysis protocols on both local single- and multi-core computers and cloud systems for high throughput data processing.

Published
2011
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21. 1100 - Dynamics of the Microbial Metaproteome in Inflammatory Bowel Disease

Author

Braun, Jonathan, primary, Brislawn, Colin, additional, Casero, David, additional, Purvine, Samuel, additional, Scott, Johanna J., additional, White, Richard A., additional, Arze, Cesar, additional, Lloyd-Price, Jason, additional, Vlamakis, Hera, additional, Xavier, Ramnik, additional, Huttenhower, Curtis, additional, Graeber, Thomas, additional, and Jansson, Janet, additional

Published
2018
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28. CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline

Author

Agrawal, Sonia, primary, Arze, Cesar, additional, Adkins, Ricky S., additional, Crabtree, Jonathan, additional, Riley, David, additional, Vangala, Mahesh, additional, Galens, Kevin, additional, Fraser, Claire M., additional, Tettelin, Hervé, additional, White, Owen, additional, Angiuoli, Samuel V., additional, Mahurkar, Anup, additional, and Fricke, W. Florian, additional

Published
2017
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29. Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Kibbe, Warren A., Arze, Cesar, Felix, Victor, Mitraka, Elvira, Bolton, Evan, Fu, Gang, Mungall, Christopher J., Binder, Janos X., Malone, James, Vasant, Drashtti, Parkinson, Helen, Schriml, Lynn M., Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Kibbe, Warren A., Arze, Cesar, Felix, Victor, Mitraka, Elvira, Bolton, Evan, Fu, Gang, Mungall, Christopher J., Binder, Janos X., Malone, James, Vasant, Drashtti, Parkinson, Helen, and Schriml, Lynn M.

Abstract

The current version of the Human Disease Ontology (DO) (http://www.disease-ontology.org) database expands the utility of the ontology for the examination and comparison of genetic variation, phenotype, protein, drug and epitope data through the lens of human disease. DO is a biomedical resource of standardized common and rare disease concepts with stable identifiers organized by disease etiology. The content of DO has had 192 revisions since 2012, including the addition of 760 terms. Thirty-two percent of all terms now include definitions. DO has expanded the number and diversity of research communities and community members by 50+ during the past two years. These community members actively submit term requests, coordinate biomedical resource disease representation and provide expert curation guidance. Since the DO 2012 NAR paper, there have been hundreds of term requests and a steady increase in the number of DO listserv members, twitter followers and DO website usage. DO is moving to a multi-editor model utilizing Protege to curate DO in web ontology language. This will enable closer collaboration with the Human Phenotype Ontology, EBI's Ontology Working Group, Mouse Genome Informatics and the Monarch Initiative among others, and enhance DO's current asserted view and multiple inferred views through reasoning.

Published
2015

30. Allelic variation contributes to bacterial host specificity

Author

Yue, Min, primary, Han, Xiangan, additional, Masi, Leon De, additional, Zhu, Chunhong, additional, Ma, Xun, additional, Zhang, Junjie, additional, Wu, Renwei, additional, Schmieder, Robert, additional, Kaushik, Radhey S., additional, Fraser, George P., additional, Zhao, Shaohua, additional, McDermott, Patrick F., additional, Weill, François-Xavier, additional, Mainil, Jacques G., additional, Arze, Cesar, additional, Fricke, W. Florian, additional, Edwards, Robert A., additional, Brisson, Dustin, additional, Zhang, Nancy R., additional, Rankin, Shelley C., additional, and Schifferli, Dieter M., additional

Published
2015
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32. Polymorphisms in Plasmodium falciparum chloroquine Resistance Transporter and Multidrug Resistance 1 Genes: Parasite Risk Factors That Affect Treatment Outcomes for P. falciparum Malaria After Artemether-Lumefantrine and Artesunate-Amodiaquine

