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Project Description
This project is about cancer genomics. Cancer can often cause a deletion or amplification of a gene. In this project, we consider deletions only. This project computes the...
My name is Dan He, first year Ph.D student.
My project is to design efficient algorithms to reconstruct CNVs (Copy Number Variations). This is joint work with Nick. Nick designed a probabilistic...
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Project Member
Hu Ye,first year graduate student from the ACCESS program.
Project Description
Common disease models include:
Dominant – One mutation on either chromosome causes the...
Description of Project
I am working on the mapper project. The point is to perform mapping of short reads to the genome for resequencing. It takes a string of certain length, and it'll try to find...
Description
The Fast Mapping with Lucene project is a short-read mapping project that uses generation of "handles" for fast lookups of short reads. Lucene refers to a high-performance search engine...
Project Description
Genlib is a C library for handling genetic data. It can perform tasks such as represent nucleotides in 2 bits. It's being developed right here at UCLA. Right now, it is a little...
Project Description
Genotypes are obtained using a microarray technology.
Make a simple genotype caller based on ratios of the probes.
Identify clusters in the genotype plots and use our own...
Project Member
My name is Matt Schuerman. I am a graduate student in Computer Science. I went to UCSD for my undergraduate education and received degrees in Physics and "The Mathematics of Computer...
Project Description
I am working on project 22: Mapping of Reads for my project along with my partner Armen Babakhanian. We will do the medium version of this project, which requires a more...
Project Member
Stephen Oakley
Project Description
Recent technology in genetic sequencing has led to short read sequencers. These sequencers produce random reads of a short fixed length from the...
Project member
Dat Bach Duong
About me
I am 3rd yr undergrad, and I study molecular cell developmental biology (mcdb) and applied math. Good background in biology and statistics/probability theory....
Hi everyone, I'm Haodong, first year graduate student of ACCESS Program. ACCESS Program represents most molecular, cellular and other life sciences programs at UCLA.
Project Description
Genetic...
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Description of the project
Imputation is a method to predict the alleles of missing single nucleotide polymorphisms (SNPs). Imputation methods use the linkage disequilibrium (LD) structure to...
About Me
My name is Kha Chu, I'm a fourth year Computer Science & Engineering major.
Project
I plan my final project to be about imputation. Due to fiscal limitations, an association study...
Genotype Calling
Biography
Ignacio Zendejas. I'm a second year MS student finishing up this quarter. My areas of interest are Machine Learning, Data Mining and Information Retrieval. I'm currently...
Introduction
Bio
James Chin, 4th year undergraduate Computer Science & Engineering major. Graduating in Fall '09 and will be working in industry for about a year, while applying for Electrical...
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Project Description
In this project, I will attempt to create a short-read mapper, trying for at least the medium-level-difficulty project. Given a reference genome of up to length 3 billion and...
Project Member
Kevin Cha
203376792
4th Year Undergrad - Computer Science
The goal of this quarter
I will be attempting to implement the relatedness estimator (Project 1). I will finish the easy...
Project Description:
Meta-Analysis is used to increase the statistical power of research studies. If two different case/control studies have M and N individuals, we can put them together to get an...
Project Member:
Lorena Topete
The goal of this quarter:
I will do the easy using 2 techniques, then compare which one was faster.
Project Description:
Short reads need to be mapped to the genome...
When genomes are being sequenced, the methods for the sequencing only reveal small samples a genome at a time. To construct a person's whole genome, it is easiest to take these samples and then...
Mapping of Reads - Easy
Outline
Obtain / Generate Input
Design and Build Program
Generate Test Cases / Test
Weekly Progress Reports
Week:
initial layout / design
Continouing design
Decide to...
Konstantinos Niktas
Me?
Second year MS graduate student trying to finish Master's project. BS in Computer Science from UCSD. Long walks on the beach, leather bound books, etc.
Project...
Project Description
In Meta analysis, our goal is to combine the statistics from different studies. For instance, if two different case/control studies have M
and N individuals, then we can put...
by Paul Servino
2nd year CS&E Major
Project Description
Choosing and Testing one SNP from one individual at a time to maximize effectiveness.
