Hanah Margalit

Professor of Computational Molecular Biology

Research Interests:
Computational molecular biology/bioinformatics. Development and use of computational approaches to analyze the information accumulated in biological databases. Main research topics: regulatory pathways - integration of genomic and proteomic data to reveal complex regulatory motifs. Molecular control and recognition mechanisms- transcription regulatory sites, DNA-protein interaction, protein-protein interaction, small RNA molecules and sense-antisense relationships, translation regulation. Determination of T-cell epitopes based on sequence and structure information.

Lab home page

Recent Publications:

1. Yeger-Lotem, E. and Margalit, H. (2003) Detection of regulatory circuits by integrating the cellular networks of protein-protein interactions and transcription regulation. Nuc Acids Res. 31:6053-6061.

2. Lithwick, G. and Margalit, H. (2003) Hirerachy of Sequence-dependent features associated with prokaryotic translation. Genome Res. 13: 2665-2673.

3. Hermjakob, H., Montecchi-Palazzi, L., Lewington, C., Mudali, S., Kerrien, S., Orchard, S., Vingron, M., Roechert, B., Roepstorff, P., Valencia, A., Margalit, H., Armstrong, J., Bairoch, A., Cesareni, G., Sherman, D., and Apweiler, R. (2004) IntAct: Ź an open source molecular interaction database. Nuc. Acids Res. 32 Database issue:D452-455.

4. Yeger-Lotem, E., Sattath, S., Kashtan, N., Itzkovitz, S., Milo, R., Pinter, R.Y., Alon, U., and Margalit, H. (2004) Network motifs in integrated cellular networks of transcription regulation and protein-protein interaction. Proc. Natl. Acad. Sci. USA. 101:5934-5939.

5. Hershberg, R, Yeger-Lotem, E. and Margalit, H. (2005) Chromosomal organization is shaped by the transcription regulation network. Trends in Genetics. 21:138-142.

6. Lithwick, G. and Margalit, H. (2005) Relative predicted protein levels of functionally associated proteins are conserved across organisms. Nuc. Acids Res. 33:1051-1057.

7. Altuvia, Y., Landgraf, P., Lithwick, G., Elefant, N., Pfeffer, S., Aravin, A., Brownstein, MJ., Tuschl, T., Margalit, H. (2005) Clustering and conservation patterns of human microRNAs. Nuc. Acids Res. 33: 2697-2706.

8. Kaplan, T., Friedman, N. and Margalit, H. (2005) Ab initio prediction of transcription factor targets using structural knowledge. PLoS Computational Biology. 1:e1.

Courses:

Undergraduate:
- Bioinformatics : Computational sequence analysis of biomolecules
- Seminar in research approaches in computational biology
Graduate:
- Structure and Function of Proteins

Email:
hanah@md.huji.ac.il

Phone:
Telephone: 972-2-6758614 / 6758647
Fax: 972-2-6784010 / 6757308

1.	Yeger-Lotem, E. and Margalit, H. (2003) Detection of regulatory circuits by integrating the cellular networks of protein-protein interactions and transcription regulation. Nuc Acids Res. 31:6053-6061.
2.	Lithwick, G. and Margalit, H. (2003) Hirerachy of Sequence-dependent features associated with prokaryotic translation. Genome Res. 13: 2665-2673.
3.	Hermjakob, H., Montecchi-Palazzi, L., Lewington, C., Mudali, S., Kerrien, S., Orchard, S., Vingron, M., Roechert, B., Roepstorff, P., Valencia, A., Margalit, H., Armstrong, J., Bairoch, A., Cesareni, G., Sherman, D., and Apweiler, R. (2004) IntAct: Ź an open source molecular interaction database. Nuc. Acids Res. 32 Database issue:D452-455.
4.	Yeger-Lotem, E., Sattath, S., Kashtan, N., Itzkovitz, S., Milo, R., Pinter, R.Y., Alon, U., and Margalit, H. (2004) Network motifs in integrated cellular networks of transcription regulation and protein-protein interaction. Proc. Natl. Acad. Sci. USA. 101:5934-5939.
5.	Hershberg, R, Yeger-Lotem, E. and Margalit, H. (2005) Chromosomal organization is shaped by the transcription regulation network. Trends in Genetics. 21:138-142.
6.	Lithwick, G. and Margalit, H. (2005) Relative predicted protein levels of functionally associated proteins are conserved across organisms. Nuc. Acids Res. 33:1051-1057.
7.	Altuvia, Y., Landgraf, P., Lithwick, G., Elefant, N., Pfeffer, S., Aravin, A., Brownstein, MJ., Tuschl, T., Margalit, H. (2005) Clustering and conservation patterns of human microRNAs. Nuc. Acids Res. 33: 2697-2706.
8.	Kaplan, T., Friedman, N. and Margalit, H. (2005) Ab initio prediction of transcription factor targets using structural knowledge. PLoS Computational Biology. 1:e1.