1. Understanding the microbial processes that control carbon sequestration in the ocean; bio-mechanistic understanding of the biological pump.
2. Investigating the enzymatic processes behind sulfur-gas production in the ocean and elucidating the broader biological factors influencing their emissions from marine ecosystems.
3. Symbiotic interactions between algae and bacteria and their impact on nutrient transformation and circulation.
4. Plankton adaptation to life in a fluctuating environment (e.g., in response to shifts in nutrient quality, micronutrient availability, light intensity, or temperature)
5. Plankton adaptation to life in suspension; growth and survival without surfaces.

1. Structure determination of membrane proteins by FTIR spectroscopy
2. Structure and function of viral ion channels

1. Mechanisms by which enteric bacterial pathogens attack epithelial host cells and how the host cells defend themselves
2. Mechanisms of human enteric diseases
3. Developing new technologies to diagnose and combat infectious/inflammatory diseases of the human gut  

1. Signal Transduction in neuronal cells: the molecular mechanism of transmitting an extracellular signal to the nucleus

2. Activation of transcription factors during neuronal activation of voltage-gated calcium channels: a mechanistic connection to autism

3. Developing new molecules for the treatment of neurodegenerative disease such a Alzheimer’s and Parkinson’s

4. Preventing oxidative stress and premature apoptosis; the importance of inflammation

1. The roles of autophagy in plant metabolism during plant development.
2. The roles of autophagy in plant metabolism during stress and recovery.
3. Modulating autophagy to increase plant yield and shelf life.

In the Micro-Flight Laboratory we use ultra-fast cameras and advanced image analysis methods to measure the flight of insects and their correction maneuvers. 

Our main research questions are:

1. Experimental research on flight in small and fast scales: How do insects control their flight?
2. How do insects represent information on their own orientation?
3. How do insects combine sensory information from multiple modalities during flight?
4. What are the neural and genetic mechanisms that determine flight control in insects?
5. Can we build tiny insect-like flying robots?

1. Life in the Tamarix (= the Eshel tree) leaf microbiome
2. Molecularly engineered bacterial biosensors for environmental monitoring 
3. Microbial detection of buried landmines and other explosive devices

1. Characterizing of the importance and function of bHLH transcription factors during the development of the embryonic nervous system (e.g. the cerebellum, Parkinson’s-related dopaminergic neurons and the spinal cord), using genetically engineered mice and chick embryos.
2. Discovering the molecular mechanism through which bHLH transcription factors act.
3. Applying the knowledge on normal embryonic development t to direct the fate of stem cells (as a tool for treating diseases like Parkinson’s).
4. Identification and study of disease caused by mutations in bHLH transcription factors.

1. The use of pluripotent stem cells to study human genetic disorders
2. The tumorigenicity of human stem cells
3. Haploid human pluripotent stem cells

1. Discovering and modifying immune metabolic pathways involved in aging.
2. The role of the gut microbiome in aging and ischemic stroke.
3. The function and structure of the enteric nervous and glial systems. 
4. Harnessing the intestinal immune system to fight brain tumors.
5. Utilizing microbiome-associated metabolites as a potential approach to treat neurodegenerative diseases. 

1. The interplay between biological clocks, sleep, and social behavior
2. The temporal organization of insect societies
3. The adaptive significance of circadian clocks
4. What does it take to make a social insect? Using the comparative approach to understand the molecular, physiological, and neuronal modifications during the evolution of insect societies
5. Social, hormonal, and molecular mechanisms controlling body size and their influence on the social organization of bumblebees 
6. Hormones and social behavior in bees
7. The involvement of RNA editing and mircoRNA in the regulation of complex behavior in bees
8. Social and molecular mechanisms regulating body size and caste differentiation in bumblebees

• Systematic mapping of the chloroplast protein import system
• Elucidating the genetic network that drives retrograde signaling during chloroplast proteotoxic stress 
• Elucidating guiding principles of the Chlamydomonas-plant microbiota ecosystem

1. Nuclear lamins regulate oxidative homeostasis in health and disease.
2. Nucleus mechanotransduction: applied mechanical forces stabilize the nuclear lamina and direct cell fate decision making.
3. Mapping matrix directed protein interactome of A-type lamins using genetic code expansion.
4. Single-cell analysis of matrix-directed differentiation of mesenchymal stem cells.
5. Mechanobiological profiling and regulation of oocyte maturation and embryo preimplantation development.
6. Morphokinetic analysis of human embryo preimplantation development (computational).
7. Developing machine-learning classifiers for evaluating the developmental potential of embryos during early preimplantation stages (computational).

