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Title Author(s) Volume, Issuesort descending Pages Type of Publication Year DOI
Limited sampling hampers ñbig dataî estimation of species richness in a tropical biodiversity hotspot Engemann, Kristine, Brian J. Enquist, Brody Sandel, Brad Boyle, Peter M. JÀrgensen, Naia... Journal 2015 doi: 10.1002/ece3.1405
Multi-scale phylogenetic structure in coastal dune plant communities across the globe Brunbjerg, Ane Kirstine, Jeannine Cavender-Bares, Wolf L. Eiserhardt, Rasmus Ejrn_s, Lonnie W.... rtt069 Journal 2014 doi: 10.1093/jpe/rtt069
Obstacles and Avenues Facing Phyloinformatic Research Piel, William H. 28-29 Conference Proceedings 2008
Plant genetics and interspecific competitive interactions determine ectomycorrhizal fungal community responses to climate change Gehring, Catherine, Dulce Flores-RenterÕa, Christopher M. Sthultz, Tierra M. Leonard, Lluvia Flores... Journal 2013 doi: 10.1111/mec.12503
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
Identification of GCN4 homologues in maize using a bioinformatics approach Scott, Taylor Dissertation 2014
Population genetics of Setaria viridis, a new model system Huang, Pu, Maximilian Feldman, Stephan Schroder, Bochra A. Bahri, Xianmin Diao, Hui Zhi, Matt Estep... Journal 2014 doi: 10.1111/mec.12907
The iPlant Collaborative Website Collaborative, iPlant Website 2008
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
Toward Scalable Systems for Big Data Analytics: A Technology Tutorial Hu, Han, Yonggang Wen, Tat-Seng Chua, and Xuelong Li Journal 2014 doi: 10.1109/ACCESS.2014.2332453
Order-Preserving Sux Trees and Their Algorithmic Applications Crochemore, Maxime, Costas S. Iliopoulos, Tomasz Kociumaka, Marcin Kubica, Alessio Langiu, Solon P... Technical Report 2013
BAC-Based Sequencing of the Aegilops tauschii Genome Dvorak, Jan et al Conference Proceedings 2015
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
Globus Nexus: A Platform-as-a-Service provider of research identity, profile, and group management Chard, Kyle, Mattias Lidman, Brendan McCollam, Josh Bryan, Rachana Ananthakrishnan, Steven Tuecke,... Journal 2015 doi: 10.1016/j.future.2015.09.006
Flash Demo: Secure, Collaborative, Management of Your Life Sciences Data with the Data Store DeBarry, Jermey W485 Conference Proceedings 2015
An interactive tool for semi-automated leaf annotation Minervini, Massimo, Mario Valerio Giuffrida, and Sotirios A. Tsaftaris Conference Proceedings 2015
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
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
Islands and Integrals: Processes of Diversification in an Island Archipelago and Bayesian Methods of Comparative Phylogeographical Model Choice Oaks, J. R. Dissertation 2013
Tales from the trenches: can user support tools make a difference? James, Doug, Robert McLay, Si Liu, R. Todd Evans, William L. Barth, Antia Lamas-Linares, Reuben... 2 Conference Proceedings 2015 doi: 10.1145/2834996.2834998
Concepts in Distributed Data Management or History of the DICE Group Moore, Reagan W., Arcot Rajasekar, Michael Wan, and Wayne Schroeder Technical Report 2015
Phylogeny, divergence times, and historical biogeography of the angiosperm family Saxifragaceae Deng, Jia-bin, Bryan T. Drew, Evgeny V. Mavrodiev, Matthew A. Gitzendanner, Pamela S. Soltis, and... Journal 2015 doi: 10.1016/j.ympev.2014.11.011
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
Integrating image-based phenomics and association analysis to dissect the genetic architecture of temporal salinity responses in rice Malachy, T. Campbell, C. Knecht Avi, Bettina Berger, J. Brien Chris, Dong Wang, and Harkamal Walia 450 Journal 2015 doi: 10.1104/pp.15.00450
Using Students' Own DNA Sequences to Explore Human Evolution Micklos, Dave W693 Conference Proceedings 2015
