@article{Eldin2017From, journal={Clinical microbiology reviews}, doi={10.1128/CMR.00045-16}, isbn={0893-8512}, issn={1098-6618}, number=1, pmid=27856520, title={From Q Fever to Coxiella burnetii Infection: a Paradigm Change.}, volume=30, author={Eldin, Carole and Mélenotte, Cléa and Mediannikov, Oleg and Ghigo, Eric and Million, Matthieu and Edouard, Sophie and Mege, Jean-Louis and Maurin, Max and Raoult, Didier}, pages={115--190}, date=2017, year=2017, } @article{Ruiz2014Vaccination, journal={Frontiers in Microbiology}, doi={10.3389/fmicb.2014.00726}, isbn={1664-302x}, issn={1664302X}, number={DEC}, pmid=25566235, title={Vaccination against Q fever for biodefense and public health indications}, volume=5, author={Ruiz, Sara and Wolfe, Daniel N.}, pages={1--7}, date=2014, year=2014, } @article{Raoult2000Q, title={Q fever 1985-1998. Clinical and epidemiologic features of 1,383 infections}, author={Raoult, D and Tissot Dupont, H and Foucault, C and Gouvernet, J and Fournier, PE and Bernit, E and Stein, A and Nesri, M and Harle, JR and Weiller, PJ}, pages={109--23}, date=2000, year=2000, } @article{Parker2006Seminar, journal={Lancet}, doi={10.1016/S0140-6736(06)68266-4}, isbn={1474-547X (Electronic){\textbackslash}r0140-6736 (Linking)}, issn=01406736, pmid=16503466, title={Seminar Q fever}, volume=367, author={Parker, Neil R and Barralet, Jennifer H and Bell, Alan Morton}, pages={679--88}, date=2006, year=2006, } @misc{0Q, title={Q Fever in the United States}, url={https://www.cdc.gov/qfever/stats/index.html}, note={[Online; accessed 2018-09-20]}, date=0000, year=0, } @article{Madariaga2003Q, journal={Lancet Infectious Diseases}, doi={10.1016/S1473-3099(03)00804-1}, isbn={1473-3099 (Print){\textbackslash}r1473-3099 (Linking)}, issn=14733099, number=11, pmid=14592601, title={Q fever: A biological weapon in your backyard}, volume=3, author={Madariaga, Miguel G. and Rezai, Katayoun and Trenholme, Gordon M. and Weinstein, Robert A.}, pages={709--721}, date=2003, year=2003, } @article{Control2002Public, number=2, title={Public Health Assessment of Potential Biological Terrorism Agents}, volume=8, author={Control, Disease and Mor-, Mmwr Morb and Rep, Wkly and Dw, Henderson and Fc, Belton and Sverdlovsk, The and Control, Disease and Morb, Mmwr and Wkly, Mortal and Control, Disease and Morb, Mmwr and Wkly, Mortal and Ja, Jernigan}, pages={225--230}, date=2002, year=2002, } @article{Woldehiwet2004Q, journal={Research in Veterinary Science}, doi={10.1016/j.rvsc.2003.09.001}, isbn={0034-5288 (Print){\textbackslash}r0034-5288 (Linking)}, issn=00345288, number=2, pmid=15196898, title={Q fever (coxiellosis): Epidemiology and pathogenesis}, volume=77, author={Woldehiwet, Zerai}, pages={93--100}, date=2004, year=2004, } @article{Opsteegh2013Inactivation, journal={Journal of Basic Microbiology}, doi={10.1002/jobm.201200211}, issn={0233111X}, title={Inactivation or clearance of Coxiella burnetii in rat serum samples to enable safe serological testing}, volume=53, author={Opsteegh, Marieke and de Heer, Lianne and van den Berg, Harold and van der Giessen, Joke}, pages={796--798}, date=2013, year=2013, } @article{Marmion1990Marmion, journal={Epidemiol Infect.}, issn={0950-2688}, number=2, pmid=2323360, title={Marmion BP, Ormsbee RA, Kyrkou M. Vaccine prophylaxis of abattoir-associated Q fever: eight years' experience in Australian abattoirs.}, volume=104, author={Marmion, B P and Ormsbee, R A and Kyrkou, M and Wright, J and Worswick, D A and Izzo, A A and Esterman, A and Feery, B and Shapiro, R A}, pages={275--87}, date=1990, year=1990, } @article{Chiu2007review, journal={New South Wales public health bulletin}, doi={10.1071/nb07057}, issn={1034-7674}, number={7-8}, pmid=17854543, title={A review of the efficacy of human Q fever vaccine registered in Australia.}, volume=18, author={Chiu, Clayton K. and Durrheim, David N.}, pages={133--6}, date=2007, year=2007, } @article{Schoffelen2013Limited, journal={Journal of Infection}, doi={10.1016/j.jinf.2013.08.008}, issn=01634453, number=6, publisher={Elsevier Ltd}, title={Limited humoral and cellular responses to Qfever vaccination in older adults with risk factors for chronic Q fever}, volume=67, author={Schoffelen, Teske and Herremans, Tineke and Sprong, Tom and Nabuurs-Franssen, Marrigje and Wever, Peter C. and Joosten, Leo A B and Netea, Mihai G. and van der Meer, Jos W M and Bijlmer, Henk A. and Van Deuren, Marcel}, pages={565--573}, date=2013, year=2013, } @article{Kazár1982Immunogenicity, journal={Bulletin of the World Health Organization}, issn={0042-9686}, number=3, pmid=6982774, title={Immunogenicity and reactogenicity of a Q fever chemovaccine in persons professionally exposed to Q fever in Czechoslovakia.