@article{brochu_wang_tollison_pyo_thomas_tseng_law_picker_gale_geraghty_et al._2022, title={Alternative splicing and genetic variation of mhc-e: implications for rhesus cytomegalovirus-based vaccines}, volume={5}, ISSN={["2399-3642"]}, DOI={10.1038/s42003-022-04344-2}, number={1}, journal={COMMUNICATIONS BIOLOGY}, author={Brochu, Hayden and Wang, Ruihan and Tollison, Tammy and Pyo, Chul-Woo and Thomas, Alexander and Tseng, Elizabeth and Law, Lynn and Picker, Louis J. and Gale, Michael and Geraghty, Daniel E. and et al.}, year={2022}, month={Dec} }
 @article{wu_jiang_zou_sun_wu_cui_huntress_peng_li_2022, title={Coupling high-throughput mapping with proteomics analysis delineates cis-regulatory elements at high resolution}, volume={50}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkab890}, number={1}, journal={NUCLEIC ACIDS RESEARCH}, author={Wu, Ting and Jiang, Danli and Zou, Meijuan and Sun, Wei and Wu, Di and Cui, Jing and Huntress, Ian and Peng, Xinxia and Li, Gang}, year={2022}, month={Jan} }
 @article{huang_callahan_wu_holloway_brochu_lu_peng_tzeng_2022, title={Phylogeny-guided microbiome OTU-specific association test (POST)}, volume={10}, ISSN={["2049-2618"]}, DOI={10.1186/s40168-022-01266-3}, number={1}, journal={MICROBIOME}, author={Huang, Caizhi and Callahan, Benjamin John and Wu, Michael C. and Holloway, Shannon T. and Brochu, Hayden and Lu, Wenbin and Peng, Xinxia and Tzeng, Jung-Ying}, year={2022}, month={Jun} }
 @article{liu_hufnagel_catherine m. o'connell_goonetilleke_mokashi_waterboer_tollison_peng_wiesenfeld_hillier_et al._2022, title={Reduced Endometrial Ascension and Enhanced Reinfection Associated With Immunoglobulin G Antibodies to Specific Chlamydia trachomatis Proteins in Women at Risk for Chlamydia}, volume={225}, ISSN={["1537-6613"]}, DOI={10.1093/infdis/jiab496}, number={5}, journal={JOURNAL OF INFECTIOUS DISEASES}, author={Liu, Chuwen and Hufnagel, Katrin and Catherine M. O'Connell and Goonetilleke, Nilu and Mokashi, Neha and Waterboer, Tim and Tollison, Tammy S. and Peng, Xinxia and Wiesenfeld, Harold C. and Hillier, Sharon L. and et al.}, year={2022}, month={Mar}, pages={846–855} }
 @article{walsh_tollison_brochu_shaw_diveley_chou_law_kirk_gale_peng_2022, title={Single-Cell-Based High-Throughput Ig and TCR Repertoire Sequencing Analysis in Rhesus Macaques}, volume={208}, ISSN={["1550-6606"]}, url={https://doi.org/10.4049/jimmunol.2100824}, DOI={10.4049/jimmunol.2100824}, number={3}, journal={JOURNAL OF IMMUNOLOGY}, author={Walsh, Evan S. and Tollison, Tammy S. and Brochu, Hayden N. and Shaw, Brian I and Diveley, Kayleigh R. and Chou, Hsuan and Law, Lynn and Kirk, Allan D. and Gale, Michael, Jr. and Peng, Xinxia}, year={2022}, month={Feb}, pages={762–771} }
 @article{dawson_rasmussen_peng_lanzas_2021, title={Inferring environmental transmission using phylodynamics: a case-study using simulated evolution of an enteric pathogen}, volume={18}, ISSN={["1742-5662"]}, url={https://doi.org/10.1098/rsif.2021.0041}, DOI={10.1098/rsif.2021.0041}, number={179}, journal={JOURNAL OF THE ROYAL SOCIETY INTERFACE}, author={Dawson, Daniel and Rasmussen, David and Peng, Xinxia and Lanzas, Cristina}, year={2021}, month={Jun} }
 @article{barrenas_hansen_law_driscoll_green_smith_chang_golez_urion_peng_et al._2021, title={Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy}, volume={17}, ISSN={["1553-7374"]}, url={https://doi.org/10.1371/journal.ppat.1009278}, DOI={10.1371/journal.ppat.1009278}, number={7}, journal={PLOS PATHOGENS}, publisher={Public Library of Science (PLoS)}, author={Barrenas, Fredrik and Hansen, Scott G. and Law, Lynn and Driscoll, Connor and Green, Richard R. and Smith, Elise and Chang, Jean and Golez, Inah and Urion, Taryn and Peng, Xinxia and et al.}, editor={Silvestri, GuidoEditor}, year={2021}, month={Jul} }
