Hooman Hefzi, Ph.D. - Related publications

Affiliations: 
2013-2018 Bioengineering University of California, San Diego, La Jolla, CA 
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Yilmaz LS, Li X, Nanda S, Fox B, Schroeder F, Walhout AJ. Modeling tissue-relevant Caenorhabditis elegans metabolism at network, pathway, reaction, and metabolite levels. Molecular Systems Biology. 16: e9649. PMID 33022146 DOI: 10.15252/msb.20209649   
2020 Zhao T, Lyu S, Lu G, Juan L, Zeng X, Wei Z, Hao J, Peng J. SC2disease: a manually curated database of single-cell transcriptome for human diseases. Nucleic Acids Research. PMID 33010177 DOI: 10.1093/nar/gkaa838   
2020 Tarbier M, Mackowiak SD, Frade J, Catuara-Solarz S, Biryukova I, Gelali E, Menéndez DB, Zapata L, Ossowski S, Bienko M, Gallant CJ, Friedländer MR. Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells. Nature Communications. 11: 5445. PMID 33116115 DOI: 10.1038/s41467-020-19011-5   
2020 Ayers MC, Sherman ZN, Gallagher JEG. Oxidative Stress Responses and Nutrient Starvation in MCHM Treated . G3 (Bethesda, Md.). PMID 33109726 DOI: 10.1534/g3.120.401661   
2020 Adlat S, Sah RK, Hayel F, Chen Y, Bah FB, Al-Azab M, Bahadar N, Myint M, Oo ZM, Nasser MI, Zhang L, Feng X, Zheng Y. Global transcriptome study of Dip2B-deficient mouse embryonic lung fibroblast reveals its important roles in cell proliferation and development. Computational and Structural Biotechnology Journal. 18: 2381-2390. PMID 33005301 DOI: 10.1016/j.csbj.2020.08.030   
2020 Fang L, Li Y, Ma L, Xu Q, Tan F, Chen G. GRNdb: decoding the gene regulatory networks in diverse human and mouse conditions. Nucleic Acids Research. PMID 33151298 DOI: 10.1093/nar/gkaa995   
2020 Anzai T, Imamura S, Ishihama A, Shimada T. Expanded roles of pyruvate-sensing PdhR in transcription regulation of the K-12 genome: fatty acid catabolism and cell motility. Microbial Genomics. PMID 32975502 DOI: 10.1099/mgen.0.000442   
2020 Men S, Yu Y. Prospects for Use of Single-Cell Sequencing to Assess DNA Methylation in Asthma. Medical Science Monitor : International Medical Journal of Experimental and Clinical Research. 26: e925514. PMID 33009362 DOI: 10.12659/MSM.925514   
2020 Sun Y, Yu Q, Li L, Mei Z, Zhou B, Liu S, Pan T, Wu L, Lei Y, Liu L, Drmanac R, Ma K, Liu S. Single-cell RNA profiling links ncRNAs to spatiotemporal gene expression during C. elegans embryogenesis. Scientific Reports. 10: 18863. PMID 33139759 DOI: 10.1038/s41598-020-75801-3   
2020 Keaveney MK, Rahsepar B, Tseng HA, Fernandez FR, Mount RA, Ta T, White JA, Berg J, Han X. CamKIIα Positive Interneurons Identified via A microRNA Based Viral Gene Targeting Strategy. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. PMID 33158963 DOI: 10.1523/JNEUROSCI.2570-19.2020   
2020 Modesto P, Fernandez JLC, Martini I, Zoccola R, Pugliano MC, Ciucis CG, Goria M, Ferrari A, Razzuoli E. Characterization of D-17 Canine Osteosarcoma Cell Line and Evaluation of Its Ability to Response to Infective Stressor Used as Alternative Anticancer Therapy. Animals : An Open Access Journal From Mdpi. 10. PMID 33126659 DOI: 10.3390/ani10111981   
2020 Yoo SM, Jung SW, Yeom J, Lee SY, Na D. Tunable Gene Expression System Independent of Downstream Coding Sequence. Acs Synthetic Biology. PMID 33124809 DOI: 10.1021/acssynbio.0c00029   
