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David S Roos - Publications

Affiliations: 
Biology University of Pennsylvania, Philadelphia, PA, United States 
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54 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 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 Neglected Tropical Diseases. 17: e0011058. PMID 36656904 DOI: 10.1371/journal.pntd.0011058  0.751
2022 Nevers Y, Jones TEM, Jyothi D, Yates B, Ferret M, Portell-Silva L, Codo L, Cosentino S, Marcet-Houben M, Vlasova A, Poidevin L, Kress A, Hickman M, Persson E, Piližota I, ... ... Roos DS, et al. The Quest for Orthologs orthology benchmark service in 2022. Nucleic Acids Research. PMID 35552456 DOI: 10.1093/nar/gkac330  0.393
2021 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. Current Opinion in Insect Science. 50: 100860. PMID 34864248 DOI: 10.1016/j.cois.2021.11.008  0.567
2021 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, ... ... Roos DS, et al. VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. Nucleic Acids Research. PMID 34718728 DOI: 10.1093/nar/gkab929  0.657
2019 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 Research. 3: 1661. PMID 32047873 DOI: 10.12688/gatesopenres.13087.1  0.65
2018 Basenko EY, Pulman JA, Shanmugasundram A, Harb OS, Crouch K, Starns D, Warrenfeltz S, Aurrecoechea C, Stoeckert CJ, Kissinger JC, Roos DS, Hertz-Fowler C. FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes. Journal of Fungi (Basel, Switzerland). 4. PMID 30152809 DOI: 10.3390/Jof4010039  0.762
2018 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 in Molecular Biology (Clifton, N.J.). 1757: 69-113. PMID 29761457 DOI: 10.1007/978-1-4939-7737-6_5  0.715
2017 Oliveira FS, Brestelli J, Cade S, Zheng J, Iodice J, Fischer S, Aurrecoechea C, Kissinger JC, Brunk BP, Stoeckert CJ, Fernandes GR, Roos DS, Beiting DP. MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments. Nucleic Acids Research. PMID 29106667 DOI: 10.1093/Nar/Gkx1027  0.61
2016 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, ... ... Roos DS, et al. EuPathDB: the eukaryotic pathogen genomics database resource. Nucleic Acids Research. PMID 27903906 DOI: 10.1093/Nar/Gkw1105  0.731
2016 Lorenzi H, Khan A, Behnke MS, Namasivayam S, Swapna LS, Hadjithomas M, Karamycheva S, Pinney D, Brunk BP, Ajioka JW, Ajzenberg D, Boothroyd JC, Boyle JP, Dardé ML, Diaz-Miranda MA, ... ... Roos DS, et al. Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes. Nature Communications. 7: 10147. PMID 26738725 DOI: 10.1038/Ncomms10147  0.595
2015 Carlton JM, Volkman SK, Uplekar S, Hupalo DN, Pereira Alves JM, Cui L, Donnelly M, Roos DS, Harb OS, Acosta M, Read A, Ribolla PE, Singh OP, Valecha N, Wassmer SC, et al. Population Genetics, Evolutionary Genomics, and Genome-Wide Studies of Malaria: A View Across the International Centers of Excellence for Malaria Research. The American Journal of Tropical Medicine and Hygiene. 93: 87-98. PMID 26259940 DOI: 10.4269/Ajtmh.15-0049  0.418
2015 Woo YH, Ansari H, Otto TD, Klinger CM, Kolisko M, Michálek J, Saxena A, Shanmugam D, Tayyrov A, Veluchamy A, Ali S, Bernal A, del Campo J, Cihlář J, Flegontov P, ... ... Roos DS, et al. Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. Elife. 4: e06974. PMID 26175406 DOI: 10.7554/Elife.06974  0.471
2015 Krishna R, Xia D, Sanderson S, Shanmugasundram A, Vermont S, Bernal A, Daniel-Naguib G, Ghali F, Brunk BP, Roos DS, Wastling JM, Jones AR. A large-scale proteogenomics study of apicomplexan pathogens-Toxoplasma gondii and Neospora caninum. Proteomics. PMID 25867681 DOI: 10.1002/pmic.201400553  0.325