 @article{barrenäs_hansen_law_driscoll_green_smith_chang_golez_urion_peng_et al._2021, title={Sustained IL-15 response signature predicts RhCMV/SIV vaccine efficacy}, volume={1}, url={https://doi.org/10.1101/2021.01.11.426199}, DOI={10.1101/2021.01.11.426199}, publisher={Cold Spring Harbor Laboratory}, author={Barrenäs, Fredrik and Hansen, Scott G. and Law, Lynn and Driscoll, Connor and Green, Richard R. and Smith, Elise and Chang, Jean and Golez, Inah and Urion, Taryn and Peng, Xinxia and et al.}, year={2021}, month={Jan} }
 @article{nagarajan_cho_gyorke_nagarajan_ezzell_brochu_huntress_harrell_peng_2021, title={Tumor Necrosis Factor Alpha-Induced Interleukin-1 Alpha Synthesis and Cell Death Is Increased in Mouse Epithelial Cells Infected With Chlamydia muridarum}, volume={224}, ISSN={["1537-6613"]}, DOI={10.1093/infdis/jiab168}, journal={JOURNAL OF INFECTIOUS DISEASES}, author={Nagarajan, Uma M. and Cho, Crescentia and Gyorke, Clare E. and Nagarajan, Shanmugam and Ezzell, J. Ashley and Brochu, Hayden and Huntress, Ian and Harrell, Erin and Peng, Xinxia}, year={2021}, month={Aug}, pages={S47–S55} }
 @article{dinh_paudel_brochu_popowski_gracieux_cores_huang_hensley_harrell_vandergriff_et al._2020, title={Inhalation of lung spheroid cell secretome and exosomes promotes lung repair in pulmonary fibrosis}, volume={11}, ISSN={["2041-1723"]}, url={http://dx.doi.org/10.1038/s41467-020-14344-7}, DOI={10.1038/s41467-020-14344-7}, number={1}, journal={NATURE COMMUNICATIONS}, publisher={Springer Science and Business Media LLC}, author={Dinh, Phuong-Uyen C. and Paudel, Dipti and Brochu, Hayden and Popowski, Kristen D. and Gracieux, M. Cyndell and Cores, Jhon and Huang, Ke and Hensley, M. Taylor and Harrell, Erin and Vandergriff, Adam C. and et al.}, year={2020}, month={Feb} }
 @article{brochu_tseng_smith_thomas_jones_diveley_law_hansen_picker_gale_et al._2020, title={Systematic Profiling of Full-Length Ig and TCR Repertoire Diversity in Rhesus Macaque through Long Read Transcriptome Sequencing}, volume={204}, ISSN={["1550-6606"]}, DOI={10.4049/jimmunol.1901256}, number={12}, journal={JOURNAL OF IMMUNOLOGY}, author={Brochu, Hayden N. and Tseng, Elizabeth and Smith, Elise and Thomas, Matthew J. and Jones, Aiden M. and Diveley, Kayleigh R. and Law, Lynn and Hansen, Scott G. and Picker, Louis J. and Gale, Michael, Jr. and et al.}, year={2020}, month={Jun}, pages={3434–3444} }
 @article{martinez_fong_li_yang_jennewein_weiner_harrell_mangold_goswami_seage_et al._2019, title={Fc Characteristics Mediate Selective Placental Transfer of IgG in HIV-Infected Women}, volume={178}, ISSN={["1097-4172"]}, DOI={10.1016/j.cell.2019.05.046}, number={1}, journal={CELL}, author={Martinez, David R. and Fong, Youyi and Li, Shuk Hang and Yang, Fang and Jennewein, Madeleine F. and Weiner, Joshua A. and Harrell, Erin A. and Mangold, Jesse F. and Goswami, Ria and Seage, George R., III and et al.}, year={2019}, month={Jun}, pages={190-+} }
 @article{li_gilbert_carpp_pyo_janes_fong_shen_neidich_goodman_decamp_et al._2019, title={Fc Gamma Receptor Polymorphisms Modulated the Vaccine Effect on HIV-1 Risk in the HVTN 505 HIV Vaccine Trial}, volume={93}, ISSN={["1098-5514"]}, DOI={10.1128/JVI.02041-18}, number={21}, journal={JOURNAL OF VIROLOGY}, author={Li, Shuying S. and Gilbert, Peter B. and Carpp, Lindsay N. and Pyo, Chul-Woo and Janes, Holly and Fong, Youyi and Shen, Xiaoying and Neidich, Scott D. and Goodman, Derrick and deCamp, Allan and et al.}, year={2019}, month={Nov} }
 @article{barrenas_raehtz_xu_law_green_silvestri_bosinger_nishida_li_lu_et al._2019, title={Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control}, volume={10}, ISSN={["2041-1723"]}, DOI={10.1038/s41467-019-12987-9}, journal={NATURE COMMUNICATIONS}, author={Barrenas, Fredrik and Raehtz, Kevin and Xu, Cuiling and Law, Lynn and Green, Richard R. and Silvestri, Guido and Bosinger, Steven E. and Nishida, Andrew and Li, Qingsheng and Lu, Wuxun and et al.}, year={2019}, month={Nov} }
