D. Perkins

L. Palmer, A. Litonjua, M. Gillman, 2006, Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology.

Immunodominance is altered in T cell receptor (beta-chain) transgenic mice without the generation of a hole in the repertoire.

J. Seidman, D. Fruman, D. Perkins, 1991, Journal of immunology.

In vitro antioxidant activities of Rhodobacter sphaeroides and protective effect on Caco-2 cell line model

Zuming Li, Jun Sun, Z. Bai, 2018, Applied Microbiology and Biotechnology.

Expression of GLUT-2 cDNA in human B lymphocytes: analysis of glucose transport using flow cytometry.

S. Gullans, S. Hebert, D. Cohen, 1992, Biochimica et biophysica acta.

Allergic Pulmonary Inflammation Promotes Airway Hyperresponsiveness and B/Rel Transcription Factors: c-Rel k NF-De

G. T. Sanctis, L. Kobzik, Hongzhen He, 1999 .

Regulation of cytotoxic T lymphocyte antigen 4 by cyclic AMP.

P. Finn, D. Perkins, Ko-Wei Lin, 2013, American journal of respiratory cell and molecular biology.

T cells and lung injury. Impact of rapamycin.

Jennifer M. Kwan, Halvor S. McGee, P. Finn, 2014, American journal of respiratory cell and molecular biology.

(R)-albuterol decreases immune responses: role of activated T cells

Hongzhen He, P. Finn, D. Perkins, 2008, Respiratory research.

The Allograft Defines the Type of Rejection (Acute versus Chronic) in the Face of an Established Effector Immune Response1

D. Perkins, Z. Dai, G. Chalasani, 2004, The Journal of Immunology.

Costimulation and allergic responses: immune and bioinformatic analyses.

P. Finn, D. Perkins, V. Jain, 2008, Pharmacology & therapeutics.

Infant home endotoxin is associated with reduced allergen-stimulated lymphocyte proliferation and IL-13 production in childhood.

D. Gold, L. Ryan, D. Milton, 2005, The Journal of allergy and clinical immunology.

Inhibition of T cell costimulation abrogates airway hyperresponsiveness in a murine model.

D. Christiani, G. T. Sanctis, L. Kobzik, 1996, The Journal of clinical investigation.

Surfactant protein D deficiency influences allergic immune responses

K. Haley, P. Finn, D. Perkins, 2004, Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology.

Nuclear Factor Kappa B Activation in Human Cord Blood Mononuclear Cells

L. Palmer, M. Gillman, D. Gold, 2004, Pediatric Research.

CD23 and allergic pulmonary inflammation: potential role as an inhibitor.

D. Christiani, H. Kikutani, L. Kobzik, 1999, American journal of respiratory cell and molecular biology.

Elevated Allergen-Induced IL-13 Secretion Predicts IgE Elevation in Children Ages 2–5 Years

D. Gold, P. Finn, D. Perkins, 2005, Journal of Clinical Immunology.

Atopic asthma: differential activation phenotypes among memory T helper cells

E. Israel, D. Christiani, P. Finn, 2001, Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology.

Both CD80 and CD86 co-stimulatory molecules regulate allergic pulmonary inflammation.

P. Linsley, M. Sayegh, L. Kobzik, 1998, International immunology.

Absence of clinical GVHD and the in vivo induction of regulatory T cells after transplantation of facilitating cells.

J. Glickman, Y. Colson, D. Perkins, 2004, Blood.

Absence of Clinical GVHD and the In Vivo Induction of Regulatory T cells following Facilitating Cell Transplantation

J. Glickman, Y. Colson, D. Perkins, 2004 .

Inhibition of NF-κB-Dependent T Cell Activation Abrogates Acute Allograft Rejection1

M. Boothby, J. Stone, P. Finn, 2001, The Journal of Immunology.

Administration of Pentoxifylline During Allergen Sensitization Dissociates Pulmonary Allergic Inflammation from Airway Hyperresponsiveness1

Hongzhen He, P. Finn, D. Perkins, 2001, The Journal of Immunology.

