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List of works by Arnab Pain

A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data

scientific article

A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains

scientific article

A comprehensive evaluation of rodent malaria parasite genomes and gene expression

scientific article

A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses

scientific article

A fast and cost-effective microsampling protocol incorporating reduced animal usage for time-series transcriptomics in rodent malaria parasites

scholarly article published 20 June 2018

A fast and cost-effective microsampling protocol incorporating reduced animal usage for time-series transcriptomics in rodent malaria parasites

scientific article published on 25 January 2019

A feast of protozoan genomes.

scientific article

A genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic

scientific article published on 22 August 2020

A landscape of genomic alterations at the root of a near-untreatable tuberculosis epidemic

scientific article published on 04 February 2020

A multiple genome analysis of Mycobacterium tuberculosis reveals specific novel genes and mutations associated with pyrazinamide resistance

scientific article published on 11 October 2017

A non-sense mutation in Cd36 gene is associated with protection from severe malaria.

scientific article published in May 2001

A promoter polymorphism in the gene encoding interleukin-12 p40 (IL12B) is associated with mortality from cerebral malaria and with reduced nitric oxide production

scientific article

A promoter-level mammalian expression atlas

scientific article

A proportion of mutations fixed in the genomes of in vitro selected isogenic drug-resistant Mycobacterium tuberculosis mutants can be detected as minority variants in the parent culture

scientific article

A reference genome and methylome for the Plasmodium knowlesi A1-H.1 line

scientific article published on 16 December 2017

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains.

scientific article

A scalable pipeline for highly effective genetic modification of a malaria parasite

scientific article

A selenocysteine tRNA and SECIS element in Plasmodium falciparum

scientific article

Accelerating early anti-tuberculosis drug discovery by creating mycobacterial indicator strains that predict mode of action

scientific article published on 16 April 2018

Adaptation of the genetically tractable malaria pathogen Plasmodium knowlesi to continuous culture in human erythrocytes

scientific article published on 24 December 2012

Advances in the genomics of ticks and tick-borne pathogens

scientific article published on 26 July 2007

Alteration of host cell phenotype by Theileria annulata and Theileria parva: mining for manipulators in the parasite genomes

scientific article

Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations

scientific article published on 18 September 2017

Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry

scientific article published in October 2002

Analysis of the role of recA in phenotypic switching of Pseudomonas tolaasii.

scientific article

Antennal transcriptome sequencing and identification of candidate chemoreceptor proteins from an invasive pest, the American palm weevil, Rhynchophorus palmarum ⬇️

scientific article published on 15 April 2021

Assembly of the genome of the disease vector Aedes aegypti onto a genetic linkage map allows mapping of genes affecting disease transmission

scientific article published on 30 January 2014

Author Correction: Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis.

scientific article published on 19 April 2018

Candidate Essential Genes in Burkholderia cenocepacia J2315 Identified by Genome-Wide TraDIS

scientific article

Characterization and gene expression analysis of the cir multi-gene family of Plasmodium chabaudi chabaudi (AS).

scientific article

Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan

article

Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites

scientific article

Clonal expansion across the seas as seen through CPLP-TB database: A joint effort in cataloguing Mycobacterium tuberculosis genetic diversity in Portuguese-speaking countries

article

Comparative Apicomplexan genomics

scientific article published in 2005

Comparative Genomic and Transcriptomic Analyses of Mycobacterium kansasii Subtypes Provide New Insights Into Their Pathogenicity and Taxonomy

scientific article published on 24 March 2020

Comparative genome analysis of three eukaryotic parasites with differing abilities to transform leukocytes reveals key mediators of Theileria-induced leukocyte transformation

scientific article

Comparative genomics of the Rab protein family in Apicomplexan parasites

scientific article published on 08 February 2008

Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy

scientific article published in 2012

Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans

scientific article published on 10 September 2009

Complete genome sequence of Mycobacterium fortuitum subsp. fortuitum type strain DSM46621

scientific article published on November 2012

Complete genome sequence of Mycobacterium phlei type strain RIVM601174.

scientific article

Complete genome sequence of Mycobacterium vaccae type strain ATCC 25954.