 @article{catherine m. o'connell_brochu_girardi_harrell_jones_darville_sena_peng_2019, title={Simultaneous profiling of sexually transmitted bacterial pathogens, microbiome, and concordant host response in cervical samples using whole transcriptome sequencing analysis}, volume={6}, ISSN={["2311-2638"]}, DOI={10.15698/mic2019.03.672}, number={3}, journal={MICROBIAL CELL}, author={Catherine M. O'Connell and Brochu, Hayden and Girardi, Jenna and Harrell, Erin and Jones, Aiden and Darville, Toni and Sena, Arlene C. and Peng, Xinxia}, year={2019}, month={Mar}, pages={177–183} }
 @article{martinez_fouda_peng_ackerman_permar_2018, title={Noncanonical placental Fc receptors: What is their role in modulating transplacental transfer of maternal IgG?}, volume={14}, ISSN={1553-7374}, url={http://dx.doi.org/10.1371/journal.ppat.1007161}, DOI={10.1371/journal.ppat.1007161}, number={8}, journal={PLOS Pathogens}, publisher={Public Library of Science (PLoS)}, author={Martinez, David R. and Fouda, Genevieve G. and Peng, Xinxia and Ackerman, Margaret E. and Permar, Sallie R.}, editor={Sheppard, Donald C.Editor}, year={2018}, month={Aug}, pages={e1007161} }
 @misc{lemler_brochu_yang_harrell_peng_2017, title={Elucidating the role of host long non-coding RNA during viral infection: Challenges and paths forward}, volume={5}, number={4}, journal={Vaccines}, author={Lemler, D. J. and Brochu, H. N. and Yang, F. and Harrell, E. A. and Peng, X. X.}, year={2017} }
 @article{forero_fenstermacher_wohlgemuth_nishida_carter_smith_peng_hayes_francis_treanor_et al._2017, title={Evaluation of the innate immune responses to influenza and live-attenuated influenza vaccine infection in primary differentiated human nasal epithelial cells}, volume={35}, ISSN={0264-410X}, url={http://dx.doi.org/10.1016/j.vaccine.2017.09.058}, DOI={10.1016/j.vaccine.2017.09.058}, number={45}, journal={Vaccine}, publisher={Elsevier BV}, author={Forero, Adriana and Fenstermacher, Katherine and Wohlgemuth, Nicholas and Nishida, Andrew and Carter, Victoria and Smith, Elise A. and Peng, Xinxia and Hayes, Melissa and Francis, Doreen and Treanor, John and et al.}, year={2017}, month={Oct}, pages={6112–6121} }
 @article{peng_li_gilbert_geraghty_katze_2016, title={FCGR2C Polymorphisms Associated with HIV-1 Vaccine Protection Are Linked to Altered Gene Expression of Fc-γ Receptors in Human B Cells}, volume={11}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0152425}, DOI={10.1371/journal.pone.0152425}, number={3}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Peng, Xinxia and Li, Shuying S. and Gilbert, Peter B. and Geraghty, Daniel E. and Katze, Michael G.}, editor={Tang, JianmingEditor}, year={2016}, month={Mar}, pages={e0152425} }
 @article{tisoncik-go_gasper_kyle_eisfeld_selinger_hatta_morrison_korth_zink_kim_et al._2016, title={Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism}, volume={19}, ISSN={1931-3128}, url={http://dx.doi.org/10.1016/j.chom.2016.01.002}, DOI={10.1016/j.chom.2016.01.002}, number={2}, journal={Cell Host & Microbe}, publisher={Elsevier BV}, author={Tisoncik-Go, Jennifer and Gasper, David J. and Kyle, Jennifer E. and Eisfeld, Amie J. and Selinger, Christian and Hatta, Masato and Morrison, Juliet and Korth, Marcus J. and Zink, Erika M. and Kim, Young-Mo and et al.}, year={2016}, month={Feb}, pages={254–266} }
 @article{peng_pyo_thomas_pyon_law_wang_geraghty_katze_2015, place={New Orleans}, title={Quantitative expression analysis of rhesus macaque MHC alleles}, volume={194}, number={113}, journal={Journal of Immunology}, author={Peng, X. and Pyo, C. and Thomas, M. and Pyon, Y. and Law, L. and Wang, R. and Geraghty, D. and Katze, M.}, year={2015} }
 @article{josset_tchitchek_gralinski_ferris_eisfeld_green_thomas_tisoncik-go_schroth_kawaoka_et al._2014, title={Annotation of long non-coding RNAs expressed in Collaborative Cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts}, volume={11}, ISSN={1547-6286 1555-8584}, url={http://dx.doi.org/10.4161/rna.29442}, DOI={10.4161/rna.29442}, number={7}, journal={RNA Biology}, publisher={Informa UK Limited}, author={Josset, Laurence and Tchitchek, Nicolas and Gralinski, Lisa E and Ferris, Martin T and Eisfeld, Amie J and Green, Richard R and Thomas, Matthew J and Tisoncik-Go, Jennifer and Schroth, Gary P and Kawaoka, Yoshihiro and et al.}, year={2014}, month={Jun}, pages={875–890} }