Plant High-Throughput Phenotyping Using Photogrammertry and 3D Modeling Techniques An, Nan Dissertation 2015
New whole genome de novo assemblies of three divergent strains of rice (O. sativa) documents novel gene space of aus and indica Schatz, Michael C., Lyza G. Maron, Joshua C. Stein, Alejandro Hernandez Wences, James Gurtowski,... Journal 2014 doi: 10.1101/003764
Data mining with iPlant: A meeting report from the 2013 GARNet workshop, Data mining with iPlant Martin, Lisa, Charis Cook, Naim Matasci, Jason Williams and Ruth Bastow Journal 2014 doi: 10.1093/jxb/eru402
Nordic Lifewatch Cooperation Final Report Hanssen, F., T. Heggberget, J. Bladt, D. Endresen, M. Forsius, et al Technical Report 2015
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
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 i5k Workspace@ NAL„enabling genomic data access, visualization and curation of arthropod genomes Poelchau, Monica, Christopher Childers, Gary Moore, Vijaya Tsavatapalli, Jay Evans, Chien-Yueh Lee... gku983 Journal 2014 doi: 10.1093/nar/gku983
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
Designing and Evaluating Scientific Workflows for Big Data Interactions Etemadpour, Ronak, Paul Murray, Matthew Bomhoff, Eric Lyons, and Angus Graeme Forbes Journal 2015
A community contribution framework for sharing materials data with Materials Project Huck, Patrick, Anubhav Jain, Dan Gunter, Donald Winston, and Kristin Persson 535-541 2015 doi: 10.1109/eScience.2015.75
Faster diversification on land than sea helps explain global biodiversity patterns among habitats and animal phyla Wiens John J Journal 2015 doi: 10.1111/ele.12503
Biotechnology and Genomics: Exploiting the Potential of CWR Walley, Peter G., and Jonathan D. Moore 212-223 Chapter 2015
Cold truths: how winter drives responses of terrestrial organisms to climate change Williams, Caroline M., Hugh AL Henry, and Brent J. Sinclair Journal 2014 doi: 10.1111/brv.12105
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
Cost-aware cloud provisioning Chard, Ryan, Kyle Chard, Kris Bubendorfer, Lukasz Lacinski, Ravi Madduri, and Ian Foster 136-144 Conference Proceedings 2015 doi: 10.1109/eScience.2015.67
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
Overivew of the iPlant Collaborative Vaughn, Matthew Conference Proceedings 2015
Pheno2GRN: a workflow for phenotype to gene network study and reverse engineering comparison Weinandt, Nick, Laura M. Jackson, Etienne Z. Gnimpieba, and Carol Lushbough 797-804 2014 doi: 10.1145/2649387.2660851
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
PHysiological Responses of N2-Fixing Legumes to Water Limitation Gonzalez, Esther M., Estibaliz Larrainzar, Daniel Marino, Stefanie Wienkoop, Erena Gil-Quintana,... May-33 Chapter 2015 doi: 10.1007/978-3-319-06212-9_2
Viral dark matter and virus_host interactions resolved from publicly available microbial genomes Roux, Simon, Steven J Hallam, Tanja Woyke, Matthew B Sullivan Journal 2015 doi: 10.7554/eLife.08490
Viromes, not gene markers for studying dsDNA viral communities Sullivan, Matthew B. Journal 2014 doi: 10.1128/JVI.03289-14
Transport Function of Rice Amino Acid Permeases (AAPs) Taylor, Margaret R., Anke Reinders, and John M. Ward pcv053 Journal 2015 doi: 10.1093/pcp/pcv053
Legume information system (LegumeInfo. org): a key component of a set of federated data resources for the legume family Dash, Sudhansu, Jacqueline D. Campbell, Ethalinda KS Cannon, Alan M. Cleary, Wei Huang, Scott R.... gkv1159 Journal 2015 doi: 10.1093/nar/gkv1159
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
Allele Workbench: Transcriptome Pipeline and Interactive Graphics for Allele-Specific Expression Soderlund, Carol, William M. Nelson, and Stephen A. Goff Journal 2014 doi: 10.1371/journal.pone.0115740