Our lab deals with a host of topics in the general fields of molecular evolution and genetics. Among the topics that are currently pursued are:

1. Human evolution. Recent advances in ancient DNA sequencing yielded genomes (either shotgun sequences with varying degrees of coverage, or SNP arrays) of many ancient anatomically modern humans, as well as of Neanderthals and Denisovans. This open unique opportunities to study the genetic aspects of the very recent lag of our own evolution.
2. Paleo-epigenetics. We developed a technique to reconstruct full DNA methylation maps from high-coverage ancient genomes, and use it to study evolutionary changes in gene regulation, ancient environments and phenotypic adaptations.
3. Paleo-genetics. We study the genetic structure of ancient populations in Israel.
4. RNA biology. We are studying many aspects of RNA biology, including splicing, nonsense-mediated decay, 3'-end processing, and circular RNAs.
5. Multivariate data analysis. My lab is also active in some fields of applied mathematics: multivariate analysis, statistical pattern recognition, data visualization, and machine learning.

1. The evolution of developmental pathways and comparative embryology as a tool for studying evolutionary processes.
2. Early stages of embryonic patterning in arthropods and the evolution of the segmental body plan.
3. The evolution of the arthropod head and the distinction between head and trunk.
4. Comparative genomics of model and non-model systems..
5. Historical biogeography of Israel, using the National invertebrate collection.

1. Molecular Characterization of a cocaine-responsive neuronal ensemble in the nucleus accumbens.
2. Synaptic and circuit-level characterization of a cocaine-responsive neuronal ensemble in the nucleus accumbens.
3. Functional interrogation of the transcriptional networks underlying the formation and maintenance of addiction.
4. The role of the claustrum in selective attention
5. The role of the claustrum in reward and addiction
6. Internal connectivity of the claustrum and its role in segregating attention

1. Neural basis of pain-free surgery
2. Brainstem control of arousal and consciousness
3. Neural pathways for transition to unconsciousness in anesthesia
4. Spinal processes in anesthesia: analgesia and atonia  
5. Sleep, fainting and coma. 

1. Epigenetics and chromatin in cancer
2. The molecular basis for changes in DNA methylation in cancer
3. The role of DNA methylation in repression of human transposable elements
4. Histones and their modifications in transcriptional control
5. Cancer causing mutations in chromatin modifiers 

1. Development of intrinsically active variants of the MAP kinases p38 and ERK.
2. Revealing the mechanisms of activation of p38 and ERK through the use of the engineered active variants.
3. Revealing the specific roles of ERK1 and ERK2 in cancer in cell lines and in transgenic mice.
4. Revealing the specific role of p38 in chronic inflammatory diseases in cell lines and in transgenic mice.

1. Coral-alga interactions under changing environmental conditions.
2. The effect of marine heat waves on the physiology of reef-building corals
3. Coral response to light flashes in shallow coastal environments
4. Metabolism of sugars with increasing temperature

1. Empirically modeling plant microbiome assembly and dynamics
2. Plant microbiome deconstruction and optimization
3. Desert plant and soil metagenomics

1. Molecular mechanisms underlying the high regeneration ability of the sea anemone Nematostella.
2. A comparison between the processes of embryonic development and regeneration
3. Cthrc1 genes: function in Nematostella, evolution in animals (metazoans) and protein structure.
4. The ADAMTS metalloproteases in development and regeneration in sea anemones and other cnidarians 
5. Inversion of body polarity – two headed Nematostella polyps

1. Physical-biological interactions in the coral reefs and plankton.
2. Behavioral ecology of fish that form social groups. 
3. Vertical mixing and plankton dynamics in the ocean.
4. Ecological long-term monitoring in the sea.