Analysis of T-cell activation after bronchial allergen challenge in patients with atopic asthma.

E. Israel, D. Christiani, P. Finn, 1998, The Journal of allergy and clinical immunology.

Donor and Recipient Ethnicity Impacts Renal Graft Adverse Outcomes

Ahmed A. Metwally, Jennifer M. Kwan, Zahraa Hajjiri, 2018, Journal of Racial and Ethnic Health Disparities.

Allergen-induced cytokine production, atopic disease, IgE, and wheeze in children.

T. Platts-Mills, D. Gold, Hongzhen He, 2003, The Journal of allergy and clinical immunology.

Selective elimination of non-lpr lymphoid cells in mice undergoing lpr-mediated graft-vs-host disease.

A. Marshak‐Rothstein, D. Perkins, J. Michaelson, 1987, Journal of immunology.

Long non-coding RNAs ( lncRNAs ) NEAT 1 and MALAT 1 are differentially expressed in severe COVID-19 patients : An integrated single-cell analysis

D. Perkins, C. Vagts, V. Raguveer, 2022 .

B7-1 (CD80) and B7-2 (CD86) have complementary roles in mediating allergic pulmonary inflammation and airway hyperresponsiveness.

A. Sharpe, L. Kobzik, P. Finn, 2000, American journal of respiratory cell and molecular biology.

Immunodominance: intramolecular competition between T cell epitopes.

G. Berriz, M. Gefter, J. Smith, 1991, Journal of immunology.

Gene Co-expression Networks Identifies Common Hub Genes Between Cutaneous Sarcoidosis and Discoid Lupus Erythematosus

P. Finn, D. Perkins, N. Sweiss, 2020, Frontiers in Medicine.

Fas modulation of apoptosis during negative selection of thymocytes.

P. Finn, D. Perkins, J. Castro, 1996, Immunity.

Regulation of CTLA-4 expression during T cell activation.

J. Bluestone, Y. Wang, Z. Wang, 1996, Journal of immunology.

T‐cell activation in autoimmune and inflammatory diseases

D. Perkins, 1998, Current opinion in nephrology and hypertension.

Analysis of robust innate immune response after transplantation in the absence of adaptive immunity1

J. Stone, Hongzhen He, D. Perkins, 2002, Transplantation.

Fetal Cord Blood: Aspects of Heightened Immune Responses

A. Litonjua, M. Gillman, D. Gold, 2005, Journal of Clinical Immunology.

Anti-CD25 mAb administration prevents spontaneous liver transplant tolerance.

J. Reyes, A. Thomson, W. Li, 2006, Transplantation proceedings.

Altered transcription factor targeting is associated with differential peripheral blood mononuclear cell proportions in sarcoidosis

P. Finn, D. Perkins, N. Sweiss, 2022, Frontiers in Immunology.

The role of Foxp3+ regulatory T cells in liver transplant tolerance.

J. Reyes, A. Thomson, W. Li, 2006, Transplantation proceedings.

CD45RB Ligation Inhibits Allergic Pulmonary Inflammation by Inducing CTLA4 Transcription1

S. Makani, Hongzhen He, D. Rothstein, 2007, The Journal of Immunology.

CTLA4 Transcription Pulmonary Inflammation by Inducing CD45RB Ligation Inhibits Allergic

S. Makani, Hongzhen He, D. Rothstein, 2007 .

T Cell Pathways Involving CTLA4 Contribute To a Model of Acute Lung Injury

S. Makani, P. Finn, D. Perkins, 2010, The Journal of Immunology.

Contribute To a Model of Acute Lung Injury T Cell Pathways Involving CTLA4

S. Makani, P. Finn, D. Perkins, 2022 .

Analysis of Exosomal MicroRNA Dynamics in Response to Rhinovirus Challenge in a Longitudinal Case-Control Study of Asthma

R. Lutter, A. Sinha, P. Finn, 2022, Viruses.

Surfactant Protein D-Mediated Decrease of Allergen-Induced Inflammation Is Dependent upon CTLA4

E. Crouch, P. Finn, D. Perkins, 2010, The Journal of Immunology.

Established Effector Immune Response (Acute versus Chronic) in the Face of an The Allograft Defines the Type of Rejection

D. Perkins, Z. Dai, G. Chalasani, 2004 .

The lpr gene is associated with resistance to engraftment by lymphoid but not erythroid stem cells from normal mice.

