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J. Thimmapuram · SciRah

Researcher profile · Semantic Scholar

J. Thimmapuram

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J. Thimmapuram — researcher profile on SciRah

h-index: 35
Works: 99
Citations: 4,878

Most-cited papers

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
Ray Ming, S. Hou, Yun Feng, Qing-Yi Yu +81 more
2008Nature1,085 citations Open access
Semantic Scholar
Genomic insights into the Ixodes scapularis tick vector of Lyme disease
Monika Gulia-Nuss, Andrew B. Nuss, Jason M. Meyer, D. Sonenshine +89 more
2016Nature Communications486 citations Open access
Semantic Scholar
Analysis of 16S rRNA Amplicon Sequencing Options on the Roche/454 Next-Generation Titanium Sequencing Platform
H. Tamaki, C. Wright, Xiang-Zhen Li, Qiaoyan Lin +5 more
2011PLoS ONE247 citations Open access
Semantic Scholar
Transcriptome analysis identifies novel responses and potential regulatory genes involved in seasonal dormancy transitions of leafy spurge (Euphorbia esula L.)
D. Horvath, W. Chao, J. Suttle, J. Thimmapuram +1 more
2008BMC Genomics206 citations Open access
Semantic Scholar
MED18 interaction with distinct transcription factors regulates multiple plant functions
Zhi-Bing Lai, Craig Schluttenhofer, Ketaki P. Bhide, Jacob Shreve +4 more
2014Nature Communications156 citations Open access
Semantic Scholar
Transcriptome pathways unique to dehydration tolerant relatives of modern wheat
Neslihan Z. Ergen, J. Thimmapuram, H. Bohnert, H. Budak
2009Functional & Integrative Genomics153 citations Open access
Semantic Scholar
The Songbird Neurogenomics (SoNG) Initiative: Community-based tools and strategies for study of brain gene function and evolution
Kirstin L. Replogle, A. Arnold, Gregory F Ball, M. Band +19 more
2008BMC Genomics139 citations Open access
Semantic Scholar
Diversity and Strain Specificity of Plant Cell Wall Degrading Enzymes Revealed by the Draft Genome of Ruminococcus flavefaciens FD-1
Margret E. Berg Miller, D. Antonopoulos, M. T. Rincón, M. Band +12 more
2009PLoS ONE136 citations Open access
Semantic Scholar
CYCLIN-DEPENDENT KINASE8 Differentially Regulates Plant Immunity to Fungal Pathogens through Kinase-Dependent and -Independent Functions in Arabidopsis[C][W]
Yingfang Zhu, Craig M Schluttenhoffer, Pengcheng Wang, F. Fu +5 more
2014The Plant Cell99 citations Open access
Semantic Scholar
Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies
Shaolin Wang, E. Peatman, J. Abernathy, G. Waldbieser +37 more
2010Genome Biology97 citations Open access
Semantic Scholar
Identification of a plastidial phenylalanine exporter that influences flux distribution through the phenylalanine biosynthetic network
Joshua R. Widhalm, M. Gutensohn, Heejin Yoo, Funmilayo Adebesin +10 more
2015Nature Communications91 citations Open access
Semantic Scholar
Gene expression in developing watermelon fruit
W. Wechter, Amnon Levi, K. Harris, Angela R. Davis +9 more
2008BMC Genomics90 citations Open access
Semantic Scholar
Low X/Y divergence in four pairs of papaya sex-linked genes.
Qing-Yi Yu, S. Hou, F. Feltus, Meghan R. Jones +12 more
2008The Plant Journal85 citations Open access
Semantic Scholar
Channel catfish BAC-end sequences for marker development and assessment of syntenic conservation with other fish species.
Peng Xu, Shaolin Wang, Lei Liu, E. Peatman +4 more
2006Animal Genetics85 citations
Semantic Scholar
Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle
D. Larkin, H. Daetwyler, Alvaro G. Hernandez, C. Wright +13 more
2012Proceedings of the National Academy of Sciences of the United States of America84 citations Open access
Semantic Scholar
Endogenous siRNAs and noncoding RNA-derived small RNAs are expressed in adult mouse hippocampus and are up-regulated in olfactory discrimination training.
N. Smalheiser, Giovanni Lugli, J. Thimmapuram, E. Cook +1 more
2011RNA: A publication of the RNA Society76 citations Open access
Semantic Scholar
