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List of works by Makedonka Mitreva

400000 nematode ESTs on the Net.

scientific article

A Multi-Omics Database for Parasitic Nematodes and Trematodes

scientific article published on 01 January 2018

A catalog of reference genomes from the human microbiome

scientific article

A framework for human microbiome research

scientific article

A nuclear single-nucleotide polymorphism (SNP) potentially useful for the separation of Rhodnius prolixus from members of the Rhodnius robustus cryptic species complex (Hemiptera: Reduviidae)

scientific article (publication date: March 2013)

A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing

scientific article

A survey of SL1-spliced transcripts from the root-lesion nematode Pratylenchus penetrans.

scientific article

A transcriptomic analysis of the phylum Nematoda

article

A vertebrate case study of the quality of assemblies derived from next-generation sequences

scientific article

Alpha-gliadin genes from the A, B, and D genomes of wheat contain different sets of celiac disease epitopes

scientific article

An Integrated Multiomics Approach to Identify Candidate Antigens for Serodiagnosis of Human Onchocerciasis

scientific article published on 15 October 2015

An expressed sequence tag analysis of the life-cycle of the parasitic nematode Strongyloides ratti.

scientific article published on 18 April 2005

Analysis of the transcriptome of adult Dictyocaulus filaria and comparison with Dictyocaulus viviparus, with a focus on molecules involved in host-parasite interactions

scientific article published on 31 January 2014

Brugia malayi: effects of radiation and culture on gene expression in infective larvae.

scientific article

Changes in duodenal tissue-associated microbiota following hookworm infection and consecutive gluten challenges in humans with coeliac disease

scientific article

Characterization of parasite-specific indels and their proposed relevance for selective anthelminthic drug targeting.

scientific article published on 29 January 2016

Characterizing Ancylostoma caninum transcriptome and exploring nematode parasitic adaptation

scientific article

Comparative and demographic analysis of orang-utan genomes

scientific article

Comparative genomics of gene expression in the parasitic and free-living nematodes Strongyloides stercoralis and Caenorhabditis elegans

scientific article published on February 2004

Comparative genomics of nematodes

scientific article published on 01 October 2005

Compartmentalization of functions and predicted miRNA regulation among contiguous regions of the nematode intestine.

scientific article

Conservation and diversification of the transcriptomes of adult Paragonimus westermani and P. skrjabini

scientific article published on 13 September 2016

Conservation and global distribution of non-canonical antigens in Enterotoxigenic Escherichia coli

scientific article published on 22 November 2019

Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem

scientific article

Cracking the nodule worm code advances knowledge of parasite biology and biotechnology to tackle major diseases of livestock

scientific article published on 27 May 2015

De novo Assembly of the Brugia malayi Genome Using Long Reads from a Single MinION Flowcell

scientific article published on 20 December 2019

Deep insights into Dictyocaulus viviparus transcriptomes provides unique prospects for new drug targets and disease intervention

scientific article published on 22 December 2010

Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles.

scientific article

Dictyocaulus viviparus genome, variome and transcriptome elucidate lungworm biology and support future intervention

scientific article published on 9 February 2016

Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia.

scientific article published on 28 February 2018

Direct experimental manipulation of intestinal cells in Ascaris suum, with minor influences on the global transcriptome.

scientific article published on 18 February 2017

Discovery of anthelmintic drug targets and drugs using chokepoints in nematode metabolic pathways

scientific article

Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines

scientific article

Downregulation of the Syk Signaling Pathway in Intestinal Dendritic Cells Is Sufficient To Induce Dendritic Cells That Inhibit Colitis.

scientific article published on 24 August 2016

Draft genome of the filarial nematode parasite Brugia malayi

scientific article

Dynamic changes in the subgingival microbiome and their potential for diagnosis and prognosis of periodontitis

scientific article

Endosymbiont DNA in endobacteria-free filarial nematodes indicates ancient horizontal genetic transfer

scientific article (publication date: 9 June 2010)

Enterotoxigenic Escherichia coli heat-labile toxin drives enteropathic changes in small intestinal epithelia

scientific article published in 2022

Evolution of coreceptor utilization to escape CCR5 antagonist therapy.

scientific article

Experimental hookworm infection and escalating gluten challenges are associated with increased microbial richness in celiac subjects

scientific article published on 18 September 2015

Exploration of bacterial community classes in major human habitats

scientific article (publication date: 7 May 2014)

Exploring metazoan evolution through dynamic and holistic changes in protein families and domains.

scientific article

Exploring the transcriptome of the burrowing nematode Radopholus similis.

