Methods in Molecular Biology

Become Competent in Generating RNA-Seq Heat Maps in One Day for Novices Without Prior R Experience.  2239:269-303. 2021

Biological Network Mining.  2328:139-151. 2021

Dynamic Regulatory Event Mining by iDREM in Large-Scale Multi-omics Datasets During Biotic and Abiotic Stress in Plants.  2328:191-202. 2021

Efficient protocols for fabricating a large human cardiac muscle patch from human induced pluripotent stem cells.  2158:187-197. 2021

Evaluating Reprogramming Efficiency and Pluripotency of the Established Human iPSCS by Pluripotency Markers.  2239:235-249. 2021

Inference of Gene Regulatory Network from Single-Cell Transcriptomic Data Using pySCENIC.  2328:171-182. 2021

Isolation of Nucleoli for Characterization of Nucleolar Contents to Uncover Clues to Metastatic Progression.  2294:269-274. 2021

Mito-SinCe² Approach to Analyze Mitochondrial Structure–Function Relationship in Single Cells.  2275:415-432. 2021

Recent Approaches and Strategies in the Generation of Anti-human Cytomegalovirus Vaccines.  2244:403-463. 2021

Reprogramming Human Fibroblasts to Induced Pluripotent Stem Cells Using the GFP-Marked Lentiviral Vectors in the Chemically Defined Medium.  2239:101-116. 2021

Assays for neuronal defects caused by early formation of α-synuclein inclusions in primary cultured neurons.  1948:1-14. 2019

Dot blot analysis for measuring global n⁶-methyladenosine modification of RNA.  1870:263-271. 2019

Fractionation of subcellular compartments from human brain tissue.  1941:201-223. 2019

Functional characterization of apolipoproteins in the HCV life cycle.  1911:235-246. 2019

Generation of suicide gene-modified chimeric antigen receptor-redirected T-cells for cancer immunotherapy.  1895:57-73. 2019

In Vitro Adhesion, Invasion, and Transcytosis of Streptococcus pneumoniae with Host Cells.  1968:137-146. 2019

NADPH oxidases and aging models of lung fibrosis.  1982:487-496. 2019

Rna modification regulatory genes in DNA damage.  1870:249-262. 2019

SubILM injection of AAV for gene delivery to the retina.  1950:249-262. 2019

Structural variant breakpoint detection with novoBreak.  1833:129-141. 2018

Tertiary Lymphoid Structures Among the World of Noncanonical Ectopic Lymphoid Organizations.  1845:1-15. 2018

Assessment of MiRNA regulation of endothelial progenitor cell mediated angiogenesis.  1553:305-314. 2017

Large-scale RNA interference screening to identify transcriptional regulators of a tumor suppressor gene.  1507:261-268. 2017

Mapping protein-protein interaction using high-throughput yeast 2-hybrid.  1610:217-230. 2017

Transcriptional analysis-based integrative genomics approach to identify tumor-promoting metabolic genes.  1507:269-276. 2017

Animal cap assay for TGF-β Signaling.  1344:261-274. 2016

Expression of epitope-tagged proteins in mammalian cells in culture.  1474:3-24. 2016

Factors affecting the use of human tissues in biomedical research: Implications in the design and operation of a biorepository.  1381:1-38. 2016

High-throughput humanized mouse models for evaluation of HIV-1 therapeutics and pathogenesis.  1354:221-235. 2016

Characterization of intracellular aggresomes by fluorescent microscopy.  1258:307-317. 2015

Fabrication of a myocardial patch with cells differentiated from human-induced pluripotent stem cells.  1299:103-114. 2015

Identification of follicular T helper cells in tissue sections.  1291:13-25. 2015

In vitro and in vivo assays for studying histone ubiquitination and deubiquitination.  1288:213-230. 2015

Purification of active RNA polymerase I from yeast.  1276:281-289. 2015

Robust HPV-18 production in organotypic cultures of primary human keratinocytes.  1249:93-109. 2015

Structure and function of macroalgal natural products.  1308:39-73. 2015

iCaspase 9 suicide gene system.  1317:87-105. 2015

A user’s guide to the ribosomal DNA in Saccharomyces cerevisiae.  1205:303-328. 2014

History of electrophysiology and the patch clamp.  1183:1-19. 2014

Identification and use of fluorescent dyes for plant cell wall imaging using high-throughput screening.  1056:103-109. 2014

