The following message is official and has been approved by the appropriate authorities to be posted to this list. Dear MCB Students,
There are still two MCB URAP opportunities for fall 2005. Apply right away if you're interested. http://research.berkeley.edu:16080/urap/projects/index.lasso ~Anne ************* Professor Yang Dan Neural correlates of visual perception Deadline for this project (only) is extended to Thursday, September 15th, 5 PM. Applicants should enter a URAP application on line. Activate it by submitting paper copy directly to the faculty member's departmental mailbox. Apply as soon as possible. Do not wait until the deadline. The goal of our lab is to understand the structure, function and plasticity of the mammalian visual system. To this end, we use a combination of electrophysiological, psychophysical and computational techniques to analyze how visual information is coded in the spiking activity of neurons in the visual cortex. Many studies in visual coding have been carried out in anesthetized preparations, with the intrinsic limitation that one can't ask important questions such as (i) how do visual neuron responses correlate with the perception of the visual stimulus? (ii) do neurons in anesthetized and awake animals respond similarly to visual stimuli? (iii) how are visual neuron responses modulated by the behavioral significance of the visual stimulus? In order to be able to address these questions, we have become interested in developing visually-guided behavioral experiments in rats, with the goal of later combining these experiments with recordings from the rat visual cortex. We are now starting to run behavioral experiments in which rats are being trained to discriminate between different visual stimuli and we plan to evaluate the effect of different surround cues on this discrimination. This paradigm will complement other paradigms that we are interested in developing in the lab. Qualifications: Undergraduates working on this project will be expected to be involved in the development of the experimental paradigms as well as animal training and data analysis. Since this is still a new area for the lab, interested undergraduates will also have the opportunity to join other members of the lab as they develop software and new equipment for the behavioral tasks. The nature of the project requires that the student conducts experiments a minimum of 2 hrs per day, 6 days a week and assist a weekly lab meeting of 1.5hrs. Weekly Hours: more than 12 hrsRelated website: http://mcb.berkeley.edu/faculty/NEU/dany.html OR Professor Steven Brenner Project 1: Computational Approaches to Structural & Functional Genomics Deadline for this project (only) is extended to Thursday, September 15th, 5 PM. Applicants should enter a URAP application on line. Activate it by submitting paper copy directly to the faculty member's departmental mailbox. Apply as soon as possible. Do not wait until the deadline. We develop computational methods for the analysis and integration of molecular sequence and structure. Our aim is to understand organismal biology by interpreting the information encoded in complete genomes. This work is presently focused on the areas of structural and functional genomics. Structural genomics projects attempt to provide an experimental structure or a good theoretical model for every tractable protein in all completed genomes. Our work involves organizing proteins into families according to homology; classifying proteins and RNA according to structure; predicting structure from homology and constructing atomic coordinate models; providing information resources for structural genomics; developing methods for selection of proteins for experimental characterization; and analyzing solved structures to detect homology and functional information. We study computational functional genomics by creating algorithms using molecular sequence, structure, phylogeny, expression, and splicing information to infer the functions of genes. This work includes the use of gene genealogies to trace gene histories and functional divergences; reverse-genomics comparison of multiple complete genomes to locate genes associated with characterized cellular or biochemical functions; creation of databases of genomic information; integration and evaluation of splice data from various sources to make functional predictions; and continued refinement of sequence comparison methods. We also combine sequence comparison with expression and other experimental data to improve molecular and cellular functional characterization. Undergraduate projects are available in several of the group's areas of interest and will be tailored to the abilities and interests of the student apprentice and current membership of the