scientific article

Complete genome sequence of Mycobacterium xenopi type strain RIVM700367.

scientific article

Comprehensive evaluation of Toxoplasma gondii VEG and Neospora caninum LIV genomes with tachyzoite stage transcriptome and proteome defines novel transcript features

scientific article

Defining the protein interaction network of human malaria parasite Plasmodium falciparum ⬇️

scientific article published on 08 December 2011

Development of the myzozoan aquatic parasite <i>Perkinsus marinus</i> as a versatile experimental genetic model organism

Developmental transition of Plasmodium sporozoites into liver-stage forms is regulated by the RNA binding protein Pumilio 2.

scientific article

Differential var gene expression in the organs of patients dying of falciparum malaria

scientific article

Discovering, Characterizing, and Applying Acyl Homoserine Lactone-Quenching Enzymes to Mitigate Microbe-Associated Problems Under Saline Conditions

scientific article published on 17 April 2019

Divergent mitochondrial respiratory chains in phototrophic relatives of apicomplexan parasites.

scientific article

Diversity of extracellular proteins during the transition from the 'proto-apicomplexan' alveolates to the apicomplexan obligate parasites

scientific article

Draft Genome Sequences of Pseudomonas fluorescens BS2 and Pusillimonas noertemannii BS8, Soil Bacteria That Cooperate To Degrade the Poly-γ-d-Glutamic Acid Anthrax Capsule

scientific article

Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei

scientific article published on 31 July 2015

Emergence of Indigenous Artemisinin-Resistant Plasmodium falciparum in Africa

scientific article published on 22 February 2017

Emergence of multidrug-resistant Mycobacterium tuberculosis of the Beijing lineage in Portugal and Guinea-Bissau: a snapshot of moving clones by whole-genome sequencing

scientific article published on 01 December 2020

Endosymbiosis undone by stepwise elimination of the plastid in a parasitic dinoflagellate

scientific article

Enteric Infections Circulating during Hajj Seasons, 2011-2013

scientific article published on October 2017

Erratum: CORRIGENDUM: Genome variation and evolution of the malaria parasite Plasmodium falciparum

scientific article published in March 2007

Erratum: Corrigendum: Genome variation and evolution of the malaria parasite Plasmodium falciparum

scientific article published in April 2007

Erratum: Corrigendum: Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

scientific article published in Nature

Essential Role of the ESX-5 Secretion System in Outer Membrane Permeability of Pathogenic Mycobacteria

scientific article published on 4 May 2015

Eukaryotes: not beyond compare

scientific article published in 2004

Exome and Transcriptome Sequencing of Aedes aegypti Identifies a Locus That Confers Resistance to Brugia malayi and Alters the Immune Response

scientific article

Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites

scientific article

Expression analysis of the Theileria parva subtelomere-encoded variable secreted protein gene family.

scientific article

First report of Klebsiella quasipneumoniae harboring bla KPC-2 in Saudi Arabia

scientific article published on 19 December 2019

Functional characterization of the Plasmodium falciparum and P. berghei homologues of macrophage migration inhibitory factor

scientific article published on 11 December 2006

Functional pangenome analysis suggests inhibition of the protein E as a readily available therapy for COVID-2019

scientific article

Fungi behaving badly

scientific article published in 2005

GZMA and RASGRP1 are novel tumor suppressors that counter dissemination of Theileria annulata-transformed macrophages

Genes involved in sex pheromone biosynthesis of Ephestia cautella, an important food storage pest, are determined by transcriptome sequencing.

scientific article published on 18 July 2015

Genetic Determinants Associated With in Vivo Survival of Burkholderia cenocepacia in the Caenorhabditis elegans Model.

scientific article

Genetic tool development in marine protists: emerging model organisms for experimental cell biology

scientific article published on 06 April 2020

Genetics and malaria--more questions than answers.

