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Title Author(s) Volume, Issue Pages Type of Publication Year DOIsort descending
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 rate Tauriello, Gerardo, Heather M. Meyer, Richard S. Smith, Petros Koumoutasakos, and Adrienne H.K.... Technical Report 2015
A Bioinformatics Approach to Systemic Lupus Erythematosus and Autoimmunity Siefert, John 2015
A Statistical Model for Recreational Trails in Aerial Images Andrew Predohl, Scott Morris, and Kobus Barnard Conference Proceedings 2013
Introducing Undergraduate Students to Gene and Genome Structure through Gene Annotation Buckner, Brent W695 Conference Proceedings 2015
Does the climatic variability hypothesis explain the longitudinal range size gradient in North American trees? Donoghue, John Conference Proceedings 2012
Enhancing the Effectiveness of Team Science Committee on the Science of Team Science; Board on Behavioral, Cognitive, and Sensory Sciences;... 6 Journal 2015
Mammalian Model Species Trees for 1X Model Condition for Mirarab et. al. Mirarab, Sivash, Md Shamsuzzoha Bayzid, Bastien Boussau, and Tandy Warnow Repository 2014
CartograTree: Connection Forest Tree Genomes, Phenotypes, and Environment Hans Vasquez-Gross, Ben Figueroa, John Yu, Damian Gessler, David Neale, Jill Wegrzyn P0992 Conference Proceedings 2013
Leafy Spurge Genomics: A Model Perennial Weed to Investigate Development, Stress Responses, and Invasiveness Horvath, David, James V. Anderson, Wun S. Chao, Michael E. Foley, and MÙnevver Do_ramaci 63-78 Chapter 2015
The DOE Systems Biology Knowledgebase: Progress Toward a System for Collaborative and Reproducible Inference and Modeling of Biological Function in Plant Research Cottingham, Robert W. et al P1138 Conference Proceedings 2015
The Arabidopsis Information Portal: A First Glimpse Vaughn, Matt P11455 Conference Proceedings 2014
An interactive tool for semi-automated leaf annotation Minervini, Massimo, Mario Valerio Giuffrida, and Sotirios A. Tsaftaris Conference Proceedings 2015
Biological Computing Using the iPlant Discovery Environment Stein, Joshua, Jerry Lu, Christos Noutsos, Liya Wang, Roger Barthelson, Fusheng Wei, Naim Matasci... P0963 Conference Proceedings 2013
Cyberinfrastructure for Life Sciences - iAnimal resources for genomics and other data driven biology Koltes, J.E., J. Reecy, J. Carson, F. McCarthy, E. Fritz-Waters, J. Williams, E. Lyons, C.F. Baes,... Accepted Conference Proceedings 2014
Accordion: Multi-Scale Recipes for Adaptive Detection of Duplication Lewis, Russell, and John H. Hartman Conference Proceedings 2015
SynFind: compiling syntenic regions across any set of genomes on demand Tang, Haibao, Matthew D. Bomhoff, Evan Briones, Liangsheng Zhang, James C. Schnable, and Eric Lyons evv219 Journal 2015
Identification of SNPs in Water Buffalo using next generation sequencing data Fritz ER, J.E. Koltes, and JM Reecy. W113 Conference Proceedings 2013
Linking environmental filtering and disequilibrium to biogeography with a community climate framework Blonder, Benjamin, David Nogu_s-Bravo, Michael K. Borregaard, John C. Donoghue, Peter M. JÀrgensen... 96, No. 4 972-985 Journal 2015
Nordic Lifewatch Cooperation Final Report Hanssen, F., T. Heggberget, J. Bladt, D. Endresen, M. Forsius, et al Technical Report 2015
Whole Genome Comparisons with Oryza and Brachypodium using CoGe and SynMap Lyons, Eric, Haibao Tang, James C. Schnable W268 Conference Proceedings 2012
Protocol for the Generation of a Transcription Factor Open Reading Frame Collection (TFome) Gray, John, Brett Burdo et al 5, No. 15 Journal 2015
Hydrologic Data Sharing Using Open Source Softwareand Low-Cost Electronics Sadler, Jeffery Michael Journal 2015
Enabling Phenotypic Image Analysis Using Shared Cyberinfrastructure Miller, Nathan W418 Conference Proceedings 2012
Case Study: Enabling Forest Tree Genomics through Association Studies with the use of SSWAP Vasquez-Gross, Hans, Jacob Zieve, Damian Gessler, David Neale, and Jill Wegrzyn W462 Conference Proceedings 2014
Frontiers in Plant Systems Biology Gutierrez, Rodrigo A. Conference Proceedings 2008
Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching Peterson, M. P., J. T. Malloy, V. P. Buonaccorsi, and J. H. Marden Journal 2015
A unified global gene family classification resource for plants and its utility for comparative genomics, genome annotation, and gene family studies Der, Joshua P. P10032 Conference Proceedings 2014
