Xinxia Peng

Alternative splicing and genetic variation of mhc-e: implications for rhesus cytomegalovirus-based vaccines

COMMUNICATIONS BIOLOGY, 5(1).

Coupling high-throughput mapping with proteomics analysis delineates cis-regulatory elements at high resolution

NUCLEIC ACIDS RESEARCH, 50(1).

Phylogeny-guided microbiome OTU-specific association test (POST)

MICROBIOME, 10(1).

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.

Single-Cell-Based High-Throughput Ig and TCR Repertoire Sequencing Analysis in Rhesus Macaques

JOURNAL OF IMMUNOLOGY, 208(3), 762–771.

Inferring environmental transmission using phylodynamics: a case-study using simulated evolution of an enteric pathogen

JOURNAL OF THE ROYAL SOCIETY INTERFACE, 18(179).

Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy

PLOS PATHOGENS, 17(7).

Sustained IL-15 response signature predicts RhCMV/SIV vaccine efficacy

Barrenäs, F., Hansen, S. G., Law, L., Driscoll, C., Green, R. R., Smith, E., … Gale, M., Jr. (2021, January 11). (Vol. 1). Vol. 1.

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.

Inhalation of lung spheroid cell secretome and exosomes promotes lung repair in pulmonary fibrosis

NATURE COMMUNICATIONS, 11(1).

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.

Fc Characteristics Mediate Selective Placental Transfer of IgG in HIV-Infected Women

CELL, 178(1), 190-+.

Fc Gamma Receptor Polymorphisms Modulated the Vaccine Effect on HIV-1 Risk in the HVTN 505 HIV Vaccine Trial

JOURNAL OF VIROLOGY, 93(21).

Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control

NATURE COMMUNICATIONS, 10.

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.

Noncanonical placental Fc receptors: What is their role in modulating transplacental transfer of maternal IgG?

PLOS Pathogens, 14(8), e1007161.

Elucidating the role of host long non-coding RNA during viral infection: Challenges and paths forward

[Review of ]. Vaccines, 5(4).

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.

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.

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.

Quantitative expression analysis of rhesus macaque MHC alleles

Journal of Immunology, 194(113).

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.

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.

Deep Sequencing of HIV-Infected Cells: Insights into Nascent Transcription and Host-Directed Therapy

Journal of Virology, 88(16), 8768–8782.

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.

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.

Infection with MERS-CoV Causes Lethal Pneumonia in the Common Marmoset

PLoS Pathogens, 10(8), e1004250.

The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease

Nature Biotechnology, 32(12), 1250–1255.

Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR)

Nucleic Acids Research, 43(D1), D737–D742.

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.

A new approach to bias correction in RNA-Seq

Bioinformatics, 28(7), 921–928.

Compression of next-generation sequencing reads aided by highly efficient de novo assembly

Nucleic Acids Research, 40(22), e171–e171.

The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics

Nucleic Acids Research, 41(D1), D906–D914.

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).

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).

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.

MicroRNA Expression and Virulence in Pandemic Influenza Virus-Infected Mice

Journal of Virology, 84(6), 3023–3032.

SAP1 is a critical post-transcriptional regulator of infectivity in malaria parasite sporozoite stages

Molecular Microbiology, 79(4), 929–939.

Unique Signatures of Long Noncoding RNA Expression in Response to Virus Infection and Altered Innate Immune Signaling

MBio, 1(5).

Computational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human livers

BMC Genomics, 10(1), 373.

Host cell transcriptional profiling during malaria liver stage infection reveals a coordinated and sequential set of biological events

BMC Genomics, 10(1), 270.

Lethal Influenza Virus Infection in Macaques Is Associated with Early Dysregulation of Inflammatory Related Genes

PLoS Pathogens, 5(10), e1000604.

P58IPK: A Novel “CIHD” Member of the Host Innate Defense Response against Pathogenic Virus Infection

PLoS Pathogens, 5(5), e1000438.

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.

The Type I interferon receptor protects against influenza virus replication while the Type II receptor is dispensible

Cytokine, 48(1-2), 83.

Virus–host interactions: from systems biology to translational research

Current Opinion in Microbiology, 12(4), 432–438.

A combined transcriptome and proteome survey of malaria parasite liver stages

Proceedings of the National Academy of Sciences, 105(1), 305–310.

Assessment and improvement of the Plasmodium yoelii yoelii genome annotation through comparative analysis

Bioinformatics, 24(13), i383–i389.

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.

Detecting Network Motifs in Gene Co-expression Networks Through Integration of Protein Domain Information

In Methods of Microarray Data Analysis V (pp. 89–102).

GeneKeyDB: A lightweight, gene-centric, relational database to support data mining environments

BMC Bioinformatics, 6(1), 72.