Works (52)

Updated: March 28th, 2024 15:14

2024 article

Pre-challenge gut microbial signature predicts RhCMV/SIV vaccine efficacy in rhesus macaques

Brochu, H. N., Smith, E., Jeong, S., Carlson, M., Hansen, S. G., Tisoncik-Go, J., … Peng, X. (2024, February 28).

By: H. Brochu n, E. Smith*, S. Jeong n, M. Carlson*, S. Hansen*, J. Tisoncik-Go*, L. Law*, L. Picker*, M. Gale*, X. Peng n

co-author countries: United States of America 🇺🇸
Source: ORCID
Added: March 1, 2024

2022 journal article

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

COMMUNICATIONS BIOLOGY, 5(1).

By: H. Brochu n, R. Wang*, T. Tollison n, C. Pyo*, A. Thomas*, E. Tseng*, L. Law*, L. Picker* ...

co-author countries: United States of America 🇺🇸
MeSH headings : Animals; Humans; Alternative Splicing; Cytomegalovirus; Cytomegalovirus Vaccines; Genetic Variation; Macaca mulatta; Simian Immunodeficiency Virus; Histocompatibility Antigens Class I / genetics
Sources: Web Of Science, ORCID
Added: January 17, 2023

2022 journal article

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

NUCLEIC ACIDS RESEARCH, 50(1).

By: T. Wu*, D. Jiang*, M. Zou*, W. Sun*, D. Wu, J. Cui*, I. Huntress n, X. Peng n, G. Li*

co-author countries: China 🇨🇳 United States of America 🇺🇸
MeSH headings : Chromosome Mapping / methods; Gene Expression Regulation; Genome, Human; High-Throughput Nucleotide Sequencing / methods; Humans; Regulatory Sequences, Nucleic Acid
Sources: Web Of Science, ORCID
Added: February 14, 2022

2022 journal article

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

MICROBIOME, 10(1).

By: C. Huang n, B. Callahan n, M. Wu*, S. Holloway n, H. Brochu n, W. Lu n, X. Peng n, J. Tzeng n

co-author countries: United States of America 🇺🇸
author keywords: Association test; Phylogenetic tree; Kernel machine regression
MeSH headings : Computational Biology / methods; Computer Simulation; Female; Humans; Infant, Newborn; Microbiota / genetics; Phylogeny; Premature Birth
Sources: Web Of Science, ORCID
Added: June 20, 2022

2022 journal article

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.

By: C. Liu*, K. Hufnagel*, . Catherine M. O'Connell*, N. Goonetilleke*, N. Mokashi*, T. Waterboer*, T. Tollison n, X. Peng n ...

co-author countries: Germany 🇩🇪 United States of America 🇺🇸
author keywords: Chlamydia; genital tract; antibody; serology; endometrium; immunoproteome
MeSH headings : Antibodies, Bacterial; Chlamydia Infections; Chlamydia trachomatis; Female; Humans; Immunoglobulin G; Reinfection
Sources: Web Of Science, ORCID
Added: March 21, 2022

2022 journal article

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

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

co-author countries: United States of America 🇺🇸
MeSH headings : Animals; Gene Expression Profiling; High-Throughput Nucleotide Sequencing; Immunoglobulins / genetics; Macaca mulatta; Receptors, Antigen, T-Cell, alpha-beta / genetics; Receptors, Antigen, T-Cell, gamma-delta / genetics; Single-Cell Analysis; T-Lymphocytes / immunology; Transcriptome / genetics; VDJ Exons / genetics
Sources: Web Of Science, ORCID
Added: February 28, 2022

2021 journal article

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

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

By: D. Dawson n, D. Rasmussen n, X. Peng n & C. Lanzas n

co-author countries: United States of America 🇺🇸
author keywords: environmental transmission; disease transmission modelling; phylodynamics; whole-genome sequencing
MeSH headings : Epidemics; Phylogeny; Probability
Sources: Web Of Science, ORCID
Added: June 9, 2021

2021 journal article

Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy

PLOS PATHOGENS, 17(7).

By: F. Barrenas*, S. Hansen*, L. Law*, C. Driscoll*, R. Green*, E. Smith*, J. Chang*, I. Golez* ...

co-author countries: Sweden 🇸🇪 United States of America 🇺🇸

Ed(s): G. Silvestri

MeSH headings : Animals; CD8-Positive T-Lymphocytes / immunology; Cytomegalovirus; Female; Genetic Vectors; Interleukin-15 / immunology; Macaca mulatta; Male; SAIDS Vaccines / immunology; Simian Acquired Immunodeficiency Syndrome / prevention & control; Simian Immunodeficiency Virus / immunology
Sources: Web Of Science, ORCID
Added: July 26, 2021

2021 article

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.

By: F. Barrenäs*, S. Hansen*, L. Law*, C. Driscoll*, R. Green*, E. Smith*, J. Chang*, I. Golez* ...

co-author countries: Sweden 🇸🇪 United States of America 🇺🇸
Source: ORCID
Added: March 15, 2023

2021 journal article

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.

