Jessica Kissinger

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Jessica Kissinger is a Distinguished Research Professor at the Franklin College of Arts and Sciences, University of Georgia and director of the Institute of Bioinformatics. Her research focus is on the evolution, assembly and data curation of protozoan parasite genomes, particularly Cryptosporidium, Toxoplasma gondii and Plasmodium.

Biography

Kissinger obtained her PhD at Indiana University Bloomington in 1995. [1] During her PostDoc she worked with David Roos to help establish the Eukaryotic Pathogen Database (EuPathDB) series of genome collections, including the malaria specific PlasmoDB, for easy querying and access by scientists. [2] [3] Since its launch in 1999 the database has accrued 9TB of data, has been received renewed grant contributions by the NIH at every funding cycle, and now receives 6 million searches a year from 13,000 individuals. [4] Most recently Kissinger and Roos were awarded a grant that is expected to total US$23.4million for maintaining the resource. [4] The success of EuPathDB has led to the creation of Clinical Epidemiology Database (ClinEpiDB) based on the same framework, alongside Christian Stoekert and Christiane Hertz-Fowler. [5]

In 2008, while an associate professor, she was made a National Associate of the National Academies of Sciences, Engineering, and Medicine. [6] She helped to establish the Institute of Bioinformatics at the University of Georgia and then became director. [7] In 2016 she was awarded the Richard F. Reiff Internationalization Award by the University (alongside fellow professor Rose Chepyator-Thomson) for her international collaborations, opening up data internationally, and for being a member of the steering group for the West African International Centers of Excellence for Malaria Research at the National Institutes of Health. [7]

Beyond the creation of databases, Kissinger focuses on the analysis and comparison of parasite genomes. Using genome assemblies from across the Apicomplexa (which includes malaria and toxoplasmosis parasites) it was shown that genetic synteny (genes arranged in the same groupings in different genomes) was substantially less than expected from animal genomes, suggesting that the parasite genomes have undergone major rearrangements or that their most recent common ancestor is more ancient than previously thought. [8] In 2012 her lab helped develop a computational tool, MCScanX, to identify synteny across genomes, which has been cited >650 times. [9] [10]

Kissinger continues to make big data obtained from investigations into parasites as accessible as it can be. The Malaria Host-Pathogen Interaction Center, a collaboration with Emory University, funded by the National Institute of Allergy and Infectious Diseases and headed by Mary Galinski, is embarking on a major project to characterise many thousands of malaria-mammal associations and Kissinger is involved in converting this data into a format that can be used by everyone. [11] She said of the project: "The goal of my team is to integrate the terabytes of data being produced on both the host and the parasite and make it accessible to our mathematical modelers, who are looking for patterns and signals, as well as the global malaria research community to guarantee that this large investment has the biggest impact possible on malaria research". [11]

Related Research Articles

<span class="mw-page-title-main">Apicomplexa</span> Phylum of parasitic alveolates

The Apicomplexa are organisms of a large phylum of mainly parasitic alveolates. Most possess a unique form of organelle structure that comprises a type of non-photosynthetic plastid called an apicoplast—with an apical complex membrane. The organelle's apical shape is an adaptation that the apicomplexan applies in penetrating a host cell.

<span class="mw-page-title-main">BioPerl</span> Collection of Perl modules for bioinformatics

BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It has played an integral role in the Human Genome Project.

<span class="mw-page-title-main">Comparative genomics</span> Field of biological research

Comparative genomics is a branch of biological research that examines genome sequences across a spectrum of species, spanning from humans and mice to a diverse array of organisms from bacteria to chimpanzees. This large-scale holistic approach compares two or more genomes to discover the similarities and differences between the genomes and to study the biology of the individual genomes. Comparison of whole genome sequences provides a highly detailed view of how organisms are related to each other at the gene level. By comparing whole genome sequences, researchers gain insights into genetic relationships between organisms and study evolutionary changes. The major principle of comparative genomics is that common features of two organisms will often be encoded within the DNA that is evolutionarily conserved between them. Therefore, Comparative genomics provides a powerful tool for studying evolutionary changes among organisms, helping to identify genes that are conserved or common among species, as well as genes that give unique characteristics of each organism. Moreover, these studies can be performed at different levels of the genomes to obtain multiple perspectives about the organisms.

