Gramene's impact on plant research in 2015-2016

Gramene database ( offers resources for conducting comparative studies on plant genomes and pathways. Over the years, we have made efforts to reach out to the various communities of plant scientists and have assisted many individuals in using various tools/and resources available from the Gramene. We have also established connection between ours and other publicly available data sources. In year 2015 and 2016, Gramene has been cited ~90 times by various researchers. Here we are listing some of the articles which cited Gramene and / or used Gramene resources for their research. We thank all of our users and collaborators.

Citation of Gramene in Year 2016 and 2015:

1. PoplarGene: poplar gene network and resource for mining functional information for genes from woody plants By: Liu, Qi; Ding, Changjun; Chu, Yanguang; et al.,  SCIENTIFIC REPORTS   Volume: 6,  Article Number: 31356, Published: AUG 12 2016

2. Identification of two novel powdery mildew resistance loci, Ren6 and Ren7, from the wild Chinese grape species Vitis piasezkii By: Pap, Daniel; Riaz, Summaira; Dry, Ian B.; et al., BMC PLANT BIOLOGY,  Volume: 16,  Article Number: 170, Published: JUL 29 2016.

3. A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses  By: Jiao, Yinping; Burke, John; Chopra, Ratan; et al.PLANT CELL   Volume: 28   Issue: 7,   Pages: 1551-1562   Published: JUL 2016.

4. Fine mapping of qKW7, a major QTL for kernel weight and kernel width in maize, confirmed by the combined analytic approaches of linkage and association analysis By: Li, Xin; Li, Yong-xiang; Chen, Lin; et al., EUPHYTICA   Volume: 210   Issue: 2   Pages: 221-232   Published: JUL 2016.

5. Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing By: Wang, Bo; Tseng, Elizabeth; Regulski, Michael; et al., NATURE COMMUNICATIONS   Volume: 7     Article Number: 11708   Published: JUN 2016.

6. PGP repository: a plant phenomics and genomics data publication infrastructure By: Arend, Daniel; Junker, Astrid; Scholz, Uwe; et al., DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION     Article Number: baw033   Published: APR 17 2016

7. The big five of the monocot genomes By: Haberer, Georg; Mayer, Klaus F. X.; Spannagl, Manuel, CURRENT OPINION IN PLANT BIOLOGY   Volume: 30   Pages: 33-40   Published: APR 2016.

8. Translational genomics for plant breeding with the genome sequence explosion By: Kang, Yang Jae; Lee, Taeyoung; Lee, Jayern; et al., PLANT BIOTECHNOLOGY JOURNAL   Volume: 14   Issue: 4   Pages: 1057-1069   Published: APR 2016.

9. Germplasm dynamics: the role of ecotypic diversity in shaping the patterns of genetic variation in Lolium perenne By: Blackmore, T.; Thorogood, D.; Skot, L.; et al., SCIENTIFIC REPORTS   Volume: 6     Article Number: 22603   Published: MAR 3 2016

10.       FragariaCyc: A Metabolic Pathway Database for Woodland Strawberry Fragaria vesca By: Naithani, Sushma; Partipilo, Christina M.; Raja, Rajani; et al., FRONTIERS IN PLANT SCIENCE   Volume: 7     Article Number: 242   Published: MAR 4 2016

11. Variation in cooking and eating quality traits in Japanese rice germplasm accessions By: Hori, Kiyosumi; Suzuki, Keitaro; Iijima, Ken; et al., BREEDING SCIENCE   Volume: 66   Issue: 2   Pages: 309-318   Published: MAR 2016

12. Ensembl comparative genomics resources By: Herrero, Javier; Muffato, Matthieu; Beal, Kathryn; et al., DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION     Article Number: bav096   Published: FEB 20 2016

13. MaizeGDB update: new tools, data and interface for the maize model organism database By: Andorf, Carson M.; Cannon, Ethalinda K.; Portwood, John L., II; et al., NUCLEIC ACIDS RESEARCH   Volume: 44   Issue: D1   Pages: D1195-D1201   Published: JAN 4 2016