}, volume=60, author={Kazár, J and Brezina, R. and Palanová, A and Tvrdá, B. and Schramek, S.}, pages={389--94}, date=1982, year=1982, } @article{Maurin1999Q, journal={Clinical Microbiology Reviews}, doi={citeulike-article-id:8656513}, isbn={0893-8512{\textbackslash}r1098-6618}, issn=08938512, number=4, pmid=10515901, title={Q fever}, volume=12, author={Maurin, M. and Raoult, D.}, pages={518--553}, date=1999, year=1999, } @article{Isken2013Implementation, journal={Vaccine}, doi={10.1016/j.vaccine.2013.03.062}, issn={0264-410X}, number=23, publisher={Elsevier Ltd}, title={Implementation of a Q fever vaccination program for high-risk patients in the Netherlands}, volume=31, author={Isken, Leslie D and Kraaij-dirkzwager, Marleen and Bondt, Patricia E Vermeer-de and Rümke, Hans C and Wijkmans, Clementine and Opstelten, Wim and Timen, Aura}, pages={2617--2622}, date=2013, year=2013, } @book{CSL Biotherapies2009guide, address={Parkville, ABN 66120398067}, title={A guide to Q fever and Q fever vaccination}, author={CSL Biotherapies}, editor={Marmion, Barrie and Spelman, Denis}, date=2009, year=2009, } @article{Chen2011Identification, journal={PLoS ONE}, doi={10.1371/journal.pone.0017712}, isbn={1932-6203 (Electronic){\textbackslash}n1932-6203 (Linking)}, issn=19326203, number=3, pmid=21423609, title={Identification of CD4+ T cell epitopes in C. burnetii antigens targeted by antibody responses}, volume=6, author={Chen, Chen and Dow, Courtney and Wang, Peng and Sidney, John and Read, Amanda and Harmsen, Allen and Samuel, James E. and Peters, Bjoern}, date=2011, year=2011, } @article{Chen2009systematic, journal={Clinical Microbiology and Infection}, doi={10.1111/j.1469-0691.2008.02206.x}, isbn={1469-0691}, issn={1198743X}, number={SUPPL. 2}, pmid=19281461, publisher={European Society of Clinical Microbiology and Infectious Diseases}, title={A systematic approach to evaluate humoral and cellular immune responses to Coxiella burnetii immunoreactive antigens}, volume=15, author={Chen, C. and Bouman, T. J. and Beare, P. A. and Mertens, K. and Zhang, G. Q. and Russell-Lodrigue, K. E. and Hogaboam, J. P. and Peters, B. and Felgner, P. L. and Brown, W. C. and Heinzen, R. A. and Hendrix, L. R. and Samuel, J. E.}, pages={156--157}, date=2009, year=2009, } @article{Reeves2017Q-vaxcelerate:, journal={Human Vaccines and Immunotherapeutics}, doi={10.1080/21645515.2017.1371377}, issn={2164554X}, number=12, title={Q-vaxcelerate: A distributed development approach for a new Coxiella burnetii vaccine}, volume=13, author={Reeves, P.M. and Paul, S.R. and Sluder, A.E. and Brauns, T.A. and Poznansky, M.C.}, date=2017, year=2017, } @article{Xiong2017Identification, journal={Journal of Infectious Diseases}, doi={10.1093/infdis/jiw470}, isbn={1537-6613 (Electronic) 0022-1899 (Linking)}, issn=15376613, number=10, pmid=27703037, title={Identification of Coxiella burnetii CD8 + T-Cell Epitopes and Delivery by Attenuated Listeria monocytogenes as a Vaccine Vector in a C57BL/6 Mouse Model}, volume=215, author={Xiong, Xiaolu and Jiao, Jun and Gregory, Anthony E. and Wang, Pengcheng and Bi, Yujing and Wang, Xiaoyi and Jiang, Yongqiang and Wen, Bohai and Portnoy, Daniel A. and Samuel, James E. and Chen, Chen}, pages={1580--1589}, date=2017, year=2017, } @article{Moise2013Immunization, journal={Human Vaccines and Immunotherapeutics}, doi={10.4161/hv.26511}, isbn={2164-554X (Electronic)}, issn=21645515, number=10, pmid=24045788, title={Immunization with cross-conserved H1N1 influenza CD4+T-cell epitopes lowers viral burden in HLA DR3 transgenic mice}, volume=9, author={Moise, Leonard and Tassone, Ryan and Latimer, Howard and Terry, Frances and Levitz, Lauren and Haran, John P. and Ross, Ted M. and Boyle, Christine and Martin, William D. and De Groot, Anne S.}, pages={2060--2068}, date=2013, year=2013, } @article{Bounds2017immunoinformatics-derived, journal={Human Vaccines and Immunotherapeutics}, doi={10.1080/21645515.2017.1329788}, issn={2164554X}, number=12, pmid=28575582, publisher={Taylor & Francis}, title={An immunoinformatics-derived DNA vaccine encoding human class II T cell epitopes of Ebola virus, Sudan virus, and Venezuelan equine encephalitis virus is immunogenic in HLA transgenic mice}, volume=13, author={Bounds, Callie E. and Terry, Frances E. and Moise, Leonard and Hannaman, Drew and Martin, William D. and De Groot, Anne S. and Suschak, John J. and Dupuy, Lesley C. and Schmaljohn, Connie S.