TitleAuthor(s)Biology Publication?Type of PublicationPublicationYearPublish DateVolume, IssuePagesDOIURLAcknowledges iPlant by Name?Acknowledges Grant #Mentions Atmosphere?Mentions Bisque?Mentions Data Commons?Mentions Data Store?Mentions Discovery Environment?Mentions DNA Subway?Mentions Powered by Program?Mentions Science APIs?Mentions Spacial Data Infrastructure?Comments
Transcriptome-mining for single-copy nuclear markers in fernsRothfels, Carl J., Anders Larsson, Fay-Wei Li, Erin M. Sigel, Layne Huiet, Dylan O. Burge, Markus Ruhsam et al.YesJournalPLoS ONE2013Oct 08 20138, No. 10e76957doi: 10.1371/journal.pone.0076957http://dx.doi.org/10.1371/journal.pone.0076957YYear 6
Obstacles and Avenues Facing Phyloinformatic ResearchPiel, William H.YesConference ProceedingsProceedings of TDWG 20082008Oct 04 200828-29 http://www.tdwg.org/fileadmin/2008conference/documents/Proceedings2008.pdf#page=28YiPlantv1
Understanding angiosperm diversification using small and large phylogenetic treesSmith, Stephen A., Jeremy M. Beaulieu, Alexandros Stamatakis, and Michael J. DonoghueYesJournalAmerican Journal of Botany2011Feb 11 201198, No. 3404-414doi: 10.3732/ajb.1000481http://dx.doi.org/10.3732/ajb.1000481YiPlantv1
RAxML-Light: a tool for computing terabyte phylogeniesStamatakis, Alexandros, Andre J. Aberer, C. Goll, Stephen A. Smith, Simon A. Berger, and Fernando Izquierdo-CarrascoYesJournalBioinformatics2012May 18 201228, No. 152064-2066doi: 10.1093/bioinformatics/bts309http://dx.doi.org/10.1093/bioinformatics/bts309YiPlantv1
The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular PlantsBanks, Jo Ann, Tomoaki Nishiyama, Mitsuyasu Hasebe, John L. Bowman, Michael Gribskov, Claude dePamphilis, Victor A. Albert et alYesJournalScience2011Apr 08 2011332, No. 6032960-963doi: 10.1126/science.1203810http://dx.doi.org/10.1126/science.1203810YiPlantv1
Distributional Changes in the Western Burrowing Owl (Athene cunicularia hypugaea) in North America from 1967 to 2008Macias-Duarte, Alberto, and Courtney J. ConwayYesJournalJournal of Raptor Research2015Mar 01 201549, No. 175-83doi: 10.3356/JRR-14-00004.1http://dx.doi.org/10.3356/JRR-14-00004.1YYear 7
A Credential Store for Multi-tenant Science GatewaysKanewala, Thejaka Amila, Suresh Marru, Jim Basney, and Marlon PierceCluster, Cloud and Grid Computing (CCGrid), 2014 14th IEEE/ACM International Symposium on2014May 29 2014 445-454doi: 10.1109/CCGrid.2014.95http://dx.doi.org/10.1109/CCGrid.2014.95Year 7
Biotechnology and Genomics: Exploiting the Potential of CWRWalley, Peter G., and Jonathan D. MooreYesChapterCrop Wild Relatives and Climate Change2015Aug 31 2015212-223http://eu.wiley.com/WileyCDA/WileyTitle/productCd-1118854330.htmlQ3 2015
Pheno2GRN: a workflow for phenotype to gene network study and reverse engineering comparisonWeinandt, Nick, Laura M. Jackson, Etienne Z. Gnimpieba, and Carol Lushbough Proceeding BCB '14 Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics2014Oct 30 2014797-804doi: 10.1145/2649387.2660851http://dx.doi.org/10.1145/2649387.2660851YesYear 7
Role of Bioinformatic Tools and Databases in Cotton ResearchYu, Jing, and Dorrie MainJournal2015Aug 06 201557doi: 10.2134/agronmonogr57.2013.0043http://dx.doi.org/10.2134/agronmonogr57.2013.0043Q3 2015
A GWAS platform built on iPlant cyber-infrastructureWang, Liya, Doreen Ware, Carol Lushbough, Nirav Merchant, and Lincoln SteinYesJournalbioRxiv2014Feb 20 2014doi: 10.1101/002881http://dx.doi.org/10.1101/002881YYear 6
A genome-wide association study platform built on iPlant cyber-infrastructureWang, Liya, Doreen Ware, Carol Lushbough, Nirav Merchant, and Lincoln SteinYesConcurrency and Computation: Practice and Experience2014Mar 06 2014 doi: 10.1002/cpe.3236http://dx.doi.org/10.1002/cpe.3236Year 6
Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related OntologiesWalls, Ramona L., John Deck, Robert Guralnick, Steve Baskauf, Reed Beaman, Stanley Blum, Shawn Bowers, Pier Luigi Buttigieg, Neil Davies, Dag Endresen, Maria Alejandra Gandolfo, Robert Hanner, Alyssa Janning, Leonard Krishtalka, Andr_a Matsunaga, Peter Midford,Norman Morrison, Äamonn ”. Tuama, Mark Schildhauer, Barry Smith, Brian J. Stucky, Andrea Thomer, John Wieczorek, Jamie Whitacre, and John WooleyYesJournalPLOS ONE2014Mar 03 20149, No. 3e89606doi: 10.1371/journal.pone.0089606http://dx.doi.org/10.1371/journal.pone.0089606YYear 6
CartograTree: connecting tree genomes, phenotypes and environmentVasquez_Gross, Hans A., John J. Yu, Ben Figueroa, Damian DG Gessler, David B. Neale, and Jill L. WegrzynYesJournalMolecular Ecology Resources2013Feb 25 201313, No. 3528-537doi: 10.1111/1755-0998.12067http://dx.doi.org/10.1111/1755-0998.12067YiPlant v1 Final
The Arabidopsis oligopeptidases TOP1 and TOP2 are salicylic acid targets that modulate SA-mediated signaling and the immune responseMoreau, Magali, Timothy Westlake, Giulio Zampogna, George Popescu, Miaoying Tian, Christos Noutsos, and Sorina PopescuYesJournalThe Plant Journal2013Aug 28 2013doi: 10.1111/tpj.12320http://dx.doi.org/10.1111/tpj.12320YiPlant v1 Final
The relationships among GC content, nucleosome occupancy, and exon sizeWang, Liya, Lincoln D. Stein, Doreen WareYesTechnical ReportarXiv preprint2014May 31 2014 http://arxiv.org/pdf/1404.2487.pdfYYear 6
Comprehensive analysis of imprinted genes in maize reveals limited conservation with other species and allelic variation forimprintingWaters, Amanda J., Paul Bilinski, Steve R. Eichten, Matthew W. Vaughn, Jeffrey Ross-Ibarra, Mary Gehring, and Nathan M. SpringerYesTechnical ReportCornel University Open Access e-Print Library (arXiv)2013Dec 31 2013 http://arxiv.org/pdf/1307.7678.pdfYiPlant v1 Final
Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other speciesWaters, Amanda J., Paul Bilinski, Steven R. Eichten, Matthew W. Vaughn, Jeffrey Ross-Ibarra, Mary Gehring, and Nathan M. SpringerYesJournalProceedings of the National Academy of Sciences2013Nov 11 2013 201309182doi: 10.1073/pnas.1309182110http://dx.doi.org/10.1073/pnas.1309182110YYear 6
Systematic land cover bias in Collection 5 MODIS cloud mask and derived products„A global overviewWilson, Adam M., Benoit Parmentier, and Walter JetzYesJournalRemote Sensing of Environment2014Nov 23 2013141149-154doi: 10.1016/j.rse.2013.10.025http://dx.doi.org/10.1016/j.rse.2013.10.025YYear 6
On automatically tagging web documents from examplesWoodward, Nicholas Joel, Weijia Xu, and Kent NorsworthyConference ProceedingsProceeding of of the 35th international ACM SIGIR conference on Research and development in information retrieval2012 1111-1112doi: 10.1145/2348283.2348494http://dx.doi.org/10.1145/2348283.2348494YiPlantv1
Mining for Meaning: Visualization Approaches to Deciphering Arabidopsis Stress Responses in Roots and ShootsZhou, Lecong, Christopher Franck, Kuan Yang, Guillaume Pilot, Lenwood S. Heath, and Ruth GreneYesJournalOMICS: A Journal of Integrative Biology2012Apr 05 201216, No. 4208-228doi: 10.1089/omi.2011.0111http://dx.doi.org/10.1089/omi.2011.0111YYesiPlantv1
A Long PCR-Based Approach for DNA Enrichment Prior to Next-Generation Sequencing for Systematic StudiesUribe-Convers, Simon, Justin R. Duke, Michael J. Moore, and David C. TankYesJournalApplications in Plant Sciences2014Jan 07 20142, No. 1doi: 10.3732/apps.1300063http://dx.doi.org/10.3732/apps.1300063YYear 6
Unleashing the Genome of Brassica RapaTang, Haibao, and Eric LyonsYesJournalFrontiers in Plant Science2012Jul 31 20123172doi: 10.3389/fpls.2012.00172http://dx.doi.org/10.3389/fpls.2012.00172YiPlantv1
Habitat area and climate stability determine geographical variation in plant species range sizesMorueta_Holme, Naia, Brian J. Enquist, Brian J. McGill, Brad Boyle, Peter M. JÀrgensen, Jeffrey E. Ott, Robert K. Peet et al.YesJournalEcology Letters2013Oct 03 2013doi: 10.1111/ele.12184http://dx.doi.org/10.1111/ele.12184YYear 6
Evolutionary Inferences from Phylogenies: A Review of MethodsO'Meara, Brian C.YesJournalAnnual Review of Ecology, Evolution, and Systematics2012Sep 04 201243267-285doi: 10.1146/annurev-ecolsys-110411-160331http://dx.doi.org/10.1146/annurev-ecolsys-110411-160331YiPlantv1
Using the iPlant Collaborative Discovery EnvironmentOliver, Shannon L., Andrew J. Lenards, Roger A. Barthelson, Nirav Merchant, Sheldon J. McKayYesChapterCurrent Protocols in Bioinformatics2013Jun 01 201322-Jandoi: 10.1002/0471250953.bi0122s42http://dx.doi.org/10.1002/0471250953.bi0122s42YiPlant v1 Final
Rex: A toolset for reproducing software experimentsPerianayagam, Somu, Gregory R. Andrews, and John H. HartmanConference ProceedingsProceedings from the 2010 IEEE International Conference on Bioinformatics and Biomedicine2010 613-617doi: 10.1109/BIBM.2010.5706639http://dx.doi.org/10.1109/BIBM.2010.5706639YiPlantv1
A Semantic Foundation for Provenance ManagementRam, Sudha and Jun LiuEditorialJournal on Data Semantics2012Mar 28 20121, No. 117-Novdoi: 10.1007/s13740-012-0002-0http://dx.doi.org/10.1007/s13740-012-0002-0YiPlantv1
EarthEnv-DEM90: A nearly-global, void-free, multi-scale smoothed, 90m digital elevation model from fused ASTER and SRTM dataRobinson, Natalie, James Regetz, and Robert P. GuralnickYesJournalISPRS Journal of Photogrammetry and Remote Sensing2014Nov 28 20138757_67doi: 10.1016/j.isprsjprs.2013.11.002http://dx.doi.org/10.1016/j.isprsjprs.2013.11.002YYear 6
Viral dark matter and virus-host interactions resolved from publicly available microbial genomesRuhfel, Brad R., Matthew A. Gitzendanner, Pamela S. Soltis, Douglas E. Soltis, and J. Gordon BurleighYesJournalBMC evolutionary biology2014Feb 17 201414, No. 123doi: 10.1186/1471-2148-14-23http://dx.doi.org/10.1186/1471-2148-14-23YYear 6
Genome-wide analysis of syntenic gene deletion in the grassesSchnable, James C., Michael Freeling, and Eric LyonsYesJournalGenome Biology and Evolution2012Jan 17 20124, No. 3265-277doi: 10.1093/gbe/evs009http://dx.doi.org/10.1093/gbe/evs009YiPlantv1
iPlant Atmosphere: A Gateway to Cloud Infrastructure for the Plant SciencesSkidmore, Edwin, Seung-jin Kim, Sangeeta Kuchimanchi, Sriramu Singaram, Nirav Merchant, and Dan StanzioneConference ProceedingsProceedings of the 2011 ACM workshop on Gateway computing environmentsPages 59-64.2011 59-64doi: 10.1145/2110486.2110495http://dx.doi.org/10.1145/2110486.2110495YiPlantv1
The iPlant Collaborative: Cyberinfrastructure to Feed the WorldStanzione, DanJournalComputer2011Sep 22 201144, No. 1144-52doi: 10.1109/MC.2011.297http://dx.doi.org/10.1109/MC.2011.297YiPlantv1
A Targeted Enrichment Strategy for Massively Parallel Sequencing of Angiosperm Plastid GenomesStull, Gregory W., Michael J. Moore, Venkata S. Mandala, Norman A. Douglas, Heather-Rose Kates, Xinshuai Qi, Samuel F. Brockington, Pamela S. Soltis, Douglas E. Soltis, and Matthew A. GitzendannerYesJournalApplications in Plant Sciences2013Jan 31 20131, No. 2doi: 10.3732/apps.1200497http://dx.doi.org/10.3732/apps.1200497YiPlant v1 Final
New whole genome de novo assemblies of three divergent strains of rice (O. sativa) documents novel gene space of aus and indicaSchatz, Michael C., Lyza G. Maron, Joshua C. Stein, Alejandro Hernandez Wences, James Gurtowski, Eric Biggers, Hayan Lee et al.YesJournalbioRxiv2014Apr 02 2014doi: 10.1101/003764http://dx.doi.org/10.1101/003764YYear 6
Factors Influencing Adoption and Non-Adoption of Cyberinfrastructure by the Research CommunityBrown, Susan A., and Sherry ThatcherConference ProceedingsProceedings of The 15th Pacific Asia Conference on Information Systems (PACIS 2011), Brisbane, Australia2011 31 http://projects.business.uq.edu.au/pacis2011/papers/PACIS2011-021.pdfYiPlantv1
Linking biological databases semantically for knowledge discoveryRam, Sudha, Kunpeng Zhang, and Wei WeiChapterAdvances in Conceptual Modeling_Challenges and Opportunities, Lecture Notes in Computer Science2008523222-32doi: 10.1007/978-3-540-87991-6_4http://dx.doi.org/10.1007/978-3-540-87991-6_4YiPlantv1
