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List of works by John Kenneth Baillie

A Hybrid Architecture (CO-CONNECT) to Facilitate Rapid Discovery and Access to Data Across the United Kingdom in Response to the COVID-19 Pandemic: Development Study

scientific article published in 2022

A gene expression atlas of the domestic pig

scientific article

A promoter-level mammalian expression atlas

scientific article

Activated protein C: controversy and hope in the treatment of sepsis.

scientific article published on November 2007

Amplicon based MinION sequencing of SARS-CoV-2 and metagenomic characterisation of nasopharyngeal swabs from patients with COVID-19

scientific article (preprint)

An atlas of active enhancers across human cell types and tissues

scientific article

An expression atlas of human primary cells: inference of gene function from coexpression networks

scientific article

An updated systematic review of the role of host genetics in susceptibility to influenza

scientific article

Analysis of SARS-CoV-2 in Nasopharyngeal Samples from Patients with COVID-19 Illustrates Population Variation and Diverse Phenotypes, Placing the Growth Properties of Variants of Concern in Context with Other Lineages

scientific article published in 2022

Analysis of SARS-CoV-2 known and novel subgenomic mRNAs in cell culture, animal model, and clinical samples using LeTRS, a bioinformatic tool to identify unique sequence identifiers

scientific article published on 01 May 2022

Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease.

scientific article

Antiviral combinations for severe influenza.

scientific article

Association of Country Income Level With the Characteristics and Outcomes of Critically Ill Patients Hospitalized With Acute Kidney Injury and COVID-19

scientific article published in 2023

Broad and strong memory CD4 + and CD8 + T cells induced by SARS-CoV-2 in UK convalescent COVID-19 patients

scientific article published on 08 June 2020

COVID-19 symptoms at hospital admission vary with age and sex: results from the ISARIC prospective multinational observational study

scientific article

Change in plasma vascular endothelial growth factor during onset and recovery from acute mountain sickness

scientific article published on 04 August 2006

Clinical characteristics of children and young people admitted to hospital with covid-19 in United Kingdom: prospective multicentre observational cohort study

scientific article published on 27 August 2020

Clinical evidence does not support corticosteroid treatment for 2019-nCoV lung injury

scientific article published on 07 February 2020

Co-Infections, Secondary Infections, and Antimicrobial Usage in Hospitalised Patients with COVID-19 from the ISARIC WHO CCP-UK Study: A Prospective, Multicentre Cohort Study

scientific article published in 2021

Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity

scientific article published on 10 December 2021

Complete genome sequence of methicillin-sensitive Staphylococcus aureus containing a heterogeneic staphylococcal cassette chromosome element

scientific article published on 23 March 2013

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

scientific article

Deciding authorship order.

scientific article published on 16 December 2013

Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma

scientific article published on March 2013

Endogenous urate production augments plasma antioxidant capacity in healthy lowland subjects exposed to high altitude.

scientific article

Endothelial nitric oxide synthase polymorphisms do not influence pulmonary artery systolic pressure at altitude

article

Erratum to: Thromboelastometry and platelet function during acclimatisation to high altitude

scientific article published on 4 April 2018

Ethnicity and Outcomes from COVID-19: The ISARIC CCP-UK Prospective Observational Cohort Study of Hospitalised Patients

scientific article published in 2020

Expression of mesenchyme-specific gene signatures by follicular dendritic cells: insights from the meta-analysis of microarray data from multiple mouse cell populations

scientific article

FANTOM5 CAGE profiles of human and mouse samples

scientific article published on 29 August 2017

Features of 16,749 hospitalised UK patients with COVID-19 using the ISARIC WHO Clinical Characterisation Protocol

scientific article published on 28 April 2020

Features of 20 133 UK patients in hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: prospective observational cohort study

scientific article published on 22 May 2020

Functional annotation of human long noncoding RNAs via molecular phenotyping

scientific article published on 27 July 2020

Functional clustering and lineage markers: insights into cellular differentiation and gene function from large-scale microarray studies of purified primary cell populations

scientific article published on 06 March 2010

Gateways to the FANTOM5 promoter level mammalian expression atlas

scientific article

Genetic mechanisms of critical illness in Covid-19

scientific article published on 11 December 2020

Genome-wide CRISPR screen identifies host dependency factors for influenza A virus infection

scientific article published on 09 January 2020

Heteroresistance at the single-cell level: adapting to antibiotic stress through a population-based strategy and growth-controlled interphenotypic coordination

scientific article published on 11 February 2014

High altitude adaptation in Daghestani populations from the Caucasus

scientific article published on 9 September 2011

High altitude pulmonary oedema.

