Hamid Bolouri - Related publications

Institute for Systems Biology, Seattle, WA, United States 
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Ben Guebila M, Lopes-Ramos CM, Weighill D, Sonawane AR, Burkholz R, Shamsaei B, Platig J, Glass K, Kuijjer ML, Quackenbush J. GRAND: a database of gene regulatory network models across human conditions. Nucleic Acids Research. PMID 34508353 DOI: 10.1093/nar/gkab778   
2021 Qi HX, Shen QD, Zhao HY, Qi GZ, Gao L. Network-based analysis revealed significant interactions between risk genes of severe COVID-19 and host genes interacted with SARS-CoV-2 proteins. Briefings in Bioinformatics. PMID 34535795 DOI: 10.1093/bib/bbab372   
2021 Cuesta-Astroz Y, Gischkow Rucatti G, Murgas L, SanMartín CD, Sanhueza M, Martin AJM. Filtering of Data-Driven Gene Regulatory Networks Using as a Case Study. Frontiers in Genetics. 12: 649764. PMID 34394179 DOI: 10.3389/fgene.2021.649764   
2021 Kwon MJ, Steiniger C, Cairns TC, Wisecaver JH, Lind AL, Pohl C, Regner C, Rokas A, Meyer V. Beyond the Biosynthetic Gene Cluster Paradigm: Genome-Wide Coexpression Networks Connect Clustered and Unclustered Transcription Factors to Secondary Metabolic Pathways. Microbiology Spectrum. e0089821. PMID 34523946 DOI: 10.1128/Spectrum.00898-21   
2021 Pio G, Mignone P, Magazzù G, Zampieri G, Ceci M, Angione C. Integrating genome-scale metabolic modelling and transfer learning for human gene regulatory network reconstruction. Bioinformatics (Oxford, England). PMID 34499112 DOI: 10.1093/bioinformatics/btab647   
2021 Saha S, Soliman A, Rajasekaran S. A Novel Pathway Network Analytics Method Based on Graph Theory. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 34448623 DOI: 10.1089/cmb.2021.0257   
2021 Azim R, Wang S. Cell-specific gene association network construction from single-cell RNA sequence. Cell Cycle (Georgetown, Tex.). 1-16. PMID 34530677 DOI: 10.1080/15384101.2021.1978265   
2021 Zhang Q, Li K, Yang Y, Li B, Jiang L, He X, Jin Y, Zhao G. Transcriptional differentiation driving Cucumis sativus-Botrytis cinerea interactions based on the Skellam model and Bayesian networks. Amb Express. 11: 138. PMID 34669064 DOI: 10.1186/s13568-021-01296-4   
2021 Zhou C, Guo H, Cao S. Gene Network Analysis of Alzheimer's Disease Based on Network and Statistical Methods. Entropy (Basel, Switzerland). 23. PMID 34682089 DOI: 10.3390/e23101365   
2021 Goszczynski DE, Tinetti PS, Choi YH, Hinrichs K, Ross PJ. Genome activation in equine in vitro-produced embryos. Biology of Reproduction. PMID 34515744 DOI: 10.1093/biolre/ioab173   
2021 Meiler A, Marchiano F, Haering M, Weitkunat M, Schnorrer F, Habermann BH. AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators. Scientific Reports. 11: 15463. PMID 34326396 DOI: 10.1038/s41598-021-94805-1   
2021 Kim DS, Risca VI, Reynolds DL, Chappell J, Rubin AJ, Jung N, Donohue LKH, Lopez-Pajares V, Kathiria A, Shi M, Zhao Z, Deep H, Sharmin M, Rao D, Lin S, et al. The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation. Nature Genetics. PMID 34650237 DOI: 10.1038/s41588-021-00947-3   
2021 Liu X, Tang N, Xu F, Chen Z, Zhang X, Ye J, Liao Y, Zhang W, Kim SU, Wu P, Cao Z. SMRT and Illumina RNA sequencing reveal the complexity of terpenoid biosynthesis in Zanthoxylum armatum. Tree Physiology. PMID 34448876 DOI: 10.1093/treephys/tpab114   