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
Phylogenetic Analysis with the iPlant Discovery Environment Matasci, Naim, Sheldon J. McKay Chapter 2013 doi: 10.1002/0471250953.bi0613s42
Cyberinfrastructure: Applications and Challenges Tong, Qiuhui, Bo Yuan, and Xiu Li 2014
Flash Talk: An Ontology Approach to Comparative Phenomics in Plants Huala, Eva et al W487 Conference Proceedings 2015
Gramene 2016: comparative plant genomics and pathway resources Tello-Ruiz, Marcela K., Joshua Stein, Sharon Wei, Justin Preece, Andrew Olson, Sushma Naithani,... gkv1179 Journal 2015 doi: 10.1093/nar/gkv1179
Undergraduate Genomics Research through GCAT-SEEK: The Genome Consortium for Active Teaching Using Next-Generation Sequencing Buonaccorsi, Vincent W697 Conference Proceedings 2015
Adaptive divergence in the monkey flower Mimulus guttatus is maintained by a chromosomal inversion Twyford, Alex D., and Jannice Friedman 1558-5646 Journal 2015 doi: 10.1111/evo.12663
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
Using multi_timescale methods and satellite_derived land surface temperature for the interpolation of daily maximum air temperature in Oregon Parmentier, Benoit, Brian J. McGill, Adam M. Wilson, James Regetz, Walter Jetz, Robert Guralnick,... Journal 2015 doi: 10.1002/joc.4251
Guest editors_ introduction to the first issue on Experimental Software Engineering in the Cloud (ESEiC) Van Gorp, Pieter, and Louis Rose Journal 2013 doi: 10.1016/j.scico.2013.12.007
Automated update, revision and quality control of the Zea mays genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes Law, MeiYee, Kevin L. Childs, Michael S. Campbell, Joshua C. Stein, Carson Holt, Nicholas Panchy,... 114 Journal 2014 doi: :10.1104/pp.114.245027
HPC-ABDS High Performance Computing Enhanced Apache Big Data Stack Fox, G.C., U. Qiu, S. Kamburugamuve, S. Jha, et al. 1057-1066 Conference Proceedings 2015 doi: 10.1109/CCGrid.2015.122
Serving national scientific communities -genome analysis as an example. Stewart, C.A. Conference Proceedings 2014
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
Keynote: The iPlant Collaborative: A Life Sciences Cyberinfrastructure for the 21st Century Stanzione, Dan Conference Proceedings 2013
Jetstream: a self-provisioned, scalable science and engineering cloud environment Stewart, Craig A., Timothy M. Cockerill, Ian Foster, David Hancock, Nirav Merchant, Edwin Skidmore... 29 Conference Proceedings 2015 doi: 10.1145/2792745.2792774
Examining the causes and consequences of context-specific differential DNA methylation in maize Li, Qing, Jawon Song, Patrick T. West, Greg Zynda, Steven R. Eichten, Matthew W. Vaughn, and Nathan... 52 Journal 2015 doi: 10._1104/_pp._15._00052
Management and Visualization of Ianimal Quantitative Data Using iPlant and EPIC-CoGe Subramaniam, Sabarinath Conference Proceedings 2015
Science gateways-leveraging modeling and simulations in HPC infrastructures via increased usability Gesing, Sandra, Rion Dooley, Marlon Pierce, Jens Kruger, Richard Grunzke, Sonja Herres-Pawlis, and... 19-26 Conference Proceedings 2015 doi: 10.1109/HPCSim.2015.7237017
Frontiers in Plant Systems Biology Gutierrez, Rodrigo A. Conference Proceedings 2008
The Arabidopsis oligopeptidases TOP1 and TOP2 are salicylic acid targets that modulate SA-mediated signaling and the immune response Moreau, Magali, Timothy Westlake, Giulio Zampogna, George Popescu, Miaoying Tian, Christos Noutsos... Journal 2013 doi: 10.1111/tpj.12320
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
Design and Development of Subject Gateway with Special Reference to Chemistry Yuvaraja, R. Dissertation 2014
RNAseq reveals weed_induced PIF3_like as a candidate target to manipulate weed stress response in soybean Horvath, David P., Stephanie A. Hansen, Janet P. Moriles_Miller, Ronald Pierik, Changhui Yan, David... Journal 2015 doi: 10.1111/nph.13351
