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David S. Roos

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2010 – today

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2018
[j25]
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  - journals/nar/OliveiraBCZIFAK18
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  - https://dblp.org/rec/journals/nar/OliveiraBCZIFAK18
Francislon S. Oliveira, John Brestelli, Shon Cade, Jie Zheng, John Iodice, Steve Fischer, Cristina Aurrecoechea, Jessica C. Kissinger, Brian P. Brunk, Christian J. Stoeckert Jr., Gabriel R. Fernandes, David S. Roos, Daniel P. Beiting:
MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments. Nucleic Acids Research 46(Database-Issue): D684-D691 (2018)
2017
[j24]
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  - journals/nar/AurrecoecheaBBB17
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Cristina Aurrecoechea, Ana Barreto, Evelina Y. Basenko, John Brestelli, Brian P. Brunk, Shon Cade, Kathryn Crouch, Ryan Doherty, Dave Falke, Steve Fischer, Bindu Gajria, Omar S. Harb, Mark Heiges, Christiane Hertz-Fowler, Sufen Hu, John Iodice, Jessica C. Kissinger, Cris Lawrence, Wei Li, Deborah F. Pinney, Jane A. Pulman, David S. Roos, Achchuthan Shanmugasundram, Fatima Silva-Franco, Sascha Steinbiss, Christian J. Stoeckert Jr., Drew Spruill, Haiming Wang, Susanne Warrenfeltz, Jie Zheng:
EuPathDB: the eukaryotic pathogen genomics database resource. Nucleic Acids Research 45(Database-Issue): D581-D591 (2017)
2016
[c1]
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  - conf/icbo/ZhengCBRSJAGDSC16
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Jie Zheng, Jashon Cade, Brian P. Brunk, David S. Roos, Christian J. Stoeckert Jr., San James, Emmanuel Arinaitwe, Bryan Greenhouse, Grant Dorsey, Steven Sullivan, Jane M. Carlton, Gabriel Carrasco-Escobar, Dionicia Gamboa, Paula Maguina-Mercedes, Joseph Vinetz:
Malaria Study Data Integration and Information Retrieval Based on OBO Foundry Ontologies. ICBO/BioCreative 2016
2013
[j23]
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  - journals/nar/AurrecoecheaBBBCDFGGGGHHHIKKLPPRSSWW13
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Cristina Aurrecoechea, Ana Barreto, John Brestelli, Brian P. Brunk, Shon Cade, Ryan Doherty, Steve Fischer, Bindu Gajria, Xin Gao, Alan Gingle, Gregory R. Grant, Omar S. Harb, Mark Heiges, Sufen Hu, John Iodice, Jessica C. Kissinger, Eileen Kraemer, Wei Li, Deborah F. Pinney, Brian Pitts, David S. Roos, Ganesh Srinivasamoorthy, Christian J. Stoeckert Jr., Haiming Wang, Susanne Warrenfeltz:
EuPathDB: The Eukaryotic Pathogen database. Nucleic Acids Research 41(Database-Issue): 684-691 (2013)
[j22]
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  - journals/nar/ZerlotiniAYXLYGPBRKO13
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Adhemar Zerlotini, Eric R. G. R. Aguiar, Fudong Yu, Huayong Xu, Yixue Li, Neil D. Young, Robin B. Gasser, Anna V. Protasio, Matthew Berriman, David S. Roos, Jessica C. Kissinger, Guilherme Oliveira:
SchistoDB: an updated genome resource for the three key schistosomes of humans. Nucleic Acids Research 41(Database-Issue): 728-731 (2013)
2012
[j21]
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  - journals/bioinformatics/DessimozGRSH12
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Christophe Dessimoz, Toni Gabaldón, David S. Roos, Erik L. L. Sonnhammer, Javier Herrero:
Toward community standards in the quest for orthologs. Bioinformatics 28(6): 900-904 (2012)
[j20]
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  - journals/nar/Logan-KlumplerSBRVMCAOSPFMRWTJHPHHBMRCSHB12
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Flora J. Logan-Klumpler, Nishadi De Silva, Ulrike Böhme, Matthew B. Rogers, Giles Velarde, Jacqueline A. McQuillan, Tim Carver, Martin Aslett, Christian Olsen, Sandhya Subramanian, Isabelle Phan, Carol Farris, Siddhartha Mitra, Gowthaman Ramasamy, Haiming Wang, Adrian Tivey, Andrew Jackson, Robin Houston, Julian Parkhill, Matthew T. G. Holden, Omar S. Harb, Brian P. Brunk, Peter J. Myler, David S. Roos, Mark Carrington, Deborah F. Smith, Christiane Hertz-Fowler, Matthew Berriman:
GeneDB - an annotation database for pathogens. Nucleic Acids Research 40(Database-Issue): 98-108 (2012)
[j19]
