| Year |
Citation |
Score |
| 2020 |
Stuckel AJ, Zhang W, Zhang X, Zeng S, Dougherty U, Mustafi R, Zhang Q, Perreand E, Khare T, Joshi T, West-Szymanski DC, Bissonnette M, Khare S. Enhanced CXCR4 Expression Associates with Increased Gene Body 5-Hydroxymethylcytosine Modification but not Decreased Promoter Methylation in Colorectal Cancer. Cancers. 12. PMID 32110952 DOI: 10.3390/Cancers12030539 |
0.301 |
|
| 2019 |
Mesa AM, Mao J, Nanjappa MK, Medrano TI, Tevosian S, Yu F, Kinkade J, Lyu Z, Liu Y, Joshi T, Wang D, Rosenfeld CS, Cooke PS. Mice Lacking Uterine Enhancer of Zeste Homolog 2 Have Transcriptomic Changes Associated with Uterine Epithelial Proliferation. Physiological Genomics. PMID 31841397 DOI: 10.1152/Physiolgenomics.00098.2019 |
0.333 |
|
| 2019 |
Liu Y, Wang D, He F, Wang J, Joshi T, Xu D. Phenotype Prediction and Genome-Wide Association Study Using Deep Convolutional Neural Network of Soybean. Frontiers in Genetics. 10: 1091. PMID 31824557 DOI: 10.3389/Fgene.2019.01091 |
0.309 |
|
| 2019 |
Vats S, Kumawat S, Kumar V, Patil GB, Joshi T, Sonah H, Sharma TR, Deshmukh R. Genome Editing in Plants: Exploration of Technological Advancements and Challenges. Cells. 8. PMID 31689989 DOI: 10.3390/Cells8111386 |
0.352 |
|
| 2019 |
Rosenfeld CS, Hekman JP, Johnson JL, Lyu Z, Ortega MT, Joshi T, Mao J, Vladimirova AV, Gulevich RG, Kharlamova AV, Acland GM, Hecht EE, Wang X, Clark AG, Trut LN, et al. Hypothalamic transcriptome of tame and aggressive silver foxes (Vulpes vulpes) identifies gene expression differences shared across brain regions. Genes, Brain, and Behavior. PMID 31605445 DOI: 10.1111/Gbb.12614 |
0.367 |
|
| 2019 |
Jiang Y, Liang Y, Wang D, Xu D, Joshi T. A Dynamic Programming Approach to Integrate Gene Expression Data and Network Information for Pathway Model Generation. Bioinformatics (Oxford, England). PMID 31168616 DOI: 10.1093/Bioinformatics/Btz467 |
0.323 |
|
| 2019 |
Hans CP, Sharma N, Sen S, Zeng S, Dev R, Jiang Y, Mahajan A, Joshi T. Transcriptomics Analysis Reveals New Insights into the Roles of Notch1 Signaling on Macrophage Polarization. Scientific Reports. 9: 7999. PMID 31142802 DOI: 10.1038/S41598-019-44266-4 |
0.301 |
|
| 2019 |
Miranda C, Culp C, Škrabišová M, Joshi T, Belzile F, Grant DM, Bilyeu K. Molecular tools for detecting Pdh1 can improve soybean breeding efficiency by reducing yield losses due to pod shatter Molecular Breeding. 39. DOI: 10.1007/S11032-019-0935-1 |
0.361 |
|
| 2018 |
Galli M, Khakhar A, Lu Z, Chen Z, Sen S, Joshi T, Nemhauser JL, Schmitz RJ, Gallavotti A. The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family. Nature Communications. 9: 4526. PMID 30375394 DOI: 10.1038/S41467-018-06977-6 |
0.343 |
|
| 2018 |
Isidra-Arellano MC, Reyero-Saavedra MDR, Sánchez-Correa MDS, Pingault L, Sen S, Joshi T, Girard L, Castro-Guerrero NA, Mendoza-Cozatl DG, Libault M, Valdés-López O. Phosphate Deficiency Negatively Affects Early Steps of the Symbiosis between Common Bean and Rhizobia. Genes. 9. PMID 30326664 DOI: 10.3390/Genes9100498 |
0.368 |
|
| 2018 |
Prince SJ, Valliyodan B, Ye H, Yang M, Tai S, Hu W, Murphy M, Durnell LA, Song L, Joshi T, Liu Y, Van de Velde J, Vandepoele K, Grover Shannon J, Nguyen HT. Understanding genetic control of root system architecture in soybean: Insights into the genetic basis of lateral root number. Plant, Cell & Environment. PMID 29749073 DOI: 10.1111/Pce.13333 |
0.38 |
|
| 2017 |
Hossain MS, Kawakatsu T, Kim KD, Ning Z, Nguyen CT, Khan SM, Batek JM, Joshi T, Schmutz J, Grimwood J, Schmitz RJ, Xu D, Jackson SA, Ecker JR, Stacey G. Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs. The New Phytologist. PMID 28106918 DOI: 10.1111/Nph.14421 |
0.33 |
|
| 2017 |
