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List of works by Purvesh Khatri

119. Prospective Validation of a 3-Gene Signature for Tuberculosis Diagnosis, Predicting Progression and Evaluating Treatment Response

article

2016. TaqMan Multiplex PCR of a Seven-Gene Host Biomarker to Discriminate Bacterial from Viral Infections

article

2565. A Novel Prognostic Gene Set for the Prediction of Severe Dengue

article

A 20-Gene Set Predictive of Progression to Severe Dengue

article

A 6-mRNA host response whole-blood classifier trained on pre-pandemic data accurately predicts severity in COVID-19 and other acute viral infections

scientific article

A B-Cell Gene Signature Correlates With the Extent of Gluten-Induced Intestinal Injury in Celiac Disease

scientific article

A Human Genome-wide RNAi Screen Reveals Diverse Modulators that Mediate IRE1α-XBP1 Activation.

scientific article published on 9 February 2018

A System Biology Approach for the Steady-State Analysis of Gene Signaling Networks

article

A clinically meaningful metric of immune age derived from high-dimensional longitudinal monitoring

scientific article published on 06 March 2019

A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation

scientific article published on 14 October 2013

A community approach to mortality prediction in sepsis via gene expression analysis.

scientific article published on 15 February 2018

A comprehensive time-course-based multicohort analysis of sepsis and sterile inflammation reveals a robust diagnostic gene set

scientific article (publication date: 13 May 2015)

A drug repositioning approach identifies tricyclic antidepressants as inhibitors of small cell lung cancer and other neuroendocrine tumors.

scientific article published on 26 September 2013

A generalizable 29-mRNA neural-network classifier for acute bacterial and viral infections

scientific article published on 04 March 2020

A meta-analysis of lung cancer gene expression identifies PTK7 as a survival gene in lung adenocarcinoma

scientific article

A microarray analysis of the effects of moderate hypothermia and rewarming on gene expression by human hepatocytes (HepG2).

scientific article

A molecular atlas of innate immunity to adjuvanted and live attenuated vaccines, in mice

scientific article published on 27 January 2022

A multi-cohort study of the immune factors associated with M. tuberculosis infection outcomes

scientific article published in Nature

A novel signaling pathway impact analysis.

scientific article

A robust gene expression signature for NASH in liver expression data

scientific article published on 16 February 2022

A semantic analysis of the annotations of the human genome

scientific article published on 14 June 2005

A systems biology approach for pathway level analysis

scientific article

An integrative approach unveils FOSL1 as an oncogene vulnerability in KRAS-driven lung and pancreatic cancer.

scientific article published on 21 February 2017

Antigen Identification for Orphan T Cell Receptors Expressed on Tumor-Infiltrating Lymphocytes.

scientific article published on 20 December 2017

Applications of Translational Bioinformatics in Transplantation ⬇️

scientific article (publication date: August 2011)

Assessing the functional bias of commercial microarrays using the onto-compare database.

scientific article published on March 2003

Assessment of Validity of a Blood-Based 3-Gene Signature Score for Progression and Diagnosis of Tuberculosis, Disease Severity, and Treatment Response

scientific article published on 05 October 2018

Author Correction: A multi-cohort study of the immune factors associated with M. tuberculosis infection outcomes

scientific article published in Nature

Babel's tower revisited: a universal resource for cross-referencing across annotation databases

scientific article published on 26 October 2006

Benchmarking Sepsis Gene Expression Diagnostics Using Public Data.

scientific article

Biomarkers in solid organ transplantation: establishing personalized transplantation medicine

scientific article published on 8 June 2011

Blood transcriptional signatures for tuberculosis diagnosis: a glass half-empty perspective - Authors' reply.

scientific article published in June 2016

CD22 blockade restores homeostatic microglial phagocytosis in ageing brains

scientific article published on 03 April 2019

Cell type-specific gene expression differences in complex tissues

scientific article published on 07 March 2010

Cell-centred meta-analysis reveals baseline predictors of anti-TNFα non-response in biopsy and blood of patients with IBD.

scientific article published on 4 April 2018

Cellular senescence impairs the reversibility of pulmonary arterial hypertension

scientific article published on 01 July 2020

Chemical Space Mimicry for Drug Discovery

scientific article

Combined inhibition of BET family proteins and histone deacetylases as a potential epigenetics-based therapy for pancreatic ductal adenocarcinoma

scientific article published on 21 September 2015

Compact RNA sensors for increasingly complex functions of multiple inputs

scientific article published on 16 January 2024

Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants

scientific article

Complement pathway amplifies caspase-11-dependent cell death and endotoxin-induced sepsis severity.

