Soybean Knowledge Base (SoyKB): We have developed Soybean Knowledge Base (SoyKB), a comprehensive all-inclusive web resource for bridging soybean translational genomics and molecular breeding. Many genome-scale data are available in soybean including genomic sequence, transcriptomics (microarray, RNA-seq), proteomics and metabolomics datasets, together with growing knowledge of soybean in gene, microRNAs, pathways, and phenotypes. This represents rich and resourceful information which can provide valuable insights, if mined in an innovative and integrative manner and thus, the need for informatics resources to achieve that. SoyKB can be publicly accessed at http://soykb.org.
SoyKB handles the management and integration of soybean genomics and multi-omics data along with gene function annotations, biological pathway and trait information. It has many useful tools including Affymetrix probeID search, gene family search, multiple gene/metabolite analysis, motif prediction tool, protein 3D structure viewer and download/upload capacity for experimental data and annotations. It has a user-friendly web interface together with genome browser and pathway viewer, which display data in an intuitive manner to the soybean researchers, breeders and consumers. It also provides new innovative tools for soybean breeding including a graphical chromosome visualizer targeted towards ease of navigation for breeders. SoyKB also has many new data analysis and visualization tools for RNA-seq and proteomics expression datasets including heatmaps, scatter plots and hierarchical clustering. It also provides new suite of tools for differential expression analysis of omics datasets. Various new types of data including DNA methylation, fast neutron mutations, phosphorylation, genotype by sequencing (GBS) data for molecular breeding and phenotypic inferences have also been incorporated.
SoyKB is powered by the iPlant Cyber-Infrastructure. The website is hosted on the iPlant's advanced computing infrastructure established to leverage and support the data analysis capabilities and analysis pipeline functionalities being developed in SoyKB. We are also working on expanding the SoyKB infrastructure to KBCommons to collaborate with researchers working on other plants and agriculturally important species such as maize, grapes etc. to be able to setup similar systems for the organisms of their interest.
Next generation resequencing data analysis for SNP identification and trait discovery: With the advances in next generation sequencing (NGS) technology and significant reduction in sequencing costs it is now possible to sequence large sets of crop germplasm and generate whole genome scale structural variations and genotypic data. In depth bioinformatics analysis of the genotypic data can provide better understanding of the links with the observed phenotypic changes. This approach can be used to further understand and study different traits for the improvement of crops by design.
We have conducted resequencing of 300+ soybean germplasm lines in collaboration with Dr. Nguyen's lab, selected for major traits including oil, protein, soybean cyst nematode resistance (SCN), abiotic stress resistance (drought, heat and salt) and root system architecture. We have developed a bioinformatics analysis pipeline using high performance computing infrastructure and workflows on IPlant and TACC resources and identifying SNPs, insertions, and deletions by comparisons against the soybean reference genome, Williams 82 using GATK. We are also performing in depth trait discovery analysis using downstream analysis pipelines to identify copy number variations, structural variations, SNP effects and genotype to phenotype predictions for understanding the SNPs significant for phenotypic changes.
Multi-Omics data integration methods for integration of rna-seq transcriptomics, proteomics and metabolomics data in soybean and maize.
Gene function prediction and pathway modeling using high-throughput omics data.
Next generation sequencing data analysis in plants and mammals for understanding relationships between methylation and rna-seq expression.
Mirna and Transcription factor identification in Glycine max.
Data mining and analysis of multi-omics based biological networks.
We have several ongoing collaborations with researchers and labs from Computer Science, Plant Sciences, Animal Sciences and Clinicians, involving research in the plant genomics, health informatics and biomedical fields.
Yan Z, Hossain MS, Valdés-López O, Hoang N, Zhai J, Wang J, Libault M, Brechenmacher L, Findley S, Joshi T, Qi L, Sherrier DJ, Ji T, Meyers B, Xu D, Stacey G. Identification and functional characterization of soybean root hair microRNAs expressed in response to Bradyrhizobium japonicum infection. Journal of Plant Biotechnology. 2015. Plant Biotechnology Journal (2015), pp. 1–10.
Prince SJ, Li S, Qiu D, Maldonado dos santos JV, Chai C, Joshi T, Patil G, Valliyodan B, Vuong T, Murphy M, Krampis K, Tucker DM, Biyashev R, Dorrance AE, Maroof MAS, Xu D, Shannon G, NguyenHT. Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean. BMC Genomics. 2015. In Press.
