Joseph R. Fontana, Ph.D. - Related publications

2010 Biology University of California, San Diego, La Jolla, CA 
General Biology
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50 most relevant papers in past 60 days:
Year Citation  Score
2019 Wang Z, Feng X, Li SC. SCDevDB: A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes. Frontiers in Genetics. 10: 903. PMID 31611909 DOI: 10.3389/fgene.2019.00903   
2019 Román Á, Golz JF, Webb AA, Graham IA, Haydon MJ. Combining GAL4 GFP enhancer trap with split luciferase to measure spatiotemporal promoter activity in Arabidopsis. The Plant Journal : For Cell and Molecular Biology. PMID 31692146 DOI: 10.1111/tpj.14603   
2019 Ding H, Grüll MP, Mulligan ME, Lang AS, Beatty JT. Induction of gene transfer agent (RcGTA) gene expression is a bistable stochastic process repressed by an extracellular calcium-binding RTX protein homologue. Journal of Bacteriology. PMID 31501287 DOI: 10.1128/JB.00430-19   
2019 Zhou J, Schor IE, Yao V, Theesfeld CL, Marco-Ferreres R, Tadych A, Furlong EEM, Troyanskaya OG. Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development. Plos Genetics. 15: e1008382. PMID 31553718 DOI: 10.1371/journal.pgen.1008382   
2019 Jones DAB, John E, Rybak K, Phan HTT, Singh KB, Lin SY, Solomon PS, Oliver RP, Tan KC. A specific fungal transcription factor controls effector gene expression and orchestrates the establishment of the necrotrophic pathogen lifestyle on wheat. Scientific Reports. 9: 15884. PMID 31685928 DOI: 10.1038/s41598-019-52444-7   
2019 Furches A, Kainer D, Weighill D, Large A, Jones P, Walker AM, Romero J, Gazolla JGFM, Joubert W, Shah M, Streich J, Ranjan P, Schmutz J, Sreedasyam A, Macaya-Sanz D, et al. Finding New Cell Wall Regulatory Genes in Using Multiple Lines of Evidence. Frontiers in Plant Science. 10: 1249. PMID 31649710 DOI: 10.3389/fpls.2019.01249   
2019 Farhadi A, Ho GH, Sawyer DP, Bourdeau RW, Shapiro MG. Ultrasound imaging of gene expression in mammalian cells. Science (New York, N.Y.). 365: 1469-1475. PMID 31604277 DOI: 10.1126/science.aax4804   
2019 Papatheodorou I, Moreno P, Manning J, Fuentes AM, George N, Fexova S, Fonseca NA, Füllgrabe A, Green M, Huang N, Huerta L, Iqbal H, Jianu M, Mohammed S, Zhao L, et al. Expression Atlas update: from tissues to single cells. Nucleic Acids Research. PMID 31665515 DOI: 10.1093/nar/gkz947   
2019 Huang T, Huang X, Shi B, Yao M. GEREDB: Gene expression regulation database curated by mining abstracts from literature. Journal of Bioinformatics and Computational Biology. 17: 1950024. PMID 31617460 DOI: 10.1142/S0219720019500240   
2019 Lin Y, Ghazanfar S, Strbenac D, Wang A, Patrick E, Lin DM, Speed T, Yang JYH, Yang P. Evaluating stably expressed genes in single cells. Gigascience. 8. PMID 31531674 DOI: 10.1093/gigascience/giz106   
2019 Liew LC, Narsai R, Wang Y, Berkowitz O, Whelan J, Lewsey MG. Temporal tissue-specific regulation of transcriptomes during barley (Hordeum vulgare) seed germination. The Plant Journal : For Cell and Molecular Biology. PMID 31628689 DOI: 10.1111/tpj.14574   
2019 Vgontzas A, Renthal W. Migraine-associated gene expression in cell types of the central and peripheral nervous system. Cephalalgia : An International Journal of Headache. 333102419877834. PMID 31660761 DOI: 10.1177/0333102419877834   