Analyzing big data with simple flowcharts and questioning techniques Goller, C. Conference Proceedings 2014
Transcriptomic Analyses and Alternative Splicing Landscapes of Brachypodium Infected with Panicum Mosaic Virus Mandadi, Kranthi Kiran, Karen-Beth G. Scholthof P9867 Conference Proceedings 2014
Plant High-Throughput Phenotyping Using Photogrammertry and 3D Modeling Techniques An, Nan Dissertation 2015
Infrastructure for managing and analyzing biological networks derived from collections of plant images Das, Abhiram, Alexander Bucksch, and Joshua S. Weitz Poster 2014
Toward a Plant Taxonomic Name Resolution Service Boyle, Brad, Brian Enquist, Sheldon McKay, William Piel, Jerry Lu, Nicole Hopkins, Kathleen Kennedy... Conference Proceedings 2010
A Posteriori Ontology Engineering for Data-Driven Science Gessler, Damian DG, Cliff Joslyn and Karin Verspoor 18 215-244 Chapter 2013
Contribution of Epigenetic Variation to Expression Changes Among Tissues and Genotypes Eichten, Steven R. W417 Conference Proceedings 2012
Differentially expressed genes fro beef fatty acid profile in Nellore cattle Berton, Mariana P., Marcos V. A. Lemos, Hermenegildo L. J. Chiaia, et al. 93, Suppl. s3 M91 Journal 2015
Sequence Alignments and Trees for Mammalian 1X for Mirarab et. al. Mirarab, Sivash, Md Shamsuzzoha Bayzid, Bastien Boussau, and Tandy Warnow Repository 2014
iMicrobe: Advancing Clinical and Environmental Microbial Research using the iPlant Cyberinfrastructure Hurwitz, Bonnie P10931 Conference Proceedings 2014
Jetstream: A Distributed Cloud Infrastructure for Under-resourced higher education communities Fischer, Jeremy, Steven Tuecke, Ian Foster, and Craig A. Stewart Technical Report 2015
Keynote: The iPlant Collaborative: A Life Sciences Cyberinfrastructure for the 21st Century Stanzione, Dan Conference Proceedings 2013
Enabling Cloud and GRid Powered Image Phenotyping Nirav Merchant, Nathan Miller, Kris Kvilekval, Edgar Spalding, B.S. Manjunath P0111 Conference Proceedings 2013
Using Students' Own DNA Sequences to Explore Human Evolution Micklos, Dave W693 Conference Proceedings 2015
A Simple Bioinformatics Workflow for RNA-Seq Analysis and Distributed Genome Annotation Micklos, Dave W250 Conference Proceedings 2014
Leverage iPlant Computing Resources for Collaborative Genomic Research Tang, Haibao, Konstantinos Krampis W419 Conference Proceedings 2012
Next Generation Resequencing of Soybean Germplasm for Trait Discovery Joshi, Trupti Poster 2014
Lincoln Hub data and information architecture project: DATA_: Data architecture transforming access & analysis Carnaby, Penny, Stuart Charters, Paul Staincliffe, Rosie Cahalane, Matthew Laurenson, Robert Gibb,... Technical Report 2014
Biotechnology and Genomics: Exploiting the Potential of CWR Walley, Peter G., and Jonathan D. Moore 212-223 Chapter 2015
How to Use the iPlant's Discovery Environment for Your Research McKay, Sheldon W420 Conference Proceedings 2012
Flora of North Dakota Project Shipunov, Alexey, Liudmila Abramova, Joshua Beaudoin, Jinhee Choi, Dallas Fry, Ryan Perry, Vera... 15 10-Jan Journal 2015
Undergraduate Genomics Research through GCAT-SEEK: The Genome Consortium for Active Teaching Using Next-Generation Sequencing Buonaccorsi, Vincent W697 Conference Proceedings 2015
Bin Definition for Super Gene Trees for Mirarab et. al. Mirarab, Sivash, Md Shamsuzzoha Bayzid, Bastien Boussau, and Tandy Warnow Repository 2014
Analyzing big data using simple flowcharts and questioning techniques Goller, C. Presentation 2014
Resolved observations of geostationary satellites from the 6.5 m MMT Hart, Michael, Richard Rast, Stuart Jefferies, and Douglas Hope Conference Proceedings 2016
XSeDe: Accelerating Scientific Discovery Gaither, Kelly, Victor Hazlewood, Scott Lathrop, Dave Lifka, and Gregory D. Peterson 14 1521-9615 Journal 2015
Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding Xu, Dong P9990 Conference Proceedings 2014
A Statistical Model for Recreational Trails in Aerial Images Andrew Predohl, Scott Morris, and Kobus Barnard Conference Proceedings 2013
Genome annotation in the cloud through xGDBvm virtual server instances deployed at iPlant Duvick, Jon P10310 Conference Proceedings 2014