2021 Dou Z, Ma X. Inferring Functional Epigenetic Modules by Integrative Analysis of Multiple Heterogeneous Networks. Frontiers in Genetics. 12: 706952. PMID 34504516 DOI: 10.3389/fgene.2021.706952   
2021 Han Y, Hou Z, He Q, Zhang X, Yan K, Han R, Liang Z. Genome-Wide Characterization and Expression Analysis of Gene Family Under Abiotic Stress in . Frontiers in Genetics. 12: 754237. PMID 34675967 DOI: 10.3389/fgene.2021.754237   
2021 Gaudet P, Logie C, Lovering RC, Kuiper M, Lægreid A, Thomas PD. Gene Ontology representation for transcription factor functions. Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms. 194752. PMID 34461313 DOI: 10.1016/j.bbagrm.2021.194752   
2021 Duveau F, Vande Zande P, Metzger BP, Diaz CJ, Walker EA, Tryban S, Siddiq MA, Yang B, Wittkopp PJ. Mutational sources of -regulatory variation affecting gene expression in . Elife. 10. PMID 34463616 DOI: 10.7554/eLife.67806   
2021 Briggs P, Hunter AL, Yang SH, Sharrocks AD, Iqbal M. PEGS: An efficient tool for gene set enrichment within defined sets of genomic intervals. F1000research. 10: 570. PMID 34504687 DOI: 10.12688/f1000research.53926.1   
2021 Ahmed FF, Hossen MI, Sarkar MAR, Konak JN, Zohra FT, Shoyeb M, Mondal S. Genome-wide identification of DCL, AGO and RDR gene families and their associated functional regulatory elements analyses in banana (Musa acuminata). Plos One. 16: e0256873. PMID 34473743 DOI: 10.1371/journal.pone.0256873   
2021 Choi W, Lee H. Identifying disease-gene associations using a convolutional neural network-based model by embedding a biological knowledge graph with entity descriptions. Plos One. 16: e0258626. PMID 34653225 DOI: 10.1371/journal.pone.0258626   
2021 He S, Wang H, Hao X, Wu Y, Bian X, Yin M, Zhang Y, Fan W, Dai H, Yuan L, Zhang P, Chen L. Dynamic network biomarker analysis discovers IbNAC083 in initiation and regulation of sweet potato root tuberization. The Plant Journal : For Cell and Molecular Biology. PMID 34460981 DOI: 10.1111/tpj.15478   
2021 Yu CY, Mitrofanova A. Mechanism-Centric Approaches for Biomarker Detection and Precision Therapeutics in Cancer. Frontiers in Genetics. 12: 687813. PMID 34408770 DOI: 10.3389/fgene.2021.687813   
2021 Liu K, Chen S, Lu R. Identification of Important Genes Related to Ferroptosis and Hypoxia in Acute Myocardial Infarction Based on WGCNA. Bioengineered. PMID 34565282 DOI: 10.1080/21655979.2021.1984004   
2021 Wei L, He F, Zhang W, Chen W, Yu B. Analysis of master transcription factors related to Parkinson's disease through the gene transcription regulatory network. Archives of Medical Science : Ams. 17: 1184-1190. PMID 34522247 DOI: 10.5114/aoms.2019.89460   
2021 Thomas AL, Marsman J, Antony J, Schierding W, O'Sullivan JM, Horsfield JA. Transcriptional Regulation of : An Informatics Analysis. Genes. 12. PMID 34440349 DOI: 10.3390/genes12081175   
2021 Minadakis G, Muñoz-Pomer Fuentes A, Tsouloupas G, Papatheodorou I, Spyrou GM. PathExNET: A tool for extracting pathway expression networks from gene expression statistics. Computational and Structural Biotechnology Journal. 19: 4336-4344. PMID 34429851 DOI: 10.1016/j.csbj.2021.07.033   
