Jun S. Song - Related publications

Institute for Genomic Biology University of Illinois, Urbana-Champaign, Urbana-Champaign, IL 
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Wang Z, He W, Tang J, Guo F. Identification of highest-affinity binding sites of yeast transcription factor families. Journal of Chemical Information and Modeling. PMID 31944107 DOI: 10.1021/acs.jcim.9b01012   
2020 Liu W, Zhang X. Single-cell alternative splicing analysis reveals dominance of single transcript variant. Genomics. PMID 31981701 DOI: 10.1016/j.ygeno.2020.01.014   
2020 Zhang J, Liu W, Zou C, Zhao Z, Lai Y, Shi Z, Xie X, Huang G, Wang Y, Zhang X, Fan Z, Su Q, Yin J, Shen J. Targeting super-enhancer-associated oncogenes in osteosarcoma with THZ2, a covalent CDK7 inhibitor. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 31937612 DOI: 10.1158/1078-0432.CCR-19-1418   
2020 Shell Cox J, Van Dyke MW. General and Genomic DNA-Binding Specificity for the HB8 Transcription Factor TTHB023. Biomolecules. 10. PMID 31935968 DOI: 10.3390/biom10010094   
2020 Panchy NL, Lloyd JP, Shiu SH. Improved recovery of cell-cycle gene expression in Saccharomyces cerevisiae from regulatory interactions in multiple omics data. Bmc Genomics. 21: 159. PMID 32054475 DOI: 10.1186/s12864-020-6554-8   
2020 Keele GR, Quach BC, Israel JW, Chappell GA, Lewis L, Safi A, Simon JM, Cotney P, Crawford GE, Valdar W, Rusyn I, Furey TS. Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation. Plos Genetics. 16: e1008537. PMID 31961859 DOI: 10.1371/journal.pgen.1008537   
2020 Marcon BH, Spangenberg L, Bonilauri B, Robert AW, Angulski ABB, Cabo GC, Cofré AR, Bettes PSL, Dallagiovanna B, Shigunov P. Data describing the experimental design and quality control of RNA-Seq of human adipose-derived stem cells undergoing early adipogenesis and osteogenesis. Data in Brief. 28: 105053. PMID 31989002 DOI: 10.1016/j.dib.2019.105053   
2020 Anderson WD, Duarte FM, Civelek M, Guertin MJ. Defining data-driven primary transcript annotations with primaryTranscriptAnnotation in R. Bioinformatics (Oxford, England). PMID 31917388 DOI: 10.1093/bioinformatics/btaa011   
2020 Halfon MS. Silencers, Enhancers, and the Multifunctional Regulatory Genome. Trends in Genetics : Tig. PMID 31918861 DOI: 10.1016/j.tig.2019.12.005   
2020 Gulati GS, Sikandar SS, Wesche DJ, Manjunath A, Bharadwaj A, Berger MJ, Ilagan F, Kuo AH, Hsieh RW, Cai S, Zabala M, Scheeren FA, Lobo NA, Qian D, Yu FB, et al. Single-cell transcriptional diversity is a hallmark of developmental potential. Science (New York, N.Y.). 367: 405-411. PMID 31974247 DOI: 10.1126/science.aax0249   
2020 Hou TY, Nandu T, Li R, Chae M, Murakami S, Kraus WL. Characterization of basal and estrogen-regulated antisense transcription in breast cancer cells: Role in regulating sense transcription. Molecular and Cellular Endocrinology. 110746. PMID 32035111 DOI: 10.1016/j.mce.2020.110746   
2020 Wei D, Raza SHA, Zhang J, Wang X, Khan R, Ma Y, Zhang G, Luoreng Z, Zan L. Characterization of the promoter region of the bovine 3 gene: Roles of SREBF2 and PPARG. Physiological Genomics. PMID 32036767 DOI: 10.1152/physiolgenomics.00091.2019   
