GFESS Group related researchintroduction

Chu Chia HanNTHU CSBB LAB

2009/7/21 1

GFESS??????

G Genome F Function E Evolution S Sequence S Structure

2009/7/21 2

還有什麼研究沒包含在 GFESS 組裡頭呢 ???

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領軍System Biology Group

我是君天

Big map 製

作人 不要忘了我 ! 我是竹君 也是系統生

物的核心人物

2009/7/21 3

還有什麼研究沒包含在 GFESS 組裡頭呢 ???

我是台灣一哥貴中啦 !

我自成一組是實驗室”藥物設計”

的老大 !

我是台灣一哥貴中啦 !

我自成一組是實驗室”藥物設計”

的老大 !

2009/7/21 4

Basic technique you need to have

• Linear algebra• Basic Statistics• Algorithm• Data Structure• Computational Geo.• Text mining• Basic Bio background• More and more…. Don’t worry! Just learn it and you will

see something interesting!

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GFESS members

• 張承文 博士 (GFESS 帶頭 老大 嘿嘿 ! 不是我喔 !)

• 邱奕彬 學長• 朱家漢 學長 ( 我只是小小

的窗口 !)• 鄭佳揚 學姐• 賴俊吉 學長 – 好爸爸• 張智宏 學長 – 看賽車達人• 黃荃敬 學長• 李季青 學長• 馬誠佑 學長

• 黃名遠 學長• 張光延 學長• 李道政 學長

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• MuSiC:sequence alignment with constraint(the high sequence similarity case) [Dr. 盧 ]

• MSA with secondary structure information(the moderate sequence identity case)

• Matching Tool(low identity. Topology shifting, rotation…)

• FAVA [ 李奇瀚 ]• HP model [Dr. 彭 ]

Research topic 1邱奕彬 學長

2009/7/21 7

Research topic 2家漢An unknown function

protein structure

CBM Domain AD-Image DB

CBM Domain AD-Image DB

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Representational Structures

AD-Image sub-DB(1)

(1)

(2)

(3)

AD-Image sub-DB(2)

AD-Image sub-DB(3)

‧‧

(1)SSE information extraction(2)Vector transformation(3)AD-Image Construction

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exon exon5’ splice site Py tracs

U2AF

3’ ss

U11 snRNP

U12 snRNP

Branch point

M {U1,U2,U2AF} L {5’ splice site, 3’splice site, Py tracs}

M’, M M’ {U1,U2,U2AF , ⊂ U1/U4/U5, U12} L’, L L’ {5’ splice site, 3’splice site, Py tracs, ⊂ branch point, 5’ss}

exon exon

Branch point

Py tracs5’ splice site 3’ ss

U1U2

U2AF

U1U2

Text Mining

Research topic 3佳揚

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Introduction

• Re-sequencing:Mapping short sequences(reads) of new sequencing technique to known genomes assembled by old techniques.– Verify old methods.– Find new function sites on genomes.

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Research topic 4名遠

2009/7/21

Problem Definition

• Input ：– 243 Transcription factors (Targets)– 8,014 mRNA sequences (Off-target)

• Goal ：– Investigated the relationship between the phenotype and

related Targets.– Don’t affect the off-target genes– Find out the answer with as less experiments as possible

Research topic 5智宏

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研究方像 : 利用 genome profile 與 tRNA associated sequence 尋找 genomic island ( 外來 DNA)

用到的實驗室的技術 : Unique signature discovery tool ( 名遠 )

Research topic 6季青

2009/7/21 12

• 分子模擬 , 蛋白質雙硫鍵預測

• 平行運算 (CUDA), Machine learning.

Research topic 7誠佑

2009/7/21 13

DOBALI: A domain-based multiple sequence alignments tool

The inputs contain 2 information: 1. protein sequences 2. id and positions of the domains in each sequences. In some conditions, users want to observe the align ments of the same domains in sequences. DOBALI is for this purpose. It aligns the domains with the same id (color) and arrange them in the appropriate columns.

Clustalw onlyDOBALI with Clustalw

Research topic 8光延

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Other research topics

• miRNA• ….• If you interest about GFESS group, we can

discuss more details!!!• Project related work…, you can discuss with

張博士 GFESS 頭頭 !

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Thank you!

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