treePL: Divergence time estimation using penalized likelihood for large phylogeniesSmith, Stephen A., and Brian C. OÍMearaYesJournalBioinformatics2012Aug 01 201228, No. 202689-2690doi: 10.1093/bioinformatics/bts492http://dx.doi.org/10.1093/bioinformatics/bts492YiPlantv1
Towards a cyberinfrastructure for the biological sciences: progress, visions and challengesStein, Lincoln D.YesJournalNature Reviews Genetics 92008Sep 01 2008No. 9678-688doi: 10.1038/nrg2414http://dx.doi.org/10.1038/nrg2414YiPlantv1
Localizing triplet periodicity in DNA and cDNA sequencesWang, Liya, and Lincoln SteinYesJournalBMC Bioinformatics2010Nov 08 201011, No. 1550doi: 10.1186/1471-2105-11-550http://dx.doi.org/10.1186/1471-2105-11-550YiPlantv1
A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-SeqWang, Lin, Yaqing Si, Lauren K. Dedow, Ying Shao, Peng Liu, and Thomas P. BrutnellYesJournalPLoS ONE 2011Oct 19 20116, No. 10e26426doi: 10.1371/journal.pone.0026426http://dx.doi.org/10.1371/journal.pone.0026426YiPlantv1
Identifying hidden rate changes in the evolution of a binary morphological character: the evolution of plant habit in campanulid angiospermsBeaulieu, Jeremy M., Brian C. O'Meara and Michael J. DonoghueYesJournalSystems Biology2013May 14 201362, 5725-37doi: 10.1093/sysbio/syt034http://dx.doi.org/10.1093/sysbio/syt034YiPlant v1 Final
Fruit Evolution and Diversification in Campanulid AngiospermsBeaulieu, Jeremy M., Michael J. DonoghueYesJournalInternational Journal of Organic Evolution2013Jul 08 2013 doi: 10.1111/evo.12180http://dx.doi.org/10.1111/evo.12180YiPlant v1 Final
A genome triplication associated with early diversification of the core eudicotsJiao, Yuannian, Jim Leebens-Mack, Saravanaraj Ayyampalayam, John E. Bowers, Michael R. McKain, Joel McNeal, Megan Rolf et alYesGenome Biology2012Jan 26 201213, No. 1R3doi: 10.1186/gb-2012-13-1-r3http://dx.doi.org/10.1186/gb-2012-13-1-r3iPlantv1
Comprehensive data infrastructure for plant bioinformaticsJordan, Chris, Dan Stanzione, Doreen Ware, Jerry Lu, and Christos NoutsosYesConference ProceedingsCluster Computing Workshops and Posters (CLUSTER WORKSHOPS), 2010 IEEE International Conference on2010 5-Jandoi: 10.1109/CLUSTERWKSP.2010.5613093http://dx.doi.org/10.1109/CLUSTERWKSP.2010.5613093YiPlantv1
Leveraging Cloud Infrastructure for Life Sciences Research Laboratories: A Generalized ViewMerchant, Nirav, John Hartman, Sonya Lowry, Andrew Lenards, David Lowenthal, and Edwin SkidmoreYesConference ProceedingsTowards Best Practices In Cloud Computing from OOPSLA092009Dec 31 2009 53-57 http://www.soacloudbestpratices.com/Towards_best_practices_sammensatt_a5.pdf#page=59YiPlantv1
DeMoSt: a Tool for Exploring the Decomposition and the Modular Structure of OWL OntologiesDel Vescovo, Chiara, Pavel Klinov, Bijan Parsia, Ulrike Sattler, and Thomas SchneiderPoster10th International Semantic Web Conference Proceedings,Bonn, Germany2011 http://iswc2011.semanticweb.org/fileadmin/iswc/Papers/PostersDemos/iswc11pd_submission_75.pdfYiPlantv1
FASTS: FAcets Structured Tag Space _ A Novel Approach to Organize and Reuse Social Bookmarking TagsRam, Sudha, and Wei WeiChapterGlobal Persepctives on Design Science Research, Lecture Notes in Computer Science20106105426-438doi: 10.1007/978-3-642-13335-0_29http://dx.doi.org/10.1007/978-3-642-13335-0_29YiPlantv1
How social is social bookmarking?Ram, Sudha, and Wei WeiConference ProceedingsBusiness Applications of Social Network Analysis (BASNA), 2010 IEEE International Workshop on2010Dec 15 2010 8-Jandoi: 10.1109/BASNA.2010.5730302http://dx.doi.org/10.1109/BASNA.2010.5730302YiPlantv1
Managing Knowledge in a Changing Scientific Landscape: The Impact of CyberinfrastructureBrown, Susan A., Sherry Thatcher, and Yan DangConference ProceedingsSystem Sciences (HICSS), 2010 43rd Hawaii International Conference on2010 10-Jandoi: 10.1109/HICSS.2010.263http://dx.doi.org/10.1109/HICSS.2010.263YiPlantv1
Decomposition and Modular Structure of BioPortal OntologiesDel Vescovo, Chiara, Damian DG Gessler, Pavel Klinov, Bijan Parsia, Ulrike Sattler, Thomas Schneider, and Andrew WingetYesChapterThe Semantic Web_ISWC 2011, Lecture Notes in Computer Science20117031130-145doi: 10.1007/978-3-642-25073-6_9http://dx.doi.org/10.1007/978-3-642-25073-6_9YiPlantv1
A Posteriori Ontology Engineering for Data-Driven ScienceGessler, Damian DG, Cliff Joslyn and Karin VerspoorYesChapterData-Intensive Science201318215-244YYear 6
SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web servicesGessler, Damian DG, Gary S. Schiltz, Greg D. May, Shulamit Avraham, Christopher D. Town, David Grant, and Rex T. NelsonCJournalBMC Bioinformatics2009Sep 23 200910309doi: 10.1186/1471-2105-10-309http://dx.doi.org/10.1186/1471-2105-10-309YiPlantv1
My-Plant.org: A phylogenetically structured social networkHanlon, Matthew R., Stephen Mock, Praveen Nuthulapati, Michael B. Gonzales, Pamela Soltis, Douglas Soltis, Lucas C. Majure, A. Payton, Brent Mishler, S. Tremblay, T. Madsen, R. Olmstead, R. McCourt, M. Wojciechowski, and Nirav MerchantConference ProceedingsGateway Computing Environments Workshop (GCE)2010 8-Jandoi: 10.1109/GCE.2010.5676118http://dx.doi.org/10.1109/GCE.2010.5676118YiPlantv1
Incrementally Updateable and Persistent Decomposition of OWL OntologiesKlinov, Pavel, Chiara Del Vescovo, and Thomas SchneiderYesConference ProceedingsProceedings of OWL: Experiences and Directions Workshop, CEUR Workshop Proceedings 2012Dec 31 20128497 http://ceur-ws.org/Vol-849/paper_7.pdfYiPlantv1
W7 Model of Provenance and Its Use in the Context of WikipediaLiu, JunDissertationThe University of Arizona Campus Repository, UA Theses and Dissertations, Dissertations2011Dec 31 2011 http://arizona.openrepository.com/arizona/handle/10150/145314YiPlantv1
Who does what: Collaboration patterns in the wikipedia and their impact on article qualityLiu, Jun, and Sudha RamJournalACM Transactions on Management Information Systems (TMIS)2011Jun 01 20112, No. 211doi: 10.1145/1985347.1985352http://dx.doi.org/10.1145/1985347.1985352YiPlantv1
Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for bioinformatics resource discovery and disparate data and service integrationNelson, Rex T., Shulamit Avraham, Randy C. Shoemaker, Gregory D. May, Doreen Ware, and Damian DG GesslerJournalBioData Mining2010Jun 04 20103, No. 13doi: 10.1186/1756-0381-3-3http://dx.doi.org/10.1186/1756-0381-3-3YiPlantv1
A few standing for many: embryo receptor-like kinasesNodine, Michael D., Anthony C. Bryan, Adriana Racolta, Keith V. Jerosky, and Frans E. TaxYesTrends in Plant Science2011Apr 01 201116, No. 4211-217doi: 10.1016/j.tplants.2011.01.005http://dx.doi.org/10.1016/j.tplants.2011.01.005iPlantv1
Provenance Management in BioSciencesRam, Sudha, and Jun LiuChapterAdvances in Conceptual Modeling_Applications and Challenges, Lecture Notes in Computer Science2010641354-64doi: 10.1007/978-3-642-16385-2_8http://dx.doi.org/10.1007/978-3-642-16385-2_8YiPlantv1
Recipes 2.0: Building for Today and TomorrowDooley, Rion, Matthew R. HanlonYesConference ProceedingsProceedings of the 5th International Workshop on Science Gateways (IWSG 2013)2013993, No. 16 http://ceur-ws.org/Vol-993/paper16.pdfYYear 6
Phylogeny, divergence times, and historical biogeography of the angiosperm family SaxifragaceaeDeng, Jia-bin, Bryan T. Drew, Evgeny V. Mavrodiev, Matthew A. Gitzendanner, Pamela S. Soltis, and Douglas E. SoltisYesJournalMolecular Phylogenetics and Evolution2015Feb 01 2015doi: 10.1016/j.ympev.2014.11.011http://dx.doi.org/10.1016/j.ympev.2014.11.011YYear 7
Order-Preserving Incomplete Sux Trees and Order-Preserving IndexesCrochemore, Maxime, Costas S. Iliopoulos, Tomasz Kociumaka, Marcin Kubica, Alessio Langiu, Solon P. Pissis, Jakub Radoszewski, Wojciech Rytter, and Tomasz WalenYesTechnical ReportSpires 2013 draft2013 http://students.mimuw.edu.pl/~kociumaka/files/spire2013_draft.pdfYYear 6
Order-Preserving Sux Trees and Their Algorithmic ApplicationsCrochemore, Maxime, Costas S. Iliopoulos, Tomasz Kociumaka, Marcin Kubica, Alessio Langiu, Solon P. Pissis, Jakub Radoszewski, Wojciech Rytter, and Tomasz WaleYesTechnical ReportCornel University Library2013Mar 27 2013 http://arxiv.org/pdf/1303.6872.pdfYiPlant v1 Final
Software-as-a-Service: The iPlant Foundation APIDooley, Rion, Matthew Vaughn, Dan Stanzione, Steve Terry, and Edwin SkidmoreConference ProceedingsProceedings from the 5th Workshop on Many-Task Computing on Grids and Supercomputers (MTAGS) 20122012 7 http://datasys.cs.iit.edu/events/MTAGS12/p07.pdfYiPlantv1
Your Data, Your Way: The iPlant Foundation API Data ServicesDooley, Rion, Matthew Vaughn, Steven Terry, Dan Stanzione, Edwin Skidmore, Nirav MerchantConference ProceedingsProceedings of The Third International Workshop on Data Intensive Computing in the Clouds (DataCloud 2012)2012 3 http://www.cse.buffalo.edu/faculty/tkosar/DataCloud2012/papers/datacloud2012_paper_3.pdfYiPlantv1
lonomics Atlas - A Tool To Explore Interconnected Ionomic, Genomic and Environmental DataDragut, Eduard C., Mourad Ouzzani, Amgad Madkour, Nabeel Mohamed, Peter Baker, and David E. SaltYesConference ProceedingsProceedings of the 21st ACM international conference on Information and knowledge management2012 2680-2682doi: 10.1145/2396761.2398724http://dx.doi.org/10.1145/2396761.2398724YiPlantv1
Variation in DNA Methylation Patterns is More Common among Maize Inbreds than among TissuesEichten, Steven R., Matthew W. Vaughn, Peter J. Hermanson and Nathan M. SpringerYesJournalThe Plant Genome2013Jan 07 2013doi: 10.3835/plantgenome2012.06.0009http://dx.doi.org/10.3835/plantgenome2012.06.0009YiPlant v1 Final
Spreading of Heterochromatin Is Limited to Specific Families of Maize RetrotransposonsEichten, Steven R., Nathanael A. Ellis, Irina Makarevitch, Cheng-Ting Yeh, Jonathan I. Gent, Lin Guo, Karen M. McGinnis, Xiaoyu Zhang, Patrick S. Schnable, Matthew W. Vaughn, R. Kelly Dawe, Nathan M. SpringerYesJournalPLoS Genetics2012Dec 13 20128, No. 12e1003127doi: 10.1371/journal.pgen.1003127http://dx.doi.org/10.1371/journal.pgen.1003127YiPlantv1
PeakRanger: A cloud-enabled peak caller for ChIP-seq dataFeng, Xin, Robert Grossman, and Lincoln SteinYesJournalBMC Bioinformatics2011May 09 201112, No. 1139doi: 10.1186/1471-2105-12-139http://dx.doi.org/10.1186/1471-2105-12-139YiPlantv1
Simultaneous cell tracking and image alignment in 3D CLSM imagery of growing Arabidopsis thaliana sepalsFick, R.H.J., D. Fedorov, A.H.K. Roeder, B.S. ManjunathYesConference ProceedingsBiomedical Imaging (ISBI), 2013 IEEE 10th International Symposium on2013 914-917doi: 10.1109/ISBI.2013.6556624http://dx.doi.org/10.1109/ISBI.2013.6556624YiPlant v1 Final
The iPlant Collaborative WebsiteCollaborative, iPlantWebsite2008 http://www.iplantcollaborative.orgYiPlantv1
Tree template matching in unranked ordered treesChristou, Michalis, Tomà_ Flouri, Costas S. Iliopoulos, Jan Janou_ek, Bo_ivoj Melichar, Solon P. Pissis, Jan __àrekYesJournalJournal of Discrete Algorithms, Available online 13 February 20132013May 01 20132051-60doi: 10.1016/j.jda.2013.02.001http://dx.doi.org/10.1016/j.jda.2013.02.001YiPlant v1 Final
Computing all subtree repeats in ordered treesChristou, Michalis, Maxime Crochemore, Tomà_ Flouri, Costas S. Iliopoulos, Jan Janou_ek, Bo_ivoj Melichar, and Solon P. PissisYesJournalInformation Processing Letters2012Dec 31 2012112, No. 24958-962doi: 10.1016/j.ipl.2012.09.001http://dx.doi.org/10.1016/j.ipl.2012.09.001YiPlantv1
A Scalable Parallel Implementation of the Neighbor Joining Algorithm for Phylogenetic TreesMcLay, Robert, Dan Stanzione, S. J. Mckay, and Travis WheelerYesConference ProceedingsICCABS Conference, Orlando, FL2011Dec 31 2011 https://pods.iplantcollaborative.org/wiki/download/attachments/7510864/NINJA-Windjammer-pub.pdfYiPlantv1