 @article{peng_pipes_xiong_green_jones_ruzzo_schroth_mason_palermo_katze_2014, title={Assessment and improvement of Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data}, volume={43}, ISSN={0047-2565}, url={http://dx.doi.org/10.1111/jmp.12125}, DOI={10.1111/jmp.12125}, number={5}, journal={Journal of Medical Primatology}, publisher={Wiley}, author={Peng, Xinxia and Pipes, Lenore and Xiong, Hao and Green, Richard R. and Jones, Daniel C. and Ruzzo, Walter L. and Schroth, Gary P. and Mason, Christopher E. and Palermo, Robert E. and Katze, Michael G.}, year={2014}, month={May}, pages={317–328} }
 @article{peng_sova_green_thomas_korth_proll_xu_cheng_yi_chen_et al._2014, title={Deep Sequencing of HIV-Infected Cells: Insights into Nascent Transcription and Host-Directed Therapy}, volume={88}, ISSN={0022-538X 1098-5514}, url={http://dx.doi.org/10.1128/jvi.00768-14}, DOI={10.1128/jvi.00768-14}, number={16}, journal={Journal of Virology}, publisher={American Society for Microbiology}, author={Peng, X. and Sova, P. and Green, R. R. and Thomas, M. J. and Korth, M. J. and Proll, S. and Xu, J. and Cheng, Y. and Yi, K. and Chen, L. and et al.}, year={2014}, month={May}, pages={8768–8782} }
 @article{barrenas_palermo_agricola_agy_aicher_carter_flanary_green_mclain_li_et al._2014, title={Deep Transcriptional Sequencing of Mucosal Challenge Compartment from Rhesus Macaques Acutely Infected with Simian Immunodeficiency Virus Implicates Loss of Cell Adhesion Preceding Immune Activation}, volume={88}, ISSN={0022-538X 1098-5514}, url={http://dx.doi.org/10.1128/jvi.00543-14}, DOI={10.1128/jvi.00543-14}, abstractNote={ABSTRACT}, number={14}, journal={Journal of Virology}, publisher={American Society for Microbiology}, author={Barrenas, Fredrik and Palermo, Robert E. and Agricola, Brian and Agy, Michael B. and Aicher, Lauri and Carter, Victoria and Flanary, Leon and Green, Richard R. and McLain, Randy and Li, Qingsheng and et al.}, editor={Silvestri, G.Editor}, year={2014}, month={May}, pages={7962–7972} }
 @article{xiong_morrison_ferris_gralinski_whitmore_green_thomas_tisoncik-go_schroth_pardo-manuel de villena_et al._2014, title={Genomic Profiling of Collaborative Cross Founder Mice Infected with Respiratory Viruses Reveals Novel Transcripts and Infection-Related Strain-Specific Gene and Isoform Expression}, volume={4}, ISSN={2160-1836}, url={http://dx.doi.org/10.1534/g3.114.011759}, DOI={10.1534/g3.114.011759}, number={8}, journal={G3: Genes|Genomes|Genetics}, publisher={Genetics Society of America}, author={Xiong, Hao and Morrison, Juliet and Ferris, Martin T. and Gralinski, Lisa E. and Whitmore, Alan C. and Green, Richard and Thomas, Matthew J. and Tisoncik-Go, Jennifer and Schroth, Gary P. and Pardo-Manuel de Villena, Fernando and et al.}, year={2014}, month={Jun}, pages={1429–1444} }
 @article{falzarano_de wit_feldmann_rasmussen_okumura_peng_thomas_van doremalen_haddock_nagy_et al._2014, title={Infection with MERS-CoV Causes Lethal Pneumonia in the Common Marmoset}, volume={10}, ISSN={1553-7374}, url={http://dx.doi.org/10.1371/journal.ppat.1004250}, DOI={10.1371/journal.ppat.1004250}, number={8}, journal={PLoS Pathogens}, publisher={Public Library of Science (PLoS)}, author={Falzarano, Darryl and de Wit, Emmie and Feldmann, Friederike and Rasmussen, Angela L. and Okumura, Atsushi and Peng, Xinxia and Thomas, Matthew J. and van Doremalen, Neeltje and Haddock, Elaine and Nagy, Lee and et al.}, editor={Denison, Mark R.Editor}, year={2014}, month={Aug}, pages={e1004250} }
 @article{peng_alföldi_gori_eisfeld_tyler_tisoncik-go_brawand_law_skunca_hatta_et al._2014, title={The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease}, volume={32}, ISSN={1087-0156 1546-1696}, url={http://dx.doi.org/10.1038/nbt.3079}, DOI={10.1038/nbt.3079}, number={12}, journal={Nature Biotechnology}, publisher={Springer Nature}, author={Peng, Xinxia and Alföldi, Jessica and Gori, Kevin and Eisfeld, Amie J and Tyler, Scott R and Tisoncik-Go, Jennifer and Brawand, David and Law, G Lynn and Skunca, Nives and Hatta, Masato and et al.}, year={2014}, month={Nov}, pages={1250–1255} }
