Publications

Harb, OS*, McDowell, MA, Roos, DS.  VEuPathDB Resources: A Platform for Free Online Data Exploration, Integration, and Analysis. In: Setubal, J.C., Stadler, P.F., Stoye, J. (eds) Comparative Genomics. Methods in Molecular Biology, vol 2802. 2024 Jun 1. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3838-5_19

 Basenko EY, Shanmugasundram A, Böhme U, Starns D, Wilkinson PA, Davison HR, Crouch K, Maslen G, Harb OS, Amos B, McDowell MA, Kissinger JC, Roos DS, Jones A. What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species. Genetics. 2024 Mar 26:iyae035. doi: 10.1093/genetics/iyae035.

Alvarez-Jarreta J, Amos B, Aurrecoechea C, Bah S, Barba M, Barreto A, Basenko EY, Belnap R, Blevins A, Böhme U, Brestelli J, Brown S, Callan D, Campbell LI, Christophides GK, Crouch K, Davison HR, DeBarry JD, Demko R, Doherty R, Duan Y, Dundore W, Dyer S, Falke D, Fischer S, Gajria B, Galdi D, Giraldo-Calderón GI, Harb OS*, Harper E, Helb D, Howington C, Hu S, Humphrey J, Iodice J, Jones A, Judkins J, Kelly SA, Kissinger JC, Kittur N, Kwon DK, Lamoureux K, Li W, Lodha D, MacCallum RM, Maslen G, McDowell MA, Myers J, Nural MV, Roos DS, Rund SSC, Shanmugasundram A, Sitnik V, Spruill D, Starns D, Tomko SS, Wang H, Warrenfeltz S, Wieck R, Wilkinson PA, Zheng J. VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023. Nucleic Acids Res. 2023 Nov 11.

Shanmugasundram A, Starns D, Böhme U, Amos B, Wilkinson PA, Harb OS, Warrenfeltz S, Kissinger JC, McDowell MA, Roos DS, Crouch K, Jones AR. TriTrypDB: An integrated functional genomics resource for kinetoplastida. PLoS Negl Trop Dis. 2023 Jan;17(1):e0011058.

Giraldo-Calderón GI, Harb OS, Kelly SA, Rund SS, Roos DS, McDowell MA. VectorBase.org updates: bioinformatic resources for invertebrate vectors of human pathogens and related organisms. Curr Opin Insect Sci. 2022 Apr;50:100860. 

Amos B, Aurrecoechea C, Barba M, Barreto A, Basenko EY, Bażant W, Belnap R, Blevins AS, Böhme U, Brestelli J, Brunk BP, Caddick M, Callan D, Campbell L, Christensen MB, Christophides GK, Crouch K, Davis K, DeBarry J, Doherty R, Duan Y, Dunn M, Falke D, Fisher S, Flicek P, Fox B, Gajria B, Giraldo-Calderón GI, Harb OS*, Harper E, Hertz-Fowler C, Hickman MJ, Howington C, Hu S, Humphrey J, Iodice J, Jones A, Judkins J, Kelly SA, Kissinger JC, Kwon DK, Lamoureux K, Lawson D, Li W, Lies K, Lodha D, Long J, MacCallum RM, Maslen G, McDowell MA, Nabrzyski J, Roos DS, Rund SSC, Schulman SW, Shanmugasundram A, Sitnik V, Spruill D, Starns D, Stoeckert CJ, Tomko SS, Wang H, Warrenfeltz S, Wieck R, Wilkinson PA, Xu L, Zheng J. VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. Nucleic Acids Res. 2022 Jan 7;50(D1):D898-D911. 

Ruhamyankaka E, Brunk BP, Dorsey G, Harb OS, Helb DA, Judkins J, Kissinger JC, Lindsay B, Roos DS, San EJ, Stoeckert CJ, Zheng J, Tomko SS. ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies. Gates Open Res. 2019;3:1661. 

Harb OS*, Roos DS. ToxoDB: Functional Genomics Resource for Toxoplasma and Related Organisms. Methods Mol Biol. 2020;2071:27-47.

Harb OS, Kissinger J, Roos D. ToxoDB: the functional genomic resource for Toxoplasma and related organisms. In: Weiss L, Kim K, editors. Toxoplasma gondii [Internet] 3 ed. NA: Academic Press; 2020. Chapter 23; p.1021-1041.