Unlimited Thirst for Genome Sequencing, Data Interrpetation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement Dhanapal, Arun Prabhu and Mahalingam Govindaraj 684321 Journal 2015
Progress in Sequencing the Genome of an Invasive Polyploid Weed (Leafy Spurge) Horvath, David, James V. Anderson, Munevver Dogramaci, Brian Scheffler P9780 Conference Proceedings 2014
Concepts in Distributed Data Management or History of the DICE Group Moore, Reagan W., Arcot Rajasekar, Michael Wan, and Wayne Schroeder Technical Report 2015
The iPlant Collaborative McKay, Sheldon, Eric Lyons, Haibao Tang, Nathan Miller, Steven R. Eichten, Stephen A. Goff, Dan... W416 Conference Proceedings 2012
Serving national scientific communities -genome analysis as an example. Stewart, C.A. Conference Proceedings 2014
Overcoming the Limitations Posed by TCR‘_ Repertoire Modeling through a GPU-based In-Silico DNA Recombination Algorithm Striemer, G, H Krovi, A Akoglu, B Vincent, B Hopson, J Frelinger, and A Buntzman Parallel Technical Sessions 6 Conference Proceedings 2014
Designing and Evaluating Scientific Workflows for Big Data Interactions Etemadpour, Ronak, Paul Murray, Matthew Bomhoff, Eric Lyons, and Angus Graeme Forbes Journal 2015
Introducing Genome Browsers, Genome Structure, and Gene Annotation Buckner, Brent P10952 Conference Proceedings 2014
Genomics and Biological Big Data: Facing Current and Future Challenges around Data and Software Sharing and Reproducibility Gesing, Sandra, Thomas Richard Connor, and Ian Taylor 1511.02689 Technical Report 2015
The genomic repertoir of complex and polyploid cereal genomes Spannagl, Manuel Dissertation 2015
Avian Model Species Trees for 1X Model Condition for Mirarab et. al. Mirarab, Sivash, Md Shamsuzzoha Bayzid, Bastien Boussau, and Tandy Warnow Repository 2014
Gene Exression in Inbred and Hybrid Mice, Young and Old Goff, Stephen A., Qi Cai, Janko Nikolich-Zugich, David Galbraith W325 Conference Proceedings 2013
AgroPortal: a proposition for ontology-based services in the agronomic domain Jonquet, Cl_ment, Esther Dzal_-Yeumo, Elizabeth Arnaud, and Pierre Larmande Conference Proceedings 2015
The Globus Galaxies Platform: Delivering Science Gateways as a Service Madduri Ravi, Kyle Chard, Ryan Chard, Lukasz Lacinski, Alex Rodriguez, Dinanath Sulakhe, David... 5313 Technical Report 2015
EPIC CoGE- a unified browser for Epigenetics Lyons, Eric, Matthew Bomhoff, Fan Li, Brian D. Gregory W514 Conference Proceedings 2013
Software-as-a-Service: The iPlant Foundation API Dooley, Rion, Matthew Vaughn, Dan Stanzione, Steve Terry, and Edwin Skidmore 7 Conference Proceedings 2012
DNA Subway _ An Educational Bioinformatics Platform for Gene and Genome Analysis: DNA Barcoding, and RNASeq Williams, J., S. McKay, M. Khalfan, C. Ghiban, U. Hilgert, S. Lauter, E.S. Jeong, and D. Micklos Accepted Conference Proceedings 2014
An optimal algorithm for computing all subtree repeats in trees Flouri, TomÇaØs, Kassian Kobert, Solon P. Pissis, and Alexandros Stamatakis Technical Report 2013
Implications of uniformly distributed, empirically informed priors for phylogeographical model selection: A reply to Hickerson et al Oaks, Jamie R., Charles W. Linkem, and Jeet Sukumaran arXiv:1402.6397 [q-bio.PE] Journal 2014
Using Clouds for Technical Computing Fox, Geoggrey, Dennis Gannon Technical Report 2013
Leveraging iPlant Cyberinfrastructure for a New Data-Driven Research Community Carson, James et al P1113 Conference Proceedings 2015
Sociometric methods for relevancy analysis of Long Tail Science Data Rajasekar, Arcot, Sharlini Sankaran, Howard Lander, Tom Carsey, Jonathan Crabtree, Hye-Chung Kum,... 1 Conference Proceedings 2013
Large-Scale Next-Generation Resequencing of Soybean Germplasm for Trait Discovery Liu, Yang et al. P0696 Conference Proceedings 2014
Color Based Classification of Circular Markers for the Identification of Experimental Units Narjala, Lakshmi Lab Report 2013
Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissues as Revealed by Deep Sequencing Kakumanu, Akshay etd-07062012-131158 Master's Thesis 2012
Transposable Elements, Gene Discovery, and DNA Barcoding (Yellow and Blue Lines) Burnette, James. Conference Proceedings 2015
DNA Subway Yellow and Blue Lines: TEs, Gene Discovery and DNA Barcoding Burnette, James. P1143 Conference Proceedings 2015
Latest Technology in Irrigation Management in Nursery Production McDonald, John, and Steve Hart Journal 2014