Araport: the Arabidopsis Information Portal Krishnakumar, Vivek, Matthew R. Hanlon, Sergio Contrino, Erik S. Ferlanti, Svetlana Karamycheva,... gku1200 Journal 2014 doi: 10.1093/nar/gku1200
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
Components of the Arabidopsis nuclear pore complex play multiple diverse roles in control of plant growth Parry, Geraint eru346 Journal 2014 doi: 10.1093/jxb/eru346
A Statistical Model for Recreational Trails in Aerial Images Andrew Predohl, Scott Morris, and Kobus Barnard Conference Proceedings 2013
Habitat area and climate stability determine geographical variation in plant species range sizes Morueta_Holme, Naia, Brian J. Enquist, Brian J. McGill, Brad Boyle, Peter M. JÀrgensen, Jeffrey E.... Journal 2013 doi: 10.1111/ele.12184
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
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
Finely-grained annotated datasets for image-based plant phenotyping Minervini, Massimo, Andreas Fischbach, Hannon Scharr, and Sotirios A. Tsaftaris Journal 2015 doi: 10.1016/j.patrec.2015.10.013
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
Multiple polyploidy events in the early radiation of nodulating and non-nodulating legumes Cannon, Steven B., Michael R. McKain, Alex Harkess, Matthew N. Nelson, Sudhansu Dash, Michael K.... msu296 Journal 2014 doi: 10.1093/molbev/msu296
A Statistical Model for Recreational Trails in Aerial Images Andrew Predohl, Scott Morris, and Kobus Barnard Conference Proceedings 2013
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
Applying high-throughput phenotyping in plant-insect interations: picturing more resistant crops Goggin, Fiona, L., Argelia Lorence, and Christopher Topp Journal 2015 doi: 10.1016/j.cois.2015.03.002
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
Infrastructure for managing and analyzing biological networks derived from collections of plant images Das, Abhiram, Alexander Bucksch, and Joshua S. Weitz Poster 2014
Functional Analysis of Your RNAseq Data McCarthy, Fiona W480 Conference Proceedings 2015
Crop Systems Biology: Where Are We and Where to Go? Yin, Xinyou, and Paul C. Struik 219-227 Chapter 2015 doi: 10.1007/978-3-319-20562-5_10
Avian Model Species Trees for 1X Model Condition for Mirarab et. al. Mirarab, Sivash, Md Shamsuzzoha Bayzid, Bastien Boussau, and Tandy Warnow Repository 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
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
Using genic sequence capture in combination with a syntenic pseudo genome to map a deletion mutant in a wheat species Gardiner, Laura_Jayne, Piotr Gawro_ski, Lisa Olohan, Thorsten Schnurbusch, Neil Hall, and Anthony... Journal 2014 doi: 10.1111/tpj.12660
Identification and characterization of DNA methylation variation within maize Eichten, Steven Richard. Dissertation 2013
Variation in DNA Methylation Patterns is More Common among Maize Inbreds than among Tissues Eichten, Steven R., Matthew W. Vaughn, Peter J. Hermanson and Nathan M. Springer Journal 2013 doi: 10.3835/plantgenome2012.06.0009
Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum VanBuren, Robert, Doug Bryant, Patrick P. Edger, Haibao Tang, Diane Burgess, Dinakar Challabathula... Journal 2015 doi: 10.1038/nature15714
Databases of the marine metagenomics Mineta, Katshuhiko, and Takashi Gojobori Journal 2015 doi: 10.1016/j.gene.2015.10.035
Metabolomic profiling of the nectars of Aquilegia pubescens and A. canadensis Noutsos, Christos, et al Journal 2015 doi: 10.1371/journal.pone.0124501
Towards revealing the functions of all genes in plants Rhee, Seung Yon, and Marek Mutwil Journal 2013 doi: 10.1016/j.tplants.2013.10.006