scientific article published in February 2001

Genome Sequence of Theileria parva, a Bovine Pathogen That Transforms Lymphocytes

scientific article

Genome Sequence of a Multidrug-Resistant Strain of Stenotrophomonas maltophilia with Carbapenem Resistance, Isolated from King Abdullah Medical City, Makkah, Saudi Arabia

scientific article published on 15 October 2015

Genome Sequences of the Oxytetracycline Production Strain Streptomyces rimosus R6-500 and Two Mutants with Chromosomal Rearrangements ⬇️

scientific article published on 17 July 2014

Genome of the Host-Cell Transforming Parasite Theileria annulata Compared with T. parva

scientific article

Genome sequence of the human malaria parasite Plasmodium falciparum

scientific article

Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts.

scientific article

Genome variation and evolution of the malaria parasite Plasmodium falciparum

scientific article published on 10 December 2006

Genome-scale comparison of expanded gene families in Plasmodium ovale wallikeri and Plasmodium ovale curtisi with Plasmodium malariae and with other Plasmodium species

scientific article published on 5 July 2016

Genome-wide RIP-Chip analysis of translational repressor-bound mRNAs in the Plasmodium gametocyte

scientific article (publication date: 3 November 2014)

Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

scientific article

Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum

scientific article

Genome-wide functional analysis of Plasmodium protein phosphatases reveals key regulators of parasite development and differentiation

scientific article (publication date: 9 July 2014)

Genome-wide mutagenesis and multi-drug resistance in American trypanosomes induced by the front-line drug benznidazole

scientific article published on 31 October 2017

Genome-wide transposon mutagenesis indicates that Mycobacterium marinum customizes its virulence mechanisms for survival and replication in different hosts

scientific article published on 17 February 2015

Genomes beyond compare

scientific article published on 01 August 2004

Genomic adaptation: a fungal perspective

scientific article published in 2008

Genomic analysis of the causative agents of coccidiosis in domestic chickens

scientific article

Genomic and Phenotypic Analyses Reveal the Emergence of an Atypical Salmonella enterica Serovar Senftenberg Variant in China

scientific article published on 25 May 2016

Genomic diversity of drug-resistant Mycobacterium tuberculosis isolates in Lisbon Portugal: Towards tuberculosis genomic epidemiology

article

Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations

scientific article

Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

scientific article

Genomic-scale prioritization of drug targets: the TDR Targets database

scientific article

Global transcriptome profiling and functional analysis reveal that tissue-specific constitutive overexpression of cytochrome P450s confers tolerance to imidacloprid in palm weevils in date palm fields.

scientific article published on 31 May 2019

Highly diverged novel subunit composition of apicomplexan F-type ATP synthase identified from Toxoplasma gondii

article published in 2018

Hot and sexy moulds!

scientific article published in 2006

Identification of a novel conjugative plasmid in mycobacteria that requires both type IV and type VII secretion

scientific article

Identification of the genes involved in odorant reception and detection in the palm weevil Rhynchophorus ferrugineus, an important quarantine pest, by antennal transcriptome analysis

scientific article

Insight into the genome of Aspergillus fumigatus: analysis of a 922 kb region encompassing the nitrate assimilation gene cluster

scientific article published on April 2004

Integrated transcriptomic and proteomic analysis of pathogenic mycobacteria and their esx-1 mutants reveal secretion-dependent regulation of ESX-1 substrates and WhiB6 as a transcriptional regulator

scientific article published in PLoS ONE

Light harvesting complexes of Chromera velia, photosynthetic relative of apicomplexan parasites

scientific article published on 18 February 2013

Long- and short-term selective forces on malaria parasite genomes

scientific article

Malaria parasites regulate intra-erythrocytic development duration via serpentine receptor 10 to coordinate with host rhythms

scientific article published on 02 June 2020

Metabolic pathway redundancy within the apicomplexan-dinoflagellate radiation argues against an ancient chromalveolate plastid.

scientific article published on 8 December 2015

Microfibrous silver-coated polymeric scaffolds with tunable mechanical properties

scholarly article in RSC Advances, vol. 7 no. 55, 2017

Mitochondrial genomes in <i>Perkinsus</i> decode conserved frameshifts in all genes

scientific article published in 2022

Mitochondrial genomes in <i>Perkinsus</i> decode conserved frameshifts in all genes

