A5103066997- SARS-CoV-2 and COVID-19 Research
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Advanced biosensing and bioanalysis techniques
- MicroRNA in disease regulation
- Cancer-related molecular mechanisms research
- Viral Infections and Immunology Research
- RNA Research and Splicing
- Viral-associated cancers and disorders
- Genomic variations and chromosomal abnormalities
- Hepatitis C virus research
- Legionella and Acanthamoeba research
- Vibrio bacteria research studies
- Chronic Lymphocytic Leukemia Research
- Genomics and Chromatin Dynamics
- COVID-19 Clinical Research Studies
- Genomics and Phylogenetic Studies
- Bacterial biofilms and quorum sensing
- Nanopore and Nanochannel Transport Studies
- Biosensors and Analytical Detection
- CRISPR and Genetic Engineering
- Ion Transport and Channel Regulation
- Adipose Tissue and Metabolism
- SARS-CoV-2 detection and testing
- Chromosomal and Genetic Variations
Columbia University
2014-2024
New York Genome Center
2008-2022
SUNY Oneonta
2020
New York Proton Center
2014
USA Mitchell Cancer Institute
2010
Stony Brook University
2010
Columbia University Irving Medical Center
2001-2009
Rockefeller University
2004-2005
University of Basel
2004-2005
Memorial Sloan Kettering Cancer Center
2004-2005
RNA silencing processes are guided by small RNAs that derived from double-stranded RNA. To probe for function of during infection human cells a DNA virus, we recorded the profile infected Epstein-Barr virus (EBV). We show EBV expresses several microRNA (miRNA) genes. Given miRNAs in pathways either targeting messenger degradation or repressing translation, identified viral regulators host and/or gene expression.
The genome of the Kaposi sarcoma-associated herpesvirus (KSHV or HHV8) was mapped with cosmid and phage genomic libraries from BC-1 cell line. Its nucleotide sequence determined except for a 3-kb region at right end that refractory to cloning. KSHV consists 140.5-kb-long unique coding flanked by multiple G + C-rich 801-bp terminal repeat sequences. A duplication apparently arose in parental tumor is present this culture-derived strain. At least 81 ORFs, including 66 homology saimiri 5...
Recently identified hepatitis C virus (HCV) isolates that are infectious in cell culture provide a genetic system to evaluate the significance of virus-host interactions for HCV replication. We have completed systematic RNAi screen wherein siRNAs were designed target 62 host genes encoding proteins physically interact with RNA or belong cellular pathways thought modulate infection. This includes 10 we identify this study bind NS5A. 26 these alter production >3-fold. Included set Dicer,...
We present the genomic sequence of Legionella pneumophila, bacterial agent Legionnaires' disease, a potentially fatal pneumonia acquired from aerosolized contaminated fresh water. The genome includes 45-kilobase pair element that can exist in chromosomal and episomal forms, selective expansions important gene families, genes for unexpected metabolic pathways, previously unknown candidate virulence determinants. highlight may account Legionella's ability to survive protozoa, mammalian...
A new human herpesvirus was recently identified in all forms of Kaposi's sarcoma (Kaposi's sarcoma-associated [KSHV] or 8), as well primary effusion (body cavity-based) lymphomas (PELs). 12.3-kb-long KSHV clone obtained from a PEL genomic library. Sequencing this revealed extensive homology and colinearity with the right end saimiri (HVS) genome more limited to left Epstein-Barr virus genome. Four open reading frames (ORFs) were sequenced characterized; these are homologous following viral...
SARS-CoV-2 is responsible for the current COVID-19 pandemic. On basis of our analysis hepatitis C virus and coronavirus replication, molecular structures activities viral inhibitors, we previously demonstrated that three nucleotide analogues (the triphosphates Sofosbuvir, Alovudine, AZT) inhibit SARS-CoV RNA-dependent RNA polymerase (RdRp). We also a library additional terminate synthesis catalyzed by RdRp, well-established drug target COVID-19. Here, used extension experiments to...
MicroRNAs (miRNAs) represent a family of small, regulatory, noncoding RNAs that are found in plants and animals. Here, we describe the miRNA profile zebrafish Danio rerio resolved developmental cell-type-specific manner. The profiles were obtained from larger-scale sequencing small RNA libraries prepared developmentally staged zebrafish, two adult fibroblast cell lines derived caudal fin (ZFL) liver epithelium (SJD). We identified total 154 distinct miRNAs expressed 343 genes. Other...
We describe a comprehensive quantitative measure of the splicing impact complete set RNA 6-mer sequences by deep sequencing successfully spliced transcripts. All 4096 6-mers were substituted at five positions within two different internal exons in 3-exon minigene, and millions transcripts sequenced after transfection human cells. The results allowed assignment relative strength score to each mutant molecule. effect on often depended their location; much this context could be ascribed...
Abstract Deletions of the 13q14 chromosome region are associated with B-cell chronic lymphocytic leukemia (B-CLL) and several other types cancer, suggesting presence a tumor suppressor gene. In previous studies minimal deletion (MDR) was mapped to less than 300-kilobase (kb) interval bordered by markers 173a12-82 138G4/1.3R. For identification putative gene, entire MDR (approximately 347 kb) has been sequenced, transcribed regions have identified exon trapping, EST-based full-length...
DNA sequencing by synthesis (SBS) on a solid surface during polymerase reaction can decipher many sequences in parallel. We report here method that is hybrid between the Sanger dideoxynucleotide terminating and SBS. In this approach, four nucleotides, modified as reversible terminators capping 3'-OH with small moiety so they are still recognized substrates, combined cleavable fluorescent dideoxynucleotides to perform The ratio of two sets nucleotides adjusted extension cycles proceed....
The functions of non-coding microRNAs (miRNAs) in tumorigenesis are just beginning to emerge. Previous studies from our laboratory have identified a number miRNAs that were deregulated colon cancer cell lines due the deletion p53 tumor suppressor gene. In this study, vivo significance some these was further evaluated using colorectal clinical samples. Ten ( hsa-let-7b, hsa-let-7g, hsa-miR-15b, hsa-miR-181b, hsa-miR-191, hsa-miR-200c, hsa-miR-26a, hsa-miR-27a, hsa-miR-30a-5p and hsa-miR-30c)...
Significance Efficient cost-effective single-molecule sequencing platforms will facilitate deciphering complete genome sequences, determining haplotypes, and identifying alternatively spliced mRNAs. We demonstrate a nanopore-based by synthesis approach that accurately distinguishes four DNA bases electronically detecting differentiating different polymer tags attached to the terminal phosphate of nucleotides during their incorporation into growing strand in polymerase reaction. With nanopore...