Preface First

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Preface Second

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Publications

Content

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Citing iPlant

If you would like to cite a publication that describes the iPlant Collaborative, please cite this paper:

  • Goff, Stephen A. et al., "The iPlant Collaborative: Cyberinfrastructure for Plant Biology," Frontiers in Plant Science 2 (2011), doi: 10.3389/fpls.2011.00034.

 

The following publications cite or acknowledge iPlant resources as contributing to the work or results being reported:

Alakonya, Amos, Ravi Kumar, Daniel Koenig, Seisuke Kimura, Brad Townsley, Steven Runo, Helena M. Garces et al. “Interspecific RNA Interference of SHOOT MERISTEMLESS-Like Disrupts Cuscuta pentagona Plant Parasitism,” The Plant Cell Online 24, No. 7 (2012): 3153-3166. doi: 10.1105/tpc.112.099994.

Albert, Victor A., W. Bradley Barbazuk, Joshua P. Der, James Leebens-Mack, Hong Ma, Jeffrey D. Palmer, Steve Rounsley et al. “The Amborella Genome and the Evolution of Flowering Plants,” Science 342, No. 6156 (2013): . doi: 10.1126/science.1241089.

Alice Y. Cheung, Ravi Palanivelu, Wei-Hua Tang, Hong-Wei Xue and Wei-Cai Yang. “Pollen and Plant Reproduction Biology: Blooming from East to West,” Molecular Plant 6, No. 4 (2013): 995-997. doi: 10.1093/mp/sst108.

Amrine, Katherine CH, Wesley D. Swingley, and David H. Ardell. “tRNA Signatures Reveal a Polyphyletic Origin of SAR11 Strains among Alphaproteobacteria,” PLOS Computational Biology 10, No. 2 (2014): e1003454. doi: 10.1371/journal.pcbi.1003454.

Ananthakrishnan, Rachana, Kyle Chard, Ian Foster, Steven Tuecke. “Globus Platform-as-a-Service for Collaborative Science Applications,” (2014): . https://www.globus.org/sites/default/files/Globus-Platform-as-a-Service-for-Collaborative-Science-Applications.pdf.

Arcot Rajasekar, Sharlini Sankaran, Howard Lander, Tom Carsey, Jonathan Crabtree, Hye-Chung Kum, Merce Crosas, Gary King, Justin Zhan. “Sociometric methods for relevancy analysis of Long Tail Science Data,” Proceedings of Databridge Conference 2013 1 (2013): . http://databridge.web.unc.edu/files/2013/01/Databridge-ConferenceVersion-final.pdf.

Aronson, Myla FJ, Frank A. La Sorte, Charles H. Nilon, Madhusudan Katti, Mark A. Goddard, Christopher A. Lepczyk, Paige S. Warren et al. “A global analysis of the impacts of urbanization on bird and plant diversity reveals key anthropogenic drivers,” Proceedings of the Royal Society B: Biological Sciences 281, No. 1780 (2014): 20133330. doi: 10.1098/rspb.2013.3330.

Banks, Jo Ann, Tomoaki Nishiyama, Mitsuyasu Hasebe, John L. Bowman, Michael Gribskov, Claude dePamphilis, Victor A. Albert et al. “The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants,” Science 332, No. 6032 (2011): 960-963. doi: 10.1126/science.1203810.

Barthelson, Roger, Adam J. McFarlin, Steven D. Rounsley, and Sarah Young. “Plantagora: Modeling Whole Genome Sequencing and Assembly of Plant Genomes,” PLoS ONE 6, No. 12 (2011): e28436. doi: 10.1371/journal.pone.0028436.

Barton, Carl, Costas S. Iliopoulos, Inbok Lee, Laurent Mouchard, Kunsoo Park, Solon P. Pissis. “Extending alignments with k-mismatches and ℓ-gaps,” Theoretical Computer Science (2013): . doi: 10.1016/j.tcs.2013.06.012,.

Basney, Jim, Rion Dooley, Jeff Gaynor, Suresh Marru, and Marlon Pierce. “Distributed web security for science gateways,” Proceeding GCE '11 Proceedings of the 2011 ACM workshop on Gateway computing environments (2011): 13-20. doi: 10.1145/2110486.2110489.

Bayzid, Md Shamsuzzoha, and Tandy Warnow. “Naive Binning Improves Phylogenomic Analyses,” Bioinformatics 29, No. 18 (2013): 227-2284. doi: 10.1093/bioinformatics/btt394.

Beaulieu, Jeremy M., Brian C. O'Meara and Michael J. Donoghue. “Identifying hidden rate changes in the evolution of a binary morphological character: the evolution of plant habit in campanulid angiosperms,” Systems Biology 62, 5 (2013): 725-37. doi: 10.1093/sysbio/syt034.

Beaulieu, Jeremy M., Michael J. Donoghue. “Fruit Evolution and Diversification in Campanulid Angiosperms,” International Journal of Organic Evolution (2013): . doi: 10.1111/evo.12180.

Beck, Jan, Liliana Ballesteros‐Mejia, Carsten M. Buchmann, Jürgen Dengler, Susanne A. Fritz, Bernd Gruber, Christian Hof et al. “What's on the horizon for macroecology?,” Ecography 35, No. 8 (2012): 673-683. doi: 10.1111/j.1600-0587.2012.07364.x.

Blonder, Benjamin, Vanessa Buzzard, Irena Simova, Lindsey Sloat, Brad Boyle, Rebecca Lipson, Brianna Aguilar-Beaucage et al. “The leaf-area shrinkage effect can bias paleoclimate and ecology research,” American Journal of Botany 99, No. 1 (2012): 1756-1763. doi: 10.3732/ajb.1200062.

Boyle, Brad, Nicole Hopkins, Zhenyuan Lu, Juan Antonio Raygoza Garay, Dmitry Mozzherin, Tony Rees, Naim Matasci, Martha L. Narro, William H. Piel, Sheldon J. Mckay, Sonya Lowry, Chris Freeland, Robert K. Peet, Brian J. Enquist. “The Taxonomic Name Resolution Service: an online tool for automated standardization of plant names,” BMC Bioinformatics 14, No. 16 (2013): 16. doi: 10.1186/1471-2105-14-16.

Brauer, Elizabeth K., Dharmendra K. Singh, and Sorina C. Popescu. “Next-generation plant science: putting big data to work,” Genome Biology 15, 301 (2014): . http://genomebiology.com/2014/15/1/301.

Brown, Susan A., and Sherry Thatcher. “Factors Influencing Adoption and Non-Adoption of Cyberinfrastructure by the Research Community,” Proceedings of The 15th Pacific Asia Conference on Information Systems (PACIS 2011), Brisbane, Australia (2011): 31. http://projects.business.uq.edu.au/pacis2011/papers/PACIS2011-021.pdf.

Brown, Susan A., Sherry Thatcher, and Yan Dang. “Managing Knowledge in a Changing Scientific Landscape: The Impact of Cyberinfrastructure,” System Sciences (HICSS), 2010 43rd Hawaii International Conference on (2010): 1-10. doi: 10.1109/HICSS.2010.263.

Burleigh, 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, Paúl M. Velazco, Ramona L Walls, Joanna M Wolfe, Mengjie Yu. “Next-generation phenomics for the Tree of Life,” PLOS Currents Tree of Life 5 (2013): . .

Busov, Victor. “The Promise of Genomics and Beyond,” Forestry Ideas 19, No. 2 (2013): 107-128. http://forestry-ideas.info/files/journal/Forestry_Ideas_BG_2013_19_2.pdf#page=5.

Campbell, Michael, MeiYee Law, Carson Holt, Joshua Stein, Gaurav Moghe, David Hunagel, Jikai Lei et al. “MAKER-P: a tool-kit for the rapid creation, management, and quality control of plant genome annotations,” Plant Physiology (2013): 113. doi: 10.1104/pp.113.230144.

Carey, Hannah V.. “Grand Challenges in Organismal Physiology,” Physiologist 54, Issue 5 (2011): 169. http://www.the-aps.org/mm/Publications/Journals/Physiologist/2010-present/2011/October.pdf.

Chamberlain, Scott A., and Eduard Szöcs. “taxize: taxonomic search and retrieval in R [v1; ref status,” F1000Research 2, No. 191 (2013): . doi: 10.12688/f1000research.2-191.v2.

Chen, Eric CH, Carlos FBA Najar, Chunfang Zheng, Alex Brandts, Eric Lyons, Haibao Tang, Lorenzo Carretero-Paulet, Victor A. Albert, and David Sankoff. “The dynamics of functional classes of plant genes in rediploidized ancient polyploids,” BMC Bioinformatics 14, No. 15 (2013): S19. http://rcg2013.sciencesconf.org/conference/rcg2013/19_Sankoff.pdf.

