New paper from the lab in Molecular
Biology and Evolution
. Rasmus Nielsen and his lab members found a region the
underwent strong positive selection in Inuits and other native Americans, which was likely
introgressed from an archaic population closely related to the Denisovans. David helped them
by analyzing the differences in DNA methylation patterns in this region between introgressed
and non introgressed invidivuals, and how they relate to the Denisovan methylation patterns
and to the expression level of the genes.
Fernando Racimo, David Gokhman, Matteo Fumagalli, Amy Ko, Torben Hansen, Ida Moltke,
Anders Albrechtsen, Liran Carmel, Emilia Huerta-Sánchez, Rasmus Nielsen (2016) Archaic
adaptive introgression in TBX15/WARS2, Molecular Biology and Evolution, in press.
New paper from the lab in BMC
. Fouad studied what features trigger EJC-independent NMD, and concluded
that is all about nucleotide composition around the stop codon, which determines the abundance
of RNA secondary structures that form there.
F. Zahdeh , L. Carmel (2016) The role of nucleotide composition in premature
termination codon recognition, BMC Bioinformatics 17:519.
New paper from the lab in Functional
. We helped to Dr.
and his student Topaz to analyze data about lizard mobility and body coloration.
We showed that striped body patterns characterize mobile lizards, whereas more statisc lizards tend
to have cryptic body patterns. The idea is mobile lizards and more prone to detection, and their
longitudinal stripes help to blur their shape while running.
The paper can be accessed online
at the journal website.
T. Halperin , L. Carmel , D. Hawlena (2016) Movement correlates of lizards' dorsal
pigmentation patterns, Functional Ecology, in press.
Welcome Yoav Mathov
to the lab.
Yoav starts a direct PhD program in the lab, as an ELSC student.
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.