Literature DB >> 25388105

The Eukaryotic Pathogen Databases: a functional genomic resource integrating data from human and veterinary parasites.

Omar S Harb1, David S Roos.   

Abstract

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 analysis requires access to seldom-available computational skills. As a result a number of databases have emerged to provide scientists with online tools enabling the interrogation of data without the need for sophisticated computational skills beyond basic knowledge of Internet browser utility. This chapter focuses on the Eukaryotic Pathogen Databases (EuPathDB: http://eupathdb.org) Bioinformatic Resource Center (BRC) and illustrates some of the available tools and methods.

Entities:  

Mesh:

Substances:

Year:  2015        PMID: 25388105      PMCID: PMC6157018          DOI: 10.1007/978-1-4939-1438-8_1

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  13 in total

Review 1.  TB database 2010: overview and update.

Authors:  James E Galagan; Peter Sisk; Christian Stolte; Brian Weiner; Michael Koehrsen; Farrell Wymore; T B K Reddy; Jeremy D Zucker; Reinhard Engels; Marcel Gellesch; Jeremy Hubble; Heng Jin; Lisa Larson; Maria Mao; Michael Nitzberg; Jared White; Zachariah K Zachariah; Gavin Sherlock; Catherine A Ball; Gary K Schoolnik
Journal:  Tuberculosis (Edinb)       Date:  2010-05-20       Impact factor: 3.131

2.  Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups.

Authors:  Steve Fischer; Brian P Brunk; Feng Chen; Xin Gao; Omar S Harb; John B Iodice; Dhanasekaran Shanmugam; David S Roos; Christian J Stoeckert
Journal:  Curr Protoc Bioinformatics       Date:  2011-09

3.  A combined transcriptome and proteome survey of malaria parasite liver stages.

Authors:  Alice S Tarun; Xinxia Peng; Ronald F Dumpit; Yuko Ogata; Hilda Silva-Rivera; Nelly Camargo; Thomas M Daly; Lawrence W Bergman; Stefan H I Kappe
Journal:  Proc Natl Acad Sci U S A       Date:  2008-01-02       Impact factor: 11.205

4.  OrthoMCL: identification of ortholog groups for eukaryotic genomes.

Authors:  Li Li; Christian J Stoeckert; David S Roos
Journal:  Genome Res       Date:  2003-09       Impact factor: 9.043

5.  The Strategies WDK: a graphical search interface and web development kit for functional genomics databases.

Authors:  Steve Fischer; Cristina Aurrecoechea; Brian P Brunk; Xin Gao; Omar S Harb; Eileen T Kraemer; Cary Pennington; Charles Treatman; Jessica C Kissinger; David S Roos; Christian J Stoeckert
Journal:  Database (Oxford)       Date:  2011-06-23       Impact factor: 3.451

6.  FungiDB: an integrated functional genomics database for fungi.

Authors:  Jason E Stajich; Todd Harris; Brian P Brunk; John Brestelli; Steve Fischer; Omar S Harb; Jessica C Kissinger; Wei Li; Vishal Nayak; Deborah F Pinney; Chris J Stoeckert; David S Roos
Journal:  Nucleic Acids Res       Date:  2011-11-07       Impact factor: 16.971

7.  OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups.

Authors:  Feng Chen; Aaron J Mackey; Christian J Stoeckert; David S Roos
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

8.  TriTrypDB: a functional genomic resource for the Trypanosomatidae.

Authors:  Martin Aslett; Cristina Aurrecoechea; Matthew Berriman; John Brestelli; Brian P Brunk; Mark Carrington; Daniel P Depledge; Steve Fischer; Bindu Gajria; Xin Gao; Malcolm J Gardner; Alan Gingle; Greg Grant; Omar S Harb; Mark Heiges; Christiane Hertz-Fowler; Robin Houston; Frank Innamorato; John Iodice; Jessica C Kissinger; Eileen Kraemer; Wei Li; Flora J Logan; John A Miller; Siddhartha Mitra; Peter J Myler; Vishal Nayak; Cary Pennington; Isabelle Phan; Deborah F Pinney; Gowthaman Ramasamy; Matthew B Rogers; David S Roos; Chris Ross; Dhileep Sivam; Deborah F Smith; Ganesh Srinivasamoorthy; Christian J Stoeckert; Sandhya Subramanian; Ryan Thibodeau; Adrian Tivey; Charles Treatman; Giles Velarde; Haiming Wang
Journal:  Nucleic Acids Res       Date:  2009-10-20       Impact factor: 16.971

9.  EuPathDB: a portal to eukaryotic pathogen databases.

Authors:  Cristina Aurrecoechea; John Brestelli; Brian P Brunk; Steve Fischer; Bindu Gajria; Xin Gao; Alan Gingle; Greg Grant; Omar S Harb; Mark Heiges; Frank Innamorato; John Iodice; Jessica C Kissinger; Eileen T Kraemer; Wei Li; John A Miller; Vishal Nayak; Cary Pennington; Deborah F Pinney; David S Roos; Chris Ross; Ganesh Srinivasamoorthy; Christian J Stoeckert; Ryan Thibodeau; Charles Treatman; Haiming Wang
Journal:  Nucleic Acids Res       Date:  2009-11-13       Impact factor: 16.971

