Xinxia Peng

John, K., Huntress, I., Smith, E., Chou, H., Tollison, T. S., Covarrubias, S., … Peng, X. (2024, March 29). Human long noncoding RNA,VILMIR,is induced by major respiratory viral infections and modulates the host interferon response. https://doi.org/10.1101/2024.03.25.586578

Brochu, H. N., Smith, E., Jeong, S., Carlson, M., Hansen, S. G., Tisoncik-Go, J., … Peng, X. (2024, February 28). Pre-challenge gut microbial signature predicts RhCMV/SIV vaccine efficacy in rhesus macaques. https://doi.org/10.1101/2024.02.27.582186

Brochu, H., Wang, R., Tollison, T., Pyo, C.-W., Thomas, A., Tseng, E., … Peng, X. (2022). Alternative splicing and genetic variation of mhc-e: implications for rhesus cytomegalovirus-based vaccines. COMMUNICATIONS BIOLOGY, 5(1). https://doi.org/10.1038/s42003-022-04344-2

Wu, T., Jiang, D., Zou, M., Sun, W., Wu, D., Cui, J., … Li, G. (2022). Coupling high-throughput mapping with proteomics analysis delineates cis-regulatory elements at high resolution. NUCLEIC ACIDS RESEARCH, 50(1). https://doi.org/10.1093/nar/gkab890

Huang, C., Callahan, B. J., Wu, M. C., Holloway, S. T., Brochu, H., Lu, W., … Tzeng, J.-Y. (2022). Phylogeny-guided microbiome OTU-specific association test (POST). MICROBIOME, 10(1). https://doi.org/10.1186/s40168-022-01266-3

Liu, C., Hufnagel, K., Catherine M. O'Connell, Goonetilleke, N., Mokashi, N., Waterboer, T., … Darville, T. (2022). Reduced Endometrial Ascension and Enhanced Reinfection Associated With Immunoglobulin G Antibodies to Specific Chlamydia trachomatis Proteins in Women at Risk for Chlamydia. JOURNAL OF INFECTIOUS DISEASES, 225(5), 846–855. https://doi.org/10.1093/infdis/jiab496

Walsh, E. S., Tollison, T. S., Brochu, H. N., Shaw, B. I., Diveley, K. R., Chou, H., … Peng, X. (2022). Single-Cell-Based High-Throughput Ig and TCR Repertoire Sequencing Analysis in Rhesus Macaques. JOURNAL OF IMMUNOLOGY, 208(3), 762–771. https://doi.org/10.4049/jimmunol.2100824

Dawson, D., Rasmussen, D., Peng, X., & Lanzas, C. (2021). Inferring environmental transmission using phylodynamics: a case-study using simulated evolution of an enteric pathogen. JOURNAL OF THE ROYAL SOCIETY INTERFACE, 18(179). https://doi.org/10.1098/rsif.2021.0041

Barrenas, F., Hansen, S. G., Law, L., Driscoll, C., Green, R. R., Smith, E., … Gale, M., Jr. (2021). Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy. PLOS PATHOGENS, 17(7). https://doi.org/10.1371/journal.ppat.1009278

Barrenäs, F., Hansen, S. G., Law, L., Driscoll, C., Green, R. R., Smith, E., … Gale, M., Jr. (2021, January 11). Sustained IL-15 response signature predicts RhCMV/SIV vaccine efficacy (Vol. 1). Vol. 1. https://doi.org/10.1101/2021.01.11.426199

Nagarajan, U. M., Cho, C., Gyorke, C. E., Nagarajan, S., Ezzell, J. A., Brochu, H., … Peng, X. (2021). Tumor Necrosis Factor Alpha-Induced Interleukin-1 Alpha Synthesis and Cell Death Is Increased in Mouse Epithelial Cells Infected With Chlamydia muridarum. JOURNAL OF INFECTIOUS DISEASES, 224, S47–S55. https://doi.org/10.1093/infdis/jiab168

Dinh, P.-U. C., Paudel, D., Brochu, H., Popowski, K. D., Gracieux, M. C., Cores, J., … Cheng, K. (2020). Inhalation of lung spheroid cell secretome and exosomes promotes lung repair in pulmonary fibrosis. NATURE COMMUNICATIONS, 11(1). https://doi.org/10.1038/s41467-020-14344-7