Wan J, Vuong T, Jiao Y, Joshi T, Zhang H, Cui S, Qiu J, Xu D, and Nguyen HT. Whole-genome gene expression profiling revealed genes and pathways potentially involved in regulating the interactions of soybean with cyst nematode (Heterodera glycines Ichinohe). BMC Genomics 2015, 16:148. doi:10.1186/s12864-015-1316-8.
Appel HM, Fescemyer H, Ehlting J, Weston D, Rehrig E, Joshi T, Xu D, Bohlmann J, and Schultz, J. Transcriptional responses of Arabidopsis thaliana to chewing and sucking insect herbivores. Front Plant Sci. 2014 Nov 14;5:565. doi: 10.3389/fpls.2014.00565. eCollection 2014.
Joshi T, Williamson R, Patil K, Viyanon S, Li S, Zhang Y, Qi W, Li D, Zimmer J, Illindala U, Foley S, Campbell R, Duan Y, Xu D. Virtual Physical Examination (VPE): A Multimedia System for Education in Medicine. International Journal of Functional Informatics and Personalised Medicine. 2014. In Press.
Valdes-Lopez O, Khan SM, Schmitz RJ, Cui S, Qiu J, Zhu M, Cheng JJ, Joshi T, Xu D, Diers B, Ecker JR, Stacey G. Genotypic variation of gene expression during the soybean innate immunity response. Plant Genetic Resources. 2014. In Press.
Langewisch T, Zhang H, Vincent R, Joshi T, Xu D, Bilyeu K. Major soybean maturity gene haplotypes revealed by SNPViz analysis of 72 sequenced soybean genomes. PLOS ONE. 2014. Apr 11;9(4):e94150. doi: 10.1371/journal.pone.0094150. eCollection 2014.
Joshi T, Fitzpatrick MR, Chen S, Liu Y, Zhang H, Endacott RZ, Gaudiello EC, Stacey G, Nguyen HT, Xu D. Soybean Knowledge Base (SoyKB): A web resource for integration of soybean translational genomics and molecular breeding. Nucleic Acids Research. 2014. Jan;42(Database issue):D1245-52. doi: 10.1093/nar/gkt905.
Schmitz RJ, He Y, Valdés-López O, Khan SM, Joshi T, Urich MA, Nery JR, Diers B, Xu D, Stacey G, Ecker JR. Ecker. Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Res. 2013 Oct;23(10):1663-74. doi: 10.1101/gr.152538.112.
Joshi T, Valliyodan B, Wu JH, Lee SH, Xu D, Nguyen HT. Genomic differences between cultivated soybean, G. max and its wild relative G. soja. BMC Genomics. 2013, 14(Suppl 1):S5.
Zhu M, Deng X, Joshi T, Xu D, Stacey G, Cheng J. Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells. BMC Genomics. 2012, 13:437.
Roeseler DA, Sachdev S, Buckley DM, Joshi T, Wu DK, Xu D, Hannink M, Waters ST. Waters. Elongation Factor 1 alpha1 and genes associated with Usher syndromes are down-stream targets of GBX2. Plos One. 2012; 7(11).
Joshi T, Patil K, Fitzpatrick MR, Franklin LD, Yao Q, Cook JR, Wang Z, Libault M, Brechenmacher L, Valliyodan B, Wu X, Cheng J, Stacey G, Nguyen HT, Xu D. Soybean Knowledge Base (SoyKB): A Web Resource for Soybean Translational Genomics. BMC Genomics. 2012, 13(Suppl 1):S15.
Lee EJ, Pei L, Srivastava G, Joshi T, Kushwaha G, Choi JH, Robertson KD, Wang X, Colbourne JK, Zhang L, Schroth GP, Xu D, Zhang K, Shi H. Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing. Nucleic Acids Research. 2011;39(19).
Liang Y, Zhang F, Wang J, Joshi T, Wang Y, Xu D. Prediction of Drought-Resistant Genes in Arabidopsis thaliana Using SVM-RFE. PLoS ONE. 2011;6(7):e21750. doi: 10.1371/journal.pone.0021750.
Yang H, Wang Y, Joshi T, Xu D, Yu S, & Liang Y. (2011). MicroRNA Precursor Prediction Using SVM with RNA Pairing Continuity Feature. In L. Liu, D. Wei, & Y. Li (Eds.), Interdisciplinary Research and Applications in Bioinformatics, Computational Biology, and Environmental Sciences (pp. 73-82). Hershey, PA: Medical Information Science Reference. doi:10.4018/978-1-60960-064-8.ch007.