By: U. Nagarajan*, C. Cho*, C. Gyorke*, S. Nagarajan*, J. Ezzell*, H. Brochu n, I. Huntress n, E. Harrell n, X. Peng n

co-author countries: United States of America 🇺🇸
author keywords: Chlamydia muridarum; IL-1 alpha; mouse epithelial cells; mouse model; TNF alpha
MeSH headings : Animals; Cell Death; Chlamydia Infections / immunology; Chlamydia Infections / metabolism; Chlamydia muridarum / immunology; Epithelial Cells; Female; Interleukin-1alpha / immunology; Interleukin-1alpha / metabolism; Mice; Mice, Inbred C57BL; Tumor Necrosis Factor-alpha / immunology; Tumor Necrosis Factor-alpha / metabolism
Sources: Web Of Science, ORCID
Added: September 13, 2021

2020 journal article

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

NATURE COMMUNICATIONS, 11(1).

By: P. Dinh n, D. Paudel n, H. Brochu n, K. Popowski n, M. Gracieux n, J. Cores n, K. Huang n, M. Hensley n ...

co-author countries: United States of America 🇺🇸
MeSH headings : Administration, Inhalation; Alveolar Epithelial Cells / drug effects; Alveolar Epithelial Cells / metabolism; Alveolar Epithelial Cells / pathology; Animals; Apoptosis / drug effects; Bleomycin / toxicity; Cell Proliferation; Disease Models, Animal; Exosomes / metabolism; Exosomes / transplantation; Humans; Idiopathic Pulmonary Fibrosis / chemically induced; Idiopathic Pulmonary Fibrosis / metabolism; Idiopathic Pulmonary Fibrosis / pathology; Idiopathic Pulmonary Fibrosis / therapy; Lung / cytology; Lung / metabolism; Lung Injury / chemically induced; Lung Injury / metabolism; Lung Injury / pathology; Lung Injury / therapy; Mesenchymal Stem Cells / metabolism; Mice; Myofibroblasts / cytology; Proteomics; Silicon Dioxide / toxicity; Spheroids, Cellular / metabolism
Sources: Web Of Science, ORCID
Added: March 23, 2020

2020 journal article

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.

By: H. Brochu n, E. Tseng*, E. Smith*, M. Thomas*, A. Jones n, K. Diveley n, L. Law*, S. Hansen* ...

co-author countries: United States of America 🇺🇸
MeSH headings : Animals; High-Throughput Nucleotide Sequencing / methods; Humans; Immunoglobulins / genetics; Immunoglobulins / immunology; Macaca mulatta / genetics; Macaca mulatta / immunology; Receptors, Antigen, T-Cell / immunology; Transcriptome / genetics; Transcriptome / immunology
Sources: Web Of Science, ORCID
Added: July 6, 2020

2019 journal article

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

CELL, 178(1), 190-+.

By: D. Martinez*, Y. Fong*, S. Li*, F. Yang n, M. Jennewein*, J. Weiner*, E. Harrell n, J. Mangold* ...

co-author countries: United States of America 🇺🇸
MeSH headings : Cohort Studies; Disease Progression; Female; Glycosylation; HIV / genetics; HIV Infections / immunology; HIV Infections / transmission; HIV Infections / virology; Humans; Immunoglobulin Fc Fragments / metabolism; Immunoglobulin G / blood; Infant; Infant, Newborn; Infectious Disease Transmission, Vertical; Malawi; Placenta / metabolism; Pregnancy; Pregnancy Complications, Infectious / immunology; Pregnancy Complications, Infectious / virology; Receptors, IgG / metabolism; United States; Viral Load / genetics
Sources: Web Of Science, ORCID
Added: July 15, 2019

2019 journal article

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

JOURNAL OF VIROLOGY, 93(21).

By: S. Li*, P. Gilbert*, L. Carpp*, C. Pyo*, H. Janes*, Y. Fong*, X. Shen*, S. Neidich* ...

co-author countries: United States of America 🇺🇸
author keywords: Fc gamma receptor; HIV/AIDS vaccine trial; HVTN 505; genetic polymorphisms
MeSH headings : Antibodies, Monoclonal / immunology; B-Lymphocytes / immunology; B-Lymphocytes / metabolism; B-Lymphocytes / virology; CD8-Positive T-Lymphocytes / immunology; CD8-Positive T-Lymphocytes / metabolism; CD8-Positive T-Lymphocytes / virology; Case-Control Studies; Clinical Trials, Phase II as Topic; Genetic Vectors / administration & dosage; HIV Infections / epidemiology; HIV Infections / genetics; HIV Infections / immunology; HIV Infections / virology; HIV Seropositivity; HIV-1 / genetics; HIV-1 / immunology; Humans; Incidence; Phagocytosis; Polymorphism, Single Nucleotide; Receptors, IgG / genetics; United States / epidemiology; Vaccination; Vaccines, DNA / administration & dosage; env Gene Products, Human Immunodeficiency Virus / immunology
Sources: Web Of Science, ORCID
Added: October 28, 2019

2019 journal article

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

NATURE COMMUNICATIONS, 10.

