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[BBON] 생물정보학 뉴스레터 Vol 4/7, 2008
[BBON] 생물정보학 뉴스레터 Vol 4/7, 2008 저자
등록일 2009.03.06
조회4283  인쇄  주소복사  소셜네트워크로 공유하기
키워드: BBON, 생물정보학, Bioinformatics


 

Communication Recruit Resources Events Books and Reports Gossip

[Communication]


1. 2008년 6월 국내 연구논문 발표 실적
  2006년 6월 한달 동안 PubMed에 등록된 국내 생물정보학 관련 발표 논문(제1 저자를 기준으로 한국에서 발표한 논문을 대상으로 12가지의 생물정보학 관련 keyword로 검색하여 정리한 결과)


1) 발표 논문 전체: 21편

연구주체

대학

국가기관

병원

발표논문 수

19

2

-



2) 지역별분포

지역구분

서울/경기

대전

부산

경남

발표논문 수

16

3

1

1



3) 주요 연구분야

분야

편수

분야

편수

Phylogeny & Evolution

4

Predictive Method

4

Proteome Analysis

4

Functional Genomics

2

System Biology

2

Sequence Comparison

2

Genome Annotation

1

Microarray

1

Database

1

 

 


2. 국외 뉴스
2008년 6월 주요 국외 뉴스 클리핑

날짜

내용

6.28 Complexity of Crohn's disease revealed as 'gene' count tops 30
New research has trebled the number of genetic regions known to be implicated in Crohn's disease, a form of inflammatory bowel disease, to over thirty. The research, published today in the journal Nature Genetics, has identified a number of potential new ...
6.27 Mechanism and function of humor identified by new evolutionary theory
The pattern recognition theory of humor is an evolutionary and cognitive explanation of how and why any individual finds anything funny. Effectively it explains that humor occurs when the brain recognizes a pattern that surprises it. It also identifies im ...
6.22 DNA study unlocks mystery to diverse traits in dogs
In the cover story of tomorrow's edition of the science journal Genetics, research reveals locations in a dog's DNA that contain genes that scientists believe contribute to differences in body and skull shape, weight, fur color and length -- and possibl ...
6.19 Gene-expression profiling of the effects of liver toxins
Gene-expression data from liver tissue or whole blood can be used to classify histopathologic differences in the effects of hepatotoxins. It is hoped that these findings, published in BioMed Central's open access journal Genome Biology will lead to a mor ...
6.16 Computer predicts anti-cancer molecules
A new computer-based method of analyzing cellular activity has correctly predicted the anti-tumor activity of several molecules. Research published today in BioMed Central's open access journal Molecular Cancer describes 'CoMet' -- a tool that studies ...
6.12 Centromeres cross over, a lot
Recombination at centromeres is higher than anywhere else on the chromosome, even though methyltransferases do their best to prevent it, say Jaco et al., as published in the June 16 issue of the Journal of Cell Biology. ...
6.11 Researchers reveal insights into hidden world of protein folding
Proteins, long and linear when first made, must fold into specific configurations before they can properly do their job in a cell. How they are folded is a mystery, but Stanford researcher Judith Frydman has begun prying the lid off a type of molecule cal ...


3. 국내외 전문연구동향 (국내뉴스 포함)

날짜

내용

6.27 생물정보학 이용, 천식 유발 후보유전자 발견
6.25 활유어 (amphioxus)의 게놈 해독에 성공
6.23 생명의 기원 논쟁, 다시 불붙나?
6.23 DNA로 姓을 찾는다
6.23 '머리카락' 검사로 유방암 정확히 찾아내는 검사법 개발
6.23 유전자 진단 기술, 더욱 진보한다...포항공과대학교 화학과 김병현 교수
6.20 게놈 연구, 일본 제약 시장에 IT의 물결 - 국내외 기업의 새로운 경쟁
6.18 생식세포의 탄생기구에 관련한 유전자군의 해명
6.16 '내 손 안에 병원' 스마트 바이오칩
6.13 암을 포함한 심장질환, 뇌질환 등 35가지 질환의 SNP 정보를 공개
6.9 "환자 바이오마커 따라 암 표적공격 맞춤치료"


