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Items: 45

1.

ToxoDB: Functional Genomics Resource for Toxoplasma and Related Organisms.

Harb OS, Roos DS.

Methods Mol Biol. 2020;2071:27-47. doi: 10.1007/978-1-4939-9857-9_2.

PMID:
31758445
2.

MeBoP: Advanced Training in the Biology of Parasitism for Middle Eastern Students.

Sheiner L, Harb OS.

Trends Parasitol. 2019 May;35(5):329-332. doi: 10.1016/j.pt.2019.03.001. Epub 2019 Apr 2. No abstract available.

PMID:
30948350
3.

FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes.

Basenko EY, Pulman JA, Shanmugasundram A, Harb OS, Crouch K, Starns D, Warrenfeltz S, Aurrecoechea C, Stoeckert CJ Jr, Kissinger JC, Roos DS, Hertz-Fowler C.

J Fungi (Basel). 2018 Mar 20;4(1). pii: E39. doi: 10.3390/jof4010039.

4.

EuPathDB: The Eukaryotic Pathogen Genomics Database Resource.

Warrenfeltz S, Basenko EY, Crouch K, Harb OS, Kissinger JC, Roos DS, Shanmugasundram A, Silva-Franco F.

Methods Mol Biol. 2018;1757:69-113. doi: 10.1007/978-1-4939-7737-6_5.

PMID:
29761457
5.

EuPathDB: the eukaryotic pathogen genomics database resource.

Aurrecoechea C, Barreto A, Basenko EY, Brestelli J, Brunk BP, Cade S, Crouch K, Doherty R, Falke D, Fischer S, Gajria B, Harb OS, Heiges M, Hertz-Fowler C, Hu S, Iodice J, Kissinger JC, Lawrence C, Li W, Pinney DF, Pulman JA, Roos DS, Shanmugasundram A, Silva-Franco F, Steinbiss S, Stoeckert CJ Jr, Spruill D, Wang H, Warrenfeltz S, Zheng J.

Nucleic Acids Res. 2017 Jan 4;45(D1):D581-D591. doi: 10.1093/nar/gkw1105. Epub 2016 Nov 29.

6.

Meeting Report: Fungal Genomics Meets Social Media: Highlights of the 28th Fungal Genetics Conference at Asilomar.

Momany M, Di Pietro A, Alexander WG, Barker BM, Harb OS, Kamoun S, Martin F, Pires JC, Stajich JE, Thomma BP, Unruh S.

G3 (Bethesda). 2015 Dec;5(12):2523-5. No abstract available.

7.

A Framework for Global Collaborative Data Management for Malaria Research.

Gutierrez JB, Harb OS, Zheng J, Tisch DJ, Charlebois ED, Stoeckert CJ, Sullivan SA.

Am J Trop Med Hyg. 2015 Sep;93(3 Suppl):124-132. doi: 10.4269/ajtmh.15-0003. Epub 2015 Aug 10.

8.

Population Genetics, Evolutionary Genomics, and Genome-Wide Studies of Malaria: A View Across the International Centers of Excellence for Malaria Research.

Carlton JM, Volkman SK, Uplekar S, Hupalo DN, Pereira Alves JM, Cui L, Donnelly M, Roos DS, Harb OS, Acosta M, Read A, Ribolla PEM, Singh OP, Valecha N, Wassmer SC, Ferreira M, Escalante AA.

Am J Trop Med Hyg. 2015 Sep;93(3 Suppl):87-98. doi: 10.4269/ajtmh.15-0049. Epub 2015 Aug 10.

9.

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

Harb OS, Roos DS.

Methods Mol Biol. 2015;1201:1-18. doi: 10.1007/978-1-4939-1438-8_1.

10.

Standardized metadata for human pathogen/vector genomic sequences.

Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ Jr, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH.

PLoS One. 2014 Jun 17;9(6):e99979. doi: 10.1371/journal.pone.0099979. eCollection 2014.

11.

EuPathDB: the eukaryotic pathogen database.

Aurrecoechea C, Barreto A, Brestelli J, Brunk BP, Cade S, Doherty R, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Hu S, Iodice J, Kissinger JC, Kraemer ET, Li W, Pinney DF, Pitts B, Roos DS, Srinivasamoorthy G, Stoeckert CJ Jr, Wang H, Warrenfeltz S.

Nucleic Acids Res. 2013 Jan;41(Database issue):D684-91. doi: 10.1093/nar/gks1113. Epub 2012 Nov 21.

12.

GeneDB--an annotation database for pathogens.

