Omar Harb

University of Pennsylvania | UP · Department of Biology

Babesiosis, caused by protozoan parasites of the genus Babesia, is an emerging tick-borne disease of significance for both human and animal health. Babesia parasites infect erythrocytes of vertebrate hosts where they develop and multiply rapidly to cause the pathological symptoms associated with the disease. The identification of new Babesia specie...

The Eukaryotic Pathogen, Vector and Host Informatics Resources (VEuPathDB.org) provide free online access to omic data from eukaryotic protozoan and fungal pathogens, arthropod vectors of disease, and host responses to pathogen infection. The goal of VEuPathDB is to make data easily accessible, findable, and importantly, re-usable by laboratory sci...

FungiDB (https://fungidb.org) serves as a valuable online resource that seamlessly integrates genomic and related large-scale data for a wide range of fungal and oomycete species. As an integral part of the VEuPathDB Bioinformatics Resource Center (https://veupathdb.org), FungiDB continually integrates both published and unpublished data addressing...

Babesiosis, caused by protozoan parasites of the genus Babesia, is an emerging tick-borne disease of significance for both human and animal health. Babesia parasites infect erythrocytes of vertebrate hosts where they develop and multiply rapidly to cause the pathological symptoms associated with the disease. The identification of various Babesia sp...

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) is a Bioinformatics Resource Center funded by the National Institutes of Health with additional funding from the Wellcome Trust. VEuPathDB supports >600 organisms that comprise invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant...

Babesiosis is a malaria-like disease in humans and animals that is caused by Babesia species, which are tick-transmitted apicomplexan pathogens. Babesia duncani causes severe to lethal infection in humans, but despite the risk that this parasite poses as an emerging pathogen, little is known about its biology, metabolic requirements or pathogenesis...

Parasitic diseases caused by kinetoplastid parasites are a burden to public health throughout tropical and subtropical regions of the world. TriTrypDB (https://tritrypdb.org) is a free online resource for data mining of genomic and functional data from these kinetoplastid parasites and is part of the VEuPathDB Bioinformatics Resource Center (https:...

VectorBase (VectorBase.org) is part of the VEuPathDB Bioinformatics Resource Center, providing free online access to multi-omics and population biology data, focusing on arthropod vectors and invertebrates of importance to human health. VectorBase includes genomics and functional genomics data from bed bugs, biting midges, body lice, kissing bugs,...

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising inverteb...

The concept of open data has been gaining traction as a mechanism to increase data use, ensure that data are preserved over time, and accelerate discovery. While epidemiology data sets are increasingly deposited in databases and repositories, barriers to access still remain. ClinEpiDB was constructed as an open-access online resource for clinical a...

ToxoDB is a free online resource that provides access to genomic and functional genomic data. All data is made available through an intuitive queryable interface that enables scientists to build in silico experiments and develop testable hypothesis. The resource contains 32 fully sequenced and annotated genomes, with genomic sequence from multiple...

ToxoDB (http://ToxoDB.org) is the functional genomic resource for Toxoplasma and related organisms. ToxoDB is part of the Eukaryotic Pathogen Database resources (http://EuPathDB.org) and contains genomes and functional genomic data. All EuPathDB resources including ToxoDB are freely accessible online and only require the use of a web browser. ToxoD...

The concept of open data has been gaining traction as a mechanism to increase data use, ensure that data are preserved over time, and accelerate discovery. While epidemiology data sets are increasingly deposited in databases and repositories, barriers to access still remain. ClinEpiDB was constructed as an open-access online resource for clinical a...

Fighting infections and developing novel drugs and vaccines requires advanced knowledge of pathogen’s biology. Readily accessible genomic, functional genomic, and population data aids biological and translational discovery. The Eukaryotic Pathogen Database Resources (http://eupathdb.org) are data mining resources that support hypothesis driven rese...

FungiDB (fungidb.org) is a free online resource for data mining and functional genomics analysis for fungal and oomycete species. FungiDB is part of the Eukaryotic Pathogen Genomics Database Resource (EuPathDB, eupathdb.org) platform that integrates genomic, transcriptomic, proteomic, and phenotypic datasets, and other types of data for pathogenic...

