CURRICULUM VITAE

Vered Chalifa-Caspi, Ph.D.

Bioinformatics Core Facility, Head
National Institute of Biotechnology in the Negev
Ben-Gurion University of the Negev
Beer-Sheva, 84105
Tel: 08-6479034, Fax: 08-6472983
Work:
2003-: Ben-Gurion University of the Negev, Beer-Sheva.

 Head of Bioinformatics Core Facility.
Activities: research collaborations, microarray data analysis, high-throughput sequence analysis, user support, workshops and academic courses.
Web site: http://bioinfo.bgu.ac.il 
1999-2003: Weizmann Institute of Science, Rehovot.

 Junior Staff Scientist at the Bioinformatics Unit of the Biological Services Department.
1996-1999: Weizmann Institute of Science, Rehovot.

 Post Doctoral fellow at the Molecular Genetics dept., Bioinformatics Unit and Crown Human Genome Center.
One of the founders of the GeneCards® database. 
Education:
1990-1996: Weizmann Institute of Science, Rehovot.
Department of Biological Regulation.
Laboratory of Prof. Mordechai Liscovitch.
Thesis: Isolation and Characterization of phospholipase D from brain membranes.
Ph.D. degree, Jan. 1996.
1987-1990: Weizmann Institute of Science, Rehovot.
Department of Biological Regulation.
Laboratory of Prof. Mordechai Liscovitch.
Thesis: Identification and characterization of a neutral, Magnesium stimulated phospholipase D activity in rat brain synaptic plasma membranes.
M.Sc. degree, Jan. 1990.
1984-1987: Hebrew University, Jerusalem.
Faculty of Natural Sciences.
B.Sc. degree, Aug. 1987.
Final average 91%, cum laude.
Experience and skills
Bioinformatics: DNA microarray data analysis (expression, SNP, SFP, CGH).  High-throughput sequence analysis and function prediction. Genomic databases and browsers. Advanced database searching. Human Genome Mapping. 
Software: Partek, SpotFire, GeneSpring, Affy, Limma, Affymetrix EC, dChip, Expander, David, ErmineJ, Cytoscape, UCSC Genome Browser, BioMart and numerous sequence analysis software.
Programming: Perl, SQL, R and BioConductor.
Academic semester courses at Ben-Gurion University:
  • Introduction to Bioinformatics for undergraduates (with Dr. Eitan Rubin)
  • Introduction to Bioinformatics for graduate students (with Dr. Eitan Rubin)
  • High throughput genomic analyses using DNA microarrays (with Dr. Micha Volokita)
  • Perl Programming for Bioinformatics
  • Guest lectures in other courses (Prof. Ruti Parvari, Dr. Chen Keasar, Dr. Yaakov pollack, Dr. Hanna Rapaport)
Publications
  1. Chalifa, V., Mohn, H., and M. Liscovitch (1990) A neutral phospholipase D activity from rat brain synaptic plasma membranes. Identification and partial characterization. J. Biol. Chem. 265, 17512-17519.
  2. Liscovitch, M., Chalifa, V., Danin, M. and Y. Eli (1991) Inhibition of neural phospholipase D activity by aminoglycoside antibiotics. Biochem. J. 279 , 319-321.
  3. Mohn, H., Chalifa, V., and M. Liscovitch (1992) Substrate specificity of neutral phospholipase D from rat brain studied by selective labeling of endogenous synaptic membrane phospholipids in vitro. J. Biol. Chem. 267 , 11131-11136.
  4. Danin, M., Chalifa, V., M–hn, H., Schmidt, U.S. and M. Liscovitch (1993) Brain membrane-bound phospholipase D. In Lipid Metabolism and Signaling Systems. J.N. Fain (ed.) Meth. Neurosci. 18 , 14-24.