}, pages={2824--2836}, date=2017, year=2017, } @article{Shattuck2014Partial, journal={Human Vaccines and Immunotherapeutics}, doi={10.4161/21645515.2014.985498}, isbn={2164-554X (Electronic){\textbackslash}r2164-5515 (Linking)}, issn={2164554X}, number=10, pmid=25517089, title={Partial pathogen protection by tick-bite sensitization and epitope recognition in peptide-immunized HLA DR3 transgenic mice}, volume=10, author={Shattuck, Wendy M.C. and Dyer, Megan C. and Desrosiers, Joe and Fast, Loren D. and Terry, Frances E. and Martin, William D. and Moise, Leonard and De Groot, Anne S. and Mather, Thomas N.}, pages={3048--3059}, date=2014, year=2014, } @article{Hussain-Yusuf2012analysis, journal={QJM : monthly journal of the Association of Physicians}, doi={10.1093/qjmed/hcs119}, issn={1460-2393}, number=11, pmid=22771556, title={An analysis of Q fever patients 6 years after an outbreak in Newport, Wales, UK.}, volume=105, author={Hussain-Yusuf, H and Islam, A and Healy, B and Lockhart, M and Nguyen, C and Sukocheva, O and Stenos, J and Graves, S}, pages={1067--73}, date={2012-11}, year=2012, month=11, } @article{Teunis2013Time-course, journal={Epidemiology and infection}, doi={10.1017/S0950268812000404}, issn={1469-4409}, number=1, pmid=22475210, title={Time-course of antibody responses against Coxiella burnetii following acute Q fever.}, volume=141, author={Teunis, P F M and Schimmer, B and Notermans, D W and Leenders, A C A P and Wever, P C and Kretzschmar, M E E and Schneeberger, P M}, pages={62--73}, date={2013-01}, year=2013, month=1, } @article{Andoh2007T, journal={Infection and Immunity}, doi={10.1128/IAI.01767-06}, isbn={0019-9567}, issn=00199567, number=7, pmid=17438029, title={T cells are essential for bacterial clearance, and gamma interferon, tumor necrosis factor alpha, and B cells are crucial for disease development in Coxiella burnetii infection in mice}, volume=75, author={Andoh, Masako and Zhang, Guoquan and Russell-Lodrigue, Kasi E. and Shive, Heather R. and Weeks, Brad R. and Samuel, James E.}, pages={3245--3255}, date=2007, year=2007, } @article{Zhang2007Mechanisms, journal={Journal of immunology (Baltimore, Md. : 1950)}, doi={10.4049/jimmunol.179.12.8372}, issn={0022-1767}, number=12, pmid=18056383, title={Mechanisms of vaccine-induced protective immunity against Coxiella burnetii infection in BALB/c mice.}, volume=179, author={Zhang, Guoquan and Russell-Lodrigue, Kasi E. and Andoh, Masako and Zhang, Yan and Hendrix, Laura R. and Samuel, James E.}, pages={8372--80}, date={2007-12-15}, year=2007, month=12, day=15, } @article{Read2010Role, journal={Infection and Immunity}, doi={10.1128/IAI.00101-10}, issn={0019-9567}, number=7, pmid=20351144, title={Role of CD4+ and CD8+ T Cells in Clearance of Primary Pulmonary Infection with Coxiella burnetii}, volume=78, author={Read, A. J. and Erickson, S. and Harmsen, A. G.}, pages={3019--3026}, date=2010, year=2010, } @article{Ledbetter2019MHC-II-restricted,, journal={Infection and immunity}, doi={10.1128/IAI.00824-19}, issn={1098-5522}, number={December}, pmid=31792078, title={MHC-II-restricted, CD4+ T cell-dependent and -independent mechanisms are required for vaccine-induced protective immunity against Coxiella burnetii.}, author={Ledbetter, Lindsey and Cherla, Rama and Chambers, Catherine and Zhang, Yan and Mitchell, William J and Zhang, Guoquan}, date={2019-12-02}, year=2019, month=12, day=2, } @article{Strauss1994Negative, journal={Immunogenetics}, doi={10.1007/BF00188172}, issn={0093-7711}, number=2, pmid=8026858, title={Negative and positive selection by HLA-DR3(DRw17) molecules in transgenic mice.}, volume=40, author={Strauss, G and Vignali, D A and Schönrich, Günther and Hämmerling, Günter J.}, pages={104--8}, date=1994, year=1994, } @article{Arricau-Bouvery2005Effect, journal={Vaccine}, doi={10.1016/j.vaccine.2005.04.010}, isbn={0264-410X (Print){\textbackslash}r0264-410X (Linking)}, issn={0264410X}, number=35, pmid=16005747, title={Effect of vaccination with phase I and phase II Coxiella burnetii vaccines in pregnant goats}, volume=23, author={Arricau-Bouvery, Nathalie and Souriau, Armel and Bodier, Christelle and Dufour, Philippe and Rousset, Elodie and Rodolakis, Annie}, pages={4392--4402}, date=2005, year=2005, } @article{Andoh2007T, journal={Infection and Immunity}, doi={10.1128/IAI.01767-06}, isbn={0019-9567}, issn=00199567, number=7, pmid=17438029, title={T cells are essential for bacterial clearance, and gamma interferon, tumor necrosis factor alpha, and B cells are crucial for disease development in Coxiella burnetii infection in mice}, volume=75, author={Andoh, Masako and Zhang, Guoquan and Russell-Lodrigue, Kasi E. and Shive, Heather R. and Weeks, Brad R. and Samuel, James E.