A. Marshak‐Rothstein, D. Perkins, J. Michaelson, 1987, Journal of immunology.

T cell activation in a murine model of asthma.

D. Christiani, G. T. Sanctis, L. Kobzik, 1996, The American journal of physiology.

Graft Produced Interleukin-6 Functions as a Danger Signal and Promotes Rejection After Transplantation

Y. Colson, P. Finn, D. Perkins, 2007, Transplantation.

Disruption of innate defense responses by endoglycosidase HPSE promotes cell survival

Evan J. Kyzar, C. Patil, P. Finn, 2020, bioRxiv.

Rituximab in the treatment of refractory pulmonary sarcoidosis

J. Garcia, S. Dudek, R. Baughman, 2014, European Respiratory Journal.

An optimized protocol to quantify signaling in human transitional B cells by phospho flow cytometry.

A. Chong, P. Finn, D. Perkins, 2018, Journal of immunological methods.

In vitro antioxidant activities of Rhodobacter sphaeroides and protective effect on Caco-2 cell line model

Zuming Li, Jun Sun, Z. Bai, 2018, Applied Microbiology and Biotechnology.

Iconographies supplémentaires de l'article : Associations of cord blood fatty acids with lymphocyte proliferation, IL-13, and IFN-γ

L. Palmer, M. Gillman, D. Gold, 2011 .

Associations of cord blood fatty acids with lymphocyte proliferation, IL-13, and IFN-gamma.

L. Palmer, M. Gillman, D. Gold, 2006, The Journal of allergy and clinical immunology.

Plasticity of the T Cell Receptor Repertoire in TCR β-Chain Transgenic Mice

P. Finn, D. Perkins, I. Rimm, 1996 .

Plasticity of the T cell receptor repertoire in TCR beta-chain transgenic mice.

P. Finn, D. Perkins, I. Rimm, 1996, Cellular immunology.

Differential expression of activation markers during tolerance induction by superantigens in T-cell receptor (beta-chain) transgenic mice.

P. Finn, D. Perkins, I. Rimm, 1994, Cellular immunology.

Control of cellular and humoral immune responses by peptides containing T-cell epitopes.

M. Gefter, J. Smith, D. Perkins, 1989, Cold Spring Harbor symposia on quantitative biology.

A diverse virome in kidney transplant patients contains multiple viral subtypes with distinct polymorphisms

Ahmed A. Metwally, D. Brennan, A. Rani, 2016, Scientific Reports.

Serotonin Transporter Deficiency is Associated with Dysbiosis and Changes in Metabolic Function of the Mouse Intestinal Microbiome

Ahmed A. Metwally, R. Ranjan, P. Finn, 2019, Scientific Reports.

WEVOTE: Weighted Voting Taxonomic Identification Method of Microbial Sequences

Patricia W. Finn, Yang Dai, Ahmed A. Metwally, 2016, bioRxiv.

The olfactory G protein-coupled receptor (Olfr-78/OR51E2) modulates the intestinal response to colitis.

Yinglin Xia, B. Layden, P. Finn, 2020, American journal of physiology. Cell physiology.

