Welcome Avigayel Rabin
to the lab.
Avigayel starts her PhD in our lab, jointly with the lab of
. She is going to focus on circular RNAs.
New paper from the lab in PLoS ONE
. The work was led by Prof.
from Ben-Gurion University. The paper describes a tool, LEMONS, to infer genes
intron-exon architecture from transcriptomics data from species lacking a reference sequence. The idea
is to rely on intron positional conservation and use known gene architectures from closely related
species. The paper can be accessed online
at the PLoS ONE site.
L. Levin , D. Bar-Yaacov , A. Bouskila, M. Chorev, L. Carmel, D. Mishmar (2015) LEMONS - A tool
for the identification of splice junctions in transcriptomes of organisms lacking reference genomes,
PLoS ONE 10:e0143329.
Liran Carmel gave a talk at the
From genome to gene: causality, synthesis, and evolution
that was organized by the
Jacques Loeb Centre at Ben-Gurion University, and was held in Beer-Sheva.
New paper from the lab in the database
of Nucleic Acids Research
, describing our intron-exon gene architecture
database. The paper should appear at the traditional January issue of the journal, but can already
be viewed online
M. Chorev, L. Guy and L. Carmel, JuncDB: an exon-exon junction database, Nucleic Acids
In this work, we survey our gene architecture database, which is the largest of its kind, and covers
nearly 40,000 sets of orthologous transcripts across 88 eukaryotes. See
for more details.
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.