Brochu, H. N., Tseng, E., Smith, E., Thomas, M. J., Jones, A. M., Diveley, K. R., … Peng, X. (2020). Systematic Profiling of Full-Length Ig and TCR Repertoire Diversity in Rhesus Macaque through Long Read Transcriptome Sequencing. JOURNAL OF IMMUNOLOGY, 204(12), 3434–3444. https://doi.org/10.4049/jimmunol.1901256

Martinez, D. R., Fong, Y., Li, S. H., Yang, F., Jennewein, M. F., Weiner, J. A., … Permar, S. R. (2019). Fc Characteristics Mediate Selective Placental Transfer of IgG in HIV-Infected Women. CELL, 178(1), 190-+. https://doi.org/10.1016/j.cell.2019.05.046

Li, S. S., Gilbert, P. B., Carpp, L. N., Pyo, C.-W., Janes, H., Fong, Y., … Peng, X. (2019). Fc Gamma Receptor Polymorphisms Modulated the Vaccine Effect on HIV-1 Risk in the HVTN 505 HIV Vaccine Trial. JOURNAL OF VIROLOGY, 93(21). https://doi.org/10.1128/JVI.02041-18

Barrenas, F., Raehtz, K., Xu, C., Law, L., Green, R. R., Silvestri, G., … Gale, M., Jr. (2019). Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control. NATURE COMMUNICATIONS, 10. https://doi.org/10.1038/s41467-019-12987-9

Catherine M. O'Connell, Brochu, H., Girardi, J., Harrell, E., Jones, A., Darville, T., … Peng, X. (2019). Simultaneous profiling of sexually transmitted bacterial pathogens, microbiome, and concordant host response in cervical samples using whole transcriptome sequencing analysis. MICROBIAL CELL, 6(3), 177–183. https://doi.org/10.15698/mic2019.03.672

Martinez, D. R., Fouda, G. G., Peng, X., Ackerman, M. E., & Permar, S. R. (2018). Noncanonical placental Fc receptors: What is their role in modulating transplacental transfer of maternal IgG? PLOS Pathogens, 14(8), e1007161. https://doi.org/10.1371/journal.ppat.1007161

Lemler, D. J., Brochu, H. N., Yang, F., Harrell, E. A., & Peng, X. X. (2017). [Review of Elucidating the role of host long non-coding RNA during viral infection: Challenges and paths forward]. Vaccines, 5(4).

Forero, A., Fenstermacher, K., Wohlgemuth, N., Nishida, A., Carter, V., Smith, E. A., … Pekosz, A. (2017). Evaluation of the innate immune responses to influenza and live-attenuated influenza vaccine infection in primary differentiated human nasal epithelial cells. Vaccine, 35(45), 6112–6121. https://doi.org/10.1016/j.vaccine.2017.09.058

Peng, X., Li, S. S., Gilbert, P. B., Geraghty, D. E., & Katze, M. G. (2016). FCGR2C Polymorphisms Associated with HIV-1 Vaccine Protection Are Linked to Altered Gene Expression of Fc-γ Receptors in Human B Cells. PLOS ONE, 11(3), e0152425. https://doi.org/10.1371/journal.pone.0152425

Tisoncik-Go, J., Gasper, D. J., Kyle, J. E., Eisfeld, A. J., Selinger, C., Hatta, M., … Katze, M. G. (2016). Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism. Cell Host & Microbe, 19(2), 254–266. https://doi.org/10.1016/j.chom.2016.01.002

Peng, X., Pyo, C., Thomas, M., Pyon, Y., Law, L., Wang, R., … Katze, M. (2015). Quantitative expression analysis of rhesus macaque MHC alleles. Journal of Immunology, 194(113).

Josset, L., Tchitchek, N., Gralinski, L. E., Ferris, M. T., Eisfeld, A. J., Green, R. R., … Katze, M. G. (2014). 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. RNA Biology, 11(7), 875–890. https://doi.org/10.4161/rna.29442

Peng, X., Pipes, L., Xiong, H., Green, R. R., Jones, D. C., Ruzzo, W. L., … Katze, M. G. (2014). Assessment and improvement of Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data. Journal of Medical Primatology, 43(5), 317–328. https://doi.org/10.1111/jmp.12125

Peng, X., Sova, P., Green, R. R., Thomas, M. J., Korth, M. J., Proll, S., … Katze, M. G. (2014). Deep Sequencing of HIV-Infected Cells: Insights into Nascent Transcription and Host-Directed Therapy. Journal of Virology, 88(16), 8768–8782. https://doi.org/10.1128/jvi.00768-14

