Lemler DJ, Brochu NH, Yang F, Harrell EA, Peng, X. Elucidating the Role of Host Long Non-Coding RNA during Viral Infection: Challenges and Paths Forward. Vaccines. 2017: 5(4), 37.

Tisoncik-Go J, Gasper DJ, Kyle JE, Eisfeld AJ, Selinger C, Hatta M, Morrison J, Korth MJ, Zink EM, Kim YM, Schepmoes AA, Nicora CD, Purvine SO, Weitz KK, Peng X, et al. Integrated Omics analysis of pathogenic host responses during pandemic H1N1 influenza virus infection: the crucial role of lipid metabolism. Cell host & microbe. 2016; 19(2):254-66.

Peng X, Li SS, Gilbert PB, Geraghty DE, Katze MG. FCGR2C Polymorphisms associated with HIV-1 vaccine protection are linked to altered gene expression of Fc-γ receptors in human B cells. PloS one. 2016; 11(3):e0152425.

Jones DC, Kuppusamy KT, Palpant NJ, Peng X, Murry CE, et al. Isolator: accurate and stable analysis of isoform-level expression in RNA-Seq experiments bioRxiv. 2016; 088765

Barrenas F, Raehetz K, Kristoff J, Apetrei C, Agy MB, Carter V, Flanary L, Green R, Ma D, Mclain R, Murnan R, Peng X, et al. Rhesus macaques and African green monkeys exhibit striking differences in extracellular matrix and cell adhesion gene expression during the eclipse phase of SIV infection. Journal of medical primatology 2015; 44 (5), 343-343

Law L, Yang Y, Barrenas F, Peng X, Proll S, Katze M. Applying RNA profiling and functional analysis approaches to evaluate vaccine-induced adaptive and innate immune responses in NHP SIV challenge and protection studies. Journal of medical primatology. 2015; 44 (5), 345-345

Peng X, Xiong H, Pipes L, Kelly S, Thomas M, Law L, Luo S, Langevin S, et al. Expanding the non-human primate reference transcriptome resource (NHPRTR): tissue-specific and immune cell-specific transcriptomes. Journal of medical primatology. 2015; 44 (5), 346-346

Thomas M, Proll S, Peng X, Green R, Katze M. Characterization of host transcript and viral RNA expression in non-human primates using targeted capture and sequencing on low volume blood samples. Journal of medical primatology. 2015; 44 (5), 342-343

Peng X, Pyo C, Thomas M, Pyon Y, Law Lynn, Wang R, Geraghty D, Katze M. Quantitative expression analysis of rhesus macaque MHC alleles. J immunol. 2015; 194:113.3

Peng X, Sova P, Green RR, Thomas MJ, Korth MJ, Proll S, Xu J, Cheng Y, Yi K, Chen L, Peng Z, Wang J, Palermo RE, Katze MG. 2014. Deep sequencing of HIV-infected cells: insights into nascent transcription and host-directed therapy. J Virol. 2014 Aug;88(16):8768-82.

Josset L, Tchitchek N, Gralinski LE, Ferris MT, Eisfeld AJ, Green RR, Thomas MJ, Tisoncik-Go J, Schroth GP, Kawaoka Y, Manuel de Villena FP, Baric RS, Heise MT, Peng X, Katze MG. 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. 2014; 11(7):875-90.

Barrenas F, Palermo RE, Agricola B, Agy MB, Aicher L, Carter V, Flanary L, Green RR, McLain R, Li Q, Lu W, Murnane R, Peng X, Thomas MJ, Weiss JM, Anderson DM, Katze MG. 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. 2014; 88(14):7962-72.

Peng X, Alföldi J, Gori K, Eisfeld AJ, Tyler SR, Tisoncik-Go J, Brawand D, Law GL, Skunca N, Hatta M, Gasper DJ, Kelly SM, Chang J, Thomas MJ, Johnson J, Berlin AM, Lara M, Russell P, Swofford R, Turner-Maier J, Young S, Hourlier T, Aken B, Searle S, Sun X, Yi Y, Suresh M, Tumpey TM, Siepel A, Wisely SM, Dessimoz C, Kawaoka Y, Birren BW, Lindblad-Toh K, Di Palma F, Engelhardt JF, Palermo RE, Katze MG. The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease. Nature biotechnology. 2014; 32(12):1250-5

Xiong H, Morrison J, Ferris MT, Gralinski LE, Whitmore AC, Green R, Thomas MJ, Tisoncik-Go J, Schroth GP, Pardo-Manuel de Villena F, Baric RS, Heise MT, Peng X, Katze MG. Genomic profiling of collaborative cross founder mice infected with respiratory viruses reveals novel transcripts and infection-related strain-specific gene and isoform expression. G3 (Bethesda, Md.). 2014; 4(8):1429-44.