Baldwin TT, Basenko E, Harb OS, Brown NA, Urban M, Hammond-Kosack KE, Bregitzer PP. Sharing mutants and experimental information prepublication using FgMutantDb (https://scabusa.org/FgMutantDb). Fungal Genet Biol. 2018 Jun;115:90-93.

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. FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes. J Fungi (Basel). 2018 Mar 20;4(1).

Warrenfeltz S, Basenko EY, Crouch K, Harb OS, Kissinger JC, Roos DS, Shanmugasundram A, Silva-Franco F. EuPathDB: The Eukaryotic Pathogen Genomics Database Resource. Methods Mol Biol. 2018;1757:69-113.

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. EuPathDB: the eukaryotic pathogen genomics database resource. Nucleic Acids Res. 2017 Jan 4;45(D1):D581-D591.

Harb OS, Boehme U, Crouch K, Ifeonu OO, Roos DS, Silva JC, Silva-Franco F, Svärd S, Tretina K, Weedall G. Genomics. In: Walochnik, J., Duchêne, M. (eds) Molecular Parasitology. Springer, Vienna; 2016; p.3-48.

Gutierrez JB, Harb OS, Zheng J, Tisch DJ, Charlebois ED, Stoeckert CJ, Sullivan SA. A Framework for Global Collaborative Data Management for Malaria Research. Am J Trop Med Hyg. 2015 Sep;93(3 Suppl):124-132. 

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. Population Genetics, Evolutionary Genomics, and Genome-Wide Studies of Malaria: A View Across the International Centers of Excellence for Malaria Research. Am J Trop Med Hyg. 2015 Sep;93(3 Suppl):87-98.

Warren AS, Aurrecoechea C, Brunk B, Desai P, Emrich S, Giraldo-Calderón GI, Harb OS, Hix D, Lawson D, Machi D, Mao C, McClelland M, Nordberg E, Shukla M, Vosshall LB, Wattam AR, Will R, Yoo HS, Sobral B. RNA-Rocket: an RNA-Seq analysis resource for infectious disease research. Bioinformatics. 2015 May 1;31(9):1496-8. 

Harb OS*, Roos DS. The Eukaryotic Pathogen Databases: a functional genomic resource integrating data from human and veterinary parasites. Methods Mol Biol. 2015;1201:1-18.

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. Standardized metadata for human pathogen/vector genomic sequences. PLoS One. 2014;9(6):e99979.

Harb OS*. MicrosporidiaDB: The Functional Genomic Resource for Microsporidia. In: Weiss LM, Becnel JJ, editors. Microsporidia [Internet] 1 ed. Chichester, UK: John Wiley & Sons, Inc.; 2014. p.687-693.

Harb OS*, Roos DS. ToxoDB: An Integrated Functional Genomic Resource for Toxoplasma and Other Sarcocystidae. In: Weiss LM, Kim K, editors. Toxoplasma gondii [Internet] 2 ed. NA: Academic Press; 2014. Chapter 19; p.647-662. 647-662p.

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. EuPathDB: the eukaryotic pathogen database. Nucleic Acids Res. 2013 Jan;41(Database issue):D684-91.

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. FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Res. 2012 Jan;40(Database issue):D675-81.

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. GeneDB--an annotation database for pathogens. Nucleic Acids Res. 2012 Jan;40(Database issue):D98-108. 

Fischer S, Brunk BP, Chen F, Gao X, Harb OS, Iodice JB, Shanmugam D, Roos DS, Stoeckert CJ Jr. Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups. Curr Protoc Bioinformatics. 2011 Sep;Chapter 6:6.12.1-6.12.19. 

Fischer S, Aurrecoechea C, Brunk BP, Gao X, Harb OS, Kraemer ET, Pennington C, Treatman C, Kissinger JC, Roos DS, Stoeckert CJ. The Strategies WDK: a graphical search interface and web development kit for functional genomics databases. Database (Oxford). 2011;2011:bar027. 

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 (2011) AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species. Nucleic Acids Res 39(Database issue): D612-619.

Peixoto L, Chen F, Harb OS*, Davis PH, Beiting DP, Brownback CS, Ouloguem D, Roos DS (2010) Integrative genomic approaches highlight a family of parasite-specific kinases that regulate host responses. Cell Host Microbe 8(2): 208-218.

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 (2010) EuPathDB: a portal to eukaryotic pathogen databases. Nucleic Acids Res 38(Database issue): D415-419.

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 (2010) TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Res 38(Database issue): D457-462.