Chen, Hao, and Xiangfeng Wang. “CrusView: a Java-based visualization platform for comparative genomics analyses in Brassicaceae,” Plant Physiology Preview 163, No. 1 (2013): 354-362. doi: 10.1104/pp.113.219444.

Chen, Min, Shiwen Mao, and Yunhao Liu. “Big Data: A Survey,” Mobile Networks and Applications January (2014): 1-39. http://link.springer.com/article/10.1007/s11036-013-0489-0#page-1.

Chitwooda, Daniel H., Ravi Kumara, Lauren R. Headland, Aashish Ranjan, Michael F. Covington, Yasunori Ichihashi, Daniel Fulop, José M. Jiménez-Gómez, Jie Peng, Julin N. Maloof and Neelima R. Sinha. “A Quantitative Genetic Basis for Leaf Morphology in a Set of Precisely Defined Tomato Introgression Lines[,” The Plant Cell Online 25, No. 7 (2013): 2465-2481. doi: 10.1105/tpc.113.112391.

Christou, Michalis, Tomáš Flouri, Costas S. Iliopoulos, Jan Janoušek, Bořivoj Melichar, Solon P. Pissis, Jan Žďárek. “Tree template matching in unranked ordered trees,” Journal of Discrete Algorithms, Available online 13 February 2013 20 (2013): 51-60. doi: 10.1016/j.jda.2013.02.001.

Claros, Manuel Gonzalo, Rocío Bautista, Darío Guerrero-Fernández, Hicham Benzerki, Pedro Seoane, and Noé Fernández-Pozo. “Why Assembling Plant Genome Sequences Is So Challenging,” Biology 1, No. 2 (2012): 439-459. doi: 10.3390/biology1020439.

Cole, Benjamin J., and Joanne Chory. “Image-Based Analysis of Light-Grown Seedling Hypocotyls in Arabidopsis,” High-Throughput Phenotyping in Plants (2012): 1-7. doi: 10.1007/978-1-61779-995-2_1.

Collaborative, iPlant. “The iPlant Collaborative Website,” (2008): . http://www.iplantcollaborative.org.

Committee to Develop a Research Strategy for Environmental, Health, and Safety Aspects of Engineered Nanomaterials; National Research Council. “Implementing the Research Strategy and Evaluating Progress,” A Research Strategy for Environmental, Health, and Safety Aspects of Engineered Nanomaterials (2014): . http://www.ncbi.nlm.nih.gov/books/NBK189502/.

Crivelli, Silvia, Rion Dooley, Raquell Holmes, and Stephen Mock. “Creating a gateway that enables large-scale science coopetition,” Concurrency and Computation: Practice and Experience (2014): . doi: 10.1002/cpe.3270.

Crochemore, Maxime, Costas S. Iliopoulos, Tomasz Kociumaka, Marcin Kubica, Alessio Langiu, Solon P. Pissis, Jakub Radoszewski, Wojciech Rytter, and Tomasz Wale. “Order-Preserving Sux Trees and Their Algorithmic Applications,” Cornel University Library (2013): . http://arxiv.org/pdf/1303.6872.pdf.

D’Hont, Angélique, France Denoeud, Jean-Marc Aury, Franc-Christophe Baurens, Françoise Carreel, Olivier Garsmeur, Benjamin Noel et al. “The banana (Musa acuminata) genome and the evolution of monocotyledonous plants,” Nature 488 (2012): 213-217. doi: 10.1038/nature11241.

Damian DG Gessler, Cliff Joslyn and Karin Verspoor. “A Posteriori Ontology Engineering for Data-Driven Science,” Data-Intensive Science 18 (2013): 215-244. .

Das, Abhiram, Alexander Bucksch, Charles A. Price, and Joshua S. Weitz. “ClearedLeavesDB: an online database of cleared plant leaf images,” Plant methods 10, No. 1 (2014): 8. doi: 10.1186/1746-4811-10-8.

Del Rio, Nicholas, Natalia Villanueva-Rosales, Deana Pennington, Karl Benedict, Aimee Stewart, and C. J. Grady. “Elseweb meets sadi: Supporting data-to-model integration for biodiversity forecasting,” In Discovery Informatics Symposium, AAAI Technical Report FS-13-01 (2013): . http://www.aaai.org/ocs/index.php/FSS/FSS13/paper/viewFile/7631/7488.

Del Vescovo, Chiara, Damian DG Gessler, Pavel Klinov, Bijan Parsia, Ulrike Sattler, Thomas Schneider, and Andrew Winget. “Decomposition and Modular Structure of BioPortal Ontologies,” The Semantic Web–ISWC 2011, Lecture Notes in Computer Science 7031 (2011): 130-145. doi: 10.1007/978-3-642-25073-6_9.

Del Vescovo, Chiara, Pavel Klinov, Bijan Parsia, Ulrike Sattler, and Thomas Schneider. “DeMoSt: a Tool for Exploring the Decomposition and the Modular Structure of OWL Ontologies,” 10th International Semantic Web Conference Proceedings,Bonn, Germany (2011): . http://iswc2011.semanticweb.org/fileadmin/iswc/Papers/PostersDemos/iswc11pd_submission_75.pdf.

Dhondt, Stijn, Nathalie Wuyts, and Dirk Inzé. “Cell to whole-plant phenotyping: the best is yet to come,” Trends in Plant Science 18, No. 8 (2013): 428-439. doi: 10.1016/j.tplants.2013.04.008.

Dooley, Rion, Matthew Vaughn, Dan Stanzione, Steve Terry, and Edwin Skidmore. “Software-as-a-Service: The iPlant Foundation API,” Proceedings from the 5th Workshop on Many-Task Computing on Grids and Supercomputers (MTAGS) 2012 (2012): 7. http://datasys.cs.iit.edu/events/MTAGS12/p07.pdf.

Dragut, Eduard C., Mourad Ouzzani, Amgad Madkour, Nabeel Mohamed, Peter Baker, and David E. Salt. “lonomics Atlas - A Tool To Explore Interconnected Ionomic, Genomic and Environmental Data,” Proceedings of the 21st ACM international conference on Information and knowledge management (2012): 2680-2682. doi: 10.1145/2396761.2398724.

Egan, Ashley N., Jessica Schlueter, and David M. Spooner. “Applications of next-generation sequencing in plant biology,” American Journal of Botany 99, No. 2 (2012): 175-185. doi: 10.3732/ajb.1200020.

Eichten, Steven R., Matthew W. Vaughn, Peter J. Hermanson and Nathan M. Springer. “Variation in DNA Methylation Patterns is More Common among Maize Inbreds than among Tissues,” The Plant Genome (2013): . doi: 10.3835/plantgenome2012.06.0009.

Eichten, 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. Springer. “Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons,” PLoS Genetics 8, No. 12 (2012): e1003127. doi: 10.1371/journal.pgen.1003127.

El-Gayar, Omar F., Surendra Sarnikar, and Matthew J. Wills. “A cyberinfrastructure framework for comparative effectiveness research in healthcare,” System Sciences (HICSS), 2010 43rd Hawaii International Conference on (2010): 1-9. doi: 10.1109/HICSS.2010.9.

Feltus, F. Alex. “Systems genetics: A paradigm to improve discovery of candidate genes and mechanisms underlying complex traits,” Plant Science (2014): . doi: 10.1016/j.plantsci.2014.03.003.

Feng, Xin, Robert Grossman, and Lincoln Stein. “PeakRanger: A cloud-enabled peak caller for ChIP-seq data,” BMC Bioinformatics 12, No. 1 (2011): 139. doi: 10.1186/1471-2105-12-139.

Fick, R.H.J., D. Fedorov, A.H.K. Roeder, B.S. Manjunath. “Simultaneous cell tracking and image alignment in 3D CLSM imagery of growing Arabidopsis thaliana sepals,” Biomedical Imaging (ISBI), 2013 IEEE 10th International Symposium on (2013): 914-917. doi: 10.1109/ISBI.2013.6556624.

Flouri, Tom´aˇs, Kassian Kobert, Solon P. Pissis, and Alexandros Stamatakis. “An optimal algorithm for computing all subtree repeats in trees,” Exelixis Lab Technical Report (2013): . http://sco.h-its.org/exelixis/pubs/Exelixis-RRDR-2013-5.pdf.

Flouri, Tomáš, Costas S. Iliopoulos, Kunsoo Park, and Solon P. Pissis. “GapMis-OMP: Pairwise Short-Read Alignment on Multi-core Architectures,” Artificial Intelligence Applications and Innovations (2012): 593-601. doi: 10.1007/978-3-642-33412-2_61.

Flouri, Tomáš, Costas S. Iliopoulos, Tomasz Kociumaka, Solon P. Pissis, Simon J. Puglisi, W. F. Smyth, and Wojciech Tyczyński. “Enhanced string covering,” Theoretical Computer Science (2013): . http://www.sciencedirect.com/science/article/pii/S0304397513006105.

