Matthew Slattery, Ph.D. - Related publications

Affiliations: 
2013- Biomedical Sciences University of Minnesota, Twin Cities, Minneapolis, MN 
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Poon GMK. The Non-continuum Nature of Eukaryotic Transcriptional Regulation. Advances in Experimental Medicine and Biology. PMID 33616894 DOI: 10.1007/5584_2021_618   
2021 Falak N, Imran QM, Hussain A, Yun BW. Transcription Factors as the "Blitzkrieg" of Plant Defense: A Pragmatic View of Nitric Oxide's Role in Gene Regulation. International Journal of Molecular Sciences. 22. PMID 33430258 DOI: 10.3390/ijms22020522   
2021 Crump NT, Ballabio E, Godfrey L, Thorne R, Repapi E, Kerry J, Tapia M, Hua P, Lagerholm C, Filippakopoulos P, Davies JOJ, Milne TA. BET inhibition disrupts transcription but retains enhancer-promoter contact. Nature Communications. 12: 223. PMID 33431820 DOI: 10.1038/s41467-020-20400-z   
2021 Jana T, Brodsky S, Barkai N. Speed-Specificity Trade-Offs in the Transcription Factors Search for Their Genomic Binding Sites. Trends in Genetics : Tig. PMID 33414013 DOI: 10.1016/j.tig.2020.12.001   
2021 Chandra S, Ehrlich KC, Lacey M, Baribault C, Ehrlich M. Epigenetics and expression of key genes associated with cardiac fibrosis: and . Epigenomics. PMID 33538177 DOI: 10.2217/epi-2020-0446   
2021 Browne JA, NandyMazumdar M, Paranjapye A, Leir SH, Harris A. The Bromodomain Containing 8 (BRD8) Transcriptional Network in Human Lung Epithelial Cells. Molecular and Cellular Endocrinology. 111169. PMID 33476703 DOI: 10.1016/j.mce.2021.111169   
2021 Larke MSC, Schwessinger R, Nojima T, Telenius J, Beagrie RA, Downes DJ, Oudelaar AM, Truch J, Graham B, Bender MA, Proudfoot NJ, Higgs DR, Hughes JR. Enhancers predominantly regulate gene expression during differentiation via transcription initiation. Molecular Cell. PMID 33539786 DOI: 10.1016/j.molcel.2021.01.002   
2021 Song R, Struhl K. S100A8/S100A9 cytokine acts as a transcriptional coactivator during breast cellular transformation. Science Advances. 7. PMID 33523865 DOI: 10.1126/sciadv.abe5357   
2021 Xu G, Lyu H, Yi Y, Peng Y, Feng Q, Song Q, Gong C, Peng X, Palli SR, Zheng S. Intragenic DNA methylation regulates insect gene expression and reproduction through the MBD/Tip60 complex. Iscience. 24: 102040. PMID 33521602 DOI: 10.1016/j.isci.2021.102040   
2021 Chen L, Cao W, Aita R, Aldea D, Flores J, Gao N, Bonder EM, Ellison CE, Verzi MP. Three-dimensional interactions between enhancers and promoters during intestinal differentiation depend upon HNF4. Cell Reports. 34: 108679. PMID 33503426 DOI: 10.1016/j.celrep.2020.108679   
2021 Bright AR, van Genesen S, Li Q, Grasso A, Frölich S, van der Sande M, van Heeringen SJ, Veenstra GJC. Combinatorial transcription factor activities on open chromatin induce embryonic heterogeneity in vertebrates. The Embo Journal. e104913. PMID 33555045 DOI: 10.15252/embj.2020104913   
2021 Pieplow A, Dastaw M, Sakuma T, Sakamoto N, Yamamoto T, Yajima M, Oulhen N, Wessel GM. CRISPR-Cas9 editing of non-coding genomic loci as a means of controlling gene expression in the sea urchin. Developmental Biology. PMID 33482173 DOI: 10.1016/j.ydbio.2021.01.003   