  5. Liscovitch, M., Chalifa, V., Pertile, P., Chen, C.-S. and L.C. Cantley (1994) Novel function of phosphatidylinositol 4,5-bisphosphate as a cofactor for brain membrane phospholipase D. J. Biol. Chem. 269 , 21403-21406.
  6. Liscovitch, M., Chalifa, V., Pertile, P., Chen, C.-S. and L.C. Cantley (1994) Novel function of phosphatidylinositol 4,5-bisphosphate as a cofactor for brain membrane phospholipase D. J. Biol. Chem. 269 , 21403-21406.
  7. Liscovitch, M. and V. Chalifa (1994) Signal-activated Phospholipase D. In Signal- activated phospholipases , M. Liscovitch (ed.), R.G. Landes Co., Austin. pp. 31-63.
  8. Pertile, P., Liscovitch, M., Chalifa, V., and L.C. Cantley (1995) Phosphatidylinositol 4,5-bisphosphate synthesis is required for activation of phospholipase D in U937 cells. J. Biol. Chem. 270 , 5130-5135.
  9. Klein, J., Chalifa, V., Liscovitch, M., and K. L–ffelholz (1995) Role of phospholipase D activation in nervous system physiology and pathophysiology. J. Neurochem. 65 , 1445-1455.
  10. Liscovitch, M. and V. Chalifa-Caspi (1996) Enzymology of mammalian phospholipases D: in vitro studies. Chem. Phys. Lipids 80 , 37-44.
  11. Chalifa-Caspi, V., Eli, Y., and M. Liscovitch (1998) Kinetic analysis of partially purified rat brain phospholipase D activity in mixed micelles. Activation by phosphatidylinositol 4,5- bisphosphate. Neurochem. Res. 23 , 589-599.
  12. Chalifa-Caspi, V., Rebhan, M., Prilusky, J. and D. Lancet (1997) The Unified Database (UDB): a novel genome integration concept. Genome Digest , July, 15.
  13. Rebhan, M., Chalifa-Caspi, V., Prilusky, J. and D. Lancet (1997) GeneCards: integrating information about genes, proteins and diseases. Trends in Genetics 13 , 163.
  14. Rebhan, M., Chalifa-Caspi, V., Prilusky, J. and D. Lancet (1998). GeneCards: A novel functional genomics compendium with automated data mining and query reformulation support. Bioinformatics , 14:656-664.
  15. Ben-Asher, E., Chalifa-Caspi, V., Horn-Saban, S., Avidan, N., Olender, Z., Adato, A., Glusman, G., Safran, M., Rubinstein, M., Lancet, D. (2000). Harvesting the human genome: the Israeli perspective. Israel Medical Association Journal, 2:657-664.
  16. Marilyn Safran, Irina Solomon, Orit Shmueli, Michal Lapidot, Shai Shen-Orr, Avital Adato, Uri Ben-Dor, Nir Esterman, Naomi Rosen, Inga Peter, Tsviya Olender, Vered Chalifa-Caspi and Doron Lancet (2002). GeneCards 2002: Towards a complete, object-oriented, human gene compendium. Bioinformatics 18:1542-3.
  17. Safran, M., Chalifa-Caspi, V., Shmueli, O., Olender, T., Lapidot, M., Rosen, N., Shmoish, M., Peter, Y., Glusman, G., Feldmesser, E., Adato, A., Peter, I., Khen, M., Atarot, T., Groner, Y., and Lancet, D. (2003) Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE. Nucleic Acids Research 31(1): p. 142-146.
  18. Naomi Rosen, Vered Chalifa-Caspi, Orit Shmueli, Avital Adato, Michal Lapidot, Julie Stampnitzky, Marilyn Safran, and Doron Lancet (2003). GeneLoc: Exon-based integration of human genome maps. Bioinformatics 19 Suppl 1: p. I222-I224.
  19. Shmueli, O., Horn-Saban, S., Chalifa-Caspi, V., Shmoish, M., Ophir, R., Benjamin-Rodrig, H., Safran, M., Domany, E., Lancet, D. (2003) GeneNote: whole genome expression profiles in normal human tissues. Comptes Rendus Biologies 326, pp. 1067-1072.
  20. Chalifa-Caspi, V., Shmueli, O., Benjamin-Rodrig, H., Rosen, N., Shmoish, M., Yanai, I., Ophir, R., Kats, P., Safran, M., and Lancet, D. (2003) GeneAnnot: Interfacing GeneCards with high throughput gene expression compendia. Briefings in Bioinformatics 4, pp. 349-360. 