PUmPER: Phylogenies Updated PerpetuallyIzquierdo-Carrasco, F., J. Cazes, S. A. Smith, and A. StamatakisYesJournalBioinformatics2014Jan 28 2014btu053 http://bioinformatics.oxfordjournals.org/content/early/2014/01/28/bioinformatics.btu053.full.pdfYYear 6
Using the Generic Syteny Browser (GBrowse_syn)McKay, Sheldon J., Ismael A. Vergara, and Jason E. StajichYesChapterCurrent protocols in bioinformatics2010Sep 01 201012-Sepdoi: 10.1002/0471250953.bi0912s31http://dx.doi.org/10.1002/0471250953.bi0912s31YiPlantv1
Comparative genomics with maize and other grasses: from genes to genomes!Schnable, James C., and Eric LyonsYesJournalMaydica2012Sep 01 201256, No. 2 http://www.maydica.org/articles/56_1763.pdfYiPlantv1
Extending alignments with k-mismatches and _-gapsBarton, Carl, Costas S. Iliopoulos, Inbok Lee, Laurent Mouchard, Kunsoo Park, Solon P. PissisYesJournalTheoretical Computer Science2013Jul 01 2013doi: 10.1016/j.tcs.2013.06.012,http://dx.doi.org/10.1016/j.tcs.2013.06.012,YiPlant v1 Final
Naive Binning Improves Phylogenomic AnalysesBayzid, Md Shamsuzzoha, and Tandy WarnowYesJournalBioinformatics2013Jul 09 201329, No. 18227-2284doi: 10.1093/bioinformatics/btt394http://dx.doi.org/10.1093/bioinformatics/btt394YiPlant v1 Final
The leaf-area shrinkage effect can bias paleoclimate and ecology researchBlonder, Benjamin, Vanessa Buzzard, Irena Simova, Lindsey Sloat, Brad Boyle, Rebecca Lipson, Brianna Aguilar-Beaucage et alYesJournalAmerican Journal of Botany2012Oct 15 201299, No. 11756-1763doi: 10.3732/ajb.1200062http://dx.doi.org/10.3732/ajb.1200062YiPlantv1
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Next-generation phenomics for the Tree of LifeBurleigh, J. Gordon, Kenzley Alphonse, Andrew J Alverson, Holly M Bik, Carrine Blank, Andrea L Cirranello, Hong Cui, Marymegan Daly, Thomas G Dietterich, Gail Gasparich, Jed Irvine, Matthew Julius, Seth Kaufman, Edith Law, Jing Liu, Lisa Moore, Maureen A O'Leary, Maria Passarotti, Sonali Ranade, Nancy B Simmons, Dennis W. Stevenson, Robert W Thacker, Edward C Theriot, Sinisa Todorovic, PaÏl M. Velazco, Ramona L Walls, Joanna M Wolfe, Mengjie YuYesJournalPLOS Currents Tree of Life2013Jun 26 20135doi: 10.1371/currents.tol.085c713acafc8711b2ff7010a4b03733http://dx.doi.org/10.1371/currents.tol.085c713acafc8711b2ff7010a4b03733YYear 6
MAKER-P: a tool-kit for the rapid creation, management, and quality control of plant genome annotationsCampbell, Michael, MeiYee Law, Carson Holt, Joshua Stein, Gaurav Moghe, David Hunagel, Jikai Lei et alYesJournalPlant Physiology2013Dec 06 2013164, No. 2513-524doi: 10.1104/pp.113.230144http://dx.doi.org/10.1104/pp.113.230144YYear 6
An Efficient and Scalable Implementation of SNP-Pair Interaction Testing for Genetic Association StudiesKoesterke, Lars, Dan Stanzione, Matt Vaughn, Stephen M. Welch, Waclaw Kusnierczyk, Jinliang Yang, Cheng-Ting Yeh, Dan Nettleton, and Patrick S. SchnableYesConference ProceedingsParallel and Distributed Processing Workshops and Phd Forum (IPDPSW), 2011 IEEE International Symposium on2011 523-530doi: 10.1109/IPDPS.2011.190http://dx.doi.org/10.1109/IPDPS.2011.190YiPlantv1
An optimal algorithm for computing all subtree repeats in treesFlouri, TomÇaØs, Kassian Kobert, Solon P. Pissis, and Alexandros StamatakisYesTechnical ReportExelixis Lab Technical Report2013 http://sco.h-its.org/exelixis/pubs/Exelixis-RRDR-2013-5.pdfYiPlant v1 Final
Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissues as Revealed by Deep SequencingKakumanu, AkshayYesMaster's ThesisDigital Library and Archives, Electronic Theses and Dissertations at Virginia Tech2012Jun 28 2012etd-07062012-131158 http://scholar.lib.vt.edu/theses/available/etd-07062012-131158/YiPlantv1
Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissue Revealed by RNA-SeqKakumanu, Akshay, Madana MR Ambavaram, Curtis Klumas, Arjun Krishnan, Utlwang Batlang, Elijah Myers, Ruth Grene, and Andy PereiraYesJournalPlant Physiology2012Jul 26 2012160, No. 2846-867doi: 10.1104/pp.112.200444http://dx.doi.org/10.1104/pp.112.200444YiPlantv1
Client-side Backprojection of Presentation Slides into Educational VideoKharitonova, Yekaterina, Qiyam Tung, Alexander Danehy, Alon Efrat, and Kobus BarnardPosterProceedings of the 20th ACM international conference on Multimedia2012 1005-1008doi: 10.1145/2393347.2396368http://dx.doi.org/10.1145/2393347.2396368YiPlantv1
Fast Algorithm for Partial Covers in WordsKociumaka, Tomasz, Solon P. Pissis, Jakub Radoszewski, Wojciech Rytter, and Tomasz WaleChapterCombinatorial Pattern Matching, Lecture Notes in Computer Science2013Dec 31 20137922177-188 http://students.mimuw.edu.pl/~kociumaka/files/cpm2013_paper.pdfYiPlant v1 Final
Cyclotide discovery in Gentianales revisited - identification and characterization of cyclic cystine-knot peptides and their phylogenetic distribution in Rubiaceae plantsKoehbach, Johannes, Alfred F. Attah, Andreas Berger, Roland Hellinger, Toni M. Kutchan, Eric J. Carpenter, Megan Rolf, Mubo A. Sonibare, Jones O. Moody, Gane Ka-Shu Wong, Steven Dessein, Harald Greger, Christian W. GruberYesJournalBiopolymers: Peptide Science2013doi: 10.1002/bip.22328http://dx.doi.org/10.1002/bip.22328YYear 6
Building an environment to facilitate discoveries for plant sciencesLenards, Andrew, Nirav Merchant, and Dan StanzioneConference ProceedingsProceedings of the 2011 ACM workshop on Gateway computing environments2011 51-58doi: 10.1145/2110486.2110494http://dx.doi.org/10.1145/2110486.2110494YiPlantv1
Life science data analysis workflow development using the bioextract server leveraging the iPlant collaborative cyberinfrastructureLushbough, Carol M., Etienne Z. Gnimpieba, and Rion DooleyYesJournalConcurrency and Computation: Practice and Experience2014Feb 27 2014 doi: 10.1002/cpe.3237http://dx.doi.org/10.1002/cpe.3237YYear 6
Angiosperm Phylogeny Based on 18S/26S rDNA Sequence Data: Constructing a Large Data Set Using Next-Generation Sequence DataMaia, Vitor H., Matthew A. Gitzendanner, Pamela S. Soltis, Gane Ka-Shu Wong, and Douglas E. SoltisYesJournalInternational Journal of Plant Sciences2014May 29 2014175, No. 6613-650doi: 10.1086/676675http://www.jstor.org/stable/10.1086/676675YYear 7
Cloud Computing with iPlant AtmosphereMcKay, Sheldon J., Edwin J. Skidmore, Christopher J. LaRose, Andre W. Mercer, and Christos NoutsosJournalCurrent Protocols in Bioinformatics2013Oct 15 201315-Sepdoi: 10.1002/0471250953.bi0915s43http://dx.doi.org/10.1002/0471250953.bi0915s43YYear 6
Structure-Forming Corals and Sponges and Their Use as Fish Habitat in Bering Sea Submarine CanyonsMiller, Robert J., John Hocevar, Robert P. Stone, and Dmitry V. FedorovYesJournalPLoS One2012Mar 21 20127, No. 3e33885doi: 10.1371/journal.pone.0033885http://dx.doi.org/10.1371/journal.pone.0033885YiPlantv1
Phylogenetic Analysis with the iPlant Discovery EnvironmentMatasci, Naim, Sheldon J. McKayYesChapterCurrent Protocols in Bioinformatics2013Jun 01 2013doi: 10.1002/0471250953.bi0613s42http://dx.doi.org/10.1002/0471250953.bi0613s42YYear 6
Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breedingJoshi, Trupti, Michael R. Fitzpatrick, Shiyuan Chen, Yang Liu, Hongxin Zhang, Ryan Z. Endacott, Eric C. Gaudiello, Gary Stacey, Henry T. Nguyen, and Dong XuYesJournalNucleic acids research2013Oct 16 2013gkt905doi: 10.1093/nar/gkt905http://dx.doi.org/10.1093/nar/gkt905YYear 6
Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant TranscriptomesJohnson, Marc TJ, Eric J. Carpenter, Zhijian Tian, Richard Bruskiewich, Jason N. Burris, Charlotte T. Carrigan, Mark W. Chase et alYesJournalPLoS One2012Nov 21 20127, No. 11e50226doi: 10.1371/journal.pone.0050226http://dx.doi.org/10.1371/journal.pone.0050226YiPlantv1
New and E_cient Approaches to the Quasiperiodic Characterisation of a StringFlouri, Tomàs, Costas S. Iliopoulos, Tomasz Kociumaka, Solon P. Pissis, Simon J. Puglisi, William F. Smyth, and Wojciech TyczynskiYesConference ProceedingsProceedings of the Prague Stringology Conference 20122012 78-88 http://www.stringology.org/papers/PSC2012.pdf#page=83YiPlantv1
GapMis-OMP: Pairwise Short-Read Alignment on Multi-core ArchitecturesFlouri, Tomà_, Costas S. Iliopoulos, Kunsoo Park, and Solon P. PissisYesChapterArtificial Intelligence Applications and Innovations2012 593-601doi: 10.1007/978-3-642-33412-2_61http://dx.doi.org/10.1007/978-3-642-33412-2_61YiPlantv1
Enhanced string coveringFlouri, Tomà_, Costas S. Iliopoulos, Tomasz Kociumaka, Solon P. Pissis, Simon J. Puglisi, W. F. Smyth, and Wojciech Tyczy_skiYesJournalTheoretical Computer Science2013Dec 31 2013 http://www.sciencedirect.com/science/article/pii/S0304397513006105YYear 6
Transcriptome map of mouse isochores in embryonic and neonatal cortexFrousios, Kimon, Costas S. Iliopoulos, German Tischler, Sophia Kossida, Solon P. Pissis, and Stilianos ArhondakisYesJournalGenomics2012Feb 01 2012101, No. 2120-124doi: 10.1016/j.ygeno.2012.11.006http://dx.doi.org/10.1016/j.ygeno.2012.11.006YiPlantv1
iPlant SSWAP (Simple Semantic Web Architecture and Protocol) enables semantic pipelines for biodiversity.Gessler, Damian DG, Blazej Bulka, Evren Sirin, Hans Vasquez-Gross, John Yu, and Jill WegrzynYesConference ProceedingsS4BioDiv Semantics for Biodiversity. Proc. of the First Intl Workshop on Semantics for Biodiversity. CEUR Workshop Proceedings.2013979 http://ceur-ws.org/Vol-979/WS_s4biodiv2013_paper_9.pdfYiPlant v1 Final
iPlant Semantic Web Platform uses SSWAP (Simple Semantic Web Architecture and Protocol) to enable Semantic Pipelines across Distributed Web and High Performance Computing ResourcesGessler, Damian DG, Blazej Bulka, Evren Sirin, Yan Kang, Pavel Klinov, Hans Vasquez-Gross, John Yu, and Jill WegrzynPosterSemantic Web Challenge 2012, The 11th International Semantic Web Conferene2012 http://challenge.semanticweb.org/2012/submissions/swc2012_submission_18.pdfYiPlantv1
The iPlant Collaborative: cyberinfrastructure for plant biologyGoff, Stephen A., Matthew Vaughn, Sheldon McKay, Eric Lyons, Ann E. Stapleton, Damian Gessler, Naim Matasci et alJournalFrontiers in Plant Genetics and Genomics2011Jul 25 2011234doi: 10.3389/fpls.2011.00034http://dx.doi.org/10.3389/fpls.2011.00034YiPlantv1
Association between the geographic distribution during the last glacial maximum of Asian wild rice, Oryza rufipogon (Poaceae), and its current genetic variationHuang, Pu, and Barbara A. SchaalYesJournalAmerican Journal of Botany2012Oct 10 201299, No. 111866-1874doi: 10.3732/ajb.1200348http://dx.doi.org/10.3732/ajb.1200348YiPlantv1
Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shapeIchihashi, Yasunori, Jos_ Antonio Aguilar-MartÕnez, Moran Farhi, Daniel H. Chitwood, Ravi Kumar, Lee V. Millon, Jie Peng, Julin N. Maloof, and Neelima R. SinhaYesJournalProceedings of the National Academy of Sciences2014May 14 2014 201402835doi: 10.1073/pnas.1402835111http://dx.doi.org/10.1073/pnas.1402835111YYear 7
Inference of Many-Taxon PhylogeniesIzquierdo-Carrasco, FernandoYesDissertationHeidelberg Institute for Theoretical Studies2014Mar 06 2014 http://sco.h-its.org/exelixis/pubs/dissFernando.pdfYYear 7
A generic Vectorization Scheme and a GPU kernel for the Phylogenetic Likelihood LibraryIzquierdo-Carrasco, Fernando, Nikolaos Alachiotis, Simon Berger, TomaÇs Flouri, Solon P. Pissis, and Alexandros StamatakisYesExelixis Lab Technical Report2013 http://sco.h-its.org/exelixis/pubs/Exelixis-RRDR-2013-3.pdfiPlant v1 Final
It's more than stamp collecting: how genome sequencing can unify biological researchRichards, StephenJournalTrends in Genetics2015May 20 2015doi: 10.1016/j.tig.2015.04.007http://dx.doi.org/10.1016/j.tig.2015.04.007YYear 7
A web semantic for SBML mergeThavappiragasam, MathialakanThesisUniversity of South Dakota2014Nov 25 2014 http://gradworks.umi.com/15/66/1566784.htmlYYesYear 7
Seed dispersal by ungulates as an ecological filter: a trait_based meta_analysisAlbert, Aur_lie, Alistair G. Auffret, Eric Cosyns, Sara AO Cousins, Bram D'hondt, Carsten Eichberg, Amy E. Eycott et alYesJournalOikos2015Apr 04 2015doi: 10.1111/oik.02512http://dx.doi.org/10.1111/oik.02512YYesYear 7
