Profossor C. Lee and professor J. Majewski conduct research in alterbative splicing using bioinformatics method.
Professor Lee : http://www.uclaaccess.ucla.edu/UCLAACCESS/Web/Faculty.aspx?ri=434
Professor J. Majewski: http://genomequebec.mcgill.ca/majewski/
Need a review of their method and focus.
Professor Black, Doug also engage research in alternative splicing, from a more traditional chemical and biological perspective
Friday, October 27, 2006
Sunday, October 22, 2006
Bioinformatics -- Andy Baxevanis Ouellette BFF
Baxevanis, A.D and Ouellette B.F.F coauthored a book Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. This book is updated to the 3rd edition in 2005.
Baxevanis's previous work focus on computation analyis of disease-causing mutations from a structural standpoint, using innovative approaches to deduce the prisece structure change in protein cause by a specific genetic mutation. (What method?)
During the early development of microarray, Baxevanis's group developed the first publicly available program to restore and analyze microarray data.
Now, Baxevanis's group the group developed a software program known as GeneLink, which enables researchers to analyze large data sets from studies of complex-trait genetic disorders, such as cancer, diabetes, and hypertension, which involve many genes along with environmental factors.
Quelette is the head of UBC Bioinformatics Centre (UBiC) and this graduate program is worth of time to have a look.
Baxevanis's previous work focus on computation analyis of disease-causing mutations from a structural standpoint, using innovative approaches to deduce the prisece structure change in protein cause by a specific genetic mutation. (What method?)
During the early development of microarray, Baxevanis's group developed the first publicly available program to restore and analyze microarray data.
Now, Baxevanis's group the group developed a software program known as GeneLink, which enables researchers to analyze large data sets from studies of complex-trait genetic disorders, such as cancer, diabetes, and hypertension, which involve many genes along with environmental factors.
Quelette is the head of UBC Bioinformatics Centre (UBiC) and this graduate program is worth of time to have a look.
Saturday, October 21, 2006
Bioinformatics -- Philip E. Bourne , Helge Weissig
This post is about Philip E. Bourne , Helge Weissig, two pioneer in structural bioinformatics. They coauthored a book Structural Bioinformatics. P.E.Bourne sumerize his lab's goal as follows in UCSD.
Helge Weissig's work centers around the research and education in strutural bioinformatics. His personal wedsite provide good directions on resoures in this field and a serise introductory courses
http://www.bioinformaticscourses.com/
P.E.Burne's group develop and maintain several databases"Our goal is to undertake in silico bioinformatics-related research and education. Along the way we develop resources, for example, the RCSB Protein Data Bank(PDB) and the Immune Epitope Database (IEDB), for use by the community. We view these resources as being as important as disseminating our science through the scientific literature. We firmly support open access to the scientific literature through our work with the Public Library of Science and free access to our software"
Biological Structure | |
| The single worldwide source of primary structural data on biological macromolecules determined experimentally. Developed in collaboration with |
| The main goal of this resource is to better understand principles behind structural domains identified from 3D coordinates ref . |
| Pair-wise structure comparisons based on the Combinatorial Extension (CE). |
| Compilation of recurring protein substructures. | |
| Use of structure comparison to extend the coverage of GO terms in the PDB. | |
| Automated classification of protein-DNA complexes of known structure. | |
| Starting from CE pair wise alignments a multi-structure alignment is computed using a |
| Signal Transduction | |
| A compilation of structures, structure alignments, sequences and sequence alignments for the protein kinase family. |
| Apoptosis | |
| Known domains involved in apoptosis and associated sequence alignments. | |
| Immunology | |
| Information that facilitates the dissemination of immune epitope information, the generation of new research tools, diagnostic techniques, vaccines and therapeutics for emerging and re-emerging diseases. |
Helge Weissig's work centers around the research and education in strutural bioinformatics. His personal wedsite provide good directions on resoures in this field and a serise introductory courses
http://www.bioinformaticscourses.com/
Friday, October 20, 2006
Bioinformatics -- Sean Eddy
Sean Eddy's most significant contribution is that he suggests and developed many tools based on probabilistic models of biological sequence and structure. Hidden Markov models (stochastic regular grammars) are useful for primary structure analysis of proteins and DNA. Stochastic context-free grammars are ideal for analysis of RNA secondary structure.