Scavenger Receptors SR-AI/II and MARCO Limit Pulmonary Dendritic Cell Migration and Allergic Airway Inflammation1

S. Shapiro, A. Imrich, K. Tryggvason, 2007, The Journal of Immunology.

Limit Pulmonary Dendritic Cell Migration Scavenger Receptors SR-AI/II and MARCO

S. Shapiro, A. Imrich, K. Tryggvason, 2007 .

Host and gut microbial tryptophan metabolism and type 2 diabetes: an integrative analysis of host genetics, diet, gut microbiome and circulating metabolites in cohort studies

J. Manson, F. Hu, E. Boerwinkle, 2021, Gut.

Microbiome: Allergic Diseases of Childhood

P. Finn, D. Perkins, B. Turturice, 2018 .

Long non-coding RNAs (lncRNAs) NEAT1 and MALAT1 are differentially expressed in severe COVID-19 patients: An integrated single-cell analysis

P. Finn, D. Perkins, C. Vagts, 2022, PloS one.

Perinatal Bacterial Exposure Contributes to IL‐13 Aeroallergen Response

A. Litonjua, D. Gold, E. Oken, 2017, American journal of respiratory cell and molecular biology.

Declining Pulmonary Function in Interstitial Lung Disease Linked to Lymphocyte Dysfunction.

P. Finn, D. Perkins, C. Ascoli, 2020, American journal of respiratory and critical care medicine.

A Circulating MicroRNA Signature Serves as a Diagnostic and Prognostic Indicator in Sarcoidosis

Ahmed A. Metwally, P. Finn, D. Perkins, 2017, American journal of respiratory cell and molecular biology.

Synergistic induction of CTLA-4 expression by costimulation with TCR plus CD28 signals mediated by increased transcription and messenger ribonucleic acid stability.

Z. Wang, P. Finn, D. Perkins, 1997, Journal of immunology.

Re-sampling strategy to improve the estimation of number of null hypotheses in FDR control under strong correlation structures

Xin Lu, David L. Perkins, Xin Lu, 2007, BMC Bioinformatics.

Long non-coding RNAs (lncRNAs) NEAT1 and MALAT1 are differentially expressed in severe COVID-19 patients: An integrated single cell analysis

P. Finn, D. Perkins, C. Vagts, 2021, medRxiv.

Detection of Differential Abundance Intervals in Longitudinal Metagenomic Data Using Negative Binomial Smoothing Spline ANOVA

Patricia W. Finn, Yang Dai, Ahmed A. Metwally, 2017, BCB.

Comparison of class I‐ and II‐restricted T cell recognition of the identical peptide

G. Berriz, M. Gefter, D. Perkins, 1991, European journal of immunology.

Identical peptides recognized by MHC class I- and II-restricted T cells

M. Gefter, J. Smith, D. Perkins, 1989, The Journal of experimental medicine.

Prolonged Allograft Survival in TNF Receptor 1-Deficient Recipients Is Due to Immunoregulatory Effects, Not to Inhibition of Direct Antigraft Cytotoxicity1

K. Haley, J. Stone, Hongzhen He, 2002, The Journal of Immunology.

CD45 ligation expands Tregs by promoting interactions with DCs.

Y. Wan, R. Flavell, C. Rudd, 2014, The Journal of clinical investigation.

Toll-like receptor 4 or 2 agonists decrease allergic inflammation.

Hongzhen He, P. Finn, D. Perkins, 2005, American journal of respiratory cell and molecular biology.

Molecular profiling of the role of the NF‐κB family of transcription factors during alloimmunity

T. Mueller, M. Boothby, Hongzhen He, 2002, Journal of leukocyte biology.

TLR2 and TLR4 stimulation differentially induce cytokine secretion in human neonatal, adult, and murine mononuclear cells.

M. Gillman, D. Gold, Hongzhen He, 2004, Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research.

Fenfluramine-induced gene dysregulation in human pulmonary artery smooth muscle and endothelial cells

Wei Zhang, W. Yao, J. Yuan, 2011, Pulmonary circulation.

Differentiation of stress, metabolism, communication, and defense responses following transplantation

J. Lederer, D. Perkins, Chunyan Ma, 2003, Journal of leukocyte biology.

NF-kappa B/Rel transcription factors: c-Rel promotes airway hyperresponsiveness and allergic pulmonary inflammation.