Multidrug-Resistant Mycobacterium tuberculosis of the Latin American Mediterranean Lineage, Wrongly Identified as Mycobacterium pinnipedii (Spoligotype International Type 863 [SIT863]), Causing Active Tuberculosis in South Brazil

scientific article

Mutations in ppe38 block PE_PGRS secretion and increase virulence of Mycobacterium tuberculosis

scientific article published on 15 January 2018

Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance.

scientific article

New Initiatives for Management of Red Palm Weevil Threats to Historical Arabian Date Palms*

article by Muhammad Mukhtar et al published December 2011 in The Florida Entomologist

New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq

scientific article

Normocyte-binding protein required for human erythrocyte invasion by the zoonotic malaria parasite Plasmodium knowlesi

scientific article published on 14 June 2016

Novel tumour suppressor roles for GZMA and RASGRP1 in Theileria annulata-transformed macrophages and human B-lymphoma cells

scientific article published on 24 August 2020

Outcomes, infectiousness, and transmission dynamics of patients with extensively drug-resistant tuberculosis and home-discharged patients with programmatically incurable tuberculosis: a prospective cohort study

scientific article

PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis

scientific article published on 13 May 2015

Plant killers on the spot

article

Plasmodium P-Type Cyclin CYC3 Modulates Endomitotic Growth during Oocyst Development in Mosquitoes

scientific article (publication date: November 2015)

Plasmodium falciparum antigenic variation: relationships between in vivo selection, acquired antibody response, and disease severity

scientific article published on 12 August 2005

Plasmodium falciparum var gene expression is modified by host immunity

scientific article published on 11 December 2009

Plasmodium falciparum-infected erythrocytes modulate the maturation of dendritic cells.

scientific article published on July 1999

Plasmodium genomics: latest milestone

scientific article published in March 2009

Plasmodium kinesin-8X associates with mitotic spindles and is essential for oocyst development during parasite proliferation and transmission.

scientific article published in October 2019

Platelet-mediated clumping of Plasmodium falciparum-infected erythrocytes is a common adhesive phenotype and is associated with severe malaria

scientific article

PolyTB: a genomic variation map for Mycobacterium tuberculosis

scientific article

Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi

scientific article

Population genomics reveals that an anthropophilic population of Aedes aegypti mosquitoes in West Africa recently gave rise to American and Asian populations of this major disease vector

scientific article (publication date: 28 February 2017)

Progenitor strain introduction of Mycobacterium bovis at the wildlife-livestock interface can lead to clonal expansion of the disease in a single ecosystem.

scientific article published on 12 April 2017

Protein phosphatase 1 regulates atypical mitotic and meiotic division in Plasmodium sexual stages

scientific article published on 18 June 2021

Proteogenomic Investigation of Strain Variation in Clinical Mycobacterium tuberculosis Isolates

scientific article published on 18 August 2017

Proteomes and transcriptomes of the Apicomplexa--where's the message?

scientific article

Proteomic Investigation of Rhizoctonia solani AG 4 Identifies Secretome and Mycelial Proteins with Roles in Plant Cell Wall Degradation and Virulence

article

Proteomic profiling of the brain of mice with experimental cerebral malaria

scientific article published on 5 June 2017

Proteomic profiling of the plasma of Gambian children with cerebral malaria

scientific article published on 24 September 2018

Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology

scientific article published on 15 April 2020

Quantitative Seq-LGS: Genome-Wide Identification of Genetic Drivers of Multiple Phenotypes in Malaria Parasites

scholarly article published 30 September 2016

READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation ⬇️

scientific article published on November 28, 2012

Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences

scientific article published on 27 May 2015

Rapid identification of genes controlling virulence and immunity in malaria parasites.

scientific article

Re-evaluating the green versus red signal in eukaryotes with secondary plastid of red algal origin

scientific article published on 16 May 2012

Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages

scientific article

Recombinations in staphylococcal cassette chromosome mec elements compromise the molecular detection of methicillin resistance in Staphylococcus aureus

scientific article

Recruitment of EB1, a master regulator of microtubule dynamics, to the surface of the Theileria annulata schizont

scientific article (publication date: May 2013)

