Avi Ma'ayan, Ph.D. - Related publications

2006 Icahn School of Medicine at Mount Sinai, New York, NY, United States 
Cellular signaling systems
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 García-Ruiz S, Gil-Martínez AL, Cisterna A, Jurado-Ruiz F, Reynolds RH, , Cookson MR, Hardy J, Ryten M, Botía JA. CoExp: A Web Tool for the Exploitation of Co-expression Networks. Frontiers in Genetics. 12: 630187. PMID 33719340 DOI: 10.3389/fgene.2021.630187   
2021 Pham TH, Qiu Y, Zeng J, Xie L, Zhang P. A deep learning framework for high-throughput mechanism-driven phenotype compound screening and its application to COVID-19 drug repurposing. Nature Machine Intelligence. 3: 247-257. PMID 33796820 DOI: 10.1038/s42256-020-00285-9   
2021 Sánchez JA, Gil-Martinez AL, Cisterna A, García-Ruíz S, Gómez-Pascual A, Reynolds RH, Nalls M, Hardy J, Ryten M, Botía JA. Modeling multifunctionality of genes with secondary gene co-expression networks in human brain provides novel disease insights. Bioinformatics (Oxford, England). PMID 33734320 DOI: 10.1093/bioinformatics/btab175   
2021 Wu B, Jiang X, Huang Y, Ying X, Zhang H, Liu B, Li Z, Qi D, Ji W, Cai X. Integrated Analysis of mRNA-mA-protein Profiles Reveals Novel Insights into the Mechanisms for Cadmium-induced Urothelial Transformation. Biomarkers : Biochemical Indicators of Exposure, Response, and Susceptibility to Chemicals. 1-23. PMID 33830842 DOI: 10.1080/1354750X.2021.1913513   
2021 Zhang R, Atwal GS, Lim WK. Noise regularization removes correlation artifacts in single-cell RNA-seq data preprocessing. Patterns (New York, N.Y.). 2: 100211. PMID 33748795 DOI: 10.1016/j.patter.2021.100211   
2021 Xie J, Deng Z, Alahdal M, Liu J, Zhao Z, Chen X, Wang G, Hu X, Duan L, Wang D, Li W. Screening and verification of hub genes involved in osteoarthritis using bioinformatics. Experimental and Therapeutic Medicine. 21: 330. PMID 33732303 DOI: 10.3892/etm.2021.9761   
2021 Liu L, Yu Y, Hu LL, Dong QB, Hu F, Zhu LJ, Liang Q, Yu LL, Bao HH, Cheng XS. Potential Target Genes in the Development of Atrial Fibrillation: A Comprehensive Bioinformatics Analysis. Medical Science Monitor : International Medical Journal of Experimental and Clinical Research. 27: e928366. PMID 33741890 DOI: 10.12659/MSM.928366   
2021 Liu Y, Huang Z, Cheng G, Shou Y, Xu J, Liu D, Yang H, Liang H, Zhang X. Development of a four-gene prognostic model for clear cell renal cell carcinoma based on transcriptome analysis. Genomics. PMID 33838279 DOI: 10.1016/j.ygeno.2021.04.005   
2021 Meng L, He X, Hong Q, Qiao B, Zhang X, Wu B, Zhang X, Wei Y, Li J, Ye Z, Xiao Y. , , and as Prognostic Factors in Head and Neck Squamous Cell Carcinoma Are Involved in the Remodeling of the Tumor Microenvironment. Frontiers in Oncology. 11: 618187. PMID 33692955 DOI: 10.3389/fonc.2021.618187   
2021 Yin W, Mendoza L, Monzon-Sandoval J, Urrutia AO, Gutierrez H. Emergence of co-expression in gene regulatory networks. Plos One. 16: e0247671. PMID 33793561 DOI: 10.1371/journal.pone.0247671   
2021 He H, Yu F, Shen W, Chen K, Zhang L, Lou S, Zhang Q, Chen S, Yuan X, Jia X, Zhou Y. The Novel Key Genes of Non-obstructive Azoospermia Affect Spermatogenesis: Transcriptomic Analysis Based on RNA-Seq and scRNA-Seq Data. Frontiers in Genetics. 12: 608629. PMID 33732283 DOI: 10.3389/fgene.2021.608629   