Flouri, Tomás, Costas S. Iliopoulos, Tomasz Kociumaka, Solon P. Pissis, Simon J. Puglisi, William F. Smyth, and Wojciech Tyczynski. “New and Efficient Approaches to the Quasiperiodic Characterisation of a String,” Proceedings of the Prague Stringology Conference 2012 (2012): 78-88. http://www.stringology.org/papers/PSC2012.pdf#page=83.

Fox, Geoggrey, Dennis Gannon. “Using Clouds for Technical Computing,” Community Grids Lab, Pervasive Technology Labs at Indiana University (2013): . http://grids.ucs.indiana.edu/ptliupages/publications/Clouds_Technical_Computing_Review.pdf.

Frousios, Kimon, Costas S. Iliopoulos, German Tischler, Sophia Kossida, Solon P. Pissis, and Stilianos Arhondakis. “Transcriptome map of mouse isochores in embryonic and neonatal cortex,” Genomics 101, No. 2 (2012): 120-124. doi: 10.1016/j.ygeno.2012.11.006.

Galbraith, David W., Jeffrey L. Bennetzen, Elizabeth A. Kellogg, J. Chris Pires, and Pamela S. Soltis. “The Genomes of All Angiosperms: A Call for a Coordinated Global Census,” Journal of Botany 2011 (2011): 10. doi: 10.1155/2011/646198.

Geser, G., Y. Jaques, Nikos Manouselis, Vassilis Protonotarios, J. Keizer, and M. Sicilia. “Building Blocks for a Data Infrastructure and Services to Empower Agricultural Research Communities,” Agris on-line Papers in Economics and Informatics 4, No. 4 (2012): 11-18. http://online.agris.cz/files/2012/agris_on-line_2012_4_geser_jaques_manouselis_protonotarios_keizer_sicilia.pdf.

Gessler, Damian DG, Blazej Bulka, Evren Sirin, Hans Vasquez-Gross, John Yu, and Jill Wegrzyn. “iPlant SSWAP (Simple Semantic Web Architecture and Protocol) enables semantic pipelines for biodiversity.,” S4BioDiv Semantics for Biodiversity. Proc. of the First Intl Workshop on Semantics for Biodiversity. CEUR Workshop Proceedings. 979 (2013): . http://ceur-ws.org/Vol-979/WS_s4biodiv2013_paper_9.pdf.

Gessler, Damian DG, Blazej Bulka, Evren Sirin, Yan Kang, Pavel Klinov, Hans Vasquez-Gross, John Yu, and Jill Wegrzyn. “iPlant Semantic Web Platform uses SSWAP (Simple Semantic Web Architecture and Protocol) to enable Semantic Pipelines across Distributed Web and High Performance Computing Resources,” Semantic Web Challenge 2012, The 11th International Semantic Web Conferene (2012): . http://challenge.semanticweb.org/2012/submissions/swc2012_submission_18.pdf.

Gessler, Damian DG, Gary S. Schiltz, Greg D. May, Shulamit Avraham, Christopher D. Town, David Grant, and Rex T. Nelson. “SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services,” BMC Bioinformatics 10 (2009): 309. doi: 10.1186/1471-2105-10-309.

Gnimpieba, Etienne Z., Brent S. Anderson, Abalo Chango, and Carol M. Lushbough. “RESTful API in Life Science Research Systems and Data Integration Challenges: Linking Metabolic Pathway, Metabolic Network, Gene and Publication,” Journal of Communication and Computer 10 (2013): 1196-1199. http://www.davidpublishing.com/davidpublishing/Upfile/12/9/2013/2013120984556665.pdf.

Gnimpieba, Etienne Z., Douglas Jennewein, Luke Fuhrman, and Carol M. Lushbough. “Bioinformatics Knowledge Transmission (training, learning, and teaching): overview and flexible comparison of computer based training approaches,” arXiv 1310.8383 (2013): . http://arxiv.org/abs/1310.8383.

Gnimpieba, Etienne Z., Douglas Jennewein, Luke Fuhrman, and Carol M. Lushbough. “Multidisciplinarity in Knowledge Transmision Management System (KTMS) evaluation,” Proceedings from the The 2013 International Conference on e-Learning, e-Business, Enterprise Information Systems, and e-Government (2013): EEE7278. http://world-comp.org/p2013/EEE7278.pdf.

Goff, Stephen A., and Qifa Zhang. “Heterosis in elite hybrid rice: speculation on the genetic and biochemical mechanisms,” Current Opinion in Plant Biology 16, No. 2 (2013): 221-227. doi: 10.1016/j.pbi.2013.03.009.

Goff, Stephen A., Matthew Vaughn, Sheldon McKay, Eric Lyons, Ann E. Stapleton, Damian Gessler, Naim Matasci et al. “The iPlant Collaborative: cyberinfrastructure for plant biology,” Frontiers in Plant Genetics and Genomics 2 (2011): 34. doi: 10.3389/fpls.2011.00034.

Gorton, Ian. “Cyberinfrastructures: Where Scientific Research and Software Engineering Collide,” Computer 1 (2013): . http://doi.ieeecomputersociety.org/10.1109/MC.2013.336.

Gorton, Ian, Yan Liu, Carina Lansing, Todd Elsethagen, and Kerstin Kleese van Dam. “Build less code deliver more science: an experience report on composing scientific environments using component-based and commodity software platforms,” Proceeding CBSE '13 Proceedings of the 16th International ACM Sigsoft symposium on Component-based software engineering (2013): 159-168. doi: 10.1145/2465449.2465452.

Hanlon, 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 Merchant. “My-Plant.org: A phylogenetically structured social network,” Gateway Computing Environments Workshop (GCE) (2010): 1-8. doi: 10.1109/GCE.2010.5676118.

Harris, Stephen E., Marissa Bellino. “DNA Barcoding from NYC to Belize,” Science 342, No. 6156 (2013): 1462-1463. doi: 10.1126/science.1230006.

Hofberger, Johannes A., Eric Lyons, Patrick P. Edger, J. Chris Pires, and M. Eric Schranz. “Whole Genome and Tandem Duplicate Retention facilitated Glucosinolate Pathway Diversification in the Mustard Family,” Genome Biology and Evolution evt162 (2013): . doi: 10.1093/gbe/evt162.

Holuigue, Loreto, Jean-Philippe Vielle-Calzada, and Rodrigo A. Gutiérrez. “Crops in all shapes and sizes,” Genome Biology 9 No. 9 (2008): 319. doi: 10.1186/gb-2008-9-9-319.

Ibarra-Laclette, Enrique, Eric Lyons, Gustavo Hernández-Guzmán, Claudia Anahí Pérez-Torres, Lorenzo Carretero-Paulet, Tien-Hao Chang, Tianying Lan, Andreanna J. Welch, María Jazmín Abraham Juárez, June Simpson, Araceli Fernández-Cortés, Mario Arteaga-Vázquez, Elsa Góngora-Castillo, Gustavo Acevedo-Hernández, Stephan C. Schuster, Heinz Himmelbauer, André E. Minoche, Sen Xu, Michael Lynch, Araceli Oropeza-Aburto, Sergio Alan Cervantes-Pérez, María de Jesús Ortega-Estrada, Jacob Israel Cervantes-Luevano, Todd P. Michael, Todd Mockler, Douglas Bryant, Alfredo Herrera-Estrella, Victor A. Albert , and Luis Herrera-Estrella. “Architecture and evolution of a minute plant genome,” Nature 498 (2013): 94-98. doi: 10.1038/nature12132.

Izquierdo-Carrasco, F., J. Cazes, S. A. Smith, and A. Stamatakis. “PUmPER: Phylogenies Updated Perpetually,” Bioinformatics (2014): btu053. http://bioinformatics.oxfordjournals.org/content/early/2014/01/28/bioinformatics.btu053.full.pdf.

Izquierdo-Carrasco, Fernando, Nikolaos Alachiotis, Simon Berger, Toma´s Flouri, Solon P. Pissis, and Alexandros Stamatakis. “A generic Vectorization Scheme and a GPU kernel for the Phylogenetic Likelihood Library,” Exelixis Lab Technical Report (2013): . http://sco.h-its.org/exelixis/pubs/Exelixis-RRDR-2013-3.pdf.

Jiao, Yuannian, Jim Leebens-Mack, Saravanaraj Ayyampalayam, John E. Bowers, Michael R. McKain, Joel McNeal, Megan Rolf et al. “A genome triplication associated with early diversification of the core eudicots,” Genome Biology 13, No. 1 (2012): R3. doi: 10.1186/gb-2012-13-1-r3.