2021 Lenz J, Liefke R, Funk J, Shoup S, Nist A, Stiewe T, Schulz R, Tokusumi Y, Albert L, Raifer H, Förstemann K, Vázquez O, Tokusumi T, Fossett N, Brehm A. Ush regulates hemocyte-specific gene expression, fatty acid metabolism and cell cycle progression and cooperates with dNuRD to orchestrate hematopoiesis. Plos Genetics. 17: e1009318. PMID 33600407 DOI: 10.1371/journal.pgen.1009318   
2021 Blevins WR, Ruiz-Orera J, Messeguer X, Blasco-Moreno B, Villanueva-Cañas JL, Espinar L, Díez J, Carey LB, Albà MM. Uncovering de novo gene birth in yeast using deep transcriptomics. Nature Communications. 12: 604. PMID 33504782 DOI: 10.1038/s41467-021-20911-3   
2021 Roy D, Sadanandom A. SUMO mediated regulation of transcription factors as a mechanism for transducing environmental cues into cellular signaling in plants. Cellular and Molecular Life Sciences : Cmls. PMID 33452901 DOI: 10.1007/s00018-020-03723-4   
2021 Chen H, Franklin Pugh B. What do transcription factors interact with? Journal of Molecular Biology. 166883. PMID 33621520 DOI: 10.1016/j.jmb.2021.166883   
2021 Lee Z, Raabe M, Hu WS. Epigenomic features revealed by ATAC-seq impact transgene expression in CHO cells. Biotechnology and Bioengineering. PMID 33521928 DOI: 10.1002/bit.27701   
2021 Lee Z, Raabe M, Hu WS. Epigenomic features revealed by ATAC-seq impact transgene expression in CHO cells. Biotechnology and Bioengineering. PMID 33521928 DOI: 10.1002/bit.27701   
2021 Morrison M, Razo-Mejia M, Phillips R. Reconciling kinetic and thermodynamic models of bacterial transcription. Plos Computational Biology. 17: e1008572. PMID 33465069 DOI: 10.1371/journal.pcbi.1008572   
2021 Trouillon J, Ragno M, Simon V, Attrée I, Elsen S. Transcription Inhibitors with XRE DNA-Binding and Cupin Signal-Sensing Domains Drive Metabolic Diversification in . Msystems. 6. PMID 33436508 DOI: 10.1128/mSystems.00753-20   
2021 Boulanger M, Chakraborty M, Tempé D, Piechaczyk M, Bossis G. SUMO and Transcriptional Regulation: The Lessons of Large-Scale Proteomic, Modifomic and Genomic Studies. Molecules (Basel, Switzerland). 26. PMID 33562565 DOI: 10.3390/molecules26040828   
2021 Wang Z, Wang P, Li Y, Peng H, Zhu Y, Mohandas N, Liu J. Interplay between cofactors and transcription factors in hematopoiesis and hematological malignancies. Signal Transduction and Targeted Therapy. 6: 24. PMID 33468999 DOI: 10.1038/s41392-020-00422-1   
2021 Her YR, Wang L, Chepelev I, Manterola M, Berkovits B, Cui K, Zhao K, Wolgemuth DJ. Genome-wide chromatin occupancy of BRDT and gene expression analysis suggest transcriptional partners and specific epigenetic landscapes that regulate gene expression during spermatogenesis. Molecular Reproduction and Development. PMID 33469999 DOI: 10.1002/mrd.23449   
2021 Chen HQ, Chen DJ, Li Y, Han F, Jiang X, Cao J, Liu JY, Liu WB. DNA methylation and hydroxymethylation associated with gene expression regulatory network during 3-methylcholanthrene induced lung cell malignant transformation. The Science of the Total Environment. 771: 144839. PMID 33545462 DOI: 10.1016/j.scitotenv.2020.144839   
2021 McNamara AV, Awais R, Momiji H, Dunham L, Featherstone K, Harper CV, Adamson AA, Semprini S, Jones NA, Spiller DG, Mullins JJ, Finkenstädt BF, Rand D, White MRH, Davis JRE. Transcription factor Pit-1 affects transcriptional timing in the dual-promoter human prolactin gene. Endocrinology. PMID 33388754 DOI: 10.1210/endocr/bqaa249   