group. Students should expect to spend at least 10 hours per week on the project. Qualifications: The ideal student will have a strong molecular biology background and considerable programming experience. Applicants with GPA less than 3.6 will be considered only in exceptional circumstances. Weekly Hours: 9-12 hrsRelated website: http://compbio.berkeley.edu --- Project 2: Critical evaluation of software that predicts structural characteristics of proteins from sequence Deadline for this project (only) is extended to Thursday, September 15th, 5 PM. Applicants should enter a URAP application on line. Activate it by submitting paper copy directly to the faculty member's departmental mailbox. Apply as soon as possible. Do not wait until the deadline. Much publicly available prediction software has only been tested on small sets of proteins, which may not adequately represent the diversity of proteins encoded by entire genomes. Similar prediction algorithms should be tested on large, diverse data sets, and the accuracy of the predictions should be critically evaluated in order to determine which algorithms are useful for predictions on a genomic scale. Applicants with Java programming ability may write classes to interface useful prediction software with a larger molecular biology class library. Qualifications: The ideal student will have a strong molecular biology background and considerable programming experience. Applicants with GPA under 3.6 will be considered only in exceptional circumstances. Weekly Hours: 9-12 hrs Related website: http://compbio.berkeley.edu --- Project 3: Investigation of the role of alternative splicing by analysis of data integrated from existing and new data sources. Deadline for this project (only) is extended to Thursday, September 15th, 5 PM. Applicants should enter a URAP application on line. Activate it by submitting paper copy directly to the faculty member's departmental mailbox. Apply as soon as possible. Do not wait until the deadline. The role of splicing and alternative splicing in human gene expression remains enigmatic. Recent work in our lab has shown that some alternate isoforms may have dramatically different fates than others. Current goals include development of tools for classifying alternate isoforms and extending recent results. Qualifications: The ideal student will have a strong molecular biology background and considerable programming experience. Applicants with GPA under 3.6 will be considered only in exceptional circumstances. Weekly Hours: 9-12 hrs Related website: http://compbio.berkeley.edu --- Project 4: Improving the Prediction of Protein Structure from Sequence Deadline for this project (only) is extended to Thursday, September 15th, 5 PM. Applicants should enter a URAP application on line. Activate it by submitting paper copy directly to the faculty member's departmental mailbox. Apply as soon as possible. Do not wait until the deadline. Protein threading is a computational method that can predict the structure of many proteins given only the amino acid sequence. We are interested in improving the accuracy of threading by incorporating data from mass spectroscopy experiments that are relatively quick and easy to perform. Applicant will write code and analyze data, and should have a basic understanding of molecular biology. Qualifications: The ideal student will have a strong molecular biology background and considerable programming experience. Applicants with GPA under 3.6 will be considered only in exceptional circumstances. Weekly Hours: 9-12 hrs Related website: http://compbio.berkeley.edu -- ^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^ Anne Aaboe phone: (510) 643-7473 Undergraduate Advising Manager fax: (510) 643-2208 Molecular & Cell Biology email: [EMAIL PROTECTED] 2083 Valley Life Sciences, #3200 web: mcb.berkeley.edu/undergrad Berkeley, CA 94720 --============_-1085392431==_ma============ Content-Type: text/html; charset="us-ascii" <!doctype html public "-//W3C//DTD W3 HTML//EN"> <html><head><style type="text/css"><!-- blockquote, dl, ul, ol, li { padding-top: 0 ; padding-bottom: 0 } --></style><title>OPEN URAP, fall 2005 - deadline tomorrow</title></head><body> <div>Dear MCB Students,</div> <div><br></div> <div>There are still two MCB URAP opportunities for fall 2005. Apply right away. http://research.berkeley.edu:16080/urap/projects/index.lasso</div> <div><br></div> <div>~Anne</div> <div>*************</div> <div><font color="#000000"><b>Professor Yang Dan<br> Neural correlates of visual perception</b><br> <i>Deadline for this project (only) is extended to Thursday, September 15th, 5 PM. Applicants should enter a URAP application on line. Activate it by submitting paper copy directly to the faculty member's departmental mailbox. Apply as soon as possible. Do not wait until the deadline.