2021 Guo W, Zheng X, Hua L, Zheng X, Zhang Y, Sun B, Tao Z, Gao J. Screening and bioinformatical analysis of differentially expressed genes in nasopharyngeal carcinoma. Journal of Cancer. 12: 1867-1883. PMID 33753985 DOI: 10.7150/jca.48979   
2021 Hu D, Jiang J, Lin Z, Zhang C, Moonasar N, Qian S. Identification of key genes and pathways in scleral extracellular matrix remodeling in glaucoma: Potential therapeutic agents discovered using bioinformatics analysis. International Journal of Medical Sciences. 18: 1554-1565. PMID 33746571 DOI: 10.7150/ijms.52846   
2021 Zhang ZQ, Wu WW, Chen JD, Zhang GY, Lin JY, Wu YK, Zhang Y, Su YA, Li JT, Si TM. Weighted Gene Coexpression Network Analysis Reveals Essential Genes and Pathways in Bipolar Disorder. Frontiers in Psychiatry. 12: 553305. PMID 33815158 DOI: 10.3389/fpsyt.2021.553305   
2021 Qiao Y, Zhang B, Liu Y. Identification of Potential Diagnostic Gene Targets for Pediatric Sepsis Based on Bioinformatics and Machine Learning. Frontiers in Pediatrics. 9: 576585. PMID 33748037 DOI: 10.3389/fped.2021.576585   
2021 Haellman V, Saxena P, Jiang Y, Fussenegger M. Rational design and optimization of synthetic gene switches for controlling cell-fate decisions in pluripotent stem cells. Metabolic Engineering. 65: 99-110. PMID 33744461 DOI: 10.1016/j.ymben.2021.03.009   
2021 Kwon AT, Mohri K, Takizawa S, Arakawa T, Takahashi M, Kaczkowski B, Furuno M, Suzuki H, Tagami S, Mukai H, Arner E. Development of p53 Knockout U87MG Cell Line for Unbiased Drug Delivery Testing System Using CRISPR-Cas9 and Transcriptomic Analysis. Journal of Biotechnology. PMID 33836165 DOI: 10.1016/j.jbiotec.2021.03.017   
2021 Kim BK, Lee HS, Lee SY, Park HW. Different Biological Pathways Between Good and Poor Inhaled Corticosteroid Responses in Asthma. Frontiers in Medicine. 8: 652824. PMID 33816533 DOI: 10.3389/fmed.2021.652824   
2021 Greco FV, Pandi A, Erb TJ, Grierson CS, Gorochowski TE. Harnessing the central dogma for stringent multi-level control of gene expression. Nature Communications. 12: 1738. PMID 33741937 DOI: 10.1038/s41467-021-21995-7   
2021 Xie Z, Bailey A, Kuleshov MV, Clarke DJB, Evangelista JE, Jenkins SL, Lachmann A, Wojciechowicz ML, Kropiwnicki E, Jagodnik KM, Jeon M, Ma'ayan A. Gene Set Knowledge Discovery with Enrichr. Current Protocols. 1: e90. PMID 33780170 DOI: 10.1002/cpz1.90   
2021 Babal YK, Kandemir B, Kurnaz IA. Gene Regulatory Network of ETS Domain Transcription Factors in Different Stages of Glioma. Journal of Personalized Medicine. 11. PMID 33671331 DOI: 10.3390/jpm11020138   
2021 Pant N, Madhumita M, Paul S. CorGO: An Integrated Method for Clustering Functionally Similar Genes. Interdisciplinary Sciences, Computational Life Sciences. PMID 33761117 DOI: 10.1007/s12539-021-00424-9   
2021 Wang L, Man S, Bian Y. Bioinformatics analysis of biomarkers of aristolochic acid-induced early nephrotoxicity in embryonic stem cells. Experimental and Therapeutic Medicine. 21: 508. PMID 33791017 DOI: 10.3892/etm.2021.9939   