ViewBS: a powerful toolkit for visualization of high-throughput bisulfite sequencing data
Xiaosan Huang, Shao-Ling Zhang, Kongqing Li, J. Thimmapuram +2 more
2017Bioinform.66 citations Open access
Semantic Scholar
Identification and analysis of common bean (Phaseolus vulgaris L.) transcriptomes by massively parallel pyrosequencing
V. Kalavacharla, Zhan-Ji Liu, B. Meyers, J. Thimmapuram +1 more
2011BMC Plant Biology63 citations Open access
Semantic Scholar
Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction
Zachary T. Herbert, Jamie P. Kershner, Vincent L. Butty, J. Thimmapuram +17 more
2017BMC Genomics58 citations Open access
Semantic Scholar
Characterization of an EST Database for the Perennial Weed Leafy Spurge: An Important Resource for Weed Biology Research
James V. Anderson, D. Horvath, W. Chao, M. Foley +7 more
2007Weed science58 citations
Semantic Scholar
Sampling the Waterhemp (Amaranthus tuberculatus) Genome Using Pyrosequencing Technology
Ryan M. Lee, J. Thimmapuram, Kate A. Thinglum, G. Gong +5 more
2009Weed science55 citations
Semantic Scholar
Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population1[W][OPEN]
Bryan W. Penning, Robert W. Sykes, Nicholas C. Babcock, Christopher K. Dugard +14 more
2014Plant Physiology52 citations Open access
Semantic Scholar
Development and application of microsatellite markers for genomic analysis of papaya
M. Eustice, Qing-Yi Yu, Chun-Wan J. Lai, S. Hou +6 more
2008Tree Genetics & Genomes52 citations
Semantic Scholar
Comparative analysis of the root transcriptomes of cultivated sweetpotato (Ipomoea batatas [L.] Lam) and its wild ancestor (Ipomoea trifida [Kunth] G. Don)
S. Ponniah, J. Thimmapuram, Ketaki P. Bhide, V. Kalavacharla +1 more
2017BMC Plant Biology48 citations Open access
Semantic Scholar
The origin and biosynthesis of the naphthalenoid moiety of juglone in black walnut
Rachel M. McCoy, S. Utturkar, Joseph W. Crook, J. Thimmapuram +1 more
2018Horticulture Research47 citations Open access
Semantic Scholar
Coordination of MicroRNAs, PhasiRNAs, and NB‐LRR Genes in Response to a Plant Pathogen: Insights from Analyses of a Set of Soybean Rps Gene Near‐Isogenic Lines
Meixia Zhao, C. Cai, J. Zhai, F. Lin +6 more
2015The Plant Genome46 citations Open access
Semantic Scholar
Effect of high-fat diet on secreted milk transcriptome in midlactation mice.
Y. Chen, J. Wang, S. Yang, S. Utturkar +8 more
2017Physiological Genomics45 citations Open access
Semantic Scholar
Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability
B. Bushman, S. Larson, M. Tuna, M. West +6 more
2011Theoretical and Applied Genetics45 citations
Semantic Scholar
The bench scientist's guide to statistical analysis of RNA-Seq data
Craig R. Yendrek, E. Ainsworth, J. Thimmapuram
2012BMC Research Notes44 citations Open access
Semantic Scholar
Genome-Wide Profiling of Histone Modifications (H3K9me2 and H4K12ac) and Gene Expression in Rust (Uromyces appendiculatus) Inoculated Common Bean (Phaseolus vulgaris L.)
V. Ayyappan, V. Kalavacharla, J. Thimmapuram, Ketaki P. Bhide +6 more
2015PLoS ONE43 citations Open access
Semantic Scholar
Genes expressed during the development and ripening of watermelon fruit
A. Levi, A. Davis, A. Hernandez, P. Wechter +6 more
2006Plant Cell Reports41 citations
Semantic Scholar
A Study of Alterations in DNA Epigenetic Modifications (5mC and 5hmC) and Gene Expression Influenced by Simulated Microgravity in Human Lymphoblastoid Cells
Basudev Chowdhury, Arun S. Seetharam, Zhiping Wang, Yunlong Liu +3 more
2016PLoS ONE39 citations Open access
Semantic Scholar
Development and annotation of perennial Triticeae ESTs and SSR markers.
B. Bushman, S. Larson, I. W. Mott, Paul F. Cliften +9 more
2008Genome39 citations
Semantic Scholar
Proteomics and metabolomics profiling of meat exudate to determine the impact of postmortem aging on oxidative stability of beef muscles.
D. Setyabrata, D. Ma, Shao-Jun Xie, J. Thimmapuram +3 more