SBMLChecker, a Semantic approach for SBML model reliability evaluationThavappiragasam, Mathialakan, Carol M. Lushbough, and Etienne Z. GnimpiebaYesConference Proceedings2014Dec 06 2014 http://worldcomp-proceedings.com/proc/p2014/BIC7255.pdfYYesYear 7
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Data integration in biological research: an overviewLapatas, Vasileios, Michalis Stefanidakis, Rafael C. Jimenez, Allegra Via, and Maria Victoria SchneiderYesJournalJournal of Biological Research-Thessaloniki2015Sep 02 201522, No. 116-Jandoi: 10.1186/s40709-015-0032-5http://dx.doi.org/10.1186/s40709-015-0032-5YYes
Flash Demo: Atmosphere Cloud Computing - Applied to Visualizing RNA-Seq DataChougule, KapeelConference ProceedingsProceedings of Plant and Animal Genome XXIII2015Jan 12 2015W483 https://pag.confex.com/pag/xxiii/webprogram/Paper17300.htmlYYesYear 7
Accordion: Multi-Scale Recipes for Adaptive Detection of DuplicationLewis, Russell, and John H. HartmanConference ProceedingsIn 7th USENIX Workshop on Hot Topics in Storage and File Systems (HotStorage 15)2015Jul 13 2015https://www.usenix.org/system/files/conference/hotstorage15/hotstorage15-lewis.pdfYYQ3 2015
RNA-seq gene and transcript expression analysis using the BioExtract server and iPlant collaborativeGnimpieba, Etienne A., Abalo Chango, and Carol M. LushboughConference ProceedingsBCB '14 Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics2014Oct 30 2014 661-669doi: 10.1145/2649387.2660822http://dx.doi.org/10.1145/2649387.2660822YYesYear 7
Proximal hyperspectral sensing and data analysis approaches for field-based plant phenomicsThorp, K. R., M. A. Gore, P. Andrade-Sanchez, A. E. Carmo-Silva, S. M. Welch, J. W. White, and A. N. FrenchYesJournalComputers and Electronics in Agriculture2015Oct 31 2015118225-236doi: 10.1016/j.compag.2015.09.005http://dx.doi.org/10.1016/j.compag.2015.09.005YY
Wild-Type N-Ras, Overexpressed in Basal-like Breast Cancer, Promotes Tumor Formation by Inducing IL-8 Secretion via JAK2 ActivationZheng, Ze-Yi, Lin Tian, Wen Bu, Cheng Fan, Xia Gao, Hai Wang, Yi-Hua Liao et alYesJournalCell Reports2015Jul 09 2015doi: 10.1016/j.celrep.2015.06.044http://dx.doi.org/10.1016/j.celrep.2015.06.044YYQ3 2015
Applying high-throughput phenotyping in plant-insect interations: picturing more resistant cropsGoggin, Fiona, L., Argelia Lorence, and Christopher ToppYesJournalCurrent Opinion in Insect Science2015Mar 19 2015doi: 10.1016/j.cois.2015.03.002http://dx.doi.org/10.1016/j.cois.2015.03.002YYesYear 7
The pineapple genome and the evolution of CAM photosynthesisMing, Ray, Robert VanBuren, Ching Man Wai, Haibao Tang, Michael C. Schatz, John E. Bowers, Eric Lyons et alJournalNature genetics2015Nov 02 2015doi: 10.1038/ng.3435http://dx.doi.org/10.1038/ng.3435YYesYes
Flash Demo: Secure, Collaborative, Management of Your Life Sciences Data with the Data StoreDeBarry, JermeyConference ProceedingsProceedings of Plant and Animal Genome XXIII2015Jan 12 2015W485 https://pag.confex.com/pag/xxiii/webprogram/Paper17299.htmlYYesYear 7
Differentially expressed genes fro beef fatty acid profile in Nellore cattleBerton, Mariana P., Marcos V. A. Lemos, Hermenegildo L. J. Chiaia, et al.YesJournalJournal of Animal Science2015Aug 07 201593, Suppl. s3M91http://www.researchgate.net/profile/Ana_Geraldo/publication/280307183_Heat_storage_and_HSP_expression_of_Holstein_females__an_in_vivo_study/links/55b0f3e108aed621ddfd276e.pdfYYesQ3 2015
Integrating image-based phenomics and association analysis to dissect the genetic architecture of temporal salinity responses in riceMalachy, T. Campbell, C. Knecht Avi, Bettina Berger, J. Brien Chris, Dong Wang, and Harkamal WaliaYesJournalPlant Physiology2015Jun 25 2015450doi: 10.1104/pp.15.00450http://dx.doi.org/10.1104/pp.15.00450YYesQ3 2015
AgroPortal: a proposition for ontology-based services in the agronomic domainJonquet, Cl_ment, Esther Dzal_-Yeumo, Elizabeth Arnaud, and Pierre LarmandeConference ProceedingsAtelier IN-OVIVE 3ième _dition2015Jun 29 2015http://www.lirmm.fr/~jonquet/publications/documents/Article_InOvive2015_AgroPortal.pdfYQ3 2015
A community contribution framework for sharing materials data with Materials ProjectHuck, Patrick, Anubhav Jain, Dan Gunter, Donald Winston, and Kristin PerssonIn e-Science (e-Science), 2015 IEEE 11th International Conference on2015Sep 04 2015535-541doi: 10.1109/eScience.2015.75http://dx.doi.org/10.1109/eScience.2015.75YesYesYes
Overivew of the iPlant CollaborativeVaughn, MatthewConference ProceedingsProceedings of Plant and Animal Genome XXIII2015Jan 12 2015 https://pag.confex.com/pag/xxiii/webprogram/Paper17211.htmlYYear 7
Legume information system (LegumeInfo. org): a key component of a set of federated data resources for the legume familyDash, Sudhansu, Jacqueline D. Campbell, Ethalinda KS Cannon, Alan M. Cleary, Wei Huang, Scott R. Kalberer, Vijay Karingula et alYesJournalNucleic Acids Research2015Oct 19 2015gkv1159doi: 10.1093/nar/gkv1159http://dx.doi.org/10.1093/nar/gkv1159YYes
Editorial: Plant and Cell Physicology's 2015 Database IssueOhyanagi, Hajime, Takeshi Obayashi, and Kentaro Yano.YesJournalPlant and Cell Physicology2015Jan 20 201556, No. 16-Aprdoi: 10.1093/pcp/pcu206http://dx.doi.org/10.1093/pcp/pcu206YYesYear 7
Using multi_timescale methods and satellite_derived land surface temperature for the interpolation of daily maximum air temperature in OregonParmentier, Benoit, Brian J. McGill, Adam M. Wilson, James Regetz, Walter Jetz, Robert Guralnick, Mao_Ning Tuanmu, and Mark SchildhauerYesJournalInternational Journal of Climatology2015Jan 27 2015doi: 10.1002/joc.4251http://dx.doi.org/10.1002/joc.4251YYYear 7
Jetstream: a self-provisioned, scalable science and engineering cloud environmentStewart, Craig A., Timothy M. Cockerill, Ian Foster, David Hancock, Nirav Merchant, Edwin Skidmore, Daniel Stanzione et alConference ProceedingsIn Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure2015Aug 03 201529doi: 10.1145/2792745.2792774http://dx.doi.org/10.1145/2792745.2792774YYesQ3 2015
Supplemental Text for The multi-level analysis of Arabidopsis sepal growth reveals that cells are variable in timing of growth but not the maximum relative growth rateTauriello, Gerardo, Heather M. Meyer, Richard S. Smith, Petros Koumoutasakos, and Adrienne H.K. RoederTechnical Report2015Aug 28 2014http://n.ethz.ch/~gerardot/download/CSE/Sepals/Text_S1.pdfYYesQ3 2015
Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four BiomesDocherty, Kathryn M., Hannah M. Borton, Noelle Espinosa, Martha Gebhardt, Juliana Gil-Loaiza, Jessica LM Gutknecht, Patrick W. Maes et alJournalPloS one2015Nov 04 201510, No. 1e0135352doi: 10.1371/journal.pone.0135352http://dx.doi.org/10.1371/journal.pone.0135352YYes
Leveraging iPlant Cyberinfrastructure for a New Data-Driven Research CommunityCarson, James et alConference ProceedingsProceedings of Plant and Animal Genome XXIII2015Jan 12 2015P1113 https://pag.confex.com/pag/xxiii/webprogram/Paper15848.htmlYYear 7
Utilizing iPlant to Unearth Long Non-Coding RNAs and Characterize Their Evolution in the Plant Family BrassicaceaeNelson, Andrew D. et alConference ProceedingsProceedings of Plant and Animal Genome XXIII2015Jan 12 2015W486 https://pag.confex.com/pag/xxiii/webprogram/Paper16865.htmlYYesYesYear 7
Adaptive divergence in the monkey flower Mimulus guttatus is maintained by a chromosomal inversionTwyford, Alex D., and Jannice FriedmanYesJournalInternational Journal of Organic Evolution2015Apr 20 20151558-5646doi: 10.1111/evo.12663http://dx.doi.org/10.1111/evo.12663YYesYear 7
Identification and Development of Data Standards for Maize Field Phenotypic Measurements: Working with the GxE Subgroup of ht eGenomes2Fields InitiativeGardiner, Jack, et al.Conference ProceedingsProceedings from Plant and Animal Genome XXIII2015Jan 12 2015P0516 https://pag.confex.com/pag/xxiii/webprogram/Paper15771.htmlYYesYear 7
Meeting report: advancing practical applications of biodiversity ontologiesWalls, Ramona L., Robert Guralnick, John Deck, Adam Buntzman, Pier L. Buttigieg, Neil Davies, Michael W. Denslow et al.YesJournalStandards in Genomic Sciences2014Dec 08 20149, No. 117doi: 10.1186/1944-3277-9-17http://dx.doi.org/10.1186/1944-3277-9-17YYear 7
A Hybrid Approach to Assemble and Annotate the Brassica rapa Transcriptome in the Cloud through the iPlant Collaborative and XSEDEDevisetty, Upendra KumarConference ProceedingsProceedings of Plant and Animal Genome XXIII2015Jan 12 2015W482 https://pag.confex.com/pag/xxiii/webprogram/Paper17195.htmlYYesYesYesYear 7
Multiple polyploidy events in the early radiation of nodulating and non-nodulating legumesCannon, Steven B., Michael R. McKain, Alex Harkess, Matthew N. Nelson, Sudhansu Dash, Michael K. Deyholos, Yanhui Peng et alJournalMolecular biology and evolution2014Oct 17 2014msu296doi: 10.1093/molbev/msu296http://dx.doi.org/10.1093/molbev/msu296YYesYear 7
Functional Analysis of Your RNAseq DataMcCarthy, Fiona Conference ProceedingsProceedings of Plant and Animal Genome XXIII2015Jan 12 2015W480 https://pag.confex.com/pag/xxiii/webprogram/Paper16866.htmlYYear 7
Genomics and Biological Big Data: Facing Current and Future Challenges around Data and Software Sharing and ReproducibilityGesing, Sandra, Thomas Richard Connor, and Ian TaylorTechnical ReportarXiv preprint arXiv2015Nov 14 20151511.02689http://arxiv.org/pdf/1511.02689.pdfYYesYes
Apache Airavata as a Laboratory Architecture and Case Study for Component-Based Gateway MiddlewareMarru, Suresh, Marlon Pierce, Sudhakar Pamidighantam, and Chathuri Wimalesena.Conference ProceedingsConference Proceedings from The Science of Cyberinfrastructure: Research, Experience, Applications and Models (SCREAM-15), at Portland, OR.2015Jun 25 2015doi: 10.1145/2753524.2753529http://dx.doi.org/10.1145/2753524.2753529YYesQ3 2015
PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid SequencesMirarab Siavash, Nguyen Nam, Sheng Guo, Li-San Wang, Junhyong Kim, and Tandy WarnowJournalJournal of Computational Biology2014Dec 30 2014doi: 10.1089/cmb.2014.0156http://dx.doi.org/10.1089/cmb.2014.0156YYear 7
Optimization Techniques For Next-Generation Sequencing Data AnalysisCaciula, AdrianYesDissertationScholar Works @ Georgia State University, Computer Science Dissertations2014Aug 12 201487 http://scholarworks.gsu.edu/cgi/viewcontent.cgi?article=1088&context=cs_dissYYesYear 7
Viral dark matter and virus_host interactions resolved from publicly available microbial genomesRoux, Simon, Steven J Hallam, Tanja Woyke, Matthew B SullivanJournaleLife2015Jul 22 2015doi: 10.7554/eLife.08490http://dx.doi.org/10.7554/eLife.08490YYesQ3 2015
Using iPlant Tools and Plastome Sequencing As a Springboard into Comparative Genomics: Plastome Organization and Sequence for the Mimosoid Legume Leucaena trichandraBailey, DonovanConference ProceedingsProceedings of Plant and Animal Genome XXIII2015Jan 12 2015W484 https://pag.confex.com/pag/xxiii/webprogram/Paper17194.htmlYYear 7
Developing Content for the Arabidopsis Information PortalVaughn, Matt et al.Conference ProceedingsProceedings from Plant and Animal Genome XXIII2015Jan 12 2015 P0792 https://pag.confex.com/pag/xxiii/webprogram/Paper16142.htmlYYesYear 7
A Cloud-Based Platform for Supporting Research CollaborationMcGregor, A., D. Bennett, S. Majumdar, B. Nandy, J. O. Melendez, M. St-Hilaire, D. Lau, and J. LiuCloud Computing (CLOUD), 2015 IEEE 8th International Conference2015Aug 24 20151107-1110doi: 10.1109/CLOUD.2015.162http://dx.doi.org/10.1109/CLOUD.2015.162YesQ3 2015
Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stressBelamkar, Vikas, Nathan T. Weeks, Arvind K. Bharti, Andrew D. Farmer, Michelle A. Graham, and Steven B. CannonYesJournalBMC genomics2014Nov 03 201415, No. 1950doi: 10.1186/1471-2164-15-950http://dx.doi.org/10.1186/1471-2164-15-950YYesYesYear 7