Order-Preserving Sux Trees and Their Algorithmic Applications Crochemore, Maxime, Costas S. Iliopoulos, Tomasz Kociumaka, Marcin Kubica, Alessio Langiu, Solon P... Technical Report 2013
Flash Talk: An Ontology Approach to Comparative Phenomics in Plants Huala, Eva et al W487 Conference Proceedings 2015
SBMLChecker, a Semantic approach for SBML model reliability evaluation Thavappiragasam, Mathialakan, Carol M. Lushbough, and Etienne Z. Gnimpieba Conference Proceedings 2014
Multidisciplinarity in Knowledge Transmision Management System (KTMS) evaluation Gnimpieba, Etienne Z., Douglas Jennewein, Luke Fuhrman, and Carol M. Lushbough EEE7278 Conference Proceedings 2013
The dynamics of functional classes of plant genes in rediploidized ancient polyploids Chen, Eric CH, Carlos FBA Najar, Chunfang Zheng, Alex Brandts, Eric Lyons, Haibao Tang, Lorenzo... 14, No. 15 S19 Conference Proceedings 2013
PASTA: ultra-large multiple sequence alignment Mirarab, Siavash, Nam Nguyen, and Tandy Warnow Technical Report 2014
Next-generation plant science: putting big data to work Brauer, Elizabeth K., Dharmendra K. Singh, and Sorina C. Popescu 15, 301 Journal 2014
Enhanced string covering Flouri, Tomà_, Costas S. Iliopoulos, Tomasz Kociumaka, Solon P. Pissis, Simon J. Puglisi, W. F.... Journal 2013
Functional Analysis of Your RNAseq Data McCarthy, Fiona W480 Conference Proceedings 2015
VegBank: a permanent online repository for international plot and relev_ data Lee, Michael T., and Robert K. Peet. 66 Conference Proceedings 2013
Inference of Many-Taxon Phylogenies Izquierdo-Carrasco, Fernando Dissertation 2014
Simplifying Genome Annotation and Examples of Large-Scale Projects in DNA Barcoding (Red and Blue Lines) Micklos, Dave Conference Proceedings 2015
Globus Platform-as-a-Service for Collaborative Science Applications Ananthakrishnan, Rachana, Kyle Chard, Ian Foster, Steven Tuecke Journal 2014
Cyberinfrastructure: Applications and Challenges Tong, Qiuhui, Bo Yuan, and Xiu Li 2014
Characterization of a plant gene family expanded in glycine max Snoderly-Foster, Lisa Dissertation 2014
Fast Algorithm for Partial Covers in Words Kociumaka, Tomasz, Solon P. Pissis, Jakub Radoszewski, Wojciech Rytter, and Tomasz Wale 7922 177-188 Chapter 2013
Grand Challenges in Organismal Physiology Carey, Hannah V. 54, Issue 5 169 Editorial 2011
BAC-Based Sequencing of the Aegilops tauschii Genome Dvorak, Jan et al Conference Proceedings 2015
Recipes 2.0: Building for Today and Tomorrow Dooley, Rion, Matthew R. Hanlon 993, No. 16 Conference Proceedings 2013
Comprehensive analysis of imprinted genes in maize reveals limited conservation with other species and allelic variation forimprinting Waters, Amanda J., Paul Bilinski, Steve R. Eichten, Matthew W. Vaughn, Jeffrey Ross-Ibarra, Mary... Technical Report 2013
Identification and Development of Data Standards for Maize Field Phenotypic Measurements: Working with the GxE Subgroup of ht eGenomes2Fields Initiative Gardiner, Jack, et al. P0516 Conference Proceedings 2015
An Improved Approximate-Bayesian Model-choice Method for Estimating Shared Evolutionary History Oaks, Jamie R. arXiv:1402.6303 [q-bio.PE] Journal 2014
Cyberinfrastructures: Where Scientific Research and Software Engineering Collide Gorton, Ian 1 Journal 2013
Implementing the Research Strategy and Evaluating Progress Committee to Develop a Research Strategy for Environmental, Health, and Safety Aspects of... Technical Report 2014
iPlant Semantic Web Platform uses SSWAP (Simple Semantic Web Architecture and Protocol) to enable Semantic Pipelines across Distributed Web and High Performance Computing Resources Gessler, Damian DG, Blazej Bulka, Evren Sirin, Yan Kang, Pavel Klinov, Hans Vasquez-Gross, John Yu... Poster 2012
The potential of genomics in plant systematics Soltis, Douglas E., Matthew A. Gitzendanner, Gregory Stull, Michael Chester, Andre Chanderbali,... 62, No. 5 886-898 Journal 2013
The Databridge Rajasekar, Arcot, Hye-Chung Kum, Merce Crosas, Jonathan Crabtree, Sharlini Sankaran, Howard Lander... 2, No. 1 Journal 2013
Binning Code for Mirarab et. al. Mirarab, Sivash, Md Shamsuzzoha Bayzid, Bastien Boussau, and Tandy Warnow Repository 2014
W7 Model of Provenance and Its Use in the Context of Wikipedia Liu, Jun Dissertation 2011
Large Dataset Analysis for Undergraduates: Discovery Environment, RNA-Seq and Leaf Senescence in< em> Arabidopsis thaliana</em>(Green Line) Brusslan, Judy A Conference Proceedings 2015