2014 Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, ... ... Roos DS, et al. Standardized metadata for human pathogen/vector genomic sequences. Plos One. 9: e99979. PMID 24936976 DOI: 10.1371/Journal.Pone.0099979  0.699
2013 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, ... ... Roos DS, et al. EuPathDB: the eukaryotic pathogen database. Nucleic Acids Research. 41: D684-91. PMID 23175615 DOI: 10.1093/Nar/Gks1113  0.707
2013 Zerlotini A, Aguiar ER, Yu F, Xu H, Li Y, Young ND, Gasser RB, Protasio AV, Berriman M, Roos DS, Kissinger JC, Oliveira G. SchistoDB: an updated genome resource for the three key schistosomes of humans. Nucleic Acids Research. 41: D728-31. PMID 23161692 DOI: 10.1093/Nar/Gks1087  0.752
2012 Reid AJ, Vermont SJ, Cotton JA, Harris D, Hill-Cawthorne GA, Könen-Waisman S, Latham SM, Mourier T, Norton R, Quail MA, Sanders M, Shanmugam D, Sohal A, Wasmuth JD, Brunk B, ... ... Roos DS, et al. Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy. Plos Pathogens. 8: e1002567. PMID 22457617 DOI: 10.1371/Journal.Ppat.1002567  0.363
2012 Magariños MP, Carmona SJ, Crowther GJ, Ralph SA, Roos DS, Shanmugam D, Van Voorhis WC, Agüero F. TDR Targets: a chemogenomics resource for neglected diseases. Nucleic Acids Research. 40: D1118-27. PMID 22116064 DOI: 10.1093/Nar/Gkr1053  0.477
2012 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, ... ... Roos D, et al. GeneDB--an annotation database for pathogens. Nucleic Acids Research. 40: D98-108. PMID 22116062 DOI: 10.1093/Nar/Gkr1032  0.63
2012 Stajich JE, Harris T, Brunk BP, Brestelli J, Fischer S, Harb OS, Kissinger JC, Li W, Nayak V, Pinney DF, Stoeckert CJ, Roos DS. FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Research. 40: D675-81. PMID 22064857 DOI: 10.1093/Nar/Gkr918  0.745
2011 Coyne RS, Hannick L, Shanmugam D, Hostetler JB, Brami D, Joardar VS, Johnson J, Radune D, Singh I, Badger JH, Kumar U, Saier M, Wang Y, Cai H, Gu J, ... ... Roos DS, et al. Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control. Genome Biology. 12: R100. PMID 22004680 DOI: 10.1186/Gb-2011-12-10-R100  0.409
2011 Fischer S, Brunk BP, Chen F, Gao X, Harb OS, Iodice JB, Shanmugam D, Roos DS, Stoeckert CJ. Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups. Current Protocols in Bioinformatics. Unit 6.12.1-19. PMID 21901743 DOI: 10.1002/0471250953.Bi0612S35  0.364
2011 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 : the Journal of Biological Databases and Curation. 2011: bar027. PMID 21705364 DOI: 10.1093/Database/Bar027  0.663
2011 Parsons M, Myler PJ, Berriman M, Roos DS, Stuart KD. Identity crisis? The need for systematic gene IDs. Trends in Parasitology. 27: 183-4. PMID 21474380 DOI: 10.1016/J.Pt.2011.02.007  0.493
2011 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, ... ... Roos DS, et al. AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species. Nucleic Acids Research. 39: D612-9. PMID 20974635 DOI: 10.1093/Nar/Gkq1006  0.721
2010 Bahl A, Davis PH, Behnke M, Dzierszinski F, Jagalur M, Chen F, Shanmugam D, White MW, Kulp D, Roos DS. A novel multifunctional oligonucleotide microarray for Toxoplasma gondii Bmc Genomics. 11. PMID 20974003 DOI: 10.1186/1471-2164-11-603  0.376
2010 Crowther GJ, Shanmugam D, Carmona SJ, Doyle MA, Hertz-Fowler C, Berriman M, Nwaka S, Ralph SA, Roos DS, Van Voorhis WC, Agüero F. Identification of attractive drug targets in neglected-disease pathogens using an in silico approach. Plos Neglected Tropical Diseases. 4: e804. PMID 20808766 DOI: 10.1371/Journal.Pntd.0000804  0.39