4. PubMed에 소개된 생물정보학관련 5월 주요리뷰(편집자 주)

저자

제목

Michor F. Mathematical models of cancer stem cells.
J Clin Oncol. 2008 Jun 10;26(17) : 2854-61. Review.
Aoki-Kinoshita KF. An introduction to bioinformatics for glycomics research.
PLoS Comput Biol. 2008 May 30;4(5) : e1000075.
De Schutter E. Why are computational neuroscience and systems biology so separate?
PLoS Comput Biol. 2008 May 30;4(5) : e1000078
Oksenberg JR, Baranzini SE, Sawcer S, Hauser SL. The genetics of multiple sclerosis: SNPs to pathways to pathogenesis.
Nat Rev Genet. 2008 Jul;9(7):516-26. Epub 2008 Jun 10
Dahl KN, Ribeiro AJ, Lammerding J. Nuclear shape, mechanics, and mechanotransduction.
Circ Res. Circ Res. 2008 Jun 6;102(11) : 1307-18
Guo S, Wu J, Ding M, Feng J. Uncovering interactions in the frequency domain.
PLoS Comput Biol. 2008 May 30;4(5) : e1000087


5. PLoS Computational Biology Journals(편집자 주: Editor's Pick)
제목 요약
Regulation of Signal Duration and the Statistical Dynamics of Kinase Activation by Scaffold Proteins The authors use a computational approach to simulate the behavior of a model signal transduction module (a kinase cascade) in the presence of scaffolding proteins, revealing mechanisms for how scaffolds can dynamically regulate the timing of cell signaling.
PLos Computational Biology 2008 June 4;(6) : e10000099
Machine-Learning Approaches for Classifying Haplogroup from Y Chromosome STR Data Schlecht et al. use modern machine-learning algorithms to assign a sampled Y chromosome to a haplogroup by scoring a relatively small number of Y-linked short tandem repeats (STRs). This novel alternative to SNP analysis provides deep ancestry information in a cost-effective and accurate manner.
PLos Computational Biology 2008 June 4;(6) : e10000093


6. Bioinformatics 저널 주요논문(편집자 주, IF, 인용지수=4.894)
Number Title
Bioinformatics
Volume 24, Number 11
Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches
2008 24(11) :1339-1343
Annotation-Modules: a tool for finding significant combinations of multisource annotations for gene lists
2008 24(11) :1386-1393
Bioinformatics
Volume 24, Number 12
Cytoscape ESP: simple search of complex biological networks
2008 24(12) :1465-1466
jSquid: a Java applet for graphical on-line network exploration
2008 24(12) :1467-1468

* Korean Scientist in Bioinformatics Journal (2008 / 6)

성 명

제 목

Jung-jae Kim, Piotr Pezik, and Dietrich Rebholz-Schuhmann MedEvi: Retrieving textual evidence of relations between biomedical concepts from Medline Bioinformatics Advance Access published on April 9, 2008
Bioinformatics 2008 24(11) :1410-1412
Soyang Ha, Young-Ju Seo, Min-Seok Kwon, Byung-Ha Chang, Cheol-Kyu Han, and Jeong-Hyeok Yoon IDMap: facilitating the detection of potential leads with therapeutic targets Bioinformatics Advance Access published on April 15, 2008
Bioinformatics 2008 24(11) :1413-1415


7. BMC Journals
  7-1. BMC Bioinformatics (IF, 인용지수 = 3.62)

제 목

요 약

Better resolution of chromosome rearrangements By comparing an organism's chromosomes to those of closely related species using a segmentation algorithm, breakpoints can be precisely delimited and their internal structure described, providing insights into the mechanisms and evolutionary properties of chromosomal rearrangements.
BMC Bioinformatics 2008, 9 : 286
Visualization of genetic variations Using the new software toolkit VariVis, curators of online locus-specific databases can now generate graphical models of gene sequences and their mutations to encourage greater understanding of the data and facilitate access.
BMC Bioinformatics 2008, 9 : 206
Mind the GAPscreener PubMed abstracts can now be effectively screened for articles related to human genetic association studies and genome epidemiology using GAPscreener, a free java-based tool.
BMC Bioinformatics 2008, 9 : 205

참고: BMC Bioinformatics: Most viewed articles in past 30 days
  7-2. BMC Genomics Research highlights (Impact Factor=4.03)

제 목

요 약

Baseline variation in toxicogenomic data An inter-laboratory meta-analysis of more that 500 microarrays from the liver and kidney of control rats defined key sources of variability in control animals and will aid in the efficient design of future toxicogenomics experiments.
BMC Genomics 2008, 9 : 285
Earthworm genetics takes on soil toxins Earthworms exposed to cadmium, the herbicide atrazine or the polyaromatic hydrocarbon fluoroanthene can be distinguished from worms not exposed to pollutants by their characteristic genetic profiles, a novel means of monitoring contaminated soil ecosystems
BMC Genomics 2008, 9 : 266
Hidden layers of human small RNAs Unbiased sequencing of 19 to 40 nucleotide-long RNAs in human cells suggests the existence of small RNAs originating from longer, more well-characterized non-coding RNAs, such as tRNAs, and also reveals six previously unknown miRNAs.
BMC Genomics 2008, 9 : 157

