Fergal J. Duffy

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CycloPs: Generating Virtual Libraries of Cyclized and Constrained Peptides Including Nonnatural Amino Acids

Marc Devocelle, Denis C. Shields, Fergal J. Duffy, 2011, J. Chem. Inf. Model..

TIN - A Combinatorial Compound Collection of Synthetically Feasible Multicomponent Synthesis Products

Tim Heinemann, Dermot Cox, David Toomey, 2011, J. Chem. Inf. Model..

Virtual Screening Using Combinatorial Cyclic Peptide Libraries Reveals Protein Interfaces Readily Targetable by Cyclic Peptides

Marc Devocelle, Denis C. Shields, Fergal J. Duffy, 2015, J. Chem. Inf. Model..

Virtual Screening of Constrained Cyclic Peptides as Mimics of Known Protein binding Peptides and Short linear Motifs

Marc Devocelle, Denis C. Shields, Fergal J. Duffy, 2012 .

Computational survey of peptides derived from disulphide-bonded protein loops that may serve as mediators of protein-protein interactions

Marc Devocelle, Denis C. Shields, Fergal J. Duffy, 2014, BMC Bioinformatics.

GlycoProfileAssigner: automated structural assignment with error estimation for glycan LC data

Pauline M. Rudd, Fergal J. Duffy, P. Rudd, 2015, Bioinform..

Metabolite changes in blood predict the onset of tuberculosis

Michel R. Klein, Jane Hughes, Gerhard Walzl, 2018, Nature Communications.

Immunometabolic Signatures Predict Risk of Progression to Active Tuberculosis and Disease Outcome

Daniel E. Zak, Fergal J. Duffy, D. Zak, 2019, Front. Immunol..

Plasma N-glycans in colorectal cancer risk

Fergal J. Duffy, F. Agakov, M. Perola, 2018, Scientific Reports.

A contained Mycobacterium tuberculosis mouse infection model predicts active disease and containment in humans

Fergal J. Duffy, E. Gold, A. Aderem, 2021 .

Computational approaches to developing short cyclic peptide modulators of protein-protein interactions.

Fergal J. Duffy, D. Shields, M. Devocelle, 2015, Methods in molecular biology.

Detection of Tuberculosis Recurrence, Diagnosis and Treatment Response by a Blood Transcriptomic Risk Signature in HIV-Infected Persons on Antiretroviral Therapy

Daniel E. Zak, Fergal J. Duffy, D. Zak, 2019, Front. Microbiol..

Contained Mycobacterium tuberculosis infection induces concomitant and heterologous protection

Fergal J. Duffy, Courtney R. Plumlee, E. Gold, 2020, PLoS pathogens.

Determinants of brain swelling in pediatric and adult cerebral malaria

Fergal J. Duffy, Joseph D. Smith, Kami Kim, 2021, JCI insight.

Linking EPCR-Binding PfEMP1 to Brain Swelling in Pediatric Cerebral Malaria.

Fergal J. Duffy, Joseph D. Smith, Ian J. C. MacCormick, 2017, Cell host & microbe.

Systems analysis of immune responses to attenuated P. falciparum malaria sporozoite vaccination reveals excessive inflammatory signatures correlating with impaired immunity

Fergal J. Duffy, K. Stuart, M. McElrath, 2021, bioRxiv.

Longitudinal immune profiling after radiation-attenuated sporozoite vaccination reveals coordinated immune processes correlated with malaria protection

Fergal J. Duffy, E. Newell, J. Aitchison, 2022, Frontiers in Immunology.

Preimmunization correlates of protection shared across malaria vaccine trials in adults

Fergal J. Duffy, J. Aitchison, M. Neal, 2021, medRxiv.

Use of a Contained Mycobacterium tuberculosis Mouse Infection Model to Predict Active Disease and Containment in Humans

Fergal J. Duffy, E. Gold, A. Aderem, 2021, The Journal of infectious diseases.

Ultra-low Dose Aerosol Infection of Mice with Mycobacterium tuberculosis More Closely Models Human Tuberculosis.

Michael Y. Gerner, Daniel E. Zak, Fergal J. Duffy, 2020, Cell host & microbe.

Predicting Binding within Disordered Protein Regions to Structurally Characterised Peptide-Binding Domains

Gianluca Pollastri, Denis C. Shields, Waqasuddin Khan, 2013, PloS one.

Computational Opportunities and Challenges in Finding Cyclic Peptide Modulators of Protein-Protein Interactions.

Nicolae-Viorel Buchete, Fergal J. Duffy, Fergal Duffy, 2019, Methods in molecular biology.

Early whole blood transcriptional responses to radiation-attenuated Plasmodium falciparum sporozoite vaccination in malaria naïve and malaria pre-exposed adult volunteers

Fergal J. Duffy, S. Hoffman, J. Aitchison, 2021, Malaria journal.

A Serum Circulating miRNA Signature for Short-Term Risk of Progression to Active Tuberculosis Among Household Contacts

Fergal J. Duffy, D. Zak, S. Kaufmann, 2018, Front. Immunol..

Progression to active Tuberculosis among household contacts

Fergal J. Duffy, D. Zak, S. Kaufmann, 2018 .

Four‐Gene Pan‐African Blood Signature Predicts Progression to Tuberculosis

Daniel E. Zak, Fergal J. Duffy, D. Zak, 2018, American journal of respiratory and critical care medicine.

The Peripheral Blood Transcriptome Is Correlated With PET Measures of Lung Inflammation During Successful Tuberculosis Treatment

Daniel E. Zak, Fergal J. Duffy, D. Zak, 2021, Frontiers in Immunology.

Latent Mycobacterium tuberculosis infection provides protection for the host by changing the activation state of the innate immune system

Fergal J. Duffy, Courtney R. Plumlee, E. Gold, 2019, bioRxiv.

Distinct immune responses associated with vaccination status and protection outcomes after malaria challenge

Fergal J. Duffy, J. Aitchison, J. Carnes, 2022, bioRxiv.

Plasma N-glycans in colorectal cancer risk

Fergal J. Duffy, F. Agakov, M. Perola, 2018, Scientific Reports.

Meta-analysis of Plasmodium falciparum var Signatures Contributing to Severe Malaria in African Children and Indian Adults

Fergal J. Duffy, Joseph D. Smith, P. Rathod, 2019, mBio.

Neutrophil degranulation, NETosis and platelet degranulation pathway genes are co-induced in whole blood up to six months before tuberculosis diagnosis

Daniel E. Zak, Fergal J. Duffy, D. Zak, 2022, bioRxiv.

Angiotensin II receptor I auto-antibodies following SARS-CoV-2 infection

Fergal J. Duffy, Samantha J. Hardy, Ingrid A. Beck, 2021, medRxiv.

Multinomial modelling of TB/HIV co-infection yields a robust predictive signature and generates hypotheses about the HIV+TB+ disease state

Daniel E. Zak, Fergal J. Duffy, D. Zak, 2018, bioRxiv.

Mycobacterium tuberculosis infection associated immune perturbations correlate with antiretroviral immunity

Fergal J. Duffy, K. Metzner, H. Günthard, 2023, bioRxiv.

Title: Four-gene pan-African blood signature predicts progression to tuberculosis

Fergal J. Duffy, T. Ottenhoff, M. Hatherill, 2019 .

Mycobacterium tuberculosis infection associated immune perturbations correlate with antiretroviral immunity

Fergal J. Duffy, K. Metzner, H. Günthard, 2023, bioRxiv.