</i><br> The goal of our lab is to understand the structure, function and plasticity of the mammalian visual system. To this end, we use a combination of electrophysiological, psychophysical and computational techniques to analyze how visual information is coded in the spiking activity of neurons in the visual cortex. Many studies in visual coding have been carried out in anesthetized preparations, with the intrinsic limitation that one can't ask important questions such as (i) how do visual neuron responses correlate with the perception of the visual stimulus? (ii) do neurons in anesthetized and awake animals respond similarly to visual stimuli? (iii) how are visual neuron responses modulated by the behavioral significance of the visual stimulus? In order to be able to address these questions, we have become interested in developing visually-guided behavioral experiments in rats, with the goal of later combining these experiments with recordings from the rat visual cortex. We are now starting to run behavioral experiments in which rats are being trained to discriminate between different visual stimuli and we plan to evaluate the effect of different surround cues on this discrimination. This paradigm will complement other paradigms that we are interested in developing in the lab.<br> <br> Qualifications: Undergraduates working on this project will be expected to be involved in the development of the experimental paradigms as well as animal training and data analysis. Since this is still a new area for the lab, interested undergraduates will also have the opportunity to join other members of the lab as they develop software and new equipment for the behavioral tasks. The nature of the project requires that the student conducts experiments a minimum of 2 hrs per day, 6 days a week and assist a weekly lab meeting of 1.5hrs.</font><br> <font color="#000000"></font></div> <div><font color="#000000">Weekly Hours: more than 12 hrsRelated website:</font><font color="#2405EF"><u> http://mcb.berkeley.edu/faculty/NEU/dany.html</u></font></div> <div><br></div> <div>OR</div> <div><br></div> <div><font color="#000000"><b>Professor Steven Brenner<br> Project 1: Computational Approaches to Structural & Functional Genomics</b><br> <i>Deadline for this project (only) is extended to Thursday, September 15th, 5 PM. Applicants should enter a URAP application on line. Activate it by submitting paper copy directly to the faculty member's departmental mailbox. Apply as soon as possible. Do not wait until the deadline.</i><br> We develop computational methods for the analysis and integration of molecular sequence and structure. Our aim is to understand organismal biology by interpreting the information encoded in complete genomes. This work is presently focused on the areas of structural and functional genomics.<br> <br> Structural genomics projects attempt to provide an experimental structure or a good theoretical model for every tractable protein in all completed genomes. Our work involves organizing proteins into families according to homology; classifying proteins and RNA according to structure; predicting structure from homology and constructing atomic coordinate models; providing information resources for structural genomics; developing methods for selection of proteins for experimental characterization; and analyzing solved structures to detect homology and functional information.<br> <br> We study computational functional genomics by creating algorithms using molecular sequence, structure, phylogeny, expression, and splicing information to infer the functions of genes. This work includes the use of gene genealogies to trace gene histories and functional divergences; reverse-genomics comparison of multiple complete genomes to locate genes associated with characterized cellular or biochemical functions; creation of databases of genomic information; integration and evaluation of splice data from various sources to make functional predictions; and continued refinement of sequence comparison methods. We also combine sequence comparison with expression and other experimental data to improve molecular and cellular functional characterization.</font></div> <div><font color="#000000"><br> Undergraduate projects are available in several of the group's areas of interest and will be tailored to the abilities and interests of the student apprentice and current membership of the group. Students should expect to spend at least 10 hours per week on the project.<br> <br> Qualifications: The ideal student will have a strong molecular biology background and considerable programming experience. Applicants with GPA less than 3.6 will be considered only in exceptional circumstances.