In vitro investigation of the roles of the proinflammatory cytokines tumor necrosis factor-α and interleukin-1 in murine osteoclastogenesis..  1155:109-123. 2014

Monitoring side-chain dynamics of proteins using ²H relaxation.  1084:3-27. 2014

Monitoring side-chain dynamics of proteins using²H relaxation.  1084:3-27. 2014

Optimal handling of bone tumor specimens.  1180:353-368. 2014

Phenomic assessment of genetic buffering by kinetic analysis of cell arrays.  1205:187-208. 2014

Recent approaches and strategies in the generation of antihuman cytomegalovirus vaccines.  1119:311-348. 2014

Reduced representation bisulfite sequencing to identify global alteration of DNA methylation.  1176:23-31. 2014

Reduced representation bisulfite sequencing to identify global alteration of DNA methylation..  1176:23-31. 2014

Isolation of murine postnatal brain microglia for phenotypic characterization using magnetic cell separation technology.  1041:33-39. 2013

Assessment of mitochondrial damage in retinal cells and tissues using quantitative polymerase chain reaction for mitochondrial DNA damage and extracellular flux assay for mitochondrial respiration activity.  935:227-243. 2013

Analysis of biomarkers of caloric restriction in aging cells.  1048:19-29. 2013

Cell senescence culturing methods.  1048:1-10. 2013

Chemokine-dependent signaling pathways in the peripheral nervous system.  1013:17-30. 2013

Genome-wide RNAi screening to identify regulators of oncogene-induced cellular senescence.  965:373-382. 2013

Induction of cellular senescence by oncogenic RAS.  1048:127-133. 2013

Structural and biochemical analysis of a bacterial glycosyltransferase.  1022:29-39. 2013

Use of the cockroach antigen model of acute asthma to determine the ammunomodulatory role of early exposure to gastrointestinal infection.  1032:271-286. 2013

Influenza virus titration, antigenic characterization, and serological Mmethods for antibody detection.  865:25-51. 2012

Protocol for analyzing human leukocyte antigen variants and sexually transmitted infections: From genotyping to immunoassays.  903:359-380. 2012

Dissociated cell culture for testing effects of carbon nanotubes on neuronal growth.  846:261-276. 2012

Cell culturing of Caenorhabditis elegans glial cells for the assessment of cytosolic Ca ²⁺ dynamics.  814:153-174. 2012

ELISA methodology to quantify astrocyte production of cytokines/chemokines in vitro.  814:235-249. 2012

Quantitative analysis of transcription elongation by RNA polymerase i in vitro.  809:579-591. 2012

Chromatin immunoprecipitation to characterize the epigenetic profiles of imprinted domains.  925:159-172. 2012

Chromatin immunoprecipitation to characterize the epigenetic profiles of imprinted domains..  925:159-172. 2012

Dynamic light scattering to study allosteric regulation.  796:175-186. 2012

In vitro biochemical assays to monitor rhodopsin function.  884:167-181. 2012

In vitro biochemical assays to monitor rhodopsin function.  884:167-181. 2012

Measuring rodent electroretinograms to assess retinal function.  884:265-276. 2012

Measuring rodent electroretinograms to assess retinal function.  884:265-276. 2012

Multiparameter flow cytometry and bioanalytics for B cell profiling in systemic lupus erythematosus.  900:109-134. 2012

Adeno-associated virus mediated gene therapy for retinal degenerative diseases.  807:179-218. 2011

Methylated-CpG Island recovery assay.  791:125-133. 2011

Advances in epigenetic technology.  791:1-10. 2011

Combined chromatin immunoprecipitation and bisulfite methylation sequencing analysis.  791:239-251. 2011

DNA methylation detection: Bisulfite genomic sequencing analysis.  791:11-21. 2011

Modeling dopamine neuron degeneration in caenorhabditis elegans.  793:129-148. 2011

Nasal potential difference measurements to assess CFTR ion channel activity..  741:69-86. 2011

Data mining methods in Omics-based biomarker discovery..  719:511-526. 2011

Contemporary approaches to Alzheimer's disease and frontotemporal dementia..  670:1-9. 2011

Quantifying biomarkers of cognitive dysfunction and neuronal network hyperexcitability in mouse models of Alzheimer's disease: depletion of calcium-dependent proteins and inhibitory hippocampal remodeling..  670:245-262. 2011

