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Submissions from 2019

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fagin: synteny-based phylostratigraphy and finer classification of young genes, Zebulun Arendsee, Jing Li, Urminder Singh, Priyanka Bhandary, Arun Seetharam, and Eve Syrkin Wurtele

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synder: inferring genomic orthologs from synteny maps, Zebulun Arendsee, Andrew Wilkey, Urminder Singh, Jing Li, Manhoi Hur, and Eve Syrkin Wurtele

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A Functional Unfolded Protein Response Is Required for Normal Vegetative Development, Yan Bao, Diane C. Bassham, and Stephen H. Howell

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Auxin Induces Widespread Proteome Remodeling in Arabidopsis Seedlings, Natalie M. Clark, Zhouxin Shen, Steven P. Briggs, Justin W. Walley, and Dior R. Kelley

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Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future, Colleen Doherty, Justin Walley, Eve Wurtele, and et al.

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Development and application of a quantitative bioassay to evaluate maize silk resistance to corn earworm herbivory among progenies derived from Peruvian landrace Piura, Miriam D. Lopez, Tesia S. Dennison, Tina M. Paque, Marna D. Yandeau-Nelson, Craig A. Abel, and Nick Lauter

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Linking Autophagy to Abiotic and Biotic Stress Responses, Santiago Signorelli, Lukasz Pawel Tarkowski, Wim Van den Ende, and Diane C. Bassham

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Altering the Substrate Specificity of Acetyl-CoA Synthetase by Rational Mutagenesis of the Carboxylate Binding Pocket, Naazneen Sofeo, Jason H. Hart, Brandon Butler, David J. Oliver, Marna D. Yandeau-Nelson, and Basil J. Nikolau

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Identification of transcription factors that regulate ATG8 expression and autophagy in Arabidopsis, Ping Wang, Trevor M. Nolan, Yanhai Yin, and Diane C. Bassham

Submissions from 2018

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Using Arabidopsis Mesophyll Protoplasts to Study Unfolded Protein Response Signaling, Yan Bao and Diane C. Bassham

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IRE1B degrades RNAs encoding proteins that interfere with the induction of autophagy by ER stress in Arabidopsis thaliana, Yan Bao, Yunting Pu, Xiang Yu, Brian D. Gregory, Renu Srivastava, Stephen H. Howell, and Diane C. Bassham

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Identification of Active Site Residues Implies a Two-step Catalytic Mechanism for Acyl-ACP Thioesterase, Fuyuan Jing, Marna D. Yandeau-Nelson, and Basil J. Nikolau

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Two distinct domains contribute to the substrate acyl chain length selectivity of plant acyl-ACP thioesterase, Fuyuan Jing, Le Zhao, Marna D. Yandeau-Nelson, and Basil J. Nikolau

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E3 ubiquitin ligases: key regulators of hormone signaling in plants, Dior R. Kelley

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From Arabidopsis to Crops: The Arabidopsis QQS Orphan Gene Modulates Nitrogen Allocation Across Species, Seth O'Conner, Andrea Neudorf, Wenguang Zheng, Mingsheng Qi, Xuefeng Zhao, Chuanlong Du, Dan Nettleton, and Ling Li

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Epigenetic regulators Rbbp4 and Hdac1 are overexpressed in a zebrafish model of RB1 embryonal brain tumor, and are required for neural progenitor survival and proliferation, Laura E. Schultz, Jeffrey A. Haltom, Maira P. Almeida, Wesley A. Wierson, Staci L. Solin, Trevor J. Weiss, Jordan A. Helmer, Elizabeth J. Sandquist, Heather R. Shive, and Maura McGrail

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Retinoblastoma binding protein 4 maintains cycling neural stem cells and prevents DNA damage and Tp53-dependent apoptosis in rb1 mutant neural progenitors, Laura E. Schultz-Rogers, Maira P. Almeida, Wesley a. Wierson, Marcel Kool, and Maura McGrail

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Dynamics of Autophagosome Formation, Junmarie Soto-Burgos, Xiaohong Zhuang, Liwen Jiang, and Diane C. Bassham

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Cellular Dynamics: Cellular Systems in the Time Domain, Dan Szymanski, Diane Bassham, Teun Munnik, and Wataru Sakamoto

