Patrick D. McMullen, Ph.D. - Related publications

Chemical and Biological Engineering Northwestern University, Evanston, IL 
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50 most relevant papers in past 60 days:
Year Citation  Score
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 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 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 Jackson CA, Castro DM, Saldi GA, Bonneau R, Gresham D. Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments. Elife. 9. PMID 31985403 DOI: 10.7554/eLife.51254   
2020 Chiang S, Shinohara H, Huang JH, Tsai HK, Okada M. Inferring the transcriptional regulatory mechanism of signal-dependent gene expression via an integrative computational approach. Febs Letters. PMID 32052437 DOI: 10.1002/1873-3468.13757   
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 Gomez-Cano L, Gomez-Cano F, Dillon FM, Alers-Velazquez R, Doseff AI, Grotewold E, Gray J. Discovery of modules involved in the biosynthesis and regulation of maize phenolic compounds. Plant Science : An International Journal of Experimental Plant Biology. 291: 110364. PMID 31928683 DOI: 10.1016/j.plantsci.2019.110364   
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 Yuan Y, Zhang B, Tang X, Zhang J, Lin J. Comparative Transcriptome Analysis of Different Species Reveals Active Ingredients-Related Genes and Pathways. International Journal of Molecular Sciences. 21. PMID 32013237 DOI: 10.3390/ijms21030861   
2020 Wang J, Liu H, Xie G, Cai W, Xu J. Identification of hub genes and key pathways of dietary advanced glycation end products‑induced non‑alcoholic fatty liver disease by bioinformatics analysis and animal experiments. Molecular Medicine Reports. 21: 685-694. PMID 31974594 DOI: 10.3892/mmr.2019.10872   
2020 Bannon DI, Bao W, Turner SD, McCain WC, Dennis W, Wolfinger R, Perkins E, Abounader R. Gene expression in mouse muscle over time after nickel pellet implantation. Metallomics : Integrated Biometal Science. PMID 32065191 DOI: 10.1039/c9mt00289h   
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 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 Cao Z, Grima R. Analytical distributions for detailed models of stochastic gene expression in eukaryotic cells. Proceedings of the National Academy of Sciences of the United States of America. PMID 32071224 DOI: 10.1073/pnas.1910888117   
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 Jost M, Santos DA, Saunders RA, Horlbeck MA, Hawkins JS, Scaria SM, Norman TM, Hussmann JA, Liem CR, Gross CA, Weissman JS. Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs. Nature Biotechnology. PMID 31932729 DOI: 10.1038/s41587-019-0387-5   
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 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 Xia Y, Li J, Li S, Khodahemmati S, Ghaffar M, Chen S, Sheng W. Identification of Pathways and Genes in the Process of E6/E7 Induced Carcinogenesis of Esophageal Epithelial Cells. Journal of Medical Virology. PMID 31916268 DOI: 10.1002/jmv.25667   
2020 Bhushan R, Rani A, Ali A, Singh VK, Dubey PK. Bioinformatics enrichment analysis of genes and pathways related to maternal type 1 diabetes associated with adverse fetal outcomes. Journal of Diabetes and Its Complications. 107556. PMID 32046932 DOI: 10.1016/j.jdiacomp.2020.107556   
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 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 Lim H, Xie L. A New Weighted Imputed Neighborhood-regularized Tri-factorization One-class Collaborative Filtering Algorithm: Application to Target Gene Prediction of Transcription Factors. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 31995498 DOI: 10.1109/TCBB.2020.2968442   
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 Hurtado C, Acevedo Sáenz LY, Vásquez Trespalacios EM, Urrego R, Jenks S, Sanz I, Vásquez G. DNA methylation changes on immune cells in Systemic Lupus Erythematosus. Autoimmunity. 1-8. PMID 32019373 DOI: 10.1080/08916934.2020.1722108   
2020 Bolt CC, Duboule D. The regulatory landscapes of developmental genes. Development (Cambridge, England). 147. PMID 32014867 DOI: 10.1242/dev.171736   
2020 Wang G, Cheng H, Li M, Zhang C, Deng W, Li T. Selection and Validation of Reliable Reference Genes for Tolypocladium guangdongense Gene Expression Analysis under Differentially Developmental Stages and Temperature Stresses. Gene. 144380. PMID 31978511 DOI: 10.1016/j.gene.2020.144380   
2020 Luo R, Zheng Z, Yang C, Zhang X, Cheng L, Su G, Bai C, Li G. Comparative Transcriptome Analysis Provides Insights into the Polyunsaturated Fatty Acid Synthesis Regulation of Transgenic Sheep. International Journal of Molecular Sciences. 21. PMID 32046209 DOI: 10.3390/ijms21031121   