G. T. Sanctis, L. Kobzik, P. Finn, 1999, Journal of immunology.

Pertussis toxin prevents the induction of peripheral T cell anergy and enhances the T cell response to an encephalitogenic peptide of myelin basic protein.

M. Gefter, D. Perkins, T. Kamradt, 1991, Journal of Immunology.

Analysis of the Major Histocompatibility Complex in Graft Rejection Revisited by Gene Expression Profiles

T. Mueller, K. Haley, Hongzhen He, 2004, Transplantation.

Silencing of immunodominant epitopes by contiguous sequences in complex synthetic peptides.

M. Gefter, J. Smith, D. Perkins, 1992, Cellular immunology.

Bronchiolitis obliterans syndrome susceptibility and the pulmonary microbiome.

Ahmed A. Metwally, J. Belperio, P. Finn, 2018, The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation.

Evidence for an intrinsic B cell defect in lpr/lpr mice apparent in neonatal chimeras.

A. Marshak‐Rothstein, D. Perkins, J. Michaelson, 1990, Journal of immunology.

Air Pollution, Neonatal Immune Responses, and Potential Joint Effects of Maternal Depression

B. Coull, M. McCormick, L. Kubzansky, 2021, International journal of environmental research and public health.

Analysis of differential immune responses induced by innate and adaptive immunity following transplantation

Hongzhen He, D. Perkins, James R. Stone, 2003, Immunology.

Multiomic Strategies Reveal Diversity and Important Functional Aspects of Human Gut Microbiome

A. Rani, R. Ranjan, P. Finn, 2018, BioMed research international.

Taxonomic Classification at the Strain Level using a Species-of-Interest $\boldsymbol{k}$-mer Database

Patricia W. Finn, Mladen R. Rasic, Ahmed A. Metwally, 2019, 2019 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI).

Analysis of cytokine functions in graft rejection by gene expression profiles1

K. Haley, Hongzhen He, P. Finn, 2003, Transplantation.

Evaluating bacterial and functional diversity of human gut microbiota by complementary metagenomics and metatranscriptomics

A. Rani, R. Ranjan, P. Finn, 2018, bioRxiv.

Lower perinatal exposure to Proteobacteria is an independent predictor of early childhood wheezing.

A. Litonjua, D. Gold, S. Rifas-Shiman, 2019, The Journal of allergy and clinical immunology.

Restriction of the TCR repertoire inhibits the development of memory T cells and prevents autoimmunity in lpr mice.

V. Kelley, A. Marshak‐Rothstein, P. Finn, 1996, Journal of immunology.

Modulation of gene expression by alloimmune networks following murine heart transplantation

T. Mueller, P. Finn, D. Perkins, 2004, Molecular Genetics and Genomics.

MetaLonDA: a flexible R package for identifying time intervals of differentially abundant features in metagenomic longitudinal studies

Ahmed A. Metwally, Yang Dai, P. Finn, 2018, Microbiome.

Healthful eating patterns, serum metabolite profile and risk of diabetes in a population-based prospective study of US Hispanics/Latinos

F. Hu, E. Boerwinkle, R. Burk, 2022, Diabetologia.

Precision Subtypes of T Cell-Mediated Rejection Identified by Molecular Profiles

Zahraa Hajjiri, P. Finn, D. Perkins, 2015, Front. Immunol..

Neonatal immune responses to TLR2 stimulation: Influence of maternal atopy on Foxp3 and IL-10 expression

E. Lieberman, M. Gillman, D. Gold, 2006, Respiratory research.

Long non-coding RNAs (lncRNAs) NEAT1 and MALAT1 are differentially expressed in severe COVID-19 patients: An integrated single cell analysis

P. Finn, D. Perkins, C. Vagts, 2021, medRxiv.

Immune response to the mRNA COVID-19 vaccine in hemodialysis patients: cohort study

P. Finn, D. Perkins, M. Ghassemi, 2023, medRxiv.

The Combined Effects of Zafirlukast, Prednisone, and Inhaled Budesonide on IL-13 and IFN-γ Secretion

E. Israel, P. Finn, D. Perkins, 2005, Journal of Clinical Immunology.

Analysis of the Innate and Adaptive Phases of Allograft Rejection by Cluster Analysis of Transcriptional Profiles1

T. Mueller, D. Perkins, Chunyan Ma, 2002, The Journal of Immunology.

The graft response to transplantation: a gene expression profile analysis.