Logan-Klumpler FJ, De Silva N, Boehme U, Rogers MB, Velarde G, McQuillan JA, Carver T, Aslett M, Olsen C, Subramanian S, Phan I, Farris C, Mitra S, Ramasamy G, Wang H, Tivey A, Jackson A, Houston R, Parkhill J, Holden M, Harb OS, Brunk BP, Myler PJ, Roos D, Carrington M, Smith DF, Hertz-Fowler C, Berriman M.

Nucleic Acids Res. 2012 Jan;40(Database issue):D98-108. doi: 10.1093/nar/gkr1032. Epub 2011 Nov 23.

13.

FungiDB: an integrated functional genomics database for fungi.

Stajich JE, Harris T, Brunk BP, Brestelli J, Fischer S, Harb OS, Kissinger JC, Li W, Nayak V, Pinney DF, Stoeckert CJ Jr, Roos DS.

Nucleic Acids Res. 2012 Jan;40(Database issue):D675-81. doi: 10.1093/nar/gkr918. Epub 2011 Nov 7.

14.

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

Fischer S, Brunk BP, Chen F, Gao X, Harb OS, Iodice JB, Shanmugam D, Roos DS, Stoeckert CJ Jr.

Curr Protoc Bioinformatics. 2011 Sep;Chapter 6:Unit 6.12.1-19. doi: 10.1002/0471250953.bi0612s35.

15.

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

Fischer S, Aurrecoechea C, Brunk BP, Gao X, Harb OS, Kraemer ET, Pennington C, Treatman C, Kissinger JC, Roos DS, Stoeckert CJ.

Database (Oxford). 2011 Jun 23;2011:bar027. doi: 10.1093/database/bar027. Print 2011.

16.

Fosmidomycin uptake into Plasmodium and Babesia-infected erythrocytes is facilitated by parasite-induced new permeability pathways.

Baumeister S, Wiesner J, Reichenberg A, Hintz M, Bietz S, Harb OS, Roos DS, Kordes M, Friesen J, Matuschewski K, Lingelbach K, Jomaa H, Seeber F.

PLoS One. 2011 May 4;6(5):e19334. doi: 10.1371/journal.pone.0019334.

17.

AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species.

Aurrecoechea C, Barreto A, Brestelli J, Brunk BP, Caler EV, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Iodice J, Kissinger JC, Kraemer ET, Li W, Nayak V, Pennington C, Pinney DF, Pitts B, Roos DS, Srinivasamoorthy G, Stoeckert CJ Jr, Treatman C, Wang H.

Nucleic Acids Res. 2011 Jan;39(Database issue):D612-9. doi: 10.1093/nar/gkq1006. Epub 2010 Oct 24.

18.

Integrative genomic approaches highlight a family of parasite-specific kinases that regulate host responses.

Peixoto L, Chen F, Harb OS, Davis PH, Beiting DP, Brownback CS, Ouloguem D, Roos DS.

Cell Host Microbe. 2010 Aug 19;8(2):208-18. doi: 10.1016/j.chom.2010.07.004.

19.

EuPathDB: a portal to eukaryotic pathogen databases.

Aurrecoechea C, Brestelli J, Brunk BP, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer ET, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Srinivasamoorthy G, Stoeckert CJ Jr, Thibodeau R, Treatman C, Wang H.

Nucleic Acids Res. 2010 Jan;38(Database issue):D415-9. doi: 10.1093/nar/gkp941. Epub 2009 Nov 13.

20.

TriTrypDB: a functional genomic resource for the Trypanosomatidae.

Aslett M, Aurrecoechea C, Berriman M, Brestelli J, Brunk BP, Carrington M, Depledge DP, Fischer S, Gajria B, Gao X, Gardner MJ, Gingle A, Grant G, Harb OS, Heiges M, Hertz-Fowler C, Houston R, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Logan FJ, Miller JA, Mitra S, Myler PJ, Nayak V, Pennington C, Phan I, Pinney DF, Ramasamy G, Rogers MB, Roos DS, Ross C, Sivam D, Smith DF, Srinivasamoorthy G, Stoeckert CJ Jr, Subramanian S, Thibodeau R, Tivey A, Treatman C, Velarde G, Wang H.

Nucleic Acids Res. 2010 Jan;38(Database issue):D457-62. doi: 10.1093/nar/gkp851. Epub 2009 Oct 20.

21.

Pyruvate kinase type-II isozyme in Plasmodium falciparum localizes to the apicoplast.

Maeda T, Saito T, Harb OS, Roos DS, Takeo S, Suzuki H, Tsuboi T, Takeuchi T, Asai T.

Parasitol Int. 2009 Mar;58(1):101-5. doi: 10.1016/j.parint.2008.10.005. Epub 2008 Oct 31.

22.