Joshi T, Wang J, Zhang H, Chen S, Zeng S, Xu B, Xu D. The Evolution of Soybean Knowledge Base (SoyKB). Methods in Molecular Biology (Clifton, N.J.). 1533: 149-159. PMID 27987168 DOI: 10.1007/978-1-4939-6658-5_7 |
0.355 |
|
| 2016 |
Seeve CM, Cho IJ, Hearne LB, Srivastava GP, Joshi T, Smith DO, Sharp RE, Oliver MJ. Water deficit-induced changes in transcription factor expression in maize seedlings. Plant, Cell & Environment. PMID 28039925 DOI: 10.1111/Pce.12891 |
0.345 |
|
| 2016 |
Liu Y, Khan SM, Wang J, Rynge M, Zhang Y, Zeng S, Chen S, Maldonado Dos Santos JV, Valliyodan B, Calyam PP, Merchant N, Nguyen HT, Xu D, Joshi T. PGen: large-scale genomic variations analysis workflow and browser in SoyKB. Bmc Bioinformatics. 17: 337. PMID 27766951 DOI: 10.1186/S12859-016-1227-Y |
0.334 |
|
| 2016 |
Valdés-López O, Batek J, Gomez-Hernandez N, Nguyen CT, Isidra-Arellano MC, Zhang N, Joshi T, Xu D, Hixson KK, Weitz KK, Aldrich JT, Paša-Tolić L, Stacey G. Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles. Frontiers in Plant Science. 7: 517. PMID 27200004 DOI: 10.3389/Fpls.2016.00517 |
0.331 |
|
| 2016 |
Valliyodan B, Dan Qiu, Patil G, Zeng P, Huang J, Dai L, Chen C, Li Y, Joshi T, Song L, Vuong TD, Musket TA, Xu D, Shannon JG, Shifeng C, et al. Landscape of genomic diversity and trait discovery in soybean. Scientific Reports. 6: 23598. PMID 27029319 DOI: 10.1038/Srep23598 |
0.364 |
|
| 2016 |
Maldonado Dos Santos JV, Valliyodan B, Joshi T, Khan SM, Liu Y, Wang J, Vuong TD, Oliveira MF, Marcelino-Guimarães FC, Xu D, Nguyen HT, Abdelnoor RV. Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing. Bmc Genomics. 17: 110. PMID 26872939 DOI: 10.1186/S12864-016-2431-X |
0.328 |
|
| 2016 |
Song L, Prince S, Valliyodan B, Joshi T, Maldonado Dos Santos JV, Wang J, Lin L, Wan J, Wang Y, Xu D, Nguyen HT. Genome-wide transcriptome analysis of soybean primary root under varying water-deficit conditions. Bmc Genomics. 17: 57. PMID 26769043 DOI: 10.1186/S12864-016-2378-Y |
0.332 |
|
| 2015 |
Wang J, Joshi T, Valliyodan B, Shi H, Liang Y, Nguyen HT, Zhang J, Xu D. A Bayesian model for detection of high-order interactions among genetic variants in genome-wide association studies. Bmc Genomics. 16: 1011. PMID 26607428 DOI: 10.1186/S12864-015-2217-6 |
0.349 |
|
| 2015 |
Prince SJ, Joshi T, Mutava RN, Syed N, Joao Vitor Mdos S, Patil G, Song L, Wang J, Lin L, Chen W, Shannon JG, Valliyodan B, Xu D, Nguyen HT. Comparative analysis of the drought-responsive transcriptome in soybean lines contrasting for canopy wilting. Plant Science : An International Journal of Experimental Plant Biology. 240: 65-78. PMID 26475188 DOI: 10.1016/J.Plantsci.2015.08.017 |
0.398 |
|
| 2015 |
Syed NH, Prince SJ, Mutava RN, Patil G, Li S, Chen W, Babu V, Joshi T, Khan S, Nguyen HT. Core clock, SUB1, and ABAR genes mediate flooding and drought responses via alternative splicing in soybean. Journal of Experimental Botany. PMID 26314767 DOI: 10.1093/Jxb/Erv407 |
0.366 |
|
| 2015 |
Chai C, Wang Y, Joshi T, Valliyodan B, Prince S, Michel L, Xu D, Nguyen HT. Soybean transcription factor ORFeome associated with drought resistance: a valuable resource to accelerate research on abiotic stress resistance. Bmc Genomics. 16: 596. PMID 26268547 DOI: 10.1186/S12864-015-1743-6 |
0.388 |
|
| 2015 |
Patil G, Valliyodan B, Deshmukh R, Prince S, Nicander B, Zhao M, Sonah H, Song L, Lin L, Chaudhary J, Liu Y, Joshi T, Xu D, Nguyen HT. Soybean (Glycine max) SWEET gene family: insights through comparative genomics, transcriptome profiling and whole genome re-sequence analysis. Bmc Genomics. 16: 520. PMID 26162601 DOI: 10.1186/S12864-015-1730-Y |
0.44 |
|
| 2015 |
