Researchers, Medicine

Name Research interests
Dr. Shahar Alon

Spatial genomics is a new field that seeks to map the physical position of millions of RNA molecules in cells and tissues and correlate them to normal and pathological conditions. We developed a technology for RNA sequencing inside tissues, which allows studying RNA molecules with unprecedented detail. We use this technology to unravel how molecular content is stored within cells in space in order to understand the function of complex tissues. 

Prof. Ehud Banin

Bacterial Biofilms

Biofilms are microbial communities embedded in a self-produced extracellular polymeric matrix. It is now well recognized that cells undergo profound changes in the transition from free-living to matrix-embedded (biofilm) communities. An important characteristic of microbial biofilms is their innate resistance to immune system- and antibiotic-killing. This has made microbial biofilms a common and difficult-to-treat cause of medical infections. Several chronic infections have been shown to be mediated by biofilms such as the respiratory infections caused by Pseudomonas aeruginosa in the cystic fibrosis (CF) lung and Staphylococcal lesions in endocarditis. Biofilms are also a major cause of infections associated with medical implants mainly by Staphylococcus epidermidisStaphylococcus aureus, and P. aeruginosa. It has been estimated that 65% of the bacterial infections treated in hospitals are caused by bacterial biofilms. Thus, there is an urgent need to discover innovative treatments for biofilm-associated infections. The current understanding of how biofilms develop and how they acquire increased resistance is still in its initial stages. Our research focuses on understanding the basic aspects of the signals and processes involved in biofilm development with a goal of finding new methods of treating biofilm-related infections. The aims are:

1) To characterize how biofilms develop, with a focus on the role of iron as a signal in biofilm development.

2) To understand the mechanisms by which biofilms obtain increased resistance to antimicrobial therapy.

3) To understand the role of inter- and intra-species cell-cell communication in mixed species biofilm interactions.

4) To discover novel compounds that effectively eradicate biofilms.

We implement an array of physiological, biochemical, and genetic tools combined with novel technologies that allow controlled and reproducible biofilm growth to characterize bacterial biofilms and compare them to the non-biofilm communities.

Prof. Chaya Brodie

1.Studying the role of protein kinase C in the regulation of cellular growth, differentiation and apoptosis.

2.Studying the molecular mechanisms underlying the development of brain tumors: Exploring signal transduction pathways involved in glial cell transformation and identification of novel proteins and genes expressed in brain tumors;  development of in vivo and in vitro models of brain tumors; development of novel diagnostic and therapeutic approaches for brain tumors; studying the role of stem cells in the development of brain tumors and their use as a vehicle in gene therapy.

3.The bi-directional interaction between the nervous and immune systems and the role of this interaction in the function of neuronal and glial cells during physiological and pathological conditions.

Prof. Aryeh Frimer

1. The synthesis of strained olefins and their photosensitized reactions with singlet and triplet oxygen.

2. The organic chemistry of active oxygen species within organic media, liposomal lipid bilayers, and biomembranes.

3. The preparation of high temperature thermo-oxidatively stable aerospace polymers.

4. The preparation, characterization and neutralization of green reduced sensitivity high energy compounds.

Dr. Doron Gerber

Viruses use very complex interaction networks to interface and hijack host machinery in order to do their bidding. Mapping protein interaction topologies represents a fundamental step towards understanding these biological processes. Over the last 3 years, I have developed quantitative high-throughput microfluidic tools and applied them to study protein interaction networks. These tools allow us to shed light on difficult biological questions with clinical implications. In many aspects, these questions could not be readily addressed with conventional methods (membrane protein expression, etc.). Viruses modulate host networks on the genometranscriptome and proteome levels. I would like to discover such viral-host interfaces by mapping viral protein interaction networks with the host genome, transcriptome and proteome. My research is guided by several questions: (1) What are the common "tools" viruses use to hijack host network? (2) How do these "tools" evolve? (3) How can we modulate or "turn off" these interfaces? (4) Can we mimic these "tools" in order to interface with cellular networks?  

A proof of concept of this methodology can be found in Einav and Gerber et al., 2008. In this paper, we used the same microfluidic platform to characterize a new function for a membrane protein from Hepatitis C virus, as well as find inhibitors to this new function. In less than 2 years, we now already have a compound that successfully passed preliminary clinical trials.