By: F. Barrenas*, K. Raehtz*, C. Xu*, L. Law*, R. Green*, G. Silvestri*, S. Bosinger*, A. Nishida* ...

co-author countries: Poland 🇵🇱 Sweden 🇸🇪 United States of America 🇺🇸
MeSH headings : Animals; Chlorocebus aethiops / genetics; Chlorocebus aethiops / immunology; Disease Progression; Fibronectins / immunology; Fibronectins / metabolism; Intestinal Mucosa / immunology; Intestinal Mucosa / metabolism; Macaca mulatta / genetics; Macaca mulatta / immunology; Macrophages / immunology; Macrophages / metabolism; Rectum / immunology; Rectum / metabolism; Simian Acquired Immunodeficiency Syndrome / immunology; Simian Immunodeficiency Virus; Systems Biology; Transcriptome; Transforming Growth Factor beta / genetics; Transforming Growth Factor beta / immunology; Wound Healing / genetics; Wound Healing / immunology
Sources: Web Of Science, ORCID
Added: November 25, 2019

2019 journal article

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.

By: . Catherine M. O'Connell*, H. Brochu n, J. Girardi*, E. Harrell n, A. Jones n, T. Darville*, A. Sena*, X. Peng n

co-author countries: United States of America 🇺🇸
author keywords: RNA-seq; chlamydia; gonorrhea; natural infection; microbiome
Sources: Web Of Science, ORCID
Added: March 18, 2019

2018 journal article

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

PLOS Pathogens, 14(8), e1007161.

co-author countries: United States of America 🇺🇸

Ed(s): D. Sheppard

MeSH headings : Animals; Female; Humans; Immunoglobulin G / immunology; Immunoglobulin G / metabolism; Maternal-Fetal Exchange / immunology; Placenta / immunology; Placenta / metabolism; Pregnancy; Receptors, Fc / immunology
Sources: Crossref, ORCID
Added: July 20, 2019

2017 review

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

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

By: D. Lemler, H. Brochu, F. Yang, E. Harrell & X. Peng

Source: NC State University Libraries
Added: August 6, 2018

2017 journal article

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.

By: A. Forero*, K. Fenstermacher*, N. Wohlgemuth*, A. Nishida*, V. Carter*, E. Smith*, X. Peng*, M. Hayes* ...

co-author countries: United States of America 🇺🇸
author keywords: Influenza virus; Host response; Live-attenuated vaccine; Inflammation; Interferon; Epithelial cells
MeSH headings : Animals; Antigen-Presenting Cells / immunology; Cell Line; Dogs; Epithelial Cells / immunology; Epithelial Cells / virology; Humans; Immunity, Innate / immunology; Influenza A Virus, H3N2 Subtype / immunology; Influenza Vaccines / immunology; Influenza, Human / immunology; Influenza, Human / prevention & control; Leukocytes, Mononuclear; Madin Darby Canine Kidney Cells; Nasal Mucosa / immunology; Nasal Mucosa / virology; T-Lymphocytes / immunology; Vaccines, Attenuated / immunology
Sources: Crossref, ORCID
Added: July 20, 2019

2016 journal article

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.

By: X. Peng*, S. Li*, P. Gilbert*, D. Geraghty* & M. Katze*

co-author countries: United States of America 🇺🇸

Ed(s): J. Tang

MeSH headings : AIDS Vaccines / therapeutic use; Alleles; Alternative Splicing; B-Lymphocytes / cytology; B-Lymphocytes / metabolism; B-Lymphocytes / virology; Europe; Gene Deletion; Gene Expression Profiling; Gene Expression Regulation; HIV Infections / genetics; HIV Infections / prevention & control; HIV-1; Homozygote; Humans; Polymorphism, Genetic; Polymorphism, Single Nucleotide; Quantitative Trait Loci; Receptors, Fc; Receptors, IgG / biosynthesis; Receptors, IgG / genetics; Receptors, Immunologic / genetics; Receptors, Immunologic / metabolism; Sequence Analysis, RNA
Sources: Crossref, ORCID
Added: July 20, 2019

2016 journal article

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.

co-author countries: France 🇫🇷 Japan 🇯🇵 United States of America 🇺🇸
MeSH headings : Animals; Disease Models, Animal; Ferrets; Gene Expression; Host-Pathogen Interactions; Humans; Influenza A Virus, H1N1 Subtype / physiology; Influenza, Human / epidemiology; Influenza, Human / genetics; Influenza, Human / metabolism; Influenza, Human / pathology; Lipid Metabolism; Lipids / chemistry; Lung / metabolism; Lung / pathology; Lung / virology; Metabolomics
Sources: Crossref, ORCID
Added: July 20, 2019

2015 journal article

Quantitative expression analysis of rhesus macaque MHC alleles

Journal of Immunology, 194(113).