참고: BMC Genomics: Most viewed articles in past 30 days

[Recruit]

주) BioJob에 등록된 구인 정보에 bioinformatics, genomics, proteomics를 검색해서 나오는 자료를 시간 순으로 정리 해서 사용 (마감날짜 기준 6월 15일 이후 자료임)

방식

형태

채용기관

학위

분야

마감일

계약직

연구원

인제대학교
기초의과학연구센터

Bs

Genomics
Bioinformatics
생물학관련모든분야

7/11

계약직

PostDoc

서울대학교 의과대학 의과학과

Ph.D.

Genetics
Genomics

7/14

계약직

연구원

포가연구원

Bs

Biology
Molecular_Biology
Proteomics

7/15

계약직

연구원

충남대학교 의과대학

MS

생물학관련모든분야
Microbiology
Proteomics

7/15

계약직

연구원

충남대학교 의과대학

Ph.D._Candidate

생물학관련모든분야
Microbiology
Proteomics

7/15

계약직

연구원

충남대학교 의과대학

MS_Candidate

생물학관련모든분야
Microbiology
Proteomics

7/15

계약직

PostDoc

연세대 게놈연구소

Ph.D.

Cancer_Biology
Genomics
Molecular_Biology

7/15

계약직

연구원

질병관리본부

MS

Bioinformatics

7/20

계약직

연구원

건국대학교
바이오식의약연구센타

MS

Proteomics
Biochemistry
Molecular_Biology

7/20

계약직

연구원

울산의대/서울아산병원

MS

Proteomics
생물학관련모든분야

7/30

계약직

연구원

극지연구소

MS

Proteomics
Environmental_Science
생물학관련모든분야

7/31

정규직

경력사원

부일메디텍

Bs

생물학관련모든분야
Clinical_Research
Genomics

7/31

계약직

연구원

화순전남대병원

MS

Genomics
Bioinformatics
Molecular_Biology

7/31

계약직

PostDoc

한국과학기술연구원-
프로테오믹스사업단

Ph.D._Candidate

Cancer_Biology
Proteomics

8/31



[Resources] 최근 주요 저널에 소개된 리소스

제목

관련URL

MITOMASTER: a bioinformatics tool for the analysis of mitochondrial DNA sequences http://mammag.web.uci.edu/twiki/bin/view/Mitomaster
EagleView: a genome assembly viewer for next-generation sequencing technologies. http://bioinformatics.bc.edu/marthlab/EagleView
MemBrain: improving the accuracy of predicting transmembrane helices http://chou.med.harvard.edu/bioinf/MemBrain/
DNAlive: A tool for the physical analysis of DNA at the genomic scale http://mmb.pcb.ub.es/DNAlive/
StAR: a simple tool for the statistical comparison of ROC curves http://protein.bio.puc.cl/cardex/servers/roc/home.php
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments http://www.babelomics.org/
bioNMF: a web-based tool for nonnegative matrix factorization in biology. http://bionmf.dacya.ucm.es./
PRIMEGENS-v2: Genome-wide primer design for analyzing DNA methylation patterns of CpG islands. http://digbio.missouri.edu/primegens/
Automated Discovery and Phylogenetic Analysis of New Toxin-Antitoxin Systems http://ueg.ulb.ac.be/tiq/
ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses http://www.bio-miblab.org/arraywiki
Noisy: identification of problematic columns in multiple sequence alignments. http://www.bioinf.uni-leipzig.de/Software/noisy/
Mango: multiple alignment with N gapped oligos. http://www.bioinfo.org.cn/mango/
PoooL: An efficient method for estimating haplotype frequencies from large DNA pools http://staff.ustc.edu.cn/~ynyang/poool/
GMODWeb: a web framework for the generic model organism database http://genome.ucla.edu/turnkey/
Web Server To Identify Similarity of Amino Acid Motifs to Compounds (SAAMCO). http://bioware.ucd.ie/
The PhyLoTA Browser: Processing GenBank for Molecular Phylogenetics Research http://loco.biosci.arizona.edu/pb/
MPIDB: The microbial protein interaction database. http://www.jcvi.org/mpidb/about.php
FishMap: a community resource for zebrafish genomics. http://fishmap.igib.res.in/
Anni 2.0: a multipurpose text-mining tool for the life sciences. http://biosemantics.org/index.php?page=anni-2-0
PURE: a PubMed article recommendation system based on content-based filtering http://www.bic.kyoto-u.ac.jp/pathway/mami/out/PURE.tar.gz
KFC Server: interactive forecasting of protein interaction hot spots. http://kfc.mitchell-lab.org/
NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways http://rsat.ulb.ac.be/rsat/index_neat.html
xREI: a phylo-grammar visualization webserver. http://harmony.biowiki.org/xrei/
BIOSMILE web search: a web application for annotating biomedical entities and relations. http://bioservices.cse.yzu.edu.tw/BWS/
DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. http://cssb.biology.gatech.edu/skolnick/webservice/DBD-Hunter/
BioLit: integrating biological literature with databases http://biolit.ucsd.edu
Protein ligand interaction database (PLID). http://203.199.182.73/gnsmmg/databases/plid/


