4th Asian Young Researchers Conference on Computational and Omics Biology

The 4th Asian Young Researchers Conference on Computational and Omics Biology is jointly organized by the Joint-International Society for Computational Biology Student Council ISCB-SC Regional Student Group RSG Japan, Korea and Singapore; young researchers in Taiwan and the GCOE program “Genome BigBang” of The University of Tokyo, Japan.

The 4th AYRCOB aims to achieve a 2-fold objective:

1) To provide an avenue of exposure for students who are interested in the areas Computational and Omics Biology to participate in lectures of current topics from leading scientists of the field.

2) To establish international collaboration through interaction and discussion with fellow participants.

** Travel expenses of selected ORAL presenters will be FULLY COVERED by the conference sponsors! **

** Latest Annoucements **

Conference Proceedings

Please click here for the PDF format of the Conference Proceedings.

Conference Schedule

Please click here for a PDF format of the conference schedule.

Airport Charter Arrangement for Participants Staying at Nostalgia Hotel, and GCOE supported Oral Presenters on 30th November 2010

Please note that the charter service is ONLY available on 30th November 2010 from Changi Airport to Nostalgia Hotel at Tiong Bahru.

Dear Nostalgia Hotel guests and GCOE supported Orals,

I have included a link here for you all to take a look on how to get around the airport:
http://www.changiairport.com/getting-around/getting-around-the-airport

For your information, 30th november is more of a free and easy day. For Nostalgia hotel guests and speakers (invited and oral), depending on which charter bus you take to the hotel, after you check in, you are on your own for the rest of the day.

We have arranged for 2 buses to pick up everyone, 1 at 4pm and the other at 8pm.

IMPORTANT: The pick up point is at Changi airport terminal 3. Depending on which flight is taken, you all will arrive at terminal 1, 2 or 3. I would require those arriving at terminal 1 and 2 to take a sky train to terminal 3. Once you reach terminal 3, go to the Macdonalds at terminal 3. AYRCOB personnel will be there.

30th November 1st wave from 12.05pm onwards:
1) For those arriving from 12pm-3pm, you will need to take a sky train to terminal 3 if your arrival is not at terminal 3 and meet us at the Macdonalds there. When the last person arrive at 3pm plus, all can take the 4pm bus to the hotel. After checking in to hotel, it is free and easy. You may want to explore the Tiong Bahru market which is just next door for some hawker food. Just ask the hotel concierge for directions. Alternatively, you can dine at the hotel at a 15% discount.

30th November 2nd wave from 5.20pm onwards:
1) For those arriving from 4pm-7.30pm, you will need to take a sky train to terminal 3 if your arrival is not at terminal 3 and meet us at the Macdonalds there. When the last person arrive at 7pm plus, all can take the 8pm bus to the hotel. After checking in to hotel, it is free and easy. Dinner can be taken near the hotel. Ask the hotel concierge for any cafes/restaurents nearby. Alternatively, you can dine at the hotel (for those who have not taken),at 15% discount.

1st-3rd December
Breakfast will be served from 1st-3rd December at the hotel. Enquire about it when you check in and you will be given further directions (eg breakfast coupons, time of breakfast etc).

The bus to biopolis leaves from 7.45am to 8am from the hotel. Be prepared by then.
Breakfast and Lunch are provided from 1st-3rd December at the conference venue.

Dinner is on your own for all conference days.

The local committe have prepared a special dinner at Nostalgia hotel for our special guests (INVITATION ONLY) on the 2nd of december. Invited guests will receive a dinner invitation coupon.

For General AYRCOB Participants

Below are some information that could be help for travelling from the airport to the conference venue or your accomdation and from your accomdation to the conference venue.

Singapore Changi Airport

Singapore Changi Airport (IATA: SIN, ICAO: WSSS), Changi International Airport, or simply Changi Airport, is the main airport in Singapore. A major aviation hub in Southeast Asia, it is about 17.2 kilometres (10.7 mi) north-east from the commercial centre in Changi, on a 13 square kilometres (5.0 sq mi) site. Singapore Changi Airport is easily accessible with many modes of transportation available to and from the Airport. For drivers, car parks are available at every Terminal of the airport as well.