}, pages={3245--3255}, date=2007, year=2007, } @article{Samusik2016Automated, journal={Nature methods}, doi={10.1038/nmeth.3863}, isbn={1548-7105 (Electronic) 1548-7091 (Linking)}, issn={1548-7105}, number=6, pmid=27183440, title={Automated mapping of phenotype space with single-cell data.}, volume=13, author={Samusik, Nikolay and Good, Zinaida and Spitzer, Matthew H and Davis, Kara L and Nolan, Garry P}, pages={493--496}, date=2016, year=2016, } @article{Zou2005Regularization, journal={J. Royal Stat. Soc. B}, number={Part 2}, title={Regularization and Variable Selection via the Elastic Nets}, volume=67, author={Zou, H and Hastie, T}, pages={301--320}, date=2005, year=2005, } @article{Maaten2008Visualizing, journal={Journal of Machine Learning Research}, title={Visualizing Data using \{\vphantom{\}}t-SNE\vphantom{\{}\}}, volume=9, author={van der Maaten, Laurens and Hinton, Geoffrey}, pages={2579--2605}, date=2008, year=2008, } @article{Krzywinski2009Circos:, journal={Genome research}, doi={10.1101/gr.092759.109}, issn={1549-5469}, number=9, pmid=19541911, title={Circos: an information aesthetic for comparative genomics.}, volume=19, author={Krzywinski, Martin and Schein, Jacqueline and Birol, Inanç and Connors, Joseph and Gascoyne, Randy and Horsman, Doug and Jones, Steven J. and Marra, Marco A.}, pages={1639--45}, date={2009-09}, year=2009, month=9, } @article{Shaham2017Removal, journal={Bioinformatics}, doi={10.1093/bioinformatics/btx196}, issn={1367-4803}, number=16, pmid=28419223, title={Removal of batch effects using distribution-matching residual networks}, volume=33, author={Shaham, Uri and Stanton, Kelly P. and Zhao, Jun and Li, Huamin and Raddassi, Khadir and Montgomery, Ruth and Kluger, Yuval}, editor={Wren, Jonathan}, pages={2539--2546}, date={2017-08-15}, year=2017, month=8, day=15, } @article{Amodio2019Exploring, journal={Nature methods}, doi={10.1038/s41592-019-0576-7}, issn={1548-7105}, number={November}, pmid=31591579, publisher={Springer US}, title={Exploring single-cell data with deep multitasking neural networks.}, volume=16, author={Amodio, Matthew and van Dijk, David and Srinivasan, Krishnan and Chen, William S. and Mohsen, Hussein and Moon, Kevin R. and Campbell, Allison and Zhao, Yujiao and Wang, Xiaomei and Venkataswamy, Manjunatha and Desai, Anita and Ravi, V. and Kumar, Priti and Montgomery, Ruth and Wolf, Guy and Krishnaswamy, Smita}, date={2019-10-07}, year=2019, month=10, day=7, } @article{Gassen2019CytoNorm:, journal={Cytometry Part A}, doi={10.1002/cyto.a.23904}, issn=15524930, title={CytoNorm: A Normalization Algorithm for Cytometry Data}, author={Van Gassen, Sofie and Gaudilliere, Brice and Angst, Martin S. and Saeys, Yvan and Aghaeepour, Nima}, date=2019, year=2019, } @article{Gautreau2017SPADEVizR:, journal={Bioinformatics}, doi={10.1093/bioinformatics/btw708}, issn=14602059, number=5, pmid=27993789, title={SPADEVizR: An R package for visualization, analysis and integration of SPADE results}, volume=33, author={Gautreau, Guillaume and Pejoski, David and Le Grand, Roger and Cosma, Antonio and Beignon, Anne Sophie and Tchitchek, Nicolas}, pages={779--781}, date=2017, year=2017, } @article{Zou2005Regularization, journal={J. Royal Stat. Soc. B}, number={Part 2}, title={Regularization and Variable Selection via the Elastic Nets}, volume=67, author={Zou, H and Hastie, T}, pages={301--320}, date=2005, year=2005, } @article{Aghaeepour2017immune, journal={Science immunology}, doi={10.1126/sciimmunol.aan2946}, issn={2470-9468}, number=15, pmid=28864494, title={An immune clock of human pregnancy.}, volume=2, author={Aghaeepour, Nima and Ganio, Edward A and Mcilwain, David and Tsai, Amy S and Tingle, Martha and Van Gassen, Sofie and Gaudilliere, Dyani K and Baca, Quentin and McNeil, Leslie and Okada, Robin and Ghaemi, Mohammad S and Furman, David and Wong, Ronald J and Winn, Virginia D and Druzin, Maurice L and El-Sayed, Yaser Y and Quaintance, Cecele and Gibbs, Ronald and Darmstadt, Gary L and Shaw, Gary M and Stevenson, David K and Tibshirani, Robert and Nolan, Garry P and Lewis, David B and Angst, Martin S and Gaudilliere, Brice}, pages={1--21}, date={2017-09-01}, year=2017, month=9, day=1, } @article{Bamezai0Mouse, journal={Archivum immunologiae et therapiae experimentalis}, issn={0004-069X}, number=4, pmid=15467490, title={Mouse Ly-6 proteins and their extended family: markers of cell differentiation and regulators of cell signaling.}, volume=52, author={Bamezai, Anil}, pages={255--66}, date=0000, year=0, } @article{Gumley1995Tissue, journal={Immunology and cell biology}, doi={10.1038/icb.1995.45}, issn={0818-9641}, number=4, pmid=7493764, title={Tissue expression, structure and function of the murine Ly-6 family of molecules.