Falzarano D, de Wit E, Feldmann F, Rasmussen AL, Okumura A, Peng X, Thomas MJ, van Doremalen N, Haddock E, Nagy L, LaCasse R, Liu T, Zhu J, McLellan JS, Scott DP, Katze MG, Feldmann H, Munster VJ. Infection with MERS-CoV causes lethal pneumonia in the common marmoset. PLoS pathogens. 2014; 10(8):e1004250.

Peng X, Thierry-Mieg J, Thierry-Mieg D, Nishida A, Pipes L, Bozinoski M, et al. Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR). Nucleic acids research. 2014; 43, D737–D742

Bosinger S, Langevin S, Peng X, Ortiz A, Folkner K, Dawoud R, Patel N, et al. Comprehensive transcriptome analysis of the T cell compartment in primate hosts of HIV and SIV. Journal of medical primatology. 2014; 43 (5), 386-386

Barrenas F, Palermo R, Agricola B, Agy M, Anderson D, Aicher L, Carter V, Flanary L, Green R, McLain R, Li Q, Lu W, Murane R, Peng X, et al. Early Response to mucosal SIV challenge in rhesus macaques. Journal of medical primatology. 2014; 43 (5), 388-388

Tyler SR, Peng X, Katze MG, Engelhardt J. Similar pathways are enriched in transcriptomes of CR ferret and human lung. Pediatric pulmonology. 2014; 49, 283

Peng X, Pipes L, Xiong H, Green RR, Jones DC, Ruzzo WL, Schroth GP, Mason CE,Palermo RE, Katze MG. Assessment and improvement of Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data. Journal of medical primatology. 2014;43(5):317-28.

Bruce AG, Ryan JT, Thomas MJ, Peng X, Grundhoff A, Tsai CC, Rose TM. 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. 2013; 87(24):13676-93.

Pipes L, Li S, Bozinoski M, Palermo R, Peng X, Blood P, Kelly S, Weiss JM, Thierry-Mieg J, Thierry-Mieg D, Zumbo P, Chen R, Schroth GP, Mason CE, Katze MG. The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics. Nucleic acids research. 2013; 41(Database issue):D906-14.

Jones DC, Ruzzo WL, Peng X, Katze MG. Compression of next-generation sequencing reads aided by highly efficient de novo assembly. Nucleic acids research. 2012; 40(22):e171

Jones DC, Ruzzo WL, Peng X, Katze MG. A new approach to bias correction in RNA-Seq. Bioinformatics (Oxford, England). 2012; 28(7):921-8

Chang ST, Sova P, Peng X, Weiss J, Law GL, Palermo RE, Katze MG.MBio. 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. Sep 20;2(5).

Aly AS, Lindner SE, MacKellar DC, Peng X, Kappe SH. SAP1 is a critical post-transcriptional regulator of infectivity in malaria parasite sporozoite stages. Molecular microbiology. 2011; 79(4):929-39.

Peng X, Gralinski L, Ferris MT, Frieman MB, Thomas MJ, Proll S, Korth MJ, Tisoncik JR, Heise M, Luo S, Schroth GP, Tumpey TM, Li C, Kawaoka Y, Baric RS, Katze MG. Integrative deep sequencing of the mouse lung transcriptome reveals differential expression of diverse classes of small RNAs in response to respiratory virus infection. mBio. 2011; 2(6).

Peng X, Gralinski L, Armour CD, Ferris MT, Thomas MJ, Proll S, Bradel-Tretheway BG, Korth MJ, Castle JC, Biery MC, Bouzek HK, Haynor DR, Frieman MB, Heise M, Raymond CK, Baric RS, Katze MG. Unique signatures of long noncoding RNA expression in response to virus infection and altered innate immune signaling. mBio. 2010; 1(5).

Cilloniz C, Pantin-Jackwood MJ, Ni C, Goodman AG, Peng X, Proll SC, Carter VS, Rosenzweig ER, Szretter KJ, Katz JM, Korth MJ, Swayne DE, Tumpey TM, Katze MG. Lethal dissemination of H5N1 influenza virus is associated with dysregulation of inflammation and lipoxin signaling in a mouse model of infection. Journal of virology. 2010; 84(15):7613-24.

Li Y, Chan EY, Li J, Ni C, Peng X, Rosenzweig E, Tumpey TM, Katze MG. MicroRNA expression and virulence in pandemic influenza virus-infected mice. Journal of virology. 2010; 84(6):3023-32.