Bin Definition for Super Gene Trees for Mirarab et. al. Mirarab, Sivash, Md Shamsuzzoha Bayzid, Bastien Boussau, and Tandy Warnow Repository 2014
Seed dispersal by ungulates as an ecological filter: a trait_based meta_analysis Albert, Aur_lie, Alistair G. Auffret, Eric Cosyns, Sara AO Cousins, Bram D'hondt, Carsten... Journal 2015 doi: 10.1111/oik.02512
Comparative genomic de_convolution of the cotton genome revealed a decaploid ancestor and widespread chromosomal fractionation Wang, Xiyin, Hui Guo, Jinpeng Wang, Tianyu Lei, Tao Liu, Zhenyi Wang, Yuxian Li et al Journal 2015 doi: 10.1111/nph.13689
Leaf phenomics: a systematic reverse genetic screen for Arabidopsis leaf mutants Wilson_Sànchez, David, Silvia Rubio_DÕaz, Rafael Mu_oz_Viana, Jos_ Manuel P_rez_P_rez, Sara... Journal 2014 doi: 10.1111/tpj.12595
Apache Airavata as a Laboratory Architecture and Case Study for Component-Based Gateway Middleware Marru, Suresh, Marlon Pierce, Sudhakar Pamidighantam, and Chathuri Wimalesena. Conference Proceedings 2015 doi: 10.1145/2753524.2753529
Binning Code for Mirarab et. al. Mirarab, Sivash, Md Shamsuzzoha Bayzid, Bastien Boussau, and Tandy Warnow Repository 2014
Unraveling Genomic Complexity at a Quantitative Disesase Resistance Locus in Maize Jamann, Tiffany M., Jesse A. Poland, Judith M. Kolkman, Laurie G. Smith, and Rebecca J. Nelson genetics-114 Journal 2014 doi: 10.1534/genetics.114.167486
A web semantic for SBML merge Thavappiragasam, Mathialakan Thesis 2014
Next Generation Resequencing of Soybean Germplasm for Trait Discovery Joshi, Trupti Poster 2014
Plant Thermoregulation: Energetics, Trait_Environment Interactions, and Carbon Economics Michaletz, Sean T., Michael D. Weiser, Jizhong Zhou, Michael Kaspari, Brent R. Helliker, and Brian... Journal 2015 doi: 10.1016/j.tree.2015.09.006
A resource for characterizing genome-wide bindng and putative target genes of transciption factors expressed during secondary growth and wood formation in Populus Liu, Lijun, Trevor Ramsay, Matthew Zinkgraf, David Sundell, Nathaniel Robert Street, Vladimir... Journal 2015 doi: 10.1111/tpj.12850
Large-Scale Next-Generation Resequencing of Soybean Germplasm for Trait Discovery Liu, Yang et al. P0696 Conference Proceedings 2014
PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences Mirarab Siavash, Nguyen Nam, Sheng Guo, Li-San Wang, Junhyong Kim, and Tandy Warnow Journal 2014 doi: 10.1089/cmb.2014.0156
Mammalian Model Species Trees for 1X Model Condition for Mirarab et. al. Mirarab, Sivash, Md Shamsuzzoha Bayzid, Bastien Boussau, and Tandy Warnow Repository 2014
It's more than stamp collecting: how genome sequencing can unify biological research Richards, Stephen Journal 2015 doi: 10.1016/j.tig.2015.04.007
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
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
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
Extracting complex lesion phenotypes in Zea mays Kelly, Derek, Avimanyou Vatsa, Wade Mayham, and Toni Kazic 12-Jan Journal 2015 doi: 10.1007/s00138-015-0718-6
An optimal algorithm for computing all subtree repeats in trees Flouri, TomÇaØs, Kassian Kobert, Solon P. Pissis, and Alexandros Stamatakis Technical Report 2013
Introducing Undergraduate Students to Gene and Genome Structure through Gene Annotation Buckner, Brent W695 Conference Proceedings 2015
From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data Li, Jilong, Jie Hou, Lin Sun, Jordan Maximillian Wilkins, Yuan Lu, Chad E. Niederhuth, Benjamin... Journal 2015 doi: 10.1371/journal.pone.0125000
The publication and reproducibility challenges of shared data Poldrack, Russell A., and Jean-Baptiste Poline Journal 2014 doi: 10.1016/j.tics.2014.11.008
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