Motivation
A Machine Learning...
Project Member
Lin Song, one year graduate student from the ACCESS program.
Project Discription
Multiple Phenotypes are often collected to study certain diseases, and some of them are intermediate...
Welcome to the Personalized Medicine Project page. I am Rui, a first year graduate student of ACCESS program, an umbrella biological program.
Project Description
This Project is to help doctor...
About me
My name is Frank Chen, a 4th year graduating senior in Computer Science. If everything goes on track, I plan to graduate and take a nice break from school by working and playing. Then it's...
Introduction
Project Member
My name is Sharon. I'm a 4th year undergrad in Computer Science and Engineering. If nothing goes wrong, I'll be graduating after this quarter, so this is one of my last...
Project Description
This project is designed to compute the risk for a certain individual of having various diseases based on their genetic makeup assuming independence. The goal is to give...
page name++ Project List
Read Mapping Lorena Topete
Read Mapping - James Chin [http://cs124project-2009.wikidot.com/james-chin-read-mapper]
Sample Project — Eun Yong Kang project link
Mapping of...
Project: Mapping of Reads
Our current sequencing technology only has the ability to produce random "short" reads of 30 bases within each chromosome, which can contain hundreds of million bases. The...
I have created a simple set of python functions that let you simulate genomic sequence and create "mapping" files. You can insert random sequence however you wish and generate a set of reads at a...
Project Description (final presentation: nfurlotte224FinalPresentation.ppt)
Genomic variation plays a major role in determining many of our characteristics. Everything from hair color to disease...
Description of the project
- Relatedness estimator is find out given the genotypes of several individuals, how all of them are related. Parents transmit 1 chromosome to each child. Siblings share...
Project Member
George Wang
The goal of this quarter
- To implement the relatedness estimator (Project 1).
About me
- I am a 4th year undergraudate in CSE major.
The Schedule for the quarter /...
Project Description
Parents transmit 1 chromosome to each child. This result in approximately 50% resemblance of DNA between siblings. Relatedness between 2 or more people can be estimated...
Project Description
Because parents transmit chromosomes directly to their children, we should be able to determine relationships between individuals based on their genotypes. Looking at...
Description
I am working on Final Project 1: Relatedness Estimator.
About Me
I am a first year biochemistry graduate student.
Goal for end of quarter
The starting goal for this project is to...
Project Description
Sequencing the genome is a relatively expensive and time-consuming task. The cost of reading the genome is reduced by reading many short segments of it, rather than the entire...
Instead of sequencing the entirety of a person's DNA at once, sequencing technology takes advantage of a technique called "short reads" that registers small portions of a person's DNA sequence....
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Project Description
Short reads are mapped to the genome and then compared to identify SNPs. However, some reads have errors and the errors could look like SNPs. Luckily SNPs will occur in many...
+ Paragraph Description of the project:
I'm going to be doing the short sequence read mapper project, medium difficulty. For this project I will align reads of length 30 to a genome up to size 3...
Project Member
My name is Supritha Sundaram. I am a third year computer science major.
Project Discription
My project is the Relatedness Estimator. I am going to be working on constructing a method...
Project Description:
With the number of disease causing associations being discovered, we can measure the risk of an individual having the disease. How do we do this? What assumptions do we need to...
Project Member
Eun Yong Kang
The goal of this quarter
The Schedule for the quarter
Project Description
Related Papers
April 19 2008
Sample Project started!
April 21 2008
What I did this...
How to create your project page
Create your own wikidot account, if you do not have one. There is a create account link at the top of wikidot page. click here
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A Wiki ([ˈwiː.kiː] <wee-kee> or [ˈwɪ.kiː] <wick-ey>) is a type of website that allows users to add, remove, or otherwise edit...
Welcome to my project page~
I hope you enjoy.
Project Description
The winner's curse is a phenomenon first observed in economics in which a party at auction overestimates the value of an item. It...
Project Member
Xuan Luo
Project Description
I looked at two-stage design. I optimized for the maximal power given a particular cost, and looked at the shape of the curve and what it...
