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Title Author(s) Volume, Issue Pagessort descending Type of Publication Year DOI
The Encyclopedia of Life v2: Providing Global Access to Knowledge About Life on Earth Parr, Cynthia S., Mr Nathan Wilson, Mr Patrick Leary, Katja S. Schulz, Ms Kristen Lans, Ms Lisa... 2 Journal 2014 doi: 10.3897/BDJ.2.e1079
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
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
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
EPIC CoGE- a unified browser for Epigenetics Lyons, Eric, Matthew Bomhoff, Fan Li, Brian D. Gregory W514 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 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
Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding Joshi, Trupti, Michael R. Fitzpatrick, Shiyuan Chen, Yang Liu, Hongxin Zhang, Ryan Z. Endacott,... gkt905 Journal 2013 doi: 10.1093/nar/gkt905
taxize: taxonomic search and retrieval in R [v1; ref status Chamberlain, Scott A., and Eduard Sz_cs 2, No. 191 Journal 2013 doi: 10.12688/f1000research.2-191.v2
The iPlant Collaborative Website Collaborative, iPlant Website 2008
Enabling Cloud and GRid Powered Image Phenotyping Nirav Merchant, Nathan Miller, Kris Kvilekval, Edgar Spalding, B.S. Manjunath P0111 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
African Orphan Crops Consortium_a NEPAD-led initiative Makinde, Diran January Essay 2014
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
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
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
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
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
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
Transcriptomic Analyses and Alternative Splicing Landscapes of Brachypodium Infected with Panicum Mosaic Virus Mandadi, Kranthi Kiran, Karen-Beth G. Scholthof P9867 Conference Proceedings 2014
Transposable Elements, Gene Discovery, and DNA Barcoding (Yellow and Blue Lines) Burnette, James. Conference Proceedings 2015
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
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
Latest Technology in Irrigation Management in Nursery Production McDonald, John, and Steve Hart Journal 2014
Optimization Techniques For Next-Generation Sequencing Data Analysis Caciula, Adrian 87 Dissertation 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
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
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
Concepts in Distributed Data Management or History of the DICE Group Moore, Reagan W., Arcot Rajasekar, Michael Wan, and Wayne Schroeder Technical Report 2015
Data sharing and its implications for academic libraries Kim, Jeonghyun 114, No. 11/12 Journal 2013
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
An Improved Approximate-Bayesian Model-choice Method for Estimating Shared Evolutionary History Oaks, Jamie R. arXiv:1402.6303 [q-bio.PE] Journal 2014
The iPlant Collaborative McKay, Sheldon, Eric Lyons, Haibao Tang, Nathan Miller, Steven R. Eichten, Stephen A. Goff, Dan... W416 Conference Proceedings 2012
Bringing Authentic Genomics Research into the Classroom: Analysis of Maize Stress Response (Green Line) Makarevitch, Irina Conference Proceedings 2015
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
Plant High-Throughput Phenotyping Using Photogrammertry and 3D Modeling Techniques An, Nan Dissertation 2015
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
A Simple Bioinformatics Workflow for RNA-Seq Analysis and Distributed Genome Annotation Micklos, Dave W250 Conference Proceedings 2014
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
Simplifying Genome Annotation and Examples of Large-Scale Projects in DNA Barcoding (Red and Blue Lines) Micklos, Dave Conference Proceedings 2015
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
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
Enabling Phenotypic Image Analysis Using Shared Cyberinfrastructure Miller, Nathan W418 Conference Proceedings 2012
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
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