In silico identification of specialized secretory-organelle proteins in apicomplexan parasites and in vivo validation in Toxoplasma gondii.

Chen Z, Harb OS, Roos DS.

PLoS One. 2008;3(10):e3611. doi: 10.1371/journal.pone.0003611. Epub 2008 Oct 31.

23.

PlasmoDB: a functional genomic database for malaria parasites.

Aurrecoechea C, Brestelli J, Brunk BP, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Stoeckert CJ Jr, Treatman C, Wang H.

Nucleic Acids Res. 2009 Jan;37(Database issue):D539-43. doi: 10.1093/nar/gkn814. Epub 2008 Oct 28.

24.

GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis.

Aurrecoechea C, Brestelli J, Brunk BP, Carlton JM, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Miller JA, Morrison HG, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Stoeckert CJ Jr, Sullivan S, Treatman C, Wang H.

Nucleic Acids Res. 2009 Jan;37(Database issue):D526-30. doi: 10.1093/nar/gkn631. Epub 2008 Sep 29.

25.
26.

Initiation and termination of NF-kappaB signaling by the intracellular protozoan parasite Toxoplasma gondii.

Shapira S, Harb OS, Margarit J, Matrajt M, Han J, Hoffmann A, Freedman B, May MJ, Roos DS, Hunter CA.

J Cell Sci. 2005 Aug 1;118(Pt 15):3501-8.

27.

Toxoplasma gondii Hsp90 is a potential drug target whose expression and subcellular localization are developmentally regulated.

Echeverria PC, Matrajt M, Harb OS, Zappia MP, Costas MA, Roos DS, Dubremetz JF, Angel SO.

J Mol Biol. 2005 Jul 22;350(4):723-34.

PMID:
15967463
28.

Multiple functionally redundant signals mediate targeting to the apicoplast in the apicomplexan parasite Toxoplasma gondii.

Harb OS, Chatterjee B, Fraunholz MJ, Crawford MJ, Nishi M, Roos DS.

Eukaryot Cell. 2004 Jun;3(3):663-74.

29.

The NF-kappaB signaling pathway: immune evasion and immunoregulation during toxoplasmosis.

Shapira S, Harb OS, Caamano J, Hunter CA.

Int J Parasitol. 2004 Mar 9;34(3):393-400. Review.

PMID:
15055212
30.

Mining the Plasmodium genome database to define organellar function: what does the apicoplast do?

Roos DS, Crawford MJ, Donald RG, Fraunholz M, Harb OS, He CY, Kissinger JC, Shaw MK, Striepen B.

Philos Trans R Soc Lond B Biol Sci. 2002 Jan 29;357(1417):35-46.

32.

Subcellular localization of acetyl-CoA carboxylase in the apicomplexan parasite Toxoplasma gondii.

Jelenska J, Crawford MJ, Harb OS, Zuther E, Haselkorn R, Roos DS, Gornicki P.

Proc Natl Acad Sci U S A. 2001 Feb 27;98(5):2723-8. Epub 2001 Feb 13. Erratum in: Proc Natl Acad Sci U S A 2002 Mar 5;99(5):3356.

33.

From protozoa to mammalian cells: a new paradigm in the life cycle of intracellular bacterial pathogens.

Harb OS, Gao LY, Abu Kwaik Y.

Environ Microbiol. 2000 Jun;2(3):251-65. Review.

PMID:
11200426
35.

Probing the microenvironment of intracellular bacterial pathogens.

Harb OS, Abu Kwaik Y.

Microbes Infect. 1999 May;1(6):445-53. Review.

PMID:
10602677
36.
37.

Phenotypic modulation by intracellular bacterial pathogens.

Kwaik YA, Harb OS.

Electrophoresis. 1999 Aug;20(11):2248-58. Review.

PMID:
10493129
38.

Signal transduction in the protozoan host Hartmannella vermiformis upon attachment and invasion by Legionella micdadei.

Abu Kwaik Y, Venkataraman C, Harb OS, Gao LY.

Appl Environ Microbiol. 1998 Sep;64(9):3134-9.

39.

Invasion of protozoa by Legionella pneumophila and its role in bacterial ecology and pathogenesis.

Abu Kwaik Y, Gao LY, Stone BJ, Venkataraman C, Harb OS.

Appl Environ Microbiol. 1998 Sep;64(9):3127-33. Review. No abstract available.

42.

Heterogeneity in the attachment and uptake mechanisms of the Legionnaires' disease bacterium, Legionella pneumophila, by protozoan hosts.

Harb OS, Venkataraman C, Haack BJ, Gao LY, Kwaik YA.

Appl Environ Microbiol. 1998 Jan;64(1):126-32.

44.

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