His work in this area is summerized his book
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
by Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme Mitchison
Now, he focus on identifying novel structural and catalytic RNAs. He proposed the "modern RNA hypothesis" stating that: far from being a few scattered relics, RNAs are in fact in widespread use in modern organisms in a variety of roles. We now argue for a “modern RNA world” hypothesis: many of the RNAs we see today are modern inventions, highly adapted to regulatory roles in complex organisms.
His work include include the HMMER profile HMM search software and the Pfam protein domain database; the Infernal structural profile SCFG search software for RNAs and the Rfam RNA domain database; and the QRNA genefinding program for ncRNA genes.
He also apply probabilistic modeling and other computational algorithms to identify interesting genetic features in large-scale DNA sequence.His work in this area is summerized his book
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
by Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme Mitchison
Now, he focus on identifying novel structural and catalytic RNAs. He proposed the "modern RNA hypothesis" stating that: far from being a few scattered relics, RNAs are in fact in widespread use in modern organisms in a variety of roles. We now argue for a “modern RNA world” hypothesis: many of the RNAs we see today are modern inventions, highly adapted to regulatory roles in complex organisms.
Monday, September 04, 2006
Quotations: Microarray: Quality Control
Today I read a paper Microarray: Quality Control in Nature , and copy some quotations of masters in these field. Funny? Maybe, we need a master to lead the way.
The challenge is no longer how to generate these vast bodies of genomic data, but rather in how to best collect, manage, and analyze the data.
Changing these algorithms (used to convert spot flurescence to gene-expression estimates.) can make a difference, and you can turn an experiement that looks just so-so into something that looks powerful and precise.
We are facing too many options for analyzing the same data set, and there has not been adequate scientific vetting of the capabilities and and limitations of available methods.
High-quality samples and high-tech instrumentation alone won't save the microarray experiment. Some of the most fundamental challenges lie in gleaning biological signicance from mounds of data and designing experiments with a statistically sound foundation
The challenge is no longer how to generate these vast bodies of genomic data, but rather in how to best collect, manage, and analyze the data.
by John Quackenbush
Changing these algorithms (used to convert spot flurescence to gene-expression estimates.) can make a difference, and you can turn an experiement that looks just so-so into something that looks powerful and precise.
by Rafael S. Irizarry
We are facing too many options for analyzing the same data set, and there has not been adequate scientific vetting of the capabilities and and limitations of available methods.
by Leming Shi
High-quality samples and high-tech instrumentation alone won't save the microarray experiment. Some of the most fundamental challenges lie in gleaning biological signicance from mounds of data and designing experiments with a statistically sound foundation
by Michael Eisenstein
Wednesday, August 30, 2006
I am playing gample
These days I have been spending hours surfing the websites of Graduate school in order to find a right school in the meaning that I will be proud of entering it and it will be satisfactory of accepting me. There are so many schools and so many mentors that I can not make a choice. I am just playing a gamble.
When I decided to enter an university three years ago, I didn't have such a tough time because my family helped me and the universities are in China. But this time, I am going to study in America which I have never been and is unfamiliar with. It is said America has many good schools and more opportunities. Like the people on the boat of Mayflower, I cherish this dream and take the risk to pursue it.
This morning, my roommates, who is also preparing to study overseas, told me he dreamed that I reveived many offers last night. I hope it is a good signal to me.
When I decided to enter an university three years ago, I didn't have such a tough time because my family helped me and the universities are in China. But this time, I am going to study in America which I have never been and is unfamiliar with. It is said America has many good schools and more opportunities. Like the people on the boat of Mayflower, I cherish this dream and take the risk to pursue it.
This morning, my roommates, who is also preparing to study overseas, told me he dreamed that I reveived many offers last night. I hope it is a good signal to me.
Thursday, August 24, 2006
When gmail disabled
Were your gmail disabled? I noticed a discusion about this problem. If you have any browser extensions, toolbars, or third party software intended to interact with Gmail, especially when such software involves too much data transfer, Google may decide to disable your gmail account, some temporaliry, some for ever. Goole list some example, such as GmailFS, Greasemonkey. I myself understand the justice of google's actions, and believe that google won't betray its don't be evil motto, thought I noticed greasemonkey, one of my favourite firefox extensions, is on google's blacklist .