Optimizing the PCIT algorithm on stampede's Xeon and Xeon Phi processors for faster discovery of biological networks Koesterke, Lars, K. Milfeld, M.W. Vaughn, D. Stanzione, J.E. Koltes, N.T. Weeks, J.M. Reecy 14 Conference Proceedings 2013 doi: 10.1145/2484762.2484794
Future of portable devices for plant pathogen diagnosis Nezhad, Amir Sanati Royal Society of Chemstry Journal 2014 doi: 10.1039/C4LC00487F
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
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
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
Globus Platform-as-a-Service for Collaborative Science Applications Ananthakrishnan, Rachana, Kyle Chard, Ian Foster, Steven Tuecke Journal 2014
Overivew of the iPlant Collaborative Vaughn, Matthew Conference Proceedings 2015
Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) Ming, Ray, Robert VanBuren, Yanling Liu, Mei Yang, Yuepeng Han, Lei-Ting Li, Qiong Zhang, Min-Jeong... 14, No. R41 Journal 2013 doi: 10.1186/gb-2013-14-5-r41
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
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
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
Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases Wollbrett, Julien, Pierre Larmande, Fr_d_ric de Lamotte, and Manuel Ruiz 14, No. 126 Journal 2013 doi: 10.1186/1471-2105-14-126
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
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
The Evolution of Genome Structure Tang, Haibao, and Eric Lyons 1, No. 1 Journal 2012 doi: 10.4172/ievj.1000e105
Role of Bioinformatic Tools and Databases in Cotton Research Yu, Jing, and Dorrie Main 57 Journal 2015 doi: 10.2134/agronmonogr57.2013.0043
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
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
The Arabidopsis Information Portal: A First Glimpse Vaughn, Matt P11455 Conference Proceedings 2014
Phylogenetic Analysis with the iPlant Discovery Environment Matasci, Naim, Sheldon J. McKay Chapter 2013 doi: 10.1002/0471250953.bi0613s42
Big Data: Related Technologies, Challenges and Future Prospects Chen, Min, Shiwen Mao, Yin Zhang, and Victor CM Leung Journal 2014 doi: 10.4236/jcc.2014.26001
Cyberinfrastructure: Applications and Challenges Tong, Qiuhui, Bo Yuan, and Xiu Li 2014
Taking the Phenomics Revolution into the Field Mogel, Karl Haro von Editorial 2013 doi: 10.2134/csa2013-58-3-1
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
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
Serving national scientific communities -genome analysis as an example. Stewart, C.A. Conference Proceedings 2014
Leverage iPlant Computing Resources for Collaborative Genomic Research Tang, Haibao, Konstantinos Krampis W419 Conference Proceedings 2012
Embedding CIPRES science gateway capabilities in phylogenetics software environments Miller, Mark A., Terri Schwartz, Wayne Pfeiffer 40 Conference Proceedings 2013 doi: 10.1145/2484762.2484806
Keynote: The iPlant Collaborative: A Life Sciences Cyberinfrastructure for the 21st Century Stanzione, Dan Conference Proceedings 2013
Recipes 2.0: Building for Today and Tomorrow Dooley, Rion, Matthew R. Hanlon 993, No. 16 Conference Proceedings 2013
The Databridge Rajasekar, Arcot, Hye-Chung Kum, Merce Crosas, Jonathan Crabtree, Sharlini Sankaran, Howard Lander... 2, No. 1 Journal 2013
Management and Visualization of Ianimal Quantitative Data Using iPlant and EPIC-CoGe Subramaniam, Sabarinath Conference Proceedings 2015
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
Leveraging the national cyberinfrastructure for biomedical research LeDuc, Richard, Matthew Vaughn, John M. Fonner, Michael Sullivan, James G. Williams, Philip D.... Journal 2013 doi: 10.1136/amiajnl-2013-002059
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
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
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
W7 Model of Provenance and Its Use in the Context of Wikipedia Liu, Jun Dissertation 2011
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
Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses Hurwitz, Bonnie L., Anton H. Westveld, Jennifer R. Brum, and Matthew B. Sullivan Journal 2014 doi: 10.1073/pnas.1319778111
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
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
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