By: X. Peng, C. Pyo, M. Thomas, Y. Pyon, L. Law, R. Wang, D. Geraghty, M. Katze

Source: NC State University Libraries
Added: September 9, 2019

2014 journal article

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.

By: L. Josset*, N. Tchitchek*, L. Gralinski*, M. Ferris*, A. Eisfeld*, R. Green*, M. Thomas*, J. Tisoncik-Go* ...

co-author countries: Russian Federation 🇷🇺 United States of America 🇺🇸
author keywords: long non-coding rna; influenza virus; sars-cov; rna-seq; interferon; collaborative cross
MeSH headings : Animals; Antiviral Agents / administration & dosage; Antiviral Agents / pharmacology; Cell Line; Female; Gene Expression Profiling; Gene Expression Regulation / drug effects; Influenza A virus / drug effects; Influenza A virus / physiology; Interferon-alpha / administration & dosage; Interferon-alpha / pharmacology; Lung / metabolism; Lung / virology; Mice; Mice, Inbred C57BL; Molecular Sequence Annotation; RNA Virus Infections / drug therapy; RNA Virus Infections / genetics; RNA Virus Infections / virology; RNA, Long Noncoding / genetics; Severe acute respiratory syndrome-related coronavirus / drug effects; Severe acute respiratory syndrome-related coronavirus / physiology; Sequence Analysis, RNA
Sources: Crossref, ORCID
Added: July 20, 2019

2014 journal article

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.

co-author countries: United States of America 🇺🇸
author keywords: intergenic transcripts; non-coding RNA; non-polyadenylated RNA; RNAseq
MeSH headings : Animals; Ebolavirus / physiology; Hemorrhagic Fever, Ebola / genetics; Hemorrhagic Fever, Ebola / virology; High-Throughput Nucleotide Sequencing; India; Macaca fascicularis; Macaca mulatta; Mauritius; Molecular Sequence Data; Monkey Diseases / genetics; Monkey Diseases / virology; RNA, Untranslated / genetics; RNA, Untranslated / metabolism; Sequence Analysis, RNA; Simian Acquired Immunodeficiency Syndrome / genetics; Simian Acquired Immunodeficiency Syndrome / virology; Simian Immunodeficiency Virus / physiology; Transcriptome
Sources: Crossref, ORCID
Added: July 20, 2019

2014 journal article

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

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

By: X. Peng*, P. Sova*, R. Green*, M. Thomas*, M. Korth*, S. Proll*, J. Xu*, Y. Cheng* ...

co-author countries: China 🇨🇳 United States of America 🇺🇸
MeSH headings : CD4-Positive T-Lymphocytes / virology; Cell Line; Gene Expression Profiling / methods; Gene Expression Regulation / genetics; HIV Infections / genetics; HIV Infections / virology; HIV-1 / genetics; High-Throughput Nucleotide Sequencing / methods; Humans; RNA / genetics; RNA, Messenger / genetics; Transcription, Genetic / genetics; Virus Replication / genetics
Sources: Crossref, ORCID
Added: July 20, 2019

2014 journal article

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.

By: F. Barrenas*, R. Palermo*, B. Agricola*, M. Agy*, L. Aicher*, V. Carter*, L. Flanary*, R. Green* ...

co-author countries: Sweden 🇸🇪 United States of America 🇺🇸

Ed(s): G. Silvestri

MeSH headings : Animals; B-Lymphocytes / immunology; Cell Adhesion; Claudins / metabolism; Cytoskeleton / metabolism; Gene Expression Profiling; Host-Pathogen Interactions; Intestinal Mucosa / immunology; Intestinal Mucosa / physiology; Intestinal Mucosa / virology; Killer Cells, Natural / immunology; Macaca mulatta; Male; Rectum / immunology; Rectum / virology; Simian Immunodeficiency Virus / immunology; T-Lymphocytes / immunology; Time Factors
Sources: Crossref, ORCID
Added: July 20, 2019

2014 journal article

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.

By: H. Xiong*, J. Morrison*, M. Ferris*, L. Gralinski*, A. Whitmore*, R. Green*, M. Thomas*, J. Tisoncik-Go* ...

co-author countries: United States of America 🇺🇸
author keywords: RNA-seq; mouse transcriptome annotation; isoform differential expression; collaborative cross; viral infection
MeSH headings : Animals; Female; Gene Expression Profiling; Gene Expression Regulation; Genome; Influenza A virus; Lung / metabolism; Lung / virology; Mice; Orthomyxoviridae Infections / genetics; Orthomyxoviridae Infections / virology; Phenotype; RNA / genetics; Severe acute respiratory syndrome-related coronavirus; Sequence Analysis, RNA; Severe Acute Respiratory Syndrome / genetics; Severe Acute Respiratory Syndrome / virology; Species Specificity; Viral Load
Sources: Crossref, ORCID
Added: July 20, 2019

2014 journal article

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

PLoS Pathogens, 10(8), e1004250.