Link for information for getting aroung the airport: http://www.changiairport.com/getting-around/getting-around-the-airport

Please see To and From Airport for more information for transport on to and from Changi Airport.

Some helpful Directions

Participants can get around Singapore with the help of the online guide “Go There SG” website at http://gothere.sg/directions. The online guide is very simple to use. Just key in your current location in Singapore and the destination of your choice.

We have gathered that some participants could be staying at clark quay, chinatown and little india area. Below are some general directions from the airport to these 3 areas:

From airport to Clark Quay area by MRT: http://gothere.sg/directions#changi airport:clark quay

From airport to Chinatown: http://gothere.sg/directions#changi airport:chinatown

From airport to Little India: http://gothere.sg/directions#changi airport:little india

To Conference Venue, Biopolis

The nearest MRT station to Biopolis is Buona Vista MRT station.

From Clark Quay to Buona Vista MRT Station: http://gothere.sg/directions#clark quay:@1.3034278957663791, 103.79206008835697

From Chinatown to Buona Vista MRT Station: http://gothere.sg/directions#chinatown:@1.3034278957663791, 103.79206008835697

From Little India to Buona Vista MRT Station: http://gothere.sg/directions#little india:@1.3034278957663791, 103.79206008835697

Singapore’s Mass Rapid Transit Network

SMRT operates three main rail lines, the North South Line which runs from Marina Bay Station to Jurong East Station via Woodlands Station, and the East West Line which runs from Pasir Ris Station to Joo Koon Station, and the Circle Line, which runs from Dhoby Ghaut Station to Marymount Station.

If you wish to connect to the North East Line, simply change trains at Dhoby Ghaut Station, Outram Park Station or Serangoon Station. For commuters headed to the Singapore Expo Centre or travellers bound for Singapore Changi Airport, hop on board the Singapore Changi Airport Express which calls at Tanah Merah Station.

Connecting town and heartlands

Bukit Panjang Light Rapid Transit (BPLRT) is the first Light Rapid Transit (LRT) system to be built in Singapore. The fully automated BPLRT system which covers 7.8km of elevated guideways is a modern and convenient feeder service.

All 14 stations on the BPLRT line are conveniently located within 400m of most apartment blocks in Bukit Panjang and Choa Chu Kang estates. Covered linkways protect you from the elements whilst access to amenities and other modes of transportation such as the MRT and bus provide the convenience and connectivity you are looking for.

Please see the SMRT Trains Website for more information on travelling on MRT in Singapore.

Instructions for GCOE Supported Oral Presentations


Dear GCOE Supported Oral Presenters,

We are pleased to inform you that you have been selected for Oral presentation with Travel support for the 4th AYRCOB 2010 in Singapore.
Thank you very much for submitting your abstract and being part of the 4th AYRCOB.

There are a few instructions to follow to confirm your acceptance and your travel support as follows:

1) Please indicate if you would accept the offer for oral presentation and reply by 10th November 2010 with an indication of your acceptance and a MS-word format of your abstract to submit@ayrcob.org. The e-mail subject should indicate “Acceptance of oral presentation_NAME”. Please note that if you do not send the formatted abstract to the proceeding managers by 10th November 2010, your abstract will not be included in the AYRCOB pro ceedings. For the the MS-word formatting details, please refer to the attached Final Abstract guidelines file. Please kindly check the content and spelling of your abstract by yourself because the proceedings managers will not do any proof-reading for any participants.