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Autophagy in crop plants: what's new beyond Arabidopsis?, Jie Tang and Diane C. Bassham

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GeneWeld: a method for efficient targeted integration directed by short homology, Wesley A. Wierson, Jordan M. Welker, Maira P. Almeida, Carla A. Mann, Dennis A. Webster, Melanie E. Torrie, Trevor J. Weiss, Macy K. Vollbrecht, Merrina Lan, Kenna C. McKeighan, Zhitao MIng, Alec Wehmeier, Christopher S. Mikelson, Jeffrey A. Haltom, Kristen M. Kwan, Chi-­Bin Chien, Darius Balciunas, Stephen C. Ekker, Karl J. Clark, Beau R. Webber, Branden Moriarity, Staci L. Solin, Daniel F. Carlson, Drena L. Dobbs, Maura McGrail, and Jeffrey J. Essner

Submissions from 2017

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Raising orphans from a metadata morass: a researcher's guide to re-use of public ’omics data, Priyanka Bhandary, Arun S. Seetharam, Zebulun Arendsee, Manhoi Hur, and Eve Syrkin Wurtele

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Students’ Use of Optional Online Reviews and Its Relationship to Summative Assessment Outcomes in Introductory Biology, Shana K. Carpenter, Shuebur Rahman, Terry J.S. Lund, Patrick I. Armstrong, Monica H. Lamm, Robert D. Reason, and Clark R. Coffman

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An Agrobacterium-delivered CRISPR/Cas9 system for high-frequency targeted mutagenesis in maize, Si Nian Char, Anjanasree K. Neelakandan, Hartinio Nahampun, Bronwyn Frame, Marcy Main, Martin H. Spalding, Philip W. Becraft, Blake C. Meyers, Virginia Walbot, Kan Wang, and Bing Yang

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High spatial resolution mass spectrometry imaging reveals the genetically programmed, developmental modification of the distribution of thylakoid membrane lipids among individual cells of maize leaf, Maria Emilia Duenas, Adam T. Klein, Liza E. Alexander, Marna D. Yandeau-Nelson, Basil J. Nikolau, and Young Jin Lee

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Evaluating the Quick Fix: Weight Loss Drugs and Cellular Respiration, Pamela L. Freeman, Jennifer A. Maki, Kara R. Thoemke, Monica H. Lamm, and Clark R. Coffman

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The 3-hydroxyacyl-ACP dehydratase component of the plant mitochondrial fatty acid synthase system, Xin Guan, Yozo Okazaki, Andrew Lithio, Ling Li, Xuefeng Zhao, Huanan Jin, Dan Nettleton, Kazuki Saito, and Basil J. Nikolau

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Peruvian Window-Leaved Peperomia Taxa Display Unique Crystal Macropatterns in High-Altitude Environments, Harry T. Horner, Stefan Wanke, Birgit Oelschlägel, and Marie-Stéphanie Samain

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Single cell transcriptome profiling of developing chick retinal cells, Lauren A. Laboissonniere, Gregory M. Martin, Jillian J. Goetz, Ran Bi, Brock Pope, Kallie Weinand, Laura Ellson, Diane Fru, Miranda Lee, Andrea K. Wester, Peng Liu, and Jeffrey M. Trimarchi

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Single-cell RNA-Seq of Defined Subsets of Retinal Ganglion Cells, Lauren A. Laboissonniere, Takuma Sonoda, Seul Ki Lee, Jeffrey M. Trimarchi, and Tiffany M. Schmidt

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A robust and efficient method for the extraction of plant extracellular surface lipids as applied to the analysis of silks and seedling leaves of maize, Derek M. Loneman, Layton Peddicord, Amani Al-Rashid, Basil J. Nikolau, Nick Lauter, and Marna D. Yandeau-Nelson

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Lasting Retinal Injury in a Mouse Model of Blast-Induced Trauma, Najiba Mammadova, Shivani Ghaisas, Gary Zenitsky, Donald S. Sakaguchi, Anumantha Kanthasamy, Justin J. Greenlee, and M. Heather West Greenlee

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Wind Energy Conversion by Plant-Inspired Designs, Michael A. McCloskey, Curtis L. Mosher, and Eric R. Henderson