Joshi T, Yao Q, Franklin LD, Brechenmacher L, Valliyodan B, Stacey G, Nguyen H, Xu D. SoyMetDB: The Soybean Metabolome Database. Proceedings of IEEE International Conference on Bioinformatics & Biomedicine (BIBM 2010), Hong Kong, pp 203-208, Dec 2010.
Wu X, Ren C, Joshi T, Vuong T, Xu D, Nguyen HT. SNP discovery by high-throughput sequencing in soybean. BMC Genomics. 2010, 11:469.
Libault M, Farmer A, Joshi T, Takahashi K, Langley RJ, Franklin LD, He J, Xu D, May G, Stacey G. An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Plant J. 2010 Jul 1;63(1):86-99.
Joshi T, Yan Z, Libault M, Jeong DH, Park S, Green PJ, Sherrier DJ, Farmer A, May G, Meyers BC, Xu D, Stacey G. Prediction of novel miRNAs and associated target genes in Glycine max. BMC Bioinformatics, 11(Suppl 1):S14, 2010.
Guttikonda SK, Joshi T, Bisht NC, Chen H, An YQ, Pandey S, Xu D, Yu O. Whole Genome Co-expression Analysis of Soybean Cytochrome P450 Genes Identifies Nodulation-Specific P450 Monooxygenases. BMC Plant Biology. 10:243. 2010.
Wang Z, Libault M, Joshi T, Valliyodan B, Nguyen HT, Xu D, Stacey G, Cheng J. SoyDB: A Knowledge Database of Soybean Transcription Factors, BMC: Plant Biology. 2010, 10:14.
Hajduch M, Hearne LB, Miernyk JA, Casteel JE, Joshi T, Agrawal GK, Song Z, Zhou M, Xu D, Thelen JJ.Systems Analysis of Seed Filling in Arabidopsis: Using General Linear Modeling to Assess Concordance of Transcript and Protein Expression. Plant Physiology, April 2010, Vol. 152, pp. 1 -10.
Libault M, Joshi T, Benedito VA, Xu D, Udvardi MK, Stacey G. Legume transcription factor genes; what makes legumes so special?. Plant Physiology. 2009; 151:991-1001.
Libault M, Joshi T, Takahashi K, Hurley-Sommer A, Puricelli K, Blake S, Finger RE, Taylor CG, Xu D, Nguyen HT, Stacey G. Large scale analysis of soybean regulatory gene expression identifies a Myb gene involved in soybean nodule development. Plant Physiology. 2009; 151:1207-1220.
Srivastava G, Joshi T, Song Z, Zhang C, Lin GN, Li P, Ross A, Popescu M, Liu J, Qiu J, and Xu D. “GO-based Gene Function and Network Characterization", in, "Ontology-Based Data Mining in Biomedical Research", Mihail Popescu and Dong Xu eds. Artech House, Norwood, MA, USA. 83-111, 2009.
Thibivilliers S, Joshi T, Campbell KB, Scheffler B, Xu D, Cooper B, Nguyen HT, Stacey G. Generation of Phaseolus vulgaris ESTs and investigation of their regulation upon Uromyces appendiculatus infection. BMC Plant Biology. 2009, 9:46 (27 Apr 2009).
Chen M, Mooney BP, Hajduch M, Joshi T, Zhou M, Xu D, Thelen JJ. System Analysis of An Arabidopsis Mutant Altered in de novo Fatty Acid Synthesis Reveals Diverse Changes in Seed Composition and Metabolic Regulation. Plant Physiology. 150:27-41, 2009.
Brechenmacher L, Lee J, Sachdev S, Song Z, Nguyen TH, Joshi T, Oehrle N, Libault M, Mooney B, Xu D, Cooper B, Stacey G. Establishment of a Protein Reference Map for Soybean Root Hair Cells. Plant Physiology. February 2009, Vol. 149, pp. 670 -682.
Zhang C, Joshi T, Lin GN, Xu D. An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data. International Journal of Computational Biology and Drug Design, Volume 1, Number 3, 26 November 2008 , pp. 254-274(21).
Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S,Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS,Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence, Genome Biology, 9(Suppl 1):S2 (27 June 2008).