John Deck, Katherine Barker, Reed Beaman, Pier Luigi Buttigieg, Gabriele Dröge, Robert Guralnick, Chuck Miller, Éamonn Ó Tuama, Zack Murrell, Cynthia Parr0, Bob Robbins, Dmitry Schigel, Brian Stucky, Ramona Walls, John Wieczorek, John Wooley. “Clarifying Concepts and Terms in Biodiversity Informatics,” Standards in Genomic Science 8, No. 2 (2013): . doi: 10.4056/sigs.3907833.

Johnson, Marc TJ, Eric J. Carpenter, Zhijian Tian, Richard Bruskiewich, Jason N. Burris, Charlotte T. Carrigan, Mark W. Chase et al. “Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes,” PLoS One 7, No. 11 (2012): e50226. doi: 10.1371/journal.pone.0050226.

Jordan, Chris, Dan Stanzione, Doreen Ware, Jerry Lu, and Christos Noutsos. “Comprehensive data infrastructure for plant bioinformatics,” Cluster Computing Workshops and Posters (CLUSTER WORKSHOPS), 2010 IEEE International Conference on (2010): 1-5. doi: 10.1109/CLUSTERWKSP.2010.5613093.

Jordan, Chris, Maria Esteva, David Walling, Tomilsav Urban, and Sivakumar Kulasekaran. “Responses to Data Management Requirements at the National Scale,” Research Data Management (2013): 64. http://www.clir.org/pubs/reports/pub160/pub160.pdf#page=73.

Joshi, Trupti, Michael R. Fitzpatrick, Shiyuan Chen, Yang Liu, Hongxin Zhang, Ryan Z. Endacott, Eric C. Gaudiello, Gary Stacey, Henry T. Nguyen, and Dong Xu. “Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding,” Nucleic acids research gkt905 (2013): . doi: 10.1093/nar/gkt905.

Joshi, Trupti, Michael R. Fitzpatrick, Shiyuan Chen, Yang Liu, Hongxin Zhang, Ryan Z. Endacott, Eric C. Gaudiello, Gary Stacey, Henry T. Nguyen, and Dong Xu. “Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding,” Nucleic acids research 42, No. 1 (2013): D1245-D1252. doi: 10.1109/BIBM.2013.6732755.

Kakumanu, Akshay. “Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissues as Revealed by Deep Sequencing,” Digital Library and Archives, Electronic Theses and Dissertations at Virginia Tech etd-07062012-131158 (2012): . http://scholar.lib.vt.edu/theses/available/etd-07062012-131158/.

Kakumanu, Akshay, Madana MR Ambavaram, Curtis Klumas, Arjun Krishnan, Utlwang Batlang, Elijah Myers, Ruth Grene, and Andy Pereira. “Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissue Revealed by RNA-Seq,” Plant Physiology 160, No. 2 (2012): 846-867. doi: 10.1104/pp.112.200444.

Kharitonova, Yekaterina, Qiyam Tung, Alexander Danehy, Alon Efrat, and Kobus Barnard. “Client-side Backprojection of Presentation Slides into Educational Video,” Proceedings of the 20th ACM international conference on Multimedia (2012): 1005-1008. doi: 10.1145/2393347.2396368.

Khoury, Colin K., Stephanie Greene, John Wiersema, Nigel Maxted, Andy Jarvis, and Paul C. Struik. “An Inventory of Crop Wild Relatives of the United States,” Crop Science 53, No. 4 (2013): 1496-1508. doi: 10.2135/cropsci2012.10.0585.

Kim, Jeonghyun. “Data sharing and its implications for academic libraries,” New Library World 114, No. 11/12 (2013): . http://www.emeraldinsight.com/journals.htm?articleid=17097171&show=abstract.

Klinov, Pavel, Chiara Del Vescovo, and Thomas Schneider. “Incrementally Updateable and Persistent Decomposition of OWL Ontologies,” Proceedings of OWL: Experiences and Directions Workshop, CEUR Workshop Proceedings 849 (2012): 7. http://ceur-ws.org/Vol-849/paper_7.pdf.

Kluyver, T. A. and Osborne, C. P.. “Taxonome: a software package for linking biological species data.,” Ecology and Evolution 3, No. 5 (2013): 1262-1265. doi: 10.1002/ece3.529.

Kociumaka, Tomasz, Solon P. Pissis, Jakub Radoszewski, Wojciech Rytter, and Tomasz Wale. “Fast Algorithm for Partial Covers in Words,” Combinatorial Pattern Matching, Lecture Notes in Computer Science 7922 (2013): 177-188. http://students.mimuw.edu.pl/~kociumaka/files/cpm2013_paper.pdf.

Koehbach, 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. Gruber. “Cyclotide discovery in Gentianales revisited - identification and characterization of cyclic cystine-knot peptides and their phylogenetic distribution in Rubiaceae plants,” Biopolymers: Peptide Science (2013): . doi: 10.1002/bip.22328.

Koeniga, Daniel, José M. Jiménez-Gómeza, Seisuke Kimuraa, Daniel Fulopa, Daniel H. Chitwooda, Lauren R. Headlanda, Ravi Kumara, Michael F. Covingtona, Upendra Kumar Devisettya, An V. Tata, Takayuki Tohgee, Anthony Bolgerf, Korbinian Schneeberger, Stephan Ossowski, Christa Lanzb, Guangyan Xiongi, Mallorie Taylor-Teeplesa, Siobhan M. Bradya, Markus Paulyi, Detlef Weigel, Björn Usadel, Alisdair R. Ferniee, Jie Pengm, Neelima R. Sinhaa, and Julin N. Maloof. “Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato,” Proceedings of the National Academy of Sciences 110, No. 28 (2013): E2655-2662. doi: 10.1073/pnas.1309606110.

Koesterke, Lars, Dan Stanzione, Matt Vaughn, Stephen M. Welch, Waclaw Kusnierczyk, Jinliang Yang, Cheng-Ting Yeh, Dan Nettleton, and Patrick S. Schnable. “An Efficient and Scalable Implementation of SNP-Pair Interaction Testing for Genetic Association Studies,” Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW), 2011 IEEE International Symposium on (2011): 523-530. doi: 10.1109/IPDPS.2011.190.

Koesterke, Lars, James E. Koltes, Nathan T. Weeks, Kent Milfeld, Matthew W. Vaughn, James M. Reecy, and Dan Stanzione. “Discovery of biological networks using an optimized partial correlation coefficient with information theory algorithm on Stampede's Xeon and Xeon Phi processors,” Concurrency and Computation: Practice and Experience (2014): . doi: 10.1002/cpe.3252.

Koesterke, Lars, K. Milfeld, M.W. Vaughn, D. Stanzione, J.E. Koltes, N.T. Weeks, J.M. Reecy. “Optimizing the PCIT algorithm on stampede's Xeon and Xeon Phi processors for faster discovery of biological networks,” Proceeding XSEDE '13 Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery 14 (2013): . doi: 10.1145/2484762.2484794.

Kolker, Eugene, Elizabeth Stewart, and Vural Ozdemir. “Opportunities and Challenges for the Life Sciences Community,” OMICS: A Journal of Integrative Biology 16, No. 3 (2012): 138-147. doi: 10.1089/omi.2011.0152.

Kültz, Dietmar, David F. Clayton, Gene E. Robinson, Craig Albertson, Hannah V. Carey, Molly E. Cummings, Ken Dewar, Scott V. Edwards, Hans A. Hofmann, Louis J. Gross, Joel G. Kingsolver, Michael J. Meaney, Barney A. Schlinger, Alexander W. Shingleton, Marla B. Sokolowski, George N. Somero, Daniel C. Stanzione and Anne E. Todgham. “New Frontiers for Organismal Biology,” BioScience 63, No. 6 (2013): 464-471. doi: 10.1525/bio.2013.63.6.8.

Kvilekval, Kristian, Dmitry Fedorov, Utkarsh Gaur, Steve Goff, Nirav Merchant, B. S. Manjunath, and Ambuj K. Singh. “Bisque: Advances in Bioimage Databases,” IEEE Data Engineering Bulletin 35, No. 3 (2012): 56-64. http://sites.computer.org/debull/A12sept/bisque.pdf.

LeDuc, Richard, Matthew Vaughn, John M. Fonner, Michael Sullivan, James G. Williams, Philip D. Blood, James Taylor, and William Barnett. “Leveraging the national cyberinfrastructure for biomedical research,” Journal of American Medical Informatics Association (2013): . doi: 10.1136/amiajnl-2013-002059.

Lee, Michael T., and Robert K. Peet.. “VegBank: a permanent online repository for international plot and relevé data,” Arctic Vegetation Archive (AVA) Workshop (2013): 66. http://www.researchgate.net/publication/257021400_Arctic_Vegetation_Archive_(AVA)_Workshop_Proceedings/file/5046352432d6cd73cb.pdf#page=66.

Lenards, Andrew, Nirav Merchant, and Dan Stanzione. “Building an environment to facilitate discoveries for plant sciences,” Proceedings of the 2011 ACM workshop on Gateway computing environments (2011): 51-58. doi: 10.1145/2110486.2110494.