There is no comprehensive storage for generated mutants of Fusarium graminearum or data associated with these mutants. Instead researchers relied on several independent and non-integrated databases. FgMutantDb was designed as a simple spreadsheet that is accessible globally on the web that will function as a centralized source of information on F....

The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconf...

In the last decade, the rise of affordable high-throughput sequencing technologies has led to rapid advances across the biological sciences. At the time of writing, annotated reference genomes are available for most clades of eukaryotic pathogens. Over 550 genomes, including unannotated sequences, are available in total. This has greatly facilitate...

The 28th Fungal Genetics Conference was held March 17−22, 2015, at the Asilomar Conference Center in Pacific Grove, California (http://www.genetics-gsa.org/fungal/2015/index.shtml). Arguably the most popular of international fungal genetics conferences, the Asilomar meeting reached its registration cap 2 days before the early bird deadline, with 91...

The study of the three protagonists in malaria-the Plasmodium parasite, the Anopheles mosquito, and the human host-is key to developing methods to control and eventually eliminate the disease. Genomic technologies, including the recent development of next-generation sequencing, enable interrogation of this triangle to an unprecedented level of scru...

Data generated during the course of research activities carried out by the International Centers of Excellence for Malaria Research (ICEMR) is heterogeneous, large, and multi-scaled. The complexity of federated and global data operations and the diverse uses planned for the data pose tremendous challenges and opportunities for collaborative researc...

RNA-Seq is a method for profiling transcription using high-throughput sequencing and is an important component of many research projects that wish to study transcript isoforms, condition specific expression, and transcriptional structure. The methods, tools, and technologies employed to perform RNA-Seq analysis continue to change, creating a bioinf...

Over the past 20 years, advances in high-throughput biological techniques and the availability of computational resources including fast Internet access have resulted in an explosion of large genome-scale data sets "big data." While such data are readily available for download and personal use and analysis from a variety of repositories, often such...

The genomics era has been succeeded by the “Omics” era, making public databases an essential tool for all investigators. The ToxoDB team works closely with the Toxoplasma scientific community to organize genomics, transcriptomics, proteomics, epigenomics and other high throughput data for the scientific community. This chapter introduces the resour...

Motivation RNA-Seq is a method for profiling transcription using high-throughput sequencing and is an important component of many research projects that wish to study transcript isoforms, condition specific expression, and transcriptional structure. The methods, tools, and technologies employed to perform RNA-Seq analysis continue to change, creati...

High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenet...

GeneDB (http://www.genedb.org) is a genome database for prokaryotic and eukaryotic pathogens and closely related organisms. The resource provides a portal to genome sequence and annotation data, which is primarily generated by the Pathogen Genomics group at the Wellcome Trust Sanger Institute. It combines data from completed and ongoing genome proj...

EuPathDB (http://eupathdb.org) resources include 11 databases supporting eukaryotic pathogen genomic and functional genomic data, isolate data and phylogenomics. EuPathDB resources are built using the same infrastructure and provide a sophisticated search strategy system enabling complex interrogations of underlying data. Recent advances in EuPathD...

GeneDB (http://www.genedb.org) is a genome database for prokaryotic and eukaryotic pathogens and closely related organisms. The resource provides a portal to genome sequence and annotation data, which is primarily generated by the Pathogen Genomics group at the Wellcome Trust Sanger Institute. It combines data from completed and ongoing genome proj...

FungiDB (http://FungiDB.org) is a functional genomic resource for pan-fungal genomes that was developed in partnership with the Eukaryotic Pathogen Bioinformatic resource center (http://EuPathDB.org). FungiDB uses the same infrastructure and user interface as EuPathDB, which allows for sophisticated and integrated searches to be performed using an...

OrthoMCL is an algorithm for grouping proteins into ortholog groups based on their sequence similarity. OrthoMCL-DB is a public database that allows users to browse and view ortholog groups that were pre-computed using the OrthoMCL algorithm. Version 4 of this database contained 116,536 ortholog groups clustered from 1,270,853 proteins obtained fro...