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Selective Autophagy of BES1 Mediated by DSK2 Balances Plant Growth and Survival, Trevor M. Nolan, Benjamin Brennan, Mengran Yang, Jiani Chen, Mingcai Zhang, Zhaohu Li, Xuelu Wang, Diane C. Bassham, Justin Walley, and Yanhai Yin

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TOR-Dependent and -Independent Pathways Regulate Autophagy in Arabidopsis thaliana, Yunting Pu, Xinjuan Luo, and Diane C. Bassham

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Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment, Sweta Roy-Carson, Kevin Natukunda, Hsien-chao Chou, Narinder Pal, Caitlin Farris, Stephan Q. Schneider, and Julie A. Kuhlman

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TNO1, a TGN-localized SNARE-interacting protein, modulates root skewing in Arabidopsis thaliana, Rahul Roy and Diane C. Bassham

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Vascular Endothelial Growth Factor A and Leptin Expression Associated with Ectopic Proliferation and Retinal Dysplasia in Zebrafish Optic Pathway Tumors, Laura E. Schultz, Staci L. Solin, Welsey A. Wierson, Janna M. Lovan, Judith Syrkin-Nikolau, Deborah E. Lincow, Andrew J. Severin, Donald S. Sakaguchi, and Maura McGrail

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SnRK1 activates autophagy via the TOR signaling pathway in Arabidopsis thaliana, Junmarie Soto-Burgos and Diane C. Bassham

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Microscopic Characterization of a Transposon-Induced Male-Sterile, Female-Sterile Mutant in Glycine max L., Katherine A. Thilges, Mark A. Chamberlin, Marc C. Albertsen, and Harry T. Horner

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Comparative Proteomics of Rubber Latex Revealed Multiple Protein Species of REF/SRPP Family Respond Diversely to Ethylene Stimulation among Different Rubber Tree Clones, Zheng Tong, Dan Wang, Yong Sun, Qian Yang, Xueru Meng, Limin Wang, Weiqiang Feng, Ling Li, Eve Syrkin Wurtele, and Xuchu Wang

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Sequence-Based Prediction of RNA-Binding Residues in Proteins, Rasna R. Walia, Yasser EL-Manzalawy, Vasant G. Honavar, and Drena Dobbs

Submissions from 2016

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Identification of G protein-coupled receptors required for vitellogenin uptake into the oocytes of the red flour beetle, Tribolium castaneum, Hua Bai and Subba R. Palli

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Mutations in TUBB8 and Human Oocyte Meiotic Arrest, Ruizhi Feng, Qing Sang, Yanping Kuang, Xiaoxi Sun, Zheng Yan, Shaozhen Zhang, Juanzi Shi, Guoling Tian, Anna Luchniak, Yusuke Fukuda, Bin Li, Min Yu, Junling Chen, Yao Xu, Luo Guo, Ronggui Qu, Xueqian Wang, Zhaogui Sun, Miao Liu, Huijuan Shi, Hongyan Wang, Yi Feng, Ruijin Shao, Renjie Chai, Qiaoli Li, Qinghe Xing, Rui Zhang, Eva Nogales, Li Jin, Lin He, Mohan L. Gupta Jr., Nicholas J. Cowan, and Lei Wang

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Polo-Like Kinase 3 Appears Dispensable for Normal Retinal Development Despite Robust Embryonic Expression, Jillian J. Goetz, Lauren A. Laboissonniere, Andrea K. Wester, Madison R. Lynch, and Jeffrey M. Trimarchi

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NKD Transcription Factors Are Central Regulators of Maize Endosperm Development, Bryan C. Gontarek, Anjanasree K. Neelakandan, Hao Wu, and Philip W. Becraft

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A Clade-Specific Arabidopsis Gene Connects Primary Metabolism and Senescence, Dallas C. Jones, Wenguang Zheng, Sheng Huang, Chuanlong Du, Xuefeng Zhao, Ragothaman M. Yennamalli, Taner Z. Sen, Dan Nettleton, Eve S. Wurtele, and Ling Li

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Opportunistic proteolytic processing of carbonic anhydrase 1 from Chlamydomonas in Arabidopsis reveals a novel route for protein maturation, Parijat S. Juvale, Ryan L. Wagner, and Martin H. Spalding

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The Plastid Casein Kinase 2 Phosphorylates Rubisco Activase at the Thr-78 Site but Is Not Essential for Regulation of Rubisco Activation State, Sang Y. Kim, Kyle W. Bender, Berkley J. Walker, Raymond E. Zielinski, Martin H. Spalding, Donald R. Ort, and Steven C. Huber

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Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition), Daniel J. Klionsky, Kotb Abdelmohsen, Diane C. Bassham, Anumantha Kanthasamy, Gustavo C. Macintosh, Hua Bai, and et. al.

