Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.cmm.msu.ru/FBB/year_02/science_1/diplom_2006/FoxChase.doc Дата изменения: Wed Dec 28 15:33:10 2005 Дата индексирования: Sat Dec 22 07:27:40 2007 Кодировка: koi8-r

Два проекта на диплом (годовых) от Fox Chase Cancer Center


Приглашаются два студента на 1 год - с лета 2006 до лета 2007г. для
выполнения дипломной работы в Fox Chase Cancer Center, США . Для этого
необходимо будет взять отпуск на год (о форме отпуска договариваться с
Петром Владимировичем).

С осени 2007года, после завершения дипломной работы, - продолжение учебы на
5м курсе и защита диплома.

Такой план одобрен деканатом 26 дек. 2005.


В идеале это должны быть совместные проекты FCCC-ФБиБи.


С вопросами можно обращаться к М.С.Гельфанду (/\/\ мг ) .


1) Roland Dunbrack: Protein structure prediction using Bayesian methods


My group develops methods for protein structure prediction and applies
these methods to problems of biological and clinical interest. We use
professional programming practices, including the use of C# and object-
oriented C++ developed in the Visual Studio environment and .Net. The
students should be encouraged to check out our webpages:


http://dunbrack.fccc.edu and especially http://dunbrack.fccc.edu/molide


They can also check out our published work:


http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=search&term=dunb
rack-r


Some specific topics:


- Methods for building 3-dimensional models of repeat proteins, such as
armadillo and HEAT repeats


- Visualization tools for molecular modeling, especially sequence
conservation superposed on structure for inclusion in our MolIDE program
(http://dunbrack.fccc.edu/molide)


- Structure modeling of families of proteins involved in cancer


- Development of automated modeling tools from multiple templates,
especially for large families with many known structures (e.g. antibodies,
kinases)


- Modeling of protein complexes from known protein complex structures


- Graph theory and computational geometry algorithms for protein modeling


2) J. Robert Beck: Integration of Biomedical Data


The Fox Chase Cancer Center has undertaken the creation of a data warehouse
to link clinical, outcomes, genetic, and functional genomics data to
support outcomes and translational research. This project is in the
prototype stage, with initial work focusing on bringing together data from
diverse information systems. The next step in the project will be to begin
linking diverse clinical data, as well as genotyping and gene expression
data. In order to bring these data types together, significant effort in
the area of biomedical and bioinformatics vocabularies, as well as in
syntactic relationships between systems is required. The project for an MSU
student will focus on development of semantic links between diverse data
types, utilizing the National Library of Medicine Metathesaurus and the
National Cancer Institute caBIG Enterprise Vocabulary Services. The work
will be focused initially on data for specific cancers, including lung and
prostate, with the requirement that semantics to be applicable in the
broader domain wherever feasible. The project will involve both high-level
ontological analysis and coding for prototyping.


The student will work directly with Dr. J. Robert Beck, who heads the data
warehouse project. In addition, the student should expect to work with
other members of the team, including Dr. Eric Ross, head of biostatistics,
Dr. Michael Ochs, head of bioinformatics, and the new biomedical
informatics faculty member (search is presently underway at Fox Chase). The
student will also be expected to interact with postdoctoral fellows and
graduate students working within these research groups.