By: D. Falzarano*, E. de Wit*, F. Feldmann*, A. Rasmussen*, A. Okumura*, X. Peng*, M. Thomas*, N. van Doremalen* ...

co-author countries: Canada 🇨🇦 United States of America 🇺🇸

Ed(s): M. Denison

MeSH headings : Animals; Callithrix; Coronavirus Infections / pathology; Coronavirus Infections / virology; Disease Models, Animal; Immunohistochemistry; Male; Middle East Respiratory Syndrome Coronavirus; Pneumonia, Viral / pathology; Pneumonia, Viral / virology; Real-Time Polymerase Chain Reaction
Sources: Crossref, ORCID
Added: July 20, 2019

2014 journal article

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

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

By: X. Peng*, J. Alföldi*, K. Gori*, A. Eisfeld*, S. Tyler*, J. Tisoncik-Go*, D. Brawand*, G. Law* ...

co-author countries: Switzerland 🇨🇭 United Kingdom of Great Britain and Northern Ireland 🇬🇧 Sweden 🇸🇪 United States of America 🇺🇸
MeSH headings : Animals; Base Sequence; Chromosome Mapping; Disease Models, Animal; Ferrets / genetics; Genome; High-Throughput Nucleotide Sequencing; Humans; Influenza, Human / genetics; Influenza, Human / transmission; Influenza, Human / virology; Molecular Sequence Annotation; Molecular Sequence Data; Orthomyxoviridae / genetics; Orthomyxoviridae / pathogenicity; Sequence Analysis, DNA
Sources: Crossref, ORCID
Added: July 20, 2019

2014 journal article

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

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

By: X. Peng*, J. Thierry-Mieg*, D. Thierry-Mieg*, A. Nishida*, L. Pipes*, M. Bozinoski*, M. Thomas*, S. Kelly* ...

co-author countries: United States of America 🇺🇸
MeSH headings : Animals; Databases, Genetic; Gene Expression Profiling; Internet; Macaca; Molecular Sequence Annotation; Organ Specificity; Primates / genetics; Reference Standards; Sequence Alignment / standards; Sequence Analysis, RNA
Sources: Crossref, ORCID
Added: July 20, 2019

2013 journal article

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.

By: A. Bruce, J. Ryan, M. Thomas*, X. Peng*, A. Grundhoff*, C. Tsai*, T. Rose*

co-author countries: Germany 🇩🇪 United States of America 🇺🇸
MeSH headings : Amino Acid Sequence; Animals; Base Sequence; Female; Genome, Viral; Herpesvirus 8, Human / chemistry; Herpesvirus 8, Human / classification; Herpesvirus 8, Human / genetics; Herpesvirus 8, Human / isolation & purification; High-Throughput Nucleotide Sequencing; Macaca nemestrina / virology; Molecular Sequence Data; Open Reading Frames; Phylogeny; Primate Diseases / virology; Rhadinovirus / chemistry; Rhadinovirus / classification; Rhadinovirus / genetics; Sarcoma, Kaposi / veterinary; Sarcoma, Kaposi / virology; Sequence Alignment; Viral Proteins / chemistry; Viral Proteins / genetics
Sources: Crossref, ORCID
Added: July 20, 2019

2012 journal article

A new approach to bias correction in RNA-Seq

Bioinformatics, 28(7), 921–928.

By: D. Jones*, W. Ruzzo*, X. Peng* & M. Katze*

co-author countries: United States of America 🇺🇸
MeSH headings : Bayes Theorem; Computational Biology / methods; Humans; Models, Statistical; Molecular Sequence Annotation; RNA / genetics; Sequence Analysis, RNA / methods; Software
Sources: Crossref, ORCID
Added: July 20, 2019

2012 journal article

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

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

By: D. Jones*, W. Ruzzo*, X. Peng* & M. Katze*

co-author countries: United States of America 🇺🇸
MeSH headings : Algorithms; Data Compression / methods; High-Throughput Nucleotide Sequencing / methods; Probability; Software
Sources: Crossref, ORCID
Added: July 20, 2019

2012 journal article

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

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

By: L. Pipes, S. Li, M. Bozinoski, R. Palermo, X. Peng*, P. Blood, S. Kelly, J. Weiss ...

MeSH headings : Animals; Databases, Nucleic Acid; Genome, Human; Genomics; Humans; Internet; Primates / genetics; Primates / metabolism; Sequence Alignment; Sequence Analysis, RNA; Transcriptome
Sources: Crossref, ORCID
Added: July 20, 2019

2011 journal article

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).

By: X. Peng*, L. Gralinski*, M. Ferris*, M. Frieman*, M. Thomas*, S. Proll*, M. Korth*, J. Tisoncik* ...

co-author countries: Japan 🇯🇵 United States of America 🇺🇸

Ed(s): B. Cullen & T. Dermody

MeSH headings : Animals; Coronavirus Infections / immunology; Gene Expression Regulation; High-Throughput Nucleotide Sequencing; Lung / immunology; Lung / virology; Mice; Mice, Inbred C57BL; MicroRNAs / biosynthesis; MicroRNAs / genetics; Orthomyxoviridae Infections / immunology; RNA, Small Nucleolar; Transcriptome
Sources: Crossref, ORCID
Added: July 20, 2019

2011 journal article

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).