Contemporary approaches to Alzheimer's disease and frontotemporal dementia.  670:1-9. 2011

Determination of s-nitrosothiols in biological fluids by chemiluminescence..  704:27-37. 2011

Quantifying biomarkers of cognitive dysfunction and neuronal network hyperexcitability in mouse models of Alzheimer's disease: Depletion of calcium-dependent proteins and inhibitory hippocampal remodeling.  670:245-262. 2011

Step-by-step in situ hybridization method for localizing gene expression changes in the brain.  670:207-230. 2011

Study of GPCR-protein interactions using gel overlay assays and glutathione-S-transferase-fusion protein pull-downs.  746:347-355. 2011

Subnuclear localization and intranuclear trafficking of transcription factors..  647:77-93. 2010

Transient expression of epitope-tagged proteins in mammalian cells.  657:43-61. 2010

Gene therapy to improve migration of T cells to the tumor site..  651:103-118. 2010

Assessment of antioxidant activity of eugenol in vitro and in vivo..  610:165-180. 2010

Measurement of plasma nitrite by chemiluminescence..  610:41-49. 2010

Organizational issues in providing high-quality human tissues and clinical information for the support of biomedical research..  576:1-30. 2010

Sequencing of the rat genome and databases..  597:33-53. 2010

Subnuclear localization and intranuclear trafficking of transcription factors.  647:77-93. 2010

Construction of unmarked deletion mutants in mycobacteria..  465:279-295. 2009

Generation of parasite antigens for use in toll-like receptor research.  517:401-413. 2009

Microarray analysis of DNA replication timing.  556:191-203. 2009

Mitochondrial DNA polymorphism and risk of cancer.  471:291-303. 2009

Mucosal antibody responses to HIV.  485:333-345. 2009

Blue native-gel electrophoresis proteomics..  519:241-258. 2009

Connecting protein interaction data, mutations, and disease using bioinformatics..  541:449-461. 2009

Histochemistry and lipid profiling combine for insights into aging and age-related maculopathy..  580:267-281. 2009

Imaging systems for westerns: chemiluminescence vs. infrared detection..  536:499-513. 2009

In vitro and in vivo assays for studying histone ubiquitination and deubiquitination..  523:295-309. 2009

Proteomics study of the hepatitis C virus replication complex..  510:185-193. 2009

Chromatin immunoprecipitation assays: application of ChIP-on-chip for defining dynamic transcriptional mechanisms in bone cells..  455:165-176. 2008

In situ nuclear organization of regulatory machinery..  455:239-259. 2008

Proteomic approaches to identify and characterize alterations to the mitochondrial proteome in alcoholic liver disease..  447:369-380. 2008

Chromatin immunoprecipitation assays: Application of chip-on-chip for defining dynamic transcriptional mechanisms in bone cells.  455:165-176. 2008

Construction of unmarked deletion mutants in mycobacteria.  465:279-295. 2008

In situ nuclear organization of regulatory machinery.  455:239-259. 2008

Proteomic approaches to identify and characterize alterations to the mitochondrial proteome in alcoholic liver disease.  447:369-380. 2008

2D gel proteomics: An approach to study age-related differences in protein abundance or isoform complexity in biological samples.  371:349-391. 2007

A method to detect DNA methyltransferase I gene transcription in vitro in aging systems.  371:73-80. 2007

A method to study the expression of DNA methyltransferases in aging systems in vitro.  371:81-87. 2007

Aging cell culture: Methods and observations.  371:9-19. 2007

Mapping genetic polymorphisms affecting natural variation in Drosophila longevity.  371:307-320. 2007

Methods for nutrigenomics and longevity studies in Drosophila effects of diets high in sucrose, palmitic acid, soy, or beef.  371:111-141. 2007

Quantitative trait locus (QTL) mapping in aging systems.  371:321-348. 2007

Techniques for analysis of biological aging.  371:1-7. 2007

Integrated high-resolution genome-wide analysis of gene dosage and gene expression in human brain tumors.  377:187-202. 2007

Interpreting microarray results with gene ontology and MeSH.  377:223-241. 2007

2D gel proteomics: an approach to study age-related differences in protein abundance or isoform complexity in biological samples..  371:349-391. 2007

Characterization of cis-regulatory elements and transcription factor binding: gel mobility shift assay..  366:183-201. 2007