scientific article published on March 2011

Hospital-acquired SARS-CoV-2 infection in the UK's first COVID-19 pandemic wave

scientific article published in 2021

Host susceptibility to severe influenza A virus infection

scientific article published on 05 September 2019

Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

scientific article

Hypoxia Modulates Platelet Purinergic Signalling Pathways

scientific article published on 13 December 2019

Hypoxia shapes the immune landscape in lung injury and promotes the persistence of inflammation

scientific article published on 27 May 2022

IFITM3 restricts the morbidity and mortality associated with influenza

scientific article

Identification of novel genes selectively expressed in the follicle-associated epithelium from the meta-analysis of transcriptomics data from multiple mouse cell and tissue populations.

scientific article

Incidence and predictors of acute mountain sickness among trekkers on Mount Kilimanjaro.

scientific article published on January 2010

Inflammatory profiles across the spectrum of disease reveal a distinct role for GM-CSF in severe COVID-19

scholarly article by Ryan S Thwaites published in 2021

Influenza--time to target the host?

scientific article published on July 2013

Is somatic retrotransposition a parasitic or symbiotic phenomenon?

scientific article published on November 2011

Letter to the Editor: Response to Luke Fletcher and Philip Peyton regarding "Predictive validity of a novel non-invasive estimation of effective shunt fraction in critically ill patients"

scientific article published on 01 October 2020

Linking protein to phenotype with Mendelian Randomization detects 38 proteins with causal roles in human diseases and traits

scientific article published on 06 July 2020

Long Covid in adults discharged from UK hospitals after Covid-19: A prospective, multicentre cohort study using the ISARIC WHO Clinical Characterisation Protocol

scientific article

Long Covid in adults discharged from UK hospitals after Covid-19: A prospective, multicentre cohort study using the ISARIC WHO Clinical Characterisation Protocol

scientific article published in 2021

Mapping of SARS-CoV-2 IgM and IgG in gingival crevicular fluid: Antibody dynamics and linkage to severity of COVID-19 in hospital inpatients

scientific article published in 2022

Measurement errors caused by incompatibility of apparatus

scientific article published on 01 November 2009

Meta-analysis of lineage-specific gene expression signatures in mouse leukocyte populations

article

Microglial brain region-dependent diversity and selective regional sensitivities to aging.

scientific article published on 18 January 2016

Middle East Respiratory Syndrome.

scientific article

Modelling mutational and selection pressures on dinucleotides in eukaryotic phyla--selection against CpG and UpA in cytoplasmically expressed RNA and in RNA viruses

scientific article

Morphine, Gabapentin, or Their Combination for Neuropathic Pain

scientific article published on 01 June 2005

Multiomic definition of generalizable endotypes in human acute pancreatitis

NT-proBNP does not rise on acute ascent to high altitude

article

Network analysis reveals distinct clinical syndromes underlying acute mountain sickness

scientific article published on 22 January 2014

Neutralising antibodies to SARS coronavirus 2 in Scottish blood donors - a pilot study of the value of serology to determine population exposure

scientific article published on 17 April 2020

Neutrophils Fuel Effective Immune Responses through Gluconeogenesis and Glycogenesis

scientific article published on 01 December 2020

Open source clinical science for emerging infections

scientific article published in January 2014

Oral antioxidant supplementation does not prevent acute mountain sickness: double blind, randomized placebo-controlled trial.