2020 Jing H, Chen Y, Liang W, Chen M, Qiu C, Guo MY. Effects of Selenium on MAC-T Cells in Bovine Mastitis: Transcriptome Analysis of Exosomal mRNA Interactions. Biological Trace Element Research. PMID 33098075 DOI: 10.1007/s12011-020-02439-7   
2020 Sharma S, Dincer C, Weidemüller P, Wright GJ, Petsalaki E. CEN-tools: an integrative platform to identify the contexts of essential genes. Molecular Systems Biology. 16: e9698. PMID 33073517 DOI: 10.15252/msb.20209698   
2020 Banaganapalli B, Mansour H, Mohammed A, Alharthi AM, Aljuaid NM, Nasser KK, Ahmad A, Saadah OI, Al-Aama JY, Elango R, Shaik NA. Exploring celiac disease candidate pathways by global gene expression profiling and gene network cluster analysis. Scientific Reports. 10: 16290. PMID 33004927 DOI: 10.1038/s41598-020-73288-6   
2020 Li J, Zhang C, Yuan X, Ren Z, Yu Z. Correlations between stemness indices for hepatocellular carcinoma, clinical characteristics, and prognosis. American Journal of Translational Research. 12: 5496-5510. PMID 33042433   
2020 Xu H, Wang J, Liang Y, Fu Y, Li S, Huang J, Xu H, Zou W, Chen B. TriTag: an integrative tool to correlate chromatin dynamics and gene expression in living cells. Nucleic Acids Research. PMID 33104788 DOI: 10.1093/nar/gkaa906   
2020 Ahmed M, Min DS, Kim DR. Curated gene expression dataset of differentiating 3T3-L1 adipocytes under pharmacological and genetic perturbations. Adipocyte. 9: 600-608. PMID 33016192 DOI: 10.1080/21623945.2020.1829852   
2020 Ma S, Zhang B, LaFave LM, Earl AS, Chiang Z, Hu Y, Ding J, Brack A, Kartha VK, Tay T, Law T, Lareau C, Hsu YC, Regev A, Buenrostro JD. Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin. Cell. PMID 33098772 DOI: 10.1016/j.cell.2020.09.056   
2020 Lu J, Huang XY, Wang YH, Xie JW, Wang JB, Lin JX, Chen QY, Cao LL, Li P, Huang CM, Zheng CH. POC1A acts as a promising prognostic biomarker associated with high tumor immune cell infiltration in gastric cancer. Aging. 12: 18982-19011. PMID 33052878 DOI: 10.18632/aging.103624   
2020 Eisenhut P, Mebrahtu A, Moradi Barzadd M, Thalén N, Klanert G, Weinguny M, Sandegren A, Su C, Hatton D, Borth N, Rockberg J. Systematic use of synthetic 5'-UTR RNA structures to tune protein translation improves yield and quality of complex proteins in mammalian cell factories. Nucleic Acids Research. PMID 33051690 DOI: 10.1093/nar/gkaa847   
2020 Tian R, Liu Y, Cao Y, Zhang Z, Li J, Liu L, Du G, Chen J. Titrating bacterial growth and chemical biosynthesis for efficient N-acetylglucosamine and N-acetylneuraminic acid bioproduction. Nature Communications. 11: 5078. PMID 33033266 DOI: 10.1038/s41467-020-18960-1   
2020 Qu Y, Jiang J, Yang X, Tang C. Protocol for Titrating Gene Expression Levels in Budding Yeast. Star Protocols. 1: 100082. PMID 33111115 DOI: 10.1016/j.xpro.2020.100082   
2020 Brown CY, Sadlon T, Hope CM, Wong YY, Wong S, Liu N, Withers H, Brown K, Bandara V, Gundsambuu B, Pederson S, Breen J, Robertson SA, Forrest A, Beyer M, et al. Molecular Insights Into Regulatory T-Cell Adaptation to Self, Environment, and Host Tissues: Plasticity or Loss of Function in Autoimmune Disease. Frontiers in Immunology. 11: 1269. PMID 33072063 DOI: 10.3389/fimmu.2020.01269   
2020 Song Y, Liu X, Wang F, Wang X, Cheng G, Peng C. Identification of Metastasis-Associated Biomarkers in Synovial Sarcoma Using Bioinformatics Analysis. Frontiers in Genetics. 11: 530892. PMID 33061942 DOI: 10.3389/fgene.2020.530892   