By: S. Chang*, P. Sova*, X. Peng*, J. Weiss*, G. Law*, R. Palermo*, M. Katze*

co-author countries: United States of America 🇺🇸

Ed(s): D. Unutmaz & T. Dermody

MeSH headings : CD4-Positive T-Lymphocytes / immunology; CD4-Positive T-Lymphocytes / virology; Cell Line; Down-Regulation; HIV Infections / genetics; HIV Infections / immunology; HIV Infections / metabolism; HIV Infections / virology; HIV-1 / genetics; HIV-1 / physiology; Humans; Lymphocyte Activation; RNA Processing, Post-Transcriptional; RNA Transport; RNA, Untranslated / genetics; RNA, Untranslated / metabolism; RNA, Viral / genetics; RNA, Viral / metabolism; Sequence Analysis, DNA; Virus Replication
Sources: Crossref, ORCID
Added: July 20, 2019

2010 journal article

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.

By: C. Cilloniz*, M. Pantin-Jackwood*, C. Ni*, A. Goodman*, X. Peng*, S. Proll*, V. Carter*, E. Rosenzweig* ...

co-author countries: United States of America 🇺🇸
MeSH headings : Animals; Female; Gene Expression Regulation; Inflammation / immunology; Inflammation / pathology; Influenza A Virus, H1N1 Subtype / immunology; Influenza A Virus, H1N1 Subtype / pathogenicity; Influenza A Virus, H5N1 Subtype / immunology; Influenza A Virus, H5N1 Subtype / pathogenicity; Lipoxins / immunology; Lung / pathology; Lung / virology; Mice; Orthomyxoviridae Infections / immunology; Orthomyxoviridae Infections / mortality; Orthomyxoviridae Infections / pathology; Orthomyxoviridae Infections / virology; Signal Transduction; Survival Analysis; Virulence
Sources: Crossref, ORCID
Added: July 20, 2019

2010 journal article

MicroRNA Expression and Virulence in Pandemic Influenza Virus-Infected Mice

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

By: Y. Li, E. Chan, J. Li*, C. Ni, X. Peng*, E. Rosenzweig, T. Tumpey*, M. Katze*

co-author countries: United States of America 🇺🇸
MeSH headings : Animals; Cyclic AMP Response Element-Binding Protein / metabolism; Disease Outbreaks; Gene Expression Profiling; Gene Expression Regulation; Humans; Influenza A Virus, H1N1 Subtype / genetics; Influenza A Virus, H1N1 Subtype / immunology; Influenza A Virus, H1N1 Subtype / pathogenicity; Influenza, Human / epidemiology; Influenza, Human / immunology; Influenza, Human / virology; Interferon Type I / immunology; Lung / immunology; Lung / physiology; Lung / virology; Mice; MicroRNAs / genetics; MicroRNAs / immunology; Oligonucleotide Array Sequence Analysis; Orthomyxoviridae / genetics; Orthomyxoviridae / immunology; Orthomyxoviridae / pathogenicity; Orthomyxoviridae Infections / epidemiology; Orthomyxoviridae Infections / immunology; Orthomyxoviridae Infections / virology
Sources: Crossref, ORCID
Added: July 20, 2019

2010 journal article

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

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

By: A. Aly*, S. Lindner*, D. MacKellar*, X. Peng* & S. Kappe*

co-author countries: Saudi Arabia 🇸🇦 United States of America 🇺🇸
MeSH headings : Animals; Cytoplasm / metabolism; Female; Gene Deletion; Gene Expression Profiling; Gene Expression Regulation; Genes, Protozoan; Malaria / parasitology; Mice; Mice, Inbred BALB C; Oligonucleotide Array Sequence Analysis; Plasmodium yoelii / genetics; Plasmodium yoelii / growth & development; Plasmodium yoelii / pathogenicity; Protozoan Proteins / genetics; Protozoan Proteins / metabolism; RNA Processing, Post-Transcriptional; RNA, Protozoan / genetics; Sporozoites / growth & development
Sources: Crossref, ORCID
Added: July 20, 2019

2010 journal article

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

MBio, 1(5).

By: X. Peng*, L. Gralinski*, C. Armour*, M. Ferris*, M. Thomas*, S. Proll*, B. Bradel-Tretheway*, M. Korth* ...

co-author countries: United States of America 🇺🇸

Ed(s): N. Sonenberg & T. Dermody

MeSH headings : Animals; Disease Models, Animal; Gene Expression Profiling; Gene Expression Regulation; Immunity, Innate; Mice; RNA, Untranslated / biosynthesis; Severe acute respiratory syndrome-related coronavirus / immunology; Severe acute respiratory syndrome-related coronavirus / pathogenicity; Severe Acute Respiratory Syndrome / immunology; Severe Acute Respiratory Syndrome / pathology; Severe Acute Respiratory Syndrome / virology; Signal Transduction; Transcription, Genetic
Sources: Crossref, ORCID
Added: July 20, 2019

2009 journal article

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

BMC Genomics, 10(1), 373.