Elseweb meets sadi: Supporting data-to-model integration for biodiversity forecasting Del Rio, Nicholas, Natalia Villanueva-Rosales, Deana Pennington, Karl Benedict, Aimee Stewart, and... Journal 2013
Using iPlant Tools and Plastome Sequencing As a Springboard into Comparative Genomics: Plastome Organization and Sequence for the Mimosoid Legume Leucaena trichandra Bailey, Donovan W484 Conference Proceedings 2015
Overivew of the iPlant Collaborative Vaughn, Matthew Conference Proceedings 2015
Design and Development of Subject Gateway with Special Reference to Chemistry Yuvaraja, R. Dissertation 2014
Cyberinfrastructure for Life Sciences - iAnimal resources for genomics and other data driven biology Reecy, J., J.P. Carson, F. McCarthy, J.E. Koltes, E. Friz-Waters, J. Williams, E. Lyons, C.F. Baes... Accepted 9911 Conference Proceedings 2014
The iPlant Collaborative Website Collaborative, iPlant Website 2008
Report of the final external review of the Generation Challenge Programme Sachdeva, Paramjit S., Gregory O. Edmeades, Rita H. Mumm, Antoni Rafalski, and Ben Bennett Technical Report 2014
Managing, Analysing and Integrating Big Data in medical bioinformatics: open problems and future perspectives Merelli, Ivan, Horacio P_rez-Sànchez, Sandra Gesing, and Daniele DÍAgostino Submitted Journal 2014
A Specimen-based View of the World: Using the Biological Collections Ontology to Model Biodiversity Collections Walls, Ramona, John Deck, Robert Guralnick, and Andrea Matsunaga 8 Journal 2014
Management and Visualization of Ianimal Quantitative Data Using iPlant and EPIC-CoGe Subramaniam, Sabarinath Conference Proceedings 2015
Flash Demo: Atmosphere Cloud Computing - Applied to Visualizing RNA-Seq Data Chougule, Kapeel W483 Conference Proceedings 2015
The Librarian & the Big Data: Bridging the Gap Rajasekar, Arcot. Paper 6. Conference Proceedings 2014
Extensible Generic Data Management Software Moore, Reagan W. 1309.5372 Technical Report 2013
PUmPER: Phylogenies Updated Perpetually Izquierdo-Carrasco, F., J. Cazes, S. A. Smith, and A. Stamatakis btu053 Journal 2014
Identification of GCN4 homologues in maize using a bioinformatics approach Scott, Taylor Dissertation 2014
Avian Dopamine Receptors DRD1a and DRD1b Arise from an Ancient Vertebrate Whole Genome Duplication Haug-Baltzell, Asher K., Eric Lyons, Fiona McCarthy, and Erich Jarvis P0402 Conference Proceedings 2015
Sustainable Software Development for Next-Gen Sequencing (NGS) Bioinformatics on Emerging Platforms Swenson, Shel, Yogesh Simmhan, Viktor Prasanna, Manish Parashar, Jason Riedy, David Bader, and... 1309, No. 1828 Technical Report 2013
Bringing Authentic Genomics Research into the Classroom: Analysis of Maize Stress Response (Green Line) Makarevitch, Irina Conference Proceedings 2015
Identification and characterization of DNA methylation variation within maize Eichten, Steven Richard. Dissertation 2013
The Promise of Genomics and Beyond Busov, Victor 19, No. 2 107-128 Journal 2013
A global analysis of the impacts of urbanization on bird and plant diversity reveals key anthropogenic drivers Sushinsky, Peter Werner, Marten Winter, Ian MacGregor-Fors KÙhn, Mark McDonnell, Ulla M_rtberg,... 281 20133330 Conference Proceedings 2014
The relationships among GC content, nucleosome occupancy, and exon size Wang, Liya, Lincoln D. Stein, Doreen Ware Technical Report 2014
A web semantic for SBML merge Thavappiragasam, Mathialakan Thesis 2014
Bisque: Advances in Bioimage Databases Kvilekval, Kristian, Dmitry Fedorov, Utkarsh Gaur, Steve Goff, Nirav Merchant, B. S. Manjunath, and... 35, No. 3 56-64 Bulletin 2012
Islands and Integrals: Processes of Diversification in an Island Archipelago and Bayesian Methods of Comparative Phylogeographical Model Choice Oaks, J. R. Dissertation 2013
Data sharing and its implications for academic libraries Kim, Jeonghyun 114, No. 11/12 Journal 2013
Obstacles and Avenues Facing Phyloinformatic Research Piel, William H. 28-29 Conference Proceedings 2008
Factors Influencing Adoption and Non-Adoption of Cyberinfrastructure by the Research Community Brown, Susan A., and Sherry Thatcher 31 Conference Proceedings 2011
Big Data: A Survey Chen, Min, Shiwen Mao, and Yunhao Liu January Jan-39 Journal 2014
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 Wegrzyn 979 Conference Proceedings 2013