2023Food Chemistry: X38 citations Open access
Semantic Scholar
Transcriptomics in Erigeron canadensis reveals rapid photosynthetic and hormonal responses to auxin herbicide application
Cara L. McCauley, S. McAdam, Ketaki P. Bhide, J. Thimmapuram +2 more
2020Journal of Experimental Botany36 citations Open access
Semantic Scholar
The impact of orally administered phages on host immune response and surrounding microbial communities
Yingying Hong, J. Thimmapuram, Jiayi Zhang, Clayton K. Collings +3 more
2016Bacteriophage34 citations Open access
Semantic Scholar
Changes in β-1,3-glucanase mRNA levels in peach in response to treatment with pathogen culture filtrates, wounding, and other elicitors
A. Zemanek, T. Ko, J. Thimmapuram, F. Hammerschlag +1 more
200234 citations
Semantic Scholar
Transcriptome Sequencing of the Blind Subterranean Mole Rat, Spalax galili: Utility and Potential for the Discovery of Novel Evolutionary Patterns
Assaf Malik, A. Korol, S. Hübner, Alvaro G. Hernandez +6 more
2011PLoS ONE33 citations Open access
Semantic Scholar
Comparative Analysis and Functional Annotation of a Large Expressed Sequence Tag Collection of Apple
K. Gašić, D. O. González, J. Thimmapuram, Lei Liu +17 more
200932 citations Open access
Semantic Scholar
Bicistronic and fused monocistronic transcripts are derived from adjacent loci in the Arabidopsis genome.
J. Thimmapuram, H. Duan, Lei Liu, M. Schuler
2005RNA: A publication of the RNA Society25 citations Open access
Semantic Scholar
Nodulation patterns of actinorhizal plants in the family rosaceae
S. Kohls, J. Thimmapuram, C. Buschena, M. W. Paschke +1 more
1994Plant and Soil25 citations
Semantic Scholar
Transcriptomic and proteomic dynamics in the metabolism of a diazotrophic cyanobacterium, Cyanothece sp. PCC 7822 during a diurnal light–dark cycle
D. Welkie, Xiao-Hui Zhang, Meng Markillie, Ronald C. Taylor +8 more
2014BMC Genomics24 citations Open access
Semantic Scholar
Genes controlling plant growth habit in Leymus (Triticeae): maize barren stalk1 (ba1), rice lax panicle, and wheat tiller inhibition (tin3) genes as possible candidates
P. Kaur, S. Larson, B. Bushman, R. Wang +5 more
2008Functional & Integrative Genomics24 citations
Semantic Scholar
Global analysis of switchgrass (Panicum virgatum L.) transcriptomes in response to interactive effects of drought and heat stresses
Rita K. Hayford, D. Serba, Shao-Jun Xie, V. Ayyappan +4 more
2022BMC Plant Biology23 citations Open access
Semantic Scholar
Single-cell transcriptomics unveils skin cell specific antifungal immune responses and IL-1Ra- IL-1R immune evasion strategies of emerging fungal pathogen Candida auris
Abishek Balakumar, Diprasom Das, Abhishek Datta, Abtar Mishra +8 more
2024bioRxiv22 citations Open access
Semantic Scholar
Ten simple rules for providing effective bioinformatics research support
Judit Kumuthini, M. Chimenti, S. Nahnsen, A. Peltzer +9 more
2020PLoS Comput. Biol.22 citations Open access
Semantic Scholar
Mitochondrial Small RNAs that are Up-Regulated in Hippocampus during Olfactory Discrimination Training in Mice
N. Smalheiser, Giovanni Lugli, J. Thimmapuram, E. Cook +1 more
2011Mitochondrion (Amsterdam. Print)21 citations Open access
Semantic Scholar
Auxin and ABA act as central regulators of developmental networks associated with paradormancy in Canada thistle (Cirsium arvense)
James V. Anderson, M. Doğramacı, D. Horvath, M. Foley +6 more
2012Functional & Integrative Genomics20 citations
Semantic Scholar
Investigation of the Transcriptome of Prairie Cord Grass, a New Cellulosic Biomass Crop
K. Gedye, J. Gonzalez-Hernandez, Y. Ban, Xi-Jin Ge +6 more
201020 citations Open access
Semantic Scholar
Metatranscriptomic profiles of Eastern subterranean termites, Reticulitermes flavipes (Kollar) fed on second generation feedstocks
S. P. Rajarapu, Jacob Shreve, Ketaki P. Bhide, J. Thimmapuram +1 more
2015BMC Genomics18 citations Open access
Semantic Scholar

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