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  - journals/nar/StajichHBBFHKLNPSR12
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Jason E. Stajich, Todd W. Harris, Brian P. Brunk, John Brestelli, Steve Fischer, Omar S. Harb, Jessica C. Kissinger, Wei Li, Vishal Nayak, Deborah F. Pinney, Christian J. Stoeckert Jr., David S. Roos:
FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Research 40(Database-Issue): 675-681 (2012)
[j18]
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  - journals/nar/MagarinosCCRRSVA12
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María P. Magariños, Santiago J. Carmona, Gregory J. Crowther, Stuart A. Ralph, David S. Roos, Dhanasekaran Shanmugam, Wesley C. Van Voorhis, Fernán Agüero:
TDR Targets: a chemogenomics resource for neglected diseases. Nucleic Acids Research 40(Database-Issue): 1118-1127 (2012)
2011
[j17]
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  - journals/biodb/FischerABGHKPTKRS11
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Steve Fischer, Cristina Aurrecoechea, Brian P. Brunk, Xin Gao, Omar S. Harb, Eileen Kraemer, Cary Pennington, Charles Treatman, Jessica C. Kissinger, David S. Roos, Christian J. Stoeckert Jr.:
The strategies WDK: a graphical search interface and web development kit for functional genomics databases. Database 2011 (2011)
[j16]
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  - journals/nar/AurrecoecheaBBBCFGGGGHHIKKLNPPPRSSTW11
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Cristina Aurrecoechea, Ana Barreto, John Brestelli, Brian P. Brunk, Elisabet V. Caler, Steve Fischer, Bindu Gajria, Xin Gao, Alan Gingle, Gregory R. Grant, Omar S. Harb, Mark Heiges, John Iodice, Jessica C. Kissinger, Eileen Kraemer, Wei Li, Vishal Nayak, Cary Pennington, Deborah F. Pinney, Brian Pitts, David S. Roos, Ganesh Srinivasamoorthy, Christian J. Stoeckert Jr., Charles Treatman, Haiming Wang:
AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species. Nucleic Acids Research 39(Database-Issue): 612-619 (2011)
2010
[j15]
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  - journals/bmcbi/MagarinosOCSDRCHNBRVA10
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María P. Magariños, John P. Overington, Santiago J. Carmona, Dhanasekaran Shanmugam, Maria A. Doyle, Stuart A. Ralph, Gregory J. Crowther, Christiane Hertz-Fowler, Solomon Nwaka, Matthew Berriman, David S. Roos, Wesley C. Van Voorhis, Fernán Agüero:
Designing and implementing chemoinformatic approaches in TDR Targets Database: linking genes to chemical compounds in tropical disease causing pathogens. BMC Bioinformatics 11(S-10): O10 (2010)
[j14]
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  - journals/nar/AurrecoecheaBBFGGGGHHIIKKLMNPPRRSSTTW10
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Cristina Aurrecoechea, John Brestelli, Brian P. Brunk, Steve Fischer, Bindu Gajria, Xin Gao, Alan Gingle, Gregory R. Grant, Omar S. Harb, Mark Heiges, Frank Innamorato, John Iodice, Jessica C. Kissinger, Eileen Kraemer, Wei Li, John A. Miller, Vishal Nayak, Cary Pennington, Deborah F. Pinney, David S. Roos, Chris Ross, Ganesh Srinivasamoorthy, Christian J. Stoeckert Jr., Ryan Thibodeau, Charles Treatman, Haiming Wang:
EuPathDB: a portal to eukaryotic pathogen databases. Nucleic Acids Research 38(Database-Issue): 415-419 (2010)
[j13]
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  - journals/nar/AslettAB10
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Martin Aslett, Cristina Aurrecoechea, Matthew Berriman, John Brestelli, Brian P. Brunk, Mark Carrington, Daniel P. Depledge, Steve Fischer, Bindu Gajria, Xin Gao, Malcolm J. Gardner, Alan Gingle, Gregory R. Grant, Omar S. Harb, Mark Heiges, Christiane Hertz-Fowler, Robin Houston, Frank Innamorato, John Iodice, Jessica C. Kissinger, Eileen Kraemer, Wei Li, Flora J. Logan, John A. Miller, Siddhartha Mitra, Peter J. Myler, Vishal Nayak, Cary Pennington, Isabelle Phan, Deborah F. Pinney, Gowthaman Ramasamy, Matthew B. Rogers, David S. Roos, Chris Ross, Dhileep Sivam, Deborah F. Smith, Ganesh Srinivasamoorthy, Christian J. Stoeckert Jr., Sandhya Subramanian, Ryan Thibodeau, Adrian Tivey, Charles Treatman, Giles Velarde, Haiming Wang:
TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Research 38(Database-Issue): 457-462 (2010)