14. Ensembl Genomes 2016: more genomes, more complexity By: Kersey, Paul Julian; Allen, James E.; Armean, Irina; et al., NUCLEIC ACIDS RESEARCH   Volume: 44   Issue: D1   Pages: D574-D580   Published: JAN 4 2016

15. Information Commons for Rice (IC4R) By: Zhang, Zhang; Hu, Songnian; He, Hang; et al., Group Author(s): IC4R Project Consortium , NUCLEIC ACIDS RESEARCH   Volume: 44   Issue: D1   Pages: D1172-D1180   Published: JAN 4 2016

16. Finding the Subcellular Location of Barley, Wheat, Rice and Maize Proteins: The Compendium of Crop Proteins with Annotated Locations (cropPAL)  By: Hooper, Cornelia M.; Castleden, Ian R.; Aryamanesh, Nader; et al., PLANT AND CELL PHYSIOLOGY   Volume: 57   Issue: 1     Published: JAN 2016

17. NABIC: A New Access Portal to Search, Visualize, and Share Agricultural Genomics Data By: Seol, Young-Joo; Lee, Tae-Ho; Park, Dong-Suk; et al., EVOLUTIONARY BIOINFORMATICS   Volume: 12   Pages: 51-58   Published: 201

18. Defining the RNA-binding glycine-rich (RBG) gene superfamily: new insights into nomenclature, phylogeny, and evolutionary trends obtained by genome-wide comparative analysis of Arabidopsis, Chinese cabbage, rice and maize genomes  By: Krishnamurthy, Panneerselvam; Kim, Jin A.; Jeong, Mi-; et al., MOLECULAR GENETICS AND GENOMICS   Volume: 290   Issue: 6   Pages: 2279-2295   Published: DEC 2015

19. Genome-wide identification and evolutionary analyses of bZIP transcription factors in wheat and its relatives and expression profiles of anther development related TabZIP genes By: Li, Xueyin; Gao, Shiqing; Tang, Yimiao; et al., BMC GENOMICS   Volume: 16     Article Number: 976   Published: NOV 18 2015

20. Quantitative trait loci (QTL) and candidate genes associated with trace element concentrations in perennial grasses grown on phytotoxic soil contaminated with heavy metalsBy: Yun, Lan; Larson, Steven R.; Jensen, Kevin B.; et al., PLANT AND SOIL   Volume: 396   Issue: 1-2   Pages: 277-296   Published: NOV 2015

21. Genetics and physiology of cell wall polysaccharides in the model C-4 grass, Setaria viridis spp By: Ermawar, Riksfardini A.; Collins, Helen M.; Byrt, Caitlin S.; et al., BMC PLANT BIOLOGY   Volume: 15     Article Number: 236   Published: OCT 2 2015

22. Small-scale gene duplications played a major role in the recent evolution of wheat chromosome 3B , By: Glover, Natasha M.; Daron, Josquin; Pingault, Lise; et al., GENOME BIOLOGY   Volume: 16     Article Number: 188   Published: SEP 9 2015

23. Disease Resistance Gene Analogs (RGAs) in Plants By: Sekhwal, Manoj Kumar; Li, Pingchuan; Lam, Irene; et al., INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES   Volume: 16   Issue: 8   Pages: 19248-19290   Published: AUG 2015

24. Characteristics of Plant Essential Genes Allow for within-and between-Species Prediction of Lethal Mutant Phenotypes By: Lloyd, John P.; Seddon, Alexander E.; Moghe, Gaurav D.; et al., PLANT CELL   Volume: 27   Issue: 8   Pages: 2133-2147   Published: AUG 2015

25. Targeted Sequencing Reveals Large-Scale Sequence Polymorphism in Maize Candidate Genes for Biomass Production and Composition By: Muraya, Moses M.; Schmutzer, Thomas; Ulpinnis, Chris; et al., PLOS ONE   Volume: 10   Issue: 7     Article Number: e0132120   Published: JUL 7 2015.