2) Please also send the following information to gcoe@cb.k.u-tokyo.ac.jp and arita@k.u-tokyo.ac.jp as soon as possible. Kindly note that you have to send to the two emails to secure your air ticket booking. The e-mail subject should indicate “Travel details_4th AYRCOB_NAME”.
- A Photocopy of the 1st page of your passport. (We would require your passport name and number to book air tickets.)
For the passport copy, please specify which is your first, middle and lastname. If your first name and last name is accidently treated in reverse,the air ticket will be invalid, so specifying will be really important.
- Institute address and the nearest airport
- Attached file of the photocopy


Please take note that air tickets will be reserved by the GCOE office. The departure day is Tuesday, 30th November 2010, and the return day is
either Friday, 3rd December 2010 midnight or Saturday, 4th December 2010.

3) Please fill up the attached hotel reservation form with your credit card or debit card details and email/fax the completed form to Colleen Chan of Nostalgia Hotel, Singapore at colleen.chan@hotelnostalgia.com.sg (e-mail) or 65 6808 1815 (fax) by 15th November 2010. The e-mail subject should indicate “4th AYRCOB Hotel Reservation_NAME” should you be sending the completed form by e-mail to the hotel. You will be reimbursed the cost of the hotel accomdation after the conference.

4) Please fill up the 外国送金支払先情報 form for your reimbursement and send to gcoe@cb.k.u-tokyo.ac.jp and arita@k.u-tokyo.ac.jp .
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Poster Presentations


Dear Poster Presenters,

We are pleased to inform you that you have been selected for Poster presentation for the 4th AYRCOB 2010 in Singapore.
Thank you very much for submitting your abstract and being part of the 4th AYRCOB.

1) Please indicate if you would accept the offer for poster presentati on and reply by 10th November 2010 with an indication of your acceptance and a MS-word format of your abstract to submit@ayrcob.org. Please note that if you do not send the formatted abstract to the proceeding managers by 10th November 2010, your abstract will not be included in the AYRCOB proceedings. For the the MS-word formatting details, please refer to the attached guidelines file. Please kindly check the content and spelling of your abstract by yourself because the proceedings
managers will not do any proof-reading for any participants.

2) Please book your own air ticket and hotel accomdation (applicable to overseas poster presenters).


Abstracts Acceptance Notification

Dear all, we thank you for your submissions to the 4th AYRCOB. It has been a pleasure reviewing all the high quality abstracts submitted. Due to overwhelming response,we could only made the announcements of the selected abstracts for oral and poster presentation will be made on today, 6th of November 2010. We apologise for the delay.

Selected Oral Presentations as follows:

Takeshi H. Saito

Data driven modeling of immediate early genes regulation by MAPKs

Durai Sundar

Getting a handhold on designing proteins for human therapeutics

Jittima Piriyapongsa

Correlation-based filtering technique coupled with machine learning for detecting gene-gene interaction in genome-wide association study

Inkyung Jung

LinkNMF: Discovery of chromatin signatures through analysis of genome-wide chromatin architecture in human genome

Zhibo Gao

Multi-omics analysis of a colon cancer

Jae Wan Jang

Dentifying structural factors affecting ligand selectivity to three 5-HT2 receptor subtypes : homology modeling and protein-ligand docking

Hsing-Jen Sun

Discovering monotonic genes from multiclass and time-series microarray data

Pongsakorn Wangkumhang

An efficient machine learning based framework to select minimal set of informative markers for bovine breed classification

Yen-Kuang Chen

Identify Membrane Protein Types by Support Vector Machines Using Physical and Biochemical Properties

Marsia Gustiananda

What T cells see in bird flu virus: Immunoinformatic analysis to identify CTL-based influenza vaccine candidates

Minho Lee

High Throughput Docking for Yeast Proteome and Drugs

Kahori Takane

Computational Prediction and Experimental Validation of Evolutionary Conserved microRNA Target Genes in Bilaterian Animals

Sun-Gou Ji

Functional Gene Network of a Pathogenic Bacterium; Pseudomonas aeruginosa

Lim Shen Jean

Intrinsically disordered residues as a possible feature determining the specificity of NF-κB proteins

Shou-Cheng Yen

Discovering sequence patterns that are relevant to protein localization

Shin Young Yim

A Gene Expression Signature of Congenital Muscular Torticollis and Its Correlation with MRI Findings