 @article{peng_thierry-mieg_thierry-mieg_nishida_pipes_bozinoski_thomas_kelly_weiss_raveendran_et al._2014, title={Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR)}, volume={43}, ISSN={1362-4962 0305-1048}, url={http://dx.doi.org/10.1093/nar/gku1110}, DOI={10.1093/nar/gku1110}, number={D1}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, author={Peng, Xinxia and Thierry-Mieg, Jean and Thierry-Mieg, Danielle and Nishida, Andrew and Pipes, Lenore and Bozinoski, Marjan and Thomas, Matthew J. and Kelly, Sara and Weiss, Jeffrey M. and Raveendran, Muthuswamy and et al.}, year={2014}, month={Nov}, pages={D737–D742} }
 @article{bruce_ryan_thomas_peng_grundhoff_tsai_rose_2013, title={Next-Generation Sequence Analysis of the Genome of RFHVMn, the Macaque Homolog of Kaposi's Sarcoma (KS)-Associated Herpesvirus, from a KS-Like Tumor of a Pig-Tailed Macaque}, volume={87}, ISSN={0022-538X}, url={http://dx.doi.org/10.1128/jvi.02331-13}, DOI={10.1128/jvi.02331-13}, number={24}, journal={Journal of Virology}, publisher={American Society for Microbiology}, author={Bruce, A. G. and Ryan, J. T. and Thomas, M. J. and Peng, X. and Grundhoff, A. and Tsai, C.-C. and Rose, T. M.}, year={2013}, month={Oct}, pages={13676–13693} }
 @article{jones_ruzzo_peng_katze_2012, title={A new approach to bias correction in RNA-Seq}, volume={28}, ISSN={1460-2059 1367-4803}, url={http://dx.doi.org/10.1093/bioinformatics/bts055}, DOI={10.1093/bioinformatics/bts055}, number={7}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Jones, Daniel C. and Ruzzo, Walter L. and Peng, Xinxia and Katze, Michael G.}, year={2012}, month={Jan}, pages={921–928} }
 @article{jones_ruzzo_peng_katze_2012, title={Compression of next-generation sequencing reads aided by highly efficient de novo assembly}, volume={40}, ISSN={1362-4962 0305-1048}, url={http://dx.doi.org/10.1093/nar/gks754}, DOI={10.1093/nar/gks754}, number={22}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, author={Jones, Daniel C. and Ruzzo, Walter L. and Peng, Xinxia and Katze, Michael G.}, year={2012}, month={Aug}, pages={e171–e171} }
 @article{pipes_li_bozinoski_palermo_peng_blood_kelly_weiss_thierry-mieg_thierry-mieg_et al._2012, title={The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics}, volume={41}, ISSN={0305-1048 1362-4962}, url={http://dx.doi.org/10.1093/nar/gks1268}, DOI={10.1093/nar/gks1268}, number={D1}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, author={Pipes, Lenore and Li, Sheng and Bozinoski, Marjan and Palermo, Robert and Peng, Xinxia and Blood, Phillip and Kelly, Sara and Weiss, Jeffrey M. and Thierry-Mieg, Jean and Thierry-Mieg, Danielle and et al.}, year={2012}, month={Nov}, pages={D906–D914} }
 @article{peng_gralinski_ferris_frieman_thomas_proll_korth_tisoncik_heise_luo_et al._2011, title={Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection}, volume={2}, ISSN={2150-7511}, url={http://dx.doi.org/10.1128/mbio.00198-11}, DOI={10.1128/mbio.00198-11}, abstractNote={ABSTRACT
               <jats:p>We previously reported widespread differential expression of long non-protein-coding RNAs (ncRNAs) in response to virus infection. Here, we expanded the study through small RNA transcriptome sequencing analysis of the host response to both severe acute respiratory syndrome coronavirus (SARS-CoV) and influenza virus infections across four founder mouse strains of the Collaborative Cross, a recombinant inbred mouse resource for mapping complex traits. We observed differential expression of over 200 small RNAs of diverse classes during infection. A majority of identified microRNAs (miRNAs) showed divergent changes in expression across mouse strains with respect to SARS-CoV and influenza virus infections and responded differently to a highly pathogenic reconstructed 1918 virus compared to a minimally pathogenic seasonal influenza virus isolate. Novel insights into miRNA expression changes, including the association with pathogenic outcomes and large differences between <jats:italic>in vivo