2020 Lee TA, Bailey-Serres J. Conserved and nuanced hierarchy of gene regulatory response to hypoxia. The New Phytologist. PMID 31953954 DOI: 10.1111/nph.16437   
2020 Wilkinson M, Darmanis S, Pisco AO, Huber G. Persistent features of intermittent transcription. Scientific Reports. 10: 3138. PMID 32081955 DOI: 10.1038/s41598-020-60094-3   
2020 Li K, Liu Y, Cao H, Zhang Y, Gu Z, Liu X, Yu A, Kaphle P, Dickerson KE, Ni M, Xu J. Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing. Nature Communications. 11: 485. PMID 31980609 DOI: 10.1038/s41467-020-14362-5   
2020 Chen PM, Li JR, Liu CC, Tang FY, Chiang EI. Metabolic Pathways Enhancement Confers Poor Prognosis in p53 Exon Mutant Hepatocellular Carcinoma. Cancer Informatics. 19: 1176935119899913. PMID 31933519 DOI: 10.1177/1176935119899913   
2020 Xia B, Yan Y, Baron M, Wagner F, Barkley D, Chiodin M, Kim SY, Keefe DL, Alukal JP, Boeke JD, Yanai I. Widespread Transcriptional Scanning in the Testis Modulates Gene Evolution Rates. Cell. 180: 248-262.e21. PMID 31978344 DOI: 10.1016/j.cell.2019.12.015   
2020 Tian D, Zhang R, Zhang Y, Zhu X, Ma J. MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome. Genome Research. PMID 31907193 DOI: 10.1101/gr.250316.119   
2020 Hofvander J, Jo VY, Fletcher CDM, Puls F, Flucke U, Nilsson J, Magnusson L, Mertens F. PHF1 fusions cause distinct gene expression and chromatin accessibility profiles in ossifying fibromyxoid tumors and mesenchymal cells. Modern Pathology : An Official Journal of the United States and Canadian Academy of Pathology, Inc. PMID 31932680 DOI: 10.1038/s41379-020-0457-8   
2020 Zhang Y, Huang J, Li X, Fang C, Wang L. Identification of Functional Transcriptional Binding Sites within Chicken Gene Promoter and Screening Its Regulators. Genes. 11. PMID 32050731 DOI: 10.3390/genes11020186   
2020 Ban M, Liao W, Baker A, Compston A, Thorpe J, Molyneux P, Fraser M, Khadake J, Jones J, Coles A, Sawcer S. Transcript specific regulation of expression influences susceptibility to multiple sclerosis. European Journal of Human Genetics : Ejhg. PMID 31932686 DOI: 10.1038/s41431-019-0569-0   
2020 Chen Y, Liao LD, Wu ZY, Yang Q, Guo JC, He JZ, Wang SH, Xu XE, Wu JY, Pan F, Lin DC, Xu LY, Li EM. Identification of key genes by integrating DNA methylation and next-generation transcriptome sequencing for esophageal squamous cell carcinoma. Aging. 12. PMID 31962291 DOI: 10.18632/aging.102686   
2020 Bolt CC, Duboule D. The regulatory landscapes of developmental genes. Development (Cambridge, England). 147. PMID 32014867 DOI: 10.1242/dev.171736   
2020 Turgeon PJ, Chan GC, Chen L, Jamal AN, Yan MS, Ho JJD, Yuan L, Ibeh N, Ku KH, Cybulsky MI, Aird WC, Marsden PA. Epigenetic Heterogeneity and Mitotic Heritability Prime Endothelial Cell Gene Induction. Journal of Immunology (Baltimore, Md. : 1950). PMID 31996458 DOI: 10.4049/jimmunol.1900744   
2020 Zhao S, Yu M. Identification of as a Potential Prognostic Biomarker and Correlating with Immune Infiltrates in Cervical Squamous Cell Carcinoma. Dna and Cell Biology. PMID 31977248 DOI: 10.1089/dna.2019.5129   
2020 Meng J, Gao L, Zhang M, Gao S, Fan S, Liang C. Systematic investigation of the prognostic value of cell division cycle-associated proteins for clear cell renal cell carcinoma patients. Biomarkers in Medicine. PMID 31955607 DOI: 10.2217/bmm-2019-0498   
