Active Projects
Intron positional conservation (Michal Chorev).
  • Build database.
  • map miRNAs on introns.
  • map snoRNAs on introns.
  • compute density of regulatory elements.
  • study positional bias of conservation.
  • Check probability of a gene to have zero introns, relative to the probability to have any number of introns that is greater than zero.
The splicing code (Noa Cohen).
  • Compare the two groups of introns:
    • length
    • GC-content
    • chromosome
    • strand
    • % repeats
    • identifying motifs
    • splicing signal strength
  • Write Matlab code for detecting BP
PTC recognition (Maayan Kreitzman).
  • Delineate pretermination codon distribution versus intron positions
  • Collaborate with Ilana on the tiling array data
  • According to prevailing theory, we are not supposed to see depletion of intorns in 3'UTRs of Drosophila. This should be easy to check. More generally, we should check 3'UTR intron abundance in lower eukaryotes.
  • We can look for Alu repeats in the 3'UTR, as a mechanism to generate a fold back.
Miosis in yeast (Ayal Gussow).
  • Duplicate key to Irit (Ayal).
  • Set a lecture with Mira (Ayal).
  • See that the 64-bit computer arrives (Liran).
  • Build simulation of translocations. Pick a chromosome with good coverage, simulate a translocation of fixed length (800bp, 1000bp maybe) from random location, and keep the coverage profile around the entire region of translocation (Ayal).
U12 evolution (Lotem Guy).
  • Integrate U12 information with main database (Lotem, Michal).
  • Study power in exponential distribution of the expression levels (Lotem).
  • Enhance statistical tests for depletion of U12 introns in highly expressed genes (Lotem).
  • Run EREM on U2, on U12, and on the integrated data (Lotem).
  • Build trinary evolutionary model (?).
Disease in Chr 17 (Irit Kisslov, Ayal Gussow).
  • How indels are observed and detected in BWA?
  • How SNPs are analyzed against databases in BWA results? In Bowtie results? How to distinct between known SNPs and sample-specific SNPs?
  • Map indels and SNPs into annotated exons.
  • What is the coverage level of the exons with respect to the annotations?
Inflammation (Stalled).
  • Find out what is special about small RNA measurements in 454. In what way it is different from other kinds of measurements.
  • Learn how to use Matlab to read SFF files. What is the content of these files.
  • Are the short reads in the fasta files simply the small RNAs?
Active Grants
  • Marie Curie International Reintegration Grants (IRG). Functional implications of the remarkable conservation of eukaryotic gene architecture.
    Grant number: PIRG05-GA-2009-248639.
    Acronym: FUNCTIONARCHITECTURE.
    Starting date: 01-Jan-2010.
    End date: 31-Dec-2013.
The Daphnia Genome Project
Conferences
Sites with a collection of conferences: Specific conferences:
Grants:
Tips for writing grants

Grants that can be submitted all year round:
DFG Bilateral project
The DFG funds bilateral Israeli-German research projects since the 1960s. In this scheme the principal investigator in Germany applies for and receives funds destined for his Israeli co-investigators. The work of the DFG serves all branches of science and the humanities to reflect its role as the self-governing organization of German science and research. The DFG is Germany`s national research foundation and geared at German scientists only. However: Israeli scientists may be added to a research proposal as "subcontractors." More details in ARD.
Swiss National Science Foundation - International short visits
The "International Short Visits" of the Swiss National Science Foundation (SNSF) allow for researchers working in Switzerland to go abroad, or for researchers from elsewhere to come to Switzerland. The visits can last between one week and three months and are limited to one person (the visiting fellow) going to one institution (the host institution). The visiting fellow and a person from the host institution (the host) are co-applicants of the proposal. More details in ARD.
Information on funded grants:
Item Computer Retrieval of Information on Scientific Projects (CRISP)
  Lists all grants funded by the US Public Helath Service, which includes the NIH, SAMHSA (Substance Abuse and Mental Health Services Administration), CDC, FDA, HRSA (Health Resources and Services Administration), and AHCPR (Agency for Health Care Policy and Research).
Item NSF
  Projects funded by the NSF since 1989.
Item Current Research Information System [CRIS] (the US Department of Agriculture)
Item Nasa Awards Taskbook (the National Aeronautics and Space Administration)
Item Community of Science
  Most federally funded grants, as well as those projects funded by the UK's Medical Research Council. Registration of the institute is required.

