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Publications

2020

  • Rani A, Ranjan R, Metwally AA, Brennan DC, Perkins DL, Finn PW, “Abundance of Multidrug Resistance Efflux Pumps in the Urinary Metagenome of Kidney Transplant Patients.” BioMed Res Int, 2020.[paper]

  • Metwally AA, Ascoli C, Turturice B, Rani A, Ranjan R, Chen Y, Schott C, Faro A, Ferkol TW, Perkins DL, Finn PW, “Pediatric Lung Transplantation: Dynamics of the Microbiome and Bronchiolitis Obliterans in Cystic Fibrosis.” J Heart Lung Transplant, 2020.[paper]

2019

  • An J, Yang C, Li Z, Finn PW, Perkins DL, Sun J, Bai Z, Gao L, Zhang M, Ren D, “In vitro antioxidant activities of Rhodobacter sphaeroides and protective effect on Caco-2 cell line model.” Appl Microbiol Biotechnol, 2019.[paper]

  • Turturice BA, Gold DR, Litonjua AA, Oken E, Rifas-Shiman S, Perkins DL, Finn PW, “Lower Perinatal Exposure to Proteobacteria is an Independent Predictor of Early Childhood Wheezing.” J Allergy Clin Immunol, 2019.[paper]

  • Wu Q, Turturice B, Wagner S, Huang Y, Gupta PK, Schott C, Metwally A, Ranjan R, Perkins D, Alegre ML, Finn P, Budinger GRS, Shilling R, Bharat A, “Gut Microbiota Can Impact Chronic Murine Lung Allograft Rejection.” Am J Respir Cell Mol Biol, 2019.[paper]

  • Metwally AA, Yu PS, Reiman D, Dai Y, Perkins DL, Finn PW, “Utilizing longitudinal microbiome taxonomic profiles to predict food allergy via Long Short-Term Memory networks.” PLoS Comput Biol, 2019.[paper]

  • Singhal M, Turturice BA, Manzella CR, Ranjan R, Metwally AA, Theorell J, Huang Y, Alrefai WA, Dudeja PK, Finn PW, Perkins DL, Gill RK, “Serotonin Transporter Deficiency is Associated with Dysbiosis and Changes in Metabolic Function of the Mouse Intestinal Microbiome.” Sci Rep, 2019.[paper]

  • Eldeirawi K, Kunzweiler C, Zenk S, Finn P, Nyenhuis S, Rosenberg N, Persky V, “Associations of urban greenness with asthma and respiratory symptoms in Mexican American children.” Ann Allergy Asthma Immunol, 2019.[paper]

  • Hahn J, Gold DR, Coull BA, McCormick MC, Finn PW, Perkins DL, Rich-Edwards JW, Rifas Shiman SL, Oken E, Kubzansky LD, “Prenatal Maternal Depression and Neonatal Immune Responses.” Psychosom Med, 2019.[paper]

  • Rasic MR, Metwally AA, Perkins DL, Finn PW, “Taxonomic Classification at the Strain Level using a Species-of-Interest k-mer Database.” 2019 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI). Chicago, IL, USA. [paper]

  • Schott CA, Ascoli C, Huang Y, Perkins DL, Finn PW; ACCESS Research Group, “Declining Pulmonary Function in Interstitial Lung Disease Linked to Lymphocyte Dysfunction.” Am J Respir Crit Care Med, 2019.[paper]

2018

  • Schott C, Weigt SS, Turturice BA, Metwally A, Belperio J, Perkins DL, Finn PW, “Pulmonary Microbiome Phenotypes Linked to Bronchiolitis Obliterans Susceptibility.” J Heart Lung Transplant, 2018.[paper]

  • Zwang NA, Ganesh BB, Cardenas KT, Chong AS, Perkins DL, Finn PW, “An optimized protocol to quantify signaling in human transitional B cells by phospho flow cytometry.” J Immunol Methods, 2018. [paper]

  • Ranjan R, Rani A, Perkins DL, Finn PW, “Multiomic strategies reveal diversity and important functional aspects of human gut microbiome.” BioMed Research International. Biomed Res Int. 2018. [paper]

  • Schott C, Weigt SS, Turturice BA, Metwally A, Belperio J, Finn PW, Perkins DL, “Bronchiolitis obliterans syndrome susceptibility and the pulmonary microbiome”, The Journal of Heart and Lung Transplantation. 2018. [paper]

  • Kwan J, Hajjiri Z, Chen Y, Metwally AA, Perkins DL, Finn PW, “Donor and Recipient Ethnicity Impacts Renal Graft Adverse Outcomes.” Journal of Racial and Ethnic Health Disparities, 2017. [paper]

  • Metwally AA, Yang J, Ascoli C, Dai Y, Finn PW, Perkins DL, “MetaLonDA: a flexible R package for identifying time  intervals of differentially abundant features in metagenomic longitudinal studies”, Microbiome, 2018. [paper]

  • Aktas ON, Turturice B, Perkins DL, Finn PW. Microbiome: Allergic Diseases of Childhood. In Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases * ger, Boston, MA. [paper]

2017

  • Ascoli C, Huang Y, Schott C, Turturice BA, Metwally AA, Perkins DL, Finn PW, ACCESS Research Group, “A Circulating Micro-RNA Signature Serves as a Diagnostic and Prognostic Indicator in Sarcoidosis.” American Journal of Respiratory Cell and Molecular Biology, 2017. [paper]

