Multivariable association discovery in population-scale meta-omics studies von Mallick, Himel, Rahnavard, Ali, McIver, Lauren J, Ma, Siyuan, Zhang, Yancong, Nguyen, Long H, Tickle, Timothy L, Weingart, George, Ren, Boyu, Schwager, Emma H, Chatterjee, Suvo, Thompson, Kelsey N, Wilkinson, Jeremy E, Subramanian, Ayshwarya, Lu, Yiren, Waldron, Levi, Paulson, Joseph N, Franzosa, Eric A, Bravo, Hector Corrada, Huttenhower, Curtis

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MetaPhlAn2 for enhanced metagenomic taxonomic profiling von Truong, Duy Tin, Franzosa, Eric A, Tickle, Timothy L, Scholz, Matthias, Weingart, George, Pasolli, Edoardo, Tett, Adrian, Huttenhower, Curtis, Segata, Nicola

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Compact graphical representation of phylogenetic data and metadata with GraPhlAn von Asnicar, Francesco, Weingart, George, Tickle, Timothy L, Huttenhower, Curtis, Segata, Nicola

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Biogeography of the Intestinal Mucosal and Lumenal Microbiome in the Rhesus Macaque von Yasuda, Koji, Oh, Keunyoung, Ren, Boyu, Tickle, Timothy L., Franzosa, Eric A., Wachtman, Lynn M., Miller, Andrew D., Westmoreland, Susan V., Mansfield, Keith G., Vallender, Eric J., Miller, Gregory M., Rowlett, James K., Gevers, Dirk, Huttenhower, Curtis, Morgan, Xochitl C.

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Computational meta'omics for microbial community studies von Segata, Nicola, Boernigen, Daniela, Tickle, Timothy L, Morgan, Xochitl C, Garrett, Wendy S, Huttenhower, Curtis

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A statistical model for describing and simulating microbial community profiles von Ma, Siyuan, Ren, Boyu, Mallick, Himel, Moon, Yo Sup, Schwager, Emma, Maharjan, Sagun, Tickle, Timothy L, Lu, Yiren, Carmody, Rachel N, Franzosa, Eric A, Janson, Lucas, Huttenhower, Curtis

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Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes von Lavaert, Marieke, Liang, Kai Ling, Vandamme, Niels, Park, Jong-Eun, Roels, Juliette, Kowalczyk, Monica S., Li, Bo, Ashenberg, Orr, Tabaka, Marcin, Dionne, Danielle, Tickle, Timothy L., Slyper, Michal, Rozenblatt-Rosen, Orit, Vandekerckhove, Bart, Leclercq, Georges, Regev, Aviv, Van Vlierberghe, Pieter, Guilliams, Martin, Teichmann, Sarah A., Saeys, Yvan, Taghon, Tom

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The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation von Wallrapp, Antonia, Riesenfeld, Samantha J., Burkett, Patrick R., Abdulnour, Raja-Elie E., Nyman, Jackson, Dionne, Danielle, Hofree, Matan, Cuoco, Michael S., Rodman, Christopher, Farouq, Daneyal, Haas, Brian J., Tickle, Timothy L., Trombetta, John J., Baral, Pankaj, Klose, Christoph S. N., Mahlakõiv, Tanel, Artis, David, Rozenblatt-Rosen, Orit, Chiu, Isaac M., Levy, Bruce D., Kowalczyk, Monika S., Regev, Aviv, Kuchroo, Vijay K.

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Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature von Haberman, Yael, Tickle, Timothy L, Dexheimer, Phillip J, Kim, Mi-Ok, Tang, Dora, Karns, Rebekah, Baldassano, Robert N, Noe, Joshua D, Rosh, Joel, Markowitz, James, Heyman, Melvin B, Griffiths, Anne M, Crandall, Wallace V, Mack, David R, Baker, Susan S, Huttenhower, Curtis, Keljo, David J, Hyams, Jeffrey S, Kugathasan, Subra, Walters, Thomas D, Aronow, Bruce, Xavier, Ramnik J, Gevers, Dirk, Denson, Lee A

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Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes von Yassour, Moran, Lim, Mi Young, Yun, Hyun Sun, Tickle, Timothy L, Sung, Joohon, Song, Yun-Mi, Lee, Kayoung, Franzosa, Eric A, Morgan, Xochitl C, Gevers, Dirk, Lander, Eric S, Xavier, Ramnik J, Birren, Bruce W, Ko, GwangPyo, Huttenhower, Curtis

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A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors von Bryant, Donald M., Johnson, Kimberly, DiTommaso, Tia, Tickle, Timothy, Couger, Matthew Brian, Payzin-Dogru, Duygu, Lee, Tae J., Leigh, Nicholas D., Kuo, Tzu-Hsing, Davis, Francis G., Bateman, Joel, Bryant, Sevara, Guzikowski, Anna R., Tsai, Stephanie L., Coyne, Steven, Ye, William W., Freeman, Robert M., Peshkin, Leonid, Tabin, Clifford J., Regev, Aviv, Haas, Brian J., Whited, Jessica L.