1. Identification and characterization of novel genes involved in familial breast and ovarian cancers.
2. Uncovering DNA damage response regulation. 
3. Identification of novel cancer therapeutic drugs.
4. Characterizing the interplay between estrogen, breast cancer and genomic instability.

1. The molecular basis of the circadian (~24 hour) oscillator in plants
2. The adaptive significance of circadian rhythms 
3. Understanding how environmental signals entrain (set) the circadian oscillator
4. Cell-specific circadian rhythms

1. Modeling gene drive spillovers
2. Ancient population genomics of immune-related processes
3. Genetics of fragmentation processes in population networks
4. Conservation genomics
5. Predicting phenotypes of past populations from ancient genomes
6. Machine learning methods for predicting conservation risks from genomic data

1. The molecular basis of aging, longevity, and age-related diseases.
2. Identifying novel genes involved in cellular and organismal aging.
3. Developing the turquoise killifish, the shortest-lived vertebrate, as a genetic model for experimental aging.
4. Applying cutting-edge molecular and genomic approaches in the killifish and human cells (such as single-cell RNA-seq, CRISPR screens, Mass-spectrometry).
5. Modeling age-associated diseases (e.g. neurodegeneration, decline in immune function) in the turquoise killifish using CRISPR/Cas9 genome editing.
6. Live-imaging of aging-related process by generating fluorescent transgenic killifish.
7. Exploring the effect of early life-history traits, such as age at sexual maturity, on the rate of aging.

1. The relation between cell adhesiveness and growth control in malignant lymphoma cells.
2. Molecular mechanisms involved in the selection of non-malignant variant cells from malignant cell populations.
3. Different approaches to reversal of multi-drug resistance of malignant cells. Growth regulation of malignant lymphoma.
4. Metastasis of malignant lymphoma.

1. Motor control of the flexible arms of the octopus - inspiration for soft robotics.
2. Neurobiology of learning and memory in an advanced invertebrate - the Octopus

1. Species diversity, Population and Community Ecology.
2. Conservation Biology and Applied Ecology.
3. Plant Ecology and Plant-Animal interactions.
4. Macroecology and Global Change Biology. 

1. Cross-linking and Mass-spectrometry for the study of protein-protein interactions in the mammalian cortex.
2. Cross-linking and Mass-spectrometry for the study of protein-protein interactions in the cancer cell-lines. 

1. Do trees repell their own kind more in tropical forests?
2. Do interactions between species maintain high species diversity?
3. How can we evaluate the competition between tree species that inhabit the same habitat?
4. How many species can potentially coexist in tropical and temperate forests?

1. The mechanisms underlying different patterns of chromosomal instability in cancer. 

• How alterations in the transcriptional profile, DNA replication timing and the 3D genome organization drive tumorigenesis?
• The involvement of chromosomal fragile sites in the genomic instability in cancer.

2. Personalized medicine approach for the treatment of rare genetic diseases – CF as a model.

• Establishment of patient-derived cellular models that will serve as a pre-clinical tool to predict the therapeutic response of CF patients carrying rare mutations to novel therapies.
• Development of novel therapeutic approaches for CF patients carrying nonsense mutations  -  RNA transcript stabilization by epigenetic modulation.

1. Dynamics of light capture and photosynthesis by marine phytoplankton
2. Photosynthesis in desert sand crust microorganisms – physiological principles and biotechnological applications  

1. The role of the microbiome in host evolution
2. Ecology and evolution of species on a patchy landscape: meta-population dynamics
3. Conservation of fragmented populations: ecology, genetics, and behavior
4. Human prehistory from an ecological perspective

1. Dynamic structural biology of alpha-Synuclein
2. Control over cytotoxic phase-separated bio-condensates
3. Rational design of inhibitors of cytotoxic alpha-Synuclein species
4. Fluorescent probe design

1. Recruitment of the immune system to attack cancer cells.
2. Expression of anti-cancer proteins in plant cells (in collaboration with Prof. Oded Shoseyov from the faculty of Agriculture

1. Bioinformatics methods for global classification of protein sequences, structure and function inference.
2. Evolution of viruses and co-evolution of hosts.
3. Synaptic proteins and translation regulation.
4. Neurotoxins as cell modulators - computational approach.
5. Proteomics methods for neuronal cell differentiation.
6. Machine learning tools for functional prediction. 
7. MicroRNA as a key for cancer diagnosis.
8. Fat cells as sensors for cell metabolic homeostasis.

