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EuPathDB: The Eukaryotic Pathogen Genomics Database Resource [chapter]

Susanne Warrenfeltz, Evelina Y. Basenko, Kathryn Crouch, Omar S. Harb, Jessica C. Kissinger, David S. Roos, Achchuthan Shanmugasundram, Fatima Silva-Franco
2018 Msphere  
s=7b88206dd42007c8).  ...  s=859df329f857438e (B) The result table contains a column of Transcript IDs.  ... 
doi:10.1007/978-1-4939-7737-6_5 pmid:29761457 fatcat:c6zfevdra5c7xn7f3qozklsy6i

Ontology Driven Data Collection for EuPathDB

Jie Zheng, Omar S. Harb, Christian J. Stoeckert Jr.
2011 International Conference on Biomedical Ontology  
dblp:conf/icbo/ZhengHS11 fatcat:bsl2rbu5rnc7pmffecu3b2aste

The Eukaryotic Pathogen Databases: A Functional Genomic Resource Integrating Data from Human and Veterinary Parasites [chapter]

Omar S. Harb, David S. Roos
2014 Msphere  
s=a905e36f634f7b42 1. T. cruzi has an expanded family of trans-sialidases.  ...  There are two places where you can enter a gene ID(s): a. The "Gene ID" search box at the top of the home page (Fig. 5a) . b.  ... 
doi:10.1007/978-1-4939-1438-8_1 pmid:25388105 pmcid:PMC6157018 fatcat:ntn2vegwp5hp3b7wbnygjowl4q

Acinetobacter baumannii Infections in Hospitalized Patients, Treatment Outcomes

Diaa Alrahmany, Ahmed F. Omar, Gehan Harb, Wasim S. El El Nekidy, Islam M. Ghazi
2021 Antibiotics  
Acinetobacter baumannii (AB), an opportunistic pathogen, could develop into serious infections with high mortality and financial burden. The debate surrounding the selection of effective antibiotic treatment necessitates studies to define the optimal approach. This study aims to compare the clinical outcomes of commonly used treatment regimens in hospitalized patients
doi:10.3390/antibiotics10060630 pmid:34070398 fatcat:spnnua54nbdlrh6izlipkqyehi

In Silico Identification of Specialized Secretory-Organelle Proteins in Apicomplexan Parasites and In Vivo Validation in Toxoplasma gondii

ZhongQiang Chen, Omar S. Harb, David S. Roos, Clotilde K. S. Carlow
2008 PLoS ONE  
adhesive domains noted above were extracted from the iPfam [47] database (ftp://ftp.sanger.ac.uk/pub/ databases/Pfam/releases/Pfam20.0/database_files/interactions. txt.gz) if (and only if) PDB structure(s)  ... 
doi:10.1371/journal.pone.0003611 pmid:18974850 pmcid:PMC2575384 fatcat:3f3scutffjhzhhuwy7urkf3vyu

Multiple Functionally Redundant Signals Mediate Targeting to the Apicoplast in the Apicomplexan ParasiteToxoplasma gondii

Omar S. Harb, Bithi Chatterjee, Martin J. Fraunholz, Michael J. Crawford, Manami Nishi, David S. Roos
2004 Eukaryotic Cell  
Other mutations within the TP 672 HARB ET AL. EUKARYOT.  ...  Red highlighting indicates the V-(V/S)-S-F motif that may be associated with release from the ER. The mature FNR gene is indicated, with conserved amino acids shown in red.  ... 
doi:10.1128/ec.3.3.663-674.2004 pmid:15189987 pmcid:PMC420125 fatcat:c26jcedmt5hzjl62z5kge3mlwy

Infections in G6PD-Deficient Hospitalized Patients—Prevalence, Risk Factors, and Related Mortality

Diaa Alrahmany, Ahmed F. Omar, Salima R. S. Al-Maqbali, Gehan Harb, Islam M. Ghazi
2022 Antibiotics  
A C I N E T O B A C T E R S P . E . C O L I K L E B S I E L L A S P . P . M I R A B I L I S P S E U D O M O N A S S P .  ...  Meanwhile, Gram-positive bacteria accounted for (28%) of the cases, mainly CoNS, S. aureus, Enterococcus sp., MRSA, and Streptococcus sp., while fungal infections were detected in 8% of the samples, with  ... 
doi:10.3390/antibiotics11070934 pmid:35884188 pmcid:PMC9312035 fatcat:kd4cczqxofgx3dhihxuy2py3qq

Integrative Genomic Approaches Highlight a Family of Parasite-Specific Kinases that Regulate Host Responses

Lucia Peixoto, Feng Chen, Omar S. Harb, Paul H. Davis, Daniel P. Beiting, Catie Small Brownback, Dinkorma Ouloguem, David S. Roos
2010 Cell Host and Microbe  
. +, putative catalytic triad; S, putative signal peptide or signal anchor; y, nuclear localization signal (low confidence Figure 6 ).  ... 
doi:10.1016/j.chom.2010.07.004 pmid:20709297 pmcid:PMC2963626 fatcat:fxcb2iir2vduniz4rxyuzr4ieu

ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies

Emmanuel Ruhamyankaka, Brian P. Brunk, Grant Dorsey, Omar S. Harb, Danica A. Helb, John Judkins, Jessica C. Kissinger, Brianna Lindsay, David S. Roos, Emmanuel James San, Christian J. Stoeckert, Jie Zheng (+1 others)
2020 Gates Open Research  
As data are selected, the data available for other variables in that Search Wizard step and any downstream steps are dynamically updated so the user can visualize the impact of their selection(s) on other  ... 
doi:10.12688/gatesopenres.13087.2 fatcat:gmul6zzsejgaljkysuvfh5t2zm

Fosmidomycin Uptake into Plasmodium and Babesia-Infected Erythrocytes Is Facilitated by Parasite-Induced New Permeability Pathways

Stefan Baumeister, Jochen Wiesner, Armin Reichenberg, Martin Hintz, Sven Bietz, Omar S. Harb, David S. Roos, Maximilian Kordes, Johannes Friesen, Kai Matuschewski, Klaus Lingelbach, Hassan Jomaa (+2 others)
2011 PLoS ONE  
Citation: Baumeister S, Wiesner J, Reichenberg A, Hintz M, Bietz S, et al. (2011) Fosmidomycin Uptake into Plasmodium and Babesia-Infected Erythrocytes Is Facilitated by Parasite-Induced New Permeability  ...  Real time PCR was performed in triplicates, with 1 cycle of 95uC for 15 min, followed by 40 cycles of 95uC for 15 s, 55uC for 15 s, and 60uC for 45 s.  ...  S. National Institutes of Health, Bethesda, Maryland, USA, http://rsb.info.nih.gov/ij/, 1997-2009) was used. Uptake assays Human erythrocytes/P. falciparum.  ... 
doi:10.1371/journal.pone.0019334 pmid:21573242 pmcid:PMC3087763 fatcat:xgpvam3gevabhdeibylzaqqweq

A Framework for Global Collaborative Data Management for Malaria Research

Juan B. Gutierrez, Edwin D. Charlebois, Christian J. Stoeckert, Steven A. Sullivan, Omar S. Harb, Jie Zheng, Daniel J. Tisch
2015 American Journal of Tropical Medicine and Hygiene  
Omar S. Harb, Jie Zheng, and Christian J. Stoeckert Jr., Institute for Biomedical Informatics, University of Pennsylvania, PA, E-mails: oharb@ upenn.edu, jiezheng@upenn.edu, and stoeckrt@upenn.edu.  ...  s=2d611e1195d75ca7.  ...  s=2d611e1195d75ca7. systems across many sites in low-and middle-income countries; similarly, the Demographic and Health Survey 24 offers comparable nationally representative household surveys from more  ... 
doi:10.4269/ajtmh.15-0003 pmid:26259944 pmcid:PMC4574270 fatcat:r3qsmylxizhavfcuvlxxeueisa

ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies

Emmanuel Ruhamyankaka, Brian P. Brunk, Grant Dorsey, Omar S. Harb, Danica A. Helb, John Judkins, Jessica C. Kissinger, Brianna Lindsay, David S. Roos, Emmanuel James San, Christian J. Stoeckert, Jie Zheng (+1 others)
2019 Gates Open Research  
As data are selected, the data available for other variables in that Search Wizard step and any downstream steps are dynamically updated so the user can visualize the impact of their selection(s) on other  ... 
doi:10.12688/gatesopenres.13087.1 pmid:32047873 pmcid:PMC6993508 fatcat:u3rviq57fncdnlbe65vplnva6i

RNA-Rocket: An RNA-Seq Analysis Resource for Infectious Disease Research [article]

Andrew S. Warren, Cristina Aurrecoechea, Brian Brunk, Prerak Desai, Scott Emrich, Gloria I. Giraldo-Calderón, Omar Harb, Deborah Hix, Daniel Lawson, Dustin Machi, Chunhong Mao, Michael McClelland (+7 others)
2014 biorxiv/medrxiv   pre-print
The site features an interactive concept diagram, which highlights the appropriate processing step(s), based on the concept that the user is interested in.  ... 
doi:10.1101/007963 fatcat:xyrluiosarc4toiu3q24qqiwpy

EuPathDB: a portal to eukaryotic pathogen databases

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 (+14 others)
2009 Nucleic Acids Research  
EuPathDB (http://EuPathDB.org; formerly ApiDB) is an integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. The most recent release of EuPathDB
more » ... ncludes updates and changes affecting data content, infrastructure and the user interface, improving data access and enhancing the user experience. EuPathDB currently supports more than 80 searches and the recentlyimplemented 'search strategy' system enables users to construct complex multi-step searches via a graphical interface. Search results are dynamically displayed as the strategy is constructed or modified, and can be downloaded, saved, revised, or shared with other database users.
doi:10.1093/nar/gkp941 pmid:19914931 pmcid:PMC2808945 fatcat:wvtdhudoo5fgjiclufxahkzhuy

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

Michelle Momany, Antonio Di Pietro, William G. Alexander, Bridget M. Barker, Omar S. Harb, Sophien Kamoun, Francis Martin, J. Chris Pires, Jason E Stajich, Bart P. H. J. Thomma, Sarah Unruh
2015 G3: Genes, Genomes, Genetics  
Nicholas Buchler (Duke University) presented a thought-provoking analysis of the evolution of cell-cycle control in eukaryotes, showing that the SBF transcription factor, a major regulator of the G1/S  ... 
doi:10.1534/g3.115.024158 pmid:27034999 pmcid:PMC4683624 fatcat:mv2thojrwbbgjldhocyoe4xki4
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