Lisch, Damon. “How important are transposons for plant evolution?,” Nature Reviews Genetics 4, No. 1 (2012): 49-61. doi: 10.1038/nrg3374.

Liu, Jun. “W7 Model of Provenance and Its Use in the Context of Wikipedia,” The University of Arizona Campus Repository, UA Theses and Dissertations, Dissertations (2011): . http://arizona.openrepository.com/arizona/handle/10150/145314.

Liu, Jun, and Sudha Ram. “Who does what: Collaboration patterns in the wikipedia and their impact on article quality,” ACM Transactions on Management Information Systems (TMIS) 2, No. 2 (2011): 11. doi: 10.1145/1985347.1985352.

López, R., and Juan Félix San-Juan. “An e-Science project in Astrodynamics and Celestial Mechanics fields,” Computer Physics Communications 184, No. 5 (2013): 1381-1386. doi: 10.1016/j.cpc.2013.01.003.

Lushbough, Carol M., Etienne Z. Gnimpieba, and Rion Dooley. “Life science data analysis workflow development using the bioextract server leveraging the iPlant collaborative cyberinfrastructure,” Concurrency and Computation: Practice and Experience (2014): . doi: 10.1002/cpe.3237.

Macilwain, Colin. “Systems Biology: Evolving into the Mainstream,” Cell 144, No. 6 (2011): 839-841. doi: 10.1016/j.cell.2011.02.044.

Makinde, Diran. “African Orphan Crops Consortium–a NEPAD-led initiative,” Viewpoints, Biosciences for Farming in Africa January (2014): . http://b4fa.org/wp-content/uploads/2014/01/Viewpoints-Makinde.pdf.

Mark A. Miller, Terri Schwartz, Wayne Pfeiffer. “Embedding CIPRES science gateway capabilities in phylogenetics software environments,” Proceeding XSEDE '13 Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery, Article No. 40, ACM New York, NY, USA ©2013 40 (2013): . doi: 10.1145/2484762.2484806.

Maxime Crochemore, Costas S. Iliopoulos, Tomasz Kociumaka, Marcin Kubica, Alessio Langiu, Solon P. Pissis, Jakub Radoszewski, Wojciech Rytter, and Tomasz Walen. “Order-Preserving Incomplete Sux Trees and Order-Preserving Indexes,” Spires 2013 draft (2013): . http://students.mimuw.edu.pl/~kociumaka/files/spire2013_draft.pdf.

McCarthy, Fiona M., Eric Lyons. “From data to function: Functinal modeling of poultry genomics data,” Poultry Science 92, No. 9 (2013): 2519-2529. doi: 10.3382/ps.2012-02808.

Schatz, Michael C., Lyza G. Maron, Joshua C. Stein, Alejandro Hernandez Wences, James Gurtowski, Eric Biggers, Hayan Lee et al.. “New whole genome de novo assemblies of three divergent strains of rice (O. sativa) documents novel gene space of aus and indica,” bioRxiv (2014): . doi: 10.1101/003764.

McDonald, John, and Steve Hart. “Latest Technology in Irrigation Management in Nursery Production,” ISHS Acta Horticulturae 1014: Proceedings of the International Plant Propagators' Society (2014): . http://www.actahort.org/members/showpdf?booknrarnr=1014_16.

McKay, Sheldon J., Edwin J. Skidmore, Christopher J. LaRose, Andre W. Mercer, and Christos Noutsos. “Cloud Computing with iPlant Atmosphere,” Current Protocols in Bioinformatics (2013): 9-15. doi: 10.1002/0471250953.bi0915s43.

McKay, Sheldon J., Ismael A. Vergara, and Jason E. Stajich. “Using the Generic Syteny Browser (GBrowse_syn),” Current protocols in bioinformatics (2010): 9-12. doi: 10.1002/0471250953.bi0912s31.

McLay, Robert, Dan Stanzione, S. J. Mckay, and Travis Wheeler. “A Scalable Parallel Implementation of the Neighbor Joining Algorithm for Phylogenetic Trees,” ICCABS Conference, Orlando, FL (2011): . https://pods.iplantcollaborative.org/wiki/download/attachments/7510864/NINJA-Windjammer-pub.pdf.

Melicher, Dacotah, Alex S. Torson, Ian Dworkin, and Julia H. Bowsher. “A pipeline for the de novo assembly of the Themira biloba (Sepsidae: Diptera) transcriptome using a multiple k-mer length approach,” BMC genomics 15, No. 1 (2014): 188. doi: 10.1186/1471-2164-15-188.

Micklos, David, Susan Lauter, and Amy Nisselle. “Lessons from a Science Education Portal,” Science 334, No. 6063 (2011): 1657-1658. doi: 10.1126/science.1197074.

Miller, Allison J., Naim Matasci, Heidi Schwaninger, Mallikarjuna K. Aradhya, Bernard Prins, Gan-Yuan Zhong, Charles Simon, Edward S. Buckler, and Sean Myles. “Vitis Phylogenomics: Hybridization Intensities from a SNP Array Outperform Genotype Calls,” PLOS ONE 8, No. 11 (2013): e78680. doi: 10.1371/journal.pone.0078680.

Miller, Mark A., Wayne Pfeiffer, and Terri Schwartz. “The CIPRES science gateway: enabling high-impact science for phylogenetics researchers with limited resources,” Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond (2012): 39. doi: 10.1145/2335755.2335836.

Miller, Robert J., John Hocevar, Robert P. Stone, and Dmitry V. Fedorov. “Structure-Forming Corals and Sponges and Their Use as Fish Habitat in Bering Sea Submarine Canyons,” PLoS One 7, No. 3 (2012): e33885. doi: 10.1371/journal.pone.0033885.

Minervini, Massimo, Mohammed M. Abdelsamea, Sotirios A. Tsaftaris. “Image-based plant phenotyping with incremental learning and active contours,” Ecological Informatics (2013): . doi: 10.1016/j.ecoinf.2013.07.004.

Mirarab, Siavash, Nam Nguyen, and Tandy Warnow. “PASTA: ultra-large multiple sequence alignment,” University of Texas, Austin (2014): . http://www.cs.utexas.edu/~smirarab/papers/pasta.pdf.

Mogel, Karl Haro von . “Taking the Phenomics Revolution into the Field,” Crops, Soils, Agronomy News Magazine (2013): . doi: 10.2134/csa2013-58-3-1.

Mohan, Anup, Thomas Hacker, Gregory P. Rodgers. “Developing a high-volume batch submission system for earthquake engineering,” Proceeding XSEDE '13 Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery, Article No. 51, ACM New York, NY, USA ©2013 51 (2013): . doi: 10.1145/2484762.2484784.

Mohan, Anup, Thomas Hacker, Gregory P. Rodgers, and Tanzima Islam. “Batchsubmit: a high-volume batch submission system for earthquake engineering simulation,” Concurrency and Computation: Practice and Experience (2014): . doi: 10.1002/cpe.3234.

Moore, Reagan W.. “Extensible Generic Data Management Software,” arXiv 1309.5372 (2013): . http://arxiv.org/abs/1309.5372.

Moore, Reagan W., and Arcot Rajsekar. “iRODS: Data Sharing Technology Integrating Communities of Practice,” Geoscience and Remote Sensing Symposium (IGARSS), 2010 IEEE International (2010): 1984-1987. doi: 10.1109/IGARSS.2010.5649894.

Moore, Reagan, and William L. Anderson. “ASIS&T research data access and preservation summit: Conference summary,” Bulletin of the American Society for Information Science and Technology 36, No. 6 (2010): 42-45. doi: 10.1002/bult.2010.1720360611.

Moreau, Magali, Timothy Westlake, Giulio Zampogna, George Popescu, Miaoying Tian, Christos Noutsos, and Sorina Popescu. “The Arabidopsis oligopeptidases TOP1 and TOP2 are salicylic acid targets that modulate SA-mediated signaling and the immune response,” The Plant Journal (2013): . doi: 10.1111/tpj.12320.

Morueta‐Holme, Naia, Brian J. Enquist, Brian J. McGill, Brad Boyle, Peter M. Jørgensen, Jeffrey E. Ott, Robert K. Peet et al.. “Habitat area and climate stability determine geographical variation in plant species range sizes,” Ecology Letters (2013): . doi: 10.1111/ele.12184.

Naim Matasci, Sheldon J. McKay. “Phylogenetic Analysis with the iPlant Discovery Environment,” Current Protocols in Bioinformatics (2013): . doi: 10.1002/0471250953.bi0613s42.

Nelson, Rex T., Shulamit Avraham, Randy C. Shoemaker, Gregory D. May, Doreen Ware, and Damian DG Gessler. “Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for bioinformatics resource discovery and disparate data and service integration,” BioData Mining 3, No. 1 (2010): 3. doi: 10.1186/1756-0381-3-3.