               <jats:p>
                  <jats:bold>IMPORTANCE}, number={6}, journal={mBio}, publisher={American Society for Microbiology}, author={Peng, Xinxia and Gralinski, Lisa and Ferris, Martin T. and Frieman, Matthew B. and Thomas, Matthew J. and Proll, Sean and Korth, Marcus J. and Tisoncik, Jennifer R. and Heise, Mark and Luo, Shujun and et al.}, editor={Cullen, Bryan and Dermody, Terence S.Editors}, year={2011}, month={Nov} }
 @article{chang_sova_peng_weiss_law_palermo_katze_2011, title={Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4+ T Cell Line}, volume={2}, ISSN={2150-7511}, url={http://dx.doi.org/10.1128/mbio.00134-11}, DOI={10.1128/mbio.00134-11}, abstractNote={ABSTRACT
               <jats:p>Next-generation sequencing (NGS) enables the highly sensitive measurement of whole transcriptomes. We report the first application to our knowledge of this technology to the analysis of RNA from a CD4<jats:sup>+
               <jats:p>
                  <jats:bold>IMPORTANCE}, number={5}, journal={mBio}, publisher={American Society for Microbiology}, author={Chang, Stewart T. and Sova, Pavel and Peng, Xinxia and Weiss, Jeffrey and Law, G. Lynn and Palermo, Robert E. and Katze, Michael G.}, editor={Unutmaz, Derya and Dermody, Terence S.Editors}, year={2011}, month={Sep} }
 @article{cilloniz_pantin-jackwood_ni_goodman_peng_proll_carter_rosenzweig_szretter_katz_et al._2010, title={Lethal Dissemination of H5N1 Influenza Virus Is Associated with Dysregulation of Inflammation and Lipoxin Signaling in a Mouse Model of Infection}, volume={84}, ISSN={0022-538X}, url={http://dx.doi.org/10.1128/jvi.00553-10}, DOI={10.1128/jvi.00553-10}, number={15}, journal={Journal of Virology}, publisher={American Society for Microbiology}, author={Cilloniz, C. and Pantin-Jackwood, M. J. and Ni, C. and Goodman, A. G. and Peng, X. and Proll, S. C. and Carter, V. S. and Rosenzweig, E. R. and Szretter, K. J. and Katz, J. M. and et al.}, year={2010}, month={May}, pages={7613–7624} }
 @article{li_chan_li_ni_peng_rosenzweig_tumpey_katze_2010, title={MicroRNA Expression and Virulence in Pandemic Influenza Virus-Infected Mice}, volume={84}, ISSN={0022-538X}, url={http://dx.doi.org/10.1128/jvi.02203-09}, DOI={10.1128/jvi.02203-09}, number={6}, journal={Journal of Virology}, publisher={American Society for Microbiology}, author={Li, Y. and Chan, E. Y. and Li, J. and Ni, C. and Peng, X. and Rosenzweig, E. and Tumpey, T. M. and Katze, M. G.}, year={2010}, month={Jan}, pages={3023–3032} }
 @article{aly_lindner_mackellar_peng_kappe_2010, title={SAP1 is a critical post-transcriptional regulator of infectivity in malaria parasite sporozoite stages}, volume={79}, ISSN={0950-382X}, url={http://dx.doi.org/10.1111/j.1365-2958.2010.07497.x}, DOI={10.1111/j.1365-2958.2010.07497.x}, number={4}, journal={Molecular Microbiology}, publisher={Wiley}, author={Aly, Ahmed S. I. and Lindner, Scott E. and MacKellar, Drew C. and Peng, Xinxia and Kappe, Stefan H. I.}, year={2010}, month={Dec}, pages={929–939} }
 @article{peng_gralinski_armour_ferris_thomas_proll_bradel-tretheway_korth_castle_biery_et al._2010, title={Unique Signatures of Long Noncoding RNA Expression in Response to Virus Infection and Altered Innate Immune Signaling}, volume={1}, ISSN={2150-7511}, url={http://dx.doi.org/10.1128/mbio.00206-10}, DOI={10.1128/mbio.00206-10}, abstractNote={ABSTRACT