Author

Venkatesan, Meera, Gadalla, Nahla B., Stepniewska, Kasia, Dahal, Prabin, Nsanzabana, Christian, Moriera, Clarissa, Price, Ric N., Martensson, Andreas, Rosenthal, Philip J., Dorsey, Grant, Sutherland, Colin J., Guerin, Philippe, Davis, Timothy M.E., Menard, Didier, Adam, Ishag, Ademowo, George, Arze, Cesar, Baliraine, Frederick, Berens-Riha, Nicole, Venkatesan, Meera, Gadalla, Nahla B., Stepniewska, Kasia, Dahal, Prabin, Nsanzabana, Christian, Moriera, Clarissa, Price, Ric N., Martensson, Andreas, Rosenthal, Philip J., Dorsey, Grant, Sutherland, Colin J., Guerin, Philippe, Davis, Timothy M.E., Menard, Didier, Adam, Ishag, Ademowo, George, Arze, Cesar, Baliraine, Frederick, and Berens-Riha, Nicole

Abstract

Adequate clinical and parasitologic cure by artemisinin combination therapies relies on the artemisinin component and the partner drug. Polymorphisms in the Plasmodium falciparum chloroquine resistance transporter (pfcrt) and P. falciparum multidrug resistance 1 (pfmdr1) genes are associated with decreased sensitivity to amodiaquine and lumefantrine, but effects of these polymorphisms on therapeutic responses to artesunate-amodiaquine (ASAQ) and artemether-lumefantrine (AL) have not been clearly defined. Individual patient data from 31 clinical trials were harmonized and pooled by using standardized methods from the WorldWide Antimalarial Resistance Network. Data for more than 7,000 patients were analyzed to assess relationships between parasite polymorphisms in pfcrt and pfmdr1 and clinically relevant outcomes after treatment with AL or ASAQ. Presence of the pfmdr1 gene N86 (adjusted hazards ratio = 4.74, 95% confidence interval = 2.29 – 9.78, P < 0.001) and increased pfmdr1 copy number (adjusted hazards ratio = 6.52, 95% confidence interval = 2.36–17.97, P < 0.001) were significant independent risk factors for recrudescence in patients treated with AL. AL and ASAQ exerted opposing selective effects on single-nucleotide polymorphisms in pfcrt and pfmdr1. Monitoring selection and responding to emerging signs of drug resistance are critical tools for preserving efficacy of artemisinin combination therapies; determination of the prevalence of at least pfcrt K76T and pfmdr1 N86Y should now be routine.

Published
2014

33. Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data

Author

Kibbe, Warren A., primary, Arze, Cesar, additional, Felix, Victor, additional, Mitraka, Elvira, additional, Bolton, Evan, additional, Fu, Gang, additional, Mungall, Christopher J., additional, Binder, Janos X., additional, Malone, James, additional, Vasant, Drashtti, additional, Parkinson, Helen, additional, and Schriml, Lynn M., additional

Published
2014
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34. Independent Emergence of Artemisinin Resistance Mutations Among Plasmodium falciparum in Southeast Asia

Author

Takala-Harrison, Shannon, primary, Jacob, Christopher G., additional, Arze, Cesar, additional, Cummings, Michael P., additional, Silva, Joana C., additional, Dondorp, Arjen M., additional, Fukuda, Mark M., additional, Hien, Tran Tinh, additional, Mayxay, Mayfong, additional, Noedl, Harald, additional, Nosten, Francois, additional, Kyaw, Myat P., additional, Nhien, Nguyen Thanh Thuy, additional, Imwong, Mallika, additional, Bethell, Delia, additional, Se, Youry, additional, Lon, Chanthap, additional, Tyner, Stuart D., additional, Saunders, David L., additional, Ariey, Frederic, additional, Mercereau-Puijalon, Odile, additional, Menard, Didier, additional, Newton, Paul N., additional, Khanthavong, Maniphone, additional, Hongvanthong, Bouasy, additional, Starzengruber, Peter, additional, Fuehrer, Hans-Peter, additional, Swoboda, Paul, additional, Khan, Wasif A., additional, Phyo, Aung Pyae, additional, Nyunt, Myaing M., additional, Nyunt, Myat H., additional, Brown, Tyler S., additional, Adams, Matthew, additional, Pepin, Christopher S., additional, Bailey, Jason, additional, Tan, John C., additional, Ferdig, Michael T., additional, Clark, Taane G., additional, Miotto, Olivo, additional, MacInnis, Bronwyn, additional, Kwiatkowski, Dominic P., additional, White, Nicholas J., additional, Ringwald, Pascal, additional, and Plowe, Christopher V., additional