Data Integration for the Plant Research Community: The Arabidopsis Information PortalCheng, Chia-Yi, et al.Conference ProceedingsProceedings from Plant and Animal Genome XXIII2015Jan 12 2015P0790 https://pag.confex.com/pag/xxiii/webprogram/Paper16112.htmlYYear 7
Population genetics of Setaria viridis, a new model systemHuang, Pu, Maximilian Feldman, Stephan Schroder, Bochra A. Bahri, Xianmin Diao, Hui Zhi, Matt Estep, Ivan Baxter, Katrien M. Devos, and Elizabeth A. KelloggYesJournalMolecular Ecology2014Sep 22 2014doi: 10.1111/mec.12907http://dx.doi.org/10.1111/mec.12907YYYesYear 7
Large Dataset Analysis for Undergraduates: Discovery Environment, RNA-Seq and Leaf Senescence in< em> Arabidopsis thaliana</em>(Green Line)Brusslan, Judy AConference ProceedingsIn Plant and Animal Genome XXIII Conference2015Jan 10 2015 https://pag.confex.com/pag/xxiii/webprogram/Paper17290.htmlYYesYear 7
Transposable Elements, Gene Discovery, and DNA Barcoding (Yellow and Blue Lines)Burnette, James.Conference ProceedingsIn Plant and Animal Genome XXIII Conference2015Jan 10 2015 https://pag.confex.com/pag/xxiii/webprogram/Paper17292.htmlYYesYear 7
Bringing Authentic Genomics Research into the Classroom: Analysis of Maize Stress Response (Green Line)Makarevitch, IrinaConference ProceedingsIn Plant and Animal Genome XXIII Conference2015Jan 10 2015 https://pag.confex.com/pag/xxiii/webprogram/Paper17287.htmlYYesYear 7
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Data mining with iPlant: A meeting report from the 2013 GARNet workshop, Data mining with iPlantMartin, Lisa, Charis Cook, Naim Matasci, Jason Williams and Ruth BastowJournalJournal of Experimental Biology2014Oct 17 2014doi: 10.1093/jxb/eru402http://dx.doi.org/10.1093/jxb/eru402YYYesYesYesYesYear 7
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Concepts in Distributed Data Management or History of the DICE GroupMoore, Reagan W., Arcot Rajasekar, Michael Wan, and Wayne SchroederTechnical Reportirods.org2015Jan 24 2015http://irods.org/wp-content/uploads/2015/01/DICE-History.pdfYYear 7
An interactive tool for semi-automated leaf annotationMinervini, Massimo, Mario Valerio Giuffrida, and Sotirios A. TsaftarisYesConference ProceedingsProceedings of BMVC 20152015Sep 10 2015http://bmvc2015.swansea.ac.uk/proceedings/cvppp/papers/paper006/paper006.pdfYYes
PathRings: a web-based tool for exploration of ortholog and expression data in biological pathwaysZhu, Yongnan, Liang Sun, Alexander Garbarino, Carl Schmidt, Jinglong Fang, and Jian ChenJournalBMC bioinformatics2015May 19 201516, No. 1165doi: 10.1186/s12859-015-0585-1http://dx.doi.org/10.1186/s12859-015-0585-1YYear 7
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An Ontology Approach to Comparative Phenomics in the Plants: Arabidopsis, Tomato, Maize, Rice, Soybean and MedicagoHarper, Lisa et al.Conference ProceedingsIn Proceedings of Plant and Animal Genome XXIII2015Jan 12 2015 P1123 https://pag.confex.com/pag/xxiii/webprogram/Paper15793.htmlYYear 7
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Flash Talk: An Ontology Approach to Comparative Phenomics in PlantsHuala, Eva et alConference ProceedingsProceedings of Plant and Animal Genome XXIII2015Jan 12 2015W487 https://pag.confex.com/pag/xxiii/webprogram/Paper17309.htmlYYear 7
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Science Incubators: Synthesis Centers and Their Role in the Research EcosystemRodrigo, Allen, Susan Alberts, Karen Cranston, Joel Kingsolver, Hilmar Lapp, Craig McClain, Robin Smith, Todd Vision, Jory Weintraub, Brian WiegmannYesJournalPLoS Biology 2013Jan 15 201311, No. 1e1001468doi: 10.1371/journal.pbio.1001468http://dx.doi.org/10.1371/journal.pbio.1001468YiPlant v1 Final
Biology's Dry FutureService, Robert FYesJournalScience Now2013Oct 11 2013342, No. 6155186-189doi: 10.1126/science.342.6155.186http://dx.doi.org/10.1126/science.342.6155.186YYear 6
Survey of Semantic Description of REST APIsVerborgh, Ruben, Andreas Harth, Maria Maleshkova, Steffen StadtmÙller, Thomas Steiner, Mohsen Taheriyan, and Rik Van de WalleText bookIn REST: Advanced Research Topics and Practical Applications2014Dec 05 2013 69-89doi: 10.1007/978-1-4614-9299-3_5http://dx.doi.org/10.1007/978-1-4614-9299-3_5YYear 6
Pollen and Plant Reproduction Biology: Blooming from East to WestCheung, Alice Y., Ravi Palanivelu, Wei-Hua Tang, Hong-Wei Xue and Wei-Cai YangYesJournalMolecular Plant2013Jul 01 20136, No. 4995-997doi: 10.1093/mp/sst108http://dx.doi.org/10.1093/mp/sst108YYear 6
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Color Based Classification of Circular Markers for the Identification of Experimental UnitsNarjala, Lakshmi YesLab ReportKansas State University2013Dec 31 2013 http://krex.k-state.edu/dspace/bitstream/handle/2097/16279/LakshmiNarjala2013.pdf?sequence=1YYear 6
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How to Use the iPlant's Discovery Environment for Your ResearchMcKay, Sheldon B Conference ProceedingsProceedings from Plant and Animal Gemone XX2012Jan 17 2012W420https://pag.confex.com/pag/xx/webprogram/Paper2931.htmlYYesYesiPlantv1
An ontology approach to comparative phenomics in plantsOellrich, Anika, Ramona L. Walls, Ethalinda KS Cannon, Steven B. Cannon, Laurel Cooper, Jack Gardiner, Georgios V. Gkoutos et alYesJournalPlant Methods2015Feb 25 201511, No. 110doi: 10.1186/s13007-015-0053-yhttp://dx.doi.org/10.1186/s13007-015-0053-yYYYesYear 7
SynFind: compiling syntenic regions across any set of genomes on demandTang, Haibao, Matthew D. Bomhoff, Evan Briones, Liangsheng Zhang, James C. Schnable, and Eric LyonsYesJournalGenome biology and evolution2015Nov 20 2015evv219http://gbe.oxfordjournals.org/content/early/2015/11/11/gbe.evv219.full.pdfYYYes
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A minimal model of fire-vegetation feedbacks and disturbance stochasticity generates alternative stable states in grassland_shrubland_woodland systemsBatllori, Enric, David D. Ackerly, and Max A. MortizYesJournalEnvironmental Research Letters2015Mar 19 201510, No. 334018doi: 10.1088/1748-9326/10/3/034018http://dx.doi.org/10.1088/1748-9326/10/3/034018YYear 7
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Examining the causes and consequences of context-specific differential DNA methylation in maizeLi, Qing, Jawon Song, Patrick T. West, Greg Zynda, Steven R. Eichten, Matthew W. Vaughn, and Nathan M. SpringerJournalPlant physiology2015Apr 15 201552doi: 10._1104/_pp._15._00052http:/_/_dx._doi._org/_10._1104/_pp._15._00052YYear 7
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Community Next Steps for Making Globally Unique Identifiers Work for Biocollections DataGuralnick, Robert P., Nico Cellinese, John Deck, Richard L. Pyle, John Kunze, Lyubomir Penev, Ramona Walls, Gregor Hagedorn, Donat Agosti, John Wieczorek, Terry Catapano, Roderic PageYesJournalZooKeys2015Apr 06 2015494133-154doi: 10.3897/zookeys.494.9352http://dx.doi.org/10.3897/zookeys.494.9352YYear 7
Protocol for the Generation of a Transcription Factor Open Reading Frame Collection (TFome)Gray, John, Brett Burdo et alYesJournalbio-protocol2015Aug 05 20155, No. 15http://www.bio-protocol.org/e1547YYesQ3 2015
RNA-Seq Analysis of the Effect of Kanamycin and the ABC Transporter AtWBC19 on Arabidopsis thaliana Seedlings Reveals Changes in Metal ContentMentewab, Ayalew, Kinnari Matheson, Morayo Adebiyi, Shanice Robinson, and Brianna ElstonYesJournalPloS one 2014Oct 13 20149, No. 10e109310doi: 10.1371/journal.pone.0109310http://dx.doir.org/10.1371/journal.pone.0109310YYesYear 7
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A resource for characterizing genome-wide bindng and putative target genes of transciption factors expressed during secondary growth and wood formation in PopulusLiu, Lijun, Trevor Ramsay, Matthew Zinkgraf, David Sundell, Nathaniel Robert Street, Vladimir Filkov, and Andrew Groover.YesJournalThe Plant Journal2015Apr 24 2015doi: 10.1111/tpj.12850http://dx.doi.org/10.1111/tpj.12850YYesYear 7
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From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics DataLi, Jilong, Jie Hou, Lin Sun, Jordan Maximillian Wilkins, Yuan Lu, Chad E. Niederhuth, Benjamin Ryan Merideth et alJournalPLOS One2015Apr 22 2015doi: 10.1371/journal.pone.0125000http://dx.doi.org/10.1371/journal.pone.0125000YYear 7
Next Generation Resequencing of Soybean Germplasm for Trait DiscoveryJoshi, TruptiB PosterIFLRC VI & ICLGG VII Conference2014Jul 06 2014YYear 7
Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active TeachingPeterson, M. P., J. T. Malloy, V. P. Buonaccorsi, and J. H. MardenJournalCourseSource2015Jun 01 2015https://www.researchgate.net/publication/277641426_Teaching_RNAseq_at_Undergraduate_Institutions_A_tutorial_and_R_package_from_the_Genome_Consortium_for_Active_TeachingYQ3 2015
Big Data: A SurveyChen, Min, Shiwen Mao, and Yunhao LiuJournalMobile Networks and Applications2014Jan 22 2014JanuaryJan-39 http://link.springer.com/article/10.1007/s11036-013-0489-0#page-1YYear 6
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Does the climatic variability hypothesis explain the longitudinal range size gradient in North American trees?Donoghue, John B Conference ProceedingsESA 20122012http://
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Contribution of Epigenetic Variation to Expression Changes Among Tissues and GenotypesEichten, Steven R. B Conference ProceedingsProceedings from Plant and Animal Gemone XX2012Jan 17 2012W417https://pag.confex.com/pag/xx/webprogram/Paper2921.htmlYiPlantv1
Identification of SNPs in Water Buffalo using next generation sequencing dataFritz ER, J.E. Koltes, and JM Reecy. B Conference ProceedingsProceedings from Plant and Animal Gemone XXI2013Jan 17 2013W113https://pag.confex.com/pag/xxi/webprogram/Paper6501.htmlYYesiPlantv1
Gene Exression in Inbred and Hybrid Mice, Young and OldGoff, Stephen A., Qi Cai, Janko Nikolich-Zugich, David GalbraithB Conference ProceedingsProceedings from Plant and Animal Gemone XXI2013Jan 15 2013W325https://pag.confex.com/pag/xxi/webprogram/Paper8375.htmlYYesiPlantv1
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Analyzing big data with simple flowcharts and questioning techniquesGoller, C.Conference ProceedingsProceedings from the 111th Annual meeting North Carolina Academy of Science2014Mar 29 2014YYesYear 7
Introducing Genome Browsers, Genome Structure, and Gene AnnotationBuckner, BrentB Conference ProceedingsProceedings from Plant and Animal Gemone XXII2014Jan 11 2014P10952https://pag.confex.com/pag/xxii/webprogram/Paper10952.htmlYYesYear 7
Next-generation plant science: putting big data to workBrauer, Elizabeth K., Dharmendra K. Singh, and Sorina C. PopescuYesJournalGenome Biology2014Jan 15 201415, 301 http://genomebiology.com/2014/15/1/301YYear 6
Toward a Plant Taxonomic Name Resolution ServiceBoyle, Brad, Brian Enquist, Sheldon McKay, William Piel, Jerry Lu, Nicole Hopkins, Kathleen Kennedy, Andrew Lenards, Matthew Helmke, Evan DeablB Conference ProceedingsProceedings from the TDWG 2010 Conference2010http://www.tdwg.org/fileadmin/2010conference/slides/Poster_boyle_iPlant_TNRS.pdfYYesiPlantv1
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UNIT 4.11 Genome Annotation and Curation Using MAKER and MAKER-PCampbell, Michael, Carson Hold, Barry Moore, and Mark YandellLab ProtocolCurrent Protocols in Bioinformatics2014Dec 12 2014doi: 10.1002/0471250953.bi0411s48http://dx.doi.org/10.1002/0471250953.bi0411s48YYear 7
Transport Function of Rice Amino Acid Permeases (AAPs)Taylor, Margaret R., Anke Reinders, and John M. WardJournalPlant and Cell Physiology2015Apr 22 2015pcv053doi: 10.1093/pcp/pcv053http://dx.doi.org/10.1093/pcp/pcv053YYesYear 7