scientific article published on 2 April 2008

First transcriptomic analysis of the economically important parasitic nematode, Trichostrongylus colubriformis, using a next-generation sequencing approach

scientific article published on 6 August 2010

Functional and phylogenetic characterization of proteins detected in various nematode intestinal compartments

scientific article

Gender-associated genes in filarial nematodes are important for reproduction and potential intervention targets

scientific article

Gene discovery in the adenophorean nematode Trichinella spiralis: an analysis of transcription from three life cycle stages.

scientific article

Gene diversity and genetic variation in lung flukes (genus Paragonimus).

scientific article

Gene expression analysis of ABC transporters in a resistant Cooperia oncophora isolate following in vivo and in vitro exposure to macrocyclic lactones ⬇️

scientific article published on January 2, 2013

Genome Sequence of Christensenella minuta DSM 22607T.

scientific article published on 12 January 2017

Genome Sequences of 11 Human Vaginal Actinobacteria Strains

scientific article published on 29 September 2016

Genome Sequences of 12 Bacterial Isolates Obtained from the Urine of Pregnant Women

scientific article published on 29 September 2016

Genome Sequences of 14 Firmicutes Strains Isolated from the Human Vagina

scientific article published on 29 September 2016

Genome Sequences of Nine Gram-Negative Vaginal Bacterial Isolates

scientific article published on 29 September 2016

Genome analysis of the platypus reveals unique signatures of evolution

scientific article published in Nature

Genome analysis of the platypus reveals unique signatures of evolution

scientific article

Genome of the human hookworm Necator americanus

scientific article

Genome-wide analysis reveals novel genes essential for heme homeostasis in Caenorhabditis elegans

scientific article

Genome-wide tissue-specific gene expression, co-expression and regulation of co-expressed genes in adult nematode Ascaris suum

scientific article

Genomes of Fasciola hepatica from the Americas Reveal Colonization with Neorickettsia Endobacteria Related to the Agents of Potomac Horse and Human Sennetsu Fevers.

scientific article

Genomic diversity in Onchocerca volvulus and its Wolbachia endosymbiont

scientific article

Genomic introgression mapping of field-derived multiple-anthelmintic resistance in Teladorsagia circumcincta

scientific article

Genomic variation landscape of the human gut microbiome

scientific article

HelmCoP: an online resource for helminth functional genomics and drug and vaccine targets prioritization

scientific article

Helminth genomics: The implications for human health

scientific article

Helminth-induced arginase-1 exacerbates lung inflammation and disease severity in tuberculosis

scientific article

Helminth.net: expansions to Nematode.net and an introduction to Trematode.net.

scientific article

Identification and characterization of alternative splicing in parasitic nematode transcriptomes

scientific article

Identification of hookworm DAF-16/FOXO response elements and direct gene targets

scientific article

Identification of small molecule enzyme inhibitors as broad-spectrum anthelmintics

scientific article published on 24 June 2019

Immune correlates of tuberculosis disease and risk translate across species

scientific article published on 01 January 2020

Impact of experimental hookworm infection on the human gut microbiota

scientific article

Improving eukaryotic genome annotation using single molecule mRNA sequencing

scientific article published in March 2018

Insights Into Onchocerca volvulus Population Biology Through Multilocus Immunophenotyping

scientific article published on September 2017

Integrating genomics and phylogenetics in understanding the history of Trichinella species

scientific article

Inter and intra-specific diversity of parasites that cause lymphatic filariasis

scientific article

Intestinal transcriptomes of nematodes: comparison of the parasites Ascaris suum and Haemonchus contortus with the free-living Caenorhabditis elegans

scientific article

Investigating hookworm genomes by comparative analysis of two Ancylostoma species ⬇️

scientific article

Large-scale sequencing and analytical processing of ESTs

scientific article

Life cycle stage-resolved proteomic analysis of the excretome/secretome from Strongyloides ratti--identification of stage-specific proteases

scientific article published on 30 September 2011

Massively parallel sequencing and analysis of the Necator americanus transcriptome

scientific article published on 11 May 2010

Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment

scientific article published on 30 June 2015

Metabolic reconstruction for metagenomic data and its application to the human microbiome

scientific article published in 2012

Microbial community function and biomarker discovery in the human microbiome

Mining novel effector proteins from the esophageal gland cells of Meloidogyne incognita

scientific article

Mining the secretome of the root-knot nematode Meloidogyne chitwoodi for candidate parasitism genes

scientific article

Molecular determinants archetypical to the phylum Nematoda

scientific article

NemaPath: online exploration of KEGG-based metabolic pathways for nematodes

scientific article

Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics

scientific article

Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data

scientific article (publication date: 2012)

Novel venom gene discovery in the platypus.

scientific article published on 29 September 2010

Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities

scientific article

Pan-Nematoda Transcriptomic Elucidation of Essential Intestinal Functions and Therapeutic Targets With Broad Potential.