Dr. Nitzan Gonen

• Sex Determination

• 3D Genome organisation

• CRISPR genome editing
• Stem Cell Biology
• Developing in vitro systems to model the gonads


Studying the role of the non-coding genome during sex determination

A main research interest of our lab is to understand, at the molecular level, how sex is determined during embryonic development, i.e., how does an embryo develop into either male or female.

In mammals, sex determination is genetically driven with XY individuals developing as males and XX individuals developing as females. However, if the process of sex determination is impaired, patients appear as XY females or XX males (sex reverse). These are all classified as patients with Disorders of Sex Development (DSD), with a prevalence of 1: 2500-4000 newborns.


During embryonic development, the gonads initially develop as a bipotential organ and it is the activity of several key transcription factors that directs them to develop into either testes or ovaries. In the lab, we use the mouse as a model system and are interested at understanding the regulation of these key transcription factors and how these interact with each other. We also study the role of the non-coding genome in mediating the process of sex determination and DSD pathologies.

We employ cutting-edge techniques to address these questions including CRISPR/Cas9 genome editing, transgenic mice production, advanced sequencing techniques as well as microscopy and molecular biology.


Developing an in vitro model to study the gonads

In an attempt to develop an in vitro system that allows to model the mammalian gonads we use mouse Embryonic Stem Cells (ESC) and develop differentiation protocols towards gonadal cell type of the gonads. In addition, we use similar protocols with Human ESC and induced Pluripotent Stem Cells to model DSD patients in vitro. Furthermore, we perform tissue engineering to model the testis and the spermatogenesis process using these stem cell-derived somatic cells along with germ cells in a 3D culture system.

Dr. Ayal Hendel


Genetic therapy

Genetic engineering

Developing CRISPR technology as a method of gene therapy for genetic diseases.

Prof. Tomer Kalisky

Single cell genomics and applications to stem cell biology, tissue regeneration, and cancer

Prof. Gal Kaminka

Teams of Robots, Agents and People, Data Mining and Learning, Multi-Agent Systems, AI

Prof. Jean-Paul Lellouche

1.Multifunctional Polymer Materials and Systems with Taylored Mechanical, Electrical and Optical Properties

2.Water-Compatible Surface Modifications of PET [poly(ethylene-terephthalate] Fibers by Grafted PEG Polymers, and/or Conducting Polymers

3.Smart Membrane for Hydrogen Energy Conversion: All Fuel Cell Functionalities in One Material

4.Chemically Modified Multi-, Single-, and Double-Walled Carbon Nanotubes (MWCNTs, SWCNTs, & DWCNTs) for the Reinforcement of Polymeric Matrices and Surface Functionalization/Nanostructuration

5.Nano-silencing in the cytoplasm and nucleus for killing of parasites and cancerous cells

6.Surface modifications of dental implants using inorganic particles

7.Functional bio-sensing nanostructured surfaces

8.Parylene-based artificial smart lenses fabricated using a novel solid-on-liquid deposition process

9.A Modular Active Nano-Platform for Advanced Cancer Management: Core Nanosystems, Tumor Targeting and Penetration, Molecular Imaging & Degradome-based Therapy

Prof. Yossi Mandel

The Ophthalmic Science and Engineering Lab is focused on basic and translational research in ophthalmology and visual neuroscience. Our main research interests are the field of electro-cellular interfaces, optical and electronic microdevices development, and applied science for improving diagnosis, treatment and prevention of various ophthalmic diseases. One of the central themes is the artificial introduction of visual information and its processing by the retina and the visual cortex. We further study learning and plasticity processes in the visual system in animals. Other projects include electrocellular interface with the autonomic system and application of high electrical field for solid tumor ablation (IRE - Irreversible Electroporation).

Prof. Shlomo Margel

Polymers & biopolymers; Surface chemistry; Thin films, Nanotechnology, Nabiotechnology and agro-nanotechnology; Encapsulation; Applications of magnetic and non-magnetic functional nanoparticles for medical (specific cell labeling and separation, diagnosis and therapy of cancer, multimodal contrast agents, wound healing, neurodegenerative disorders, etc.), agricultural and industrial applications.

Prof. Shulamit Michaeli

Our model systems are the trypanosomes, parasitic protozoa that are the causative agent of devastating parasitic diseases such as sleeping sickness, leishmaniasis and Chagas’ disease, which affect millions of people worldwide.

In my laboratory, we are investigating processes which are unique to the parasite and not found in the mammalian host; our hope is to find unique targets for therapy.