Tanaka K, Cho SH, Lee H, Pham AQ, Batek JM, Cui S, Qiu J, Khan SM, Joshi T, Zhang ZJ, Xu D, Stacey G. Effect of lipo-chitooligosaccharide on early growth of C4 grass seedlings. Journal of Experimental Botany. PMID 26049159 DOI: 10.1093/Jxb/Erv260 |
0.366 |
|
| 2015 |
Hossain MS, Joshi T, Stacey G. System approaches to study root hairs as a single cell plant model: current status and future perspectives. Frontiers in Plant Science. 6: 363. PMID 26042143 DOI: 10.3389/Fpls.2015.00363 |
0.371 |
|
| 2015 |
Wan J, Vuong T, Jiao Y, Joshi T, Zhang H, Xu D, Nguyen HT. Whole-genome gene expression profiling revealed genes and pathways potentially involved in regulating interactions of soybean with cyst nematode (Heterodera glycines Ichinohe). Bmc Genomics. 16: 148. PMID 25880563 DOI: 10.1186/S12864-015-1316-8 |
0.42 |
|
| 2015 |
Prince SJ, Song L, Qiu D, Maldonado Dos Santos JV, Chai C, Joshi T, Patil G, Valliyodan B, Vuong TD, Murphy M, Krampis K, Tucker DM, Biyashev R, Dorrance AE, Maroof MA, et al. Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean. Bmc Genomics. 16: 132. PMID 25765991 DOI: 10.1186/S12864-015-1334-6 |
0.359 |
|
| 2015 |
Quach TN, Nguyen HT, Valliyodan B, Joshi T, Xu D, Nguyen HT. Genome-wide expression analysis of soybean NF-Y genes reveals potential function in development and drought response. Molecular Genetics and Genomics : Mgg. 290: 1095-115. PMID 25542200 DOI: 10.1007/S00438-014-0978-2 |
0.369 |
|
| 2014 |
Appel HM, Fescemyer H, Ehlting J, Weston D, Rehrig E, Joshi T, Xu D, Bohlmann J, Schultz J. Transcriptional responses of Arabidopsis thaliana to chewing and sucking insect herbivores. Frontiers in Plant Science. 5: 565. PMID 25452759 DOI: 10.3389/Fpls.2014.00565 |
0.374 |
|
| 2014 |
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. 9: e94150. PMID 24727730 DOI: 10.1371/Journal.Pone.0094150 |
0.414 |
|
| 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. 42: D1245-52. PMID 24136998 DOI: 10.1093/Nar/Gkt905 |
0.38 |
|
| 2014 |
Valdés-López O, Khan SM, Schmitz RJ, Cui S, Qiu J, Joshi T, Xu D, Diers B, Ecker JR, Stacey G. Genotypic variation of gene expression during the soybean innate immunity response Plant Genetic Resources: Characterisation and Utilisation. 12: S27-S30. DOI: 10.1017/S1479262114000197 |
0.366 |
|
| 2014 |
Franck S, Franck WL, Birke SR, Chang WS, Sangurdekar DP, Cytryn E, Joshi T, Sadowsky M, Stacey G, Xu D, Emerich DW. Comparative transcriptomic analysis of symbiotic Bradyrhizobium japonicum Symbiosis. 63: 123-135. DOI: 10.1007/S13199-014-0294-Y |
0.392 |
|
| 2013 |
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. 14: S5. PMID 23368680 DOI: 10.1186/1471-2164-14-S1-S5 |
0.357 |
|
| 2012 |
Roeseler DA, Sachdev S, Buckley DM, Joshi T, Wu DK, Xu D, Hannink M, Waters ST. Elongation factor 1 alpha1 and genes associated with Usher syndromes are downstream targets of GBX2. Plos One. 7: e47366. PMID 23144817 DOI: 10.1371/Journal.Pone.0047366 |
0.382 |
|
| 2012 |
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. 13: 437. PMID 22938179 DOI: 10.1186/1471-2164-13-437 |
0.37 |
|
| 2012 |
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. 13: S15. PMID 22369646 DOI: 10.1186/1471-2164-13-S1-S15 |
0.38 |
|
| 2011 |
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. 6: e21750. PMID 21789178 DOI: 10.1371/Journal.Pone.0021750 |
0.407 |
|
| 2011 |
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. 39: e127. PMID 21785137 DOI: 10.1093/Nar/Gkr598 |
0.308 |
|
| 2011 |
Roeseler D, Sachdev S, Joshi T, Hwang C, Xu D, Hannink M, Waters S. GBX2 target gene identification reveals Usher syndrome genes PCD15 and USH2A Developmental Biology. 356: 264-265. DOI: 10.1016/J.Ydbio.2011.05.516 |
0.322 |
|
| 2010 |
Wu X, Ren C, Joshi T, Vuong T, Xu D, Nguyen HT. SNP discovery by high-throughput sequencing in soybean. Bmc Genomics. 11: 469. PMID 20701770 DOI: 10.1186/1471-2164-11-469 |