Brechenmacher L, Kim MY, Benitez M, Li M, Joshi T, Calla B, Lee MP, Libault M, Vodkin LO, Xu D, Lee SH, Clough SJ, Stacey G. Transcription profiling of soybean nodulation by Bradyrhizobium japonicum. Molecular Plant-Microbe Interactions. Vol.21, No. 5, 631-645, 2008.
Joshi T, Zhang C, Lin GN, Song Z, Xu D. GeneFAS : A tool for prediction of protein function using multiple sources of data. Methods Mol Biol. 2008;439:369-86. doi: 10.1007/978-1-59745-188-8_25.
Cytryn EJ, Sangurdekar DP, Streeter JG, Franck WL, Chang WS, Stacey G, Emerich DW, Joshi T, Xu D, Sadowsky MJ. Transcriptional and Physiological Responses of Bradyrhizobium japonicum to Desiccation-Induced Stress. Journal of Bacteriology, October 2007, p. 6751-6762, Vol. 189, No. 19.
Joshi T, Xu D. Quantitative assessment of relationship between sequence similarity and function similarity. BMC Genomics, Vol. 8(1):222, 2007.
Chang WS, Franck WL, Cytryn E, Jeong S, Joshi T, Emerich DW, Sadowsky MJ, Xu D, Stacey G. An Oligonucleotide Microarray Resource for Transcriptional Profiling of Bradyrhizobium japonicum. Molecular Plant-Microbe Interactions Vol. 20, No. 10, 1298-1307. 2007.
Kumar R, Qiu J, Joshi T, Valliyodan B, Xu D, Nguyen HT. Nguyen. Single Feature Polymorphism Discovery in Rice. PLoS ONE 2(3): e284. doi:10.1371/journal.pone.0000284, 2007.
Joshi T, Wan J, Palm CJ, Juneau K, Davis R, Southwick A, Ramonell KM, Stacey G, Xu D. Bioinformatics Analyses of Arabidopsis thaliana Tiling Array Expression Data In "Knowledge Discovery in Bioinformatics: Techniques, Methods and Application" edited by Yi Pan and Xiaohua (Tony) Hu, John Wiley and Sons, New York. Pages 57-70, 2007.
Wang Y, Joshi T, Zhang XS, Xu D, Chen L. Inferring Gene Regulatory Networks from Multiple Microarray Datasets. Bioinformatics. 22:2413-2420, 2006.
Wang Y, Joshi T, Xu D, Zhang XS, Chen L. "Supervised Inference of Gene Regulatory Networks by Linear Programming". Lecture Notes in Computer Science, 4115, 551-561, 2006. (Also in Proceeding of the 2006 International Conference on Intelligent Computing (ICIC 2006), Kunming, China).
Nunberg A, Bedell JA, Budiman MA, Citek RW, Clifton SW, Fulton L, Pape D, Cai Z, Joshi T, Nguyen HT, Xu D, Stacey G. Survey sequencing of soybean elucidates the genome structure and composition. Functional Plant Biology, 33, 765-773, 2006.
Joshi T, Chen Y, Alexandrov NN, Xu D. Cellular Function Prediction and Biological Pathway Discovery in Arabidopsis thaliana Using Microarray Data. International Journal of Bioinformatics Research and Applications. Vol. 1, No. 3, 2005.
Joshi T, Chen Y, Becker JM, Alexandrov N, Xu D. Genome-Scale Gene Function Prediction Using Multiple Sources of High-Throughput Data in Yeast Saccharomyces cerevisiae. OMICS: A Journal of Integrative Biology Dec 2004, Vol. 8, No. 4: 322-333.
Joshi T, Chen Y, Alexandrov N, Xu D. Cellular Function Prediction and Biological Pathway Discovery in Arabidopsis thaliana Using Microarray Data. Conf Proc IEEE Eng Med Biol Soc. 2004;4:2881-4.
Joshi T, Chen Y, Becker J, Alexandrov N, Xu Dong. Function Prediction for Hypothetical Proteins in Yeast Saccharomyces cerevisiae Using Multiple Sources of High-Throughput Data. Proceeding of the 8th World Multi-Conference on Systemics, Cybernetics and Informatics (2004). Vol. IX, 17-20.
Chen Y, Joshi T, Xu Y, Xu D. Towards Automated Derivation of Biological Pathways Using High-Throughput Biological Data. Proceeding of the 3rd IEEE Symposium on Bioinformatics and Bioengineering (2003). 18-25, IEEE/CS Press.