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Programmable DNA Nanosystem for Molecular Interrogation, Davita Mathur and Eric R. Henderson

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Comparison of Susceptible and Resistant Maize Hybrids to Colonization by Clavibacter michiganensis subsp. nebraskensis, Gladys C. Y. Mbofung, Jeff Sernett, Harry T. Horner, and Alison E. Robertson

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Polycaprolactone Microfibrous Scaffolds to Navigate Neural Stem Cells, Farrokh Sharifi, Bhavika B. Patel, Adam K. Dzuilko, Reza Montazami, Donald S. Sakaguchi, and Nastaran Hashemi

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Comparative Transcriptome Reconstruction of Four Hypericum Species Focused on Hypericin Biosynthesis, Miroslav Sotak, Odeta Czerankova, Daniel Klein, Zuzana Jurcackova, Ling Li, and Eva Cellarova

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Microbial Community and Chemical Characteristics of Swine Manure during Maturation, Steven L. Trabue, Brian J. Kerr, Bradley L. Bearson, Manhoi Hur, Timothy Parkin, Eve S. Wurtele, and Cherrie J. Ziemer

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Template-based protein–protein docking exploiting pairwise interfacial residue restraints, Li C. Xue, João P.G.L.M. Rodrigues, Drena Dobbs, Vasant Honavar, and Alexandre M.J.J. Bonvin

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Bone marrow-derived mesenchymal stem cells (MSCs) stimulate neurite outgrowth from differentiating adult hippocampal progenitor cells, Eun-Ah Ye, Sagar S. Chawla, Michael Z. Khan, and Donald S. Sakaguchi

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Genes and Small RNA Transcripts Exhibit Dosage-Dependent Expression Pattern in Maize Copy-Number Alterations, Tao Zuo, Jianbo Zhang, Andrew Lithio, Sudhansu Dash, David F. Weber, Roger Wise, Dan Nettleton, and Thomas Peterson

Submissions from 2015

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Heritable site-specific mutagenesis using TALENs in maize, Si Nian Char, Erica Unger-Wallace, Bronwyn Frame, Sarah A. Briggs, Marcy Main, Martin H. Spalding, Erik Vollbrecht, Kan Wang, and Bing Yang

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Stochastic Optical Reconstruction Microscopy Imaging of Microtubule Arrays in Intact Arabidopsis thaliana Seedling, Bin Dong, Xiaochen Yang, Shaobin Zhu, Diane C. Bassham, and Ning Fang

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Transcriptomic analyses of Onecut1 and Onecut2 deficient retinas, Jillian J. Goetz and Jeffrey M. Trimarchi

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Where Goes the BSA Endowment: A Legacy Yet to be Written, Harry T. (Jack) Horner

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ArcA Controls Metabolism, Chemotaxis, and Motility Contributing to the Pathogenicity of Avian Pathogenic Escherichia coli, Fengwei Jiang, Chunxia An, Yinli Bao, Xuefeng Zhao, Robert L. Jernigan, Andrew Lithio, Dan Nettleton, Ling Li, Eve S. Wurtele, Lisa K. Nolan, Chengping Lu, and Ganwu Li

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TALEN-Mediated Gene Editing of the Thrombospondin-1 Locus in Axolotl, Tzu-Hsing Kuo, Johanna E. Kowalko, Tia DiTommaso, Mandi Nyambi, Daniel T. Montoro, Jeffrey J. Essner, and Jessica L. Whited

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The QQS orphan gene of Arabidopsis modulates carbon and nitrogen allocation in soybean, Ling Li and Eve S. Wurtele

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QQS orphan gene regulates carbon and nitrogen partitioning across species via NF-YC interactions, Ling Li, Wenguang Zheng, Yanbing Zhu, Huaxun Ye, Buyun Tang, Zebulun W. Arendsee, Dallas Jones, Ruoran Li, Diego Ortiz, Xuefeng Zhao, Chuanlong Du, Dan Nettleton, M. Paul Scott, Maria G. Salas-Fernandez, Yanhai Yin, and Eve S. Wurtele