scientific article

Pan-phylum Comparison of Nematode Metabolic Potential

scientific article

Parasitic nematodes - from genomes to control.

scientific article published on 7 June 2007

Peptidases compartmentalized to the Ascaris suum intestinal lumen and apical intestinal membrane.

scientific article

Precise dissection of an Escherichia coli O157:H7 outbreak by single nucleotide polymorphism analysis

scientific article

Profiling of gender-regulated gene transcripts in the filarial nematode Brugia malayi by cDNA oligonucleotide array analysis

article

Proteomic analysis of Oesophagostomum dentatum (Nematoda) during larval transition, and the effects of hydrolase inhibitors on development

scientific article

Proteomics elucidates key molecules involved in exsheathment in vitro in Oesophagostomum dentatum

scientific article

RNAi effector diversity in nematodes

scientific article

Role of horizontal gene transfer in the evolution of plant parasitism among nematodes.

scientific article published on January 2009

Secreted proteomes of different developmental stages of the gastrointestinal nematode Nippostrongylus brasiliensis

scientific article

Sepsis from the gut: the enteric habitat of bacteria that cause late-onset neonatal bloodstream infections

scientific article

Sequence mining and transcript profiling to explore cyst nematode parasitism

scientific article

Silencing of germline-expressed genes by DNA elimination in somatic cells

scientific article published on November 2012

Small Molecule Inhibitors of Metabolic Enzymes Repurposed as a New Class of Anthelmintics

scientific article published on 14 May 2018

Stage-specific excretory-secretory small heat shock proteins from the parasitic nematode Strongyloides ratti--putative links to host's intestinal mucosal defense system.

scientific article published on 24 August 2011

Strategies for undertaking expressed sequence tag (EST) projects

scientific article

Structure, function and diversity of the healthy human microbiome

scientific article

Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance

scientific article

Systems biology studies of adult paragonimus lung flukes facilitate the identification of immunodominant parasite antigens

scientific article

TIMPs of parasitic helminths - a large-scale analysis of high-throughput sequence datasets

scientific article published on 30 May 2013

Tackling Hypotheticals in Helminth Genomes.

scientific article published on 14 December 2017

Targeting Lysine Deacetylases (KDACs) in Parasites

scientific article

Targeting protein-protein interactions for parasite control

scientific article (publication date: 2011)

The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia

scientific article published on 6 October 2015

The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism

scientific article

The bandit, a new DNA transposon from a hookworm-possible horizontal genetic transfer between host and parasite

scientific article

The draft genome of the parasitic nematode Trichinella spiralis

scientific article

The effect of dietary resistant starch type 2 on the microbiota and markers of gut inflammation in rural Malawi children.

scientific article published on 3 September 2015

The endosymbiont Wolbachia rebounds following antibiotic treatment

scientific article published on 08 July 2020

The genome of a blood fluke associated with human cancer ⬇️

scientific article published on January 27, 2012

The hookworm Ancylostoma ceylanicum intestinal transcriptome provides a platform for selecting drug and vaccine candidates

scientific article published on 27 September 2016

The prevalence of species and strains in the human microbiome: a resource for experimental efforts

scientific article

The transcriptomes of the cattle parasitic nematode Ostertagia ostartagi.

scientific article published on 27 February 2009

Transcription profiling reveals stage- and function-dependent expression patterns in the filarial nematode Brugia malayi.

scientific article

Transcriptome Analysis of Female and Male Xiphophorus maculatus Jp 163 A ⬇️

scientific article published on April 5, 2011

Transcriptome analyses reveal protein and domain families that delineate stage-related development in the economically important parasitic nematodes, Ostertagia ostertagi and Cooperia oncophora

scientific article

Transcriptomes and pathways associated with infectivity, survival and immunogenicity in Brugia malayi L3

scientific article published on 15 June 2009

Transcriptomic and Proteomic Analyses of a Wolbachia-Free Filarial Parasite Provide Evidence of Trans-Kingdom Horizontal Gene Transfer ⬇️

scientific article published on September 26, 2012

Transcripts analysis of the entomopathogenic nematode Steinernema carpocapsae induced in vitro with insect haemolymph

scientific article

Trichinella spiralis: Adaptation and parasitism

scientific article published on 2 July 2016

Using existing drugs as leads for broad spectrum anthelmintics targeting protein kinases

scientific article (publication date: February 2013)

Variant in a common odorant-binding protein gene is associated with bitter sensitivity in people.

scientific article published on 6 May 2017

Widespread colonization of the lung by Tropheryma whipplei in HIV infection

scientific article published on May 2013

mBLAST: Keeping up with the sequencing explosion for (meta)genome analysis

scientific article

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