Goodman AG, Zeng H, Proll SC, Peng X, Cillóniz C, Carter VS, Korth MJ, Tumpey TM, Katze MG. The alpha/beta interferon receptor provides protection against influenza virus replication but is dispensable for inflammatory response signaling. Journal of virology. 2010; 84(4):2027-37.

Diamond D, Rasmussen A, Susnow N, Datta S, Magaret C, Webb-Robertson B, Krasnoselsky A, Burnum K, Yeh M, McDermott J, Jacobs J, Gritsenko M, Bhattacharya R, Perkins J, Carithers R, Liou I, Strom S, LeCiel C, Carter V, Purdy D, Walters K, Larson A, Xinxia Peng, et al. Hepatitix C Virus infection and pathogenesis: from systems biology to translational research hepatology. Hepatology. 2010; 52 (4), 829A-830A

Cillóniz C, Shinya K, Peng X, Korth MJ, Proll SC, Aicher LD, Carter VS, Chang JH, Kobasa D, Feldmann F, Strong JE, Feldmann H, Kawaoka Y, Katze MG. Lethal influenza virus infection in macaques is associated with early dysregulation of inflammatory related genes. PLoS pathogens. 2009; 5(10):e1000604.

Peng X, Li Y, Walters KA, Rosenzweig ER, Lederer SL, Aicher LD, Proll S, Katze MG. Computational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human livers. BMC genomics. 2009; 10:373.

Peng X, Chan EY, Li Y, Diamond DL, Korth MJ, Katze MG. Virus-host interactions: from systems biology to translational research. Current opinion in microbiology. 2009; 12(4):432-8.

Albuquerque SS, Carret C, Grosso AR, Tarun AS, Peng X, Kappe SH, Prudêncio M, Mota MM. Host cell transcriptional profiling during malaria liver stage infection reveals a coordinated and sequential set of biological events. BMC genomics. 2009; 10:270.

Goodman AG, Fornek JL, Medigeshi GR, Perrone LA, Peng X, Dyer MD, Proll SC, Knoblaugh SE, Carter VS, Korth MJ, Nelson JA, Tumpey TM, Katze MG. P58(IPK): a novel "CIHD" member of the host innate defense response against pathogenic virus infection. PLoS pathogens. 2009; 5(5):e1000438.

AG Goodman, H Zeng, C Cilloniz, VS Carter, X Peng, SC Proll, et al. The Type I interferon receptor protects against influenza virus replication while the Type II receptor is dispensible. Cytokine. 2--9; 48 (1), 83

CZ Shang, YJ Chen, HW Zhang, L Zhang, J Cao, X Peng, JS Chen. Splenic autotransplantation combined with lower esophagus transaction in the treatment of hepatic cirrhosis induced portal hypertension. Zhonghua wai ke za zhi [Chinese journal of surgery]. 2009; 47 (2), 83-85

Goodman A, Fornek J, Medigeshi G, Perrone L, Peng X, Dyer M, Proll S, Knoblaugh S, et al. P58IPK: A Novel ‘‘CIHD’’ Member of the Host Innate Defense Response against Pathogenic Virus Infection. PLoS Pathogens May 2009; 5 (5), e1000438

Goodman A, Fornek J, Medigeshi G, Perrone L, Peng X, Dyer M, Proll S, Knoblaugh S, et al. P58IPK: A Novel ‘‘CIHD’’ Member of the Host Innate Defense Response against Pathogenic Virus Infection. PLoS Pathogens May 2009; 5 (5), e1000438

Mikolajczak SA, Silva-Rivera H, Peng X, Tarun AS, Camargo N, Jacobs-Lorena V, Daly TM, Bergman LW, de la Vega P, Williams J, Aly AS, Kappe SH. Distinct malaria parasite sporozoites reveal transcriptional changes that cause differential tissue infection competence in the mosquito vector and mammalian host. Molecular and cellular biology. 2008; 28(20):6196-207. PMCID: PMC2577418

Vaughan A, Chiu SY, Ramasamy G, Li L, Gardner MJ, Tarun AS, Kappe SH, Peng X. Assessment and improvement of the Plasmodium yoelii yoelii genome annotation through comparative analysis. Bioinformatics (Oxford, England). 2008; 24(13):i383-9.

Tarun AS, Peng X, Dumpit RF, Ogata Y, Silva-Rivera H, Camargo N, Daly TM, Bergman LW, Kappe SH. A combined transcriptome and proteome survey of malaria parasite liver stages. Proceedings of the National Academy of Sciences of the United States of America. 2008; 105(1):305-10.

Methods of Microarray Data Analysis V Peng X, Langston MA, Saxton AM, Baldwin NE, Snoddy JayR. New York: Springer; 2007. Chapter 7, Detecting Network Motifs in Gene Co-expression Networks Through Integration of Protein Domain Information; p.89-102.