Ningthoujam, Sanjoy Singh, Manabendra Dutta Choudhury, Kumar Singh Potsangbam, Pankaj Chetia, Lutfun Nahar, Satyajit D. Sarker, Norazah Basar, and Anupam Das Talukdar. “NoSQL Data Model for Semi‐automatic Integration of Ethnomedicinal Plant Data from Multiple Sources,” Phytochemical Analysis (2014): . doi: 10.1002/pca.2520.

Nodine, Michael D., Anthony C. Bryan, Adriana Racolta, Keith V. Jerosky, and Frans E. Tax. “A few standing for many: embryo receptor-like kinases,” Trends in Plant Science 16, No. 4 (2011): 211-217. doi: 10.1016/j.tplants.2011.01.005.

Numa, Hisataka, and Takeshi Itoh. “MEGANTE: A Web-based System for Integrated Plant Genome Annotation,” Plant and Cell Physiology (2013): pct157. doi: 10.1093/pcp/pct157.

O'Meara, Brian C.. “Evolutionary Inferences from Phylogenies: A Review of Methods,” Annual Review of Ecology, Evolution, and Systematics 43 (2012): 267-285. doi: 10.1146/annurev-ecolsys-110411-160331.

Oaks, Jamie R. . “An Improved Approximate-Bayesian Model-choice Method for Estimating Shared Evolutionary History,” arXiv preprint arXiv:1402.6303 [q-bio.PE] (2014): . http://arxiv.org/abs/1402.6303.

Oaks, Jamie R., Charles W. Linkem, and Jeet Sukumaran. “Implications of uniformly distributed, empirically informed priors for phylogeographical model selection: A reply to Hickerson et al,” arXiv preprint arXiv:1402.6397 [q-bio.PE] (2014): . http://arxiv.org/abs/1402.6397.

Okii, D., A. C. Luseko, P. Tukamuhabwa, and M. Maphosa. “Application of Bioinformatics in Crop Improvement: Annotating the Putative Soybean Rust resistance gene Rpp3 for Enhancing Marker Assisted Selection,” Journal of Proteomics and Bioinformatics 7 (2014): 001-009. doi: 10.4172/jpb.1000296.

Oliver, Shannon L., Andrew J. Lenards, Roger A. Barthelson, Nirav Merchant, Sheldon J. McKay. “Using the iPlant Collaborative Discovery Environment,” Current Protocols in Bioinformatics, Available Online: 1 June 2013. (2013): 1-22. doi: 10.1002/0471250953.bi0122s42.

Parr, Cynthia S., Robert Guralnick, Nico Cellinese, and Roderic DM Page. “Evolutionary informatics: unifying knowledge about the diversity of life,” Trends in Ecology & Evolution 27, No. 2 (2012): 94-103. doi: 10.1016/j.tree.2011.11.001.

Perianayagam, Somu, Gregory R. Andrews, and John H. Hartman. “Rex: A toolset for reproducing software experiments,” Proceedings from the 2010 IEEE International Conference on Bioinformatics and Biomedicine (2010): 613-617. doi: 10.1109/BIBM.2010.5706639.

Piel, William H.. “Obstacles and Avenues Facing Phyloinformatic Research,” Proceedings of TDWG 2008 (2008): 28-29. http://www.tdwg.org/fileadmin/2008conference/documents/Proceedings2008.pdf#page=28.

Ragupathy, Raja, Frank M. You, Sylvie Cloutier. “Arguments for standardizing transposable element annotation in plant genomes,” Trends in Plant Science 18, No. 7 (2013): 367-376. doi: 10.1016/j.tplants.2013.03.005,.

Rajasekar, Arcot.. “The Librarian & the Big Data: Bridging the Gap,” Proceedings from the 2014 e-Science Symposium at University of Massachusetts Medical School Paper 6. (2014): . http://escholarship.umassmed.edu/escience_symposium/2014/program/6.

Rajasekar, Arcot, Hao Xu, and Reagan Moore. “Note on Three Classes of Data Grid Operations,” Journal of Computer and Communications 2, No. 6 (2014): 1-6. doi: 10.4236/jcc.2014.26001.

Rajasekar, Arcot, Tom Carsey, Jonathan Crabtree, Merce Crosas, Gary King, Hye-Chung Kum, Howard Lander, Sharlini Sankaran. “Design of the DataBridge: A System for Sociometric Analysis ofLong tail Science Data,” (2013): . http://databridge.web.unc.edu/files/2013/07/DataBridgeMP-LAST.pdf.

Ram, Sudha and Jun Liu. “A Semantic Foundation for Provenance Management,” Journal on Data Semantics 1, No. 1 (2012): 11-17. doi: 10.1007/s13740-012-0002-0.

Ram, Sudha, and Jun Liu. “Provenance Management in BioSciences,” Advances in Conceptual Modeling–Applications and Challenges, Lecture Notes in Computer Science 6413 (2010): 54-64. doi: 10.1007/978-3-642-16385-2_8.

Ram, Sudha, and Wei Wei. “FASTS: FAcets Structured Tag Space – A Novel Approach to Organize and Reuse Social Bookmarking Tags,” Global Persepctives on Design Science Research, Lecture Notes in Computer Science 6105 (2010): 426-438. doi: 10.1007/978-3-642-13335-0_29.

Ram, Sudha, and Wei Wei. “How social is social bookmarking?,” Business Applications of Social Network Analysis (BASNA), 2010 IEEE International Workshop on (2010): 1-8. doi: 10.1109/BASNA.2010.5730302.

Ram, Sudha, Kunpeng Zhang, and Wei Wei. “Linking biological databases semantically for knowledge discovery,” Advances in Conceptual Modeling–Challenges and Opportunities, Lecture Notes in Computer Science 5232 (2008): 22-32. doi: 10.1007/978-3-540-87991-6_4.

Ramamoorthy, Vellaisamy, Sourabh Dhingra, Alexander Kincaid, Sourabha Shantappa, Xuehuan Feng, Ana M. Calvo. “The Putative C2H2 Transcription Factor MtfA Is a Novel Regulator of Secondary Metabolism and Morphogenesis in Aspergillus nidulans,” PLoS ONE 8, No. 9 (2013): e74122. doi: 10.1371/journal.pone.0074122.

Ray Ming, Robert VanBuren, Yanling Liu, Mei Yang, Yuepeng Han, Lei-Ting Li, Qiong Zhang, Min-Jeong Kim, Michael C Schatz, Michael Campbell, Jingping Li, John E Bowers, Haibao Tang, Eric Lyons, Ann A Ferguson, Giuseppe Narzisi, David R Nelson, Crysten E Blaby-Haas, Andrea R Gschwend, Yuannian Jiao, Joshua P Der, Fanchang Zeng, Jennifer Han, Xiang Jia Min, Karen A Hudson, Ratnesh Singh, Aleel K Grennan, Steven J Karpowicz, Jennifer R Watling, Kikukatsu Ito, et al.. “Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.),” Genome Biology 14, No. R41 (2013): . doi: 10.1186/gb-2013-14-5-r41.

Reddy, Anireddy SN, Mark F. Rogers, Dale N. Richardson, Michael Hamilton, and Asa Ben-Hur. “Deciphering the Plant Splicing Code: Experimental and Computational Approaches for Predicting Alternative Splicing and Splicing Regulatory Elements,” Frontiers in Plant Science 3 (2012): 18. doi: 10.3389/fpls.2012.00018.

Reecy, 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.. “Computational resources to facilitate variant discovery and analysis,” In ADSA-ASAS Midwest Meeting 23 (2014): . https://asas.confex.com/asas/mw14/webprogram/Paper3463.html.

Rhee, Seung Yon, and Marek Mutwil. “Towards revealing the functions of all genes in plants,” Trends in Plant Science (2013): . doi: 10.1016/j.tplants.2013.10.006.

Rion Dooley, Matthew R. Hanlon. “Recipes 2.0: Building for Today and Tomorrow,” Proceedings of the 5th International Workshop on Science Gateways (IWSG 2013) 993, No. 16 (2013): . http://ceur-ws.org/Vol-993/paper16.pdf.

Robinson, Natalie, James Regetz, and Robert P. Guralnick. “EarthEnv-DEM90: A nearly-global, void-free, multi-scale smoothed, 90m digital elevation model from fused ASTER and SRTM data,” ISPRS Journal of Photogrammetry and Remote Sensing 87 (2014): 57–67. doi: 10.1016/j.isprsjprs.2013.11.002.

Rodrigo, Allen, Susan Alberts, Karen Cranston, Joel Kingsolver, Hilmar Lapp, Craig McClain, Robin Smith, Todd Vision, Jory Weintraub, Brian Wiegmann. “Science Incubators: Synthesis Centers and Their Role in the Research Ecosystem,” PLoS Biology 11, No. 1 (2013): e1001468. doi: 10.1371/journal.pbio.1001468.