2021 Zuo D, Li C, Liu T, Yue M, Zhang J, Ning G. Construction and validation of a metabolic risk model predicting prognosis of colon cancer. Scientific Reports. 11: 6837. PMID 33767290 DOI: 10.1038/s41598-021-86286-z   
2021 Bian Q, Chen J, Wu J, Ding F, Li X, Ma Q, Zhang L, Zou X, Chen J. Bioinformatics analysis of a TF-miRNA-lncRNA regulatory network in major depressive disorder. Psychiatry Research. 299: 113842. PMID 33751989 DOI: 10.1016/j.psychres.2021.113842   
2021 Lee J, Geng S, Li S, Li L. Single Cell RNA-Seq and Machine Learning Reveal Novel Subpopulations in Low-Grade Inflammatory Monocytes With Unique Regulatory Circuits. Frontiers in Immunology. 12: 627036. PMID 33708217 DOI: 10.3389/fimmu.2021.627036   
2021 Du X, Zhang C, Yin C, Wang W, Yan X, Xie D, Zheng X, Zheng Q, Li M, Song Z. High BLM Expression Predicts Poor Clinical Outcome and Contributes to Malignant Progression in Human Cholangiocarcinoma. Frontiers in Oncology. 11: 633899. PMID 33828983 DOI: 10.3389/fonc.2021.633899   
2021 Du X, Zhang C, Yin C, Wang W, Yan X, Xie D, Zheng X, Zheng Q, Li M, Song Z. High BLM Expression Predicts Poor Clinical Outcome and Contributes to Malignant Progression in Human Cholangiocarcinoma. Frontiers in Oncology. 11: 633899. PMID 33828983 DOI: 10.3389/fonc.2021.633899   
2021 Wang J, Peng R, Zhang Z, Zhang Y, Dai Y, Sun Y. Identification and Validation of Key Genes in Hepatocellular Carcinoma by Bioinformatics Analysis. Biomed Research International. 2021: 6662114. PMID 33688500 DOI: 10.1155/2021/6662114   
2021 Bai J, Dai Y, Farinha A, Tang AY, Syal S, Vargas-Cuebas G, van Opijnen T, Isberg RR, Geisinger E. Essential gene analysis in by high-density transposon mutagenesis and CRISPR interference. Journal of Bacteriology. PMID 33782056 DOI: 10.1128/JB.00565-20   
2021 Li R, Lin CY, Guo WF, Akutsu T. Weighted minimum feedback vertex sets and implementation in human cancer genes detection. Bmc Bioinformatics. 22: 143. PMID 33752597 DOI: 10.1186/s12859-021-04062-2   
2021 Huang Z, Han Z, Wang Resource T, Shao W, Xiang S, Salama P, Rizkalla M, Huang K, Zhang J. TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining. Genomics, Proteomics & Bioinformatics. PMID 33705981 DOI: 10.1016/j.gpb.2019.05.006   
2021 Zhou Y, Sharpee TO. Hyperbolic geometry of gene expression. Iscience. 24: 102225. PMID 33748711 DOI: 10.1016/j.isci.2021.102225   
2021 Zhou Y, Sharpee TO. Hyperbolic geometry of gene expression. Iscience. 24: 102225. PMID 33748711 DOI: 10.1016/j.isci.2021.102225   
2021 Huang F, Guo H, Wei Y, Zhao X, Chen Y, Lin Z, Zhou Y, Sun P. In Silico Network Analysis of Ingredients of Cornus officinalis in Osteoporosis. Medical Science Monitor : International Medical Journal of Experimental and Clinical Research. 27: e929219. PMID 33795629 DOI: 10.12659/MSM.929219   
2021 Reed F, Larsuel ST, Mayday MY, Scanlon V, Krause DS. MRTFA: a critical protein in normal and malignant hematopoiesis and beyond. The Journal of Biological Chemistry. 100543. PMID 33722605 DOI: 10.1016/j.jbc.2021.100543   
2021 Wang L, Lin Y, Yuan Y, Liu F, Sun K. Identification of TYROBP and FCER1G as Key Genes with Prognostic Value in Clear Cell Renal Cell Carcinoma by Bioinformatics Analysis. Biochemical Genetics. PMID 33786672 DOI: 10.1007/s10528-021-10061-y   