The Arabidopsis Information Portal: A First GlimpseVaughn, MattB Conference ProceedingsProceedings from Plant and Animal Gemone XXII2014Jan 13 2014P11455https://pag.confex.com/pag/xxii/webprogram/Paper11455.htmlYYesYear 7
RESTful API in Life Science Research Systems and Data Integration Challenges: Linking Metabolic Pathway, Metabolic Network, Gene and PublicationGnimpieba, Etienne Z., Brent S. Anderson, Abalo Chango, and Carol M. LushboughJournalJournal of Communication and Computer2013Sep 09 2013101196-1199 http://www.davidpublishing.com/davidpublishing/Upfile/12/9/2013/2013120984556665.pdfYYear 6
Keynote: The iPlant Collaborative: A Life Sciences Cyberinfrastructure for the 21st CenturyStanzione, DanConference ProceedingsCBSB132013http://www.hansmann-lab.com/cbsb13/cbsb13-participants.shtmlYYiPlantv1
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Serving national scientific communities -genome analysis as an example. Stewart, C.A.B Conference ProceedingsProceedings from ZKI-Fruhjahrstagung, Berlin, Deutschland2014Mar 25 2014http://edoc.hu-berlin.de/conferences/zki2014/stewart/PDF/stewart.pdfYYear 7
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Case Study: Enabling Forest Tree Genomics through Association Studies with the use of SSWAPVasquez-Gross, Hans, Jacob Zieve, Damian Gessler, David Neale, and Jill WegrzynB Conference ProceedingsProceedings from Plant and Animal Gemone XXII2014Jan 14 2014W462https://pag.confex.com/pag/xxii/webprogram/Paper12980.htmlYYear 7
Metadata based management and sharing of distributed biomedical dataWang, Fusheng, Cristobal Vergara_Niedermayr, and Peiya LiuJournalInternational Journal of Metadata, Semantics and Ontologies2014Feb 06 20149, No. 142-57doi: 10.1504/IJMSO.2014.059126http://dx.doi.org/10.1504/IJMSO.2014.059126YYear 6
Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breedingXu, DongB Conference ProceedingsProceedings from Plant and Animal Gemone XXII2014Jan 14 2014P9990https://pag.confex.com/pag/xxii/webprogram/Paper9990.htmlYYear 7
Infrastructure for managing and analyzing biological networks derived from collections of plant imagesDas, Abhiram, Alexander Bucksch, and Joshua S. WeitzB Poster2014Dec 31 2014http://files.figshare.com/1667607/dasBigData.pdfYYesYear 7
Using Flatbed Scanners to Collect High-resolution Time-lapsed Images of the Arabidopsis Root Gravitropic ResponseSmith, Halie C., Devon J. Niewohner, Grant D. Dewey, Autumn M. Longo, Tracy L. Guy, Bradley R. Higgins, Sarah B. Daehling, Sarah C. Genrich, Christopher D. Wentworth, and Tessa L. Durham BrooksYesJournalJoVE (Journal of Visualized Experiments)2014Jan 25 201483e50878-e50878doi: 10.3791/50878http://dx.doi.org/10.3791/50878YYear 6
Computational resources to facilitate variant discovery and analysisReecy, James, C. Baes, E. Fritz-Waters, James E. Koltes, M. Dolezal, B. Bapts, C. Flury, H. Signer-Hasler, C. Stricker, Rohan L. Fernando, Dorian J. Garrick, Fritz Schmitz-Hsu, B. Gredler, and Matt Vaughn.Conference ProceedingsIn ADSA-ASAS Midwest Meeting2014Mar 18 201423 https://asas.confex.com/asas/mw14/webprogram/Paper3463.htmlYYear 6
Future of portable devices for plant pathogen diagnosisNezhad, Amir SanatiYesJournalLab on a Chip2014May 20 2014Royal Society of Chemstrydoi: 10.1039/C4LC00487Fhttp://dx.doi.org/10.1039/C4LC00487FYYear 7
iMicrobe: Advancing Clinical and Environmental Microbial Research using the iPlant CyberinfrastructureHurwitz, BonnieB Conference ProceedingsProceedings from Plant and Animal Gemone XXII2014Jan 14 2014P10931https://pag.confex.com/pag/xxii/webprogram/Paper10931.htmlYYear 7
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African Orphan Crops Consortium_a NEPAD-led initiativeMakinde, DiranYesEssayViewpoints, Biosciences for Farming in Africa2014May 31 2014January http://b4fa.org/wp-content/uploads/2014/01/Viewpoints-Makinde.pdfYYear 6
Transcriptomic Analyses and Alternative Splicing Landscapes of Brachypodium Infected with Panicum Mosaic VirusMandadi, Kranthi Kiran, Karen-Beth G. ScholthofB Conference ProceedingsProceedings from Plant and Animal Gemone XXII2014Jan 14 2014P9867https://pag.confex.com/pag/xxii/webprogram/Paper9867.htmlYYear 7
Latest Technology in Irrigation Management in Nursery ProductionMcDonald, John, and Steve HartYesJournalISHS Acta Horticulturae 1014: Proceedings of the International Plant Propagators' Society2014May 31 2014 http://www.actahort.org/members/showpdf?booknrarnr=1014_16YYear 6
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Enabling Phenotypic Image Analysis Using Shared CyberinfrastructureMiller, Nathan B Conference ProceedingsProceedings from Plant and Animal Gemone XX2012Jan 17 2012W418https://pag.confex.com/pag/xx/webprogram/Paper2923.htmlYiPlantv1
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The Plant Ontology: A Tool for Plant GenomicsCooper, Laurel and Pankaj JaiswalChapterPlant Bioinformatics: Methods and Protocols2015Nov 07 2015137489-114doi: 10.1007/978-1-4939-3167-5_5http://dx.doi.org/10.1007/978-1-4939-3167-5_5YYes
Unlimited Thirst for Genome Sequencing, Data Interrpetation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant ImprovementDhanapal, Arun Prabhu and Mahalingam GovindarajYesJournalGenetics Research International2015Mar 18 2015684321http://www.hindawi.com/journals/gri/aa/684321/YYear 7
ASIS&T research data access and preservation summit: Conference summaryMoore, Reagan, and William L. AndersonJournalBulletin of the American Society for Information Science and Technology2010Sep 01 201036, No. 642-45doi: 10.1002/bult.2010.1720360611http://dx.doi.org/10.1002/bult.2010.1720360611YiPlantv1
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The Genomes of All Angiosperms: A Call for a Coordinated Global CensusGalbraith, David W., Jeffrey L. Bennetzen, Elizabeth A. Kellogg, J. Chris Pires, and Pamela S. SoltisYesJournalJournal of Botany2011Aug 22 2011201110doi: 10.1155/2011/646198http://dx.doi.org/10.1155/2011/646198YiPlantv1
Systems Biology: Evolving into the MainstreamMacilwain, ColinYesJournalCell2011Mar 18 2011144, No. 6839-841doi: 10.1016/j.cell.2011.02.044http://dx.doi.org/10.1016/j.cell.2011.02.044YiPlantv1
Advances in the use of next-generation sequence data in plant systematics and evolutionSoltis, D. E., G. Burleigh, W. B. Barbazuk, M. J. Moore, and P. S. SoltisYesConference ProceedingsInternational Symposium on Molecular Markers in Horticulture2009Dec 31 2009859193-206 http://www.actahort.org/books/859/859_23.htmYiPlantv1
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International Climate Resilient Crops Genomics Consortium (ICRCGC) White Paper Application of Genomics to the Production of Climate Resilient Crops: Challenges and opportunitiesOrtiz, Rodomiro, David Edwards, Sean Mayes, Francis C. Ogbonnaya, Chittaranjan Kole, et alYesWhite Paper2014Aug 01 2014 http://climatechangegenomics.org/white_paper.phpYYear 7
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Characterization of a plant gene family expanded in glycine maxSnoderly-Foster, LisaDissertationMissouri University of Science and Technology Thesis2014Jul 14 2014 http://hdl.handle.net/10355/43427YYear 7
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Crop Systems Biology: Where Are We and Where to Go?Yin, Xinyou, and Paul C. StruikChapterCrop Systems Biology2015Nov 16 2015219-227doi: 10.1007/978-3-319-20562-5_10http://dx.doi.org/10.1007/978-3-319-20562-5_10Y
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Viromes, not gene markers for studying dsDNA viral communitiesSullivan, Matthew B.JournalJournal of Virology2014Dec 18 2014doi: 10.1128/JVI.03289-14http://dx.doi.org/10.1128/JVI.03289-14YYear 7
RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modificationsLyu, Ming-Ju A., Udo Gowik, Steve Kelly, Sarah Covshoff, Julia Mallmann, Peter Westhoff, Julian M. Hibberd et alYesJournalBMC Evolutionary Biology2015Jun 15 201515, No. 1116doi: 10.1186/s12862-015-0399-9http://dx.doi.org/10.1186/s12862-015-0399-9YYesQ3 2015
Image Analysis: The New Bottleneck in Plant PhenotypingMiniervini, M., H. Scharr, and S. Tsaftaris.JournalSignal Processing Magazine, IEEE2015Jun 12 201532, No. 4126-131doi: 10.1109/MSP.2015.2405111http://dx.doi.org/10.1109/MSP.2015.2405111YQ3 2015
Opportunities and Challenges for the Life Sciences CommunityKolker, Eugene, Elizabeth Stewart, and Vural OzdemirYesJournalOMICS: A Journal of Integrative Biology2012Mar 03 201216, No. 3138-147doi: 10.1089/omi.2011.0152http://dx.doi.org/10.1089/omi.2011.0152YiPlantv1
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XRAS: Allocations software as a service in XSEDEHart, David L., Amy Schuele, Ester Soriano, Maytal Dahan, and Matthew HanlonConference ProceedingsIn Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment2014Jul 18 2014 65doi: 10.1145/2616498.2616562http://dx.doi.org/10.1145/2616498.2616562YYear 7
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Management and Visualization of Ianimal Quantitative Data Using iPlant and EPIC-CoGeSubramaniam, SabarinathConference ProceedingsIn Proceeds for Plant and Animal Genome XXIII Meeting.2015Jan 10 2015 https://pag.confex.com/pag/xxiii/webprogram/Paper14925.htmlYYesYear 7
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RNA-Seq: a glance at technologies and methodologiesJazayeri, Seyed Mehdi, Luz Marina Melgarejo Munoz, and Hernan Mauricio Romero.JournalActa biol. Colomb.2015Jan 09 201520, No. 223-35doi: 10.15446/abc.v20n2.43639http://dx.doi.org/10.15446/abc.v20n2.43639YYesYear 7
iRODS: Data Sharing Technology Integrating Communities of PracticeMoore, Reagan W., and Arcot RajsekarConference ProceedingsGeoscience and Remote Sensing Symposium (IGARSS), 2010 IEEE International2010 1984-1987doi: 10.1109/IGARSS.2010.5649894http://dx.doi.org/10.1109/IGARSS.2010.5649894YiPlantv1
Extensible Generic Data Management SoftwareMoore, Reagan W.Technical ReportarXiv 2013Dec 31 20131309.5372 http://arxiv.org/abs/1309.5372YiPlant v1 Final
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Gramene 2016: comparative plant genomics and pathway resourcesTello-Ruiz, Marcela K., Joshua Stein, Sharon Wei, Justin Preece, Andrew Olson, Sushma Naithani, Vindhya Amarasinghe et alYesJournalNucleic Acids Research2015Nov 08 2015gkv1179doi: 10.1093/nar/gkv1179http://dx.doi.org/10.1093/nar/gkv1179YYes
Transcriptional analysis of phloem-associated cells of potatoLin, Tian, Coralie C. Lashbrook, Sung K. Cho, Nathaniel M. Butler, Pooja Sharma, Usha Muppirala, Andrew J. Severin, and David J. HannapelYesJournalBMC genomics2015Sep 03 201516, No. 1665doi: 10.1186/s12864-015-1844-2http://dx.doi.org/10.1186/s12864-015-1844-2YYes
DNA Subway Yellow and Blue Lines: TEs, Gene Discovery and DNA BarcodingBurnette, James.Conference ProceedingsProceedings of Plant and Animal Genome XXIII2015Jan 12 2015P1143 https://pag.confex.com/pag/xxiii/webprogram/Paper17293.htmlYYesYear 7
Semantic Bridges for Biodiversity SciencesVillanueva-Rosales, Natalia, Nicholas del Rio, Deana Pennington, and Luis Garnica ChaviraYesChapterIn The Semantic Web-ISWC 20152015Oct 24 2015310-317doi: 10.1007/978-3-319-25010-6_20http://dx.doi.org/10.1007/978-3-319-25010-6_20Y
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BAC-Based Sequencing of the Aegilops tauschii GenomeDvorak, Jan et alConference ProceedingsProceedings of Plant and Animal Genome XXIII2015Jan 10 2015 https://pag.confex.com/pag/xxiii/webprogram/Paper13960.htmlYYear 7
VirSorter: mining viral signal from microbial genomic dataRoux, Simon, Francois Enault, Bonnie L. Hurwitz, and Matthew B. Sullivan.YesJournalPeerJ2015May 28 20153e985doi: 10.7717/peerj.985https://dx.doi.org/10.7717/peerj.985YYesYear 7
The Use of DNA Barcoding in Identification of Genetic Diversity of Fish in Ugwu-Omu Nike River in EnuguNwakanma, C., G. Ude, and M.N. UnachukwuYesJournalNigerian Journal of Biotechnology2015Jun 21 20152927-33doi: 10.4314/njb.v29i1.4http://dx.doi.org/10.4314/njb.v29i1.4YYesQ3 2015