2020 Vicchio TM, Aliquò F, Ruggeri RM, Ragonese M, Giuffrida G, Cotta OR, Spagnolo F, Torre ML, Alibrandi A, Asmundo A, Angileri FF, Esposito F, Polito F, Oteri R, Aguennouz MH, et al. MicroRNAs expression in pituitary tumors: differences related to functional status, pathological features, and clinical behavior. Journal of Endocrinological Investigation. PMID 31939196 DOI: 10.1007/s40618-019-01178-4   
2020 Liu Y, Guo X, Zhao M, Ao H, Leng X, Liu M, Wu C, Ma J, Zhu J. Contributions and prognostic values of m A RNA methylation regulators in non-small-cell lung cancer. Journal of Cellular Physiology. PMID 32052446 DOI: 10.1002/jcp.29531   
2020 Zheng T, Nakamoto A, Kumano G. H3K27me3 suppresses sister-lineage somatic gene expression in late embryonic germline cells of the ascidian, Halocynthia roretzi. Developmental Biology. PMID 31904374 DOI: 10.1016/j.ydbio.2019.12.017   
2020 Yang F, Huang X, Zang R, Chen J, Fidalgo M, Sanchez-Priego C, Yang J, Caichen A, Ma F, Macfarlan T, Wang H, Gao S, Zhou H, Wang J. DUX-miR-344-ZMYM2-Mediated Activation of MERVL LTRs Induces a Totipotent 2C-like State. Cell Stem Cell. 26: 234-250.e7. PMID 32032525 DOI: 10.1016/j.stem.2020.01.004   
2020 Zhou C, Zhang J, Zhang M, Wang D, Ma Y, Wang Y, Wang Y, Huang Y, Zhang Y. Transcriptional memory inherited from donor cells is a developmental defect of bovine cloned embryos. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 34: 1637-1651. PMID 31914649 DOI: 10.1096/fj.201900578RR   
2020 Mavropoulos Papoudas S, Papanikolaou N, Nikolaou C. Monitoring the prolonged Tnf stimulation in space and time with topological-functional networks. Computational and Structural Biotechnology Journal. 18: 220-229. PMID 32021663 DOI: 10.1016/j.csbj.2020.01.001   
2020 Liu G, Ruan G, Huang M, Chen L, Sun P. Genome-wide DNA copy number profiling and bioinformatics analysis of ovarian cancer reveals key genes and pathways associated with distinct invasive/migratory capabilities. Aging. 11. PMID 31895688 DOI: 10.18632/aging.102608   
2020 Karagianni P, Moulos P, Schmidt D, Odom DT, Talianidis I. Bookmarking by Non-pioneer Transcription Factors during Liver Development Establishes Competence for Future Gene Activation. Cell Reports. 30: 1319-1328.e6. PMID 32023452 DOI: 10.1016/j.celrep.2020.01.006   
2020 Wang M, Guo J, Zhang L, Kuek V, Xu J, Zou J. Molecular structure, expression, and functional role of Clec11a in skeletal biology and cancers. Journal of Cellular Physiology. PMID 32003015 DOI: 10.1002/jcp.29600   
2020 Wragg D, Liu Q, Lin Z, Riggio V, Pugh CA, Beveridge AJ, Brown H, Hume DA, Harris SE, Deary IJ, Tenesa A, Prendergast JGD. Using regulatory variants to detect gene-gene interactions identifies networks of genes linked to cell immortalisation. Nature Communications. 11: 343. PMID 31953380 DOI: 10.1038/s41467-019-13762-6   
2020 Liu R, Liu L, Li X, Liu D, Yuan Y. Engineering yeast artificial core promoter with designated base motifs. Microbial Cell Factories. 19: 38. PMID 32070349 DOI: 10.1186/s12934-020-01305-4   