0.328 |
|
| 2010 |
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. The Plant Journal : For Cell and Molecular Biology. 63: 86-99. PMID 20408999 DOI: 10.1111/J.1365-313X.2010.04222.X |
0.428 |
|
| 2010 |
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. 152: 2078-87. PMID 20118269 DOI: 10.1104/Pp.109.152413 |
0.339 |
|
| 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. 10: 14. PMID 20082720 DOI: 10.1186/1471-2229-10-14 |
0.364 |
|
| 2010 |
Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, ... ... Joshi T, et al. Genome sequence of the palaeopolyploid soybean. Nature. 463: 178-83. PMID 20075913 DOI: 10.1038/Nature08670 |
0.376 |
|
| 2010 |
Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, ... ... Joshi T, et al. Erratum: Genome sequence of the palaeopolyploid soybean Nature. 465: 120-120. DOI: 10.1038/Nature08957 |
0.316 |
|
| 2009 |
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 putative soybean regulatory gene expression identifies a Myb gene involved in soybean nodule development. Plant Physiology. 151: 1207-20. PMID 19755542 DOI: 10.1104/Pp.109.144030 |
0.412 |
|
| 2009 |
Libault M, Joshi T, Benedito VA, Xu D, Udvardi MK, Stacey G. Legume transcription factor genes: what makes legumes so special? Plant Physiology. 151: 991-1001. PMID 19726573 DOI: 10.1104/Pp.109.144105 |
0.359 |
|
| 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. 149: 670-82. PMID 19036831 DOI: 10.1104/Pp.108.131649 |
0.313 |
|
| 2008 |
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. 1: 254-74. PMID 20054992 DOI: 10.1504/Ijcbdd.2008.021418 |
0.351 |
|
| 2008 |
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, et al. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biology. 9: S2. PMID 18613946 DOI: 10.1186/Gb-2008-9-S1-S2 |
0.373 |
|
| 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 : Mpmi. 21: 631-45. PMID 18393623 DOI: 10.1094/Mpmi-21-5-0631 |
0.395 |
|
| 2008 |
Joshi T, Zhang C, Lin GN, Song Z, Xu D. GeneFAS: A tool for prediction of gene function using multiple sources of data. Methods in Molecular Biology (Clifton, N.J.). 439: 369-86. PMID 18370116 DOI: 10.1007/978-1-59745-188-8_25 |
0.358 |
|
| 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 : Mpmi. 20: 1298-307. PMID 17918631 DOI: 10.1094/Mpmi-20-10-1298 |
0.413 |
|
| 2007 |
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. 189: 6751-62. PMID 17660288 DOI: 10.1128/Jb.00533-07 |
0.383 |
|
| 2007 |
Joshi T, Xu D. Quantitative assessment of relationship between sequence similarity and function similarity. Bmc Genomics. 8: 222. PMID 17620139 DOI: 10.1186/1471-2164-8-222 |
0.321 |
|
| 2007 |
Kumar R, Qiu J, Joshi T, Valliyodan B, Xu D, Nguyen HT. Single feature polymorphism discovery in rice. Plos One. 2: e284. PMID 17372626 DOI: 10.1371/Journal.Pone.0000284 |
0.315 |
|
| 2006 |
Nunberg A, Bedell JA, Budiman MA, Citek RW, Clifton SW, Fulton L, Pape D, Cai Z, Joshi T, Nguyen H, Xu D, Stacey G. Survey sequencing of soybean elucidates the genome structure, composition and identifies novel repeats. Functional Plant Biology : Fpb. 33: 765-773. PMID 32689287 DOI: 10.1071/Fp06106 |
0.344 |
|
| 2006 |
Wang Y, Joshi T, Zhang X, Xu D, Chen L. Inferring gene regulatory networks from multiple microarray datasets Bioinformatics. 22: 2413-2420. PMID 16864593 DOI: 10.1093/Bioinformatics/Btl396 |
0.368 |
|
| 2005 |
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. 1: 335-50. PMID 18048140 DOI: 10.1504/Ijbra.2005.007910 |
0.375 |
|
| 2004 |
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. 8: 322-333. PMID 15703479 DOI: 10.1089/Omi.2004.8.322 |
0.386 |
|
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