Barrenas, F., Palermo, R. E., Agricola, B., Agy, M. B., Aicher, L., Carter, V., … Katze, M. G. (2014). Deep Transcriptional Sequencing of Mucosal Challenge Compartment from Rhesus Macaques Acutely Infected with Simian Immunodeficiency Virus Implicates Loss of Cell Adhesion Preceding Immune Activation. Journal of Virology, 88(14), 7962–7972. https://doi.org/10.1128/jvi.00543-14

Xiong, H., Morrison, J., Ferris, M. T., Gralinski, L. E., Whitmore, A. C., Green, R., … Katze, M. G. (2014). Genomic Profiling of Collaborative Cross Founder Mice Infected with Respiratory Viruses Reveals Novel Transcripts and Infection-Related Strain-Specific Gene and Isoform Expression. G3: Genes|Genomes|Genetics, 4(8), 1429–1444. https://doi.org/10.1534/g3.114.011759

Falzarano, D., de Wit, E., Feldmann, F., Rasmussen, A. L., Okumura, A., Peng, X., … Munster, V. J. (2014). Infection with MERS-CoV Causes Lethal Pneumonia in the Common Marmoset. PLoS Pathogens, 10(8), e1004250. https://doi.org/10.1371/journal.ppat.1004250

Peng, X., Alföldi, J., Gori, K., Eisfeld, A. J., Tyler, S. R., Tisoncik-Go, J., … Katze, M. G. (2014). The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease. Nature Biotechnology, 32(12), 1250–1255. https://doi.org/10.1038/nbt.3079

Peng, X., Thierry-Mieg, J., Thierry-Mieg, D., Nishida, A., Pipes, L., Bozinoski, M., … Mason, C. E. (2014). Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR). Nucleic Acids Research, 43(D1), D737–D742. https://doi.org/10.1093/nar/gku1110

Bruce, A. G., Ryan, J. T., Thomas, M. J., Peng, X., Grundhoff, A., Tsai, C.-C., & Rose, T. M. (2013). 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. Journal of Virology, 87(24), 13676–13693. https://doi.org/10.1128/jvi.02331-13

Jones, D. C., Ruzzo, W. L., Peng, X., & Katze, M. G. (2012). A new approach to bias correction in RNA-Seq. Bioinformatics, 28(7), 921–928. https://doi.org/10.1093/bioinformatics/bts055

Jones, D. C., Ruzzo, W. L., Peng, X., & Katze, M. G. (2012). Compression of next-generation sequencing reads aided by highly efficient de novo assembly. Nucleic Acids Research, 40(22), e171–e171. https://doi.org/10.1093/nar/gks754

Pipes, L., Li, S., Bozinoski, M., Palermo, R., Peng, X., Blood, P., … Katze, M. G. (2012). The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics. Nucleic Acids Research, 41(D1), D906–D914. https://doi.org/10.1093/nar/gks1268

Peng, X., Gralinski, L., Ferris, M. T., Frieman, M. B., Thomas, M. J., Proll, S., … Katze, M. G. (2011). Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection. MBio, 2(6). https://doi.org/10.1128/mbio.00198-11

Chang, S. T., Sova, P., Peng, X., Weiss, J., Law, G. L., Palermo, R. E., & Katze, M. G. (2011). 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. MBio, 2(5). https://doi.org/10.1128/mbio.00134-11

Cilloniz, C., Pantin-Jackwood, M. J., Ni, C., Goodman, A. G., Peng, X., Proll, S. C., … Katze, M. G. (2010). Lethal Dissemination of H5N1 Influenza Virus Is Associated with Dysregulation of Inflammation and Lipoxin Signaling in a Mouse Model of Infection. Journal of Virology, 84(15), 7613–7624. https://doi.org/10.1128/jvi.00553-10

Li, Y., Chan, E. Y., Li, J., Ni, C., Peng, X., Rosenzweig, E., … Katze, M. G. (2010). MicroRNA Expression and Virulence in Pandemic Influenza Virus-Infected Mice. Journal of Virology, 84(6), 3023–3032. https://doi.org/10.1128/jvi.02203-09

Aly, A. S. I., Lindner, S. E., MacKellar, D. C., Peng, X., & Kappe, S. H. I. (2010). SAP1 is a critical post-transcriptional regulator of infectivity in malaria parasite sporozoite stages. Molecular Microbiology, 79(4), 929–939. https://doi.org/10.1111/j.1365-2958.2010.07497.x