Wataru Iwasaki

A Travelling Salesman Approach to Phylogenetic Trees

Selected Poster Presentations as follows:

Sub # Authors Title
3 Abida Shehzadi and Khalid Masood In silico study of promiscuous MHC I and MHC II binding epitopes of HCV 3a viral proteome from Punjab Pakistan and their conservancy analysis
4 Bai Xue Zheng and Hanry Yu Liver fibrosis drug discovery using high content analysis
8 Ratna Prabha and Indira Ghosh Developing Plant Stress Gene Database
10 Shanmughavel Piramanayagam Evaluation of in silico protein secondary structure prediction methods by employing statistical techniques
16 Satya Arjunan and Koichi Takahashi Cell shape and curvature can regulate the self-organized patterns in Dictyostelium discoideum
20 Sumit Raj and Pasupuleti Renuka AYURVEDIC BIOINFORMATICS: Establishing an in-silico-ayurvedic medication for Alzheimer’s disease
22 charu kapil, Dr. Amit Sharma and Dr. Mohamad Jairajpuri Impact on compositional skewness of genomes from prokaryotes and eukaryotes on Codon-usage patterns in phylogenetically unrelated AT-rich genomes
24 Eric Lee and I-Fang Chung Processing NGS Data with Web 2.0 and GPU Parallel Computing
25 Mohamed Nazir and R Manjunatha Kini Purification, structural and functional characterization of a novel anticoagulant three finger toxin from the venom of Naja siamensis
27 Fei-Hung Hung and Hung-Wen Chiu Pathway-oriented Gene Expression Profile Analysis of Human Cancer
28 disha tandon, deepak yadav and arnold emerson ISLET: Sequence Analysis Software
29 Sohyun Hwang, Seung Y. Rhee, Edward M. Marcotte and Insuk Lee AraNet: a web-based system for prediction of gene function using a probabilistic functional gene network for Arabidopsis thaliana
30 Ara Cho, Jung Eun Shim and Insuk Lee Network-based classifiers for identifying Driver-mutation-bearing cancer genes
34 Sripad Chandan Patnaik, B Shadrack Jabes and Gyan Ranjan Satpathy Design of N-phenyl-2-(pyrimidin-2-ylsulfanyl) acetamide derivatives as inhibitors against SARS virus
35 Sripadchandan Patnaik and Gyan Ranjan Satpathy Molecular Dynamics Simulations Of Sequentially Varied Human Immunodeficiency Virus-1 Tat Consensus Protein Structures
37 Sripadchandan Patnaik, B Shadrack Jabes and Gyan Ranjan Satpathy Design and study of N-phenyl-2-(pyrimidin-2-ylsulfanyl) acetamide derivatives as inhibitors against SARS virus
41 Muhammad Ilyas, Ziaur rahman and Khalid Masood Analysis of Envelope Glycoprotein E epitopes of Dengue Virus-3: A Bioinformatics approach
42 Nai-wen Chang, Chia-Lang Hsu and Ueng-Cheng Yang Quality assessment of protein-protein interactions
44 Yuan Shi, Lisa Tucker-Kellogg and Shazib Pervaiz Systematic Analysis of LY30 induced Sensitization of Cancer Cells to TRAIL
45 Hsu Jui Tse, Yen-Hua Huang and Ueng-Cheng Yang A platform to process personal genomic sequences – discovering possible SNPs on SCA patients
47 Dave Siak-Wei Ow, Hou-jiang Zhou, Denis Yong-Xiang Lim, Cara Sze-Hui Chin, Kong-Peng Lam, Shabaz Mohammed and Albert J.R. Heck A proteomic work flow based on strong-cation exchange/Ti-IMAC for mass spectrometry identification of phosphopeptides from B cells
48 Hyosil Kim Differentially Co-Expressed Gene Pairs Identify the Distinct Stages of HIV Type 1 Infection
51 Takeshi Obayashi and Kengo Kinoshita COXPRESdb: a gene coexpression database for 7 animal species
52 Chun-Hung Su, Nikhil Ranjan Pal and I-Fang Chung A modified amino acid pair approach for predicting linear B-cell epitope based on machine-learning technique
55 Shanmugam Sabarathinam, Ulaganathan Priyadharshini, Easwaran Murugesh, Jayaraman Angayarkanni and Muthusamy Palaniswamy Structural prediction and annotation of orphan enzyme pterin deaminase from rat liver (Rattus norvegicus)
59 Asfa Alli Shaik and Christopher Hogue Elusive Function of the Evolutionarily Conserved Vault Complex
63 Ya-Li Hsiao, Po-feng Chen, Cheng-Fang Tsai, Hsiang-Chuan Liu and Pei-chun Chang Coupling Effects of Amino Acids in T-cell Epitope Prediction
73 Wei-cheng Lo, Chia-Han Chu, Hsin-Wei Wang, Chi-Ching Lee, Yen-Chu Hsu, Jenn-Kang Hwang, Ping-Chiang Lyu, Tun-Wen Pai and Chuan Yi Tang The Developments of a Standard Dataset and a Precise Hinge Loop Determination Procedure for 3D Domain Swapping Proteins
76 Bhavisha Sheth and Vrinda Thaker Bioinformatics insights into Photosynthesis: Exploring light to life
82 Hanhae Kim and Insuk Lee CryptoNet: A Gene Network of Human Patogenic Fungus, Cryptococcus Neoformans
85 Gourav Nema, Avinash Shanmugam and Angela Jean Comparative Analysis for the Identification of Novel Bacterial Genes
87 Soo Cheol Lee, Hye Young Shin and Sangdun Choi Cellular network analysis of cisplatin-induced renal toxicity


