New paper from the lab appeared
online. The paper had been accepted to the webserver annual issue of Nucleic Acids
. In this work, we built a database of gene-body part associations, and
designed a webserver to browse this database, and to identify body parts enriched or
depleted within a list of genes. We expect this tool to be very useful in a variety of
evolutionary and medical studies.
David Gokhman, Guy Kelman, Adir Amartely, Guy Gershon, Shira Tsur, Liran Carmel (2017).
Gene ORGANizer: Linking Genes to the Organs They Affect, Nucleic Acids Research,
Congratualtion to David Gokhman who is the 2017 recipient of the Dan David
Prize Scholarship for the Past time dimension in the field of Archaeology and
Congratualtion to David Gokhman who recieved the prestigious Human Frontiers
Science Program (HFSP) postdoctroal award.
Our JuncDB database and
web server are referenced in OMICtools
Yoav was interviewed in Makademia (Radio show) on his work. In the fascinating interview
(in Hebrew). He talked about brain, evolution and human cognition.
Our lab deals with a host of topics in the general fields of molecular evolution
Among the topics that are currently actively pursued are:
- Recent human evolution. Recent advances in ancient DNA sequencing yielded complete high-coverage
genomes of the Neandertal and the Denisovan. We devise algorithms that predict the DNA methylation along
ancient DNA, and identifies genes that are differently activated in present-day humans.
- Gene architecture. We study conservation of gene architecture by means of intronic positional
conservation. This is an extension of the more "standard" sequence and structure evolutionary
conservation modes. We are interested in the quantification of this conservation, and in studying its
implication on our understanding of intronic functions.
We also study the evolutionary forces that have led to the wealth of gene architectures seen across the
eukaryotic domain. This includes the identification of evolutionary trends, and the study of mechanisms
of intron gain and loss.
- Splicing. We study the functional roles of splicing in general, and of alternative splicing in
particular. We develop a tool to estimate the effect of splicing on normal splicing patterns, and its
connection to human diseases.
- Massive parallel sequencing. We are involved in a number of projects that involve the analysis
of next-generation sequencing data. Among these are identifying human disease-causing
mutations, and studying the mutational spectrum of meiosis in yeast. We mainly
use resequencing and RNA-seq analysis.
- Nonsense mediated decay (NMD). We are interested in the mechanism that recognizes a premature
termination codon in mammals, and its relationship with introns in the 3'UTR.
- Phylogenetics. We are interested in various aspects of rooting phylogenetic trees.
- Systems biology. We characterize the dynamics of gene architecture in individual genes,
and are interested in studying the connections between this dynamics and other genic features.
- Multivariate data analysis. My lab is also active in some fields of applied mathematics:
multivariate analysis, statistical pattern recognition, data visualization, and machine learning.