Literature DB >> 14681426

CryptoDB: the Cryptosporidium genome resource.

Daniela Puiu1, Shinichiro Enomoto, Gregory A Buck, Mitchell S Abrahamsen, Jessica C Kissinger.   

Abstract

CryptoDB (http://CryptoDB.org) represents a collaborative effort to locate all genome data for the apicomplexan parasite Cryptosporidium parvum in a single user-friendly database. CryptoDB currently houses the genomic sequence data for both the human type 1 H strain and the bovine type 2 IOWA strain in addition to all other available EST and GSS sequences obtained from public repositories. All data are available for data mining via BLAST, keyword searches of pre-computed BLASTX results and user-defined or PROSITE motif pattern searches. Release 1.0 of CryptoDB contains approximately 19 million bases of genome sequence for the H and IOWA strains and an additional approximately 24 million bases of GSS and EST sequence obtained from other sources. Open reading frames greater than 50 and 100 amino acids have been generated for all sequences and all data are available for bulk download. This database, like other apicomplexan parasite databases, has been built utilizing the PlasmoDB model.

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Year:  2004        PMID： 14681426      PMCID： PMC308784          DOI： 10.1093/nar/gkh050

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  14 in total

1.  What's new in the library? What's new in GenBank? let PubCrawler tell you.

Authors:  K Hokamp; K Wolfe
Journal:  Trends Genet       Date:  1999-11       Impact factor: 11.639

Review 2.  Gene discovery in Cryptosporidium parvum: expressed sequence tags and genome survey sequences.

Authors:  W B Strong; R G Nelson
Journal:  Contrib Microbiol       Date:  2000

3.  Animal propagation and genomic survey of a genotype 1 isolate of Cryptosporidium parvum.

Authors:  G Widmer; D Akiyoshi; M A Buckholt; X Feng; S M Rich; K M Deary; C A Bowman; P Xu; Y Wang; X Wang; G A Buck; S Tzipori
Journal:  Mol Biochem Parasitol       Date:  2000-05       Impact factor: 1.759

4.  The Plasmodium genome database.

Authors:  Jessica C Kissinger; Brian P Brunk; Jonathan Crabtree; Martin J Fraunholz; Bindu Gajria; Arthur J Milgram; David S Pearson; Jonathan Schug; Amit Bahl; Sharon J Diskin; Hagai Ginsburg; Gregory R Grant; Dinesh Gupta; Philip Labo; Li Li; Matthew D Mailman; Shannon K McWeeney; Patricia Whetzel; Christian J Stoeckert; David S Roos
Journal:  Nature       Date:  2002-10-03       Impact factor: 49.962

5.  PROSITE: a documented database using patterns and profiles as motif descriptors.

Authors:  Christian J A Sigrist; Lorenzo Cerutti; Nicolas Hulo; Alexandre Gattiker; Laurent Falquet; Marco Pagni; Amos Bairoch; Philipp Bucher
Journal:  Brief Bioinform       Date:  2002-09       Impact factor: 11.622

6.  Preliminary profile of the Cryptosporidium parvum genome: an expressed sequence tag and genome survey sequence analysis.

Authors:  W B Strong; R G Nelson
Journal:  Mol Biochem Parasitol       Date:  2000-03-15       Impact factor: 1.759

7.  Integrated mapping, chromosomal sequencing and sequence analysis of Cryptosporidium parvum.

Authors:  Alan T Bankier; Helen F Spriggs; Berthold Fartmann; Bernard A Konfortov; Martin Madera; Christine Vogel; Sarah A Teichmann; Al Ivens; Paul H Dear
Journal:  Genome Res       Date:  2003-07-17       Impact factor: 9.043

8.  ToxoDB: accessing the Toxoplasma gondii genome.

Authors:  Jessica C Kissinger; Bindu Gajria; Li Li; Ian T Paulsen; David S Roos
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

9.  PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data.

Authors:  Amit Bahl; Brian Brunk; Jonathan Crabtree; Martin J Fraunholz; Bindu Gajria; Gregory R Grant; Hagai Ginsburg; Dinesh Gupta; Jessica C Kissinger; Philip Labo; Li Li; Matthew D Mailman; Arthur J Milgram; David S Pearson; David S Roos; Jonathan Schug; Christian J Stoeckert; Patricia Whetzel
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

10.  Cryptosporidium hominis n. sp. (Apicomplexa: Cryptosporidiidae) from Homo sapiens.

Authors:  Una M Morgan-Ryan; Abbie Fall; Lucy A Ward; Nawal Hijjawi; Irshad Sulaiman; Ronald Fayer; R C Andrew Thompson; M Olson; Altaf Lal; Lihua Xiao
Journal:  J Eukaryot Microbiol       Date:  2002 Nov-Dec       Impact factor: 3.346
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  35 in total

1.  ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites.

