Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues von Waldron, Levi D, Simpson, Peter, Parmigiani, Giovanni, Huttenhower, Curtis

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Metagenomic microbial community profiling using unique clade-specific marker genes von Segata, Nicola, Waldron, Levi D, Ballarini, Annalisa, Narasimhan, Vagheesh, Jousson, Olivier, Huttenhower, Curtis

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A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets von Koren, Omry, Knights, Daniel, Gonzalez, Antonio, Waldron, Levi D, Segata, Nicola, Knight, Rob, Huttenhower, Curtis, Ley, Ruth E

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curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome von Ganzfried, Benjamin Frederick, Riester, Markus, Haibe-Kains, Benjamin, Risch, Thomas, Tyekucheva, Svitlana, Jazic, Ina, Wang, Xin Victoria, Ahmadifar, Mahnaz, Birrer, Michael James, Parmigiani, Giovanni, Huttenhower, Curtis, Waldron, Levi D

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Composition of the Adult Digestive Tract Bacterial Microbiome Based on Seven Mouth Surfaces, Tonsils, Throat and Stool Samples von Segata, Nicholas, Haake, Susan Kinder, Mannon, Peter, Lemon, Katherine Paige, Waldron, Levi D, Gevers, Dirk, Huttenhower, Curtis, Izard, Jacques Georges

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Microbial Community Function and Biomarker Discovery in the Human Microbiome von Abubucker, Sahar, Goll, Johannes, Schubert, Alyxandria M, Cantarel, Brandi L, Rodriguez-Mueller, Beltran, Thiagarajan, Mathangi, Henrissat, Bernard, White, Owen, Kelley, Scott T, Methé, Barbara, Schloss, Patrick D, Gevers, Dirk, Mitreva, Makedonka, Izard, Jacques Georges, Waldron, Levi D, Zucker, Jeremy Daniel Hofeld, Garrett, Wendy S, Huttenhower, Curtis, Segata, Nicola

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Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals von Asnicar, Francesco, Berry, Sarah E., Valdes, Ana M., Nguyen, Long H., Piccinno, Gianmarco, Drew, David A., Leeming, Emily, Gibson, Rachel, Le Roy, Caroline, Khatib, Haya Al, Francis, Lucy, Mazidi, Mohsen, Mompeo, Olatz, Valles-Colomer, Mireia, Tett, Adrian, Beghini, Francesco, Dubois, Léonard, Bazzani, Davide, Thomas, Andrew Maltez, Mirzayi, Chloe, Khleborodova, Asya, Oh, Sehyun, Hine, Rachel, Bonnett, Christopher, Capdevila, Joan, Danzanvilliers, Serge, Giordano, Francesca, Geistlinger, Ludwig, Waldron, Levi, Davies, Richard, Hadjigeorgiou, George, Wolf, Jonathan, Ordovás, José M., Gardner, Christopher, Franks, Paul W., Chan, Andrew T., Huttenhower, Curtis, Spector, Tim D., Segata, Nicola

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Software for the Integration of Multiomics Experiments in Bioconductor von Ramos, Marcel, Schiffer, Lucas, Re, Angela, Azhar, Rimsha, Basunia, Azfar, Rodriguez, Carmen, Chan, Tiffany, Chapman, Phil, Davis, Sean R, Gomez-Cabrero, David, Culhane, Aedin C, Haibe-Kains, Benjamin, Hansen, Kasper D, Kodali, Hanish, Louis, Marie S, Mer, Arvind S, Riester, Markus, Morgan, Martin, Carey, Vince, Waldron, Levi

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Transparency and reproducibility in artificial intelligence von Haibe-Kains, Benjamin, Adam, George Alexandru, Hosny, Ahmed, Khodakarami, Farnoosh, Waldron, Levi, Wang, Bo, McIntosh, Chris, Goldenberg, Anna, Kundaje, Anshul, Greene, Casey S., Broderick, Tamara, Hoffman, Michael M., Leek, Jeffrey T., Korthauer, Keegan, Huber, Wolfgang, Brazma, Alvis, Pineau, Joelle, Tibshirani, Robert, Hastie, Trevor, Ioannidis, John P. A., Quackenbush, John, Aerts, Hugo J. W. L.