Life Sciences Cyberinfrastructure at Your Fingertips: Using Internet2 to Power Scientific Collaboration Taylor, Daniel B. W488 Conference Proceedings 2015
Incrementally Updateable and Persistent Decomposition of OWL Ontologies Klinov, Pavel, Chiara Del Vescovo, and Thomas Schneider 849 7 Conference Proceedings 2012
African Orphan Crops Consortium_a NEPAD-led initiative Makinde, Diran January Essay 2014
Your Data, Your Way: The iPlant Foundation API Data Services Dooley, Rion, Matthew Vaughn, Steven Terry, Dan Stanzione, Edwin Skidmore, Nirav Merchant 3 Conference Proceedings 2012
Building Blocks for a Data Infrastructure and Services to Empower Agricultural Research Communities Geser, G., Y. Jaques, Nikos Manouselis, Vassilis Protonotarios, J. Keizer, and M. Sicilia 4, No. 4 18-Nov Journal 2012
An Ontology Approach to Comparative Phenomics in the Plants: Arabidopsis, Tomato, Maize, Rice, Soybean and Medicago Harper, Lisa et al. P1123 Conference Proceedings 2015
Computational resources to facilitate variant discovery and analysis Reecy, James, C. Baes, E. Fritz-Waters, James E. Koltes, M. Dolezal, B. Bapts, C. Flury, H. Signer-... 23 Conference Proceedings 2014
New and E_cient Approaches to the Quasiperiodic Characterisation of a String Flouri, Tomàs, Costas S. Iliopoulos, Tomasz Kociumaka, Solon P. Pissis, Simon J. Puglisi, William F... 78-88 Conference Proceedings 2012
A Hybrid Approach to Assemble and Annotate the Brassica rapa Transcriptome in the Cloud through the iPlant Collaborative and XSEDE Devisetty, Upendra Kumar W482 Conference Proceedings 2015
Bioinformatics Knowledge Transmission (training, learning, and teaching): overview and flexible comparison of computer based training approaches Gnimpieba, Etienne Z., Douglas Jennewein, Luke Fuhrman, and Carol M. Lushbough 1310.8383 Technical Report 2013
Responses to Data Management Requirements at the National Scale Jordan, Chris, Maria Esteva, David Walling, Tomilsav Urban, and Sivakumar Kulasekaran 64 Journal 2013
Design of the DataBridge: A System for Sociometric Analysis ofLong tail Science Data Rajasekar, Arcot, Tom Carsey, Jonathan Crabtree, Merce Crosas, Gary King, Hye-Chung Kum, Howard... Lab Report 2013
DeMoSt: a Tool for Exploring the Decomposition and the Modular Structure of OWL Ontologies Del Vescovo, Chiara, Pavel Klinov, Bijan Parsia, Ulrike Sattler, and Thomas Schneider Poster 2011
A Scalable Parallel Implementation of the Neighbor Joining Algorithm for Phylogenetic Trees McLay, Robert, Dan Stanzione, S. J. Mckay, and Travis Wheeler Conference Proceedings 2011
Developing Content for the Arabidopsis Information Portal Vaughn, Matt et al. P0792 Conference Proceedings 2015
Flash Demo: Annotating genomes with MAKER-P and the iPlant Discovery Environment Subramaniam, Sabarinath W481 Conference Proceedings 2015
Sequence Alignments and Trees for Avian 1X for Mirarab et. al. Mirarab, Sivash, Md Shamsuzzoha Bayzid, Bastien Boussau, and Tandy Warnow Repository 2014
International Climate Resilient Crops Genomics Consortium (ICRCGC) White Paper Application of Genomics to the Production of Climate Resilient Crops: Challenges and opportunities Ortiz, Rodomiro, David Edwards, Sean Mayes, Francis C. Ogbonnaya, Chittaranjan Kole, et al White Paper 2014
Optimization Techniques For Next-Generation Sequencing Data Analysis Caciula, Adrian 87 Dissertation 2014
Flash Demo: Secure, Collaborative, Management of Your Life Sciences Data with the Data Store DeBarry, Jermey W485 Conference Proceedings 2015
Utilizing iPlant to Unearth Long Non-Coding RNAs and Characterize Their Evolution in the Plant Family Brassicaceae Nelson, Andrew D. et al W486 Conference Proceedings 2015
RESTful API in Life Science Research Systems and Data Integration Challenges: Linking Metabolic Pathway, Metabolic Network, Gene and Publication Gnimpieba, Etienne Z., Brent S. Anderson, Abalo Chango, and Carol M. Lushbough 10 1196-1199 Journal 2013
Order-Preserving Incomplete Sux Trees and Order-Preserving Indexes Crochemore, Maxime, Costas S. Iliopoulos, Tomasz Kociumaka, Marcin Kubica, Alessio Langiu, Solon P... Technical Report 2013
Summary of the First Workshop on Sustainable Software For Science: Practice and Experiences (WSSSPE1) Katz, Daniel S., Sou-Cheng T. Choi, Hilmar Lapp, Ketan Maheshwari, Frank Loffler, Matthew Turk,... Journal 2014