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 (2008) PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res.

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 (2008) GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis. Nucleic Acids Res.

Singh P, Vydyam P, Fang T, Estrada K, Gonzalez LM, Grande R, Kumar M, Chakravarty S, Berry V, Ranwez V, Carcy B, Depoix D, Sánchez S, Cornillot E, Abel S, Ciampossin L, Lenz T, Harb O, Sanchez-Flores A, Montero E, Le Roch KG, Lonardi S, Mamoun CB. Insights into the evolution, virulence and speciation of Babesia MO1 and Babesia divergens through multiomics analyses. Emerg Microbes Infect. 2024 Dec;13(1):2386136.

Singh P, Lonardi S, Liang Q, Vydyam P, Khabirova E, Fang T, Gihaz S, Thekkiniath J, Munshi M, Abel S, Ciampossin L, Batugedara G, Gupta M, Lu XM, Lenz T, Chakravarty S, Cornillot E, Hu Y, Ma W, Gonzalez LM, Sánchez S, Estrada K, Sánchez-Flores A, Montero E, Harb OS, Le Roch KG, Mamoun CB. (2023) Babesia duncani multi-omics identifies virulence factors and drug targets. Nat Microbiol.

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.  Fosmidomycin uptake into Plasmodium and Babesia-infected erythrocytes is facilitated by parasite-induced new permeability pathways. PLoS One. 2011 May 4;6(5):e19334. 

Maeda T, Saito T, Harb OS, Roos DS, Takeo S, Suzuki H, Tsuboi T, Takeuchi T, Asai T (2008) Pyruvate kinase type-II isozyme in Plasmodium falciparum localizes to the apicoplast. Parasitol Int.

Chen Z, Harb OS*, Roos DS (2008) In silico identification of specialized secretory-organelle proteins in apicomplexan parasites and in vivo validation in Toxoplasma gondii. PLoS ONE 3(10): e3611.

Vanchinathan P, Brewer JL, Harb OS, Boothroyd JC, Singh U (2005) Disruption of a locus encoding a nucleolar zinc finger protein decreases tachyzoite-to-bradyzoite differentiation in Toxoplasma gondii. Infect Immun 73(10): 6680-6688.

Shapira S, Harb OS, Margarit J, Matrajt M, Han J, Hoffmann A, Freedman B, May MJ, Roos DS, Hunter CA (2005) Initiation and termination of NF-kappaB signaling by the intracellular protozoan parasite Toxoplasma gondii. J Cell Sci 118(Pt 15): 3501-3508.

Echeverria PC, Matrajt M, Harb OS, Zappia MP, Costas MA, Roos DS, Dubremetz JF, Angel SO (2005) Toxoplasma gondii Hsp90 is a potential drug target whose expression and subcellular localization are developmentally regulated. J Mol Biol 350(4): 723-734.

Shapira S, Harb OS, Caamano J, Hunter CA (2004) The NF-kappaB signaling pathway: immune evasion and immunoregulation during toxoplasmosis. Int J Parasitol 34(3): 393-400.

Harb OS, Chatterjee B, Fraunholz MJ, Crawford MJ, Nishi M, Roos DS (2004) Multiple functionally redundant signals mediate targeting to the apicoplast in the apicomplexan parasite Toxoplasma gondii. Eukaryot Cell 3(3): 663-674.

Roos DS, Crawford MJ, Donald RG, Fraunholz M, Harb OS, He CY, Kissinger JC, Shaw MK, Striepen B (2002) Mining the Plasmodium genome database to define organellar function: what does the apicoplast do? Philos Trans R Soc Lond B Biol Sci 357(1417): 35-46.

Harb OS and Abu Kwaik, Y. (2002). Legionella in the Environment: Persistence, Evolution, and Pathogenicity. In Encyclopedia of Environmental Microbiology, ISBN 0-471-35450-3 ed. Bitton, G. Wiley, NY.

Tilney LG, Harb OS, Connelly PS, Robinson CG, Roy CR (2001) How the parasitic bacterium Legionella pneumophila modifies its phagosome and transforms it into rough ER: implications for conversion of plasma membrane to the ER membrane. J Cell Sci 114(Pt 24): 4637-4650.

Jelenska J, Crawford MJ, Harb OS, Zuther E, Haselkorn R, Roos DS, Gornicki P (2001) Subcellular localization of acetyl-CoA carboxylase in the apicomplexan parasite Toxoplasma gondii. Proc Natl Acad Sci U S A 98(5): 2723-2728.