2021 Karami H, Derakhshani A, Ghasemigol M, Fereidouni M, Miri-Moghaddam E, Baradaran B, Tabrizi NJ, Najafi S, Solimando AG, Marsh LM, Silvestris N, De Summa S, Paradiso AV, Racanelli V, Safarpour H. Weighted Gene Co-Expression Network Analysis Combined with Machine Learning Validation to Identify Key Modules and Hub Genes Associated with SARS-CoV-2 Infection. Journal of Clinical Medicine. 10. PMID 34441862 DOI: 10.3390/jcm10163567   
2021 Wu J, Fang X, Xia X. Identification of Key Genes and Pathways associated with Endometriosis by Weighted Gene Co-expression Network Analysis. International Journal of Medical Sciences. 18: 3425-3436. PMID 34522169 DOI: 10.7150/ijms.63541   
2021 Xia S, Ventura IM, Blaha A, Sgromo A, Han S, Izaurralde E, Long M. Rapid Gene evolution in an ancient post-transcriptional and translational regulatory system compensates for meiotic X chromosomal inactivation. Molecular Biology and Evolution. PMID 34626117 DOI: 10.1093/molbev/msab296   
2021 Liu J, He Z, Li S, Huang W, Ren Z. Network Pharmacology-Based Analysis of the Effects of (Thunb.) Pers. in Non-Small Cell Lung Cancer. Evidence-Based Complementary and Alternative Medicine : Ecam. 2021: 4341517. PMID 34497656 DOI: 10.1155/2021/4341517   
2021 Chung H, Parkhurst CN, Magee EM, Phillips D, Habibi E, Chen F, Yeung BZ, Waldman J, Artis D, Regev A. Joint single-cell measurements of nuclear proteins and RNA in vivo. Nature Methods. 18: 1204-1212. PMID 34608310 DOI: 10.1038/s41592-021-01278-1   
2021 Viswanathan R, Hartmann J, Pallares Cartes C, De Renzis S. Desensitisation of Notch signalling through dynamic adaptation in the nucleus. The Embo Journal. 40: e107245. PMID 34396565 DOI: 10.15252/embj.2020107245   
2021 Shi K, Zhu X, Wu J, Chen Y, Zhang J, Sun X. Centromere protein E as a novel biomarker and potential therapeutic target for retinoblastoma. Bioengineered. 12: 5950-5970. PMID 34482803 DOI: 10.1080/21655979.2021.1972080   
2021 Martínez-Pinteño A, Gassó P, Prohens L, Segura AG, Parellada M, Saiz-Ruiz J, Cuesta MJ, Bernardo M, Lafuente A, Mas S, Rodríguez N. Identification of as a Key Gene Involved in Antipsychotic-Induced Metabolic Dysregulation Based on Integrative Bioinformatics Analysis of Multi-Tissue Gene Expression Data. Frontiers in Pharmacology. 12: 729474. PMID 34483940 DOI: 10.3389/fphar.2021.729474   
2021 Lin Q, Munir A, Masood S, Hussain S, Naeem M, Fazal S. Gene expression profiling utilizing extremely sensitive CDNA arrays and enrichment-based network study of major bone cancer genes. Journal of Research in Medical Sciences : the Official Journal of Isfahan University of Medical Sciences. 26: 49. PMID 34484381 DOI: 10.4103/jrms.JRMS_592_20   
2021 Yang S, Fu Q, Deng H, Liu Z, Zhong J, Zhu X, Wang Q, Sun C, Wu J. Mechanisms and molecular targets of the Yu-Ping-Feng powder for allergic rhinitis, based on network pharmacology. Medicine. 100: e26929. PMID 34477124 DOI: 10.1097/MD.0000000000026929   
2021 Esmaeili S, Rostami-Nejad M, Rezaei-Tavirani M, Okhovatian F, Mehdi Zadeh-Esmaeel M, Razzagh Z, Ahmadzadeh A, Vafaee R. Evaluating of Gene Expression Alteration after Garlic Consumption, Analyzing through Bioinformatics Approach. Iranian Journal of Pharmaceutical Research : Ijpr. 20: 72-81. PMID 34400942 DOI: 10.22037/ijpr.2020.112409.13744   