11 Yukyung Jun, SooYoung Cho, Sanghyun Lee, Hyung-Seok Chol, Sungchul Jung, Youngjun Jang, Charny Park, Sangok Kim, Sanghyuk Lee and Wankyu Kim miRGator v2.0 : an integrated system for functional investigation of microRNAs
57 Kosuke Fujishima, Junichi Sugahara, Masaru Tomita and Akio Kanai Large-scale intron transposition has contributed to the late gain of introns in the deep-branching Archaea
61 Chaninya Wongwarangkana, Shuichi Asakawa and Shugo Watabe Sequencing and functional analysis of Takifugu rubripes and Oryzias latipes small RNA
70 Ying-chen Huang and I-Fang Chung Q-Motif: Phosphorylation Motifs Finding by Subtractive Clustering

Dear Poster Presenters, as some of the submissions have not placed all authors as corresponding authors hence some authors may not have received the notification about their accepted Oral or Poster presentations. Please refer above for the selected Oral and Poster presentations.

Conference Posters

Please find the conference posters below:

1. AYRCOB flyer Final

2. AYRCOB flyer Final_wo participating insitutions


APBionet Travel Fellowship


In addition to the travel grant sponsored by the Global COE program of the University of Tokyo, in order to increase participation of the 4th AYRCOB and CBAS-Symbio 2010, we welcome applications for the APBionet travel fellowship to support participants who are attending either of the 2 conferences.

Terms and conditions

These travel fellowship will be in the form of reimbursement of up to USD500 for each participant. Participants may only apply for ONE travel sponsorship: either the APBionet travel fellowship or the travel grant sponsored by the Global COE program of the University of Tokyo.

Application Process for APBionet Travel Fellowship

Please note that application for the APBionet travel fellowship is different from the application for the Global COE program travel grant. Applications for APBionet travel fellowship are to be e-mailed to submit@ayrcob.org.

A complete application should consist of: the abstract submission on the Easy Chair submission system, followed by an email with 3 attachments: abstract, a detailed CV, and a detailed description of the scholarly rationale to be considered for the travel fellowship, to submit@ayrcob.org.

The subject of the email should indicate ‘Application for APBionet Travel Fellowship_FULL NAME’.