We focus on the structure and function of RNA molecules that participate in RNA processing trans-splicing that is unique to these parasites. We are interested in the structure and function of novel anti-sense non-coding RNAs and the mechanism of a novel RNAi silencing event discovered in our laboratory, snoRNAi, which silences nucleolar RNAs. Recently, we discovered a novel stress-induced mechanism that silences the production of mRNA by abolishing trans-splicing that leads to apoptosis.  We term this process SLS, and plan to identify chemical compounds that elicit this death pathway as potential chemotherapy.

We study the mechanism of protein sorting across the ER, especially the role of the signal recognition particles (SR), since we found that the trypanosome particle carries two RNA molecules unlike all its homologues in other eukaryotes. In addition, we study unique RNA quality control mechanisms that regulate the level of non-coding RNAs.

My laboratory is also investigating nuclear RNA silencing in human cells and exploring the use of nanotechnology for gene silencing.

We were heavily involved in generating transgenic plants resistant to nematodes by expressing siRNAs to silence pathogenic plant nematodes.

We use a variety of methodologies from generating of transgenic parasites, knock-out, RNAi silencing, biochemical fractionation of RNA-protein complexes, microarray analysis of the transcriptome, and live cell imaging of RNA, proteins and more.

Prof. Uri Nir
Prof. Yarden Opatowsky

Structural Studies of Cell Signaling Assemblies

We use structural and biochemical methods to study how cytokines activate receptors to initiate precise signaling events across the cell membrane. Receptor tyrosine kinases (RTKs) are key players in the control of a wide range of cellular processes including proliferation, differentiation, migration and survival. They are composed of an extracellular domain to which specific ligands bind, a single-pass transmembrane helix, and an intracellular tyrosine kinase domain flanked by regulatory regions. We seek to understand how the extracellular event of ligand binding to the receptor is translated into an accurate intracellular response. We are also interested in structural investigations of coordinated signaling through assemblies of RTKs and co-receptors. Through the parallel use of X-ray crystallography and single-particle electron microscopy, we address basic mechanistic questions concerning the early stages of cell signaling.

Prof. Rachela Popovtzer

Smart nanoscale sensors and medical applications

 BioMEMS & ‘Lab on a Chip' devices

 Bio-imaging & Plasmonic nanoparticles

 Neural Prosthetic devices

Prof. Yaron Shav-Tal

Our research focuses on the gene expression pathway, and specifically on mRNA dynamics in living cell systems. We study dynamic cell processes on the single-molecule, single-gene and single-cell level using time-lapse fluorescent microscopy and subsequent kinetic analysis.

The primary goals of our research are to understand how genes switch "on" and "off" in normal cells and in cancer cells, how quickly are mRNAs transcribed, the kinetics of the transcription process in vivo, and their travels and destinations as they translocate within the cell. The major topics of interest in our group:

Cancer and Gene Expression

We follow gene expression in real-time by applying a variety of fluorescent tags to genes, mRNAs and proteins, and have developed a number of cell systems in which gene expression, or mRNA transcription, can be examined and quantified.

We are able to observe single genes in living cells and to quantify the action of a gene as it unfolds before our eyes. Using this approach, we can monitor the influence of promoter regions and transcription factors, on the activity of an oncogene in living cells, thereby elucidating the over-expression pathway in cancerous cells.

As the process of transcription transpires, the pre-mRNA undergoes a number of processing events such as capping, splicing and polyadenylation. Since these processes occur co-transcriptionally, it is important to determine whether they affect transcription kinetics. We are examining the real-time kinetics of the co-transcriptional process of pre-mRNA splicing using live cell imaging techniques (FRAP, photoactivation and FCS) followed by kinetic modeling for analysis of the kinetic data.

RNA Export

In order to understand how genetic information disseminates from the cell nucleus into the cytoplasm it is essential to determine the mechanisms of mRNA mobility in cells. We have been following the dynamics of mRNA nucleoplasmic translocation, as well as mRNA export in vivo. We are interested in analyzing different elements that control the export pathway, using inhibitors and knock down of specific elements considered necessary for these processes. Our analysis performed by applying single molecule approaches that allow us to quantify the interactions of molecules passing through the nuclear pore complex. We also perform screening of small molecule libraries using high-content microscopy in search of new inhibitors of the gene expression pathway.

