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conferenceDavid Gokhman gave his PhD talk today. Graduating soon ...

conferenceLiran Carmel was a keynote speaker at the Sydney Bioinformatics Research Symposium 2017 that was held at Sydney University.

scholarship Congratualtion to David Gokhman who recieved the Zuckerman fellowship for his upcoming postdoctroal studies.

scholarship David Gokhman receiving the prestigious Dan David Prize Scholarship for the Past time dimension in the field of Archaeology and Natural Sciences, at the ceremony in Tel-Aviv University.

Gene ORGANizer Gene ORGANizer was featured in LabWorm, where it collected the highest number of weekly upvotes, as well as in OMICtools.

Gene ORGANizer New paper from the lab appeared online. The paper had been accepted to the webserver annual issue of Nucleic Acids Research. 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, in press.

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.
Interview Yoav Mathov was interviewed in Makademia.

MovieLiran was 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.

Our Web Servers
Movie Gene ORGANizer connects genes to the body parts where their phenotype is observed. Given a list of genes, Gene ORGANizer finds body parts in which these genes are enriched or depleted. The paper is about to appear in the webserver issue of NAR, but can already be found online.

Movie JuncDB is a gene exon-intron architecture comparative database, covering nearly 40,000 sets of orthologous transcripts across 88 eukaryotic species. It had been published in the database issue of NAR.
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 liran.carmel @
The Hebrew University
Useful links: for more details and full list