Bioinformatics

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Dr. Vered Chalifa-Caspi
Head

The Bioinformatics Core unit provides customized data analysis services and consultation to scientists at BGU and all over Israel from both academia and industry. The aim of the facility is to help scientists advance their research using cutting edge bioinformatics methodologies. The main areas of expertise include the design and analysis of experiments that use genomic technologies (e.g., next-generation sequencing, mass spectrometry proteomics and metabolomics profiling, microarrays, and more), as well as mining and reanalysis of publicly available datasets. In addition, the facility develops software tools for automation of data analysis workflows (NeatSeq-Flow, Microbe-Flow).

De novo assembly and annotation of genomes and transcriptomes

Gene expression profiling (RNA-Seq, single cell RNA-Seq)

SNP discovery and genotyping from genome, exome and RAD-Seq sequencing

Protein-DNA interaction analysis (Chip-Seq)

Analysis of isolated bacteria and microbial communities

MAS-Spec proteomics and metabolomics profiling

Svetlitsky D., Dagan T., Chalifa-Caspi V. and Ziv-Ukelson M. (2018)
CBSFinder: Discovery of colinear syntenic blocks across thousands of prokaryotic genomes.
Bioinformatics, bty861, https://doi.org/10.1093/bioinformatics/bty861
Tayeh Z., Dudai N., Shachter A., Chalifa-Caspi V., Barak S. and Ofir R. (2018)
Molecular Mode of Action of AsteriscusGraveolens as an Anticancer Agent.
International Journal of Molecular Sciences 19(8):2162.
Sorek M., Schnyzer Y., Ben-Asher H.W., Chalifa-Caspi V., Chen C.S., Miller D.J. and Levy O. (2018)
Setting the pace: host rhythmic behaviour and gene expression patterns in the facultatively symbiotic cnidarian Aiptasiaare determined largely by Symbiodinium.
Microbiome 6:83.
Ziv T., Chalifa-Caspi V., Denekamp N., Plaschkes I., Kierszniowska S., Blais I., Admon A. and Lubzens E. (2017)
Dormancy in Embryos: Insight from Hydrated Encysted Embryos of an Aquatic Invertebrate.
Mol Cell Proteomics 16(10):1746-1769.
Gordon M., Yakunin E., Valinsky L., Chalifa-Caspi V., Moran-Gilad J. and Infections ESGfL (2017)
A bioinformatics tool for ensuring the backwards compatibility of Legionella pneumophila typing in the genomic era
Clin Microbiol Infect 23(5):306-310.