26. Transcriptome Response Signatures Associated with the Overexpression of a Mitochondrial Uncoupling Protein (AtUCP1) in Tobacco By: Nunes Laitz, Alessandra Vasconcellos; Acencio, Marcio Luis; Budzinski, Ilara G. F.; et al., PLOS ONE   Volume: 10   Issue: 6     Article Number: e0130744   Published: JUN 24 2015

27. Getting the 'MOST' out of crop improvement By: Hu, Songlin; Luebberstedt, Thomas, TRENDS IN PLANT SCIENCE   Volume: 20   Issue: 6   Pages: 372-379   Published: JUN 2015

28. Reduced susceptibility to Fusarium head blight in Brachypodium distachyon through priming with the Fusarium mycotoxin deoxynivalenol By: Bluemke, Antje; Sode, Bjoern; Ellinger, Dorothea; et al., MOLECULAR PLANT PATHOLOGY   Volume: 16   Issue: 5   Pages: 472-483   Published: JUN 2015

29. QTLMiner: QTL database curation by mining tables in literature By: Peng, Jing; Shi, Xinyi; Sun, Yiming; et al., BIOINFORMATICS   Volume: 31   Issue: 10   Pages: 1689-1691   Published: MAY 15 201

30. Genetic mapping of leaf blast resistance gene in landrace rice cultivar 'GS19769' By: Parinthawong, Nonglak; Tansian, Pennapar; Sreewongchai, Tanee, MAEJO INTERNATIONAL JOURNAL OF SCIENCE AND TECHNOLOGY   Volume: 9   Issue: 2   Pages: 278-287   Published: MAY-AUG 2015

31. Enrichment of Triticum aestivum gene annotations using ortholog cliques and gene ontologies in other plants By: Tulpan, Dan; Leger, Serge; Tchagang, Alain; et al., BMC GENOMICS   Volume: 16     Article Number: 299   Published: APR 15 2015

32. Patterns of Metabolite Changes Identified from Large-Scale Gene Perturbations in Arabidopsis Using a Genome-Scale Metabolic Network By: Kim, Taehyong; Dreher, Kate; Nilo-Poyanco, Ricardo; et al., PLANT PHYSIOLOGY   Volume: 167   Issue: 4   Pages: 1685-U890   Published: APR 2015

33. RIG: Recalibration and Interrelation of Genomic Sequence Data with the GATK By: McCormick, Ryan F.; Truong, Sandra K.; Mullet, John E., G3-GENES GENOMES GENETICS   Volume: 5   Issue: 4   Pages: 655-665   Published: APR 1 2015

34. Distribution, structure and biosynthetic gene families of (1,3;1,4)-beta-glucan in Sorghum bicolor By: Ermawar, Riksfardini A.; Collins, Helen M.; Byrt, Caitlin S.; et al., JOURNAL OF INTEGRATIVE PLANT BIOLOGY   Volume: 57   Issue: 4   Special Issue: SI   Pages: 429-445   Published: APR 2015

35. Genetic and Genomic Toolbox of Zea mays By: Nannas, Natalie J.; Dawe, R. Kelly GENETICS   Volume: 199   Issue: 3   Pages: 655-+   Published: MAR 2015

36. Comparative genomics of grass EST libraries reveals previously uncharacterized splicing events in crop plants By: Chuang, Trees-Juen; Yang, Min-Yu; Lin, Chuang-Chieh; et al., BMC PLANT BIOLOGY   Volume: 15     Article Number: 39   Published: FEB 5 2015

37. Multidimensional approaches for studying plant defence against insects: from ecology to omics and synthetic biology By: Barah, Pankaj; Bones, Atle M., JOURNAL OF EXPERIMENTAL BOTANY   Volume: 66   Issue: 2   Special Issue: SI   Pages: 479-493   Published: FEB 2015