Leveraging Cloud Infrastructure for Life Sciences Research Laboratories: A Generalized View Merchant, Nirav, John Hartman, Sonya Lowry, Andrew Lenards, David Lowenthal, and Edwin Skidmore 53-57 Conference Proceedings 2009
Advances in the use of next-generation sequence data in plant systematics and evolution Soltis, D. E., G. Burleigh, W. B. Barbazuk, M. J. Moore, and P. S. Soltis 859 193-206 Conference Proceedings 2009
A generic Vectorization Scheme and a GPU kernel for the Phylogenetic Likelihood Library Izquierdo-Carrasco, Fernando, Nikolaos Alachiotis, Simon Berger, TomaÇs Flouri, Solon P. Pissis,... 2013
Comparative genomics with maize and other grasses: from genes to genomes! Schnable, James C., and Eric Lyons 56, No. 2 Journal 2012
Data Integration for the Plant Research Community: The Arabidopsis Information Portal Cheng, Chia-Yi, et al. P0790 Conference Proceedings 2015
Re-annotation of the woodland strawberry (Fragaria vesca) genome Darwish, Omar, Rachel Shahan, Zhongchi Liu, Janet P. Slovin, and Nadim W. Alkharouf 16, No. 1 29 Journal 2015 doi: 10.1186/s12864-015-1221-1
Using the iPlant Collaborative Discovery Environment Oliver, Shannon L., Andrew J. Lenards, Roger A. Barthelson, Nirav Merchant, Sheldon J. McKay 22-Jan Chapter 2013 doi: 10.1002/0471250953.bi0122s42
UNIT 4.11 Genome Annotation and Curation Using MAKER and MAKER-P Campbell, Michael, Carson Hold, Barry Moore, and Mark Yandell Lab Protocol 2014 doi: 10.1002/0471250953.bi0411s48
Phylogenetic Analysis with the iPlant Discovery Environment Matasci, Naim, Sheldon J. McKay Chapter 2013 doi: 10.1002/0471250953.bi0613s42
Using the Generic Syteny Browser (GBrowse_syn) McKay, Sheldon J., Ismael A. Vergara, and Jason E. Stajich 12-Sep Chapter 2010 doi: 10.1002/0471250953.bi0912s31
Cloud Computing with iPlant Atmosphere McKay, Sheldon J., Edwin J. Skidmore, Christopher J. LaRose, Andre W. Mercer, and Christos Noutsos 15-Sep Journal 2013 doi: 10.1002/0471250953.bi0915s43
Geographic comparison of plant genera used in frugivory among the pitheciids Cacajao, Callicebus, Chiropotes, and Pithecia Boyle, Sarah A., Cynthia L. Thompson, Anneke Deluycker, Silvia J. Alvarez, Thiago HG Alvim, Rolando... Journal 2015 doi: 10.1002/ajp.22422
Cyclotide discovery in Gentianales revisited - identification and characterization of cyclic cystine-knot peptides and their phylogenetic distribution in Rubiaceae plants Koehbach, Johannes, Alfred F. Attah, Andreas Berger, Roland Hellinger, Toni M. Kutchan, Eric J.... Journal 2013 doi: 10.1002/bip.22328
ASIS&T research data access and preservation summit: Conference summary Moore, Reagan, and William L. Anderson 36, No. 6 42-45 Journal 2010 doi: 10.1002/bult.2010.1720360611
Batchsubmit: a high-volume batch submission system for earthquake engineering simulation Mohan, Anup, Thomas Hacker, Gregory P. Rodgers, and Tanzima Islam Journal 2014 doi: 10.1002/cpe.3234
A genome-wide association study platform built on iPlant cyber-infrastructure Wang, Liya, Doreen Ware, Carol Lushbough, Nirav Merchant, and Lincoln Stein 2014 doi: 10.1002/cpe.3236
Life science data analysis workflow development using the bioextract server leveraging the iPlant collaborative cyberinfrastructure Lushbough, Carol M., Etienne Z. Gnimpieba, and Rion Dooley Journal 2014 doi: 10.1002/cpe.3237
Discovery of biological networks using an optimized partial correlation coefficient with information theory algorithm on Stampede's Xeon and Xeon Phi processors Koesterke, Lars, James E. Koltes, Nathan T. Weeks, Kent Milfeld, Matthew W. Vaughn, James M. Reecy... Journal 2014 doi: 10.1002/cpe.3252
Creating a gateway that enables large-scale science coopetition Crivelli, Silvia, Rion Dooley, Raquell Holmes, and Stephen Mock Journal 2014 doi: 10.1002/cpe.3270
Araport: an application platform for data discovery Hanlon, Matthew R., Matthew Vaughn, Stephen Mock, Rion Dooley, Walter Moreira, Joe Stubbs, Chris... Journal 2015 doi: 10.1002/cpe.3542
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Plant Pathway Databases Jaiswal, Pankaj, and Bj_rn Usadel 137 71-87 Chapter 2015 doi: 10.1007/978-1-4939-3167-5_4
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Image-Based Analysis of Light-Grown Seedling Hypocotyls in Arabidopsis Cole, Benjamin J., and Joanne Chory 7-Jan Chapter 2012 doi: 10.1007/978-1-61779-995-2_1
