Works (53)

Updated: April 8th, 2024 06:06

2024 article

Human long noncoding RNA,VILMIR,is induced by major respiratory viral infections and modulates the host interferon response

John, K., Huntress, I., Smith, E., Chou, H., Tollison, T. S., Covarrubias, S., … Peng, X. (2024, March 29).

By: K. John n, I. Huntress n, E. Smith n, H. Chou n, T. Tollison n, S. Covarrubias*, E. Crisci n, S. Carpenter*, X. Peng n

TL;DR: The results show that VILMIR is a novel interferon-stimulated gene (ISG) that regulates the host interferon response and may be a potential therapeutic target for human respiratory viral infections upon further mechanistic investigation. (via Semantic Scholar)
Source: ORCID
Added: April 1, 2024

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

TL;DR: Findings indicate that changes in gut microbiomes are associated with RhCMV/SIV vaccine-induced protection and early host response to vaccination in rhesus macaques. (via Semantic Scholar)
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* ...

MeSH headings : Animals; Humans; Alternative Splicing; Cytomegalovirus; Cytomegalovirus Vaccines; Genetic Variation; Macaca mulatta; Simian Immunodeficiency Virus; Histocompatibility Antigens Class I / genetics
TL;DR: Using long-read sequencing, 16 Mamu-E isoforms were identified and all MamU-E splicing junctions were detected among HLA-Eisoforms in humans and the presence of G2_LTR alleles was significantly associated with the lack of RhCMV/SIV vaccine protection. (via Semantic Scholar)
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).

MeSH headings : Chromosome Mapping / methods; Gene Expression Regulation; Genome, Human; High-Throughput Nucleotide Sequencing / methods; Humans; Regulatory Sequences, Nucleic Acid
TL;DR: The utility of Reel-seq and FREP-MS analyses for the systematic identification of cis-REs at high resolution over a large region of the human genome in a systematic and continuous manner is confirmed. (via Semantic Scholar)
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

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
TL;DR: This work proposes a local collapsing test called phylogeny-guided microbiome OTU-specific association test (POST), and develops a user friendly R package POSTm, which can enhance the selection performance of associated microbiome features by improving the overall true-positive and false-positive detection. (via Semantic Scholar)
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 ...

author keywords: Chlamydia; genital tract; antibody; serology; endometrium; immunoproteome
MeSH headings : Antibodies, Bacterial; Chlamydia Infections; Chlamydia trachomatis; Female; Humans; Immunoglobulin G; Reinfection
TL;DR: Protein-specific CT antibodies are not sufficient to protect against ascending or incident infection but broad recognition of CT proteins by IgG correlates with cervical CT gene transcript abundance, suggesting CT protein abundance correlates with immunogenicity and signifies their potential as vaccine candidates. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
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.

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

author keywords: environmental transmission; disease transmission modelling; phylodynamics; whole-genome sequencing
MeSH headings : Epidemics; Phylogeny; Probability
TL;DR: It is concluded that prior knowledge of the likely ecology and population structure of pathogens in host and non-host environments is critical to fully using phylodynamic techniques. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
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* ...

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
TL;DR: It is reported that 68–1 RhCMV/SIV vector administration strikingly alters the whole blood transcriptome of vaccinated RMs, with the sustained induction of specific immune-related pathways, including immune cell, toll-like receptor (TLR), inflammasome/cell death, and interleukin-15 (IL-15) signaling, significantly correlated with subsequent vaccine efficacy. (via Semantic Scholar)
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* ...

TL;DR: It is found that arrest of viral replication after challenge significantly correlates with a vaccine-induced response to IL-15 that includes modulation of T cell, inflammation, TLR signaling, and cell death programming, suggesting that RhCMV/SIV efficacy is not based on chance, but rather, results from a coordinated and sustained vaccine-mediated induction of innate and adaptive immune pathways. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
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

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
TL;DR: The results suggest TNFα and IL-1α enhance each other's downstream effects resulting in a hyperinflammatory response to chlamydial infection and propose that biologics targeting TNF-induced IL- 1α synthesis could be used to mitigate tissue damage during chlamYDial infection. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
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 ...

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
TL;DR: It is shown that the secretome and exosomes of lung spheroid cells is effective as inhalation treatment in rodent models of lung injury and fibrosis and superior to the counterparts derived from mesenchymal stem cells. (via Semantic Scholar)
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* ...

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
TL;DR: New rhesus-specific assays are designed that remove the need for primers conventionally targeting variable regions and allow single cell level Ig and TCR repertoire analysis, and the first complete reference set for the constant regions of all known isotypes and chain types of rhesu Ig andTCR repertoires is constructed. (via Semantic Scholar)
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* ...

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
TL;DR: It is suggested that Fc region characteristics modulate the selective placental transfer of IgG, with implications for maternal vaccine design and infant health. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
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* ...

