Abhinav Kaushik PhD.
Our US based scientific advisor, Dr. Abhinav Kaushik, is currently a Research Scientist at Harvard University with the T.H. Chan School of Public Health. He has done extensive research into T cell immunity and provides valuable insight to the team.
Dr. Abhinav Kaushik previously held a prominent position at Stanford University, where his work revolves around the intricate analysis of high-dimensional datasets using cutting-edge methodologies such as single-cell Mass cytometry (CyTOF), Multiplexed imaging, gene expression, SNP calling, and DNA methylation data analysis. Proficient in various statistical modeling approaches, including linear and non-linear techniques, as well as Bayesian inference, Dr. Kaushik is recognized as a seasoned data scientist with a flair for delving into complex scientific data.
With a robust background in machine learning and AI-based methods, including deep learning, Dr. Kaushik is adept at unraveling patterns and insights from vast datasets. His research interests span a wide spectrum, from developing novel algorithms for data analysis to their practical application across diverse scientific domains.
Beyond his expertise in genomics, encompassing areas such as whole-genome assembly and variant calling, Dr. Kaushik’s expertise extends to structural biology, where he has made significant contributions through in silico analysis methods like MD simulations. His interdisciplinary approach and extensive experience make him a sought-after collaborator in tackling multifaceted challenges in scientific research.
Research articles
Dr. Kaushik’s research revolves around research into T cell immunity.
Air Pollution and Pregnancy: Insights into Immune Response, Histone Modifications, and Cytokine Signatures
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Combining avidin with CD63 improves basophil activation test accuracy in classifying peanut allergy
Background Conventional basophil activation tests (BATs) measure basophil activation by the increased expression of CD63. Previously, fluorophore‐labeled avidin, a positively‐charged molecule, was found to bind to activated basophils, which tend to expose negatively charged granule constituents during degranulation. This study further compares avid…
Untargeted metabolomic profiling in children identifies novel pathways in asthma and atopy
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Distinct and mutually exclusive Ca 2+ flux‐ and adenylyl cyclase‐inducing gene expression profiles of G‐protein‐coupled receptors on human antigen‐specific B cells
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Proinflammatory polarization of monocytes by particulate air pollutants is mediated by induction of trained immunity in pediatric asthma
Background: The impact of exposure to air pollutants, such as fine particulate matter (PM), on the immune system and its consequences on pediatric asthma, are not well understood. We investigated whether ambient levels of fine PM with aerodynamic diameter ≤2.5 microns (PM2.5 ) are associated with alterations in circulating monocytes in children wi…
Cross-reactive MHC Class I T Cell Epitopes May Dictate Heterologous Immune Responses Between Respiratory Viruses and Food Allergens
Respiratory virus infections play a major role in asthma inception, persistence, and exacerbations. There is also a close correlation between asthma and food allergy, and we hypothesize that food-allergen-induced T cell-mediated heterologous immunity likely plays a role in inducing asthma symptoms in sensitized individuals. In this study, we used t…
Single-cell, Multi-omic Analysis of Peanut-reactive CD4+ T Cells Identifies Gene Signatures Favorable for Sustained Unresponsiveness Following Peanut Oral Immunotherapy
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The Likelihood of Sustained Unresponsiveness Following Peanut Oral Immunotherapy is Linked to The Frequency of Granzyme B+ Memory CD8+ T Cells
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Multiplexed Tissue Imaging for Immune Cells Profiling During Peanut Allergy Immunotherapy
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Proinflammatory polarization of monocytes by particulate air pollutants is mediated by induction of trained immunity in pediatric asthma
The impact of exposure to air pollutants, such as fine particulate matter (PM), on the immune system and its consequences on pediatric asthma are not well understood. We investigated whether the ambient levels of fine PM with aerodynamic diameter ≤ 2.5 microns (PM ) are associated with alterations in circulating monocytes in children with or withou…
CD8 T cell differentiation status correlates with the feasibility of sustained unresponsiveness following oral immunotherapy
While food allergy oral immunotherapy (OIT) can provide safe and effective desensitization (DS), the immune mechanisms underlying development of sustained unresponsiveness (SU) following a period of avoidance are largely unknown. Here, we compare high dimensional phenotypes of innate and adaptive immune cell subsets of participants in a previously…
Pangenome Analysis of the Soilborne Fungal Phytopathogen Rhizoctonia solani and Development of a Comprehensive Web Resource: RsolaniDB
Rhizoctonia solani is a collective group of genetically and pathologically diverse basidiomycetous fungi that damage economically important crops. Its isolates are classified into 13 Anastomosis Groups (AGs) and subgroups having distinctive morphology and host ranges. The genetic factors driving the unique features of R. solani pathology are not we…