scientific article published on 03 October 2016

Comprehensive Analysis of the Unfolded Protein Response in Breast Cancer Subtypes

scientific article published on 26 July 2017

Comprehensive Validation of the FAIM3:PLAC8 Ratio in Time-matched Public Gene Expression Data

scientific article published in November 2015

Computational and Systems Immunology: A Student's Perspective

scientific article published on 06 July 2019

Computational drug repositioning of atorvastatin for ulcerative colitis

scientific article

Coordination of stress signals by the lysine methyltransferase SMYD2 promotes pancreatic cancer

scientific article published on 17 March 2016

Cross-species functional analysis of cancer-associated fibroblasts identifies a critical role for CLCF1 and IL-6 in non-small cell lung cancer in vivo.

scientific article published on 07 September 2012

Data Heterogeneity: The Enzyme to Catalyze Translational Bioinformatics?

scientific article published on 12 August 2020

Diagnostic accuracy study of a novel blood-based assay for identification of TB in people living with HIV ⬇️

scientific article published on 09 December 2020

Discovery of Distinct Immune Phenotypes Using Machine Learning in Pulmonary Arterial Hypertension

scientific article published on 01 March 2019

Disease characteristics and serological responses in patients with differing severity of COVID-19 infection: A longitudinal cohort study in Dhaka, Bangladesh

scientific article published on 04 January 2022

Diversity in immunogenomics: the value and the challenge

scientific article

EMPOWERING MULTI-COHORT GENE EXPRESSION ANALYSIS TO INCREASE REPRODUCIBILITY.

scientific article published on January 2016

Early life immunity in the era of systems biology: understanding development and disease

article

Emergent high fatality lung disease in systemic juvenile arthritis

scientific article published on 27 September 2019

FHIT, a Novel Modifier Gene in Pulmonary Arterial Hypertension

scientific article published on 01 January 2019

Future research directions in pneumonia: NHLBI working group report

journal article published in 2018

Gene Expression Analysis to Assess the Relevance of Rodent Models to Human Lung Injury

scientific article

Gene annotation bias impedes biomedical research.

scientific article

Generalizable Biomarkers in Critical Care: Toward Precision Medicine

scientific article published on June 2017

Genome-wide expression for diagnosis of pulmonary tuberculosis: a multicohort analysis

scientific article

Global functional profiling of gene expression.

scientific article published on February 2003

High-throughput quantitative histology in systemic sclerosis skin disease using computer vision

scientific article published on 14 March 2020

Hospital-acquired Pneumonia: A Host of Factors.

scientific article

Host-response-based gene signatures for tuberculosis diagnosis: A systematic comparison of 16 signatures

article

Identification of genomic signatures for the design of assays for the detection and monitoring of anthrax threats.

scientific article

Identifying uncertainty regions in Support Vector Machines using geometric margin and convex hulls

Increased monocyte count as a cellular biomarker for poor outcomes in fibrotic diseases: a retrospective, multicentre cohort study

scientific article published on 29 March 2019

Increasing reproducibility, robustness, and generalizability of biomarker selection from meta-analysis using Bayesian methodology

scientific article published on 27 June 2022

Inflammatory macrophage-associated 3-gene signature predicts subclinical allograft injury and graft survival.

scientific article published on 25 January 2018

Integrated multi-cohort transcriptional meta-analysis of neurodegenerative diseases.

scientific article

Integrated, Multi-cohort Analysis Identifies Conserved Transcriptional Signatures across Multiple Respiratory Viruses

scientific article

Integrated, multicohort analysis of systemic sclerosis identifies robust transcriptional signature of disease severity

scientific article published on 22 December 2016

Integrated, multicohort analysis reveals unified signature of systemic lupus erythematosus

scientific article published on 27 February 2020

Integration of Next–Generation Sequencing, Viral Sequencing, and Host-Response Profiling for the Diagnosis of Acute Infections.

scientific article published on 4 October 2017

Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations

scientific article published on 23 March 2018

KLRD1-expressing natural killer cells predict influenza susceptibility.

scientific article published on 14 June 2018

Leveraging heterogeneity across multiple datasets increases cell-mixture deconvolution accuracy and reduces biological and technical biases

scientific article published in Nature Communications

META-ANALYSIS OF CONTINUOUS PHENOTYPES IDENTIFIES A GENE SIGNATURE THAT CORRELATES WITH COPD DISEASE STATUS.