Integrated high-resolution genome-wide analysis of gene dosage and gene expression in human brain tumors..  377:187-202. 2007

Interpreting microarray results with gene ontology and MeSH..  377:223-242. 2007

Methods of telomerase inhibition..  405:1-7. 2007

Microarray analysis..  404:409-430. 2007

Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS)..  408:153-169. 2007

Protein crystallization..  383:337-349. 2007

Quantitative trait locus (QTL) mapping in aging systems..  371:321-348. 2007

RNA interference using a plasmid construct expressing short-hairpin RNA..  405:31-37. 2007

Retrovirus-mediated RNA interference. Targeting hTERT through stable expression of short-hairpin RNA..  405:39-46. 2007

hTERT knockdown in human embryonic kidney cells using double-stranded RNA..  405:23-29. 2007

Detection of an mRNA polymorphism by differential display..  317:279-285. 2006

Simultaneous in situ detection of RNA, DNA, and protein using tyramide-coupled immunofluorescence..  292:215-230. 2005

Analysis of in vivo gene expression using epitope-tagged proteins..  285:37-40. 2004

Assembly of DNA sequencing data..  255:319-332. 2004

Chromatin immunoprecipitation..  285:41-44. 2004

Crystallization of cytokine-receptor complexes..  249:81-92. 2004

Delivery of DNA to tumor cells in vivo using adeno-associated virus..  246:237-243. 2004

Immunofluorescence analysis using epitope-tagged proteins: in vitro system..  285:33-36. 2004

In situ immunofluorescence analysis: analyzing RNA synthesis by 5-bromouridine-5'-triphosphate labeling..  285:29-31. 2004

In situ immunofluorescence analysis: immunofluorescence microscopy..  285:23-28. 2004

Localization of epithelial sodium channels by atomic force microscopy..  242:281-289. 2004

Methods of epigenetic analysis..  287:1-8. 2004

Profiling DNA methylation by bisulfite genomic sequencing: problems and solutions..  287:169-179. 2004

Protein-deoxyribonucleic acid interactions linked to gene expression: DNase I digestion..  285:57-62. 2004

Protein-deoxyribonucleic acid interactions linked to gene expression: electrophoretic mobility shift assay..  285:45-55. 2004

Protein-deoxyribonucleic acid interactions linked to gene expression: ligation-mediated polymerase chain reaction..  285:63-67. 2004

Quality assessment of finished BAC sequences..  255:343-349. 2004

Sequence finishing..  255:333-342. 2004

Study of G-protein-coupled receptor-protein interactions using gel overlay assays and glutathione-S-transferase-fusion protein pull-downs..  259:371-378. 2004

Analysis of gene promoter regulation by tumor suppressor genes..  223:101-116. 2003

Chemical transformation of E. coli..  235:49-53. 2003

Ligase chain reaction..  226:135-150. 2003

Preparation of single-stranded DNA from phagemid vectors..  235:103-106. 2003

Purification of porins from Mycobacterium smegmatis..  228:139-150. 2003

Centriole duplication, centrosome maturation and spindle assembly in lysates of Spisula solidissima oocytes..  161:215-228. 2001

Drug-DNA interactions..  95:161-169. 2001

Drug-induced stabilization of covalent DNA topoisomerase I-DNA intermediates. DNA cleavage assays..  95:291-301. 2001

Finding genes in genomic nucleotide sequences by using bioinformatics..  175:235-247. 2001

Prediction of protein structure and function by using bioinformatics..  175:341-375. 2001

Regulatory roles of syndecans in cell adhesion and invasion..  171:495-503. 2001

Studying DNA topoisomerase I-targeted drugs in the yeast. Saccharomyces cerevisiae..  95:303-313. 2001

Application of adenoviral vectors. Analysis of eye development..  135:525-535. 2000

Introduction to DNA topoisomerases..  94:1-8. 1999

Overexpression and purification of DNA topoisomerase I from yeast..  94:179-186. 1999

Resolution of DNA molecules by one-dimensional agarose-gel electrophoresis..  94:9-17. 1999

Making and working with peroxynitrite..  100:215-230. 1998

Yeast plasmids..  62:113-130. 1997

Identification of Alternatively Spliced mRNAs and Localization of 5' Ends by Polymerase Chain Reaction Amplification..  15:189-198. 1993