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lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R von Khleborodova, Asya, Gamboa-Tuz, Samuel D, Ramos, Marcel, Segata, Nicola, Waldron, Levi, Oh, Sehyun

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Orchestrating high-throughput genomic analysis with Bioconductor von Huber, Wolfgang, Carey, Vincent J, Gentleman, Robert, Anders, Simon, Carlson, Marc, Carvalho, Benilton S, Bravo, Hector Corrada, Davis, Sean, Gatto, Laurent, Girke, Thomas, Gottardo, Raphael, Hahne, Florian, Hansen, Kasper D, Irizarry, Rafael A, Lawrence, Michael, Love, Michael I, MacDonald, James, Obenchain, Valerie, Oleś, Andrzej K, Pagès, Hervé, Reyes, Alejandro, Shannon, Paul, Smyth, Gordon K, Tenenbaum, Dan, Waldron, Levi, Morgan, Martin

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Evaluation of Oral Cavity DNA Extraction Methods on Bacterial and Fungal Microbiota von Rosenbaum, Jennifer, Usyk, Mykhaylo, Chen, Zigui, Zolnik, Christine P., Jones, Heidi E., Waldron, Levi, Dowd, Jennifer B., Thorpe, Lorna E., Burk, Robert D.

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Stem cell gene expression programs influence clinical outcome in human leukemia von Eppert, Kolja, Takenaka, Katsuto, Lechman, Eric R, Waldron, Levi, Nilsson, Björn, van Galen, Peter, Metzeler, Klaus H, Poeppl, Armando, Ling, Vicki, Beyene, Joseph, Canty, Angelo J, Danska, Jayne S, Bohlander, Stefan K, Buske, Christian, Minden, Mark D, Golub, Todd R, Jurisica, Igor, Ebert, Benjamin L, Dick, John E

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Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease von Morgan, Xochitl C, Kabakchiev, Boyko, Waldron, Levi, Tyler, Andrea D, Tickle, Timothy L, Milgrom, Raquel, Stempak, Joanne M, Gevers, Dirk, Xavier, Ramnik J, Silverberg, Mark S, Huttenhower, Curtis

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Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma von Björk, Johannes R., Bolte, Laura A., Maltez Thomas, Andrew, Lee, Karla A., Rossi, Niccolo, Wind, Thijs T., Smit, Lotte M., Armanini, Federica, Asnicar, Francesco, Blanco-Miguez, Aitor, Board, Ruth, Calbet-Llopart, Neus, Derosa, Lisa, Dhomen, Nathalie, Brooks, Kelly, Harland, Mark, Harries, Mark, Lorigan, Paul, Manghi, Paolo, Marais, Richard, Newton-Bishop, Julia, Nezi, Luigi, Pinto, Federica, Potrony, Miriam, Puig, Susana, Serra-Bellver, Patricio, Shaw, Heather M., Tamburini, Sabrina, Valpione, Sara, Waldron, Levi, Zitvogel, Laurence, Zolfo, Moreno, de Vries, Elisabeth G. E., Nathan, Paul, Fehrmann, Rudolf S. N., Spector, Tim D., Bataille, Véronique, Segata, Nicola, Hospers, Geke A. P., Weersma, Rinse K.

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Best practices to evaluate the impact of biomedical research software—metric collection beyond citations von Afiaz, Awan, Ivanov, Andrey A, Chamberlin, John, Hanauer, David, Savonen, Candace L, Goldman, Mary J, Morgan, Martin, Reich, Michael, Getka, Alexander, Holmes, Aaron, Pati, Sarthak, Knight, Dan, Boutros, Paul C, Bakas, Spyridon, Caporaso, J Gregory, Del Fiol, Guilherme, Hochheiser, Harry, Haas, Brian, Schloss, Patrick D, Eddy, James A, Albrecht, Jake, Fedorov, Andrey, Waldron, Levi, Hoffman, Ava M, Bradshaw, Richard L, Leek, Jeffrey T, Wright, Carrie