Gastrointestinal γδ T cells reveal differentially expressed transcripts and enriched pathways during peanut oral immunotherapy
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A010 MASS CYTOMETRY ANALYSIS REVEALS DAMPENING OF TH2 PHENOTYPE AMONG PEANUT-REACTIVE CD4+ T CELLS FOLLOWING PEANUT-OIT
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The genome of the zoonotic malaria parasite Plasmodium simium reveals adaptations to host switching
Background Plasmodium simium, a malaria parasite of non-human primates (NHP), was recently shown to cause zoonotic infections in humans in Brazil. We sequenced the P. simium genome to investigate its evolutionary history and to identify any genetic adaptions that may underlie the ability of this parasite to switch between host species. Results Phy…
Global survey-based assessment of lifestyle changes during the COVID-19 pandemic
Along with the major impact on public health, the COVID-19 outbreak has caused unprecedented concerns ranging from sudden loss of employment to mental stress and anxiety. We implemented a survey-based data collection platform to characterize how the COVID-19 pandemic has affected the socio-economic, physical and mental health conditions of individu…
CyAnno : A semi-automated approach for cell type annotation of mass cytometry datasets
Motivation For immune system monitoring in large-scale studies at the single-cell resolution using CyTOF, (semi-)automated computational methods are applied for annotating live cells of mixed cell types. Here, we show that the live cell pool can be highly enriched with undefined heterogeneous cells, i.e., ‘ungated’ cells, and that current semi-auto…
Homologies between SARS-CoV-2 and allergen proteins may direct T cell-mediated heterologous immune responses
The outbreak of the new severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a public health emergency. Asthma does not represent a risk factor for COVID-19 in several published cohorts. We hypothesized that the SARS-CoV-2 proteome contains T cell epitopes, which are potentially cross-reactive to allergen epitopes. We aimed at identifyin…
Global Survey-based Assessment of Lifestyle Changes During the COVID-19 Pandemic
Along with the major impact on public health, the COVID-19 outbreak has caused unprecedented concerns ranging from sudden loss of employment to mental stress and anxiety. We implemented a survey-based data collection platform to characterize how the COVID-19 pandemic has affected the socio-economic, physical and mental health conditions of individu…
The pangenome analysis of the soil-borne fungal phytopathogen Rhizoctonia solani and development of a comprehensive web resource: RsolaniDB
Rhizoctonia solani is a collective group of genetically and pathologically diverse basidiomycetous fungus that damages economically important crops. Its isolates are classified into 13 Anastomosis Groups (AGs) and subgroups having distinctive morphology and host range. The genetic factors driving the unique features of R. solani pathology are not w…
Novel tumour suppressor roles for GZMA and RASGRP1 in Theileria annulata-transformed macrophages and human B-lymphoma cells
Theileria annulata is a tick‐transmitted apicomplexan parasite that infects and transforms bovine leukocytes into disseminating tumours that cause a disease called tropical theileriosis. Using comparative transcriptomics we identified genes transcriptionally perturbed during Theileria‐induced leukocyte transformation. Dataset comparisons highlighte…
Malaria parasites regulate intra-erythrocytic development duration via serpentine receptor 10 to coordinate with host rhythms
Malaria parasites complete their intra-erythrocytic developmental cycle (IDC) in multiples of 24 h suggesting a circadian basis, but the mechanism controlling this periodicity is unknown. Combining in vivo and in vitro approaches utilizing rodent and human malaria parasites, we reveal that: (i) 57% of Plasmodium chabaudi genes exhibit daily rhythms…
Neuroserpin (NS) is predominantly expressed in brain and inhibits tissue-type plasminogen activator (tPA) with implications in brain development and memory. Nature of conformational change in pathological variants in strand 6B and helix B of NS that cause a relatively mild to severe epilepsy (and/or dementia) remains largely elusive. MD simulation…
Novel meta-analysis pipeline of heterogeneous high-throughput gene expression datasets reveals dysregulated interactions and pathways in asthma
Introduction: Asthma is a complex and chronic inflammatory disorder with varying degrees of airway inflammation. It affects ~235 million people worldwide, and about 8% of the United States population. Unlike single-gene disorders, asthma phenotypes are guided by a highly variable combination of genotypes, making it a complex disease to study comput…
The genome of the zoonotic malaria parasite Plasmodium simium reveals adaptions to host-switching
Background Plasmodium simium , a malaria parasite of non-human primates (NHP) was recently shown to cause zoonotic infections in humans in Brazil. We sequenced the P. simium genome to investigate its evolutionary history and to identify any genetic adaptions that may underlie the ability of this parasite to switch between host species. Results Phy…
Disruption of the coordination between host circadian rhythms and malaria parasite development alters the duration of the intraerythrocytic cycle