1. How do virulence factors promote the expansion of bacterial pathogens in the gut? 
2. Interaction of bacteriophages (bacterial viruses) with the microbiota and the mammalian host. 
3. Mechanisms of colonization resistance against pathogens in the intestine. 

1. The biochemistry, biology, and structural aspects of MAP kinase of canonical and alternative activation pathways.  
2. The structure, activity, and selectivity of NelD – an effector in bacterial infection.  
3. Development and optimization of anti-viral agents via structural studies.
4. Bio-engineering and refinement of biotin-based high affinity systems via protein design and manipulation. 

1. Effects of neuromodulation on dendritic computation.
2. Role of HCN channels and dendritic excitability in mice models of autism.
3. Sub cortical neural circuits controlling ultrasonic vocalizations in mice 
4. The role of dendritic computation in working memory

1. Using embryonic and induced pluripotent stem cells to model and study Huntington’s and Machado Joseph disease.
2. Epigenetic mechanisms and heterogeneity in stem cells and neuronal differentiation.
3. Paleo-epigenetics (with Prof. Liran Carmel): reconstructing DNA methylation in archaic genomes, and testing phenotypes in stem cells and minibrains.
4. Live imaging of nuclear dynamics in stem cell differentiation.
5. Histone turnover in glioblastoma.

1. Tissue Engineering. Development of a biological micro-pancreas.
2. A second generation Biopump for the secretion of Biologicals.
3. A second generation biological angiopump for the treatment of vascular diseases.
4. Discovery of novel antibiotics derived from amphibia.
5. Characterization of signals involved in skin ageing and homeostasis.
6. In vitro and in vivo ovarian micro-organs to treat human fertility.
7. Development of complex artificial scaffolds for tissue engineering.
8. Role of connective tissue in carcinogenesis.

1. The evolution of post-transcriptional regulation by microRNAs.
2. The evolution of microRNA mode of action.
3. The developmental roles of microRNAs in Cnidaria.
4. The molecular evolution of animal venom.
5. Ecological and organismal factors driving the evolution of venom and venom delivery mechanisms in sea anemones.

1. The role of RNA modifications in translation regulation – how rRNA modifications control ribosome function and its translational capacity?
2. Hematopoiesis – We aim to understand how translation-regulation controls hematopoietic stem cell function and the generation of blood cells.  
3. Ribosome hijacking during Viral infection – We explore how pathogens, like viruses, utilize the host’s ribosome to their own advantage to facilitate viral replication and disease manifestation.  

1. Movement ecology: A new transdisciplinary paradigm to study movement of organisms across multiple spatial and temporal scales.
2. Lifetime tracks of organisms, their underlying mechanisms, their use to assess the species' ecology and biology, and what elements are most critical for fitness.
3. Ecology, evolution and behavior of various phenomena related to movement – including migration, search, foraging, dispersal, wandering, exploration, navigation and spread of diseases – in birds and fruit bats.
4. The relationships between sociality and social rank, movement, performance and fitness.
5. Development of new tracking devices and data analysis tools for movement ecology.
6. Management of huge datasets in the emerging Big Data era of movement ecology.
7. Spreading of invasive plants and long-distance dispersal. 

1. Structure of PSI in various photosynthetic organisms
2. Reconstruction of artificial photosynthetic systems
3. Characterization of the protein mitoNEET which is involved in iron homeostasis

1. Transformations of sensory representations in the ascending auditory system.
2. Perception-action loops - quantifying information processing in auditory-driven behavior.
3. Statistical learning in audition.