2010 Peixoto L, Chen F, Harb OS, Davis PH, Beiting DP, Brownback CS, Ouloguem D, Roos DS. Integrative genomic approaches highlight a family of parasite-specific kinases that regulate host responses. Cell Host & Microbe. 8: 208-18. PMID 20709297 DOI: 10.1016/J.Chom.2010.07.004  0.382
2010 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, ... ... Roos DS, et al. EuPathDB: a portal to eukaryotic pathogen databases. Nucleic Acids Research. 38: D415-9. PMID 19914931 DOI: 10.1093/Nar/Gkp941  0.614
2010 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, ... ... Roos DS, et al. TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Research. 38: D457-62. PMID 19843604 DOI: 10.1093/Nar/Gkp851  0.732
2009 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, ... ... Roos DS, et al. PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Research. 37: D539-43. PMID 18957442 DOI: 10.1093/Nar/Gkn814  0.75
2009 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, ... ... Roos DS, et al. GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis. Nucleic Acids Research. 37: D526-30. PMID 18824479 DOI: 10.1093/Nar/Gkn631  0.746
2008 Agüero F, Al-Lazikani B, Aslett M, Berriman M, Buckner FS, Campbell RK, Carmona S, Carruthers IM, Chan AW, Chen F, Crowther GJ, Doyle MA, Hertz-Fowler C, Hopkins AL, McAllister G, ... ... Roos DS, et al. Genomic-scale prioritization of drug targets: the TDR Targets database. Nature Reviews. Drug Discovery. 7: 900-7. PMID 18927591 DOI: 10.1038/Nrd2684  0.397
2008 Xia D, Sanderson SJ, Jones AR, Prieto JH, Yates JR, Bromley E, Tomley FM, Lal K, Sinden RE, Brunk BP, Roos DS, Wastling JM. The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation. Genome Biology. 9: R116. PMID 18644147 DOI: 10.1186/Gb-2008-9-7-R116  0.523
2008 Gajria B, Bahl A, Brestelli J, Dommer J, Fischer S, Gao X, Heiges M, Iodice J, Kissinger JC, Mackey AJ, Pinney DF, Roos DS, Stoeckert CJ, Wang H, Brunk BP. ToxoDB: an integrated Toxoplasma gondii database resource. Nucleic Acids Research. 36: D553-6. PMID 18003657 DOI: 10.1093/Nar/Gkm981  0.717
2007 Chen F, Mackey AJ, Vermunt JK, Roos DS. Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes Plos One. 2. PMID 17440619 DOI: 10.1371/Journal.Pone.0000383  0.379
2007 Greene JM, Collins F, Lefkowitz EJ, Roos D, Scheuermann RH, Sobral B, Stevens R, White O, Di Francesco V. National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics. Infection and Immunity. 75: 3212-9. PMID 17420237 DOI: 10.1128/Iai.00105-07  0.392
2007 Vedadi M, Lew J, Artz J, Amani M, Zhao Y, Dong A, Wasney GA, Gao M, Hills T, Brokx S, Qiu W, Sharma S, Diassiti A, Alam Z, Melone M, ... ... Roos D, et al. Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms. Molecular and Biochemical Parasitology. 151: 100-10. PMID 17125854 DOI: 10.1016/J.Molbiopara.2006.10.011  0.355
2007 Aurrecoechea C, Heiges M, Wang H, Wang Z, Fischer S, Rhodes P, Miller J, Kraemer E, Stoeckert CJ, Roos DS, Kissinger JC. ApiDB: integrated resources for the apicomplexan bioinformatics resource center. Nucleic Acids Research. 35: D427-30. PMID 17098930 DOI: 10.1093/Nar/Gkl880  0.655
2006 Stoeckert CJ, Fischer S, Kissinger JC, Heiges M, Aurrecoechea C, Gajria B, Roos DS. PlasmoDB v5: new looks, new genomes. Trends in Parasitology. 22: 543-6. PMID 17029963 DOI: 10.1016/J.Pt.2006.09.005  0.656