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Semantic Bridges for Biodiversity Sciences Villanueva-Rosales, Natalia, Nicholas del Rio, Deana Pennington, and Luis Garnica Chavira 310-317 Chapter 2015 doi: 10.1007/978-3-319-25010-6_20
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FASTS: FAcets Structured Tag Space _ A Novel Approach to Organize and Reuse Social Bookmarking Tags Ram, Sudha, and Wei Wei 6105 426-438 Chapter 2010 doi: 10.1007/978-3-642-13335-0_29
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OMG! Orthologs in Multiple Genomes _ Competing Graph-Theoretical Formulations Zheng, Chunfang, Krister Swenson, Eric Lyons, and David Sankoff 6833 364-375 Chapter 2011 doi: 10.1007/978-3-642-23038-7_30
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Arabidopsis thaliana: A Model for Plant Research Sivasubramanian, R., Nitika Mukhi, and Jagreet Kaur 26-Jan Chapter 2015 doi: 10.1007/978-81-322-2283-5_1
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Field-based phenomics for plant genetics research White, Jeffrey W., Pedro Andrade-Sanchez, Michael A. Gore, Kevin F. Bronson, Terry A. Coffelt,... 133 101-112 Journal 2012 doi: 10.1016/j.fcr.2012.04.003,
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Systems genetics: A paradigm to improve discovery of candidate genes and mechanisms underlying complex traits Feltus, F. Alex Journal 2014 doi: 10.1016/j.plantsci.2014.03.003
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Extending alignments with k-mismatches and _-gaps Barton, Carl, Costas S. Iliopoulos, Inbok Lee, Laurent Mouchard, Kunsoo Park, Solon P. Pissis Journal 2013 doi: 10.1016/j.tcs.2013.06.012,
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Machine learning for Big Data analytics in plants Ma, Chuang, Hao Helen Zhang, and Xiangfeng Wang Journal 2014 doi: 10.1016/j.tplants.2014.08.004
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Transcriptome map of mouse isochores in embryonic and neonatal cortex Frousios, Kimon, Costas S. Iliopoulos, German Tischler, Sophia Kossida, Solon P. Pissis, and... 101, No. 2 120-124 Journal 2012 doi: 10.1016/j.ygeno.2012.11.006
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iBIOMES: Managing and sharing biomolecular simulation data in a distributed environment Thibault, Julien Charles, Julio C. Facelli, and Thomas E. Cheatham III 53, No. 3 726-736 Journal 2013 doi: 10.1021/ci300524j
Depth-stratified functional and taxonomic niche specialization in the ïcoreÍand ïflexibleÍPacific Ocean Virome Hurwitz, Bonnie L., Jennifer R. Brum, and Matthew B. Sullivan Journal 2014 doi: 10.1038/ismej.2014.143
Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics Brum, Jennifer R, Bonnie L Hurwitz, Oscar Schofield, Hugh W Ducklow, and Matthew B Sullivan Journal 2015 doi: 10.1038/ismej.2015.125
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Convergence of terrestrial plant production across global climate gradients Michaletz, Sean T., Dongliang Cheng, Andrew J. Kerkhoff, and Brian J. Enquist 512, No. 7512 39-43 Journal 2014 doi: 10.1038/nature13470
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A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms Werner, Gijsbert DA, William K. Cornwell, Janet I. Sprent, Jens Kattge, and E. Toby Kiers 5, No. 4087 Journal 2014 doi: 10.1038/ncomms5087
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The pineapple genome and the evolution of CAM photosynthesis Ming, Ray, Robert VanBuren, Ching Man Wai, Haibao Tang, Michael C. Schatz, John E. Bowers, Eric... Journal 2015 doi: 10.1038/ng.3435
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Mining for Meaning: Visualization Approaches to Deciphering Arabidopsis Stress Responses in Roots and Shoots Zhou, Lecong, Christopher Franck, Kuan Yang, Guillaume Pilot, Lenwood S. Heath, and Ruth Grene 16, No. 4 208-228 Journal 2012 doi: 10.1089/omi.2011.0111
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treePL: Divergence time estimation using penalized likelihood for large phylogenies Smith, Stephen A., and Brian C. OÍMeara 28, No. 20 2689-2690 Journal 2012 doi: 10.1093/bioinformatics/bts492
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Rex: A toolset for reproducing software experiments Perianayagam, Somu, Gregory R. Andrews, and John H. Hartman 613-617 Conference Proceedings 2010 doi: 10.1109/BIBM.2010.5706639
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