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welcomeWelcome Avigayel Rabin to the lab. Avigayel starts her PhD in our lab, jointly with the lab of Sebastian Kadener. She is going to focus on circular RNAs.

new paper New paper from the lab in PLoS ONE . The work was led by Prof. Dan Mishmar 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.

conferenceLiran Carmel gave a talk at the conference 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 New paper from the lab in the database issue 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 Research (2016).

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 publication #41 for more details.

Research Interests:
Our lab deals with a host of topics in the general fields of molecular evolution and genetics. 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.
MovieLiran is interviewed at London et Kirshenbaum about Otzi's helicobacter. Minutes 29:42 to 34:33.

MovieOur research on archaic gene regulation is on youtube! A narration accompanied by whiteboard animation.

MovieHUJI researchers had participated in a cooking event, with the chef Anat Lesem from Sartaki at the Mahane Yehuda market. We got to do the molecular Sorbet. Watch!
Our Web Servers
Movie Gene ORGANizer connects genes to body organs and body system. Given a list of genes, Gene ORGANizer finds body organs in which these genes are enriched or depleted. The web server is still under development, and not published yet, but it is already open for use by the community.

Movie JuncDB is a gene exon-intron architecture comparative database, covering nearly 40,000 sets of orthologous transcripts across 88 eukaryotic species. Accepted for publication at the upcoming database issue of Nucleic Acids Research, see online version.
Contact Information:
Room 2-342
Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science,
the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
telephone +972 (2) 658-5103
fax +972 (2) 658-4856
email carmell @
The Hebrew University
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