2000 – 2009

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2009
[j12]
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  - journals/nar/AurrecoecheaBBCDFGGGGHHIIKKLMMNPPRRSSTW09
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Cristina Aurrecoechea, John Brestelli, Brian P. Brunk, Jane M. Carlton, Jennifer Dommer, Steve Fischer, Bindu Gajria, Xin Gao, Alan Gingle, Gregory R. Grant, Omar S. Harb, Mark Heiges, Frank Innamorato, John Iodice, Jessica C. Kissinger, Eileen Kraemer, Wei Li, John A. Miller, Hilary G. Morrison, Vishal Nayak, Cary Pennington, Deborah F. Pinney, David S. Roos, Chris Ross, Christian J. Stoeckert Jr., Steven Sullivan, Charles Treatman, Haiming Wang:
GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis. Nucleic Acids Research 37(Database-Issue): 526-530 (2009)
[j11]
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Cristina Aurrecoechea, John Brestelli, Brian P. Brunk, Jennifer Dommer, Steve Fischer, Bindu Gajria, Xin Gao, Alan Gingle, Gregory R. Grant, Omar S. Harb, Mark Heiges, Frank Innamorato, John Iodice, Jessica C. Kissinger, Eileen Kraemer, Wei Li, John A. Miller, Vishal Nayak, Cary Pennington, Deborah F. Pinney, David S. Roos, Chris Ross, Christian J. Stoeckert Jr., Charles Treatman, Haiming Wang:
PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Research 37(Database-Issue): 539-543 (2009)
2008
[j10]
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  - journals/bioinformatics/LiuMRP08
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Qian Liu, Aaron J. Mackey, David S. Roos, Fernando C. N. Pereira:
Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction. Bioinformatics 24(5): 597-605 (2008)
[j9]
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  - journals/bmcbi/LiuCPR08
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Qian Liu, Koby Crammer, Fernando C. N. Pereira, David S. Roos:
Reranking candidate gene models with cross-species comparison for improved gene prediction. BMC Bioinformatics 9 (2008)
[j8]
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  - journals/nar/GajriaBBDFGHIKMPRSWB08
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Bindu Gajria, Amit Bahl, John Brestelli, Jennifer Dommer, Steve Fischer, Xin Gao, Mark Heiges, John Iodice, Jessica C. Kissinger, Aaron J. Mackey, Deborah F. Pinney, David S. Roos, Christian J. Stoeckert Jr., Haiming Wang, Brian P. Brunk:
ToxoDB: an integrated Toxoplasma gondii database resource. Nucleic Acids Research 36(Database-Issue): 553-556 (2008)
2007
[j7]
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  - journals/bmcbi/PeixotoR07
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Lucia Peixoto, David S. Roos:
Genomic scale analysis of lateral gene transfer in Apicomplexan parasites: insights into early eukaryotic evolution, host-pathogen interaction and drug target development. BMC Bioinformatics 8(S-8) (2007)
[j6]
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  - journals/nar/AurrecoecheaHWWFRMKSRK07
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Cristina Aurrecoechea, Mark Heiges, Haiming Wang, Zhiming Wang, Steve Fischer, Philippa Rhodes, John A. Miller, Eileen Kraemer, Christian J. Stoeckert Jr., David S. Roos, Jessica C. Kissinger:
ApiDB: integrated resources for the apicomplexan bioinformatics resource center. Nucleic Acids Research 35(Database-Issue): 427-430 (2007)
2006
[j5]
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  - journals/nar/ChenMSR06
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Feng Chen, Aaron J. Mackey, Christian J. Stoeckert Jr., David S. Roos:
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Research 34(Database-Issue): 363-368 (2006)
2004
[j4]
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  - journals/nar/LiCFPSSR04
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Li Li, Jonathan Crabtree, Steve Fischer, Deborah F. Pinney, Christian J. Stoeckert Jr., L. David Sibley, David S. Roos:
ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites. Nucleic Acids Research 32(Database-Issue): 326-328 (2004)
2003
[j3]
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  - journals/nar/BahlBCFGGGGKLLMMPRSSW03
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Amit Bahl, Brian P. 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 Jr., Patricia L. Whetzel:
PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data. Nucleic Acids Research 31(1): 212-215 (2003)
[j2]
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  - journals/nar/KissingerGLPR03
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Jessica C. Kissinger, Bindu Gajria, Li Li, Ian T. Paulsen, David S. Roos:
ToxoDB: accessing the Toxoplasma gondii genome. Nucleic Acids Research 31(1): 234-236 (2003)
2002
[j1]
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  - journals/nar/BahlBCCDFGGHKLLMMRSS03
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Amit Bahl, Brian P. Brunk, Ross L. Coppel, Jonathan Crabtree, Sharon J. Diskin, Martin J. Fraunholz, Gregory R. Grant, Dinesh Gupta, Robert L. Huestis, Jessica C. Kissinger, Philip Labo, Li Li, Shannon K. McWeeney, Arthur J. Milgram, David S. Roos, Jonathan Schug, Christian J. Stoeckert Jr.:
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(1): 87-90 (2002)

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