2020 Di Stefano M, Di Giovanni F, Pozharskaia V, Gomar-Alba M, Baù D, Carey LB, Marti-Renom MA, Mendoza M. Impact of Chromosome Fusions on 3D Genome Organization and Gene Expression in Budding Yeast. Genetics. PMID 31907200 DOI: 10.1534/genetics.119.302978   
2020 Barter MJ, Bui C, Cheung K, Falk J, Gómez R, Skelton AJ, Elliott HR, Reynard LN, Young DA. DNA hypomethylation during MSC chondrogenesis occurs predominantly at enhancer regions. Scientific Reports. 10: 1169. PMID 31980739 DOI: 10.1038/s41598-020-58093-5   
2020 Woldemeskel SA, Daitch AK, Alvarez L, Panis G, Zeinert R, Gonzalez D, Smith E, Collier J, Chien P, Cava F, Viollier PH, Goley ED. The conserved transcriptional regulator CdnL is required for metabolic homeostasis and morphogenesis in Caulobacter. Plos Genetics. 16: e1008591. PMID 31961855 DOI: 10.1371/journal.pgen.1008591   
2020 Kim TK, Lee I, Cho JH, Canine B, Keller A, Price ND, Hwang D, Carlson G, Hood L. Core transcriptional regulatory circuits in prion diseases. Molecular Brain. 13: 10. PMID 31959236 DOI: 10.1186/s13041-020-0551-3   
2020 Erickson RJB, Bandyopadhyay AA, Barnes AMT, O'Brien SA, Hu WS, Dunny GM. Single-Cell Analysis Reveals that the Enterococcal Sex Pheromone Response Results in Expression of Full-length Conjugation Operon Transcripts in All Induced Cells. Journal of Bacteriology. PMID 32041799 DOI: 10.1128/JB.00685-19   
2020 Britton CS, Sorrells TR, Johnson AD. Protein-coding changes preceded cis-regulatory gains in a newly evolved transcription circuit. Science (New York, N.Y.). 367: 96-100. PMID 31896718 DOI: 10.1126/science.aax5217   
2020 Serobyan V, Kontarakis Z, El-Brolosy MA, Welker JM, Tolstenkov O, Saadeldein AM, Retzer N, Gottschalk A, Wehman AM, Stainier DY. Transcriptional adaptation in . Elife. 9. PMID 31951195 DOI: 10.7554/eLife.50014   
2020 Fan Y, Jiang W, Ran F, Luo R, An L, Hang H. An efficient Exogenous Gene Insertion Site in CHO Cells with High Transcription Level to Enhance AID Induced Mutation. Biotechnology Journal. e1900313. PMID 31975519 DOI: 10.1002/biot.201900313   
2020 Li J, Huang Y, Cui Q, Zhou Y. m6Acorr: an online tool for the correction and comparison of mA methylation profiles. Bmc Bioinformatics. 21: 31. PMID 31996134 DOI: 10.1186/s12859-020-3380-6   
2020 Foreman R, Wollman R. Mammalian gene expression variability is explained by underlying cell state. Molecular Systems Biology. 16: e9146. PMID 32043799 DOI: 10.15252/msb.20199146   
2020 Camino EM, Weinstein ML, List MP, Vellky JE, Rebeiz M, Williams TM. Red Light/Green Light, a Dual Fluorescent Protein Reporter System To Study Enhancer-Promoter Specificity in . G3 (Bethesda, Md.). PMID 31900331 DOI: 10.1534/g3.119.401033   
2020 Xue S, Lam YM, He Z, Zheng Y, Li L, Zhang Y, Li C, Mbadhi MN, Zheng L, Cheng Z, Liu Y, Wang X, Chan LC, Ng RK, Zhang J. Histone lysine demethylase KDM5B maintains chronic myeloid leukemia via multiple epigenetic actions. Experimental Hematology. PMID 32007477 DOI: 10.1016/j.exphem.2020.01.006   
2020 Gutierrez-Arcelus M, Baglaenko Y, Arora J, Hannes S, Luo Y, Amariuta T, Teslovich N, Rao DA, Ermann J, Jonsson AH, , Navarrete C, Rich SS, Taylor KD, Rotter JI, et al. Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci. Nature Genetics. PMID 32066938 DOI: 10.1038/s41588-020-0579-4