}, volume=73, author={Gumley, T P and McKenzie, I F and Sandrin, M S}, pages={277--96}, date={1995-08}, year=1995, month=8, } @article{DeLong2018Cytokine-, journal={The Journal of Immunology}, doi={10.4049/jimmunol.1701154}, issn={0022-1767}, pmid=29358280, title={Cytokine- and TCR-Mediated Regulation of T Cell Expression of Ly6C and Sca-1}, author={DeLong, Jonathan H. and Hall, Aisling O’Hara and Konradt, Christoph and Coppock, Gaia M. and Park, Jeongho and Harms Pritchard, Gretchen and Hunter, Christopher A.}, pages={ji1701154}, date=2018, year=2018, } @article{Marshall2011Differential, journal={Immunity}, doi={10.1016/j.immuni.2011.08.016}, isbn={1074-7613}, issn=10747613, number=4, pmid=22018471, publisher={Elsevier Inc.}, title={Differential Expression of Ly6C and T-bet Distinguish Effector and Memory Th1 CD4+Cell Properties during Viral Infection}, volume=35, author={Marshall, Heather D. and Chandele, Anmol and Jung, Yong Woo and Meng, Hailong and Poholek, Amanda C. and Parish, Ian A. and Rutishauser, Rachel and Cui, Weiguo and Kleinstein, Steven H. and Craft, Joe and Kaech, Susan M.}, pages={633--646}, date=2011, year=2011, } @article{Lee2018Phenotypic, journal={Frontiers in Immunology}, doi={10.3389/fimmu.2018.00437}, issn=16643224, number={MAR}, pmid=29616017, title={Phenotypic and functional changes of peripheral Ly6C+T regulatory cells driven by conventional effector T cells}, volume=9, author={Lee, Jun Young and Kim, Juhee and Yi, Jaeu and Kim, Daeun and Kim, Hee Ok and Han, Daehee and Sprent, Jonathan and Lee, You Jeong and Surh, Charles D. and Cho, Jae Ho}, pages={1--15}, date=2018, year=2018, } @article{Goldrath2000Naive, journal={The Journal of experimental medicine}, doi={10.1084/jem.192.4.557}, isbn={0022-1007 (Print)}, issn={0022-1007}, number=4, pmid=10952725, title={Naive T cells transiently acquire a memory-like phenotype during homeostasis-driven proliferation}, volume=192, author={Goldrath, A.W. and Bogatzki, L.Y. and Bevan, M.J.}, pages={557--64}, date=2000, year=2000, } @article{Yamanouchi1998T, journal={European Journal of Immunology}, doi={10.1002/(SICI)1521-4141(199802)28:02{\textless}696::AID-IMMU696{\textgreater}3.0.CO;2-N}, isbn={0014-2980 (Print){\textbackslash}r0014-2980 (Linking)}, issn=00142980, number=2, pmid=9521080, title={A T cell activation antigen, Ly6C, induced on CD4+Th1 cells mediates an inhibitory signal for secretion of IL-2 and proliferation in peripheral immune responses}, volume=28, author={Yamanouchi, Sachiko and Kuwahara, Kazuhiko and Sakata, Atsuko and Ezaki, Taichi and Matsuoka, Shuji and Miyazaki, Jun Ichi and Hirose, Sachiko and Tamura, Toshiki and Nariuchi, Hideo and Sakaguchi, Nobuo}, pages={696--707}, date=1998, year=1998, } @article{Hu2015Functional, journal={Journal of immunology (Baltimore, Md. : 1950)}, doi={10.4049/jimmunol.1401928}, issn={1550-6606}, number=6, pmid=25662997, title={Functional heterogeneity in the CD4+ T cell response to murine γ-herpesvirus 68.}, volume=194, author={Hu, Zhuting and Blackman, Marcia A and Kaye, Kenneth M and Usherwood, Edward J}, pages={2746--56}, date={2015-03-15}, year=2015, month=3, day=15, } @article{Hänninen2011Ly6C, journal={European journal of immunology}, doi={10.1002/eji.201040760}, isbn=3582333752, issn={1521-4141}, number=3, pmid=21308682, title={Ly6C supports preferential homing of central memory CD8+ T cells into lymph nodes.}, volume=41, author={Hänninen, Arno and Maksimow, Mikael and Alam, Catharina and Morgan, David J. and Jalkanen, Sirpa}, pages={634--44}, date={2011-03}, year=2011, month=3, } @article{Walunas1995Ly-6C, journal={Journal of immunology (Baltimore, Md. : 1950)}, issn={0022-1767}, number=4, pmid=7543536, title={Ly-6C is a marker of memory CD8+ T cells.}, volume=155, author={Walunas, T L and Bruce, David S and Dustin, Lynn and Loh, D Y and Bluestone, J A}, pages={1873--83}, date={1995-08-15}, year=1995, month=8, day=15, } @article{Reynolds2015Human, journal={Frontiers in immunology}, doi={10.3389/fimmu.2015.00330}, issn={1664-3224}, number={JUN}, pmid=26124761, title={Human and Mouse Mononuclear Phagocyte Networks: A Tale of Two Species?}, volume=6, author={Reynolds, Gary and Haniffa, Muzlifah}, pages=330, date=2015, year=2015, } @article{Szabo2000novel, journal={Cell}, doi={10.1016/S0092-8674(00)80702-3}, isbn={0092-8674}, issn=00928674, number=6, pmid=10761931, title={A novel transcription factor, T-bet, directs Th1 lineage commitment.