Sequence Alignments and Trees for Mammalian 1X for Mirarab et. al. Mirarab, Sivash, Md Shamsuzzoha Bayzid, Bastien Boussau, and Tandy Warnow Repository 2014
Does the climatic variability hypothesis explain the longitudinal range size gradient in North American trees? Donoghue, John Conference Proceedings 2012
PASTA: ultra-large multiple sequence alignment Mirarab, Siavash, Nam Nguyen, and Tandy Warnow Technical Report 2014
De novo assembly and characterization of the transcriptome of the parasitic weed Cuscuta pentagona identifies genes associated with plant parasitism Ranjan, Aashish, Yasunori Ichihashi, Moran Farhi, Kristina Zumstein, Brad Townsley, Rakefet David-... 113 Journal 2014 doi: 10.1104/pp.113.234864
A Bioinformatics Approach to Systemic Lupus Erythematosus and Autoimmunity Siefert, John 2015
Life Sciences Cyberinfrastructure at Your Fingertips: Using Internet2 to Power Scientific Collaboration Taylor, Daniel B. W488 Conference Proceedings 2015
PUmPER: Phylogenies Updated Perpetually Izquierdo-Carrasco, F., J. Cazes, S. A. Smith, and A. Stamatakis btu053 Journal 2014
Authentication and Authorization Considerations for a Multi-tenant Service Heiland, Randy, Scott Koranda, Suresh Marru, Marlon, Pierce, and Von Welch 29-35 Conference Proceedings 2015 doi: 10.1145/2753524.2753534
Flash Demo: Atmosphere Cloud Computing - Applied to Visualizing RNA-Seq Data Chougule, Kapeel W483 Conference Proceedings 2015
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
Who cares about science gateways?: a large-scale survey of community use and needs Lawrence, Katherine A., Nancy Wilkins-Diehr, Julie A. Wernert, Marlon Pierce, Michael Zentner, and... 4-Jan Conference Proceedings 2014 doi: 10.1109/GCE.2014.11
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
A software tool for the input and management of phenotypic data using personal digital assistants and other mobile devices Kohl, Karin, and Jurgen Gremmels Journal 2015 doi: 10.1186/s13007-015-0069-3
Accordion: Multi-Scale Recipes for Adaptive Detection of Duplication Lewis, Russell, and John H. Hartman Conference Proceedings 2015
Enhanced string covering Flouri, Tomà_, Costas S. Iliopoulos, Tomasz Kociumaka, Solon P. Pissis, Simon J. Puglisi, W. F.... Journal 2013
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
Resolved observations of geostationary satellites from the 6.5 m MMT Hart, Michael, Richard Rast, Stuart Jefferies, and Douglas Hope Conference Proceedings 2016
The genomic repertoir of complex and polyploid cereal genomes Spannagl, Manuel Dissertation 2015
Using basic plant traits to predict ungulate seed dispersal potential Albert, Aur_lie, Anders MÎrell, M_lanie Picard, and Christophe Baltzinger Journal 2015 doi: 10.1111/ecog.00709
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,
Evidence against a Pleistocene desert refugium in the Lower Colorado River Basin Holmgren, Camille A., Julio L. Betancourt, M. Cristina Penalba, Jose Delgadillo, Kristin Zuravnsky... Journal 2014 doi: 10.1111/jbi.12337
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
Analyzing big data using simple flowcharts and questioning techniques Goller, C. Presentation 2014
Image-based plant phenotyping with incremental learning and active contours Minervini, Massimo, Mohammed M. Abdelsamea, Sotirios A. Tsaftaris Journal 2013 doi: 10.1016/j.ecoinf.2013.07.004
Wild-Type N-Ras, Overexpressed in Basal-like Breast Cancer, Promotes Tumor Formation by Inducing IL-8 Secretion via JAK2 Activation Zheng, Ze-Yi, Lin Tian, Wen Bu, Cheng Fan, Xia Gao, Hai Wang, Yi-Hua Liao et al Journal 2015 doi: 10.1016/j.celrep.2015.06.044
Responses to Data Management Requirements at the National Scale Jordan, Chris, Maria Esteva, David Walling, Tomilsav Urban, and Sivakumar Kulasekaran 64 Journal 2013
Clouds for Masses - Toward Ubiquitiousand Transparent Clouds Goscinski, Andrzej, and Philip Church 1141-1148 Conference Proceedings 2015 doi: 10.1109/CLOUD.2015.168