SARS-CoV-2 S1 and N-based serological assays reveal rapid seroconversion and induction of specific antibody response in COVID-19 patients

scientific article published on 06 October 2020

SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load

scientific article published on 01 February 2022

SVAMP: sequence variation analysis, maps and phylogeny

scientific article published on 3 April 2014

Sequence data swell for nematodes

scientific article

Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13

scientific article

Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae

scientific article

Simultaneous detection and mutation surveillance of SARS-CoV-2 and multiple respiratory viruses by rapid field-deployable sequencing

scientific article published on 31 March 2021

SnoopCGH: software for visualizing comparative genomic hybridization data

scientific article (publication date: 15 October 2009)

Specialist fungi, versatile genomes

scientific article published in 2007

Split photosystem protein, linear-mapping topology, and growth of structural complexity in the plastid genome of Chromera velia

scientific article

Strength in diversity

scientific article published in 2004

Targeted disruption of py235ebp-1: invasion of erythrocytes by Plasmodium yoelii using an alternative Py235 erythrocyte binding protein ⬇️

scientific article

The Lipopolysaccharide and β-1,3-Glucan Binding Protein Gene Is Upregulated in White Spot Virus-Infected Shrimp (Penaeus stylirostris).

scientific article published in September 2002

The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae

scientific article published on 4 June 2015

The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction

scientific article

The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode

scientific article

The genome of the simian and human malaria parasite Plasmodium knowlesi

scientific article

The genome of the social amoeba Dictyostelium discoideum

scientific article

The genomic variation landscape of globally-circulating clades of SARS-CoV-2 defines a genetic barcoding scheme

scientific article published on 23 April 2020

The lipopolysaccharide and beta-1,3-glucan binding protein gene is upregulated in white spot virus-infected shrimp (Penaeus stylirostris)

scientific article

The normal cellular prion protein is strongly expressed by myeloid dendritic cells

scientific article published on December 2001

The population structure of Vibrio cholerae from the Chandigarh Region of Northern India

scientific article (publication date: July 2014)

The rhoptry proteome of Eimeria tenella sporozoites

scientific article published on 20 December 2012

The systematic functional analysis of Plasmodium protein kinases identifies essential regulators of mosquito transmission

scientific article

Theileria highjacks JNK2 into a complex with the macroschizont GPI-anchored surface protein p104

scientific article published on 05 December 2018

Theileria parasites subvert E2F signaling to stimulate leukocyte proliferation

scientific article published on 04 March 2020

Timing of host feeding drives rhythms in parasite replication

scientific article published on 26 February 2018

Timing of host feeding drives rhythms in parasite replication

Transition of Plasmodium sporozoites into liver stage-like forms is regulated by the RNA binding protein Pumilio

scientific article (publication date: May 2011)

Translational repression of the cpw-wpc gene family in the malaria parasite Plasmodium

scientific article

Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor

scientific article published on 13 October 2016

Two nonrecombining sympatric forms of the human malaria parasite Plasmodium ovale occur globally

scientific article

Unity in diversity: lessons from Candida

scientific article published in 2009

Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting

scientific article

Variety is the spice of eukaryotic life

scientific article published in 2007

WhiB6 is required for the secretion-dependent regulation of ESX-1 substrates in pathogenic mycobacteria

Whole genome sequence analysis of Mycobacterium suricattae.

scientific article

Whole genome sequencing based characterization of extensively drug-resistant Mycobacterium tuberculosis isolates from Pakistan

scientific article

Whole genome sequencing of amplified Plasmodium knowlesi DNA from unprocessed blood reveals genetic exchange events between Malaysian Peninsular and Borneo subpopulations

scientific article published on 08 July 2019

Whole genome sequencing provides additional insights into recurrent tuberculosis classified as endogenous reactivation by IS6110 DNA fingerprinting

scientific article published on 02 July 2019

Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates

scientific article

Whole genome sequencing-based characterization of extensively drug resistant (XDR) strains of Mycobacterium tuberculosis from Pakistan

scholarly article by Zahra Hasan et al published March 2015 in International journal of mycobacteriology

iSCAN: An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2

scientific article published on 18 August 2020

miR-126-5p by direct targeting of JNK-interacting protein-2 (JIP-2) plays a key role in Theileria-infected macrophage virulence.

scientific article published on 23 March 2018

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