}, volume=100, author={Szabo, S J and Kim, S T and Costa, G L and Zhang, X and Fathman, C G and Glimcher, L H}, pages={655--669}, date=2000, year=2000, } @article{Rubtsova2013T-box, journal={Proc Natl Acad Sci U S A}, doi={10.1073/pnas.1312348110}, isbn={1091-6490 (Electronic){\textbackslash}r0027-8424 (Linking)}, issn={0027-8424}, number=34, pmid=23922396, title={T-box transcription factor T-bet, a key player in a unique type of B-cell activation essential for effective viral clearance}, volume=110, author={Rubtsova, K and Rubtsov, V A and van Dyk, L F and Kappler, J W and Marrack, P}, pages={E3216--24}, date=2013, year=2013, } @article{Mayer2008Cutting, journal={Journal of immunology (Baltimore, Md. : 1950)}, doi={10.4049/jimmunol.180.2.693}, isbn={0022-1767 (Print){\textbackslash}r0022-1767 (Linking)}, issn={0022-1767}, number=180, pmid=18178806, title={Cutting Edge: T-bet and IL-27R Are Critical for In Vivo IFN-gamma Production by CD8 T Cells during Infection}, volume=067723, author={Mayer, Katrin D and Mohrs, Katja and Reiley, William and Wittmer, Susan and Kohlmeier, Jacob E and Pearl, John E and Cooper, Andrea M and Johnson, Lawrence L and Woodland, David L and Mohrs, Markus and Reviews, Brief}, pages={693–697}, date=2008, year=2008, } @article{Lazarevic2013T-bet:, journal={Nature reviews. Immunology}, doi={10.1038/nri3536}, isbn={1474-1741 (Electronic){\textbackslash}r1474-1733 (Linking)}, issn={1474-1741}, number=11, pmid=24113868, publisher={Nature Publishing Group}, title={T-bet: a bridge between innate and adaptive immunity.}, volume=13, author={Lazarevic, Vanja and Glimcher, Laurie H and Lord, Graham M}, pages={777--89}, date=2013, year=2013, } @article{Rubtsova2013T-box, journal={Proc Natl Acad Sci U S A}, doi={10.1073/pnas.1312348110}, isbn={1091-6490 (Electronic){\textbackslash}r0027-8424 (Linking)}, issn={0027-8424}, number=34, pmid=23922396, title={T-box transcription factor T-bet, a key player in a unique type of B-cell activation essential for effective viral clearance}, volume=110, author={Rubtsova, K and Rubtsov, V A and van Dyk, L F and Kappler, J W and Marrack, P}, pages={E3216--24}, date=2013, year=2013, } @article{Lazarevic2013T-bet:, journal={Nature reviews. Immunology}, doi={10.1038/nri3536}, isbn={1474-1741 (Electronic){\textbackslash}r1474-1733 (Linking)}, issn={1474-1741}, number=11, pmid=24113868, publisher={Nature Publishing Group}, title={T-bet: a bridge between innate and adaptive immunity.}, volume=13, author={Lazarevic, Vanja and Glimcher, Laurie H and Lord, Graham M}, pages={777--89}, date=2013, year=2013, } @article{Harms Pritchard2015Diverse, journal={Journal of immunology (Baltimore, Md. : 1950)}, doi={10.4049/jimmunol.1401617}, isbn=2157462295, issn={1550-6606}, number=3, pmid=25556247, title={Diverse roles for T-bet in the effector responses required for resistance to infection.}, volume=194, author={Harms Pritchard, Gretchen and Hall, Aisling O'Hara and Christian, David A and Wagage, Sagie and Fang, Qun and Muallem, Gaia and John, Beena and Glatman Zaretsky, Arielle and Dunn, William G and Perrigoue, Jacqueline and Reiner, Steven L and Hunter, Christopher A}, pages={1131--40}, date={2015-02-01}, year=2015, month=2, day=1, } @article{Mohr2010IFN-{gamma}, journal={Proceedings of the National Academy of Sciences of the United States of America}, doi={10.1073/pnas.1004879107}, isbn={1091-6490 (Electronic){\textbackslash}n0027-8424 (Linking)}, issn={0027-8424}, number=40, pmid=20855629, title={IFN-\{\vphantom{\}}gamma\vphantom{\{}\} produced by CD8 T cells induces T-bet-dependent and -independent class switching in B cells in responses to alum-precipitated protein vaccine.}, volume=107, author={Mohr, Elodie and Cunningham, Adam F and Toellner, Kai-Michael and Bobat, Saeeda and Coughlan, Ruth E and Bird, Roger a and MacLennan, Ian C M and Serre, Karine}, pages={17292--17297}, date=2010, year=2010, } @article{Faugaret2014Granulomatous, journal={Frontiers in Cellular and Infection Microbiology}, doi={10.3389/fcimb.2014.00172}, issn={2235-2988}, number={December}, pmid=25566510, title={Granulomatous response to Coxiella burnetii, the agent of Q fever: the lessons from gene expression analysis}, volume=4, author={Faugaret, Delphine and Ben Amara, Amira and Alingrin, Julie and Daumas, Aurélie and Delaby, Amélie and Lépolard, Catherine and Raoult, Didier and Textoris, Julien and Mège, Jean-Louis}, pages={1--8}, date=2014, year=2014, } @article{Faugaret2014Granulomatous, journal={Frontiers in Cellular and Infection Microbiology}, doi={10.3389/fcimb.2014.00172}, issn={2235-2988}, number={December}, pmid=25566510, title={Granulomatous response to Coxiella burnetii, the agent of Q fever: the lessons from gene expression analysis}, volume=4, author={Faugaret, Delphine and Ben Amara, Amira and Alingrin, Julie and Daumas, Aurélie and Delaby, Amélie and Lépolard, Catherine and Raoult, Didier and Textoris, Julien and Mège, Jean-Louis}, pages={1--8}, date=2014, year=2014, } @article{Thompson1989Antibodies, journal={Journal of immunology (Baltimore, Md. : 1950)}, issn={0022-1767}, number=6, pmid=2550543, title={Antibodies to 5'-nucleotidase (CD73), a glycosyl-phosphatidylinositol-anchored protein, cause human peripheral blood T cells to proliferate.