Published
2014
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35. CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing

Author

Angiuoli, Samuel V, Angiuoli, Samuel V, Matalka, Malcolm, Gussman, Aaron, Galens, Kevin, Vangala, Mahesh, Riley, David R, Arze, Cesar, White, James R, White, Owen, Fricke, W Florian, Angiuoli, Samuel V, Angiuoli, Samuel V, Matalka, Malcolm, Gussman, Aaron, Galens, Kevin, Vangala, Mahesh, Riley, David R, Arze, Cesar, White, James R, White, Owen, and Fricke, W Florian

Abstract

Next-generation sequencing technologies have decentralized sequence acquisition, increasing the demand for new bioinformatics tools that are easy to use, portable across multiple platforms, and scalable for high-throughput applications. Cloud computing platforms provide on-demand access to computing infrastructure over the Internet and can be used in combination with custom built virtual machines to distribute pre-packaged with pre-configured software. We describe the Cloud Virtual Resource, CloVR, a new desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing. In a case study, we demonstrate the use of CloVR to automatically process next-generation sequencing data on multiple cloud computing platforms. The CloVR VM and associated architecture lowers the barrier of entry for utilizing complex analysis protocols on both local single- and multi-core computers and cloud systems for high throughput data processing.

Published
2011

36. Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia

Author

Takala-Harrison, Shannon, primary, Clark, Taane G., additional, Jacob, Christopher G., additional, Cummings, Michael P., additional, Miotto, Olivo, additional, Dondorp, Arjen M., additional, Fukuda, Mark M., additional, Nosten, Francois, additional, Noedl, Harald, additional, Imwong, Mallika, additional, Bethell, Delia, additional, Se, Youry, additional, Lon, Chanthap, additional, Tyner, Stuart D., additional, Saunders, David L., additional, Socheat, Duong, additional, Ariey, Frederic, additional, Phyo, Aung Pyae, additional, Starzengruber, Peter, additional, Fuehrer, Hans-Peter, additional, Swoboda, Paul, additional, Stepniewska, Kasia, additional, Flegg, Jennifer, additional, Arze, Cesar, additional, Cerqueira, Gustavo C., additional, Silva, Joana C., additional, Ricklefs, Stacy M., additional, Porcella, Stephen F., additional, Stephens, Robert M., additional, Adams, Matthew, additional, Kenefic, Leo J., additional, Campino, Susana, additional, Auburn, Sarah, additional, MacInnis, Bronwyn, additional, Kwiatkowski, Dominic P., additional, Su, Xin-zhuan, additional, White, Nicholas J., additional, Ringwald, Pascal, additional, and Plowe, Christopher V., additional

Published
2012
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38. Corrigendum: Allelic variation contributes to bacterial host specificity.

Author

Yue, Min, Han, Xiangan, De Masi, Leon, Zhu, Chunhong, Ma, Xun, Zhang, Junjie, Wu, Renwei, Schmieder, Robert, Kaushik, Radhey S., Fraser, George P., Zhao, Shaohua, McDermott, Patrick F., Weill, François-Xavier, Mainil, Jacques G., Arze, Cesar, Fricke, W. Florian, Edwards, Robert A., Brisson, Dustin, Zhang, Nancy R., and Rankin, Shelley C.