scientific article

Outcome of Hospitalization for COVID-19 in Patients with Interstitial Lung Disease: An International Multicenter Study

scientific article published on 02 October 2020

Outcomes of COVID-19 Related Hospitalisation Among People with HIV in the ISARIC WHO Clinical Characterisation Protocol UK Protocol: Prospective Observational Study

scientific article published in 2020

Outcomes of COVID-19 related hospitalisation among people with HIV in the ISARIC WHO Clinical Characterisation Protocol UK Protocol: prospective observational study

scientific article

Outcomes of COVID-19 related hospitalization among people with HIV in the ISARIC WHO Clinical Characterization Protocol (UK): a prospective observational study

scientific article published on 23 October 2020

Passage of pathogenic microorganisms through breathing system filters used in anaesthesia and intensive care

scientific article published in April 2010

Pericardial effusions in healthy lowlanders after acute ascent to high altitude

scientific article published on April 2006

Phosphodiesterase type 5 inhibitors in the treatment and prevention of high altitude pulmonary edema.

scientific article

Physical, cognitive, and mental health impacts of COVID-19 after hospitalisation (PHOSP-COVID): a UK multicentre, prospective cohort study

Predictive validity of a novel non-invasive estimation of effective shunt fraction in critically ill patients

scientific article published on 20 August 2019

Proteome-by-phenome Mendelian Randomisation detects 38 proteins with causal roles in human diseases and traits

Residual Lung Abnormalities after COVID-19 Hospitalization: Interim Analysis of the UKILD Post–COVID-19 Study

scientific article published in 2023

Retinal vessel tortuosity in response to hypobaric hypoxia

scientific article published in December 2012

Risk of adverse outcomes in patients with underlying respiratory conditions admitted to hospital with COVID-19: a national, multicentre prospective cohort study using the ISARIC WHO Clinical Characterisation Protocol UK

scientific article published in 2021

Risk stratification of patients admitted to hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: development and validation of the 4C Mortality Score

scientific article published on 09 September 2020

Robust, reproducible clinical patterns in hospitalised patients with COVID-19

scientific article published on 16 August 2020

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

scientific article published in March 2018

Sildenafil citrate for the prevention of high altitude hypoxic pulmonary hypertension: double blind, randomized, placebo-controlled trial.

scientific article

Simple, easily memorised "rules of thumb" for the rapid assessment of physiological compensation for respiratory acid-base disorders.

scientific article

Somatic retrotransposition alters the genetic landscape of the human brain

scientific article (publication date: 30 October 2011)

Stratified infection medicine: a call to arms

scientific article published on 01 June 2014

Targeting the host immune response to fight infection

scientific article

The 2018 Lake Louise Acute Mountain Sickness Score

article

The Search for Efficacious New Therapies in Sepsis Needs to Embrace Heterogeneity

article published in 2019

The citric acid cough threshold and the ventilatory response to carbon dioxide on ascent to high altitude

article

The effect of dexmedetomidine and clonidine on the inflammatory response in critical illness: a systematic review of animal and human studies

scientific article published on 11 December 2019

The effectiveness of convalescent plasma and hyperimmune immunoglobulin for the treatment of severe acute respiratory infections of viral etiology: a systematic review and exploratory meta-analysis

scientific article

The mechanism of action of gabapentin in neuropathic pain.

scientific article

The role of host genetic factors in respiratory tract infectious diseases: systematic review, meta-analyses and field synopsis

scientific article

The role of host genetics in susceptibility to influenza: a systematic review

scientific article

The utility of peripheral blood leucocyte ratios as biomarkers in infectious diseases: A systematic review and meta-analysis

scientific article published on 22 February 2019

The value of open-source clinical science in pandemic response: lessons from ISARIC

scientific article published in 2021

Thromboelastometry and Platelet Function during Acclimatization to High Altitude.

scientific article

Tissue Proteomic Analysis Identifies Mechanisms and Stages of Immunopathology in Fatal COVID-19

scientific article published on 01 February 2022

Tissue-specific Immunopathology in Fatal COVID-19

scientific article published on 20 November 2020

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

scientific article

Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions.

scientific article

Using imaging to combat a pandemic: rationale for developing the UK National COVID-19 Chest Imaging Database

scientific article published on 02 July 2020

Wide variation and systematic bias in expert clinicians' perceptions of prognosis following brain injury.

scientific article

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