By: X. Peng*, Y. Li*, K. Walters*, E. Rosenzweig*, S. Lederer*, L. Aicher*, S. Proll*, M. Katze*

co-author countries: United States of America 🇺🇸
MeSH headings : Adolescent; Adult; Aged; Computational Biology / methods; Gene Expression Profiling; Gene Expression Regulation; Gene Regulatory Networks; Hepacivirus / physiology; Hepatitis C / genetics; Hepatitis C / metabolism; Humans; Liver / metabolism; Liver / virology; MicroRNAs / genetics; MicroRNAs / metabolism; Middle Aged; Models, Genetic; Oligonucleotide Array Sequence Analysis; RNA, Messenger / genetics; RNA, Messenger / metabolism; Sequence Analysis, RNA / methods; Young Adult
Sources: Crossref, ORCID
Added: July 20, 2019

2009 journal article

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

BMC Genomics, 10(1), 270.

By: S. Albuquerque*, C. Carret*, A. Grosso*, A. Tarun*, X. Peng*, S. Kappe*, M. Prudêncio*, M. Mota*

co-author countries: Portugal 🇵🇹 United States of America 🇺🇸
MeSH headings : Animals; Cell Line, Tumor; Gene Expression Profiling; Hepatocytes / metabolism; Hepatocytes / parasitology; Host-Parasite Interactions / genetics; Liver / metabolism; Liver / parasitology; Malaria / genetics; Mice; Mice, Inbred BALB C; Oligonucleotide Array Sequence Analysis; Plasmodium berghei; Sporozoites; Time Factors
Sources: Crossref, ORCID
Added: July 20, 2019

2009 journal article

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

PLoS Pathogens, 5(10), e1000604.

By: C. Cillóniz*, K. Shinya*, X. Peng*, M. Korth*, S. Proll*, L. Aicher*, V. Carter*, J. Chang* ...

co-author countries: Canada 🇨🇦 Japan 🇯🇵 United States of America 🇺🇸

Ed(s): M. Diamond

MeSH headings : Animals; Bronchi / pathology; Bronchi / virology; Disease Outbreaks; Gene Expression; Gene Expression Profiling; In Situ Nick-End Labeling; Inflammation / genetics; Inflammation / virology; Influenza A Virus, H1N1 Subtype / immunology; Influenza A Virus, H5N1 Subtype / immunology; Macaca; Oligonucleotide Array Sequence Analysis; Orthomyxoviridae Infections / genetics; Orthomyxoviridae Infections / immunology; Orthomyxoviridae Infections / virology; Reverse Transcriptase Polymerase Chain Reaction
Sources: Crossref, ORCID
Added: July 20, 2019

2009 journal article

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

PLoS Pathogens, 5(5), e1000438.

By: A. Goodman*, J. Fornek*, G. Medigeshi*, L. Perrone*, X. Peng*, M. Dyer*, S. Proll*, S. Knoblaugh* ...

co-author countries: United States of America 🇺🇸

Ed(s): R. Andino

MeSH headings : Animals; Apoptosis / genetics; Eukaryotic Initiation Factor-2 / metabolism; HSP40 Heat-Shock Proteins / genetics; HSP40 Heat-Shock Proteins / metabolism; Immunity, Innate; Inflammation; Influenza A virus / pathogenicity; Influenza A virus / physiology; Interferon-beta / genetics; Interferon-beta / metabolism; Interleukin-6 / genetics; Interleukin-6 / metabolism; Lung / metabolism; Lung / pathology; Lung / virology; Mice; Mice, Knockout; Oligonucleotide Array Sequence Analysis; Orthomyxoviridae Infections / immunology; Orthomyxoviridae Infections / metabolism; Orthomyxoviridae Infections / mortality; Orthomyxoviridae Infections / virology; Phosphorylation; Virus Replication / genetics; eIF-2 Kinase / metabolism
Sources: Crossref, ORCID
Added: July 20, 2019

2009 journal article

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.

By: A. Goodman*, H. Zeng*, S. Proll*, X. Peng*, C. Cilloniz*, V. Carter*, M. Korth*, T. Tumpey*, M. Katze*

co-author countries: United States of America 🇺🇸
MeSH headings : Animals; Apoptosis / genetics; Base Sequence; Cells, Cultured; DNA, Viral / genetics; Dogs; Host-Pathogen Interactions / immunology; Inflammation / immunology; Inflammation / virology; Influenza A virus / genetics; Influenza A virus / immunology; Influenza A virus / pathogenicity; Influenza A virus / physiology; Mice; Mice, Knockout; NF-kappa B / metabolism; Orthomyxoviridae Infections / genetics; Orthomyxoviridae Infections / immunology; Receptor, Interferon alpha-beta / deficiency; Receptor, Interferon alpha-beta / genetics; Receptor, Interferon alpha-beta / physiology; STAT1 Transcription Factor / metabolism; Signal Transduction; Toll-Like Receptor 3 / metabolism; Virulence; Virus Replication / immunology; eIF-2 Kinase / metabolism
Sources: Crossref, ORCID
Added: July 20, 2019

2009 journal article

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

Cytokine, 48(1-2), 83.