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
TL;DR: It is found that host genetics, specifically Fc gamma receptor genetic variations, influenced whether receiving the DNA/rAd5 regimen was beneficial, neutral, or detrimental to an individual with respect to HIV-1 acquisition risk. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
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* ...

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
TL;DR: It is found that AGMs rapidly activate and maintain evolutionarily conserved regenerative wound healing mechanisms in mucosal tissue, which likely preserves mucosal integrity and prevents inflammatory insults that underlie immune exhaustion in RMs. (via Semantic Scholar)
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

author keywords: RNA-seq; chlamydia; gonorrhea; natural infection; microbiome
TL;DR: It is suggested that total RNA profiling will advance understanding of the interplay of pathogen, host and microbiota during natural infection and may reveal novel, outcome-relevant biomarkers. (via Semantic Scholar)
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.

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
TL;DR: A deeper understanding of the molecular mechanism(s) of IgG binding to placentally expressed Fc receptors could be important for the design of novel maternal IgG-based therapeutics and vaccines with optimal transplacental transfer efficiency. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
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* ...

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
TL;DR: Findings indicate that cell-intrinsic type III IFN-mediated innate immune responses in the nasal epithelium are not only crucial for viral clearance and attenuation, but may also play an important role in the induction of protective immune responses with live-attenuated vaccines. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
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*

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
TL;DR: The results suggest that the expression of FcγR genes is influenced by these SNPs either directly or in linkage with other causal variants, and motivate further investigations into the potential for a causal association of expression and alternative splicing of FCGR2C and other FcβR genes with the HIV-1 vaccine protection in the RV144 trial and other similar studies. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
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.

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
TL;DR: An extensive and systematic profiling of lipids, metabolites, and proteins in respiratory compartments of ferrets infected with either 1918 or 2009 human pandemic H1N1 influenza viruses finds enrichment of distinct T cell subpopulations in the trachea. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
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* ...

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
TL;DR: A broad categorization of potential lncRNA functions is provided and subsets of lncRNAs with likely key roles in respiratory virus pathogenesis are identified. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
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.

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
TL;DR: The genome annotations of rhesus ( Macaca mulatta) and cynomolgus (Macaca fascicularis) macaques, two of the most common non‐human primate animal models, are limited. (via Semantic Scholar)
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* ...

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
TL;DR: Mass sequencing is used to identify genes differentially expressed in CD4+ T cells during HIV-1 infection and shows that it is possible to identify candidate drugs for host-directed therapy against HIV/AIDS using the genomics-based approach. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
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* ...

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
TL;DR: During acute infection, a significant host response was mounted in the mucosa before inflammation was triggered, and the response has a detrimental effect on tissue integrity, causing increased permeability, tissue damage, and recruitment of SIV target cells. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
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* ...

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
TL;DR: The results reveal the complexity of the transcriptional response to viral infection, previously undocumented genomic elements, and extensive diversity in the response across mouse strains. (via Semantic Scholar)
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* ...

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
TL;DR: This is the first description of a severe, partially lethal, disease model of MERS-CoV, and as such will have a major impact on the ability to assess the efficacy of vaccines and treatment strategies as well as allowing more detailed pathogenesis studies. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
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* ...

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
TL;DR: It is shown that transcriptional changes in the CFTR-knockout ferret lung reflect pathways of early disease that cannot be readily studied in human infants with cystic fibrosis disease. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
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* ...

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
TL;DR: A major expansion of NHPRTR is described by adding 10.1 billion fragments of tissue-specific RNA-seq data, such that 88% of the reads align to human reference sequences, allowing the full list of expression abundance across all tissues for each species to be computed. (via Semantic Scholar)
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*

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
TL;DR: Sequence comparisons indicated that RFHVMn and KSHV developed in long-term synchrony with the evolution of their hosts, and both viruses phylogenetically group within the RV1 lineage of Old World primate rhadinoviruses. (via Semantic Scholar)
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*

MeSH headings : Bayes Theorem; Computational Biology / methods; Humans; Models, Statistical; Molecular Sequence Annotation; RNA / genetics; Sequence Analysis, RNA / methods; Software
TL;DR: This work presents a new method to measure and correct for protocol-specific sequence bias in RNA-Seq experiments using a simple graphical model that effectively decreases bias and increases uniformity. (via Semantic Scholar)
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*

MeSH headings : Algorithms; Data Compression / methods; High-Throughput Nucleotide Sequencing / methods; Probability; Software
TL;DR: Quip is presented, a lossless compression algorithm for next-generation sequencing data in the FASTQ and SAM/BAM formats and the first assembly-based compressor, using a novel de novo assembly algorithm. (via Semantic Scholar)
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
TL;DR: A large-scale RNA-Seq data and analysis infrastructure is described, the NHP reference transcriptome resource, which presently hosts data from 12 species of primates and is to be expanded to 15 species/subspecies spanning great apes, old world monkeys, new world monkeys and prosimians. (via Semantic Scholar)
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* ...