2006 Chen F, Mackey AJ, Stoeckert CJ, Roos DS. OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups Nucleic Acids Research.. 34. PMID 16381887 DOI: 10.1093/Nar/Gkj123  0.405
2004 Berry AE, Gardner MJ, Caspers GJ, Roos DS, Berriman M. Curation of the Plasmodium falciparum genome Trends in Parasitology. 20: 548-552. PMID 15522662 DOI: 10.1016/J.Pt.2004.09.003  0.494
2004 Matrajt M, Platt CD, Sagar AD, Lindsay A, Moulton C, Roos DS. Transcript initiation, polyadenylation, and functional promoter mapping for the dihydrofolate reductase-thymidylate synthase gene of Toxoplasma gondii. Molecular and Biochemical Parasitology. 137: 229-38. PMID 15383293 DOI: 10.1016/J.Molbiopara.2003.12.015  0.314
2004 Gunasekera AM, Patankar S, Schug J, Eisen G, Kissinger J, Roos D, Wirth DF. Widespread distribution of antisense transcripts in the Plasmodium falciparum genome. Molecular and Biochemical Parasitology. 136: 35-42. PMID 15138065 DOI: 10.1016/J.Molbiopara.2004.02.007  0.631
2004 Li L, Crabtree J, Fischer S, Pinney D, Stoeckert CJ, Sibley LD, Roos DS. ApiEST-DB: Analyzing clustered EST data of the apicomplexan parasites Nucleic Acids Research. 32. PMID 14681425 DOI: 10.1093/Nar/Gkh112  0.48
2003 Li L, Stoeckert CJ, Roos DS. OrthoMCL: Identification of ortholog groups for eukaryotic genomes Genome Research. 13: 2178-2189. PMID 12952885 DOI: 10.1101/Gr.1224503  0.512
2003 Li L, Brunk BP, Kissinger JC, Pape D, Tang K, Cole RH, Martin J, Wylie T, Dante M, Fogarty SJ, Howe DK, Liberator P, Diaz C, Anderson J, White M, ... ... Roos DS, et al. Gene discovery in the apicomplexa as revealed by EST sequencing and assembly of a comparative gene database. Genome Research. 13: 443-54. PMID 12618375 DOI: 10.1101/Gr.693203  0.56
2003 Kissinger JC, Gajria B, Li L, Paulsen IT, Roos DS. ToxoDB: accessing the Toxoplasma gondii genome. Nucleic Acids Research. 31: 234-6. PMID 12519989 DOI: 10.1093/nar/gkg072  0.694
2003 Bahl A, Brunk B, Crabtree J, Fraunholz MJ, Gajria B, Grant GR, Ginsburg H, Gupta D, Kissinger JC, Labo P, Li L, Mailman MD, Milgram AJ, Pearson DS, Roos DS, et al. PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data. Nucleic Acids Research. 31: 212-5. PMID 12519984 DOI: 10.1093/Nar/Gkg081  0.736
2002 Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, ... ... Roos DS, et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature. 419: 498-511. PMID 12368864 DOI: 10.1038/Nature01097  0.475
2002 Kissinger JC, Brunk BP, Crabtree J, Fraunholz MJ, Gajria B, Milgram AJ, Pearson DS, Schug J, Bahl A, Diskin SJ, Ginsburg H, Grant GR, Gupta D, Labo P, Li L, ... ... Roos DS, et al. The Plasmodium genome database. Nature. 419: 490-2. PMID 12368860 DOI: 10.1038/419490A  0.688
2002 Joiner KA, Roos DS. Secretory traffic in the eukaryotic parasite Toxoplasma gondii: less is more. The Journal of Cell Biology. 157: 557-63. PMID 12011107 DOI: 10.1083/jcb.200112144  0.304
2002 Roos DS, Crawford MJ, Donald RG, Fraunholz M, Harb OS, He CY, Kissinger JC, Shaw MK, Striepen B. Mining the Plasmodium genome database to define organellar function: what does the apicoplast do? Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 357: 35-46. PMID 11839180 DOI: 10.1098/rstb.2001.1047  0.663
2002 Bahl A, Brunk B, Coppel RL, Crabtree J, Diskin SJ, Fraunholz MJ, Grant GR, Gupta D, Huestis RL, Kissinger JC, Labo P, Li L, McWeeney SK, Milgram AJ, Roos DS, et al. PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished). Nucleic Acids Research. 30: 87-90. PMID 11752262 DOI: 10.1093/Nar/30.1.87  0.732
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