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MicroRNA Signature Obtained From the Comparison of Aggressive With Indolent Non-Hodgkin Lymphomas: Potential Prognostic Value in Mantle-Cell Lymphoma von GOSWAMI, Rashmi S, ATENAFU, Eshetu G, LAI, Raymond, CHURCH, Alanna J, LAM, Wilson S, BAETZ, Tara, LEBRUN, David P, SEHN, Laurie H, FARINHA, Pedro, JURISICA, Igor, BAILEY, Denis J, GASCOYNE, Randy D, YALI XUAN, CRUMP, Michael, KAMEL-REID, Suzanne, WALDRON, Levi, REIS, Patricia P, SUN, Thomas, DATTI, Alessandro, WEI XU, KURUVILLA, John, GOOD, David J

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Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space von Schatz, Michael C., Philippakis, Anthony A., Afgan, Enis, Banks, Eric, Carey, Vincent J., Carroll, Robert J., Culotti, Alessandro, Ellrott, Kyle, Goecks, Jeremy, Grossman, Robert L., Hall, Ira M., Hansen, Kasper D., Lawson, Jonathan, Leek, Jeffrey T., Luria, Anne O’Donnell, Mosher, Stephen, Morgan, Martin, Nekrutenko, Anton, O’Connor, Brian D., Osborn, Kevin, Paten, Benedict, Patterson, Candace, Tan, Frederick J., Taylor, Casey Overby, Vessio, Jennifer, Waldron, Levi, Wang, Ting, Wuichet, Kristin, Baumann, Alexander, Rula, Andrew, Kovalsy, Anton, Bernard, Clare, Caetano-Anollés, Derek, Van der Auwera, Geraldine A., Canas, Justin, Yuksel, Kaan, Herman, Kate, Taylor, M. Morgan, Simeon, Marianie, Baumann, Michael, Wang, Qi, Title, Robert, Munshi, Ruchi, Chaluvadi, Sushma, Reeves, Valerie, Disman, William, Thomas, Salin, Hajian, Allie, Kiernan, Elizabeth, Gupta, Namrata, Vosburg, Trish, Geistlinger, Ludwig, Ramos, Marcel, Oh, Sehyun, Rogers, Dave, McDade, Frances, Hastie, Mim, Turaga, Nitesh, Ostrovsky, Alexander, Mahmoud, Alexandru, Baker, Dannon, Clements, Dave, Cox, Katherine E.L., Suderman, Keith, Kucher, Nataliya, Golitsynskiy, Sergey, Zarate, Samantha, Wheelan, Sarah J., Kammers, Kai, Stevens, Ana, Hutter, Carolyn, Wellington, Christopher, Ghanaim, Elena M., Wiley, Ken L., Sen, Shurjo K., Di Francesco, Valentina, s Yuen, Deni, Walsh, Brian, Sargent, Luke, Jalili, Vahid, Chilton, John, Shepherd, Lori, Stubbs, B.J., O’Farrell, Ash, Vizzier, Benton A., Overbeck, Charles, Reid, Charles, Steinberg, David Charles, Sheets, Elizabeth A., Lucas, Julian, Blauvelt, Lon, Cabansay, Louise, Warren, Noah, Hannafious, Brian, Harris, Tim, Reddy, Radhika, Torstenson, Eric, Banasiewicz, M. Katie, Abel, Haley J., Walker, Jason

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SIMON: Open-Source Knowledge Discovery Platform von Tomic, Adriana, Tomic, Ivan, Waldron, Levi, Geistlinger, Ludwig, Kuhn, Max, Spreng, Rachel L., Dahora, Lindsay C., Seaton, Kelly E., Tomaras, Georgia, Hill, Jennifer, Duggal, Niharika A., Pollock, Ross D., Lazarus, Norman R., Harridge, Stephen D.R., Lord, Janet M., Khatri, Purvesh, Pollard, Andrew J., Davis, Mark M.

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Public data and open source tools for multi-assay genomic investigation of disease von Kannan, Lavanya, Ramos, Marcel, Re, Angela, El-Hachem, Nehme, Safikhani, Zhaleh, Gendoo, Deena M A, Davis, Sean, Gomez-Cabrero, David, Castelo, Robert, Hansen, Kasper D, Carey, Vincent J, Morgan, Martin, Culhane, Aedín C, Haibe-Kains, Benjamin, Waldron, Levi

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