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
TL;DR: These findings represent the first integrated sequencing analysis of the response of host small RNAs to virus infection and show that smallRNAs are an integrated component of complex networks involved in regulating the host response to infection. (via Semantic Scholar)
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*

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
TL;DR: The first application to the authors' knowledge of next-generation sequencing to the analysis of RNA from a CD4+ T cell line infected with intact HIV is reported, providing insights into alternative viral RNA splice events and the expression of noncoding RNAs, including microRNA host genes. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
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* ...

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
TL;DR: It is suggested that Vietnam/1203 is more pathogenic in mice as a consequence of several factors, including the early and sustained induction of the inflammatory response, the additive or synergistic effects of upregulated components of the immune response, and inhibition of lipoxin-mediated anti-inflammatory responses, which correlated with the ability of VN/ 1203 to disseminate to extrapulmonary organs. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
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*

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
TL;DR: This is the first demonstration that cellular gene expression patterns in influenza virus-infected mice may be attributed in part to microRNA regulation and that such regulation may be a contributing factor to the extreme virulence of the r1918. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
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*

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
TL;DR: A global gene expression survey is used to more comprehensively identify transcripts that are affected by SAP1 deletion, which suggests that SAP1 is involved in a selective post‐transcriptional mechanism to regulate the abundance of transcripts critical to the infectivity of sporozoites. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
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* ...

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
TL;DR: Using next-generation sequencing, a whole-transcriptome analysis of the host response to severe acute respiratory syndrome coronavirus infection across four founder mouse strains of the Collaborative Cross demonstrated that virus infection alters the expression of numerous long ncRNAs, suggesting that these RNAs may be a new class of regulatory molecules that play a role in determining the outcome of infection. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
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*

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
TL;DR: The utility of the approach to obtain new insights into post-transcriptional gene regulation at the miRNA level in complex human diseases is demonstrated as the framework for future experimental analyses is provided. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
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*

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
TL;DR: The data reveal that host cell infection by Plasmodium sporozoites leads to a coordinated and sequential set of biological events, ranging from the initial stage of stress response up to the engagement of host metabolic processes and the maintenance of cell viability throughout infection. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
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* ...

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
TL;DR: Compared pathology and global gene expression profiles in bronchial tissue from macaques infected with either the reconstructed 1918 pandemic virus or the highly pathogenic avian H5N1 virus A/Vietnam/1203/04 suggest that the severity of disease in 1918 virus-infected macaques is a consequence of the early up-regulation of cell death and inflammatory related genes, in which additive or synergistic effects likely dictate the severityof tissue damage. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
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* ...

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
TL;DR: It is reported that infection of P58IPK knockout mice with influenza virus resulted in increased lung pathology, immune cell apoptosis, PKR activation, and mortality, and it is suggested that P 58IPK represents a new class of molecule, a cellular inhibitor of the host defense (CIHD), as P56IPK is activated during virus infection to inhibit virus-induced apoptosis and inflammation to prolong host survival, even while prolonging viral replication. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
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*

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
TL;DR: Familiarity studies have identified potential pathways, via interferon regulatory factor 3 (IRF3) activation or Hoxa13, Polr2a, Nr4a1, or Ing1 induction, that contribute to this redundancy. (via Semantic Scholar)
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*

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*

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
TL;DR: New high-throughput technologies, a new philosophy for studying virus-host interactions, and the potential of systems biology to facilitate bench-to-bedside research and create novel strategies to combat disease are highlighted. (via Semantic Scholar)
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*

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
TL;DR: A comprehensive transcriptome analysis in combination with a proteomic survey of LS revealed exported parasite proteins and LS metabolic pathways including expression of FASII pathway enzymes and other pathways localized in the apicoplast as potential drug targets to prevent malaria infection. (via Semantic Scholar)
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*

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
TL;DR: A systematic assessment of the accuracy of the genome annotation based on a detailed analysis of a comprehensive set of cDNA sequences and proteomics data found that the coverage of the current annotation tends to be biased toward genes expressed in the blood stages of the parasite life cycle. (via Semantic Scholar)
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* ...

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
TL;DR: The UIS-UOS gene classification provides a framework to elucidate the infectivity and transmission success of Plasmodium sporozoites on a whole-genome scale and identify targets for vector-based transmission blocking strategies (UOS genes), as well as strategies that prevent mammalian host infection (UIS genes). (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
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*

author keywords: graph algorithms; microarray analysis; clustering; network motif; gene expression; protein domain; protein interaction; data integration
TL;DR: This work developed algorithms for constructing gene co-expression networks labeled with corresponding protein sequence domain combinations, and detected recurring network motifs with similar protein domain memberships within these labeled networks, and applied this approach to the malaria transcriptome. (via Semantic Scholar)
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*

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
TL;DR: GeneKeyDB is a gene-centered relational database developed to enhance data mining in biological data sets and can enable analysis tools and users to manipulate the intersections, unions, and differences among different data sets. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: September 9, 2019

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