2019 Wang M, Zhang J, Xu H, Golding I. Measuring transcription at a single gene copy reveals hidden drivers of bacterial individuality. Nature Microbiology. PMID 31527794 DOI: 10.1038/s41564-019-0553-z   
2019 Wan Z, Zhang X, Luo Y, Zhao B. Identification of Hepatocellular Carcinoma-Related Potential Genes and Pathways Through Bioinformatic-Based Analyses. Genetic Testing and Molecular Biomarkers. PMID 31633428 DOI: 10.1089/gtmb.2019.0063   
2019 Gan Z, Fei L, Shan N, Fu Y, Chen J. Identification and Expression Analysis of in Kiwifruit () During Postharvest Process. Plants (Basel, Switzerland). 8. PMID 31698719 DOI: 10.3390/plants8110473   
2019 Yang Y, Ahammed GJ, Wan C, Liu H, Chen R, Zhou Y. Comprehensive Analysis of TIFY Transcription Factors and Their Expression Profiles under Jasmonic Acid and Abiotic Stresses in Watermelon. International Journal of Genomics. 2019: 6813086. PMID 31662958 DOI: 10.1155/2019/6813086   
2019 Makrodimitris S, Reinders MJT, van Ham RCHJ. Metric Learning on Expression Data for Gene Function Prediction. Bioinformatics (Oxford, England). PMID 31562759 DOI: 10.1093/bioinformatics/btz731   
2019 Wang F, Liang S, Kumar T, Navin N, Chen K. SCMarker: Ab initio marker selection for single cell transcriptome profiling. Plos Computational Biology. 15: e1007445. PMID 31658262 DOI: 10.1371/journal.pcbi.1007445   
2019 Kang C, Sun F, Yan L, Li R, Bai J, Caetano-Anollés G. Genome-Wide Identification and Characterization of the Vacuolar H-ATPase Subunit H Gene Family in Crop Plants. International Journal of Molecular Sciences. 20. PMID 31623139 DOI: 10.3390/ijms20205125   
2019 Bai G, Yang DH, Cao P, Yao H, Zhang Y, Chen X, Xiao B, Li F, Wang ZY, Yang J, Xie H. Genome-Wide Identification, Gene Structure and Expression Analysis of the MADS-Box Gene Family Indicate Their Function in the Development of Tobacco (). International Journal of Molecular Sciences. 20. PMID 31614589 DOI: 10.3390/ijms20205043   
2019 Pan Y, Zhao SW, Tang XL, Wang S, Wang X, Zhang XX, Zhou JJ, Xi J. Transcriptome analysis of maize reveals potential key genes involved in the response to belowground herbivore H. parallela larvae feeding. Genome. PMID 31533014 DOI: 10.1139/gen-2019-0043   
2019 Su Y, Liu J, Liang W, Dou Y, Fu R, Li W, Feng C, Gao C, Zhang D, Kang Z, Li H. Wheat AGAMOUS LIKE 6 transcription factors function in stamen development by regulating the expression of . Development (Cambridge, England). PMID 31540915 DOI: 10.1242/dev.177527   
2019 Young AP, Landry CF, Jackson DJ, Wyeth RC. Tissue-specific evaluation of suitable reference genes for RT-qPCR in the pond snail, . Peerj. 7: e7888. PMID 31637135 DOI: 10.7717/peerj.7888   
2019 Xing Z, Luo Z, Yang H, Huang Z, Liang X. Screening and identification of key biomarkers in adrenocortical carcinoma based on bioinformatics analysis. Oncology Letters. 18: 4667-4676. PMID 31611976 DOI: 10.3892/ol.2019.10817   
2019 Ochola S, Huang J, Ali H, Shu H, Shen D, Qiu M, Wang L, Li X, Chen H, Kange A, Qutob D, Dong S. Editing of an effector gene promoter sequence impacts plant - Phytophthora interaction. Journal of Integrative Plant Biology. PMID 31691466 DOI: 10.1111/jipb.12883   