Information on available grants:
Item Grants.gov
  All federally funded grant activities. Still a work in progress.
Item Community of Science
Item Illinois Research Information Service (IRIS)
Item Grant Advisor
Item TRAM
Item Fundsnet Services
Item GrantsNet
Item Foundation Center
  private foundations, corporate-giving programs, and sources of non-profit giving.

Specific Grants:
Item BSF
  Except for the Regular research grant, there is also a start-up research grant that traditionally enjoys higher acceptance rates. Submission deadline: usually mid-November.
Item R03
  The sole purpose of the Foundation is the direct support of scholarship and research in universities and non-profit research institutions, primarily in Germany, with special emphasis on giving help to young scholars and scientists. They do not support research projects with no direct relation to disease. The following projects receive special support: (1) Functional analysis of genes for monogenous and complex genetic disease in vitro and in vivo. (2) Establishing and evaluating cell and animal models in Deseases with Genetic Basis. Analysis of ‚predisposing' genes or genes which modify the disease. Submission deadline: 16-Sep-2009.
Administration
Online report for sickness/reserve. Further information can be given by Edna Hazan 5882746, email: ednaha@savion.cc.huji.ac.il.

Instruction on transferring to Stage B PhD.
Bioinformatic tools:
All around players: Data mining: Gene Architecture: Gene data summary: Gene Expression: Gene Ontology: Genome browsers: Matlab Utilities: miRNA:
  • The MicroRNA.org website uses the miRanda algorithm to find miRNA targets. Precompiled data for known miRNAs in human, mouse, and rat.
  • Burge's TargetScan can look for targets in multiple species of both precompiled miRNAs, as well as use-provided seeds (nucleotides 2-8 of any miRNA.
Molecular Evolution: Motif discovery: Next Generation Sequencing: References: RNA folding: Tool Warehouses:
Hot Topics:
AS-disease
Human diseases related to damage to the normal splicing pattern.
AS-NMD
Possible regulatory role of AS coupled to NMD.
Evolution of spliceosomal introns
Evolution of gene architecture.
Experimental techniques
Very short summaries at the level of input/output.
Export
The mRNA export mechinary, and how it is related to splicing.
Function of spliceosomal introns
Functions associated with introns. How to reveal these function using intron positional conservation. Why other consrevation types fail.
Inflammation
What characterizes and regulates infalmmatory stress response.
Molecular Biology
General terms and concepts in molecular biology.
Molecular Evolution
Different topics in molecular evolution.
Nonsense mediated decay (NMD)
NMD, and especially its link to introns.
microRNAs
Types of sRNAs, algorithms to detect them
snoRNAs
Biology of snoRNAs
the Spliceosome
The assembly, composition, biogenesis of the spliceosome.
Splicing code
Evolution and prediction of splicing regulatory elements (SREs).
U12 introns
Evolution of U12 introns and the associated minor spliceosome.
Colleagues:
Key figures:
John Archibald John Archibald
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada.
E-mail: john.archibald@dal.ca

Laura Landweber Laura Landweber
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
E-mail: lfl@princeton.edu

Michael Lynch Michael Lynch
Department of Biology, Indiana University, Bloomington, IN, USA.
E-mail: milynch@indiana.edu

William Martin William Martin
Institut für Botanik III, Heinrich-Heine-Universität, Düsseldorf, Germany.
E-mail: w.martin@uni-duesseldorf.de
Interests: various aspects of molecular evolution, especially endosymbiosis, cell evolution, and plant evolution.
Paul Sharp Paul Sharp
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
E-mail: paul.sharp@ed.ac.uk

Ziheng Yang Ziheng Yang
Department of Biology, University College London, London, UK.
E-mail: z.yang@ucl.ac.uk

Evgeny Zdobnov Evgeny Zdobnov
The Computational Evolutionary Genomics group at the Swiss Institute of Bioinformatics, Geneva, Switzerland.
E-mail: evgeny.zdobnov@unige.ch

Jianzhi George Zhang Jianzhi George Zhang
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
E-mail: jianzhi@umich.edu