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News
scholarship Congratulations to Michal Chorev for winning the 2014 Google Anita Borg Memorial Scholarship.

July-2014
conference Liran was a keynote speaker in the AllBio/SeqAhead workshop (Epigenomics, coding and non-coding RNAs - Challenging NGS data) in Bari, Italy.

June-2014
scholarship Michal Chorev and David Gokhman presented in the SMBE conference at Puerto Rico. Both works drew much attention and interest. Here is Michal presenting ...

June-2014
new paper New paper in Science!
David Gokhman, Eitan Lavi, Kay Prüfer, Mario F. Fraga, José A. Riancho, Janet Kelso, Svante Pääbo, Eran Meshorer and Liran Carmel, Reconstructing the DNA methylation maps of the Neandertal and the Denisovan, Science (2014).

In this paper we reconstruct the full DNA methylation maps of the Neandertal and the Denisovan by harnessing the natural degradation processes of methylated and unmethylated cytosines. Comparing these ancient methylation maps to those of present-day humans, we identified ~2000 differentially methylated regions (DMRs). Particularly, we found substantial methylation changes in the HOXD cluster that may explain anatomical differences between archaic and present-day humans. Additionally, we found that DMRs are significantly more likely to be associated with diseases like Autism, Schizophrenia and Alzheimer. This study provides insight into the epigenetic landscape of our closest evolutionary relatives, and opens a window to explore the epigenomes of extinct species.
Coverage: The paper had been selected to Science Express, and was covered in more almost 300 news and science websites ,and in close to 40 countries. The coverage includes Science, Nature, The New Scientist, NBCnews, Yahoo News, and many others. We try to keep track of all references here, although the list is not complete and constantly updated.

Apr-2014
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.
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 @ cc.huji.ac.il
The Hebrew University
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