               <jats:p>Studies of the host response to virus infection typically focus on protein-coding genes. However, non-protein-coding RNAs (ncRNAs) are transcribed in mammalian cells, and the roles of many of these ncRNAs remain enigmas. Using next-generation sequencing, we performed a whole-transcriptome analysis of the host response to severe acute respiratory syndrome coronavirus (SARS-CoV) infection across four founder mouse strains of the Collaborative Cross. We observed differential expression of approximately 500 annotated, long ncRNAs and 1,000 nonannotated genomic regions during infection. Moreover, studies of a subset of these ncRNAs and genomic regions showed the following. (i) Most were similarly regulated in response to influenza virus infection. (ii) They had distinctive kinetic expression profiles in type I interferon receptor and STAT1 knockout mice during SARS-CoV infection, including unique signatures of ncRNA expression associated with lethal infection. (iii) Over 40% were similarly regulated <jats:italic>in vitro
               <jats:p>
                  <jats:bold>IMPORTANCE}, number={5}, journal={mBio}, publisher={American Society for Microbiology}, author={Peng, Xinxia and Gralinski, Lisa and Armour, Christopher D. and Ferris, Martin T. and Thomas, Matthew J. and Proll, Sean and Bradel-Tretheway, Birgit G. and Korth, Marcus J. and Castle, John C. and Biery, Matthew C. and et al.}, editor={Sonenberg, Nahum and Dermody, Terence S.Editors}, year={2010}, month={Oct} }
 @article{peng_li_walters_rosenzweig_lederer_aicher_proll_katze_2009, title={Computational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human livers}, volume={10}, ISSN={1471-2164}, url={http://dx.doi.org/10.1186/1471-2164-10-373}, DOI={10.1186/1471-2164-10-373}, number={1}, journal={BMC Genomics}, publisher={Springer Nature}, author={Peng, Xinxia and Li, Yu and Walters, Kathie-Anne and Rosenzweig, Elizabeth R and Lederer, Sharon L and Aicher, Lauri D and Proll, Sean and Katze, Michael G}, year={2009}, pages={373} }
 @article{albuquerque_carret_grosso_tarun_peng_kappe_prudêncio_mota_2009, title={Host cell transcriptional profiling during malaria liver stage infection reveals a coordinated and sequential set of biological events}, volume={10}, ISSN={1471-2164}, url={http://dx.doi.org/10.1186/1471-2164-10-270}, DOI={10.1186/1471-2164-10-270}, number={1}, journal={BMC Genomics}, publisher={Springer Nature}, author={Albuquerque, Sónia S and Carret, Céline and Grosso, Ana and Tarun, Alice S and Peng, Xinxia and Kappe, Stefan HI and Prudêncio, Miguel and Mota, Maria M}, year={2009}, pages={270} }
 @article{cillóniz_shinya_peng_korth_proll_aicher_carter_chang_kobasa_feldmann_et al._2009, title={Lethal Influenza Virus Infection in Macaques Is Associated with Early Dysregulation of Inflammatory Related Genes}, volume={5}, ISSN={1553-7374}, url={http://dx.doi.org/10.1371/journal.ppat.1000604}, DOI={10.1371/journal.ppat.1000604}, number={10}, journal={PLoS Pathogens}, publisher={Public Library of Science (PLoS)}, author={Cillóniz, Cristian and Shinya, Kyoko and Peng, Xinxia and Korth, Marcus J. and Proll, Sean C. and Aicher, Lauri D. and Carter, Victoria S. and Chang, Jean H. and Kobasa, Darwyn and Feldmann, Friedericke and et al.}, editor={Diamond, Michael S.Editor}, year={2009}, month={Oct}, pages={e1000604} }
 @article{goodman_fornek_medigeshi_perrone_peng_dyer_proll_knoblaugh_carter_korth_et al._2009, title={P58IPK: A Novel “CIHD” Member of the Host Innate Defense Response against Pathogenic Virus Infection}, volume={5}, ISSN={1553-7374}, url={http://dx.doi.org/10.1371/journal.ppat.1000438}, DOI={10.1371/journal.ppat.1000438}, number={5}, journal={PLoS Pathogens}, publisher={Public Library of Science (PLoS)}, author={Goodman, Alan G. and Fornek, Jamie L. and Medigeshi, Guruprasad R. and Perrone, Lucy A. and Peng, Xinxia and Dyer, Matthew D. and Proll, Sean C. and Knoblaugh, Sue E. and Carter, Victoria S. and Korth, Marcus J. and et al.}, editor={Andino, RaulEditor}, year={2009}, month={May}, pages={e1000438} }
 @article{goodman_zeng_proll_peng_cilloniz_carter_korth_tumpey_katze_2009, title={The Alpha/Beta Interferon Receptor Provides Protection against Influenza Virus Replication but Is Dispensable for Inflammatory Response Signaling}, volume={84}, ISSN={0022-538X}, url={http://dx.doi.org/10.1128/jvi.01595-09}, DOI={10.1128/jvi.01595-09}, number={4}, journal={Journal of Virology}, publisher={American Society for Microbiology}, author={Goodman, A. G. and Zeng, H. and Proll, S. C. and Peng, X. and Cilloniz, C. and Carter, V. S. and Korth, M. J. and Tumpey, T. M. and Katze, M. G.}, year={2009}, month={Nov}, pages={2027–2037} }
