## Former Lab Members

### Lea Tsaban

#### Lea’s HomePage

Publications:

- Kraus, S.; Kroener, A.; Tsaban, L.; (2002) IMAP – Intelligent Multimedia Authoring Tools for Electronic Publishing, AH 2002, Lecture Notes in Computer Science 2347 (2002), 527-530
- Ginodi, I.; Vider-Shalit, T.; Tsaban, L.; Louzoun, Y.; (2008) Precise score for the prediction of peptides cleaved by the proteasome, Bioinformatics 24(4):477-483
- Vider-Shalit, T.; Sarid, R.; Maman, K.; Tsaban, L.; Levi, R.; Louzoun, Y.; (2009) Viruses selectively mutate their CD8+ T-Cell epitopes-a large-scale immunomic analysis, Bioinformatics 25(12):i39-i44
- Almani, M.; Raffaeli, S.; Vider-Shalit, T.; Tsaban, L.; Fishbain, V.; Louzoun, Y.; (2009) Human self-protein CD8+ T-cell epitopes are both positively and negatively selected, European journal of immunology 39(4):1056-1065
- Itzhack, R.; Muchnik, L.; Erez, T.; Tsaban, L.; Goldenberg, J.; Solomon, S.; Louzoun, Y.; (2010) Empirical extraction of mechanisms underlying real world network generation, Physica A: Statistical Mechanics and its Applications 389(22):5308-5318
- Kovjazin, R.; Volovitz, I.; Daon, Y.; Vider-Shalit, T.; Azran, R.; Tsaban, L.; Carmon, L.; Louzoun, Y.; (2011) Signal peptides and trans-membrane regions are broadly immunogenic and have high CD8+ T cell epitope densities: Implications for vaccine development, Molecular Immunology

### Kobi Maman

**Ph.D.**

Research area:

- Studying the modulation of CTL epitopes by pathogens as immune evasion strategy.
- Developing algorithm for CTL response/ immunodominance.

Publications:

- Vider-Shalit, Tal, Ronit Sarid, Kobi Maman, Lea Tsaban, Ran Levi, and Yoram Louzoun. (2009). Viruses selectively mutate their CD8+ T-cell epitopes–a large-scale immunomic analysis. Bioinformatics 25:i39-44.
- Yaakov Maman, Antoine Blancher, Jennifer Benichou, Adi Yablonka, Sol Efroni, Yoram Louzoun. (2011) Immune induced evolutionary selection focused on a single reading frame in overlapping HBV proteins. Journal Of Virology. In Press.
- Yaakov Maman, Ran Nir-Paz, Yoram Louzoun (2011) Bacteria modulate the CD8+ T cell epitope repertoire of host cytosol-exposed proteins to manipulate the host immune response. Submitted.
- Nora C. Toussaint, Yaakov Maman, Oliver Kohlbacher and Yoram Louzoun (2011) Universal peptide vaccines – optimal peptide vaccine design based on viral sequence conservation. Submitted.
- Alexandra Agranovich , Kobi Maman , Yoram Louzoun. Escape mutations are mainly accumulated in short proteins in small viruses. ISMB-2011. Submitted.
- Yaakov Maman, Alexandra Agranovich, Tal Vider Shalit, Yoram Louzoun, Evolutionary Principles in Viral Epitopes, Lecture Notes on Mathematical Modelling in the Life Sciences 2013, pp 59-83

### Gilad Liberman

**Ph.D.**

Research area:

- In collaboration with the MRI unit of TASMC under the supervision of Dr. Dafna Ben-Bashat, we segment and classify multi-modal MRI scans into healthy and unhealthy (Lesion, edema, etc.) tissue classes, aiming for patient specific treatment of Glioblastoma Multiforme (GBM).

Publications:

- Liberman, G.; Nutov, Z.; (2007) On shredders and vertex connectivity augmentation, Journal of Discrete Algorithms 5(1):91-101
- Liberman, G.; Louzoun, Y.; Colliot, O.; Ben Bashat, D.; (2011) T1 mapping, AIF and pharmacokinetic parameter extraction from dynamic contrast enhancement MRI data, Multimodal Brain Image Analysis :76-83
- Liberman, G.; Louzoun Y.; Aizenstein O.; Blumenthal D. T.; Bokstein F.; Palmon M.; Corn B. W.; Ben Bashat D.; (2012) Automatic multi-modal MR tissue classification for the assessment of response to bevacizumab in patients with glioblastoma, in press

### Udi Hoze

Research area:

- CD4+ T-cell epitopes processing

Publications:

- Liang, X.; Hury, A.; Hoze, E.; Uliel, S.; Myslyuk, I.; Apatoff A., Unger R.; Michaeli S.; (2007) Genome-Wide Analysis of C/D and H/ACA-Like Small Nucleolar RNAs in Leishmania major Indicates Conservation among Trypanosomatids in the Repertoire and in Their rRNA Targets, Eukaryotic Cell 6(3):361-377

### Alexandra Agranovich

**Ph.D.**

Research area:

- mathematical modeling in immunology,
- optimization problems,
- population dynamics,
- predator-prey systems,
- modeling of stochastic birth-death processes with catalysis.