2021 Kubo N, Ishii H, Xiong X, Bianco S, Meitinger F, Hu R, Hocker JD, Conte M, Gorkin D, Yu M, Li B, Dixon JR, Hu M, Nicodemi M, Zhao H, et al. Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation. Nature Structural & Molecular Biology. PMID 33398174 DOI: 10.1038/s41594-020-00539-5   
2021 Xu J, Shi J, Cui X, Cui Y, Li JJ, Goel A, Chen X, Issa JP, Su J, Li W. Cellular Heterogeneity-Adjusted cLonal Methylation (CHALM) improves prediction of gene expression. Nature Communications. 12: 400. PMID 33452255 DOI: 10.1038/s41467-020-20492-7   
2021 Davies R, Liu L, Taotao S, Tuano N, Chaturvedi R, Huang KK, Itman C, Mandoli A, Qamra A, Hu C, Powell D, Daly RJ, Tan P, Rosenbluh J. CRISPRi enables isoform-specific loss-of-function screens and identification of gastric cancer-specific isoform dependencies. Genome Biology. 22: 47. PMID 33499898 DOI: 10.1186/s13059-021-02266-6   
2021 Gallaher SD, Craig RJ, Ganesan I, Purvine SO, McCorkle SR, Grimwood J, Strenkert D, Davidi L, Roth MS, Jeffers TL, Lipton MS, Niyogi KK, Schmutz J, Theg SM, Blaby-Haas CE, et al. Widespread polycistronic gene expression in green algae. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33579822 DOI: 10.1073/pnas.2017714118   
2021 Chia M, Li C, Marques S, Pelechano V, Luscombe NM, van Werven FJ. High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts. Genome Biology. 22: 34. PMID 33446241 DOI: 10.1186/s13059-020-02245-3   
2021 Cheng M, Pei D, He X, Liu Y, Zhu P, Yan X. Hydrolytic dehalogenation operon of 4-chlorobenzoate is transcriptionally regulated by the TetR-type repressor FcbR and its ligand 4-chlorobenzoyl-CoA. Applied and Environmental Microbiology. PMID 33397703 DOI: 10.1128/AEM.02652-20   
2021 Sarkar A, Mishra P, Kahveci T. Data perturbation and recovery of time series gene expression data. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 33566765 DOI: 10.1109/TCBB.2021.3058342   
2021 Kitazawa T, Machlab D, Joshi O, Maiorano N, Kohler H, Ducret S, Kessler S, Gezelius H, Soneson C, Papasaikas P, López-Bendito G, Stadler MB, Rijli FM. A unique bipartite Polycomb signature regulates stimulus-response transcription during development. Nature Genetics. PMID 33603234 DOI: 10.1038/s41588-021-00789-z   
2021 Zhao X, Luo T, Huang S, Peng N, Yin Y, Luo Z, Zhang Y. A novel transcription factor negatively regulates antioxidant response, cell wall integrity and virulence in the fungal insect pathogen, Beauveria bassiana. Environmental Microbiology. PMID 33432709 DOI: 10.1111/1462-2920.15397   
2021 Cavallaro M, Walsh MD, Jones M, Teahan J, Tiberi S, Finkenstädt B, Hebenstreit D. 3 -5 crosstalk contributes to transcriptional bursting. Genome Biology. 22: 56. PMID 33541397 DOI: 10.1186/s13059-020-02227-5   
2021 Jia T, Li F, Liu S, Dou J, Huang T. DnaJ Proteins Regulate Expression in Shoot Apical Meristem of Arabidopsis. Plants (Basel, Switzerland). 10. PMID 33445404 DOI: 10.3390/plants10010136   
2021 Zhou Q, Yu M, Tirado-Magallanes R, Li B, Kong L, Guo M, Tan ZH, Lee S, Chai L, Numata A, Benoukraf T, Fullwood MJ, Osato M, Ren B, Tenen DG. ZNF143 mediates CTCF-bound promoter-enhancer loops required for murine hematopoietic stem and progenitor cell function. Nature Communications. 12: 43. PMID 33397967 DOI: 10.1038/s41467-020-20282-1   