2021 Wang Z, Masoomi A, Xu Z, Boueiz A, Lee S, Zhao T, Bowler R, Cho M, Silverman EK, Hersh C, Dy J, Castaldi PJ. Improved prediction of smoking status via isoform-aware RNA-seq deep learning models. Plos Computational Biology. 17: e1009433. PMID 34634029 DOI: 10.1371/journal.pcbi.1009433   
2021 Zhang C, Wang T, Cui T, Liu S, Zhang B, Li X, Tang J, Wang P, Guo Y, Wang Z. Genome-Wide Phylogenetic Analysis, Expression Pattern, and Transcriptional Regulatory Network of the Pig C/EBP Gene Family. Evolutionary Bioinformatics Online. 17: 11769343211041382. PMID 34471342 DOI: 10.1177/11769343211041382   
2021 Zogopoulos VL, Saxami G, Malatras A, Angelopoulou A, Jen CH, Duddy WJ, Daras G, Hatzopoulos P, Westhead DR, Michalopoulos I. Coexpression Tool: a tool for gene coexpression analysis in . Iscience. 24: 102848. PMID 34381973 DOI: 10.1016/j.isci.2021.102848   
2021 Lambert JT, Su-Feher L, Cichewicz K, Warren TL, Zdilar I, Wang Y, Lim KJ, Haigh JL, Morse SJ, Canales CP, Stradleigh TW, Castillo Palacios E, Haghani V, Moss SD, Parolini H, et al. Parallel functional testing identifies enhancers active in early postnatal mouse brain. Elife. 10. PMID 34605404 DOI: 10.7554/eLife.69479   
2021 Xia Y, Yang J, Ma L, Yan S, Pang Y. Genome-Wide Identification and Analyses of Drought/Salt-Responsive Cytochrome Genes in . International Journal of Molecular Sciences. 22. PMID 34576120 DOI: 10.3390/ijms22189957   
2021 Wang Y, Li Z, Yang G, Cai L, Yang F, Zhang Y, Zeng Y, Ma Q, Zeng F. The Study of Alternative Splicing Events in Human Induced Pluripotent Stem Cells From a Down's Syndrome Patient. Frontiers in Cell and Developmental Biology. 9: 661381. PMID 34660567 DOI: 10.3389/fcell.2021.661381   
2021 Ding W, Chim SSC, Wang CC, Lau CSL, Leung TY. Molecular Mechanism and Pathways of Normal Human Parturition in Different Gestational Tissues: A Systematic Review of Transcriptome Studies. Frontiers in Physiology. 12: 730030. PMID 34566691 DOI: 10.3389/fphys.2021.730030   
2021 Markus BM, Boydston EA, Lourido S. CRISPR-Mediated Transcriptional Repression in Toxoplasma gondii. Msphere. e0047421. PMID 34643425 DOI: 10.1128/mSphere.00474-21   
2021 Liu Y, Cui S, Sun J, Yan X, Han D. Identification of Potential Biomarkers for Psoriasis by DNA Methylation and Gene Expression Datasets. Frontiers in Genetics. 12: 722803. PMID 34512732 DOI: 10.3389/fgene.2021.722803   
2021 Luo J, Nvsvrot T, Wang N. Comparative transcriptomic analysis uncovers conserved pathways involved in adventitious root formation in poplar. Physiology and Molecular Biology of Plants : An International Journal of Functional Plant Biology. 27: 1903-1918. PMID 34629770 DOI: 10.1007/s12298-021-01054-7   
2021 Zhou M, Guo R, Wang YF, Yang W, Li R, Lu L. Application of Weighted Gene Coexpression Network Analysis to Identify Key Modules and Hub Genes in Systemic Juvenile Idiopathic Arthritis. Biomed Research International. 2021: 9957569. PMID 34435051 DOI: 10.1155/2021/9957569   
2021 Galfrè SG, Morandin F, Pietrosanto M, Cremisi F, Helmer-Citterich M. COTAN: scRNA-seq data analysis based on gene co-expression. Nar Genomics and Bioinformatics. 3: lqab072. PMID 34396096 DOI: 10.1093/nargab/lqab072   
2021 Chu EC, Morin A, Chang THC, Nguyen T, Tsai YC, Sharma A, Liu CC, Pavlidis P. Experiment level curation of transcriptional regulatory interactions in neurodevelopment. Plos Computational Biology. 17: e1009484. PMID 34665801 DOI: 10.1371/journal.pcbi.1009484