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Genome Editing Using TALENs in Blind Mexican Cavefish, Astyanax mexicanus, Li Ma, William R. Jeffery, Jeffrey J. Essner, and Johanna E. Kowalko

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Enabling nanomaterial, nanofabrication and cellular technologies for nanoneuromedicines, Surya K. Mallapragada, Timothy M. Brenza, JoEllyn M. McMillan, Balaji Narasimhan, Donald S. Sakaguchi, Anup D. Sharma, Svitlana Zbarska, and Howard E. Gendelman

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Redesigning photosynthesis to sustainably meet global food and bioenergy demand, Donald R. Ort, Sabeeha S. Merchant, Jean Alric, Alice Barkan, Robert E. Blankenship, Ralph Bock, Roberta Croce, Maureen R. Hanson, Julian M. Hibberd, Stephen P. Long, Thomas A. Moore, James Moroney, Krishna K. Niyogi, Martin A.J. Parry, Pamela P. Peralta-Yahya, Roger C. Prince, Kevin E. Redding, Martin H. Spalding, Klass J. van Wijk, Wim F.J. Vermaas, Susanne von Caemmerer, Andreas P.M. Weber, Todd O. Yeates, Joshua S. Yuan, and Xin Guang Zhu

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Gravitropism and Lateral Root Emergence are Dependent on the Trans-Golgi Network Protein TN01, Rahul Roy and Diane C. Bassham

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High Throughput Characterization of Adult Stem Cells Engineered for Delivery of Therapeutic Factors for Neuroprotective Strategies, Anup D. Sharma, Pavel A. Brodskiy, Emma M. Petersen, Melih Dagdeviren, Eun-Ah Ye, Surya K. Mallapragada, and Donald Sakaguchi

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Rapid Tumor Induction in Zebrafish by TALEN-Mediated Somatic Inactivation of the Retinoblastoma1 Tumor Suppressor rb1, Staci L. Solin, Heather R. Shive, Kevin D. Woolard, Jeffrey J. Essner, and Maura McGrail

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Use of designer nucleases for targeted gene and genome editing in plants, Martin H. Spalding, Donald P. Weeks, and Bing Yang

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Modifications of membrane lipids in response to wounding of Arabidopsis thaliana leaves, Hieu Sy Vu, Rebecca Roston, Sunitha Shiva, Manhoi Hur, Eve S. Wurtele, Xuemin Wang, Jyoti Shah, and Ruth Welti

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Computational prediction of protein interfaces: A review of data driven methods, Li C. Xue, Drena Dobbs, Alexandre M.J.J. Bonvin, and Vasant Honavar

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Advances in metabolomic applications in plant genetics and breeding, Marna D. Yandeau-Nelson, Nick Lauter, and Olga A. Zabotina

Submissions from 2014

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G-Quadruplex (G4) Motifs in the Maize (Zea mays L.) Genome Are Enriched at Specific Locations in Thousands of Genes Coupled to Energy Status, Hypoxia, Low Sugar, and Nutrient Deprivation, Carson M. Andorf, Mykhailo Kopylov, Drena Dobbs, Karen E. Koch, M. Elizabeth Stroupe, Carolyn J. Lawrence, and Hank W. Bass

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Autophagy in plants and algae, Diane C. Bassham and Jose L. Crespo

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Loss of Gq/11 Genes Does Not Abolish Melanopsin Phototransduction, Kylie S. Chew, Tiffany M. Schmidt, Alan C. Rupp, Paulo Kofuji, and Jeffrey M. Trimarchi

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Onecut1 and Onecut2 Play Critical Roles in the Development of the Mouse Retina, Jillian J. Goetz, Gregory M. Martin, Rebecca Chowdhury, and Jeffrey M. Trimarchi

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In Memorium: William A. Jensen, 1927-2014, Jack Horner

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Multipotent adult hippocampal progenitor cells maintained as neurospheres favor differentiation toward glial lineages, Jisun Oh, Gabrielle J. Daniels, Lawrence S. Chiou, Eun-Ah Ye, Yong-Seob Jeong, and Donald S. Sakaguchi