}, volume=143, author={Thompson, Linda F and Ruedi, Julie M and Glass, Alison and Low, Martin G and Lucas, Alexander H}, pages={1815--21}, date={1989-09-15}, year=1989, month=9, day=15, } @article{Airas2000CD73, journal={Journal of immunology (Baltimore, Md. : 1950)}, doi={10.4049/jimmunol.165.10.5411}, issn={0022-1767}, number=10, pmid=11067892, title={CD73 engagement promotes lymphocyte binding to endothelial cells via a lymphocyte function-associated antigen-1-dependent mechanism.}, volume=165, author={Airas, L. and Niemelä, J and Jalkanen, S.}, pages={5411--7}, date={2000-11-15}, year=2000, month=11, day=15, } @article{Deaglio2007Adenosine, journal={The Journal of experimental medicine}, doi={10.1084/jem.20062512}, issn={0022-1007}, number=6, pmid=17502665, title={Adenosine generation catalyzed by CD39 and CD73 expressed on regulatory T cells mediates immune suppression.}, volume=204, author={Deaglio, Silvia and Dwyer, Karen M and Gao, Wenda and Friedman, David and Usheva, Anny and Erat, Anna and Chen, Jiang-Fan and Enjyoji, Keiichii and Linden, Joel and Oukka, Mohamed and Kuchroo, Vijay K and Strom, Terry B and Robson, Simon C}, pages={1257--65}, date={2007-06-11}, year=2007, month=6, day=11, } @article{Borsellino2007Expression, journal={Blood}, doi={10.1182/blood-2006-12-064527}, isbn={0006-4971, 1528-0020}, issn={0006-4971}, number=4, pmid=17449799, title={Expression of ectonucleotidase CD39 by Foxp3+ Treg cells: hydrolysis of extracellular ATP and immune suppression}, volume=110, author={Borsellino, G. and Kleinewietfeld, M. and Di Mitri, D. and Sternjak, A. and Diamantini, A. and Giometto, R. and Hopner, S. and Centonze, D. and Bernardi, G. and Dell'Acqua, M. L. and Rossini, P. M. and Battistini, L. and Rotzschke, O. and Falk, K.}, pages={1225--1232}, date={2007-08-15}, year=2007, month=8, day=15, } @article{Takenaka2016Regulation, journal={Trends in Immunology}, doi={10.1016/j.it.2016.04.009}, issn=14714981, number=7, publisher={Elsevier Ltd}, title={Regulation of the T Cell Response by CD39}, volume=37, author={Takenaka, Maisa C. and Robson, Simon and Quintana, Francisco J.}, pages={427--439}, date=2016, year=2016, } @article{Allard2017ectonucleotidases, journal={Immunological Reviews}, doi={10.1111/imr.12528}, issn=01052896, number=1, pmid=26226423, title={The ectonucleotidases CD39 and CD73: Novel checkpoint inhibitor targets}, volume=276, author={Allard, Bertrand and Longhi, Maria Serena and Robson, Simon C. and Stagg, John}, pages={121--144}, date={2017-03-14}, year=2017, month=3, day=14, } @article{Regateiro2013CD73, journal={Clinical and experimental immunology}, doi={10.1111/j.1365-2249.2012.04623.x}, issn={1365-2249}, number=1, pmid=23199317, title={CD73 and adenosine generation in the creation of regulatory microenvironments.}, volume=171, author={Regateiro, F. S. and Cobbold, S. P. and Waldmann, H.}, pages={1--7}, date={2013-01}, year=2013, month=1, } @article{Chen2009systematic, journal={Clinical Microbiology and Infection}, doi={10.1111/j.1469-0691.2008.02206.x}, isbn={1469-0691}, issn={1198743X}, number={SUPPL. 2}, publisher={European Society of Clinical Microbiology and Infectious Diseases}, title={A systematic approach to evaluate humoral and cellular immune responses to Coxiella burnetii immunoreactive antigens}, volume=15, author={Chen, C. and Bouman, T. J. and Beare, P. A. and Mertens, K. and Zhang, G. Q. and Russell-Lodrigue, K. E. and Hogaboam, J. P. and Peters, B. and Felgner, P. L. and Brown, W. C. and Heinzen, R. A. and Hendrix, L. R. and Samuel, J. E.}, pages={156--157}, date=2009, year=2009, } @article{Schaik2013Molecular, journal={Nature reviews. Microbiology}, doi={10.1038/nrmicro3049}, isbn=2122633255, issn={1740-1534}, number=8, pmid=23797173, title={Molecular pathogenesis of the obligate intracellular bacterium Coxiella burnetii.}, volume=11, author={van Schaik, Erin J and Chen, Chen and Mertens, Katja and Weber, Mary M and Samuel, James E}, pages={561--73}, date={2013-08}, year=2013, month=8, } @article{Scott1987Animal, journal={Journal of general microbiology}, doi={10.1099/00221287-133-3-691}, issn={1350-0872}, number=3, pmid=3655728, title={Animal models in Q fever: pathological responses of inbred mice to phase I Coxiella burnetii.