Harb OS, Gao LY, Abu Kwaik Y (2000) From protozoa to mammalian cells: a new paradigm in the life cycle of intracellular bacterial pathogens. Environ Microbiol 2(3): 251-265.

Harb OS, Abu Kwaik Y (2000) Characterization of a macrophage-specific infectivity locus (milA) of Legionella pneumophila. Infect Immun 68(1): 368-376.

Harb OS, Abu Kwaik Y (2000) Essential role for the Legionella pneumophila rep helicase homologue in intracellular infection of mammalian cells. Infect Immun 68(12): 6970-6978.

Kwaik YA, Harb OS (1999) Phenotypic modulation by intracellular bacterial pathogens. Electrophoresis 20(11): 2248-2258.

Harb OS, Abu Kwaik Y (1999) Probing the microenvironment of intracellular bacterial pathogens. Microbes Infect 1(6): 445-453.

Harb OS, Venkataraman C, Haack BJ, Gao LY, Kwaik YA (1998) Heterogeneity in the attachment and uptake mechanisms of the Legionnaires' disease bacterium, Legionella pneumophila, by protozoan hosts. Appl Environ Microbiol 64(1): 126-132.

Harb OS, Abu Kwaik Y (1998) Identification of the aspartate-beta-semialdehyde dehydrogenase gene of Legionella pneumophila and characterization of a null mutant. Infect Immun 66(5): 1898-1903.

Gao LY, Harb OS, Kwaik YA (1998) Identification of macrophage-specific infectivity loci (mil) of Legionella pneumophila that are not required for infectivity of protozoa. Infect Immun 66(3): 883-892.

Abu Kwaik Y, Venkataraman C, Harb OS, Gao LY (1998) Signal transduction in the protozoan host Hartmannella vermiformis upon attachment and invasion by Legionella micdadei. Appl Environ Microbiol 64(9): 3134-3139.

 Abu Kwaik Y, Gao LY, Stone BJ, Venkataraman C, Harb OS (1998) Invasion of protozoa by Legionella pneumophila and its role in bacterial ecology and pathogenesis. Appl Environ Microbiol 64(9): 3127-3133.

Gao LY, Harb OS, Abu Kwaik Y (1997) Utilization of similar mechanisms by Legionella pneumophila to parasitize two evolutionarily distant host cells, mammalian macrophages and protozoa. Infect Immun 65(11): 4738-4746.

Abu Kwaik Y, Gao LY, Harb OS, Stone BJ (1997) Transcriptional regulation of the macrophage-induced gene (gspA) of Legionella pneumophila and phenotypic characterization of a null mutant. Mol Microbiol 24(3): 629-642.

Harvey WH, Harb OS, Kosak ST, Sheaffer JC, Lowe LR, Heerema NA (1994) Interferon-alpha-2b downregulation of oncogenes H-ras, c-raf-2, c-kit, c-myc, c-myb and c-fos in ESKOL, a hairy cell leukemic line, results in temporal perturbation of signal transduction cascade. Leuk Res 18(8): 577-585

Keroack C, Cosentino RO, Teixeira TL, Lansink L, Larcombe SD, Davidge B, Serra L, de Graffenried C, Figueiredo LM, Harb OS*, Povelones ML. Scientists swarm into Woods Hole for the 10th Kinetoplastid Molecular Cell Biology Meeting. Trends Parasitol. 2024 Nov 5:S1471-4922(24)00298-8. 

Sheiner L, Harb OS*. MeBoP: Advanced Training in the Biology of Parasitism for Middle Eastern Students. Trends Parasitol. 2019 May;35(5):329-332.

Momany M, Di Pietro A, Alexander WG, Barker BM, Harb OS, Kamoun S, Martin F, Pires JC, Stajich JE, Thomma BP, Unruh S. Meeting Report: Fungal Genomics Meets Social Media: Highlights of the 28th Fungal Genetics Conference at Asilomar. G3 (Bethesda). 2015 Dec;5(12):2523-5.

Contributing author to the Instructor’s Manual accompanying Genes VIII. (2005). ISBN 0-13-144944-3 ed. Benjamin Lewin, Prentice Hall, NJ.

Harb OS Instructor's Manual [to Accompany] Essential Genes [by] Benjamin Lewin (2006). ISBN 0-13-149009-5 ed. Benjamin Lewin, Prentice Hall, NJ.