<br> <br> Weekly Hours: 9-12 hrsRelated website:</font><font color="#2405EF"><u> http://compbio.berkeley.edu</u></font><font color="#000000"><br> <br> ---<br> <b>Project 2: Critical evaluation of software that predicts structural characteristics of proteins from sequence</b><br> <i>Deadline for this project (only) is extended to Thursday, September 15th, 5 PM. Applicants should enter a URAP application on line. Activate it by submitting paper copy directly to the faculty member's departmental mailbox. Apply as soon as possible. Do not wait until the deadline.</i><br> Much publicly available prediction software has only been tested on small sets of proteins, which may not adequately represent the diversity of proteins encoded by entire genomes. Similar prediction algorithms should be tested on large, diverse data sets, and the accuracy of the predictions should be critically evaluated in order to determine which algorithms are useful for predictions on a genomic scale. Applicants with Java programming ability may write classes to interface useful prediction software with a larger molecular biology class library.<br> <br> Qualifications: The ideal student will have a strong molecular biology background and considerable programming experience. Applicants with GPA under 3.6 will be considered only in exceptional circumstances.<br> <br> Weekly Hours: 9-12 hrs<br> Related website:</font><font color="#2405EF"><u> http://compbio.berkeley.edu</u></font><font color="#000000"><br> ---<br> <b>Project 3: Investigation of the role of alternative splicing by analysis of data integrated from existing and new data sources.</b><br> <i>Deadline for this project (only) is extended to Thursday, September 15th, 5 PM. Applicants should enter a URAP application on line. Activate it by submitting paper copy directly to the faculty member's departmental mailbox. Apply as soon as possible. Do not wait until the deadline.</i><br> The role of splicing and alternative splicing in human gene expression remains enigmatic. Recent work in our lab has shown that some alternate isoforms may have dramatically different fates than others. Current goals include development of tools for classifying alternate isoforms and extending recent results.<br> <br> Qualifications: The ideal student will have a strong molecular biology background and considerable programming experience. Applicants with GPA under 3.6 will be considered only in exceptional circumstances.<br> <br> Weekly Hours: 9-12 hrs<br> Related website:</font><font color="#2405EF"><u> http://compbio.berkeley.edu</u></font><font color="#000000"><br> ---<br> <b>Project 4: Improving the Prediction of Protein Structure from Sequence</b><br> <i>Deadline for this project (only) is extended to Thursday, September 15th, 5 PM. Applicants should enter a URAP application on line. Activate it by submitting paper copy directly to the faculty member's departmental mailbox. Apply as soon as possible. Do not wait until the deadline.</i><br> Protein threading is a computational method that can predict the structure of many proteins given only the amino acid sequence. We are interested in improving the accuracy of threading by incorporating data from mass spectroscopy experiments that are relatively quick and easy to perform. Applicant will write code and analyze data, and should have a basic understanding of molecular biology.<br> <br> Qualifications: The ideal student will have a strong molecular biology background and considerable programming experience. Applicants with GPA under 3.6 will be considered only in exceptional circumstances.<br> <br> Weekly Hours: 9-12 hrs</font></div> <div><font color="#000000">Related website:</font><font color="#2405EF"><u> http://compbio.berkeley.edu</u></font></div> <x-sigsep><pre>-- </pre></x-sigsep> <div><font color="#0000FF" >^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^_^</font></div > <div><font color="#0000FF"><b>Anne Aaboe<x-tab> </x-tab><x-tab> </x-tab><x-tab> </x-tab><x-tab> </x-tab> phone: (510) 643-7473</b></font></div> <div><font color="#0000FF">Undergraduate Advising Manager <span ></span > <span ></span> fax: (510) 643-2208</font></div> <div><font color="#0000FF">Molecular & Cell Biology <span ></span > <span ></span> email: [EMAIL PROTECTED]</font></div> <div><font color="#0000FF">2083 Valley Life Sciences, #3200 web: mcb.berkeley.edu/undergrad</font></div> <div><font color="#0000FF">Berkeley, CA 94720</font></div> </body> </html> --============_-1085392431==_ma============-- ---------------------------------------------------------------- The above message does not necessarily represent the views or opinions of MCBcDNA, mcbUSA, the MCB Department, or UC Berkeley. 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