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The Neuroscience Multi-Omic Archive: a BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain von Ament, Seth A, Adkins, Ricky S, Carter, Robert, Chrysostomou, Elena, Colantuoni, Carlo, Crabtree, Jonathan, Creasy, Heather H, Degatano, Kylee, Felix, Victor, Gandt, Peter, Garden, Gwenn A, Giglio, Michelle, Herb, Brian R, Khajouei, Farzaneh, Kiernan, Elizabeth, McCracken, Carrie, McDaniel, Kennedy, Nadendla, Suvarna, Nickel, Lance, Olley, Dustin, Orvis, Joshua, Receveur, Joseph P, Schor, Mike, Sonthalia, Shreyash, Tickle, Timothy L, Way, Jessica, Hertzano, Ronna, Mahurkar, Anup A, White, Owen R

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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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Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment von Morgan, Xochitl C, Tickle, Timothy L, Sokol, Harry, Gevers, Dirk, Devaney, Kathryn L, Ward, Doyle V, Reyes, Joshua A, Shah, Samir A, LeLeiko, Neal, Snapper, Scott B, Bousvaros, Athos, Korzenik, Joshua, Sands, Bruce E, Xavier, Ramnik J, Huttenhower, Curtis

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Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission von Rooks, Michelle G, Veiga, Patrick, Wardwell-Scott, Leslie H, Tickle, Timothy, Segata, Nicola, Michaud, Monia, Gallini, Carey Ann, Beal, Chloé, van Hylckama-Vlieg, Johan ET, Ballal, Sonia A, Morgan, Xochitl C, Glickman, Jonathan N, Gevers, Dirk, Huttenhower, Curtis, Garrett, Wendy S

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Guided construction of single cell reference for human and mouse lung von Guo, Minzhe, Morley, Michael P., Jiang, Cheng, Wu, Yixin, Li, Guangyuan, Du, Yina, Zhao, Shuyang, Wagner, Andrew, Cakar, Adnan Cihan, Kouril, Michal, Jin, Kang, Gaddis, Nathan, Kitzmiller, Joseph A., Stewart, Kathleen, Basil, Maria C., Lin, Susan M., Ying, Yun, Babu, Apoorva, Wikenheiser-Brokamp, Kathryn A., Mun, Kyu Shik, Naren, Anjaparavanda P., Clair, Geremy, Adkins, Joshua N., Pryhuber, Gloria S., Misra, Ravi S., Aronow, Bruce J., Tickle, Timothy L., Salomonis, Nathan, Sun, Xin, Morrisey, Edward E., Whitsett, Jeffrey A., Xu, Yan

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MAMS: matrix and analysis metadata standards to facilitate harmonization and reproducibility of single-cell data von Sarfraz, Irzam, Wang, Yichen, Shastry, Amulya, Teh, Wei Kheng, Sokolov, Artem, Herb, Brian R, Creasy, Heather H, Virshup, Isaac, Dries, Ruben, Degatano, Kylee, Mahurkar, Anup, Schnell, Daniel J, Madrigal, Pedro, Hilton, Jason, Gehlenborg, Nils, Tickle, Timothy, Campbell, Joshua D

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Two-stage microbial community experimental design von Tickle, Timothy L, Segata, Nicola, Waldron, Levi, Weingart, Uri, Huttenhower, Curtis

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Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research von Kapoor, Muskan, Ventura, Enrique Sapena, Walsh, Amy, Sokolov, Alexey, George, Nancy, Kumari, Sunita, Provart, Nicholas J, Cole, Benjamin, Libault, Marc, Tickle, Timothy, Warren, Wesley C, Koltes, James E, Papatheodorou, Irene, Ware, Doreen, Harrison, Peter W, Elsik, Christine, Yordanova, Galabina, Burdett, Tony, Tuggle, Christopher K

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Towards the uniform distribution of null P values on Affymetrix microarrays von Fodor, Anthony A, Tickle, Timothy L, Richardson, Christine

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