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
Protocol for the Generation of a Transcription Factor Open Reading Frame Collection (TFome) Gray, John, Brett Burdo et al 5, No. 15 Journal 2015
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
Identification of dopamine receptors across the extant avian family tree and analysis with other clades uncovers a polyploid expansion among vertebrates Haug-Baltzell, Asher, Erich D. Jarvis, Fiona McCarthy, and Eric Lyons 9, No. 361 Journal 2015 doi: 10.3389/fnins.2015.00361
Infrastructure for managing and analyzing biological networks derived from collections of plant images Das, Abhiram, Alexander Bucksch, and Joshua S. Weitz Poster 2014
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 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
SBMLChecker, a Semantic approach for SBML model reliability evaluation Thavappiragasam, Mathialakan, Carol M. Lushbough, and Etienne Z. Gnimpieba Conference Proceedings 2014
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
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
Bin Definition for Super Gene Trees for Mirarab et. al. Mirarab, Sivash, Md Shamsuzzoha Bayzid, Bastien Boussau, and Tandy Warnow Repository 2014
Next-generation plant science: putting big data to work Brauer, Elizabeth K., Dharmendra K. Singh, and Sorina C. Popescu 15, 301 Journal 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
A Set of Plastid Loci for Use in Multiplex Fragment Length Genotyping for Intraspecific Variation in Pinus (Pinaceae) Wofford, Austin M., Kristen Finch, Adam Bigott, and Ann Willyard 2, No. 5 Journal 2014 doi: 10.3732/apps.1400002
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
Gene co-expression network analysis provides novel insights into myostatin regulation at three different mouse developmental timepoints Yang, Xuerong, James E. Koltes, Carissa A. Park, Daiwen Chen, and James M. Reecy 10, No. 2 Journal 2015 doi: 10.1371/journal.pone.0117607
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
Introducing Genome Browsers, Genome Structure, and Gene Annotation Buckner, Brent P10952 Conference Proceedings 2014
A web semantic for SBML merge Thavappiragasam, Mathialakan Thesis 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
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
Extensible Generic Data Management Software Moore, Reagan W. 1309.5372 Technical Report 2013
How to Use the iPlant's Discovery Environment for Your Research McKay, Sheldon W420 Conference Proceedings 2012
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
Role of genetic studies towards solving problems of human society Zulfiqar, Shumaila, Muhammad Nadeem Hafeez, Muhammad Shahzad Iqbal, and Qurban Ali 13, No. 4 Journal 2015 doi: 10.7537/j.issn.1545-0740
Implementing the Research Strategy and Evaluating Progress Committee to Develop a Research Strategy for Environmental, Health, and Safety Aspects of... Technical Report 2014
Sequence Alignments and Trees for Avian 1X for Mirarab et. al. Mirarab, Sivash, Md Shamsuzzoha Bayzid, Bastien Boussau, and Tandy Warnow Repository 2014
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
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
An optimal algorithm for computing all subtree repeats in trees Flouri, TomÇaØs, Kassian Kobert, Solon P. Pissis, and Alexandros Stamatakis Technical Report 2013
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 Review of Cloud Computing Bioinformatics Solutions for Next-Gen Sequencing Data Analysis and Research Krampis, Konstantinos, and Claudia Wultsch 2, No. 1 Journal 2015 doi: 10.1515/mngs-2015-0003
Using Clouds for Technical Computing Fox, Geoggrey, Dennis Gannon Technical Report 2013
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
A Bioinformatics Approach to Systemic Lupus Erythematosus and Autoimmunity Siefert, John 2015
Genome annotation in the cloud through xGDBvm virtual server instances deployed at iPlant Duvick, Jon P10310 Conference Proceedings 2014
Promzea: a pipeline f or discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas Liseron-Monfils, Christophe, Tim Lewis, Daniel Ashlock, Paul D McNicholas, François Fauteux,... 13, No. 24 Journal 2013 doi: 10.1186/1471-2229-13-42
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