}, volume=133, author={Scott, G H and Williams, J C and Stephenson, E H}, pages={691--700}, date=1987, year=1987, } @article{Kong1996HLA-DRB1, journal={The Journal of experimental medicine}, doi={10.1084/jem.184.3.1167}, isbn={0022-1007}, issn={0022-1007}, number=3, pmid=9064334, title={HLA-DRB1 polymorphism determines susceptibility to autoimmune thyroiditis in transgenic mice: definitive association with HLA-DRB1*0301 (DR3) gene.}, volume=184, author={Kong, Y C and Lomo, L C and Motte, R W and Giraldo, A A and Baisch, J and Strauss, G and Hämmerling, G J and David, C S}, pages={1167--72}, date={1996-09-01}, year=1996, month=9, day=1, } @article{Omsland2011Life, journal={Annual review of microbiology}, doi={10.1146/annurev-micro-090110-102927}, issn={1545-3251}, pmid=21639786, title={Life on the outside: the rescue of Coxiella burnetii from its host cell.}, volume=65, author={Omsland, Anders and Heinzen, Robert A}, pages={111--28}, date=2011, year=2011, } @article{Kersh2011Virulence, journal={Vector borne and zoonotic diseases (Larchmont, N.Y.)}, doi={10.1089/vbz.2011.0670}, issn={1557-7759}, number=11, pmid=21867419, title={Virulence of pathogenic Coxiella burnetii strains after growth in the absence of host cells.}, volume=11, author={Kersh, Gilbert J and Oliver, Lindsay D and Self, Joshua S and Fitzpatrick, Kelly A and Massung, Robert F}, pages={1433--8}, date={2011-11}, year=2011, month=11, } @article{Baeten2018Standardized, journal={PloS one}, doi={10.1371/journal.pone.0205882}, isbn=1111111111, issn={1932-6203}, number=10, pmid=30312355, title={Standardized guinea pig model for Q fever vaccine reactogenicity.}, volume=13, author={Baeten, Laurie A. and Podell, Brendan K. and Sluder, Ann E. and Garritsen, Anja and Bowen, Richard A. and Poznansky, Mark C.}, pages={e0205882}, date=2018, year=2018, } @article{Reeves2017Application, journal={FASEB journal}, doi={10.1096/fj.201700325}, number={In press.}, title={Application and utility of mass cytometry in vaccine development}, author={Reeves, Patrick M and Sluder, Ann E and Paul, Susan Raju and Scholzen, Anja and Kashiwagi, Satoshi and Poznansky, Mark C and General, Massachusetts and East, Hospital and Reeves, Patrick M and Sluder, Ann E and Paul, Susan Raju and Scholzen, Anja and Kashiwagi, Satoshi and Poznansky, Mark C}, pages={1--11}, date=2017, year=2017, } @article{Nowicka2017CyTOF, journal={F1000Research}, doi={10.12688/f1000research.11622.3}, issn={2046-1402}, pmid=28663787, title={CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets.}, volume=6, author={Nowicka, Malgorzata and Krieg, Carsten and Crowell, Helena L and Weber, Lukas M and Hartmann, Felix J and Guglietta, Silvia and Becher, Burkhard and Levesque, Mitchell P and Robinson, Mark D}, pages=748, date=2017, year=2017, } @article{Bagwell2019Automated, journal={Cytometry. Part A : the journal of the International Society for Analytical Cytology}, doi={10.1002/cyto.a.23926}, issn={1552-4930}, pmid=31737997, title={Automated Data Cleanup for Mass Cytometry.}, author={Bagwell, Charles Bruce and Inokuma, Margaret and Hunsberger, Benjamin and Herbert, Donald and Bray, Christopher and Hill, Beth and Stelzer, Gregory and Li, Stephen and Kollipara, Avinash and Ornatsky, Olga and Baranov, Vladimir}, date={2019-11-18}, year=2019, month=11, day=18, } @article{R Core Team2013R:, publisher={R Foundation for Statistical Computing}, address={Vienna, Austria}, title={R: A Language and Environment for Statistical Computing}, author={R Core Team}, date=2013, year=2013, } @article{Kolde2019pheatmap:, note={R package version 1.0.12}, title={pheatmap: Pretty Heatmaps}, author={Kolde, Raivo}, date=2019, year=2019, } @article{Charrad2014NbClust, journal={Journal of Statistical Software}, doi={10.18637/jss.v061.i06}, issn={1548-7660}, number=6, title={NbClust : An R Package for Determining the Relevant Number of Clusters in a Data Set}, volume=61, author={Charrad, Malika and Ghazzali, Nadia and Boiteau, Véronique and Niknafs, Azam}, date=2014, year=2014, } @article{Kuhn2008Building, journal={Journal of Statistical Software}, doi={10.18637/jss.v028.i05}, issn={1548-7660}, number=5, title={Building Predictive Models in R Using the caret Package}, volume=28, author={Kuhn, Max}, date=2008, year=2008, } @article{Gu2014circlize, journal={Bioinformatics}, doi={10.1093/bioinformatics/btu393}, issn={1460-2059}, number=19, title={circlize implements and enhances circular visualization in R}, volume=30, author={Gu, Zuguang and Gu, Lei and Eils, Roland and Schlesner, Matthias and Brors, Benedikt}, pages={2811--2812}, date={2014-10}, year=2014, month=10, }