Malaria parasites complete their intra-erythrocytic developmental cycle (IDC) in multiples of 24 hours (depending on the species), suggesting a circadian basis to the asexual cell cycle, but the mechanism controlling this periodicity is unknown. Combining in vivo and in vitro approaches using rodent and human malaria parasites, we reveal that: (i)…
A Novel Workflow for Semi-supervised Annotation of Cell-type Clusters in Mass Cytometry Data
Mass Cytometry by time-of-flight (CyTOF) is a widely used technology to study the variation in immune cell populations by simultaneously measuring the expression of 40-50 protein markers in millions of single cells. Traditionally, for the identification of cell types, a clustering method is employed which uses cell surface marker expression profile…
Computational prediction and experimental validation of the activator function of C2-β-D-glucopyranosyl-1,3,6,7-tetrahydroxyxanthone on pancreatic and hepatic hexokinase
This study identifies and validates hexokinase type 4 (HK4), an isozyme of hexokinase in the liver and pancreas, as an important target of C2-β-D-glucopyranosyl-1,3,6,7-tetrahydroxyxanthone (βdGT), a xanthone glucoside suggested to have antidiabetic property. In the study, we applied the computational pipeline of molecular docking followed by the m…
Role of CYP1B1, p.E229K and p.R368H mutations among 120 families with sporadic juvenile onset open-angle glaucoma
Background To determine the frequency of CYP1B1 p.E229K and p.R368H, gene mutations in a cohort of sporadic juvenile onset open-angle glaucoma (JOAG) patients and to evaluate their genotype/phenotype correlation. Methods Unrelated JOAG patients whose first-degree relatives had been examined and found to be unaffected were included in the study. The…
Exploring Heme and Hemoglobin Binding Regions of Plasmodium Heme Detoxification Protein for New Antimalarial Discovery
Hemoglobin degradation/hemozoin formation, essential steps in Plasmodium life cycle, are targets of existing antimalarials. The pathway still offers vast possibilities to be explored for new antimalarial discoveries. Here, we characterize Heme Detoxification Protein; PfHDP, a major protein involved in hemozoin formation, as a novel drug target. Usi…
An RNAi based high-throughput screening assay to identify small molecule inhibitors of Hepatitis B Virus replication
Persistent or chronic infection with the hepatitis B virus represents one of the most common viral diseases in humans. The hepatitis B virus deploys the Hepatitis B Virus X Protein (HBx) as a suppressor of host defenses consisting of RNAi-based silencing of viral genes. Because of its critical role in countering host defenses, HBx represents an att…
A hydrophobic patch surrounding Trp154 in human neuroserpin controls the helix F dynamics with implications in inhibition and aggregation
Neuroserpin (NS) mediated inhibition of tissue-type plasminogen activator (tPA) is important for brain development, synapse formation and memory. Aberrations in helix F and β-sheet A movement during inhibition can directly lead to epilepsy or dementia. Conserved W154 residue in a hydrophobic patch between helix F and β-sheet A is ideally placed to…
Altered Pathway Analyzer: A gene expression dataset analysis tool for identification and prioritization of differentially regulated and network rewired pathways
Gene connection rewiring is an essential feature of gene network dynamics. Apart from its normal functional role, it may also lead to dysregulated functional states by disturbing pathway homeostasis. Very few computational tools measure rewiring within gene co-expression and its corresponding regulatory networks in order to identify and prioritize…
Proteomic Identification and Analysis of Arginine-Methylated Proteins of Plasmodium falciparum at Asexual Blood Stages
Plasmodium falciparum undergoes a tightly regulated developmental process in human erythrocytes, and recent studies suggest an important regulatory role of post-translational modifications (PTMs). As compared to Plasmodium phosphoproteome, little is known about other PTMs in the parasite. In the present study, we performed a global analysis of asex…
Widespread occurrence of lysine methylation in Plasmodium falciparum proteins at asexual blood stages
Gene Network Rewiring to Study Melanoma Stage Progression and Elements Essential for Driving Melanoma
Metastatic melanoma patients have a poor prognosis, mainly attributable to the underlying heterogeneity in melanoma driver genes and altered gene expression profiles. These characteristics of melanoma also make the development of drugs and identification of novel drug targets for metastatic melanoma a daunting task. Systems biology offers an altern…
miRMOD: A tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data
In the past decade, the microRNAs (miRNAs) have emerged to be important regulators of gene expression across various species. Several studies have confirmed different types of post-transcriptional modifications at terminal ends of miRNAs. The reports indicate that miRNA modifications are conserved and functionally significant as it may affect miRNA…
In silico characterization and molecular dynamics simulation of Pfcyc-1, a cyclin homolog of Plasmodium falciparum
Malaria is still one of the deadly diseases resulting in deaths of millions of people worldwide and situation has become worse due to alarming rise in anti-malarial drug resistance. Genome sequence availability of Plasmodium falciparum, the main causal organism of severe malaria in humans, has enabled identification of various parasite cell cycle r…