2019 Jin X, Cao D, Wang Z, Ma L, Tian K, Liu Y, Gong Z, Zhu X, Jiang C, Li Y. Genome-wide identification and expression analyses of the LEA protein gene family in tea plant reveal their involvement in seed development and abiotic stress responses. Scientific Reports. 9: 14123. PMID 31575979 DOI: 10.1038/s41598-019-50645-8   
2019 He H, Li W, Shen B, Zhao H, Liu J, Qin J, Shi J, Yi X, Peng M, Huo R, Jin G. Gene expression changes induced by valproate in the process of rat hippocampal neural stem cells differentiation. Cell Biology International. PMID 31642547 DOI: 10.1002/cbin.11254   
2019 Wu J, Gao J, Bi W, Zhao J, Yu X, Li Z, Liu D, Liu B, Wang X. Genome-Wide Expression Profiling of Genes Associated with the -Mediated Wheat Resistance to Leaf Rust (). International Journal of Molecular Sciences. 20. PMID 31514396 DOI: 10.3390/ijms20184498   
2019 Hao Z, Zong Y, Liu H, Tu Z, Li H. Cloning, Characterization and Functional Analysis of the Gene, a Homologue of Derived from . Genes. 10. PMID 31683912 DOI: 10.3390/genes10110878   
2019 Yi Q, Liu Y, Cao M, Liu J, Xiang Q, Tan G, Zhang H, Lai G, Xie Y. Transcriptional analysis and differentially expressed gene screening of spontaneous liver tumors in CBA/CaJ mice. Gene. 144159. PMID 31629818 DOI: 10.1016/j.gene.2019.144159   
2019 Koroknai V, Szász I, Hernandez-Vargas H, Fernandez-Jimenez N, Cuenin C, Herceg Z, Vízkeleti L, Ádány R, Ecsedi S, Balázs M. DNA hypermethylation is associated with invasive phenotype of malignant melanoma. Experimental Dermatology. PMID 31602702 DOI: 10.1111/exd.14047   
2019 He S, An T, A R, Liu S. Validation of Reliable Reference Genes for RT-qPCR Studies of Target Gene Expression in During Spore Germination and Mycelial Growth and Interaction With Host Plants. Frontiers in Microbiology. 10: 2055. PMID 31551988 DOI: 10.3389/fmicb.2019.02055   
2019 Zhu M, Xie H, Wei X, Dossa K, Yu Y, Hui S, Tang G, Zeng X, Yu Y, Hu P, Wang J. WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice. Genes. 10. PMID 31533315 DOI: 10.3390/genes10090719   
2019 Bian Q, Chen J, Qiu W, Peng C, Song M, Sun X, Liu Y, Ding F, Chen J, Zhang L. Four targeted genes for predicting the prognosis of colorectal cancer: A bioinformatics analysis case. Oncology Letters. 18: 5043-5054. PMID 31612015 DOI: 10.3892/ol.2019.10866   
2019 Ruan SS, Xiao YC, He PC, Wang Y, Ma T. Identification of Potential Gene Signatures Related to Sleep Deprivation. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 31573330 DOI: 10.1089/cmb.2019.0177   
2019 Li H, Kaiser TK, Borschiwer M, Bohnenberger H, Reichardt SD, Lühder F, Walter L, Dressel R, Meijsing SH, Reichardt HM. Glucocorticoid resistance of allogeneic T cells alters the gene expression profile in the inflamed small intestine of mice suffering from acute graft-versus-host disease. The Journal of Steroid Biochemistry and Molecular Biology. 105485. PMID 31561002 DOI: 10.1016/j.jsbmb.2019.105485   
2019 Catalán A, Briscoe AD, Höhna S. Drift and Directional Selection Are the Evolutionary Forces Driving Gene Expression Divergence in Eye and Brain Tissue of Butterflies. Genetics. PMID 31467133 DOI: 10.1534/genetics.119.302493   
2019 Lin G, Yin G, Yan Y, Lin B. Identification of prognostic biomarkers for malignant melanoma using microarray datasets. Oncology Letters. 18: 5243-5254. PMID 31620197 DOI: 10.3892/ol.2019.10914   