  21. Chalifa-Caspi, V., Yanai, I., Ophir, R., Rosen, N., Shmoish, M., Benjamin-Rodrig, H., Iny Stein, T., Shmueli, O., Safran, M., and Lancet, D. (2004), GeneAnnot: Comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes. Bioinformatics 20, pp.1457-8.
  22. E. Ling, G. Feldman, M. Portnoi, R. Dagan, K. Overweg, F. Mulholland, V. Chalifa-Caspi, J. Wells and Y. Mizrachi-Nebenzahl (2004) Glycolytic enzymes associated with the cell surface of Streptococcus pneumoniae are antigenic in humans and elicit protective immune responses in the mouse. Clinical and Experimental Immunology 138, pp. 290-298.
  23. Itai Yanai, Hila Benjamin, Michael Shmoish, Vered Chalifa-Caspi, Maxim Shklar, Ron Ophir, Arren Bar-Even, Shirley Horn-Saban, Marilyn Safran, Eytan Domany, Doron Lancet and Orit Shmueli (2005) Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21(5), pp. 650-659
  24. Bose S. Kochupurakkal, Daniel Harari, Ayelet Di-Segni, Galia Maik-Rachline, Ljuba Lyass, Gal Gur, Gabriele Kerber, Ami Citri, Sara Lavi, Raya Eilam, Vered Chalifa-Caspi, Zelig Eshhar, Eli Pikarski, Ronit Pinkas-Kramarski, Sarah S. Bacus, and Yosef Yarden  (2005). Epigen: the last ligand of ErbB receptors reveals intricate relationships between affinity and mitogenicity. J. Biol. Chem.  4;280(9):8503-12.
  25. Rivka Manor, Simy Weil, Shirley Oren, Lilah Glazer, Eliahu D. Aflalo, Tomer Ventura, Vered Chalifa-Caspi, Miri Lapidot and Amir Sagi (2007) Insulin and gender: an insulin-like gene expressed exclusively in the androgenic gland of the male crayfish. General and Comparative Endocrinology 150:326-36.
  26. Arie Budovsky, Amir Abramovich, Raphael Cohen, Vered Chalifa-Caspi and Vadim Fraifeld (2007) Longevity network: construction and implications. Mechanisms of Ageing and Development, 128(1):117-24
  27. Blau Karin, Portnoi Maxim, Shagan Marilou, Kaganovich Antonina, Rom Slava, Kafka Daniel, Chalifa-Caspi Vered, Porgador Angel, Givon-Lavi Noga, Gershoni Johnny, Dagan Ron and Mizrachi Nebenzahl Yaffa. Flamingo Cadherin: A Putative Receptor to Streptococcus pneumoniae in the Host. The Journal of Infectious Diseases (in press)
  28. Cohen, R., Chalifa-Caspi, V., Williams, T.D., Auslander, M., George, S.G., Chipman, J. K., Tom, M. Estimating the efficiency of fish cross-species hybridization on cDNA microarray (submitted)
Articles in Preparation
  1. Pragya Kant, Michal Gordon, Surya Kant, Gaston Zolla, Robert Fluhr, Olga Davydov, Yair Heimer, Vered Chalifa-Caspi, and Simon Barak. A functional genomics-based screen for genes that regulate Arabidopsis responses to multiple abiotic stresses.
  2. Shechter A., Tom M., Yudkovski Y., Weil, S., Chang S.A., Chang E.S, Chalifa- Caspi, V., Berman A., Sagi A. On the search for hepatopancreatic ecdysone- responsive genes during the crayfish molt cycle: from a single gene to multigenicity
  3. Yudkovski Y., Shechter, A., Chalifa-Caspi, V., Auslander, M., Ophir, R., Dauphin-Villemant, C., Waterman, M., Sagi A., Tom, M.. Hepatopancreatic multi-transcript expression patterns in the crayfish Cherax quadricarinatus during the molt cycle.
  4. Auslander, M. Chalifa-Caspi, V., Yudkovski, Y., Ophir, R., Tom, M. Pollution-affected fish hepatic transcriptome - a potential source for novel environmental biomarkers