Ph.D.: Weizmann Institute of Science, Israel
Post-Doctorate: Weizmann Institute of Science, Israel
Position: Research Associate
Bioinformatics Core Facility – Head
Bioinformatics Core Facility
The NIBN Bioinformatics Core Facility was established in September 2003 with the aim of providing scientists with opportunities to significantly advance their research with cutting edge bioinformatics resources and methodologies.
To date, the Core Facility provides data analysis services, consultation and training to scientists all over Israel from both academia and industry. Our main areas of expertise include the analysis and re-analysis of data obtained from genomic technologies (e.g. Next Generation Sequencing, Mass spec proteomics profiling and DNA microarrays), as well as in mining biological databases, bioinformatics programming and biostatistics. In addition, assistance is provided in designing appropriate experiments using genomic technologies and in writing relevant sections in grant proposals.
Our team includes bioinformaticians and programmers with strong backgrounds in biology, bioinformatics and statistics, with much prior expertise in analyzing high-throughput genomic datasets. Our efforts are supported by the necessary hardware infrastructure, including 6-core HPC cluster nodes, access to additional 150 shared nodes with a total of 1600 cores and 1.2 Tb RAM, a web server and strong Windows workstations. Additionally, we have cutting-edge commercial software (CLC Genomics Workbench, Partek Genomics Suite, MetaCore data-mining and pathway analysis software and Blast2GO Pro for functional annotation of novel genomes) as well as the leading publicly available software in the field.
Details of our main areas of expertise and the services we provide are shown below.
Next Generation Sequencing (NGS) data analysis:
- de novo sequence assembly and annotation of novel genomes and transcriptomes
- Gene expression profiling (RNA-Seq)
- Protein-DNA and protein-RNA interaction analysis (Chip-Seq)
- Identification of epigenetic regulation sites such as methylation and histone acetylation
- Micro-RNA discovery and profiling
- Human, plant and livestock genetic analyses
- Comparative bacterial genome analyses and metagenomics
- Mining and reanalysis of NGS data from public databases
DNA microarray data analysis and meta-analysis:
- Differential gene expression analysis
- Genetic studies using SNP and CNV arrays
- Mining and reanalysis of microarray data from published studies
- Comparative analysis of multiple microarray experiments at the gene and pathway levels
Mass Spectrometry Proteomics profiling:
- Construction of a reference proteome
- Differential protein expression analysis
- Pathway and gene ontology enrichment analyses
Clinical data analysis:
- Biostatistics and statistical programming
- Machine learning
- Database development
Amir E.D., Bartal O., Morad E., Nagar T., Sheynin J., Parvari R. and Chalifa-Caspi V. (2010). KinSNP software for homozygosity mapping of disease genes using SNP microarrays. Hum Genomics 4(6):394-401.
Grafi G., Chalifa-Caspi V., Nagar T., Plaschkes I., Barak S. and Ransbotyn V. (2011). Plant response to stress meets dedifferentiation. Planta, 233(3):433-438.
Mazor M., Alkrinawi S., Chalifa-Caspi V., Manor E., Sheffield V.C., Aviram M. and Parvari R. (2011). Primary ciliary dyskinesia caused by homozygous mutation in DNAL1, encoding dynein light chain 1. Am. J. Hum. Genet. 88(5):599-607.
Ventura T., Manor R., Aflalo E.D., Chalifa-Caspi V., Weil S., Sharabi O. and Sagi A. (2013). Post-embryonic transcriptomes of the prawn Macrobrachium rosenbergii: multigenic succession through metamorphosis. PLoS One 8(1):e55322.
Bakshi S., Chalifa-Caspi V., Plaschkes I., Perevozkin I., Gurevich M. and Schwartz R. (2013). Gene expression analysis reveals functional pathways of glatiramer acetate activation. Expert Opin. Ther. Targets 17(4):351-362.
Toker L., Bersudsky Y., Plaschkes I., Chalifa-Caspi V., Berry G.T., Buccafusca R., Moechars D., Belmaker R.H. and Agam G. (2014). Inositol-Related Gene Knockouts Mimic Lithium's Effect on Mitochondrial Function. Neuropsychopharmacology 39(2):319-328.