Prof. Alexander Bolshoy
Study of HIV Latency
- Chromatin structure at HIV-1 integration sites.
- Chromatin organization of the HIV-1 promoter.
Evolution of RNA Viruses
- Interplay between conservation and variability (in HIV-1):
- How do viruses ensure robustness against genetic and environmental perturbations?
- How do viruses simultaneously achieve sufficient plasticity to adapt to changing environments?
- Overlapping Codes in RNA Viral Genomes
- Usually, the phenomenon of overlapping is explained by the need to store large quantities of information in a small genome. The model that we presented a few years ago is in general accord with previous models associating high mutation rate with message overlapping. However, unlike the previous models, our analysis suggested a direct evolutionary advantage for message overlapping under conditions of high mutation rate.
- Objective: to develop a more general evolutionary model of overlapping in retroviruses
- Population Dynamics of RNA Viruses.
- DNA linguistics.
- How to measure information contained in DNA texts.
- Sequence complexity measures
Curvature Distribution in Prokaryotes
Dr. Leonid I. Brodsky
- Algorithmic approaches to analysis of high-throughput biological data.
- Computational metabolomics
- Systems biology dynamic modeling of biological processes
- Integration of metabolome, transcriptome, and genome data
- 3D structures of proteins and their interactions with small molecules
- MicroRNA: regulation mechanisms in cell signal transduction pathways
Prof. Abraham B. Korol
- Evolutionary adaptation to stressful environments using Drosophila as a model .
- Population genetics of multilocus systems (including non-linear dynamics).
- Recombination variability, evolution of sex and recombination.
- Genome evolution and structure on the above-gene level.
- Genome mapping, including multilocus mapping and physical mapping.
- Genetics of quantitative traits and its evolutionary and practical applications.
Corresponding studies of the lab are based on intimate interaction between field observations, laboratory experimentation, and theoretical analysis (using both mathematical modeling and computer simulations). Beside Drosophila, our studies target also other organisms (in collaboration with other labs, both within and outside the Institute of Evolution) that include plants, fungi, mammals, and humans. The main fields of our activity are related to evolutionary genetics and genomics (experimental and theoretical), genome structural and functional analysis, and bioinformatics.
Dr. Sagi Snir
Our research is focused on mathematical and algorithmic solutions to problems in bioinformatics, in particular in the field of evolution. The tools we use are from fields such as combinatorial optimization, statistics and probability, mathematics, and information theory. Our research is characterized by ample collaborations with researchers from broad disciplines under the general framework of a systematic analysis of evolutionary processes aiming at finding biologically significant patterns. Below are the main field we focus at:
Phylogenetics, the reconstruction of the evolutionary history of a group of species, is increasingly integrated into modern biological areas such as preventive medicine and epidemiology. Understanding the biological mechanisms underlying the observed evolution of pathogen species is crucial for devising effective control strategies for important human, animal and plant diseases. Moreover, in light of the high mutational and speciation rates among RNA viruses, extremely accurate modeling and reconstruction is called for. Maximum Likelihood (ML) is currently considered as the most accurate phylogenetic method. In past works I developed analytical solutions to ML reconstruction. The novelty of that approach was application of algebraic geometry tools for obtaining the solution. These works have since sparked a wave of interest in the field, in particular at UC Berkeley where I later took on a position as a postdoctoral research fellow.
Another field I am pursuing is supertree reconstruction that is used for large scale phylogenetic reconstruction. Here, we developed an extremely fast method that is inspired by ideas of finding a maximum cut in a weighted graph by means of semidefinite programming (SDP). The method is used by leading labs in the world and has yielded several publications, both practical and theoretical.
Horizontal gene transfer (HGT), the passage of genetic material between genetically distant organisms, is a significant factor in microbial evolution, driving the diversification and speciation of microorganisms, especially pathogens. HGT plays a role in the emergence of novel human diseases, as well as promoting the spread of antibiotic resistance in bacteria species. The unexpectedly high frequency of HGT among prokaryotes made it a topical area in microbiology and medical research. Our research of HGT proceeds along seemingly unrelated tracks. In the first, the phylogenetic track, we have formulated several rigorous frameworks to detect and analyze HGT. These works were the first to model realistically HGT. We formulated both combinatorial and statistical models for the HGT phenomenon.
On a second, the sequence based track, we seek for intrinsic clues for HGT in the organism genomes. The advantage here is the speed of the methods and the alleviation of tasks such as sequence alignment or phylogenetic reconstruction. The method is able to trace HGT events in a community of organisms.
Sequence alignment – the grouping of homologous bases into one column – is fundamental to almost any task in comparative genomics. This translates to positing gaps in the genomic sequences to account for events of insertions and deletions (indels). The interrelationship between sequence alignment and phylogenetic reconstruction has drawn substantial attention recently. We have developed a combinatorial (as opposed to statistical) approach based on indel history. The novelty of this approach is the distinguishing between insertions and deletions and augmenting the analysis a dimension of “depth” extending it from the sequence space.
Prof. Edward N. Trifonov
- Deciphering of the codes carried by sequences.
- Sequence determinants of chromatin structure
- Modular structure of proteins
- Networks in protein sequence space
- Early molecular evolution and origin of life
The group currently studies nucleosome positioning patterns in various types of isochores, interaction between translation code and chromatin code, nature of gene splicing, evolution of protein sequences.