  • Metwally AA, Finn PWF, Dai Y, Perkins DL, “Detection of Differential Abundance Intervals in Longitudinal Metagenomic 

  • Data Using Negative Binomial Smoothing Spline ANOVA.” ACM BCB, 2017. [paper]

  • Turturice BA, McGee H, Oliver B, Baraket M, Nguyen B, Ascoli C, Ranjan R, Rani A, Perkins DL, Finn PW, “Atopic asthmatic immune phenotypes associated with airway microbiota and airway obstruction.” PLOS One, 2017. [paper]

  • Turturice BA, Ranjan R, Nguyen B, Hughes L, Andropolis K, Gold D, Litonjua A, Oken E, Perkins DL, Finn PW, “Perinatal Bacterial Exposure Contributes to IL-13 Aeroallergen Response.” American Journal of Respiratory Cell and Molecular Biology, 2017. [paper]

  • Ozturk AB, Turturice BA, Perkins DL, Finn PW. The potential for emerging microbiome-mediated therapeutics in asthma. Current allergy and asthma reports. * paper]](https://link.springer.com/article/10.1007/s11882-017-0730-1)

2016

  • Metwally AA, Dai Y, Finn PW, Perkins DL, “WEVOTE: Weighted Voting Taxonomic Identification Method of Microbial Sequences.” PLoS ONE, 2016. [paper]

  • Rani R, Ranjan R, McGee H, Metwally AA, Hajjiri Z, Brennan D, Finn PW, Perkins DL, “A diverse virome in kidney transplant patients contains multiple viral subtypes with distinct polymorphisms.” Scientific Reports, 2016. [paper]

  • Kwan J, Hajjiri Z, Metwally AA, Finn PW, Perkins DL, “Effect of the Obesity Epidemic on Kidney Transplantation: Obesity Is Independent of Diabetes as a Risk Factor for Adverse Renal Transplant Outcomes.” PLoS ONE, 2016. [paper]

  • Rani A, Ranjan R, McGee H, Andropolis K, Panchal D, Hajjiri Z, Brennan D, Finn PW, Perkins DL, “Urinary microbiome of kidney transplant patients reveals dysbiosis with potential for antibiotic resistance.” Translational Research, * /abstract)

  • Ranjan R, Rani A, Brennan D, Finn PW, Perkins DL, “Complete Genome Sequence of BK Polyomavirus Subtype Ib-1 Detected in a Kidney Transplant Patient with BK Viremia Using Shotgun Sequencing.” Genome Announcements, 2016. [paper]

  • Ranjan R, Rani R, Metwally AA, McGee H, Perkins DL, “Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing.” Biochemical and Biophysical Research Communications, 2016. [paper]

Selected Publications (-2015)

  • Kadota PO, Hajjiri Z, Finn PW, Perkins DL, “Precision subtypes of T cell-mediated rejection identified by molecular profiles.” Frontiers in immunology, 2015. [paper]

  • Camirand G, Wang Y, Lu Y, Wan Y, Lin Y, Deng S, Guz G, Perkins DL, Finn PW, Farber D, Flavell R, Shlomchik W, Lakkis F, Rudd C, Rothstein D, “CD45 ligation expands Tregs by promoting interactions with DCs.” Journal of Clinical Investigation, 2014. [paper]

  • Nakajima T, Lin K, Li J, McGee H, Kwan J, Perkins DL, Finn PW, “T cells and lung injury. Impact of rapamycin.” American Journal of Respiratory Cell and Molecular Biology, 2014. [paper]

  • Sweiss N, Lower E, Mirsaeidi M, Dudek S, Garcia J, Perkins DL, Finn PW, Baughman R, “Rituximab in the treatment of refractory pulmonary sarcoidosis.” European Respiratory Journal, 2014. [paper]

  • Verma M, Awdishu L, Lane J, Park K, Bahur B, Lwin W, McGee H, Steiner R, Finn PW, Perkins DL, “Impact of single immunosuppressive drug withdrawal on lymphocyte immunoreactivity.” Journal of Surgical Research, * /abstract)

  • Li J, Lin K, Murray F, Nakajima T, Zhao Y, Perkins DL, Finn PW, “Regulation of Cytotoxic T Lymphocyte Antigen 4 by Cyclic AMP.” American Journal of Respiratory Cell and Molecular Biology, 2012. [paper]

  • Lwin W, Park K, Wauson M, Gao Q, Finn PW, Perkins DL, Khanna A, “Systems Biology Approach to Transplant Tolerance: Proof of Concept Experiments Using RNA Interference (RNAi) to Knock Down Hub Genes in Jurkat and HeLa Cells In Vitro.” Journal of Surgical Research, * /abstract)

  • Lin K, Kai Y, Suarez C, Crouch E, Perkins DL, Finn PW, “Surfactant Protein D-Mediated Decrease of Allergen-Induced Inflammation is Dependent upon CTLA4.” Journal of Immunology, 2010. [paper]

  • Nakajima T, Suarez C, Lin K, Kai Y, Schnitzer J, Makani S, Parker N, Perkins DL, Finn PW, “T Cell Pathways Involving CTLA4 Contribute to a Model of Acute Lung Injury.” Journal of Immunology, 2010. [paper]

FinnPerkins