Publications:

- Agranovich A, Louzoun Y, Shnerb. N and Moalem S. (2006) Catalyst Induced Growth with Limited Catalyst Lifespan and Competition. Journal of theoretical biology 241(2):307-20
- Alexandra Agranovich and Yoram Louzoun (2012) Predator-prey dynamics in a uniform medium leads to directed percolation and wave-train propagation. Physical Review E 85, 031911
- Alexandra Agranovich, Tal Vider-Shalit, Yoram Louzoun. (2011) Optimal viral immune surveillance evasion strategies. Theoretical Population Biology 80(4):233-243
- Yaakov Maman, Alexandra Agranovich, Tal Vider Shalit, Yoram Louzoun, Evolutionary Principles in Viral Epitopes, Lecture Notes on Mathematical Modelling in the Life Sciences 2013, pp 59-83
- Alexandra Agranovich , Kobi Maman , Yoram Louzoun. Escape mutations are mainly accumulated in short proteins in small viruses.ISMB-2011. submitted

Seminars:

- Influence of Spatial Factor on Hysteresis in Immune system. Society for Mathematical Biology Conference 2008, Centre for Mathematical Medicine, Fields Institute, Toronto, Canada
- Predator – prey dynamics in the uniform medium lead to directed percolation and wave train propagation. Functional Differential Equations and Applications. Research workshop of the Israel Science Foundation 2010, Ariel, Israel

### Romi Magori-Cohen

**Ph.D.**

Research area:

- Bio informatics and Bio-statistics.
- Thesis: Deterministic decisions based on fuzzy receptor ligand interactions. Statistical analysis in various academic projects, such as the analysis of PET and fMRI imaging data, analysis of the relation between behavioral and physiological data.

Publications:

- Magori Cohen. R., Louzoun. Y., and Kleinstein. S. (2006) Mutation parameters from DNA sequence data using graph theoretic measures on lineage trees. Bioinformatics 22(14):e332-40.
- Final stages of preparation: Magori Cohen. R., Louzoun. Y., and Kleinstein. S. Estimating underlying biological dynamics from sequence data using graph theoretic measures of clonal trees. Bulletin of Mathematical Biology.
- James Pita, Manish Jain, Fernando Ordonez, Milind Tambe, Sarit Kraus, Reuma Magori-Cohen: Effective solutions for real-world Stackelberg games: when agents must deal with human uncertainties. AAMAS (1) 2009: 369-376
- Kedmi Maor, Herziger Yael, Galon Nadav, Magori -Cohen Reuma, Perel Marc, Batten Carrie, Braverman Yehuda, Gottlieb Yuval, Shpigel Nahum, Klement Eyal: The association of winds with the spread of EHDV in dairy cattle in Israel during an outbreak in 2006. Preventive veterinary medicine 2010;96(3-4):152-60
- Ruth Feldman, Reuma Magori Cohen, Giora Galili and Yoram Louzoun; (2011) Human Attachment is Supported by Biological Synchrony: Mother and Infant Coordinate Heart Rhythms through Episodes of Interaction Synchrony, Infant Behavior and Development 34(4):569-577.
- Weisman, O.; Magori-Cohen, R.; Louzoun, Y.; Eidelman, A.I.; Feldman, R.; (2011) Sleep-wake transitions in premature neonates predict early development. PEDIATRICS 128(4):706 -714
- Magori-Cohen, R.; Louzoun, Y.; Herziger, Y.; Oron, E.; Arazi, A.; Tuppurainen, E.; Shpigel, N.Y.; Klement, E.; Sadilkova, L.; Nepereny, J.; (2012) Mathematical modelling and evaluation of the different routes of transmission of lumpy skin disease virus, Veterinary Research 43(1)
- Cohen, R.M.; Kleinstein, S.H.; Louzoun, Y.; (2011) Somatic hypermutation targeting is influenced by location within the immunoglobulin V region, Molecular immunology 48(12):1477-1483
- Pita, J.; Jain, M.; Ordonez, F.; Tambe, M.; Kraus, S.; Magori-Cohen, R.; (2009) Quickly Learning User Characteristics for Eficient Interruptability in Agent/User Collaborative Systems, http://eprints.pascal-network.org/archive/00005090/

### Royi Itschack

**Ph.D.**

Research area:

- Complexity Science, more specifically Complex Networks. I work on new measurements and algorithms on network theory , extreme events statistics and more general aspects of modeling .
- Decoding of the visual stimuli . I worked on finding a decoder that translate a picture according the neural reaction that was received on the brain (areas V1,V2) , in this the work we focused in special algorithms in image processing and sophisticated Data mining

Publications:

- Royi Itzhack,Yelena Mogilevski and Yoram Louzoun , An optimal algorithm for counting network motifs , physica A , vol 381 ,pages 482-490,2007
- Lev Muchnik, Royi Itschak, Sorin Solomon and Yoram Louzoun (2007) Phys. Rev. E 76 , 016106, Self-emergence of knowledge trees: Extraction of the Wikipedia hierarchies Download
- Royi Itzhack, Lev Muchnik, Tom Erez , Lea Tsaban, Jacob Goldenberg, Sorin Solomon and Yoram Louzoun Submitted Diagonal attachmI ent: The Quest for the Mechanism Underlying Network Evolution

### Orit Lavi (Farhi)

**Ph.D.**

Research area:

- focused on Bio-mathematical modeling of the cell complexity.
- problems of Biochemical networks, cell signal processing and population modeling.

Publications:

- Orit Lavi, Yoram Louzoun; “What cycles the cell?: An incremental methodology for the analysis of intra-cellular mechanisms”, submitted.
- Orit Lavi, Yoram Louzoun, Eyal Klement; “Hygiene’s double-edged sword: Decreased exposure to Listeria may cause an upsurge in listeriosis”, submitted.

### Tali Vider

**Ph.D.**

Research area:

- The main goal of my research is characterization of the peptide repertoire presented to the cellular immune system and the usage of the repertoire properties for different biological applications.

Publications:

- Louzoun Y, Vider T, (2004). Score for Proteasomal Peptide Production Probability. Immunology, 1, 45-50
- Louzoun Y, Vider T and Weigert B, (2006). T-cell epitope repertoire as predicted from human and viral genomes. Molecular Immunology 43 (6; 559- 569).
- Vider- Shalit T, Raffaeli S and Louzoun Y, (2006). Virus-epitope vaccine design: Informatic matching the HLA-I polymorphism to the virus genome. The Molecular Immunology 44 (6; 1253- 1261).
- Vider- Shalit T, Fishbain V, Raffaeli S and Louzoun Y, (2006). Phase dependent immune evasion of Herpesviruses. Journal of Virology, pending minor revision.
- Raffaeli S, Vider-Shalit T, Tsaban L, Fishbain V and Louzoun Y (2006). PEPTIBASE – a novel CD8 T cell epitope database server. Bioinformatics, submmited.

### German Nudelman

**Ph.D.**

### Lev Muchnik

**Ph.D.**

### Michal Almani

**M.Sc.**

Research area:

- Networks

Publications:

- Almani M, Raffaeli S, Vider-Shalit T, Tsaban L, Fishbain V and Louzoun Y, (2008). Human self-protein CD8+ T-cell epitopes are both positively and negatively selected. European Journal of Immunology, 39 (4; 1056-65).
- Vider-Shalit T, Almani M, Sarid R and Louzoun Y, (2009). The HIV Hide and Seek Game as Revealed by Immunogenomic Analysis of Viral Epitopes. AIDS, in press.

### Mor Sinai

**M.Sc.**

My research:

Our research is to build information based method orthogonal/non-orthogonal for dimensionality reduction. Assume a data set

X⊂R^{n}xR^{m},

this data is composed of k population, we will give every population different “color”. We need to find matrix A, that will transform X so we will get good separation of the population or of the “colors”, Z=AX.

*First Step*: we will find matrix A using iterative methods

At the first step, we will find the direction A_{1} that maximizes the mutual information between Z and the “colors”. I(Z)=H(Z)+H(colors)-H(z;colors).

At the second step, we will reduce the projection of A_{1} from X, and by using the “Dimension reduction” above we will get new data

X∈R^{n}xR^{m-1}.

We will then find a direction A_{2} that minimize the mutual information on the new data and remove the projection on this dimension from the vectors. We will then continue this process n times, where n is the dimension we want to reduce our data to.

*Second stage*: we will find the same matrix A without using iterative methods.

### Hadar Davidovich

**M.Sc.**

### Shai Raffaeli

**M.Sc.**

### Elena Mogilevsky

**M.Sc.**

Research area:

- My research deals with Network analysis, such as the World Wide Web, scale free networks, biological networks etc. The main goal is to find scaling properties of network measurements using an appropriate sampling method.

Publications:

- Royi Itzhack, Yelena Mogilevski, Yoram Louzoun, An Optimal Algorithm for counting network motifs, Math department, Bar Ilan University, 52900 Ramat-Gan, Israel.

### Avital Peretz

**M.Sc.**

Research area:

- Calculation of the structural attributes of peptides presented to MHC I and the similarity between them.

### Ido Ginodi

**The hot promise for the future**

### Roy Azran

**Research assistant**

### Ran Levy

**Research assistant**

### Vered Fishbain

**Research assistant**

### Doron Cohen

**Research assistant**

### Hanan Besser

**Research assistant**

### Yubal Samoilov

**Research assistant**

### Mirav Ben Izhak

**Research assistant**

### Keren Cohen

**Research assistant**

### Adar Maimov

**Research assistant**