<span class="mw-page-title-main">Fiona Brinkman</span> Canadian medical researcher

Fiona Brinkman is a Professor in Bioinformatics and Genomics in the Department of Molecular Biology and Biochemistry at Simon Fraser University in British Columbia, Canada, and is a leader in the area of microbial bioinformatics. She is interested in developing "more sustainable, holistic approaches for infectious disease control and conservation of microbiomes".

<i>Theileria</i> Genus of single-celled organisms

Theileria is a genus of parasites that belongs to the phylum Apicomplexa, and is closely related to Plasmodium. Two Theileria species, T. annulata and T. parva, are important cattle parasites. T. annulata causes tropical theileriosis and T. parva causes East Coast fever. Theileria species are transmitted by ticks. The genomes of T. orientalis Shintoku, Theileria equi WA, Theileria annulata Ankara and Theileria parva Muguga have been sequenced and published.

UCSC Malaria Genome Browser is a bioinformatic research tool to study the malaria genome, developed by Hughes Undergraduate Research Laboratory together with the laboratory of Prof. Manuel Ares Jr. at the University of California, Santa Cruz.

The Bioinformatics Resource Centers (BRCs) are a group of five Internet-based research centers established in 2004 and funded by NIAID The BRCs were formed in response to the threats posed by emerging and re-emerging pathogens, particularly Centers for Disease Control and Prevention (CDC) Category A, B, and C pathogens, and their potential use in bioterrorism. The intention of NIAID in funding these bioinformatics centers is to assist researchers involved in the experimental characterization of such pathogens and the formation of drugs, vaccines, or diagnostic tools to combat them.

VectorBase is one of the five Bioinformatics Resource Centers (BRC) funded by the National Institute of Allergy and Infectious Diseases (NIAID), a component of the National Institutes of Health (NIH), which is an agency of the United States Department of Health and Human Services. VectorBase is focused on invertebrate vectors of human pathogens working with the sequencing centers and the research community to curate vector genomes.

Pathema was one of the eight bioinformatics resource centers funded by the National Institute of Allergy and Infectious Diseases (NIAID), a component of the National Institute of Health (NIH), which is an agency of the United States Department of Health and Human Services.

SUPERFAMILY is a database and search platform of structural and functional annotation for all proteins and genomes. It classifies amino acid sequences into known structural domains, especially into SCOP superfamilies. Domains are functional, structural, and evolutionary units that form proteins. Domains of common Ancestry are grouped into superfamilies. The domains and domain superfamilies are defined and described in SCOP. Superfamilies are groups of proteins which have structural evidence to support a common evolutionary ancestor but may not have detectable sequence homology.

PlasmoDB is a biological database for the genus Plasmodium. The database is a member of the EuPathDB project. The database contains extensive genome, proteome and metabolome information relating to malaria parasites.

<span class="mw-page-title-main">European Nucleotide Archive</span> Online database from the EBI on Nucleotides

The European Nucleotide Archive (ENA) is a repository providing free and unrestricted access to annotated DNA and RNA sequences. It also stores complementary information such as experimental procedures, details of sequence assembly and other metadata related to sequencing projects. The archive is composed of three main databases: the Sequence Read Archive, the Trace Archive and the EMBL Nucleotide Sequence Database. The ENA is produced and maintained by the European Bioinformatics Institute and is a member of the International Nucleotide Sequence Database Collaboration (INSDC) along with the DNA Data Bank of Japan and GenBank.

<span class="mw-page-title-main">Eukaryotic Pathogen Database</span>

The Eukaryotic Pathgen Database, or EuPathDB, is a database of bioinformatic and experimental data related to a variety of eukaryotic pathogens. It was established in 2006 under a National Institutes of Health program to create Bioinformatics Resource Centers to facilitate research on pathogens that may pose biodefense threats. EuPathDB stores data related to its organisms of interest and provides tools for searching through and analyzing the data. It currently consists of 14 component databases, each dedicated to a certain research topic. EuPathDB includes:

<span class="mw-page-title-main">Multiomics</span> Biological analysis approach

Multiomics, multi-omics, integrative omics, "panomics" or "pan-omics" is a biological analysis approach in which the data sets are multiple "omes", such as the genome, proteome, transcriptome, epigenome, metabolome, and microbiome ; in other words, the use of multiple omics technologies to study life in a concerted way. By combining these "omes", scientists can analyze complex biological big data to find novel associations between biological entities, pinpoint relevant biomarkers and build elaborate markers of disease and physiology. In doing so, multiomics integrates diverse omics data to find a coherently matching geno-pheno-envirotype relationship or association. The OmicTools service lists more than 99 softwares related to multiomic data analysis, as well as more than 99 databases on the topic.