scientific article published on January 2016

Methods to increase reproducibility in differential gene expression via meta-analysis

scientific article published on 14 September 2016

Multi-cohort analysis of host immune response identifies conserved protective and detrimental modules associated with severity across viruses

scientific article

Multicohort Analysis of Whole-Blood Gene Expression Data Does Not Form a Robust Diagnostic for Acute Respiratory Distress Syndrome

scientific article published in February 2018

NetPath: a public resource of curated signal transduction pathways

scientific article

New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate

scientific article

Non-HLA antibodies to immunogenic epitopes predict the evolution of chronic renal allograft injury

scientific article published on 02 February 2012

Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate

scientific article published on July 2003

Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments

scientific article published on July 2004

Onto-Tools: new additions and improvements in 2006.

scientific article published on 21 June 2007

Ontological analysis of gene expression data: current tools, limitations, and open problems

scientific article

Pediatric Sepsis Endotypes Among Adults With Sepsis

scientific article published on 6 October 2017

Pilot study of a novel serum mRNA gene panel for diagnosis of acute septic arthritis

scientific article published on 18 December 2019

Predicting novel human gene ontology annotations using semantic analysis

scientific article published on January 2010

Pregnancy-Induced Alterations in NK Cell Phenotype and Function

scientific article published on 23 October 2019

Profiling Gene Expression Using Onto-Express

article

Profiling of autoantibodies in IgA nephropathy, an integrative antibiomics approach

scientific article published on December 2011

Progressive histological damage in renal allografts is associated with expression of innate and adaptive immunity genes

scientific article published on 31 August 2011

Recent additions and improvements to the Onto-Tools

scientific article

Reliability and reproducibility issues in DNA microarray measurements

scientific article

Repression of CTSG, ELANE and PRTN3-mediated histone H3 proteolytic cleavage promotes monocyte-to-macrophage differentiation

scientific article published on 20 May 2021

Response to: 'Effectiveness and safety of ruxolitinib for the treatment of refractory systemic idiopathic juvenile arthritis like associated with interstitial lung disease: case report' by Bader-Meunier et al

scientific article published on 13 February 2020

Response to: 'Successful treatment of plasma exchange for refractory systemic juvenile idiopathic arthritis complicated with macrophage activation syndrome and severe lung disease' by Sato et al

scientific article published on 21 April 2020

Robust classification of bacterial and viral infections via integrated host gene expression diagnostics

scientific article published on July 2016

SIMON: Open-Source Knowledge Discovery Platform

scientific article published in 2021

SMYD3 links lysine methylation of MAP3K2 to Ras-driven cancer

scientific article

Septic Cardiomyopathy: Getting to the Heart of the Matter.

scientific article published on March 2017

Sex Differences in the Blood Transcriptome Identify Robust Changes in Immune Cell Proportions with Aging and Influenza Infection

scientific article published on 01 November 2019

Single cell immune profiling in transplantation research

scientific article published on 20 March 2019

Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging

scientific article published on 21 April 2018

Single-cell epigenetics – Chromatin modification atlas unveiled by mass cytometry

scientific article published on 28 June 2018

Single-cell technologies - studying rheumatic diseases one cell at a time

scientific article published on 01 June 2019

Spermatozoal RNA profiles of normal fertile men.

scientific article published on September 2002

Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans

scientific article

T cell-inducing vaccine durably prevents mucosal SHIV infection even with lower neutralizing antibody titers

scientific article published on 11 May 2020

Ten years of pathway analysis: current approaches and outstanding challenges

scientific article (publication date: 2012)

The authors reply

The authors reply

scientific article published in March 2017

The center for expanded data annotation and retrieval

scientific article

The immunoregulatory landscape of human tuberculosis granulomas

scientific article published on 20 January 2022

The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination

scientific article published on 25 June 2021

Transcriptomic similarities and differences in host response between SARS-CoV-2 and other viral infections

scholarly article by Simone A Thair published in January 2021

Unique transcriptomic response to sepsis is observed among patients of different age groups.

scientific article published on 8 September 2017

Unsupervised Analysis of Transcriptomics in Bacterial Sepsis Across Multiple Datasets Reveals Three Robust Clusters.

scientific article published on 13 March 2018

Using gene arrays in diagnosis of rejection

scientific article published on February 2009

Validation of the Sepsis MetaScore for Diagnosis of Neonatal Sepsis

scientific article published on 13 April 2017

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