Cytoplasmic mRNA

Cytoplasmic mRNAs can be translated by ribosomes, stored in granules, or degraded by a variety of surveillance mechanisms. A group of structures involved in mRNA storage and decay are cytoplasmic P-bodies. We are interested in understanding the dynamics of cytoplasmic P-bodies in living cells in relation to mRNA kinetics. Imaging the "mRNA localization" process in real-time will assist in revealing the fate of mRNAs in cells.

Prof. Orit Shefi

Neurobiological systems development: image processing and network analysis

Tissue Engineering: Developing skin grafts that enable reinnervation and regeneration

Developing devices for reagents delivery into live tissue at a microscopic resolution

Neuroprosthetic devices: Neuron-Chip interface

Dr. Amit Tzur

Cell cycle

Cell growth

Prof. Ron Unger

My research interest is the interface between Biology and Computer Science. We are interested in exploring this interface from two directions: how advanced computational techniques can help to address fundamental biological questions and how biology can inspire new computational approaches. Within this framework, we are involved in projects spanning a wide range of topics such as: Designing simple models to better understand protein structure and protein folding dynamics, studying ncRNA molecules, molecular computation and system biology. 

1) Studying simple models of protein folding: We are using simple models to address the fundamental questions related to protein folding. Such models capture the essence of the fundamental questions, while being simple enough to enable thorough computational analysis. Using this approach, we have demonstrated the usefulness of genetic algorithms for structure calculations, study the importance of local interactions, analyze protein folding assisted by chaperons, and study long-range interactions in proteins.

2) Studying ncRNA molecules: The importance of short noncoding RNA molecules (ncRNA) in controlling various biological processes became evident in the last several years. Traditional sequence analysis tools are generally not suitable to identify such molecules on a genomic scale. We use a variety of sophisticated computer science methods ranging from suffix trees to SVMs to detect, compare, and characterize ncRNA molecules. This work is done in collaboration with Prof. Shula Michaeli, an experimentalist who is working on understanding the function of ncRNA molecules in parasites.   

3) Molecular Computation:  The exquisite selectivity and specificity of complex protein-based networks suggest that similar principles can be used to devise biological systems that will be able to directly implement any logical circuit as a parallel asynchronous computation. We have designed a scheme for protein molecules that would serve as the basic computational element by functioning as a NAND logical gate, utilizing DNA tags for recognition, and phosphorylation and exonuclease reactions for information processing.

4) System Biology, the robustness of biological systems: We are analyzing genomic networks (like protein - protein interactions, genetic double mutants) in order to understand how biological systems gain their robustness. We are intrigued by the regularity of the overall features of these networks while they consist of so many different underlying components.  Thus, we look for global properties, in addition to being scale-free and local, that may induce robustness.

Prof. Gur Yaari

Computational systems biology:

Using immune repertoires as diagnostic and prognostic tools for diseases.


1. Development of nano-technologies (e.g. lab on a chip) for identification of immune repertoire patterns for diagnostics and prognostics of diseases.

2. Computational investigation of antibody-antigen interactions for antibody engineering.

3. Development and usage of advanced machine learning approaches in various fields.

Lab on a chip, investigation of nano-scale interactions and machine learning applications fit well the nano technology field


Behind the phenomenal success of the human immune system in fighting countless evolving threats lies its ability to diversify, adapt and form long term memory. Specificity is achieved by the dynamic B cells that undergo affinity maturation in response to antigens. Thus, the antibody repertoire stores information about threats that the body has encountered, and can be harnessed to provide valuable information about diseases. We develop computational pipelines tailored for antibody repertoire analyses, and apply them to samples from different clinical conditions to shed light on new disease mechanisms and improve diagnostics and prognostics.  



Dr. Nissan Yissachar

The intestinal immune system and the microbiome: communication networks and decision-making processes 

We study the cellular, molecular and genetic mechanisms that facilitate communication between cells of the immune system and their environment in the gut - the gut microbes (microbiome), the enteric nervous system, and intestinal epithelium, etc…

We aim to understand how these intercellular communication networks control immunological decision-making processes, between inflammation and immunological tolerance, in health and in autoimmune and chronic inflammatory diseases (such as inflammatory bowel diseases). 

We combine microscopy, genomics and molecular biology together with a unique gut organ culture system, that allow dissecting these host-environment interactions in real-time, ex-vivo (Yissachar et al., Cell, 2017).

In addition, we combine principles of systems biology, to understand how cells of the immune system process environmental signals in real-time (Yissachar et al., Molecular Cell, 2013).