2021 Liu Z, Wang Y, Yuan S, Wen F, Liu J, Zou L, Zhang J. Regulatory role of long non-coding RNA UCA1 in signaling pathways and its clinical applications. Oncology Letters. 21: 404. PMID 33777227 DOI: 10.3892/ol.2021.12665   
2021 Wang JC, Ramaswami G, Geschwind DH. Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility. Scientific Reports. 11: 5748. PMID 33707641 DOI: 10.1038/s41598-021-85061-4   
2021 Liu H, Qu Y, Zhou H, Zheng Z, Zhao J, Zhang J. Bioinformatic analysis of potential hub genes in gastric adenocarcinoma. Science Progress. 104: 368504211004260. PMID 33788653 DOI: 10.1177/00368504211004260   
2021 Kim SM, Rampogu S, Vetrivel P, Kulkarni AM, Ha SE, Kim HH, Lee KW, Kim GS. Transcriptome analysis of sinensetin-treated liver cancer cells guided by biological network analysis. Oncology Letters. 21: 355. PMID 33747212 DOI: 10.3892/ol.2021.12616   
2021 Li C, Lyu Y, Liu C, Yin S. The Role of PBK as a Potential Prognostic and Diagnostic Biomarker in Ovarian Cancer. Cancer Biotherapy & Radiopharmaceuticals. PMID 33794097 DOI: 10.1089/cbr.2020.4249   
2021 Wang P, Moore BM, Uygun S, Lehti-Shiu MD, Barry CS, Shiu SH. Optimizing the use of gene expression data to predict plant metabolic pathway memberships. The New Phytologist. PMID 33749860 DOI: 10.1111/nph.17355   
2021 He K, Zhang J, Liu J, Cui Y, Liu LG, Ye S, Ban Q, Pan R, Liu D. Functional genomics study of protein inhibitor of activated STAT1 in mouse hippocampal neuronal cells revealed by RNA sequencing. Aging. 13. PMID 33759814 DOI: 10.18632/aging.202749   
2021 Zhang B, Chen Z, Wang Y, Fan G, He X. Integrated bioinformatics analysis for the identification of key genes and signaling pathways in thyroid carcinoma. Experimental and Therapeutic Medicine. 21: 298. PMID 33717241 DOI: 10.3892/etm.2021.9729   
2021 Kitajima K, Kawahira N, Lee S, Tamura K, Morishita Y, Ohtsuka D. Light-induced local gene expression in primary chick cell culture system. Development, Growth & Differentiation. PMID 33733477 DOI: 10.1111/dgd.12721   
2021 Iscan E, Ekin U, Yildiz G, Oz O, Keles U, Suner A, Cakan-Akdogan G, Ozhan G, Nekulova M, Vojtesek B, Uzuner H, Karakülah G, Alotaibi H, Ozturk M. TAp73β Can Promote Hepatocellular Carcinoma Dedifferentiation. Cancers. 13. PMID 33668566 DOI: 10.3390/cancers13040783   
2021 Tian L, Chen T, Lu J, Yan J, Zhang Y, Qin P, Ding S, Zhou Y. Integrated Protein-Protein Interaction and Weighted Gene Co-expression Network Analysis Uncover Three Key Genes in Hepatoblastoma. Frontiers in Cell and Developmental Biology. 9: 631982. PMID 33718368 DOI: 10.3389/fcell.2021.631982   
2021 Zheng PF, Chen LZ, Guan YZ, Liu P. Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease. Scientific Reports. 11: 6711. PMID 33758323 DOI: 10.1038/s41598-021-86207-0   
2021 Mayère C, Neirijnck Y, Sararols P, Rands CM, Stévant I, Kühne F, Chassot AA, Chaboissier MC, Dermitzakis ET, Nef S. Single-cell transcriptomics reveal temporal dynamics of critical regulators of germ cell fate during mouse sex determination. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 35: e21452. PMID 33749946 DOI: 10.1096/fj.202002420R