Analyzing big data with simple flowcharts and questioning techniques Goller, C. Conference Proceedings 2014
Leveraging iPlant Cyberinfrastructure for a New Data-Driven Research Community Carson, James et al P1113 Conference Proceedings 2015
Transcriptional responses to fluctuating thermal regimes underpinning differences in survival in the solitary bee Megachile rotundata Torson, Alex S., George D. Yocum, Joseph P. Rinehart, William P. Kemp, and Julia H. Bowsher jeb-113829 Journal 2015 doi: 10.1242/_jeb.113829
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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
Identifying hidden rate changes in the evolution of a binary morphological character: the evolution of plant habit in campanulid angiosperms Beaulieu, Jeremy M., Brian C. O'Meara and Michael J. Donoghue 62, 5 725-37 Journal 2013 doi: 10.1093/sysbio/syt034
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
New Frontiers for Organismal Biology KÙltz, Dietmar, David F. Clayton, Gene E. Robinson, Craig Albertson, Hannah V. Carey, Molly E.... 63, No. 6 464-471 Journal 2013 doi: 10.1525/bio.2013.63.6.8
Provenance Management in BioSciences Ram, Sudha, and Jun Liu 6413 54-64 Chapter 2010 doi: 10.1007/978-3-642-16385-2_8
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
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
Application of Bioinformatics in Crop Improvement: Annotating the Putative Soybean Rust resistance gene Rpp3 for Enhancing Marker Assisted Selection Okii, D., A. C. Luseko, P. Tukamuhabwa, and M. Maphosa 7 001-009 Journal 2014 doi: 10.4172/jpb.1000296
Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes Johnson, Marc TJ, Eric J. Carpenter, Zhijian Tian, Richard Bruskiewich, Jason N. Burris, Charlotte... 7, No. 11 e50226 Journal 2012 doi: 10.1371/journal.pone.0050226
Ontology for big systems: The Ontology Summit 2012 Communiqu_ Schneider, Todd, Ali Hashemi, Mike Bennett, Mary Brady, Cory Casanave, Henson Graves, Michael... 7, No. 3 357-371 Journal 2012 doi: 10.3233/AO-2012-0111
Structure-Forming Corals and Sponges and Their Use as Fish Habitat in Bering Sea Submarine Canyons Miller, Robert J., John Hocevar, Robert P. Stone, and Dmitry V. Fedorov 7, No. 3 e33885 Journal 2012 doi: 10.1371/journal.pone.0033885
Decomposition and Modular Structure of BioPortal Ontologies Del Vescovo, Chiara, Damian DG Gessler, Pavel Klinov, Bijan Parsia, Ulrike Sattler, Thomas... 7031 130-145 Chapter 2011 doi: 10.1007/978-3-642-25073-6_9
Metadata Mapper: a web service for mapping data between independent visual analysis components, guided by perceptual rules Rogowitz, Bernice E., and Naim Matasci 786501 Conference Proceedings 2011 doi: 10.1117/12.881734
Fast Algorithm for Partial Covers in Words Kociumaka, Tomasz, Solon P. Pissis, Jakub Radoszewski, Wojciech Rytter, and Tomasz Wale 7922 177-188 Chapter 2013
Big data-a 21st century science Maginot Line? No-boundary thinking: shifting from the big data paradigm Huang, Xiuzhen, Steven F. Jennings, Barry Bruce, Alison Buchan, Liming Cai, Pengyin Chen, Carole L... 8 Journal 2015 doi: 10.1186/s13040-015-0037-5
Transcriptome-mining for single-copy nuclear markers in ferns Rothfels, Carl J., Anders Larsson, Fay-Wei Li, Erin M. Sigel, Layne Huiet, Dylan O. Burge, Markus... 8, No. 10 e76957 Journal 2013 doi: 10.1371/journal.pone.0076957
Vitis Phylogenomics: Hybridization Intensities from a SNP Array Outperform Genotype Calls Miller, Allison J., Naim Matasci, Heidi Schwaninger, Mallikarjuna K. Aradhya, Bernard Prins, Gan-... 8, No. 11 e78680 Journal 2013 doi: 10.1371/journal.pone.0078680
Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons Eichten, Steven R., Nathanael A. Ellis, Irina Makarevitch, Cheng-Ting Yeh, Jonathan I. Gent, Lin... 8, No. 12 e1003127 Journal 2012 doi: 10.1371/journal.pgen.1003127
