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Journal Articles
- 2022
[j23]Beatrice Amos, Cristina Aurrecoechea, Matthieu Barba
, Ana Barreto, Evelina Y. Basenko, Wojciech Bazant, Robert Belnap, Ann S. Blevins, Ulrike Böhme, John Brestelli, Brian P. Brunk, Mark J. Caddick, Danielle Callan, Lahcen I. Campbell, Mikkel B. Christensen, George K. Christophides, Kathryn Crouch, Kristina Davis, Jeremy D. DeBarry, Ryan Doherty, Yikun Duan, Michael Dunn, Dave Falke, Steve Fisher, Paul Flicek, Brett Fox, Bindu Gajria, Gloria I. Giraldo-Calderón, Omar S. Harb, Elizabeth Harper, Christiane Hertz-Fowler, Mark J. Hickman, Connor Howington, Sufen Hu, Jay C. Humphrey, John Iodice, Andrew R. Jones, John Judkins, Sarah A. Kelly, Jessica C. Kissinger, Dae Kun Kwon, Kristopher Lamoureux, Daniel Lawson, Wei Li, Kallie Lies, Disha Lodha, Jamie Long, Robert M. MacCallum, Gareth Maslen, Mary Ann McDowell, Jaroslaw Nabrzyski, David S. Roos, Samuel S. C. Rund, Stephanie wever Schulman, Achchuthan Shanmugasundram, Vasily Sitnik, Drew Spruill, David Starns, Christian J. Stoeckert Jr., Sheena Shah Tomko, Haiming Wang, Susanne Warrenfeltz, Robert Wieck, Paul A. Wilkinson, Lin Xu, Jie Zheng:
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. Nucleic Acids Res. 50(D1): 898-911 (2022)- 2018
- [j22]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 Res. 46(Database-Issue): D684-D691 (2018) - 2017
- [j21]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 Res. 45(Database-Issue): D581-D591 (2017) - 2016
- [j20]Sascha Steinbiss, Fatima Silva-Franco, Brian P. Brunk, Bernardo Foth, Christiane Hertz-Fowler, Matthew Berriman, Thomas D. Otto:
Companion: a web server for annotation and analysis of parasite genomes. Nucleic Acids Res. 44(Webserver-Issue): W29-W34 (2016) - 2015
- [j19]Andrew S. Warren, Cristina Aurrecoechea, Brian P. Brunk, Prerak Desai, Scott J. Emrich, Gloria I. Giraldo-Calderón, Omar S. Harb, Deborah Hix, Daniel Lawson, Dustin Machi, Chunhong Mao, Michael McClelland, Eric K. Nordberg, Maulik Shukla, Leslie B. Vosshall, Alice R. Wattam, Rebecca Will, Hyun Seung Yoo, Bruno W. S. Sobral:
RNA-Rocket: an RNA-Seq analysis resource for infectious disease research. Bioinform. 31(9): 1496-1498 (2015) - 2013
- [j18]Cristina Aurrecoechea, Ana Barreto, John Brestelli, Brian P. Brunk, Shon Cade, Ryan Doherty, Steve Fischer, Bindu Gajria, Xin Gao, Alan R. Gingle, Gregory R. Grant, Omar S. Harb, Mark Heiges, Sufen Hu, John Iodice, Jessica C. Kissinger, Eileen T. 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 Res. 41(Database-Issue): 684-691 (2013) - 2012
- [j17]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 Res. 40(Database-Issue): 98-108 (2012) - [j16]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 Res. 40(Database-Issue): 675-681 (2012) - 2011
- [j15]Steve Fischer, Cristina Aurrecoechea, Brian P. Brunk, Xin Gao, Omar S. Harb, Eileen T. 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 J. Biol. Databases Curation 2011 (2011) - [j14]Gregory R. Grant, Michael H. Farkas, Angel D. Pizarro, Nicholas F. Lahens, Jonathan Schug, Brian P. Brunk, Christian J. Stoeckert Jr., John B. Hogenesch, Eric A. Pierce:
Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinform. 27(18): 2518-2528 (2011) - [j13]Cristina Aurrecoechea, Ana Barreto, John Brestelli, Brian P. Brunk, Elisabet V. Caler, Steve Fischer, Bindu Gajria, Xin Gao, Alan R. Gingle, Gregory R. Grant, Omar S. Harb, Mark Heiges, John Iodice, Jessica C. Kissinger, Eileen T. 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 Res. 39(Database-Issue): 612-619 (2011) - 2010
- [j12]Cristina Aurrecoechea, John Brestelli, Brian P. Brunk, Steve Fischer, Bindu Gajria, Xin Gao, Alan R. Gingle, Gregory R. Grant, Omar S. Harb, Mark Heiges, Frank Innamorato, John Iodice, Jessica C. Kissinger, Eileen T. 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 Res. 38(Database-Issue): 415-419 (2010) - [j11]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 R. Gingle, Gregory R. Grant, Omar S. Harb, Mark Heiges, Christiane Hertz-Fowler, Robin Houston, Frank Innamorato, John Iodice, Jessica C. Kissinger, Eileen T. 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 Res. 38(Database-Issue): 457-462 (2010) - 2009
- [j10]Cristina Aurrecoechea, John Brestelli, Brian P. Brunk, Jane M. Carlton, Jennifer Dommer, Steve Fischer, Bindu Gajria, Xin Gao, Alan R. Gingle, Gregory R. Grant, Omar S. Harb, Mark Heiges, Frank Innamorato, John Iodice, Jessica C. Kissinger, Eileen T. 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 Res. 37(Database-Issue): 526-530 (2009) - [j9]Cristina Aurrecoechea, John Brestelli, Brian P. Brunk, Jennifer Dommer, Steve Fischer, Bindu Gajria, Xin Gao, Alan R. Gingle, Gregory R. Grant, Omar S. Harb, Mark Heiges, Frank Innamorato, John Iodice, Jessica C. Kissinger, Eileen T. 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 Res. 37(Database-Issue): 539-543 (2009) - 2008
- [j8]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 Res. 36(Database-Issue): 553-556 (2008) - 2003
- [j7]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 Res. 31(1): 212-215 (2003) - 2002
- [j6]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 Res. 30(1): 87-90 (2002) - 2001
- [j5]Christian J. Stoeckert Jr., Angel D. Pizarro, Elisabetta Manduchi, M. Gibson, Brian P. Brunk, Jonathan Crabtree, Jonathan Schug, Shai Shen-Orr, G. Christian Overton:
A relational schema for both array-based and SAGE gene expression experiments. Bioinform. 17(4): 300-308 (2001) - [j4]Susan B. Davidson, Jonathan Crabtree, Brian P. Brunk, Jonathan Schug, Val Tannen, G. Christian Overton, Christian J. Stoeckert Jr.:
K2/Kleisli and GUS: Experiments in integrated access to genomic data sources. IBM Syst. J. 40(2): 512-531 (2001) - 1999
- [j3]Steve Fischer, Jonathan Crabtree, Brian P. Brunk, M. Gibson, G. Christian Overton:
bioWidgets: data interaction components for genomics. Bioinform. 15(10): 837-846 (1999) - [j2]Christian J. Stoeckert Jr., Fidel Salas, Brian P. Brunk, G. Christian Overton:
EpoDB: a prototype database for the analysis of genes expressed during vertebrate erythropoiesis. Nucleic Acids Res. 27(1): 200-203 (1999) - 1998
- [j1]Fidel Salas, Juergen Haas, Brian P. Brunk, Christian J. Stoeckert Jr., G. Christian Overton:
EpoDB: a database of genes expressed during vertebrate erythropoiesis. Nucleic Acids Res. 26(1): 288-289 (1998)
Conference and Workshop Papers
- 2016
- [c1]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
Coauthor Index
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