To prepare an abstract, please follow the style format template (Click for format template in MS Word .doc file). Abstract must be 1 page of A4 size and prepared in English according to the format provided in the template. The name of the presenter should be indicated by an underline in the author list.

As an example, a Curriculum Vitae may include:

•English Full Name (Last Name, First name)
•Full Name in Native Language (Last Name, First name)
•Affiliation
•E-mail Address
•Education Profile
•Publication List
•Conference Presentation List
•Honors and Awards
•Other information that indicates that you are a person to be supported

Please provide your abstract, CV (A4, 1-4 pages), and the detailed description of the scholarly rationale to be considered for the travel fellowship(A4, 1 page) as English, PDF-formatted files.

Key Dates

Wednessday, 25th August 2010: Call for Abstract Opens

Monday, 13th September 2010: Website Registration open

Monday, 25th October 2010 Extended till Wednesday, 27th October 2010: Abstract Submission Deadline

Friday, 5th November 2010: Abstract Acceptance Notification

Wednesday, 10th November 2010: Abstract Acceptance Deadline

1st to 3rd December 2010: Main conference (lectures, orals, posters, and discussions)

2rd to 3rd December 2010: 1st Joint Clinical Bioinformatics Symposium and Singapore Symposium on Computational Biology 2010

Join us @ the 4th AYRCOB.

Acclaimed as a thriving cosmopolitan city that is brimming with diversity and has a multiplicity of culture, language, arts and architecture, Singapore offers a wide variety of architectural, historical, cultural, exotic dining and social venues. Join us this year for a memorable conference and a lively exchange of scientific ideas in one of Asia’s most culturally rich cities!

We extend our invitation to all undergraduate students, graduate students, and young researchers with interest in the areas of Computational and Omics Biology from Taiwan, Japan, as well as other countries to participate in lectures of current topics from leading scientists of the field, and to establish international collaboration through interaction and discussion with fellow participants.

Instructions for presenters

The conference is planning to support travel expense of about 16-20 ORAL presenters in the conference, so we are soliciting many submissions of high-quality abstracts!

If you wish to make an ORAL presentation AND to obtain full travel support, please submit your abstract, CV and recommendation letter via the Submissions page and there after register via the Registration page.

If you wish to make an ORAL presentation but DO NOT NEED to obtain travel support, please submit your abstract via the Submissions page and there after register via the Registration page.

If you wish to make a POSTER presentation (Please note that travel support is for ORAL presentations ONLY), please submit your abstract via the Submissions page and there after register via the Registration page.

To prepare an abstract, please follow the style format template (Click for format template in MS Word .doc file). Abstract must be 1 page of A4 size and prepared in English according to the format provided in the template. The name of the presenter should be indicated by an underline in the author list. Please submit a PDF version of the abstract.

For details, please refer to the Guidelines on the Submissions/Guidelines page.

Instructions for non-presenters

If you wish to participate in the conference as a non-presenter, please register via the Registration page. This is to faciliate the arrangement for lunch boxes and tea breaks, in addition to the dinner and dance on the 2nd day of the conference.

25th August 2010 – Call for abstracts

The submission of abstracts is now open. Take advantage of this opportunity to present your work at the 4th AYRCOB. Submission deadline is October 25, 2010. Please see the Guidelines for more information and submit at the Submissions web site

CBAS – SYMBIO 2010 is also being held concurrently with the 4th AYRCOB.

Bioinformatics Week

CBAS-SYMBIO 2010 is the 1st joint symposium uniting scientists working in a broad range of disciplines, including bioinformatics, computational biology, biology, medicine, systems biology, medical and health informatics. Participation at CBAS – SYMBIO 2010 will be the prime opportunity to learn about cutting-edge research in computational biology and medical informatics and to network with other members of our community.

You may sign up for CBAS-SYMBIO 2010 also during registration for 4th AYRCOB.

For more information on CBAS-SYMBIO 2010, please visit http://symbio2010.rsg.sg/.

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