Clarifying Concepts and Terms in Biodiversity Informatics Deck, John, Katherine Barker, Reed Beaman, Pier Luigi Buttigieg, Gabriele Dr_ge, Robert Guralnick,... 8, No. 2 Journal 2013 doi: 10.4056/sigs.3907833
TCW: Transcriptome Computational Workbench Soderlund, Carol, William Nelson, Mark Willer, David R. Gang 8, No. 7 e69401 Journal 2013 doi: 10.1371/journal.pone.0069401
The Putative C2H2 Transcription Factor MtfA Is a Novel Regulator of Secondary Metabolism and Morphogenesis in Aspergillus nidulans Ramamoorthy, Vellaisamy, Sourabh Dhingra, Alexander Kincaid, Sourabha Shantappa, Xuehuan Feng, Ana... 8, No. 9 e74122 Journal 2013 doi: 10.1371/journal.pone.0074122
Using Flatbed Scanners to Collect High-resolution Time-lapsed Images of the Arabidopsis Root Gravitropic Response Smith, Halie C., Devon J. Niewohner, Grant D. Dewey, Autumn M. Longo, Tracy L. Guy, Bradley R.... 83 e50878-e50878 Journal 2014 doi: 10.3791/50878
Incrementally Updateable and Persistent Decomposition of OWL Ontologies Klinov, Pavel, Chiara Del Vescovo, and Thomas Schneider 849 7 Conference Proceedings 2012
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
Optimization Techniques For Next-Generation Sequencing Data Analysis Caciula, Adrian 87 Dissertation 2014
Spatiotemporal data representation and its effect on the performance of spatial analysis in a cyberinfrastructure environment-A case study with raster zonal analysis Song, Miaomiao, Wenwen Li, Bin Zhou, and Ting Lei 87 21-Nov Journal 2016 doi: 10.1016/j.cageo.2015.11.005
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Meeting report: advancing practical applications of biodiversity ontologies Walls, Ramona L., Robert Guralnick, John Deck, Adam Buntzman, Pier L. Buttigieg, Neil Davies,... 9, No. 1 17 Journal 2014 doi: 10.1186/1944-3277-9-17
Metadata based management and sharing of distributed biomedical data Wang, Fusheng, Cristobal Vergara_Niedermayr, and Peiya Liu 9, No. 1 42-57 Journal 2014 doi: 10.1504/IJMSO.2014.059126
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From data to function: Functinal modeling of poultry genomics data McCarthy, Fiona M., Eric Lyons 92, No. 9 2519-2529 Journal 2013 doi: 10.3382/ps.2012-02808
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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
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
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
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
Whole Genome and Tandem Duplicate Retention facilitated Glucosinolate Pathway Diversification in the Mustard Family Hofberger, Johannes A., Eric Lyons, Patrick P. Edger, J. Chris Pires, and M. Eric Schranz evt162 Journal 2013 doi: 10.1093/gbe/evt162
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Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges Stein, Lincoln D. No. 9 678-688 Journal 2008 doi: 10.1038/nrg2414
Enabling Cloud and GRid Powered Image Phenotyping Nirav Merchant, Nathan Miller, Kris Kvilekval, Edgar Spalding, B.S. Manjunath P0111 Conference Proceedings 2013
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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
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iMicrobe: Advancing Clinical and Environmental Microbial Research using the iPlant Cyberinfrastructure Hurwitz, Bonnie P10931 Conference Proceedings 2014
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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
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A Simple Bioinformatics Workflow for RNA-Seq Analysis and Distributed Genome Annotation Micklos, Dave W250 Conference Proceedings 2014
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