[Events]

1. 2008년 국외 행사

행사명

기간

장소

International Symposium on Integrative Bioinformatics August 20- 22, 2008 Leucorea, Lutherstadt Wittenberg, Germany
Computational Intelligence in Bioinformatics and Bioengineering September 15-17 Sun Valley, Idaho
BCSB 2008 : "International Conference on Bioinformatics, Computational and Systems Biology" October 29-31, 2008 Venice, Italy

2. 국내 행사

행사명

날짜

장소

생물정보 데이터 분석을 위한
Perl 프로그래밍 기초
2008/07/15 한국기초과학지원연구원
대전 본원 소회의실
제 4회 통계유전워크샵 (한국유전체학회) 2008/07/21 - 26 경희대학교 의학관 강의실


[Books and Reports]

사진

상세내용

Analysis of Microarray Data: A Network-Based Approach
By Matthias Dehmer, Frank Emmert-Streib
Published 2008
Wiley-VCH
438 pages
ISBN:3527318224
Unique Chips and Systems
By Eugene John, Juan Rubio
CRC Press
370 pages
ISBN:1420051741
Genomics of Disease
J. Taylor, G. Stacey Contributor J. P. Gustafson, J. Taylor, G. Stacey
Springer
222 pages
ISBN:0387767223
Epigentics By Jorg Tost
Published 2008
Horizon Scientific Press
404 pages
ISBN:1904455239

[Gossip]

1. ISMB 2008
1) Keynote Speakers
2) ISMB 2008 Accepted Papers
3) Program
4) Highlights Track

2. 2008 Bioinformatics Research Papers by EurekAlert

-. Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis
By Ari Loytynoja and Nick Goldman.
Science, 20 June 2008: Vol. 320. no. 5883, pp. 1632 - 1635 DOI: 10.1126/science.1158395.

-. Discovering Sequence Motifs with Arbitrary Insertions and Deletions
By Martin C. Frith, et al.
PLoS Computational Biology, 4(5): e1000071. doi:10.1371/journal.pcbi.1000071 (2008).

-. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei.
By Diego Martinez, et al.
Nature Biotechnology 26, 553 - 560 Published online: 4 May 2008 | doi:10.1038/nbt1403 (2008).

-. Exon level integration of proteomics and microarray data
By Danny Bitton, et al.
BMC Bioinformatics 2008, 9:118doi:10.1186/1471-2105-9-118 (2008).

-. Geographic Patterns of Genome Admixture in Latin American Mestizos
By Sijia Wang, et al.
PLoS Genet 4(3): e1000037. doi:10.1371/journal.pgen.1000037 (2008).

-. Global Analysis of Genetic, Epigenetic and Transcriptional Polymorphisms in Arabidopsis thaliana Using Whole Genome Tiling Arrays
By Xu Zhang, et al.
PLoS Genet 4(3): e1000032. doi:10.1371/journal.pgen.1000032 (2008).

-. Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation
By Jun Z. Li, et al.
Science, Vol. 319. no. 5866, pp. 1100-1104, DOI: 10.1126/science.1153717) (2008).

-. Evolution of Complex Modular Biological Networks
By Arend Hintze and Christoph Adami.
PLoS Comput Biol 4(2): e23 doi:10.1371/journal.pcbi.0040023 (2008).

-. Genome resequencing and genetic variation
By Abraham L. Brass et al.
Science, 10.1126/science.1152725 (2008).

-. Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen
By Arend Hintze and Christoph Adami.
PLoS Comput Biol 4(2): e23 doi:10.1371/journal.pcbi.0040023 (2008).

자료 : http://www.eurekalert.org/context.php?context=bio&show=research

3. Genome Browser
UCSC genome browser tutorial

4. New Technology
Next-Generation DNA Sequencing Methods

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