Preface First

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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): .

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): .

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): .

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.

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.

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.

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.

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.

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): .

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): .

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): .

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): .

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): .

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.

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): .

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): .

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.

Fox, Geoggrey, Dennis Gannon. “Using Clouds for Technical Computing,” Community Grids Lab, Pervasive Technology Labs at Indiana University (2013): .

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.

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): .

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): .

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.

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): .

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.

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): .

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. “ 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.

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): .

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.

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): .

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): .

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.

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.

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.

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