 @article{goodman_zeng_cilloniz_carter_peng_proll_tumpey_katze_2009, title={The Type I interferon receptor protects against influenza virus replication while the Type II receptor is dispensible}, volume={48}, ISSN={1043-4666}, url={http://dx.doi.org/10.1016/j.cyto.2009.07.294}, DOI={10.1016/j.cyto.2009.07.294}, number={1-2}, journal={Cytokine}, publisher={Elsevier BV}, author={Goodman, Alan G. and Zeng, Hui and Cilloniz, Cristian and Carter, Victoria S. and Peng, Xinxia and Proll, Sean C. and Tumpey, Terrence M. and Katze, Michael G.}, year={2009}, month={Oct}, pages={83} }
 @article{peng_chan_li_diamond_korth_katze_2009, title={Virus–host interactions: from systems biology to translational research}, volume={12}, ISSN={1369-5274}, url={http://dx.doi.org/10.1016/j.mib.2009.06.003}, DOI={10.1016/j.mib.2009.06.003}, number={4}, journal={Current Opinion in Microbiology}, publisher={Elsevier BV}, author={Peng, Xinxia and Chan, Eric Y and Li, Yu and Diamond, Deborah L and Korth, Marcus J and Katze, Michael G}, year={2009}, month={Aug}, pages={432–438} }
 @article{tarun_peng_dumpit_ogata_silva-rivera_camargo_daly_bergman_kappe_2008, title={A combined transcriptome and proteome survey of malaria parasite liver stages}, volume={105}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.0710780104}, DOI={10.1073/pnas.0710780104}, number={1}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Tarun, A. S. and Peng, X. and Dumpit, R. F. and Ogata, Y. and Silva-Rivera, H. and Camargo, N. and Daly, T. M. and Bergman, L. W. and Kappe, S. H. I.}, year={2008}, month={Jan}, pages={305–310} }
 @article{vaughan_chiu_ramasamy_li_gardner_tarun_kappe_peng_2008, title={Assessment and improvement of the Plasmodium yoelii yoelii genome annotation through comparative analysis}, volume={24}, ISSN={1460-2059 1367-4803}, url={http://dx.doi.org/10.1093/bioinformatics/btn140}, DOI={10.1093/bioinformatics/btn140}, number={13}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Vaughan, Ashley and Chiu, Sum-Ying and Ramasamy, Gowthaman and Li, Ling and Gardner, Malcolm J. and Tarun, Alice S. and Kappe, Stefan H.I. and Peng, Xinxia}, year={2008}, month={Jul}, pages={i383–i389} }
 @article{mikolajczak_silva-rivera_peng_tarun_camargo_jacobs-lorena_daly_bergman_de la vega_williams_et al._2008, title={Distinct Malaria Parasite Sporozoites Reveal Transcriptional Changes That Cause Differential Tissue Infection Competence in the Mosquito Vector and Mammalian Host}, volume={28}, ISSN={0270-7306}, url={http://dx.doi.org/10.1128/mcb.00553-08}, DOI={10.1128/mcb.00553-08}, number={20}, journal={Molecular and Cellular Biology}, publisher={American Society for Microbiology}, author={Mikolajczak, S. A. and Silva-Rivera, H. and Peng, X. and Tarun, A. S. and Camargo, N. and Jacobs-Lorena, V. and Daly, T. M. and Bergman, L. W. and de la Vega, P. and Williams, J. and et al.}, year={2008}, month={Aug}, pages={6196–6207} }
 @inbook{peng_langston_saxton_baldwin_snoddy_2007, title={Detecting Network Motifs in Gene Co-expression Networks Through Integration of Protein Domain Information}, ISBN={9780387345680}, url={http://dx.doi.org/10.1007/978-0-387-34569-7_7}, DOI={10.1007/978-0-387-34569-7_7}, booktitle={Methods of Microarray Data Analysis V}, publisher={Springer US}, author={Peng, Xinxia and Langston, Michael A. and Saxton, Arnold M. and Baldwin, Nicole E. and Snoddy, Jay R.}, year={2007}, month={Feb}, pages={89–102} }
 @article{kirov_peng_baker_schmoyer_zhang_snoddy_2005, title={GeneKeyDB: A lightweight, gene-centric, relational database to support data mining environments}, volume={6}, ISSN={1471-2105}, url={http://dx.doi.org/10.1186/1471-2105-6-72}, DOI={10.1186/1471-2105-6-72}, number={1}, journal={BMC Bioinformatics}, publisher={Springer Nature}, author={Kirov, SA and Peng, X and Baker, E and Schmoyer, D and Zhang, B and Snoddy, J}, year={2005}, pages={72} }