Rogowitz, Bernice E., and Naim Matasci. “Metadata Mapper: a web service for mapping data between independent visual analysis components, guided by perceptual rules,” Proceedings from SPIE 7865, Human Vision and Electronic Imaging XVI 786501 (2011): . doi: 10.1117/12.881734.

Ruhfel, Brad R., Matthew A. Gitzendanner, Pamela S. Soltis, Douglas E. Soltis, and J. Gordon Burleigh. “From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes,” BMC evolutionary biology 14, No. 1 (2014): 23. doi: 10.1186/1471-2148-14-23.

Schaeffer, Mary L., Lisa C. Harper, Jack M. Gardiner, Carson M. Andorf, Darwin A. Campbell, Ethalinda KS Cannon, Taner Z. Sen, and Carolyn J. Lawrence. “MaizeGDB: curation and outreach go hand-in-hand,” Database: the journal of biological databases and curation 2011 (2011): bar022. doi: 10.1093/database/bar022.

Schatz, Michael C., Jan Witkowski, and W. Richard McCombie. “Current Challenges in de novo plant genome sequencing and assembly,” Genome Biology 13, No. 4 (2012): 243. doi: 10.1186/gb-2012-13-4-243.

Schnable, James C., and Eric Lyons. “Comparative genomics with maize and other grasses: from genes to genomes!,” Maydica 56, No. 2 (2012): . http://www.maydica.org/articles/56_1763.pdf.

Schnable, James C., Michael Freeling, and Eric Lyons. “Genome-wide analysis of syntenic gene deletion in the grasses,” Genome Biology and Evolution 4, No. 3 (2012): 265-277. doi: 10.1093/gbe/evs009.

Schneider, Todd, Ali Hashemi, Mike Bennett, Mary Brady, Cory Casanave, Henson Graves, Michael Gruninger, Nicola Guarino, Anatoly Levenchuk, Ernie Lucier, Leo Obrst, Steve Ray, Ram D. Sriram, Amanda Vizedom, Matthew West, Trish Whetzel, Peter Yim. “Ontology for big systems: The Ontology Summit 2012 Communiqué,” Applied Ontoloty 7, No. 3 (2012): 357-371. doi: 10.3233/AO-2012-0111.

Service, Robert F. “Biology's Dry Future,” Science 342 (2013): 186-189. http://cdn.sparkart.net/immunityproject/Content/misc/Science-2013-Service-186-9.pdf.

Service, Robert F. . “Biology's Dry Future,” Science Now 342, No. 6155 (2013): 186-189. doi: 10.1126/science.342.6155.186.

Shaffer, Christopher D., Consuelo J. Alvarez, April E. Bednarski, David Dunbar, Anya L. Goodman, Catherine Reinke, Anne G. Rosenwald et al. “A Course-Based Research Experience: How Benefits Change with Increased Investment in Instructional Time,” CBE-Life Sciences Education 13, No. 1 (2014): 111-130. doi: 10.1187/cbe-13-08-0152.

Simmerman, Scott, Jingyuan Wang, James Osborne, Kimberly Shook, Jian Huang, William Godsoe, and Theodore Simons. “Exploring similarities among many species distributions,” Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond (2012): 38. doi: 10.1145/2335755.2335835.

Skidmore, Edwin, Seung-jin Kim, Sangeeta Kuchimanchi, Sriramu Singaram, Nirav Merchant, and Dan Stanzione. “iPlant Atmosphere: A Gateway to Cloud Infrastructure for the Plant Sciences,” Proceedings of the 2011 ACM workshop on Gateway computing environmentsPages 59-64. (2011): 59-64. doi: 10.1145/2110486.2110495.

Smith, 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 Brooks. “Using Flatbed Scanners to Collect High-resolution Time-lapsed Images of the Arabidopsis Root Gravitropic Response,” JoVE (Journal of Visualized Experiments) 83 (2014): e50878-e50878. doi: 10.3791/50878.

Smith, Stephen A., and Brian C. O’Meara. “treePL: Divergence time estimation using penalized likelihood for large phylogenies,” Bioinformatics 28, No. 20 (2012): 2689-2690. doi: 10.1093/bioinformatics/bts492.

Smith, Stephen A., Jeremy M. Beaulieu, Alexandros Stamatakis, and Michael J. Donoghue. “Understanding angiosperm diversification using small and large phylogenetic trees,” American Journal of Botany 98, No. 3 (2011): 404-414. doi: 10.3732/ajb.1000481.

Soderlund, Carol, William Nelson, Mark Willer, David R. Gang. “TCW: Transcriptome Computational Workbench,” TCW: Transcriptome Computational Workbench. PLoS ONE 8, No. 7 (2013): e69401. doi: 10.1371/journal.pone.0069401.

Soltis, Douglas E., Matthew A. Gitzendanner, Gregory Stull, Michael Chester, Andre Chanderbali, Srikar Chamala, Ingrid Jordon-Thaden, Pamela S. Soltis, Patrick S. Schnable, and W. Brad Barbazuk. “The potential of genomics in plant systematics,” Taxon 62, No. 5 (2013): 886-898. http://www.ingentaconnect.com/content/iapt/tax/2013/00000062/00000005/art00005.

Soltis, Pamela S. and Douglas E. Soltis. “Angiosperm Phylogeny: A Framework for Studies of Genome Evolution,” Plant Genome Diversity 2 (2013): 1-11. doi: 10.1007/978-3-7091-1160-4_1.

Stamatakis, Alexandros, Andre J. Aberer, C. Goll, Stephen A. Smith, Simon A. Berger, and Fernando Izquierdo-Carrasco. “RAxML-Light: a tool for computing terabyte phylogenies,” Bioinformatics 28, No. 15 (2012): 2064-2066. doi: 10.1093/bioinformatics/bts309.

Stanzione, Dan. “The iPlant Collaborative: Cyberinfrastructure to Feed the World,” Computer 44, No. 11 (2011): 44-52. doi: 10.1109/MC.2011.297.

Stein, Lincoln D.. “Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges,” Nature Reviews Genetics 9 No. 9 (2008): 678-688. doi: 10.1038/nrg2414.

Stillman, Jonathon H., Mark Denny, Dianna K. Padilla, Marvalee H. Wake, Sheila Patek, and Brian Tsukimura. “Grand Opportunities: Strategies for Addressing Grand Challenges in Organismal Animal Biology,” Integrative and comparative biology 51, No. 1 (2011): 7-13. doi: 10.1093/icb/icr052.

Stoltzfus, 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 Jordan. “Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient,” BMC Bioinformatics 14, No.158 (2013): . doi: 10.1186/1471-2105-14-158.

Straub, Shannon CK, Matthew Parks, Kevin Weitemier, Mark Fishbein, Richard C. Cronn, and Aaron Liston. “Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics,” American Journal of Botany 99, No. 2 (2011): 349-364. doi: 10.3732/ajb.1100335.

Strickler, Susan R., Aureliano Bombarely, and Lukas A. Mueller. “Designing a transcriptome next-generation sequencing project for a nonmodel plant species,” American Journal of Botany 99, No. 2 (2011): 257-266. doi: 10.3732/ajb.1100292.

Stull, 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. Gitzendanner. “A Targeted Enrichment Strategy for Massively Parallel Sequencing of Angiosperm Plastid Genomes,” Applications in Plant Sciences 1, No. 2 (2013): . doi: 10.3732/apps.1200497.

Sushinsky, Peter Werner, Marten Winter, Ian MacGregor-Fors Kühn, Mark McDonnell, Ulla Mörtberg, Petr Pysek, Stefan Siebert et al.. “A global analysis of the impacts of urbanization on bird and plant diversity reveals key anthropogenic drivers,” Proceedings of the Royal Society of Biological Sciences 281 (2014): 20133330. http://www.ufz.de/export/data/1/56654_Aronson-etal_ProcRoySocB-2014.pdf.

Swenson, Shel, Yogesh Simmhan, Viktor Prasanna, Manish Parashar, Jason Riedy, David Bader, and Richard Vuduc. “Sustainable Software Development for Next-Gen Sequencing (NGS) Bioinformatics on Emerging Platforms,” Cornel University Library 1309, No. 1828 (2013): . http://arxiv.org/abs/1309.1828.

Tan, Wei, M. Brian Blake, Iman Saleh, and Schahram Dustdar. “Social-Network-Sourced Big Data Analytics,” Internet Computing, IEEE 17, No. 5 (2013): 62-69. doi: 10.1109/MIC.2013.100.

Tang, Haibao, and Eric Lyons. “The Evolution of Genome Structure,” International Journal of Evolution 1, No. 1 (2012): . doi: 10.4172/ievj.1000e105.