Sequence alignment of Dxr proteins from select bacteria and plastid or apicoplast-containing organisms. Sequences were taken from NCBI and aligned using MUSCLE at http://www.phylogeny.fr/. Residues colored in red, green and black in the E. coli sequence are also highly conserved in all other Dxr proteins and have been implicated in binding/interact...

Localization of PfDxr in early trophozoite stages of P. falciparum. For details see Fig. 1B. (TIF)

Localization of PfDxr in ring stages of P. falciparum. For details see Fig. 1B. (TIF)

Localization of PfDxr in mid-late trophozoite stages of P. falciparum. For details see Fig. 1B. (TIF)

1D- and 3D-structures of anti-plasmodial phosphonates. Structures of Fos and FR (A) and their superimposed 3D-structures (B). Aligned calculated three-dimensional conformer coordinates for Fos and FR were retrieved from PubChem (http://pubchem.ncbi.nlm.nih.gov) and visualized using Chimera [74]. (C) Structures of the two anti-plasmodial phosphonate...

Comparison of the mevalonate and DOXP pathway for the biosynthesis of the isoprenoid precursors IPP/DMAPP. The pathways shown are based on MetaCyc [71] and were drawn using the Pathway Tools software [72]. Numbers drawn in blue are enzyme EC numbers. (TIF)

Expression levels of the DOXP pathway genes in P. yoelii. The values are based on microarray data of the rodent parasite P. yoelii [24] and were extracted from the P. yoelii gene entries (accessible via the respective cross-references from the P. falciparum gene entries; see Table S1) at PlasmoDB (http://www.plasmodb.org/). M values denote the rela...

Enzymes of the DOXP pathway of isoprenoid biosynthesis in five Apicomplexa. Given are the EC numbers, enzyme names and respective accession numbers in either EuPathDB (http://eupathdb.org/eupathdb) for T. gondii, N. caninum, P. falciparum and T. parva, or NCBI (http://www.ncbi.nlm.nih.gov) for B. bovis. Designations printed in blue mean that MassSp...

Localization of PfDxr in late trophozoite stages of P. falciparum. For details see Fig. 1B. (TIF)

Localization of PfDxr in merozoites stages of P. falciparum right before lysis. For details see Fig. 1B. (TIF)

Dose-dependend inhibition of [14C]FR uptake by two NPP inhibitors (NPPB and furosemide). Uptake of [14C]FR into infected erythrocytes in the presence of different concentrations (as indicated in the figure) of NPPB (5-Nitro-2-(3-phenylpropylamino)benzoic acid) or furosemide, respectively, was determined in triplicates (see Materials & Methods). The...

Western blot analysis of rabbit anti-PfDxr antisera. The western blot of a T. gondii cell lysate with pre-immune sera from two rabbits (lanes 1 & 2) and the respective hyper-immune sera after PfDxr immunization (lanes 3 & 4) is shown. It clearly shows in lane 3 a very prominent band<50 kDa. This size correlates very well with a predicted molecular...

Physico-chemical properties of select compounds known to act on apicoplast targets in Plasmodium and/or T. gondii. Compounds were compiled from the literature [72], [73]. L-glutamic acid and pantothenic acid as physiological NPP substrates (indicated in yellow) and five other anti-plasmodials (blue) are included for comparison (see main text for de...

Highly charged compounds typically suffer from low membrane permeability and thus are generally regarded as sub-optimal drug candidates. Nonetheless, the highly charged drug fosmidomycin and its more active methyl-derivative FR900098 have proven parasiticidal activity against erythrocytic stages of the malaria parasite Plasmodium falciparum. Both c...

Web sites associated with the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) have recently introduced a graphical user interface, the Strategies WDK, intended to make advanced searching and set and interval operations easy and accessible to all users. With a design guided by usability studies, the system helps motivate researcher...

EuPathDB is a public resource of protozoan parasite genomic and functional genomic data. To address community needs, information on isolate specimens, and on genetic manipulation and phenotype data will be collected directly from scientists. In order to facilitate data exploration, exchange, sharing and reuse, such data needs to be well-structured...

AmoebaDB (http://AmoebaDB.org) and MicrosporidiaDB (http://MicrosporidiaDB.org) are new functional genomic databases serving the amoebozoa and microsporidia research communities, respectively. AmoebaDB contains the genomes of three Entamoeba species (E. dispar, E. invadens and E. histolityca) and microarray expression data for E. histolytica. Micro...