PathoPhenoDB is a biological database. The database connects pathogens to their phenotypes using multiple databases such as NCBI, Human Disease Ontology Human Phenotype Ontology, Mammalian Phenotype Ontology, PubChem, SIDER and CARD. Pathogen-disease associations were gathered mainly through the CDC and the List of Infectious Diseases page on Wikipedia. The manner by which they assigned taxonomy was semi-automatic. When mapped against NCBI Taxonomy, if the pathogen was not an exact match, it was then mapped to the parent class. PathoPhenoDB employs NPMI in order to filter pairs based on their co-occurrence statistics.

In molecular biology, MvirDB was a publicly available database that stored information on toxins, virulence factors and antibiotic resistance genes. Sources that this database used for DNA and protein information included: Tox-Prot, SCORPION, the PRINTS Virulence Factors, VFDB, TVFac, Islander, ARGO and VIDA. The database provided a BLAST tool that allowed the user to query their sequence against all DNA and protein sequences in MvirDB. Information on virulence factors could be obtained from the usage of the provided browser tool. Once the browser tool was used, the results were returned as a readable table that was organized by ascending E-Values, each of which were hyperlinked to their related page. MvirDB was implemented in an Oracle 10g relational database. MvirDB appears to have been inactive for some time, and is therefore not current. The last available snapshot was made on August 2, 2017.

Mary R. Galinski is a professor of medicine at the Emory Vaccine Center, Hubert Department of Global Health of the Rollins School of Public Health, and the Department of Medicine of the Emory University School of Medicine.

References

  1. ↑ "Jessica Kissinger | Department of Genetics". www.genetics.uga.edu. Retrieved 2019-08-02.
  2. ↑ "Parasitologist, Reprogrammed: A Profile of David Roos". The Scientist Magazine®. Retrieved 2019-08-02.
  3. ↑ Aurrecoechea, C.; Barreto, A.; Brestelli, J.; Brunk, B. P.; Cade, S.; Doherty, R.; Fischer, S.; Gajria, B.; Gao, X. (2013-01-01). "EuPathDB: The Eukaryotic Pathogen database". Nucleic Acids Research. 41 (D1): D684–D691. doi:10.1093/nar/gks1113. ISSN   0305-1048. PMC   3531183 . PMID   23175615.
  4. 1 2 Flurry, Alan (2015-01-12). "$23.4M contract to bolster pathogen genomics database". UGA Today. Retrieved 2019-08-02.
  5. ↑ "New open-access data resource aims to bolster collaboration in global infectious disease research". Penn Today. 21 February 2018. Retrieved 2019-08-02.
  6. ↑ "Jessica Kissinger, Nationial Associate of Nationial Research Council". UGA Today. 2008-11-17. Retrieved 2019-08-02.
  7. 1 2 Smith, Sue Myers (2016-04-08). "UGA faculty and staff receive awards from the Office of International Education". UGA Today. Retrieved 2019-08-02.
  8. ↑ DeBarry, J. D.; Kissinger, J. C. (2011-10-01). "Jumbled Genomes: Missing Apicomplexan Synteny". Molecular Biology and Evolution. 28 (10): 2855–2871. doi:10.1093/molbev/msr103. ISSN   0737-4038. PMC   3176833 . PMID   21504890.
  9. ↑ Wang, Y.; Tang, H.; DeBarry, J. D.; Tan, X.; Li, J.; Wang, X.; Lee, T.-h.; Jin, H.; Marler, B. (2012-04-01). "MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity". Nucleic Acids Research. 40 (7): e49. doi:10.1093/nar/gkr1293. ISSN   0305-1048. PMC   3326336 . PMID   22217600.
  10. ↑ "Jessica C Kissinger - Google Scholar Citations". scholar.google.com. Retrieved 2019-08-02.
  11. 1 2 "Emory, UGA collaborate to leverage strengths in infectious disease research". news.emory.edu. 2014-12-16. Retrieved 2019-08-02.
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