Authors:  Li Li; Jonathan Crabtree; Steve Fischer; Deborah Pinney; Christian J Stoeckert; L David Sibley; David S Roos
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

2.  Sequence and comparative genomic analysis of actin-related proteins.

Authors:  Jean Muller; Yukako Oma; Laurent Vallar; Evelyne Friederich; Olivier Poch; Barbara Winsor
Journal:  Mol Biol Cell       Date:  2005-09-29       Impact factor: 4.138

Review 3.  A hundred-year retrospective on cryptosporidiosis.

Authors:  Saul Tzipori; Giovanni Widmer
Journal:  Trends Parasitol       Date:  2008-03-07

4.  The mitochondrial ribosomal protein L13 is critical for the structural and functional integrity of the mitochondrion in Plasmodium falciparum.

Authors:  Hangjun Ke; Swati Dass; Joanne M Morrisey; Michael W Mather; Akhil B Vaidya
Journal:  J Biol Chem       Date:  2018-04-06       Impact factor: 5.157

5.  Nuclear delivery of parasite Cdg2_FLc_0220 RNA transcript to epithelial cells during Cryptosporidium parvum infection modulates host gene transcription.

Authors:  Guang-Hui Zhao; Ai-Yu Gong; Yang Wang; Xin-Tian Zhang; Min Li; Nicholas W Mathy; Xian-Ming Chen
Journal:  Vet Parasitol       Date:  2017-12-20       Impact factor: 2.738

6.  Functional characterization of an evolutionarily distinct phosphopantetheinyl transferase in the apicomplexan Cryptosporidium parvum.

Authors:  Xiaomin Cai; Dustin Herschap; Guan Zhu
Journal:  Eukaryot Cell       Date:  2005-07

7.  Delivery of Parasite RNA Transcripts Into Infected Epithelial Cells During Cryptosporidium Infection and Its Potential Impact on Host Gene Transcription.

Authors:  Yang Wang; Ai-Yu Gong; Shibin Ma; Xiqiang Chen; Yan Li; Chun-Jen Su; Dana Norall; Jing Chen; Juliane K Strauss-Soukup; Xian-Ming Chen
Journal:  J Infect Dis       Date:  2017-02-15       Impact factor: 5.226

8.  Induction of Inflammatory Responses in Splenocytes by Exosomes Released from Intestinal Epithelial Cells following Cryptosporidium parvum Infection.

Authors:  Yang Wang; Yujuan Shen; Hua Liu; Jianhai Yin; Xin-Tian Zhang; Ai-Yu Gong; Xiqiang Chen; Siyi Chen; Nicholas W Mathy; Jianping Cao; Xian-Ming Chen
Journal:  Infect Immun       Date:  2019-03-25       Impact factor: 3.441

9.  Gene transfer in the evolution of parasite nucleotide biosynthesis.

Authors:  Boris Striepen; Andrea J P Pruijssers; Jinling Huang; Catherine Li; Marc-Jan Gubbels; Nwakaso N Umejiego; Lizbeth Hedstrom; Jessica C Kissinger
Journal:  Proc Natl Acad Sci U S A       Date:  2004-02-18       Impact factor: 11.205

10.  Trans-suppression of defense DEFB1 gene in intestinal epithelial cells following Cryptosporidium parvum infection is associated with host delivery of parasite Cdg7_FLc_1000 RNA.

Authors:  Zhenping Ming; Ai-Yu Gong; Yang Wang; Xin-Tian Zhang; Min Li; Courtney E Dolata; Xian-Ming Chen
Journal:  Parasitol Res       Date:  2018-01-26       Impact factor: 2.289
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