38. The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements  By: Altenhoff, Adrian M.; Skunca, Nives; Glover, Natasha; et al., NUCLEIC ACIDS RESEARCH   Volume: 43   Issue: D1   Pages: D240-D249   Published: JAN 28 2015

39. Gene Ontology Consortium: going forward By: Blake, J. A.; Christie, K. R.; Dolan, M. E.; et al. Group Author(s): Gene Ontology Consortium , NUCLEIC ACIDS RESEARCH   Volume: 43   Issue: D1   Pages: D1049-D1056   Published: JAN 28 2015

40. The coffee genome hub: a resource for coffee genomes By: Dereeper, Alexis; Bocs, Stephanie; Rouard, Mathieu; et al., NUCLEIC ACIDS RESEARCH   Volume: 43   Issue: D1   Pages: D1028-D1035   Published: JAN 28 2015

41. PLAZA 3.0: an access point for plant comparative genomics By: Proost, Sebastian; Van Bel, Michiel; Vaneechoutte, Dries; et al. NUCLEIC ACIDS RESEARCH   Volume: 43   Issue: D1   Pages: D974-D981   Published: JAN 28 2015

42. EXPath: a database of comparative expression analysis inferring metabolic pathways for plants By: Chien, Chia-Hung; Chow, Chi-Nga; Wu, Nai-Yun; et al., BMC GENOMICS   Volume: 16   Supplement: 2     Article Number: S6   Published: JAN 21 2015

43. Triticeae Resources in Ensembl Plants By: Bolser, Dan M.; Kerhornou, Arnaud; Walts, Brandon; et al. PLANT AND CELL PHYSIOLOGY   Volume: 56   Issue: 1     Article Number: UNSP e3   Published: JAN 201

44. A Maize Database Resource that Captures Tissue-Specific and Subcellular-Localized Gene Expression, via Fluorescent Tags and Confocal Imaging (Maize Cell Genomics Database) By: Krishnakumar, Vivek; Choi, Yongwook; Beck, Erin; et al. PLANT AND CELL PHYSIOLOGY   Volume: 56   Issue: 1     Article Number: UNSP e12   Published: JAN 2015

45. MOROKOSHI: Transcriptome Database in Sorghum bicolor By: Makita, Yuko; Shimada, Setsuko; Kawashima, Mika; et al., PLANT AND CELL PHYSIOLOGY   Volume: 56   Issue: 1     Article Number: UNSP e6   Published: JAN 2015

46. The Bimodal Distribution of Genic GC Content Is Ancestral to Monocot Species By: Clement, Yves; Fustier, Margaux-Alison; Nabholz, Benoit; et al., GENOME BIOLOGY AND EVOLUTION   Volume: 7   Issue: 1   Pages: 336-348   Published: JAN 2015

47. Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes  By: Law, MeiYee; Childs, Kevin L.; Campbell, Michael S.; et al. PLANT PHYSIOLOGY   Volume: 167   Issue: 1   Pages: 25-39   Published: JAN 2015

48. Fine mapping of qHd1, a minor heading date QTL with pleiotropism for yield traits in rice (Oryza sativa L.) By: Chen, Jun-Yu; Guo, Liang; Ma, Huan; et al., THEORETICAL AND APPLIED GENETICS   Volume: 127   Issue: 11   Pages: 2515-2524   Published: NOV 2014

49. GC content evolution in coding regions of angiosperm genomes: a unifying hypothesis By: Glemin, Sylvain; Clement, Yves; David, Jacques; et al., TRENDS IN GENETICS   Volume: 30   Issue: 7   Pages: 263-270   Published: JUL 2014

50. Unique Genotypic Differences Discovered among Indigenous Bangladeshi Rice Landraces By: Yesmin, Nusrat; Elias, Sabrina M.; Rahman, Md. Sazzadur; et al., INTERNATIONAL JOURNAL OF GENOMICS     Article Number: 210328   Published: 2014