2020 Ziegler N, Bader E, Epanchintsev A, Margerie D, Kannt A, Schmoll D. AMPKβ1 and AMPKβ2 define an isoform-specific gene signature in human pluripotent stem cells, differentially mediating cardiac lineage specification. The Journal of Biological Chemistry. PMID 33067322 DOI: 10.1074/jbc.RA120.013990   
2020 Meng C, Kunliu, Lv Z, Zhang Y, Li J, Luo X, Qiang H, Li K, Liu F, Zhang B, Cui F. Inflammation and Immunity Gene Expression Profiling of Macrophages on Mineralized Collagen. Journal of Biomedical Materials Research. Part A. PMID 33089616 DOI: 10.1002/jbm.a.37124   
2020 Wu G, Xia P, Yan S, Chen D, Xie L, Fan G. Identification of unique long non-coding RNAs as putative biomarkers for chromophobe renal cell carcinoma. Personalized Medicine. PMID 33052074 DOI: 10.2217/pme-2020-0020   
2020 Borchert C, Herman A, Roth M, Brooks AC, Friedenberg SG. RNA sequencing of whole blood in dogs with primary immune-mediated hemolytic anemia (IMHA) reveals novel insights into disease pathogenesis. Plos One. 15: e0240975. PMID 33091028 DOI: 10.1371/journal.pone.0240975   
2020 Qi M, Wu Q, Liu T, Hou Y, Miao Y, Hu M, Liu Q. Hepatopancreas Transcriptome Profiling Analysis Reveals Physiological Responses to Acute Hypoxia and Reoxygenation in Juvenile Qingtian Paddy Field Carp . Frontiers in Physiology. 11: 1110. PMID 33041847 DOI: 10.3389/fphys.2020.01110   
2020 Polkoff KM, Chung J, Simpson SG, Gleason K, Piedrahita JA. Validation of Transgene Expression in Gene-Edited Pigs Using CRISPR Transcriptional Activators. The Crispr Journal. 3: 409-418. PMID 33095051 DOI: 10.1089/crispr.2020.0037   
2020 Bryja A, Sujka-Kordowska P, Konwerska A, Ciesiółka S, Wieczorkiewicz M, Bukowska D, Antosik P, Bryl R, Skowroński MT, Jaśkowski JM, Mozdziak P, Angelova Volponi A, Shibli JA, Kempisty B, Dyszkiewicz-Konwińska M. New Gene Markers Involved in Molecular Processes of Tissue Repair, Response to Wounding and Regeneration Are Differently Expressed in Fibroblasts from Porcine Oral Mucosa during Long-Term Primary Culture. Animals : An Open Access Journal From Mdpi. 10. PMID 33105567 DOI: 10.3390/ani10111938   
2020 Alexandre PA, Hudson NJ, Lehnert SA, Fortes MRS, Naval-Sánchez M, Nguyen LT, Porto-Neto LR, Reverter A. Genome-Wide Co-Expression Distributions as a Metric to Prioritize Genes of Functional Importance. Genes. 11. PMID 33092259 DOI: 10.3390/genes11101231   
2020 Wang HF, Warrier T, Farran CA, Zheng ZH, Xing QR, Fullwood MJ, Zhang LF, Li H, Xu J, Lim TM, Loh YH. Defining Essential Enhancers for Pluripotent Stem Cells Using a Features-Oriented CRISPR-Cas9 Screen. Cell Reports. 33: 108309. PMID 33113365 DOI: 10.1016/j.celrep.2020.108309   
2020 Zhu Y, Berkowitz O, Selinski J, Hartmann A, Narsai R, Wang Y, Mao P, Whelan J. Conserved and Opposite Transcriptome Patterns during Germination in and . International Journal of Molecular Sciences. 21. PMID 33036486 DOI: 10.3390/ijms21197404   
2020 Gravett AM, Dennis JL, Dalgleish AG, Copier J, Liu WM. The efficacy of chemotherapeutic drug combinations may be predicted by concordance of gene response to the single agents. Oncology Letters. 20: 321. PMID 33093925 DOI: 10.3892/ol.2020.12184   
2020 Summers DK, Perry DS, Rao B, Madhani HD. Coordinate genomic association of transcription factors controlled by an imported quorum sensing peptide in Cryptococcus neoformans. Plos Genetics. 16: e1008744. PMID 32956370 DOI: 10.1371/journal.pgen.1008744   