2019 Hu Z, Wu J, Qin L, Jin H, Lv Y, Zhang R, Xiao C, Cao Y, Zhao Y. effect on Yan Yellow Cattle preadipocyte differentiation. Animal Biotechnology. 1-10. PMID 31646946 DOI: 10.1080/10495398.2019.1679824   
2019 Shalmani A, Muhammad I, Sharif R, Zhao C, Ullah U, Zhang D, Jing XQ, Amin B, Jia P, Mobeen Tahir M, Xu Z, Chen KM, An N. Zinc Finger-Homeodomain Genes: Evolution, Functional Differentiation, and Expression Profiling Under Flowering-Related Treatments and Abiotic Stresses in Plants. Evolutionary Bioinformatics Online. 15: 1176934319867930. PMID 31523124 DOI: 10.1177/1176934319867930   
2019 Podushkina D, West NW, Golenberg EM. Utilizing multiplex fluor LAMPs to illuminate multiple gene expressions in situ. Plos One. 14: e0223333. PMID 31584968 DOI: 10.1371/journal.pone.0223333   
2019 Ge Y, Li W, Ni Q, He Y, Chu J, Wei P. Weighted Gene Co-Expression Network Analysis Identifies Hub Genes Associated with Occurrence and Prognosis of Oral Squamous Cell Carcinoma. Medical Science Monitor : International Medical Journal of Experimental and Clinical Research. 25: 7272-7288. PMID 31562292 DOI: 10.12659/MSM.916025   
2019 Magwanga RO, Kirungu JN, Lu P, Cai X, Zhou Z, Xu Y, Hou Y, Agong SG, Wang K, Liu F. Map-Based Functional Analysis of the Genes Reveals Their Roles in Enhancing Tolerance to N-Deficiency in Cotton. International Journal of Molecular Sciences. 20. PMID 31597268 DOI: 10.3390/ijms20194953   
2019 Zhu H, Ji Y, Li W, Wu M. Identification of key pathways and genes in colorectal cancer to predict the prognosis based on mRNA interaction network. Oncology Letters. 18: 3778-3786. PMID 31579079 DOI: 10.3892/ol.2019.10698   
2019 Wang B, Li J, Li X, Ou Y. Identifying prognosis and metastasis-associated genes associated with Ewing sarcoma by weighted gene co-expression network analysis. Oncology Letters. 18: 3527-3536. PMID 31516570 DOI: 10.3892/ol.2019.10681   
2019 Fraik AK, Quackenbush C, Margres MJ, Comte S, Hamilton DG, Kozakiewicz CP, Jones M, Hamede R, Hohenlohe PA, Storfer A, Kelley JL. Transcriptomics of Tasmanian Devil () Ear Tissue Reveals Homogeneous Gene Expression Patterns across a Heterogeneous Landscape. Genes. 10. PMID 31614864 DOI: 10.3390/genes10100801   
2019 Stamoulis G, Garieri M, Makrythanasis P, Letourneau A, Guipponi M, Panousis N, Sloan-Béna F, Falconnet E, Ribaux P, Borel C, Santoni F, Antonarakis SE. Single cell transcriptome in aneuploidies reveals mechanisms of gene dosage imbalance. Nature Communications. 10: 4495. PMID 31582743 DOI: 10.1038/s41467-019-12273-8   
2019 Yang Z, Wei X, He J, Sun C, Ju J, Ma J. Characterization of the Noncanonical Regulatory and Transporter Genes in Atratumycin Biosynthesis and Production in a Heterologous Host. Marine Drugs. 17. PMID 31569487 DOI: 10.3390/md17100560   
2019 Wang H, Sham P, Tong T, Pang H. Pathway-based Single-Cell RNA-Seq Classification, Clustering, and Construction of Gene-Gene Interactions Networks Using Random Forests. Ieee Journal of Biomedical and Health Informatics. PMID 31581101 DOI: 10.1109/JBHI.2019.2944865   
2019 Matualatupauw JC, O'Grada C, Hughes MF, Roche HM, Afman LA, Bouwman J. Integrated Analys of High-Fat Challenge-Induced Changes in Blood Cell Whole-Genome Gene Expression. Molecular Nutrition & Food Research. e1900101. PMID 31565847 DOI: 10.1002/mnfr.201900101