Tang, Haibao, and Eric Lyons. “Unleashing the Genome of Brassica Rapa,” Frontiers in Plant Science 3 (2012): 172. doi: 10.3389/fpls.2012.00172.

ter Steege, Hans, Nigel CA Pitman, Daniel Sabatier, Christopher Baraloto, Rafael P. Salomão, Juan Ernesto Guevara, Oliver L. Phillips et al. . “Hyperdominance in the Amazonian Tree Flora,” Science 342, No. 6156 (2013): 1243092. doi: 10.1126/science.1243092.

Thibault, Julien Charles, Julio C. Facelli, and Thomas E. Cheatham III. “iBIOMES: Managing and sharing biomolecular simulation data in a distributed environment,” Journal of Chemical Information and Modeling, Publication Date (Web): February 17, 2013 53, No. 3 (2013): 726-736. doi: 10.1021/ci300524j.

Uribe-Convers, Simon, Justin R. Duke, Michael J. Moore, and David C. Tank. “A Long PCR-Based Approach for DNA Enrichment Prior to Next-Generation Sequencing for Systematic Studies,” Applications in Plant Sciences 2, No. 1 (2014): . doi: 10.3732/apps.1300063.

Van Gorp, Pieter, and Louis Rose. “Guest editorsʼ introduction to the first issue on Experimental Software Engineering in the Cloud (ESEiC),” Science of Computer Programming (2013): . doi: 10.1016/j.scico.2013.12.007.

Vasquez‐Gross, Hans A., John J. Yu, Ben Figueroa, Damian DG Gessler, David B. Neale, and Jill L. Wegrzyn. “CartograTree: connecting tree genomes, phenotypes and environment,” Molecular Ecology Resources 13, No. 3 (2013): 528-537. doi: 10.1111/1755-0998.12067.

Verborgh, Ruben, Andreas Harth, Maria Maleshkova, Steffen Stadtmüller, Thomas Steiner, Mohsen Taheriyan, and Rik Van de Walle. “Survey of Semantic Description of REST APIs,” In REST: Advanced Research Topics and Practical Applications (2014): 69-89. doi: 10.1007/978-1-4614-9299-3_5.

Walls, 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, Andréa Matsunaga, Peter Midford,Norman Morrison, Éamonn Ó. Tuama, Mark Schildhauer, Barry Smith, Brian J. Stucky, Andrea Thomer, John Wieczorek, Jamie Whitacre, and John Wooley. “Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies,” PLOS ONE 9, No. 3 (2014): e89606. doi: 10.1371/journal.pone.0089606.

Wang Liya, Doreen Ware, Carol Lushbough, Nirav Merchant, and Lincoln Stein. “A genome-wide association study platform built on iPlant cyber-infrastructure,” Concurrency and Computation: Practice and Experience (2014): . doi: 10.1002/cpe.3236.

Wang, Liya, Lincoln D. Stein, Doreen Ware. “The relationships among GC content, nucleosome occupancy, and exon size,” arXiv preprint (2014): . http://arxiv.org/pdf/1404.2487.pdf.

Wang, Fei-Yue. “From AI to SciTS: Team Science and Research Intelligence,” Intelligent Systems, IEEE 26, No. 3 (2011): 2-4. doi: 10.1109/MIS.2011.49.

Wang, Fusheng, Cristobal Vergara–Niedermayr, and Peiya Liu. “Metadata based management and sharing of distributed biomedical data,” International Journal of Metadata, Semantics and Ontologies 9, No. 1 (2014): 42-57. doi: 10.1504/IJMSO.2014.059126.

Wang, Lin, Richard B. Peterson, and Thomas P. Brutnell. “Regulatory mechanisms underlying C4 photosynthesis,” New Phytologist 190, No. 1 (2011): 9-20. doi: 10.1111/j.1469-8137.2011.03649.x.

Wang, Lin, Yaqing Si, Lauren K. Dedow, Ying Shao, Peng Liu, and Thomas P. Brutnell. “A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq,” PLoS ONE 6, No. 10 (2011): e26426. doi: 10.1371/journal.pone.0026426.

Wang, Liya, and Lincoln D. Stein. “Modeling the evolution dynamics of exon-intron structure with a general random fragmentation process,” BMC Evolutionary Biology 13, No. 57 (2013): 1-15. doi: 10.1186/1471-2148-13-57.

Wang, Liya, and Lincoln Stein. “Localizing triplet periodicity in DNA and cDNA sequences,” BMC Bioinformatics 11, No. 1 (2010): 550. doi: 10.1186/1471-2105-11-550.

Waters, Amanda J., Paul Bilinski, Steve R. Eichten, Matthew W. Vaughn, Jeffrey Ross-Ibarra, Mary Gehring, and Nathan M. Springer. “Comprehensive analysis of imprinted genes in maize reveals limited conservation with other species and allelic variation forimprinting,” Cornel University Open Access e-Print Library (arXiv) (2013): . http://arxiv.org/pdf/1307.7678.pdf.

Waters, Amanda J., Paul Bilinski, Steven R. Eichten, Matthew W. Vaughn, Jeffrey Ross-Ibarra, Mary Gehring, and Nathan M. Springer. “Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species,” Proceedings of the National Academy of Sciences (2013): 201309182. doi: 10.1073/pnas.1309182110.

White, Jeffrey W., Pedro Andrade-Sanchez, Michael A. Gore, Kevin F. Bronson, Terry A. Coffelt, Matthew M. Conley, Kenneth A. Feldmann et al. “Field-based phenomics for plant genetics research,” Field Crops Research 133 (2012): 101-112. doi: 10.1016/j.fcr.2012.04.003,.

Wickett, Norman J., Siavash Mirarab, Nam Nguyen, Tandy Warnow, Eric Carpenter, Naim Matasci, Saravanaraj Ayyampalayam, Michael Barker, Gordon J. Burleigh, Matthew A. Gitzendanner, Brad Ruhfel, Eric Wafula, Josh Der, Sean W. Graham, Sarah Mathews, Michael Melkonian, Douglas E. Soltis, Pamela S. Soltis, Carl Rothfels, Lisa Pokorny, Jonathan Shaw, Lisa DeGironimo, Dennis Stevenson, Barbara Surek, Juan Carlos Villarreal, Béatrice Roure, Hervé Philippe, Claude W. dePamphilis, Tao Chen, Michael Deyholos, Jun Wang, Yong Zhang, Zhijian Tian, Zhixiang Yan, Xiaolei Wu, Xiao Sun, Gane Ka-Shu Wong, Jim Leebens-Mack. “A phylotranscriptomics analysis of the origin and early diversification of land plants,” PNAS One--NEED FULL CITATION (): . .

Williams, Caroline M., Hugh AL Henry, and Brent J. Sinclair. “Cold truths: how winter drives responses of terrestrial organisms to climate change,” Biological Reviews (2014): . doi: 10.1111/brv.12105.

Wilson, Adam M., Benoit Parmentier, and Walter Jetz. “Systematic land cover bias in Collection 5 MODIS cloud mask and derived products—A global overview,” Remote Sensing of Environment 141 (2014): 149-154. doi: 10.1016/j.rse.2013.10.025.

Wollbrett, Julien, Pierre Larmande, Frédéric de Lamotte, and Manuel Ruiz. “Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases,” BMC Bioinformatics 14, No. 126 (2013): . doi: 10.1186/1471-2105-14-126.

Woodward, Nicholas Joel, Weijia Xu, and Kent Norsworthy. “On automatically tagging web documents from examples,” Proceeding of of the 35th international ACM SIGIR conference on Research and development in information retrieval (2012): 1111-1112. doi: 10.1145/2348283.2348494.

Xu, Zheping, Jinzhong Cui, Zhaogai Wang, Fenghong Liu, and Guojun Liu. “The Architecture and Implementation of Biodiversity Digital Library in China,” Software Engineering (WCSE), 2010 Second World Congress on 1 (2010): 291-294. doi: 10.1109/WCSE.2010.167.

Zamer, William E. “A Cohesive Biology of Organisms is on the Horizon,” BioScience 61, No. 11 (2011): 848-849. doi: 10.1525/bio.2011.61.11.3.

Zheng, Chunfang, Krister Swenson, Eric Lyons, and David Sankoff. “OMG! Orthologs in Multiple Genomes – Competing Graph-Theoretical Formulations,” Algorithms in Bioinformatics, Lecture Notes in Computer Science 6833 (2011): 364-375. doi: 10.1007/978-3-642-23038-7_30.

Zhou, Lecong, Christopher Franck, Kuan Yang, Guillaume Pilot, Lenwood S. Heath, and Ruth Grene. “Mining for Meaning: Visualization Approaches to Deciphering Arabidopsis Stress Responses in Roots and Shoots,” OMICS: A Journal of Integrative Biology 16, No. 4 (2012): 208-228. doi: 10.1089/omi.2011.0111.