Abstract

This corrects the article DOI: 10.1038/ncomms9754 [ABSTRACT FROM AUTHOR]

Published
2017
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39. Polymorphisms in Plasmodium falciparum chloroquine resistance transporter and multidrug resistance 1 genes: parasite risk factors that affect treatment outcomes for P. falciparum malaria after artemether-lumefantrine and artesunate-amodiaquine.

Author

Venkatesan M, Gadalla NB, Stepniewska K, Dahal P, Nsanzabana C, Moriera C, Price RN, Mårtensson A, Rosenthal PJ, Dorsey G, Sutherland CJ, Guérin P, Davis TME, Ménard D, Adam I, Ademowo G, Arze C, Baliraine FN, Berens-Riha N, Björkman A, Borrmann S, Checchi F, Desai M, Dhorda M, Djimdé AA, El-Sayed BB, Eshetu T, Eyase F, Falade C, Faucher JF, Fröberg G, Grivoyannis A, Hamour S, Houzé S, Johnson J, Kamugisha E, Kariuki S, Kiechel JR, Kironde F, Kofoed PE, LeBras J, Malmberg M, Mwai L, Ngasala B, Nosten F, Nsobya SL, Nzila A, Oguike M, Otienoburu SD, Ogutu B, Ouédraogo JB, Piola P, Rombo L, Schramm B, Somé AF, Thwing J, Ursing J, Wong RPM, Zeynudin A, Zongo I, Plowe CV, Sibley CH, and Asaq Molecular Marker Study Group

Subjects
Amino Acid Substitution, Amodiaquine therapeutic use, Antimalarials pharmacology, Artemether, Artemisinins therapeutic use, Child, Child, Preschool, Chloroquine pharmacology, Datasets as Topic, Drug Combinations, Drug Resistance genetics, Drug Therapy, Combination, Ethanolamines therapeutic use, Fluorenes therapeutic use, Genetic Markers genetics, Genotype, Humans, Infant, Kaplan-Meier Estimate, Lumefantrine, Malaria, Falciparum drug therapy, Plasmodium falciparum drug effects, Risk Factors, Antimalarials therapeutic use, Malaria, Falciparum parasitology, Membrane Transport Proteins genetics, Multidrug Resistance-Associated Proteins genetics, Plasmodium falciparum genetics, Polymorphism, Genetic, Protozoan Proteins genetics
Abstract

Adequate clinical and parasitologic cure by artemisinin combination therapies relies on the artemisinin component and the partner drug. Polymorphisms in the Plasmodium falciparum chloroquine resistance transporter (pfcrt) and P. falciparum multidrug resistance 1 (pfmdr1) genes are associated with decreased sensitivity to amodiaquine and lumefantrine, but effects of these polymorphisms on therapeutic responses to artesunate-amodiaquine (ASAQ) and artemether-lumefantrine (AL) have not been clearly defined. Individual patient data from 31 clinical trials were harmonized and pooled by using standardized methods from the WorldWide Antimalarial Resistance Network. Data for more than 7,000 patients were analyzed to assess relationships between parasite polymorphisms in pfcrt and pfmdr1 and clinically relevant outcomes after treatment with AL or ASAQ. Presence of the pfmdr1 gene N86 (adjusted hazards ratio = 4.74, 95% confidence interval = 2.29 - 9.78, P < 0.001) and increased pfmdr1 copy number (adjusted hazards ratio = 6.52, 95% confidence interval = 2.36-17.97, P < 0.001 : were significant independent risk factors for recrudescence in patients treated with AL. AL and ASAQ exerted opposing selective effects on single-nucleotide polymorphisms in pfcrt and pfmdr1. Monitoring selection and responding to emerging signs of drug resistance are critical tools for preserving efficacy of artemisinin combination therapies; determination of the prevalence of at least pfcrt K76T and pfmdr1 N86Y should now be routine., (© The American Society of Tropical Medicine and Hygiene.)

Published
2014
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