10.  SchistoDB: a Schistosoma mansoni genome resource.

Authors:  Adhemar Zerlotini; Mark Heiges; Haiming Wang; Romulo L V Moraes; Anderson J Dominitini; Jerônimo C Ruiz; Jessica C Kissinger; Guilherme Oliveira
Journal:  Nucleic Acids Res       Date:  2008-10-08       Impact factor: 16.971

View more
  11 in total

1.  Generating and Maintaining Transgenic Cryptosporidium parvum Parasites.

Authors:  Mattie C Pawlowic; Sumiti Vinayak; Adam Sateriale; Carrie F Brooks; Boris Striepen
Journal:  Curr Protoc Microbiol       Date:  2017-08-11

Review 2.  Microtubule organelles in Giardia.

Authors:  Kari D Hagen; Shane G McInally; Nicholas D Hilton; Scott C Dawson
Journal:  Adv Parasitol       Date:  2020-02-05       Impact factor: 3.870

Review 3.  Cross-organism analysis using InterMine.

Authors:  Rachel Lyne; Julie Sullivan; Daniela Butano; Sergio Contrino; Joshua Heimbach; Fengyuan Hu; Alex Kalderimis; Mike Lyne; Richard N Smith; Radek Štěpán; Rama Balakrishnan; Gail Binkley; Todd Harris; Kalpana Karra; Sierra A T Moxon; Howie Motenko; Steven Neuhauser; Leyla Ruzicka; Mike Cherry; Joel Richardson; Lincoln Stein; Monte Westerfield; Elizabeth Worthey; Gos Micklem
Journal:  Genesis       Date:  2015-07-08       Impact factor: 2.487

4.  Genetic modification of the diarrhoeal pathogen Cryptosporidium parvum.

Authors:  Sumiti Vinayak; Mattie C Pawlowic; Adam Sateriale; Carrie F Brooks; Caleb J Studstill; Yael Bar-Peled; Michael J Cipriano; Boris Striepen
Journal:  Nature       Date:  2015-07-15       Impact factor: 49.962

5.  Characterizing Antibody Responses to Plasmodium vivax and Plasmodium falciparum Antigens in India Using Genome-Scale Protein Microarrays.

Authors:  Swapna Uplekar; Pavitra Nagesh Rao; Lalitha Ramanathapuram; Vikky Awasthi; Kalpana Verma; Patrick Sutton; Syed Zeeshan Ali; Ankita Patel; Sri Lakshmi Priya G; Sangamithra Ravishankaran; Nisha Desai; Nikunj Tandel; Sandhya Choubey; Punam Barla; Deena Kanagaraj; Alex Eapen; Khageswar Pradhan; Ranvir Singh; Aarti Jain; Philip L Felgner; D Huw Davies; Jane M Carlton; Jyoti Das
Journal:  PLoS Negl Trop Dis       Date:  2017-01-24

Review 6.  "Omic" investigations of protozoa and worms for a deeper understanding of the human gut "parasitome".

Authors:  Valeria Marzano; Livia Mancinelli; Giorgia Bracaglia; Federica Del Chierico; Pamela Vernocchi; Francesco Di Girolamo; Stefano Garrone; Hyppolite Tchidjou Kuekou; Patrizia D'Argenio; Bruno Dallapiccola; Andrea Urbani; Lorenza Putignani
Journal:  PLoS Negl Trop Dis       Date:  2017-11-02

7.  Evolution of the Apicomplexan Sugar Transporter Gene Family Repertoire.

Authors:  Ousman Mahmud; Jessica C Kissinger
Journal:  Int J Genomics       Date:  2017-05-07       Impact factor: 2.326

8.  Theileria parasites subvert E2F signaling to stimulate leukocyte proliferation.

Authors:  Kyle Tretina; Malak Haidar; Sally A Madsen-Bouterse; Takaya Sakura; Sara Mfarrej; Lindsay Fry; Marie Chaussepied; Arnab Pain; Donald P Knowles; Vishvanath M Nene; Doron Ginsberg; Claudia A Daubenberger; Richard P Bishop; Gordon Langsley; Joana C Silva
Journal:  Sci Rep       Date:  2020-03-04       Impact factor: 4.379

9.  The Conoid Associated Motor MyoH Is Indispensable for Toxoplasma gondii Entry and Exit from Host Cells.

Authors:  Arnault Graindorge; Karine Frénal; Damien Jacot; Julien Salamun; Jean Baptiste Marq; Dominique Soldati-Favre
Journal:  PLoS Pathog       Date:  2016-01-13       Impact factor: 6.823

Review 10.  Eight unique basal bodies in the multi-flagellated diplomonad Giardia lamblia.

Authors:  Shane G McInally; Scott C Dawson
Journal:  Cilia       Date:  2016-07-04
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.