2020 Chen W, Zhu S, Zhang Y, Xiao J, Tian D. Identification of key candidate tumor biomarkers in non-small-cell lung cancer by analysis. Oncology Letters. 19: 1008-1016. PMID 31897214 DOI: 10.3892/ol.2019.11169   
2020 Liu HB, Huang GJ, Luo MS. Transcriptome analyses identify hub genes and potential mechanisms in adenoid cystic carcinoma. Medicine. 99: e18676. PMID 31914060 DOI: 10.1097/MD.0000000000018676   
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 Blake LE, Roux J, Hernando-Herraez I, Banovich N, Garcia Perez R, Hsiao CJ, Eres I, Cuevas C, Marques-Bonet T, Gilad Y. A comparison of gene expression and DNA methylation patterns across tissues and species. Genome Research. PMID 31953346 DOI: 10.1101/gr.254904.119   
2020 Annalora AJ, Marcus CB, Iversen PL. Alternative Splicing in the Nuclear Receptor Superfamily Redirects Human Metabolic Homeostasis. Drug Metabolism and Disposition: the Biological Fate of Chemicals. PMID 31980501 DOI: 10.1124/dmd.119.089102   
2020 Chen F, Fu Q, Pu L, Hou Z, Xu Z, Zhang P, Deng T, Pang C, Liang X, Lu Y, Zhang M. Maternal transcription profiles at different stages for the development of early embryo in buffalo. Reproduction in Domestic Animals = Zuchthygiene. PMID 31971628 DOI: 10.1111/rda.13644   
2020 Singh AK, Upadhyay RC, Chandra G, Kumar S, Malakar D, Singh SV, Singh MK. Genome-wide expression analysis of the heat stress response in dermal fibroblasts of Tharparkar (zebu) and Karan-Fries (zebu × taurine) cattle. Cell Stress & Chaperones. PMID 32062819 DOI: 10.1007/s12192-020-01076-2   
2020 Zhang Y, Cao X, Li P, Fan Y, Zhang L, Li W, Liu Y. PSMC6 promotes osteoblast apoptosis through inhibiting PI3K/AKT signaling pathway activation in ovariectomy-induced osteoporosis mouse model. Journal of Cellular Physiology. PMID 32017075 DOI: 10.1002/jcp.29261   
2020 Zhou H, Yang Z, Yue J, Chen Y, Chen T, Mu T, Liu H, Bi X. Identification of potential hub genes via bioinformatics analysis combined with experimental verification in colorectal cancer. Molecular Carcinogenesis. PMID 32064687 DOI: 10.1002/mc.23165   
2020 Li D, Pan Z, Hu G, Anderson G, He S. Active module identification from multilayer weighted gene co-expression networks: a continuous optimization approach. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 32011261 DOI: 10.1109/TCBB.2020.2970400   
2020 Feldmann A, Dimitrova E, Kenney A, Lastuvkova A, Klose RJ. CDK-Mediator and FBXL19 prime developmental genes for activation by promoting atypical regulatory interactions. Nucleic Acids Research. PMID 31996894 DOI: 10.1093/nar/gkaa064   
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 Verma YK, Singh AK, Gurudutta GU. Survival genes expression analysis following ionizing radiation to LiCl treated KG1a cells. International Journal of Radiation Biology. 1-56. PMID 31985347 DOI: 10.1080/09553002.2020.1721592   
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 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 Zhou P, Pu T, Gui C, Zhang X, Gong L. Transcriptome Analysis Reveals Biosynthesis of Important Bioactive Constituents and Mechanism of Stem Formation of Dendrobium huoshanense. Scientific Reports. 10: 2857. PMID 32071345 DOI: 10.1038/s41598-020-59737-2   
2020 Shao M, Li W, Wang S, Liu Z. Identification of key genes and pathways associated with esophageal squamous cell carcinoma development based on weighted gene correlation network analysis. Journal of Cancer. 11: 1393-1402. PMID 32047546 DOI: 10.7150/jca.30699   
2020 Sanchez R, Mackenzie SA. Integrative Network Analysis of Differentially Methylated and Expressed Genes for Biomarker Identification in Leukemia. Scientific Reports. 10: 2123. PMID 32034170 DOI: 10.1038/s41598-020-58123-2   
2020 Pandelakis M, Delgado E, Ebrahimkhani MR. CRISPR-Based Synthetic Transcription Factors In Vivo: The Future of Therapeutic Cellular Programming. Cell Systems. 10: 1-14. PMID 31972154 DOI: 10.1016/j.cels.2019.10.003   
2020 Schachtschneider KM, Welge ME, Auvil LS, Chaki S, Rund LA, Madsen O, Elmore MRP, Johnson RW, Groenen MAM, Schook LB. Altered Hippocampal Epigenetic Regulation Underlying Reduced Cognitive Development in Response to Early Life Environmental Insults. Genes. 11. PMID 32033187 DOI: 10.3390/genes11020162   
2020 Li X, Zhang C, Xu X, Miao J, Yao J, Liu R, Zhao Y, Chen X, Yang Y. A single-component light sensor system allows highly tunable and direct activation of gene expression in bacterial cells. Nucleic Acids Research. PMID 31989175 DOI: 10.1093/nar/gkaa044   
2020 Ferrer-Bonsoms JA, Cassol I, Fernández-Acín P, Castilla C, Carazo F, Rubio A. ISOGO: Functional annotation of protein-coding splice variants. Scientific Reports. 10: 1069. PMID 31974522 DOI: 10.1038/s41598-020-57974-z