2020 Gómez-Saldivar G, Osuna-Luque J, Semple JI, Glauser DA, Jarriault S, Meister P. Tissue-Specific Transcription Footprinting Using NoI Dam (RAPID) in . Genetics. PMID 33037050 DOI: 10.1534/genetics.120.303774   
2020 Li L, Zhu M, Huang H, Wu J, Meng D. Identification of Hub Genes in Anaplastic Thyroid Carcinoma: Evidence From Bioinformatics Analysis. Technology in Cancer Research & Treatment. 19: 1533033820962135. PMID 33025856 DOI: 10.1177/1533033820962135   
2020 Xia K, Han C, Xu J, Liang X. Transcriptome response of Acetobacter pasteurianus Ab3 to high acetic acid stress during vinegar production. Applied Microbiology and Biotechnology. PMID 33156446 DOI: 10.1007/s00253-020-10995-0   
2020 Mason CC, Fiol CR, Baker MJ, Nadal-Melsio E, Yebra-Fernandez E, Bicalho L, Chowdhury A, Albert M, Reid AG, Claudiani S, Apperley JF, Khorashad JS. Identification of genetic targets in acute myeloid leukaemia for designing targeted therapy. British Journal of Haematology. PMID 33022753 DOI: 10.1111/bjh.17129   
2020 Ruan X, Li P, Ma Y, Jiang C, Chen Y, Shi Y, Gupta N, Seifuddin F, Pirooznia M, Ohnishi Y, Yoneda N, Nishiwaki M, Dumbovic G, Rinn JL, Higuchi Y, et al. Identification of human long non-coding RNAs associated with nonalcoholic fatty liver disease and metabolic homeostasis. The Journal of Clinical Investigation. PMID 33048844 DOI: 10.1172/JCI136336   
2020 de Souza-Guerreiro TC, Meng X, Dacheux E, Firczuk H, McCarthy J. Translational control of gene expression noise and its relationship to ageing in yeast. The Febs Journal. PMID 33090724 DOI: 10.1111/febs.15594   
2020 Kim J, T Jakobsen S, Natarajan KN, Won KJ. TENET: gene network reconstruction using transfer entropy reveals key regulatory factors from single cell transcriptomic data. Nucleic Acids Research. PMID 33170214 DOI: 10.1093/nar/gkaa1014   
2020 Dai H, Jin QQ, Li L, Chen LN. Reconstructing gene regulatory networks in single-cell transcriptomic data analysis. Zoological Research. 1-6. PMID 33124218 DOI: 10.24272/j.issn.2095-8137.2020.215   
2020 Tirloni L, Braz G, Nunes RD, Gandara ACP, Vieira LR, Assumpcao TC, Sabadin GA, da Silva RM, Guizzo MG, Machado JA, Costa EP, Santos D, Gomes HF, Moraes J, Dos Santos Mota MB, et al. A physiologic overview of the organ-specific transcriptome of the cattle tick Rhipicephalus microplus. Scientific Reports. 10: 18296. PMID 33106528 DOI: 10.1038/s41598-020-75341-w   
2020 Jasenosky LD, Nambu A, Tsytsykova AV, Ranjbar S, Haridas V, Kruidenier L, Tough DF, Goldfeld AE. Identification of a Distal Locus Enhancer Element That Controls Cell Type-Specific and Gene Expression in Human T Cells. Journal of Immunology (Baltimore, Md. : 1950). PMID 32978279 DOI: 10.4049/jimmunol.1901311   
2020 Xie J, Wu Z, Xu X, Liang G, Xu J. Screening and identification of key genes and pathways in metastatic uveal melanoma based on gene expression using bioinformatic analysis. Medicine. 99: e22974. PMID 33120861 DOI: 10.1097/MD.0000000000022974   
2020 Yan J, Shu M, Li X, Yu H, Chen S, Xie S. Prognostic Score-based Clinical Factors and Metabolism-related Biomarkers for Predicting the Progression of Hepatocellular Carcinoma. Evolutionary Bioinformatics Online. 16: 1176934320951571. PMID 33013158 DOI: 10.1177/1176934320951571   
2020 Bui TT, Lee D, Selvarajoo K. ScatLay: utilizing transcriptome-wide noise for identifying and visualizing differentially expressed genes. Scientific Reports. 10: 17483. PMID 33060728 DOI: 10.1038/s41598-020-74564-1