If your gmail is unfortunately banned by google,there is a site to complain https://mail.google.com/support/bin/request.py?lockout=1
If your gmail is unfortunately banned by google,there is a site to complain https://mail.google.com/support/bin/request.py?lockout=1
[From Google Reader] Related articles in Google Scholar
Related articles in Google Scholar
Google Scholar recently added the ability to find related articles for a paper. Its is a link Related Article together with cited by and webseach attched to each search result. if not notified by offical google blog post, I would have neglected it. Some one tried it, and writes:
Google Scholar recently added the ability to find related articles for a paper. Its is a link Related Article together with cited by and webseach attched to each search result. if not notified by offical google blog post, I would have neglected it. Some one tried it, and writes:
"so I decided to try it out with a paper from my former life as a graphics person. It was a paper in SIGGRAPH a few years ago called the "Office of the Future" and it dealt with projecting images onto surfaces that aren't exactly flat. If you predistort an image before you project it, you can often cancel out the different surfaces as you project onto them, which lets you create the appearance of a flat screen again. Here's a picture that gives you the idea. It's completely unrelated to me or the paper, but it demonstrates the concept really well (I just did a flickr search for [projection surface] and found a nice result–thanks flickr! I don't read German,... Source: http://www.mattcutts.com/blog/related-articles-in-google-scholar/ "
Wednesday, August 23, 2006
Matlab-SP3
Matlab 7 With Sp3
Matlab 7 With Sp3 (full 3 Cd ISO)
Key Features:
High-level language for technical computing
Development environment for managing code, files, and data
Interactive tools for iterative exploration, design, and problem solving
Mathematical functions for linear algebra, statistics, Fourier analysis, filtering, optimization, and numerical integration
2-D and 3-D graphics functions for visualizing data
Tools for building custom graphical user interfaces
Functions for integrating MATLAB based algorithms with external applications and languages, such as C, C++, Fortran, Java, COM, and Microsoft Excel
31 parts x 50 MB
Download links in coments.
MATLAB is a high-level technical computing language and interactive environment for algorithm development, data visualization, data analysis, and numeric computation. Using MATLAB, you can solve technical computing problems faster than with traditional programming languages, such as C, C++, and Fortran.
You can use MATLAB in a wide range of applications, including signal and image processing, communications, control design, test and measurement, financial modeling and analysis, and computational biology. Add-on toolboxes (collections of special-purpose MATLAB functions, available separately) extend the MATLAB environment to solve particular classes of problems in these application areas.
MATLAB provides a number of features for documenting and sharing your work. You can integrate your MATLAB code with other languages and applications, and distribute your MATLAB algorithms and applications.
You can use MATLAB in a wide range of applications, including signal and image processing, communications, control design, test and measurement, financial modeling and analysis, and computational biology. Add-on toolboxes (collections of special-purpose MATLAB functions, available separately) extend the MATLAB environment to solve particular classes of problems in these application areas.
MATLAB provides a number of features for documenting and sharing your work. You can integrate your MATLAB code with other languages and applications, and distribute your MATLAB algorithms and applications.
Key Features:
High-level language for technical computing
Development environment for managing code, files, and data
Interactive tools for iterative exploration, design, and problem solving
Mathematical functions for linear algebra, statistics, Fourier analysis, filtering, optimization, and numerical integration
2-D and 3-D graphics functions for visualizing data
Tools for building custom graphical user interfaces
Functions for integrating MATLAB based algorithms with external applications and languages, such as C, C++, Fortran, Java, COM, and Microsoft Excel
31 parts x 50 MB
Download links in coments.
1 Comments:
Friday, August 11, 2006
Why my blog is called warm sping harbor lab
I invent the term Warm Spring Harbor Lab myself with the inspiration of the famous Cold Spring Harbor Lab, a international biological science research institute which sees the revolution of molecular biology. WSHL is a kind joke of CSHL. Another source is that the Anhui province, in which my university locates, actually have many warm springs in the Huangshan Mountain region. The third consideration is that I am always thinking of this term. I hope to set up such a institute in China, and promote the development of science in my country.
I used to think I am the first one to invent this term. However, I google it just now and found a papers in Science magazine published in 2004 had touched this name. Unfortunately, I fall behind.
I used to think I am the first one to invent this term. However, I google it just now and found a papers in Science magazine published in 2004 had touched this name. Unfortunately, I fall behind.
Avril Lavigne
My idea changed when I come to losing grip, the first song of the album Complicated. Her style is a little like Sun Yanzi, relaxed and comfortable. I continued. the song complicated convert me to a funs of Avril. And then,Tomorrow. The voice souds so sweet that I feel my sweetheart whisp around my ears.