Apicomplexan parasites release factors via specialized secretory organelles (rhoptries, micronemes) that are thought to control host cell responses. In order to explore parasite-mediated modulation of host cell signaling pathways, we exploited a phylogenomic approach to characterize the Toxoplasma gondii kinome, defining a 44 member family of cocci...

TriTrypDB (http://tritrypdb.org) is an integrated database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. TriTrypDB is a collaborative project, utilizing the GUS/WDK computational infrastructure developed by the Eukaryotic Pathogen Bioinfor...

EuPathDB (http://EuPathDB.org; formerly ApiDB) is an integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal off...

PlasmoDB (http://PlasmoDB.org) is a functional genomic database for Plasmodium spp. that provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB belongs to a family of genomic resources that are housed under the EuPathDB (http://EuPathDB.org) Bioinformatics Resource Center (BRC) umbrella. The latest...

Bioinformatics research on Plasmodium falciparum revealed two isoforms of pyruvate kinase: type-I and type-II enzymes. The type-I enzyme shows typical glycolytic properties, while type-II enzyme is involved in fatty acid type-II biosynthesis and has been predicted to localize to the apicoplast with the targeting signal in its N-terminus. The type-I...

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List of candidate microneme proteins for Plasmodium knowlesi. (0.04 MB XLS)

List of candidate microneme proteins for Theileria parva. (0.16 MB XLS)

List of candidate microneme proteins for Babesia bovis. (0.03 MB XLS)

Detailed results of comparisons between T. gondii computational data from this study and various proteomics datasets. (0.05 MB XLS)

List of candidate microneme proteins for Theileria annulata. (0.18 MB XLS)

Detailed results of comparisons between P. falciparum computational data from this study and various proteomics datasets (see Table 2). (0.04 MB XLS)

Comparison of candidate parasite interacting partners with those published by [106] (David et al. 2007) and [107] (Dyer et al. 2007). (0.23 MB XLS)

List of human proteins reported to be engaged by P. falciparum and/or T. gondii (including those not detected by our search methods). (0.01 MB PDF)

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List of candidate microneme proteins for Plasmodium yoelii. (0.04 MB XLS)

List of candidate microneme proteins for Plasmodium berghei. (0.03 MB XLS)

Comparison of candidate human interacting partners from the Phint and Phifam datasets with those published by [106] (David et al. 2007) and [107] (Dyer et al. 2007). (0.71 MB XLS)

List of candidate microneme proteins for Plasmodium falciparum. (0.24 MB XLS)

List of candidate microneme proteins for Plasmodium vivax. (0.08 MB XLS)

List of candidate microneme proteins for Plasmodium chabaudi. (0.03 MB XLS)

Complete Phint and Phifam datasets (see Fig. 3). (1.86 MB XLS)

GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the EuPathDB (http://EuPathDB.org) family of functional genomic databases. GiardiaDB and TrichDB employ the same framework as other EuPathDB sites (CryptoDB,...

Apicomplexan parasites, including the human pathogens Toxoplasma gondii and Plasmodium falciparum, employ specialized secretory organelles (micronemes, rhoptries, dense granules) to invade and survive within host cells. Because molecules secreted from these organelles function at the host/parasite interface, their identification is important for un...

Signaling via the NF-kappaB cascade is critical for innate recognition of microbial products and immunity to infection. As a consequence, this pathway represents a strong selective pressure on infectious agents and many parasitic, bacterial and viral pathogens have evolved ways to subvert NF-kappaB signaling to promote their survival. Although the...

Two replicative forms characterize the asexual cycle of the protozoan parasite Toxoplasma gondii: rapidly growing tachyzoites and slowly dividing encysted bradyzoites. The mechanisms that regulate the transition between these two stages are not clearly understood. However, stress inducers that also activate heat shock protein expression can trigger...

During its life cycle in intermediate hosts, Toxoplasma gondii exists in two interconverting developmental stages: tachyzoites and bradyzoites. This interconversion is essential for the survival and pathogenicity of the parasite, but little is known about the