Plant High-Throughput Phenotyping Using Photogrammertry and 3D Modeling TechniquesAn, NanYesDissertationKansas State University2015Nov 09 2015http://krex.k-state.edu/dspace/bitstream/handle/2097/20493/NanAn2015.pdf?sequence=1&isAllowed=yYYes
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Guest editors_ introduction to the first issue on Experimental Software Engineering in the Cloud (ESEiC)Van Gorp, Pieter, and Louis RoseJournalScience of Computer Programming2013Dec 19 2013doi: 10.1016/j.scico.2013.12.007http://dx.doi.org/10.1016/j.scico.2013.12.007YYear 6
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Design and Development of Subject Gateway with Special Reference to ChemistryYuvaraja, R.DissertationBharathidasan University2014Jun 07 2014 7
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Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial OntologyDahdul, Wasila M., Hong Cui, Paula M. Mabee, Christopher J. Mungall, David Osumi-Sutherland, Ramona L. Walls, and Melissa A. HaendelYesJournalJournal of Biomedical Semantics2014Aug 11 20145, No. 134doi: 10.1186/2041-1480-5-34http://dx.doi.org/10.1186/2041-1480-5-34YYYear 7
Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeumVanBuren, Robert, Doug Bryant, Patrick P. Edger, Haibao Tang, Diane Burgess, Dinakar Challabathula, Kristi Spittle et alYesJournalNature2015Nov 11 2015doi: 10.1038/nature15714http://dx.doi.org/10.1038/nature15714Y
Comparative genomic de_convolution of the cotton genome revealed a decaploid ancestor and widespread chromosomal fractionationWang, Xiyin, Hui Guo, Jinpeng Wang, Tianyu Lei, Tao Liu, Zhenyi Wang, Yuxian Li et alYesJournalNew Phytologist2015Oct 07 2015doi: 10.1111/nph.13689http://dx.doi.org/10.1111/nph.13689Y
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BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library constructionTownsley, Brad Thomas, Michael F. Covington, Yasunori Ichihashi, Kristina Zumstein, and Neelima Roy SinhaYesJournalFrontiers in Plant Science2015May 08 20156366doi: 10.3389/fpls.2015.00366http://dx.doi.org/10.3389/fpls.2015.00366YYYesYear 7
An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictusPoelchau, Monica F., Xin Huang, Allison Goff, Julie Reynolds, and Peter ArmbrusterYesJournalJoVE (Journal of Visualized Experiments)2014Nov 30 201493e51961-e51961doi: 10.3791/51961http://dx.doi.org/10.3791/51961YYesYear 7
A Bioinformatics Approach to Systemic Lupus Erythematosus and AutoimmunitySiefert, JohnYesImmunology 20112015Aug 25 2015https://immunology2011.org/Education/Summer_Teachers/Docs/Archive/2015_Seifert_Final.pdfYesQ3 2015
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Managing, Analysing and Integrating Big Data in medical bioinformatics: open problems and future perspectivesMerelli, Ivan, Horacio P_rez-Sànchez, Sandra Gesing, and Daniele DÍAgostinoJournal2014Jul 31 2014Submitted http://downloads.hindawi.com/journals/bmri/aip/134023.pdfYYesYear 7
Using basic plant traits to predict ungulate seed dispersal potentialAlbert, Aur_lie, Anders MÎrell, M_lanie Picard, and Christophe BaltzingerYesJournalEcography2015Jan 29 2015doi: 10.1111/ecog.00709http://dx.doi.org/10.1111/ecog.00709YYear 7
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Finding Our Way through PhenotypesDeans, Andrew R., Suzanna E. Lewis, Eva Huala, Salvatore S. Anzaldo, Michael Ashburner, James P. Balhoff, David C. Blackburn et alYesJournalPLoS biology2015Jan 06 201513, No. 1e1002033doi: 10.1371/journal.pbio.1002033http://dx.doi.org/10.1371/journal.pbio.1002033YYear 7
OMG! Orthologs in Multiple Genomes _ Competing Graph-Theoretical FormulationsZheng, Chunfang, Krister Swenson, Eric Lyons, and David SankoffYesChapterAlgorithms in Bioinformatics, Lecture Notes in Computer Science20116833364-375doi: 10.1007/978-3-642-23038-7_30http://dx.doi.org/10.1007/978-3-642-23038-7_30YiPlantv1
Clarifying Concepts and Terms in Biodiversity InformaticsDeck, John, Katherine Barker, Reed Beaman, Pier Luigi Buttigieg, Gabriele Dr_ge, Robert Guralnick, Chuck Miller, Äamonn ” Tuama, Zack Murrell, Cynthia Parr0, Bob Robbins, Dmitry Schigel, Brian Stucky, Ramona Walls, John Wieczorek, John WooleyYesJournalStandards in Genomic Science2013May 31 20138, No. 2doi: 10.4056/sigs.3907833http://dx.doi.org/10.4056/sigs.3907833YYear 6
Heterosis in elite hybrid rice: speculation on the genetic and biochemical mechanismsGoff, Stephen A., and Qifa ZhangYesJournalCurrent Opinion in Plant Biology2013Apr 13 201316, No. 2221-227doi: 10.1016/j.pbi.2013.03.009http://dx.doi.org/10.1016/j.pbi.2013.03.009YiPlant v1 Final
Whole Genome and Tandem Duplicate Retention facilitated Glucosinolate Pathway Diversification in the Mustard FamilyHofberger, Johannes A., Eric Lyons, Patrick P. Edger, J. Chris Pires, and M. Eric SchranzYesJournalGenome Biology and Evolution2013Oct 29 2013evt162doi: 10.1093/gbe/evt162http://dx.doi.org/10.1093/gbe/evt162YYear 6
Big data-a 21st century science Maginot Line? No-boundary thinking: shifting from the big data paradigmHuang, Xiuzhen, Steven F. Jennings, Barry Bruce, Alison Buchan, Liming Cai, Pengyin Chen, Carole L. Cramer et alYesJournalBioData mining2015Feb 06 20158doi: 10.1186/s13040-015-0037-5http://dx.doi.org/10.1186/s13040-015-0037-5YYear 7
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The Evolution of Genome StructureTang, Haibao, and Eric LyonsYesJournalInternational Journal of Evolution2012Jul 03 20121, No. 1doi: 10.4172/ievj.1000e105http://dx.doi.org/10.4172/ievj.1000e105YiPlantv1
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Modeling the evolution dynamics of exon-intron structure with a general random fragmentation processWang, Liya, and Lincoln D. SteinYesJournalBMC Evolutionary Biology 2013Feb 01 201313, No. 5715-Jandoi: 10.1186/1471-2148-13-57http://dx.doi.org/10.1186/1471-2148-13-57YiPlant v1 Final
Avian Dopamine Receptors DRD1a and DRD1b Arise from an Ancient Vertebrate Whole Genome DuplicationHaug-Baltzell, Asher K., Eric Lyons, Fiona McCarthy, and Erich JarvisYesConference ProceedingsProceedings of Plant and Animal Genome XXIII2015Jan 12 2015P0402 https://pag.confex.com/pag/xxiii/webprogram/Paper16214.htmlYYesYear 7
The banana (Musa acuminata) genome and the evolution of monocotyledonous plantsDÍHont, Ang_lique, France Denoeud, Jean-Marc Aury, Franc-Christophe Baurens, Françoise Carreel, Olivier Garsmeur, Benjamin Noel et alYesJournalNature2012Jul 11 2012488213-217doi: 10.1038/nature11241http://dx.doi.org/10.1038/nature11241YiPlantv1
Managing, analysing, and integrating big data in medical bioinformatics: open problems and future perspectivesMerelli, Ivan, Horacio P_rez-Sànchez, Sandra Gesing, and Daniele DÍAgostinoJournalBioMed research international2014Dec 22 20142014doi: 10.1155/2014/825649http://dx.doi.org/10.1155/2014/825649YYear 7
The NEWT platform: an extensible plugin framework for creating ReSTful HPC APIsCholia, Shreyqa, and Terence Sun.Conference ProceedingsIn Proceedings of the 9th Gateway Computing Environments Workshop2014Nov 21 2014 17-20doi: 10.1109/GCE.2014.14http://dx.doi.org/10.1109/GCE.2014.14YYesYear 7
Elseweb meets sadi: Supporting data-to-model integration for biodiversity forecastingDel Rio, Nicholas, Natalia Villanueva-Rosales, Deana Pennington, Karl Benedict, Aimee Stewart, and C. J. GradyJournalIn Discovery Informatics Symposium, AAAI Technical Report FS-13-012013 http://www.aaai.org/ocs/index.php/FSS/FSS13/paper/viewFile/7631/7488YYear 6
Leafy Spurge Genomics: A Model Perennial Weed to Investigate Development, Stress Responses, and InvasivenessHorvath, David, James V. Anderson, Wun S. Chao, Michael E. Foley, and MÙnevver Do_ramaciChapterIn Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches2015Jul 22 201563-78http://www.springer.com/us/book/9783319171562YQ3 2015
From data to function: Functinal modeling of poultry genomics dataMcCarthy, Fiona M., Eric LyonsYesJournalPoultry Science2013Sep 01 201392, No. 92519-2529doi: 10.3382/ps.2012-02808http://dx.doi.org/10.3382/ps.2012-02808YYYear 6
Interspecific RNA Interference of SHOOT MERISTEMLESS-Like Disrupts Cuscuta pentagona Plant ParasitismAlakonya, Amos, Ravi Kumar, Daniel Koenig, Seisuke Kimura, Brad Townsley, Steven Runo, Helena M. Garces et alYesJournalThe Plant Cell Online2012Jul 01 201224, No. 73153-3166doi: 10.1105/tpc.112.099994http://dx.doi.org/10.1105/tpc.112.099994YiPlantv1
Globus Platform-as-a-Service for Collaborative Science ApplicationsAnanthakrishnan, Rachana, Kyle Chard, Ian Foster, Steven TueckeJournal2014May 31 2014 https://www.globus.org/sites/default/files/Globus-Platform-as-a-Service-for-Collaborative-Science-Applications.pdfYYear 6
CrusView: a Java-based visualization platform for comparative genomics analyses in BrassicaceaeChen, Hao, and Xiangfeng WangYesJournalPlant Physiology Preview2013Jul 01 2013163, No. 1354-362doi: 10.1104/pp.113.219444http://dx.doi.org/10.1104/pp.113.219444YiPlant v1 Final
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Why Assembling Plant Genome Sequences Is So ChallengingClaros, Manuel Gonzalo, RocÕo Bautista, DarÕo Guerrero-Fernàndez, Hicham Benzerki, Pedro Seoane, and No_ Fernàndez-PozoYesJournalBiology2012Sep 18 20121, No. 2439-459doi: 10.3390/biology1020439http://dx.doi.org/10.3390/biology1020439YiPlantv1
Cell to whole-plant phenotyping: the best is yet to comeDhondt, Stijn, Nathalie Wuyts, and Dirk Inz_YesReviewTrends in Plant Science2013May 23 201318, No. 8428-439doi: 10.1016/j.tplants.2013.04.008http://dx.doi.org/10.1016/j.tplants.2013.04.008YiPlant v1 Final
A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiospermsWerner, Gijsbert DA, William K. Cornwell, Janet I. Sprent, Jens Kattge, and E. Toby KiersYesJournalNature communications2014Jun 10 20145, No. 4087doi: 10.1038/ncomms5087http://dx.doi.org/10.1038/ncomms5087YYear 7
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Big Data: Related Technologies, Challenges and Future ProspectsChen, Min, Shiwen Mao, Yin Zhang, and Victor CM LeungJournalSpringer Briefs in Computer Science2014May 09 2014 doi: 10.4236/jcc.2014.26001http://dx.doi.org/10.1007/978-3-319-06245-7YYear 6
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Phylotastic! Making tree-of-life knowledge accessible, reusable and convenientStoltzfus, Arlin, Hilmar Lapp, Naim Matasci, Helena Deus, Brian Sidlauskas, Christian M Zmasek, Gaurav Vaidya, Enrico Pontelli, Karen Cranston, Rutger Vos, Campbell O Webb, Luke J Harmon, Megan Pirrung, Brian O'Meara, Matthew W Pennell, Siavash Mirarab, Michael S Rosenberg, James P Balhoff, Holly M Bik, Tracy A Heath, Peter E Midford, Joseph W Brown, Emily Jane McTavish, Jeet Sukumaran, Mark Westneat, Michael E Alfaro, Aaron Steele and Greg JordanYesJournalBMC Bioinformatics2013May 13 201314, No.158doi: 10.1186/1471-2105-14-158http://dx.doi.org/10.1186/1471-2105-14-158YYYear 6
Multi-scale phylogenetic structure in coastal dune plant communities across the globeBrunbjerg, Ane Kirstine, Jeannine Cavender-Bares, Wolf L. Eiserhardt, Rasmus Ejrn_s, Lonnie W. Aarssen, Hannah L. Buckley, Estelle Forey et alYesJournalJournal of Plant Ecology2014Jan 29 2014rtt069doi: 10.1093/jpe/rtt069http://dx.doi.org/10.1093/jpe/rtt069YYear 7
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The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing dataLammers, Youri, Tamara Peelen, Rutger A. Vos, and Barbara GravendeelYesJournalBMC Bioinformatics2014Feb 06 201415, No. 144doi: 10.1186/1471-2105-15-44http://dx.doi.org/10.1186/1471-2105-15-44YYear 7
An Inventory of Crop Wild Relatives of the United StatesKhoury, Colin K., Stephanie Greene, John Wiersema, Nigel Maxted, Andy Jarvis, and Paul C. StruikYesJournalCrop Science2013Apr 29 201353, No. 41496-1508doi: 10.2135/cropsci2012.10.0585http://dx.doi.org/10.2135/cropsci2012.10.0585YiPlant v1 Final