I have just listen to Avril, I can only recommend the following
- complicated
- skater boy
- tomorrow
Monday, June 26, 2006
Saturday, April 22, 2006
Avoiding RSI
Avoiding RSI: "Posted by Dr. Taraneh Razavi, M.D., Staff Doctor
From time to time, a resident physician at Google headquarters weighs in with her thoughts on healthy living. This is not medical advice, and you should check with your own doctor before pursuing any particular course of action.
There is a Chinese saying that 'To go beyond is as wrong as to fall short.' In other words, how long can you tap on that keyboard or sit in that chair before you hurt yourself. We’re not designed to remain as sedentary or perform the fine motor movements for the long uninterrupted hours that we have to do in so many of our jobs. Evidence suggests that prolonged abnormal posture and repetitive movements contribute to neck, limb and back pain. These conditions are collectively known as overuse syndromes, or repetitive stress injury (RSI).
RSI is no small matter. It accounts for 34% of all lost-workday injury and illness — and costs almost $20 billion annually, according to the Bureau of Labor Statistics. The National Academy of Sciences has concluded that an estimated $"
From time to time, a resident physician at Google headquarters weighs in with her thoughts on healthy living. This is not medical advice, and you should check with your own doctor before pursuing any particular course of action.
There is a Chinese saying that 'To go beyond is as wrong as to fall short.' In other words, how long can you tap on that keyboard or sit in that chair before you hurt yourself. We’re not designed to remain as sedentary or perform the fine motor movements for the long uninterrupted hours that we have to do in so many of our jobs. Evidence suggests that prolonged abnormal posture and repetitive movements contribute to neck, limb and back pain. These conditions are collectively known as overuse syndromes, or repetitive stress injury (RSI).
RSI is no small matter. It accounts for 34% of all lost-workday injury and illness — and costs almost $20 billion annually, according to the Bureau of Labor Statistics. The National Academy of Sciences has concluded that an estimated $"
Friday, April 21, 2006
This year's Anita Borg Scholarship winners
This year's Anita Borg Scholarship winners: "Posted by April Yu and Jennifer Bostrom, University Programs
It's that time of year when we happily announce the winners of the 2006 Google Anita Borg Memorial Scholarship. We're awarding 19 $10,000 scholarships to these outstanding young women -- graduate and undergraduate students who are completing degrees in computer science and related fields -- with our congratulations:
Brianna Bethel, University of Colorado - Boulder
G. Ayorkor Mills - Tettey, Carnegie Mellon University
Gillian Rachael Hayes, Georgia Institute of Technology
Himabindu Pucha, Purdue University
Karen Fullam, University of Texas at Austin
Kristen Walcott, University of Virginia
Kristina Chodorow, New York University
Laura Rouse, Georgia Institute of Technology
Marta Magdalena Luczynska, Massachusetts Institute of Technology
Megan Olsen, University of Massachusetts Amherst
Michele Banko, University of Washington
Neven Abou Gazala, University of Pittsburgh
Parisa Michelle Tabriz, University of Illinois, Urbana-Champaign
Rebecca Nancy Nesson, Harvard University
Shana Kay Watters, University of Minnesota
Sharmishtaa Sesha"
It's that time of year when we happily announce the winners of the 2006 Google Anita Borg Memorial Scholarship. We're awarding 19 $10,000 scholarships to these outstanding young women -- graduate and undergraduate students who are completing degrees in computer science and related fields -- with our congratulations:
Brianna Bethel, University of Colorado - Boulder
G. Ayorkor Mills - Tettey, Carnegie Mellon University
Gillian Rachael Hayes, Georgia Institute of Technology
Himabindu Pucha, Purdue University
Karen Fullam, University of Texas at Austin
Kristen Walcott, University of Virginia
Kristina Chodorow, New York University
Laura Rouse, Georgia Institute of Technology
Marta Magdalena Luczynska, Massachusetts Institute of Technology
Megan Olsen, University of Massachusetts Amherst
Michele Banko, University of Washington
Neven Abou Gazala, University of Pittsburgh
Parisa Michelle Tabriz, University of Illinois, Urbana-Champaign
Rebecca Nancy Nesson, Harvard University
Shana Kay Watters, University of Minnesota
Sharmishtaa Sesha"
Thursday, April 06, 2006
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