R. Gentleman, Jianhua Zhang, T. Mueller, 2003, Physiological genomics.

expression profile analysis The graft response to transplantation: a gene

R. Gentleman, T. Mueller, D. Perkins, 2015 .

Abundance of Multidrug Resistance Efflux Pumps in the Urinary Metagenome of Kidney Transplant Patients

Ahmed A. Metwally, D. Brennan, A. Rani, 2020, BioMed Research International.

Trimer IgG and neutralising antibody response to COVID-19 mRNA vaccination in individuals with sarcoidosis

Jessica M. Lee, P. Finn, D. Perkins, 2022, ERJ Open Research.

Atopic asthmatic immune phenotypes associated with airway microbiota and airway obstruction

A. Rani, R. Ranjan, P. Finn, 2017, PloS one.

Impact of single immunosuppressive drug withdrawal on lymphocyte immunoreactivity.

P. Finn, D. Perkins, L. Awdishu, 2014, The Journal of surgical research.

Prenatal Maternal Depression and Neonatal Immune Responses

B. Coull, M. McCormick, L. Kubzansky, 2019, Psychosomatic medicine.

Utilizing longitudinal microbiome taxonomic profiles to predict food allergy via Long Short-Term Memory networks

Philip S. Yu, Derek Reiman, Philip S Yu, 2019, PLoS Comput. Biol..

Transmission Dynamics of Large Coronavirus Disease Outbreak in Homeless Shelter, Chicago, Illinois, USA, 2020

P. Finn, D. Perkins, Elizabeth S. Davis, 2021, Emerging infectious diseases.

of Direct Antigraft Cytotoxicity Immunoregulatory Effects, Not to Inhibition Receptor 1-Deficient Recipients Is Due to Prolonged Allograft Survival in TNF

J. Stone, Hongzhen He, D. Perkins, 2001 .

Pediatric lung transplantation: Dynamics of the microbiome and bronchiolitis obliterans in cystic fibrosis.

Ahmed A. Metwally, A. Rani, T. Ferkol, 2020, The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation.

Microarray analysis of gene expression in murine cardiac graft infiltrating cells.

D. Perkins, Xin Lu, Yurong Liang, 2007, Methods in molecular biology.

Serotonin Transporter Deficiency is Associated with Dysbiosis and Changes in Metabolic Function of the Mouse Intestinal Microbiome

Ahmed A. Metwally, R. Ranjan, P. Finn, 2019, Scientific Reports.

Variable expression of WASP in B cell lines of Wiskott-Aldrich syndrome patients.

F. Finkelman, C. June, D. Perkins, 1997, Journal of immunology.

Superantigen-induced peripheral tolerance inhibits T cell responses to immunogenic peptides in TCR (beta-chain) transgenic mice.

J. Seidman, D. Perkins, I. Rimm, 1993, Journal of immunology.

A systems biology view of allograft rejection

D. Perkins, Xin Lu, 2005 .

Functional genomics of immune responses

T. Mueller, D. Perkins, C. Mckee, 2002 .

The endogenous pro-resolving mediators lipoxin A4 and resolvin E1 preserve organ function in allograft rejection.

B. Levy, J. Reilly, C. Serhan, 2011, Prostaglandins, Leukotrienes and Essential Fatty Acids.

Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing.

Ahmed A. Metwally, A. Rani, R. Ranjan, 2016, Biochemical and biophysical research communications.

MetaLonDA: a flexible R package for identifying time intervals of differentially abundant features in metagenomic longitudinal studies

Yang Dai, Christian Ascoli, Ahmed A. Metwally, 2018, Microbiome.