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Molecular and Cellular Characterization of a Zebrafish Optic Pathway Tumor Line Implicates Glia-Derived Progenitors in Tumorigenesis, Staci L. Solin, Ying Wang, Joshua Mauldin, Laura E. Schultz, Deborah E. Lincow, Pavel A. Brodskiy, Crystal A. Jones, Judith Syrkin-Nikolau, Jasmine M. Linn, Jeffrey J. Essner, Jesse M. Hostetter, Elizabeth M. Whitley, J. Douglas Cameron, Hui-Hsien Chou, Andrew J. Severin, Donald S. Sakaguchi, and Maura McGrail

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Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice, Martin H. Spalding, Huanbin Zhou, Bo Liu, Donald P. Weeks, and Bing Yang

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Computational modeling suggests dimerization of equine infectious anemia virus Rev is required for RNA binding, Chijioke N. Umunnakwe, Hyelee Loyd, Kinsey Cornick, Jerald R. Chavez, Drena Dobbs, and Susan Carpenter

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Acclimation to very-low CO2: Contribution of LCIB and LCIA to inorganic carbon uptake in Chlamydomonas reinhardtii, Yingjun Wang and Martin H. Spalding

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High-throughput fluorescence-activated cell sorting for lipid hyperaccumulating Chlamydomonas reinhardtii mutants, Bo Xie, Dan Stessman, Jason H. Hart, Haili Dong, Yingjun Wang, David A. Wright, Basil J. Nikolau, Martin H. Spalding, and Larry J. Halverson

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DockRank: Ranking docked conformations using partner-specific sequence homology-based protein interface prediction, Li C. Xue, Rafael A. Jordan, Yasser EL-Manzalawy, Drena Dobbs, and Vasant Honavar

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Transposition-mediated DNA re-replication in maize, Jianbo Zhang, Tao Zuo, Dafang Wang, and Thomas Peterson

Submissions from 2013

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Implementing Pedagogical Change in Introductory Biology Courses Through the Use of Faculty Learning Communities, Elizabeth A. Addis, Kathleen M. Quardokus, Diane C. Bassham, Philip W. Becraft, Clark R. Coffman, Jo Anne Powell-Coffman, Nancy M. Boury, and James T. Colbert

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Comprehensive analysis of correlation coefficients estimated from pooling heterogeneous microarray data, Márcia M. Almeida-de-Macedo, Nick Ransom, Yaping Feng, Jonathan Hurst, and Eve S. Wurtele

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Holocarboxylase Synthetase 1 Physically Interacts with Histone H3 in Arabidopsis, Xi Chen, Hui-Hsien Chou, and Eve S. Wurtele

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Identification and biosynthesis of acylphloroglucinols in Hypericum gentianoides, Matthew C. Crispin, Manhoi Hur, Taeseong Park, Young Hwan Kim, and Eve S. Wurtele

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Otx2 and Onecut1 Promote the Fates of Cone Photoreceptors and Horizontal Cells and Repress Rod Photoreceptors, Mark M. Emerson, Natalia Surzenko, Jillian J. Goetz, Jeffrey M. Trimarchi, and Constance L. Cepko

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Plasma-seq: a novel strategy for metastatic prostate cancer analysis, Caitlin Farris and Jeffrey M. Trimarchi

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A global approach to analysis and interpretation of metabolic data for plant natural product discovery, Manhoi Hur, Alexis Ann Campbell, Márcia M. Almeida de Macedo, Ling Li, Nick Ransom, Adarsh Jose, Matthew C. Crispin, Basil J. Nikolau, and Eve S. Wurtele

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Functional redundancy between trans-Golgi network SNARE family members in Arabidopsis thaliana, Sang-Jin Kim and Diane C. Bassham

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Complex DNA Nanostructures from Oligonucleotide Ensembles, Divita Mathur and Eric R. Henderson

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Computational Tools for Investigating RNA-Protein Interaction Partners, Usha K. Muppirala, Benjamin A. Lewis, and Drena L. Dobbs

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Molecular Mapping of D1, D2 and ms5 Revealed Linkage between the Cotyledon Color Locus D2 and the Male-Sterile Locus ms5 in Soybean, Alina Ott, Yang Yang, Madan Bhattacharyya, Harry T. Horner, Reid G. Palmer, and Devinder Sandhu