1. Characterization of novel transcription factors regulating gebe expression of steroidogenic hormones in mammalian ovaries and uterus during ovulation and fetal development during pregnancy.
2. Degradation of mitochondrial proteins following hormonal stress conditions

1. Group II introns splicing in plants organelles: Regulation of organellar gene expression
2. The roles of various RNA-binding cofactors in the splicing of organellar transcripts
3. Establishment of an in vitro splicing system for plant organellar group II introns
4. The establishment of Mitochondrial Mutant Libraries (MML’s) in plants
5. Insights into the composition and assembly of plant mitochondria respiratory complexes
6. Environmental effects on plant mitochondria biogenesis

1. Structure and function of NhaA Na+/H+ antiporter, an example of membrane proteins that comprise 30% of the proteome.
2. Structural and functional dynamics of NhaA Na+/H+ antiporter.
3. Molecular biology of adaptation to salts in bacteria.
4. Molecular biology of adaptation to pH in bacteria.

1. Maternally inherited mRNAs, and their role in development
2. The role of RNA regulation (stability, localization, translation etc.) in cellular differentiation and embryogenesis.
3. How is genetic information on mRNA regulation encoded in the genome?

1. Chromatin regulation during differentiation
2. Single cell Microfluidics technology development
3. Enhancer regulation and Epigenetics
4. Heterogeneity in biological systems
5. Computational biology
6. Chromatin and cell cycle 

1. Identification and characterization of intracellular protein quality control pathways, focusing on degradation.
2. Characterization of proteomic changes during aging, with emphasis on protein degradation.
3. Identification and characterization of DEGRONS: Signals within proteins that trigger degradation.
4. Mechanisms of membrane protein degradation by the ubiquitin-proteasome pathway.

1. Protein engineering and design
2. Protein evolution
3. Design of new therapeutic proteins from various natural scaffolds — better drugs for cancer treatment
4. Understanding basic principles of protein binding interactions

1. Mapping and characterization of genetic variations involved in brain disorders, such as autism and schizophrenia, using computational analysis of genomic data.
2. Studying genes and proteins associated with brain disorders using molecular tools.
3. Studying brain development and function using embryonic stem cells and neuronal cell lines.
4. Mouse as a model for brain disorders: influence of genes on brain and behavior.
5. Application of crispr pooled libraries to study genetic interactions.

1. Repair of DNA breaks during meiosis in yeast as a source of new mutations.

2. Involvement of error-prone DNA polymerases in mutagenicity during meiosis.

3. Evolutionary impact of enhanced mutagenicity during meiosis.

In collaboration with: Dr. Ayelet Arbel-Eden, Senior Lecturer at Hadassah Medical College (ayeletar@hadassah.ac.il).

1. Mis-regulation of RNA metabolism in the mammalian brain: From acute stress responses to neurodegenerative diseases.
2. Fire, wire and inspire rules of cholinergic signaling: From structure to mental function in health and disease.
3. Non-coding RNAs and micro-RNAs in brain-to-body communication. 

1. The endogenous spliceosome – structure and function in controlling posttranscriptional gene expression.

2. A new quality control mechanism within the endogenous spliceosome.

3. Small non-coding RNA as novel regulators of RNA processing and splicing.

4. Nuclear microRNA in cancer.

1. Structural studies of the immune recognition of Hepatitis C virus (HCV) to facilitate structural-based vaccine design. 
2. Development of a small-scale expression and solubility screening system for viral envelope glycoprotein.
3. Structural studies of the entry mechanism of HCV-related hepaciviruses.
4. Structural and biochemical studies of the interactions between the HCV envelope glycoprotein and host cell receptors.

1. Three-dimensional structure and the mechanism of action of telomerase.
2. Genetic diseases of telomere dysfunction such as dyskeratosis congenita, Hoyeraal-Hreidarsson syndrome and Coats plus.
3. How telomeres control cell proliferation and prevent cancer.
4. The role of helicases in telomere structure and maintenance.

1. Trans-generational epigenetic memory.
2. Genetic and neuronal mechanisms underlying Learning and Memory, Aging and Neurodegenerative diseases.
3. Systems Biology of how genes and neural networks shape behavioral outputs.
4. Computational Biology - how sensory systems encode the environment (experiments and theory).