Peng, X., Gralinski, L., Armour, C. D., Ferris, M. T., Thomas, M. J., Proll, S., … Katze, M. G. (2010). Unique Signatures of Long Noncoding RNA Expression in Response to Virus Infection and Altered Innate Immune Signaling. MBio, 1(5). https://doi.org/10.1128/mbio.00206-10

Peng, X., Li, Y., Walters, K.-A., Rosenzweig, E. R., Lederer, S. L., Aicher, L. D., … Katze, M. G. (2009). Computational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human livers. BMC Genomics, 10(1), 373. https://doi.org/10.1186/1471-2164-10-373

Albuquerque, S. S., Carret, C., Grosso, A., Tarun, A. S., Peng, X., Kappe, S. H. I., … Mota, M. M. (2009). Host cell transcriptional profiling during malaria liver stage infection reveals a coordinated and sequential set of biological events. BMC Genomics, 10(1), 270. https://doi.org/10.1186/1471-2164-10-270

Cillóniz, C., Shinya, K., Peng, X., Korth, M. J., Proll, S. C., Aicher, L. D., … Katze, M. G. (2009). Lethal Influenza Virus Infection in Macaques Is Associated with Early Dysregulation of Inflammatory Related Genes. PLoS Pathogens, 5(10), e1000604. https://doi.org/10.1371/journal.ppat.1000604

Goodman, A. G., Fornek, J. L., Medigeshi, G. R., Perrone, L. A., Peng, X., Dyer, M. D., … Katze, M. G. (2009). P58IPK: A Novel “CIHD” Member of the Host Innate Defense Response against Pathogenic Virus Infection. PLoS Pathogens, 5(5), e1000438. https://doi.org/10.1371/journal.ppat.1000438

Goodman, A. G., Zeng, H., Proll, S. C., Peng, X., Cilloniz, C., Carter, V. S., … Katze, M. G. (2009). The Alpha/Beta Interferon Receptor Provides Protection against Influenza Virus Replication but Is Dispensable for Inflammatory Response Signaling. Journal of Virology, 84(4), 2027–2037. https://doi.org/10.1128/jvi.01595-09

Goodman, A. G., Zeng, H., Cilloniz, C., Carter, V. S., Peng, X., Proll, S. C., … Katze, M. G. (2009). The Type I interferon receptor protects against influenza virus replication while the Type II receptor is dispensible. Cytokine, 48(1-2), 83. https://doi.org/10.1016/j.cyto.2009.07.294

Peng, X., Chan, E. Y., Li, Y., Diamond, D. L., Korth, M. J., & Katze, M. G. (2009). Virus–host interactions: from systems biology to translational research. Current Opinion in Microbiology, 12(4), 432–438. https://doi.org/10.1016/j.mib.2009.06.003

Tarun, A. S., Peng, X., Dumpit, R. F., Ogata, Y., Silva-Rivera, H., Camargo, N., … Kappe, S. H. I. (2008). A combined transcriptome and proteome survey of malaria parasite liver stages. Proceedings of the National Academy of Sciences, 105(1), 305–310. https://doi.org/10.1073/pnas.0710780104

Vaughan, A., Chiu, S.-Y., Ramasamy, G., Li, L., Gardner, M. J., Tarun, A. S., … Peng, X. (2008). Assessment and improvement of the Plasmodium yoelii yoelii genome annotation through comparative analysis. Bioinformatics, 24(13), i383–i389. https://doi.org/10.1093/bioinformatics/btn140

Mikolajczak, S. A., Silva-Rivera, H., Peng, X., Tarun, A. S., Camargo, N., Jacobs-Lorena, V., … Kappe, S. H. I. (2008). Distinct Malaria Parasite Sporozoites Reveal Transcriptional Changes That Cause Differential Tissue Infection Competence in the Mosquito Vector and Mammalian Host. Molecular and Cellular Biology, 28(20), 6196–6207. https://doi.org/10.1128/mcb.00553-08

Peng, X., Langston, M. A., Saxton, A. M., Baldwin, N. E., & Snoddy, J. R. (2007). Detecting Network Motifs in Gene Co-expression Networks Through Integration of Protein Domain Information. In Methods of Microarray Data Analysis V (pp. 89–102). https://doi.org/10.1007/978-0-387-34569-7_7

Kirov, S. A., Peng, X., Baker, E., Schmoyer, D., Zhang, B., & Snoddy, J. (2005). GeneKeyDB: A lightweight, gene-centric, relational database to support data mining environments. BMC Bioinformatics, 6(1), 72. https://doi.org/10.1186/1471-2105-6-72