2021 Morral N, Liu S, Conteh AM, Chu X, Wang Y, Dong XC, Liu Y, Linnemann AK, Wan J. Aberrant gene expression induced by a high fat diet is linked to H3K9 acetylation in the promoter-proximal region. Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms. 194691. PMID 33556624 DOI: 10.1016/j.bbagrm.2021.194691   
2021 Yu TC, Liu WL, Brinck MS, Davis JE, Shek J, Bower G, Einav T, Insigne KD, Phillips R, Kosuri S, Urtecho G. Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems. Nature Communications. 12: 325. PMID 33436562 DOI: 10.1038/s41467-020-20094-3   
2021 Yu TC, Liu WL, Brinck MS, Davis JE, Shek J, Bower G, Einav T, Insigne KD, Phillips R, Kosuri S, Urtecho G. Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems. Nature Communications. 12: 325. PMID 33436562 DOI: 10.1038/s41467-020-20094-3   
2021 Xiong YJ, Liu DY, Shen RR, Xiong Y. A short deletion in the DNA binding domain of STAT3 suppresses growth and progression of colon cancer cells. Aging. 12. PMID 33535185 DOI: 10.18632/aging.202439   
2021 Schneider N, Wieland FG, Kong D, Fischer AAM, Hörner M, Timmer J, Ye H, Weber W. Liquid-liquid phase separation of light-inducible transcription factors increases transcription activation in mammalian cells and mice. Science Advances. 7. PMID 33523844 DOI: 10.1126/sciadv.abd3568   
2021 Schneider N, Wieland FG, Kong D, Fischer AAM, Hörner M, Timmer J, Ye H, Weber W. Liquid-liquid phase separation of light-inducible transcription factors increases transcription activation in mammalian cells and mice. Science Advances. 7. PMID 33523844 DOI: 10.1126/sciadv.abd3568   
2021 Gacita AM, Fullenkamp DE, Ohiri J, Pottinger T, Puckelwartz MJ, Nobrega MA, McNally EM. Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression. Circulation. PMID 33478249 DOI: 10.1161/CIRCULATIONAHA.120.050432   
2021 Thakur V, Bains S, Kaur R, Singh K. Identification and characterization of SlbHLH, SlDof and SlWRKY transcription factors interacting with SlDPD gene involved in costunolide biosynthesis in Saussurea lappa. International Journal of Biological Macromolecules. PMID 33482203 DOI: 10.1016/j.ijbiomac.2021.01.114   
2021 Lee JY, Song J, LeBlanc L, Davis I, Kim J, Beck S. Conserved dual-mode gene regulation programs in higher eukaryotes. Nucleic Acids Research. PMID 33621342 DOI: 10.1093/nar/gkab108   
2021 Gonzalez I, Molliex A, Navarro P. Mitotic memories of gene activity. Current Opinion in Cell Biology. 69: 41-47. PMID 33454629 DOI: 10.1016/j.ceb.2020.12.009   
2021 Xie Q, Yu Q, Jobe TO, Pham A, Ge C, Guo Q, Liu J, Liu H, Zhang H, Zhao Y, Xue S, Hauser F, Schroeder JI. An amiRNA screen uncovers redundant CBF & ERF34/35 transcription factors that differentially regulate arsenite and cadmium responses. Plant, Cell & Environment. PMID 33554343 DOI: 10.1111/pce.14023   
2021 Johari YB, Mercer AC, Liu Y, Brown AJ, James DC. Design of synthetic promoters for controlled expression of therapeutic genes in retinal pigment epithelial cells. Biotechnology and Bioengineering. PMID 33580508 DOI: 10.1002/bit.27713   
2021 Koay TW, Osterhof C, Orlando IMC, Keppner A, Andre D, Yousefian S, Alonso MS, Correia M, Markworth R, Schödel J, Hankeln T, Hoogewijs D. Androglobin gene expression patterns and FOXJ1-dependent regulation indicate its functional association with ciliogenesis. The Journal of Biological Chemistry. 100291. PMID 33453283 DOI: 10.1016/j.jbc.2021.100291