By: A. Goodman*, H. Zeng*, C. Cilloniz*, V. Carter*, X. Peng*, S. Proll*, T. Tumpey*, M. Katze*

co-author countries: United States of America 🇺🇸
Sources: Crossref, ORCID
Added: August 28, 2020

2009 journal article

Virus–host interactions: from systems biology to translational research

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

By: X. Peng*, E. Chan*, Y. Li*, D. Diamond*, M. Korth* & M. Katze*

co-author countries: United States of America 🇺🇸
MeSH headings : Gene Expression Regulation; Gene Expression Regulation, Viral; Gene Knockdown Techniques; Genomics / methods; Host-Pathogen Interactions; Humans; MicroRNAs / genetics; MicroRNAs / metabolism; Proteomics / methods; RNA, Small Interfering / genetics; RNA, Small Interfering / metabolism; Sequence Analysis, DNA / methods; Systems Biology / methods; Virus Diseases / immunology; Virus Diseases / virology; Virus Physiological Phenomena; Viruses / immunology
Sources: Crossref, ORCID
Added: July 20, 2019

2008 journal article

A combined transcriptome and proteome survey of malaria parasite liver stages

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

By: A. Tarun*, X. Peng*, R. Dumpit*, Y. Ogata*, H. Silva-Rivera*, N. Camargo*, T. Daly*, L. Bergman*, S. Kappe*

co-author countries: United States of America 🇺🇸
author keywords: drug targeting; fatty acid synthesis; Plasmodium
MeSH headings : Animals; Drug Design; Fatty Acids / metabolism; Gene Expression Regulation; Green Fluorescent Proteins / chemistry; Hepatocytes / parasitology; Humans; Liver / parasitology; Malaria / parasitology; Open Reading Frames; Plasmodium yoelii / metabolism; Proteome; Proteomics / methods; Transcription, Genetic
Sources: Crossref, ORCID
Added: July 20, 2019

2008 journal article

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

Bioinformatics, 24(13), i383–i389.

By: A. Vaughan*, S. Chiu*, G. Ramasamy*, L. Li*, M. Gardner*, A. Tarun*, S. Kappe*, X. Peng*

co-author countries: United States of America 🇺🇸
MeSH headings : Algorithms; Animals; Chromosome Mapping / methods; Genome, Protozoan / genetics; Plasmodium yoelii / genetics; Reproducibility of Results; Sensitivity and Specificity; Sequence Alignment / methods; Sequence Analysis, DNA / methods
Sources: Crossref, ORCID
Added: July 20, 2019

2008 journal article

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.

By: S. Mikolajczak*, H. Silva-Rivera*, X. Peng*, A. Tarun*, N. Camargo*, V. Jacobs-Lorena*, T. Daly*, L. Bergman* ...

co-author countries: United States of America 🇺🇸
MeSH headings : Animals; Anopheles / parasitology; Gene Expression Profiling; Gene Expression Regulation; Gene Targeting; Genes, Protozoan; Hemolymph / cytology; Hemolymph / metabolism; Host-Parasite Interactions; Injections, Intravenous; Insect Vectors / parasitology; Malaria / genetics; Malaria / parasitology; Mammals / parasitology; Mice; Oocysts / cytology; Oocysts / metabolism; Parasites / cytology; Parasites / genetics; Parasites / pathogenicity; Plasmodium falciparum / genetics; Plasmodium yoelii / genetics; Protein Transport; Protozoan Proteins / genetics; Protozoan Proteins / metabolism; Salivary Glands / parasitology; Sporozoites / cytology; Sporozoites / metabolism; Transcription, Genetic
Sources: Crossref, ORCID
Added: July 20, 2019

2007 chapter

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

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

By: X. Peng*, M. Langston*, A. Saxton*, N. Baldwin* & J. Snoddy*

co-author countries: United States of America 🇺🇸
author keywords: graph algorithms; microarray analysis; clustering; network motif; gene expression; protein domain; protein interaction; data integration
Sources: Crossref, ORCID
Added: July 20, 2019

2005 journal article

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

BMC Bioinformatics, 6(1), 72.

By: S. Kirov*, X. Peng*, E. Baker*, D. Schmoyer*, B. Zhang* & J. Snoddy*

co-author countries: United States of America 🇺🇸
MeSH headings : Algorithms; Animals; Computational Biology / instrumentation; Computational Biology / methods; Computer Graphics; Computers; Data Interpretation, Statistical; Database Management Systems; Databases as Topic; Databases, Factual; Databases, Genetic; Databases, Protein; Genomics; Humans; Information Storage and Retrieval; Internet; Programming Languages; Software; Software Design; Systems Integration; User-Computer Interface
Sources: Crossref, ORCID
Added: September 9, 2019

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