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Overcoming the Limitations Posed by TCR‘_ Repertoire Modeling through a GPU-based In-Silico DNA Recombination AlgorithmStriemer, G, H Krovi, A Akoglu, B Vincent, B Hopson, J Frelinger, and A BuntzmanConference ProceedingsProceedings from the 28th IEEE International Parallel and Distributed Processing Symposium, May 19-23, 2014 Phoenix, AZ2014May 23 2014Parallel Technical Sessions 6YYear 6
Hydrologic Data Sharing Using Open Source Softwareand Low-Cost ElectronicsSadler, Jeffery MichaelJournalBYU Scholars Archives: All Theses and Dissertations2015Apr 07 2015http://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=5424&context=etdYYear 7
Islands and Integrals: Processes of Diversification in an Island Archipelago and Bayesian Methods of Comparative Phylogeographical Model ChoiceOaks, J. R. YesDissertationUniversity of Kansas, KU Scholar Works2013Dec 31 2013 http://hdl.handle.net/1808/12932YYear 6
An Improved Approximate-Bayesian Model-choice Method for Estimating Shared Evolutionary HistoryOaks, Jamie R. YesJournalarXiv preprint2014Feb 25 2014 arXiv:1402.6303 [q-bio.PE] http://arxiv.org/abs/1402.6303YYear 6
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Genomic-scale exchange of mRNA between a parasitic plant and its hostsKim, Gunjune, Megan L. LeBlanc, Eric K. Wafula, and James H. WestwoodYesJournalScience2014Aug 15 2013345, No. 6198808-811doi: 10.1126/science.1253122http://dx.doi.org/10.1126/science.1253122YiPlantv1
Genomic Distribution of H3K9me2 and DNA Methylation in a Maize GenomeWest, Patrick T., Qing Li, Lexiang Ji, Steven R. Eichten, Jawon Song, Matthew W. Vaughn, Robert J. Schmitz, and Nathan M. SpringerYesJournalPloS one2014Aug 14 20149, No. 8e105267doi: 10.1371/journal.pone.0105267http://dx.doi.org/10.1371/journal.pone.0105267YYYear 7
Annual Reports to the Governing CouncilEcological Society of AmericaYesReportReport from the ESA 99th Annual Meeting, Sacramento, California, August 9th-15th, 2014.2014Oct 31 2014 43doi: 10.1890/2014.councilreporthttp://dx.doi.org/10.1890/2014.councilreportYYear 7
Genomes of Candidatus Liberibacter solanacearum haplotype A from New Zealand and the USA suggest significant genome plasticity in the speciesThompson, Sarah M., Chris P. Johnson, Ashley Y. Lu, Rebekah A. Frampton, Kerry L. Sullivan, Mark WEJ Fiers, Ross N. Crowhurst et alYesJournalPhytopathology2015Mar 30 2015doi: 10.1094/PHYTO-12-14-0363-FIhttp://dx.doi.org/10.1094/PHYTO-12-14-0363-FIYYesYesYear 7
Bin Definition for Super Gene Trees for Mirarab et. al.Mirarab, Sivash, Md Shamsuzzoha Bayzid, Bastien Boussau, and Tandy WarnowRepositoryIDEALS2014Dec 11 2014http://hdl.handle.net/2142/55685YYear 7
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Authentication and Authorization Considerations for a Multi-tenant ServiceHeiland, Randy, Scott Koranda, Suresh Marru, Marlon, Pierce, and Von WelchConference ProceedingsProceeding SCREAM '15 Proceedings of the 1st Workshop on The Science of Cyberinfrastructure: Research, Experience, Applications and Models2015Jun 15 201529-35doi: 10.1145/2753524.2753534http://dx.doi.org/10.1145/2753524.2753534YYesQ3 2015
A software tool for the input and management of phenotypic data using personal digital assistants and other mobile devicesKohl, Karin, and Jurgen GremmelsJournalBioMed Central2015Apr 07 2015doi: 10.1186/s13007-015-0069-3http://dx.doi.org/10.1186/s13007-015-0069-3YYear 7
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De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcumFox, Samuel E., Matthew Geniza, Mamatha Hanumappa, Sushma Naithani, Chris Sullivan, Justin Preece, Vijay K. Tiwari et alYesJournalPLoS ONE 2014May 12 20149, No. 8e105275doi: 10.1371/journal.pone.0105275http://dx.doi.org/10.1371/journal.pone.0105275YYear 6
A 3' RACE Protocol to Confirm Polyadenylation SitesMa, Liuyin and Arthur G. HuntYes2014Nov 13 20141255135-144doi: 10.1007/978-1-4939-2175-1_12http://dx.doi.org/10.1007/978-1-4939-2175-1_12Year 7
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Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamicsBrum, Jennifer R, Bonnie L Hurwitz, Oscar Schofield, Hugh W Ducklow, and Matthew B SullivanJournalThe ISME Journal2015Aug 21 2015doi: 10.1038/ismej.2015.125http://dx.doi.org/10.1038/ismej.2015.125YYesQ3 2015
Allele Workbench: Transcriptome Pipeline and Interactive Graphics for Allele-Specific ExpressionSoderlund, Carol, William M. Nelson, and Stephen A. GoffJournalPLOS2014Dec 26 2014doi: 10.1371/journal.pone.0115740http://dx.doi.org/10.1371/journal.pone.0115740YYYesYear 7
Resolved observations of geostationary satellites from the 6.5 m MMTHart, Michael, Richard Rast, Stuart Jefferies, and Douglas HopeConference ProceedingsProceedings from AMOS: Advanced Maui Optical and Space Survelillance Technologies Conference2016Nov 16 2015http://www.amostech.com/TechnicalPapers/2015/Adaptive_Optics_Imaging/Hart.pdfY
neotoma: A Programmatic Interface to the Neotoma Paleoecological DatabaseGoring, Simon, Andria Dawson, Gavin L. Simpson, Karthik Ram, Russ W. Graham, Eric C. Grimm, and John W. WilliamsYesJournalOpenQuaternary2015Mar 20 20151, No. 217-Jandoi: 10.5334/oq.abhttp://dx.doi.org/10.5334/oq.abYYesYear 7
The DOE Systems Biology Knowledgebase: Progress Toward a System for Collaborative and Reproducible Inference and Modeling of Biological Function in Plant ResearchCottingham, Robert W. et alConference ProceedingsProceedings of Plant and Animal Genome XXIII2015Jan 12 2015P1138https://pag.confex.com/pag/xxiii/webprogram/Paper16317.htmlYYear 7
Clouds for Masses - Toward Ubiquitiousand Transparent CloudsGoscinski, Andrzej, and Philip ChurchConference ProceedingsCloud Computing (CLOUD), 2015 IEEE 8th International Conference on2015Aug 24 20151141-1148doi: 10.1109/CLOUD.2015.168http://dx.doi.org/10.1109/CLOUD.2015.168YYesQ3 2015
Jetstream: A Distributed Cloud Infrastructure for Under-resourced higher education communitiesFischer, Jeremy, Steven Tuecke, Ian Foster, and Craig A. StewartTechnical Reportcac.cornell.edu2015Apr 11 2015http://www.cac.cornell.edu/about/pubs/JetstreamDCIforUnderResourcedHigherEdCommunities.pdfYYYesYear 7
Optical mapping in plant comparative genomicsTang, Haibo, Eric Lyons, and Christopher D. TownYesJournalGigaScience2015Feb 10 20154, No. 13doi: 10.1186/s13742-015-0044-yhttp://dx.doi.org/10.1186/s13742-015-0044-yYYYear 7
Plantagora: Modeling Whole Genome Sequencing and Assembly of Plant GenomesBarthelson, Roger, Adam J. McFarlin, Steven D. Rounsley, and Sarah YoungYesJournalPLoS ONE2011Dec 12 20116, No. 12e28436doi: 10.1371/journal.pone.0028436http://dx.doi.org/10.1371/journal.pone.0028436YYiPlantv1
The Amborella Genome and the Evolution of Flowering PlantsAlbert, Victor A., W. Bradley Barbazuk, Joshua P. Der, James Leebens-Mack, Hong Ma, Jeffrey D. Palmer, Steve Rounsley et alYesJournalScience2013Dec 20 2013342, No. 6156doi: 10.1126/science.1241089http://dx.doi.org/10.1126/science.1241089YYear 6
Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genomeChalhoub, Boulos, France Denoeud, Shengyi Liu, Isobel AP Parkin, Haibao Tang, Xiyin Wang, Julien Chiquet et alYesJournalScience2014Aug 22 2014345, No. 6199950-953doi: 10.1126/science.1253435http://dx.doi.org/10.1126/science.1253435YYear 7
The dynamics of functional classes of plant genes in rediploidized ancient polyploidsChen, Eric CH, Carlos FBA Najar, Chunfang Zheng, Alex Brandts, Eric Lyons, Haibao Tang, Lorenzo Carretero-Paulet, Victor A. Albert, and David SankoffYesConference ProceedingsBMC Bioinformatics201314, No. 15S19 http://rcg2013.sciencesconf.org/conference/rcg2013/19_Sankoff.pdfYYear 6
Araport: an application platform for data discoveryHanlon, Matthew R., Matthew Vaughn, Stephen Mock, Rion Dooley, Walter Moreira, Joe Stubbs, Chris Town et alJournalConcurrency and Computation: Practice and Experience2015May 19 2015doi: 10.1002/cpe.3542http://dx.doi.org/10.1002/cpe.3542YYesYear 7
Meeting report: Identifying practical applications of ontologies for biodiversity informaticsDeck, John, Robert Guralnick, Ramona Walls, Stanley Blum, Melissa Haendel, Andr_a Matsunaga, and John WieczorekReportStandards in Genomic Sciences2015May 17 201510, No. 125doi: 10.1186/s40793-015-0014-0http://dx.doi.org/10.1186/s40793-015-0014-0YYear 7
A Review of Cloud Computing Bioinformatics Solutions for Next-Gen Sequencing Data Analysis and ResearchKrampis, Konstantinos, and Claudia WultschYesJournalMethods in Next Generation Sequencing2015Jul 27 20152, No. 1doi: 10.1515/mngs-2015-0003http://dx.doi.org/10.1515/mngs-2015-0003YYesQ3 2015
Undergraduate Genomics Research through GCAT-SEEK: The Genome Consortium for Active Teaching Using Next-Generation SequencingBuonaccorsi, VincentConference ProceedingsProceedings of Plant and Animal Genome XXIII2015Jan 11 2015W697https://pag.confex.com/pag/xxiii/webprogram/Paper17140.htmlYYear 7
HPC-ABDS High Performance Computing Enhanced Apache Big Data StackFox, G.C., U. Qiu, S. Kamburugamuve, S. Jha, et al.Conference ProceedingsCluster, Cloud and Grid Computing (CCGrid), 2015 15th IEEE/ACM International Symposium on2015May 07 20151057-1066doi: 10.1109/CCGrid.2015.122http://dx.doi.org/10.1109/CCGrid.2015.122YYesYesQ3 2015
Science gateways-leveraging modeling and simulations in HPC infrastructures via increased usabilityGesing, Sandra, Rion Dooley, Marlon Pierce, Jens Kruger, Richard Grunzke, Sonja Herres-Pawlis, and Alexander HoffmannConference ProceedingsIn High Performance Computing & Simulation (HPCS), 2015 International Conference on2015Jul 24 201519-26doi: 10.1109/HPCSim.2015.7237017http://dx.doi.org/10.1109/HPCSim.2015.7237017YYYesQ3 2015
Araport: the Arabidopsis Information PortalKrishnakumar, Vivek, Matthew R. Hanlon, Sergio Contrino, Erik S. Ferlanti, Svetlana Karamycheva, Maria Kim, Benjamin D. Rosen et al.YesJournalNucleic Acids Research2014Nov 04 2014gku1200doi: 10.1093/nar/gku1200http://dx.doi.org/10.1093/nar/gku1200YYesYear 7
Re-annotation of the woodland strawberry (Fragaria vesca) genomeDarwish, Omar, Rachel Shahan, Zhongchi Liu, Janet P. Slovin, and Nadim W. AlkharoufYesJournalBMC genomics2015Jan 27 201516, No. 129doi: 10.1186/s12864-015-1221-1http://dx.doi.org/10.1186/s12864-015-1221-1YYesYear 7
Identification of dopamine receptors across the extant avian family tree and analysis with other clades uncovers a polyploid expansion among vertebratesHaug-Baltzell, Asher, Erich D. Jarvis, Fiona McCarthy, and Eric LyonsJournalFrontiers in Neuroscience2015Sep 21 20159, No. 361doi: 10.3389/fnins.2015.00361http://dx.oi.org/10.3389/fnins.2015.00361YYesYes
Metabolomic profiling of the nectars of Aquilegia pubescens and A. canadensisNoutsos, Christos, et alJournalPlosOne2015May 01 2015doi: 10.1371/journal.pone.0124501http://dx.doi.org/10.1371/journal.pone.0124501YYYesYesYear 7
Gene co-expression network analysis provides novel insights into myostatin regulation at three different mouse developmental timepointsYang, Xuerong, James E. Koltes, Carissa A. Park, Daiwen Chen, and James M. ReecyYesJournalPloS one2015Feb 19 201510, No. 2doi: 10.1371/journal.pone.0117607http://dx.doi.org/10.1371/journal.pone.0117607YYesYesYear 7
Large-Scale Next-Generation Resequencing of Soybean Germplasm for Trait DiscoveryLiu, Yang et al.Conference ProceedingsProceedings from Plant and Animal Genome XXIII2014Jan 12 2015P0696 https://pag.confex.com/pag/xxiii/webprogram/Paper16113.htmlYYear 7
Flash Demo: Annotating genomes with MAKER-P and the iPlant Discovery EnvironmentSubramaniam, SabarinathConference ProceedingsProceedings of Plant and Animal Genome XXIII2015Jan 12 2015W481 https://pag.confex.com/pag/xxiii/webprogram/Paper17298.htmlYYesYear 7
Avian Model Species Trees for 1X Model Condition for Mirarab et. al.Mirarab, Sivash, Md Shamsuzzoha Bayzid, Bastien Boussau, and Tandy WarnowRepositoryIDEALS2014Dec 11 2014http://hdl.handle.net/2142/55619YYear 7