Embed Size (px)
Citation preview
82 APBN • Vol. 7 • No. 3 • 2003
www.asiabiotech.com
Bioinformatics Research
Yi-Ping Phoebe ChenCenter for Information Technology Innovation, Queensland University of Technology, Brisbane, Australia.
Geoff McLachlanDepartment of Mathematics, University of Queensland, Australia.
in Australia
Abstract
Bioinformatics is the intersection of computerscience, statistics, molecular biology and genetics. It isone of the most important emerging research areas ofthe 21st century and has already attracted worldwideinterest. It is clear that major initiatives are beingundertaken which will establish Australia both as a vitallink in the international bioinformatics community forresearch and development and also as an Asia-Pacificservice for bioinformatics. This article briefly notes somegroups carrying out bioinformatics research in Australia.
Keywords: Bioinformatics; Australia.
1 Introduction
An excellent account of bioinformatics in Australiahas been provided in the editorial of Littlejohn (2000).Since the writing of this editorial, interest inbioinformatics in Australia has increased enormously.The volume of biological data is growing exponentially,partly due to the deluge of information that has stemmedfrom the working draft of the human genome (releasedin February 2001) and other similar sequencing projects.Also, the increase in advanced computer power hasallowed groups to generate more data at a faster rate.Consequently, there are many challenging and novelproblems on the interface of modern biology andcomputational statistics that are in need of solutions.For example, there needs to be statistical methodologyand database technologies that can analyze and drawreliable inferences from these huge and complex datasets, where the biological signal is often very difficult todistinguish from the noise which can arise from manysources. There is also the need to adapt existingstatistical and computational approaches to
accommodate the often novel constraints orassumptions of bioinformatics problems.
The bioinformatics research community in Australiahas been fortunate in having one of the leadingresearchers on the international stage in the field, Prof.Terry Speed (University of California Berkeley), nowspending six months each year at the Walter & ElizaHall Institute (WEHI) in Melbourne. Research inbioinformatics at WEHI is focussed on statisticalgenetics, design and analysis of gene expression studies,biological sequence analysis, and proteomics.
At the University of Queensland (UQ), research inbioinformatics is centered in the Computational Biologyand Bioinformatics Division of the Institute of MolecularBioscience (IMB). The IMB is directed by Prof. JohnMattick whose research interests in this field includethe development of an intron and alternativesplicing database. The Computational Biology andBioinformatics Division at the IMB is directed by Prof.Mark Ragan. It is actively building critical mass in datamining, genomic and expression databases, proteinstructure/function, gene identification, molecularmodeling, comparative genomics, chemical informaticsand high-performance computing. It collaborates closelywith other initiatives at UQ: the AdvancedComputational Modeling Center, under the directionof Prof. Kevin Burrage; the Computational Biology andBioinformatics group funded by the CommonwealthDepartment of Education, Training and Youth Affairs(DETYA); the Queensland Parallel SupercomputingFoundation (QPSF) in collaboration with the AustralianPartnership in Advanced Computing (APAC); and theCenter for Statistics directed by Prof. Geoff McLachlan.There are also close collaborative ties between the
83APBN • Vol. 7 • No. 3 • 2003
Division and Dr. Phoebe Chen’s group at theQueensland University of Technology (QUT).
Research in bioinformatics at QUT is focussed inthe Center for Information Technology Innovation ledby Dr. Chen. As part of her research, Dr. Chen isundertaking ARC funded investigations with UQcollaborators on two projects: “Integrating DatabaseTechnologies and Visual Analysis in Bioinformatics forGenome Data” and “Computational Infrastructure forHigh-Throughput Genome Bioinformatics.”␣ QUT hasidentified bioinformatics as a strategic area for researchand education. Its Faculty of Information Technologyhas created a research concentration in bioinformatics.Research projects have been collaborated among theFaculty of Information Technology, the Faculty ofScience, Department of Maths and the Center forMolecular Biotechnology.
Among other groups researching bioinformatics inBrisbane, there is the UQ node of the Australian Centerfor Plant Functional Genomics, headed by Prof. KayeBasford, the Queensland Institute of Medical Research(QIMR), and the CSIRO Divisions of Livestock Industries(Dr. Brian Dalrymple) and Plant Industry (Drs. RosanneCasu and Scott Chapman). Bioinformatics research isbeing carried out also in some other CSIRO divisionseither in Brisbane or elsewhere in Australia, includingEntomology and Mathematical & Information Sciences.
The Center for Bioinformation Science at theAustralian National University (ANU), co-directed byProf. Sue Wilson and Prof. Simon Easteel, collaboratesextensively with groups within the ANU and outside.The former include the Human Genetics group at theJohn Curtin School of Medical Research and theAdvanced Data Mining Group (Dr. Marcus Hegland).The latter include the Garvan Institute of MedicalResearch, Prof. Speed’s group at the University ofCalifornia Berkeley and WEHI, and Prof. Ewens’ groupat the University of Pennsylvania. Dr. Georg Weiller isleader of the bioinformatics group in the ResearchSchool of Biological Sciences at the ANU.
Australia’s national bioinformatics service provider(ANGIS, the Australian National Genomics InformationService) is based at the University of Sydney. It is headedby Dr. Michael Poidinger. Over the years, ANGIS hasdeveloped a series of integrated bioinformaticsworkspaces. Recently, the University of Sydney hasannounced a new postgraduate course inbioinformatics. In other recent initiatives in Sydney, theGarvan Institute of Medical Research has established abioinformatics center.
The Victorian Bioinformatics Consortium (VBC) isdirected by Prof. Ross Coppel. VBC members include:Monash University, the central institution with severaldepartments and centers involved; Plant BiotechnologyCenter of Agriculture Victoria at La Trobe University;CSIRO Mathematical and Information Sciences; thePeter MacCallum Cancer Institute (directed by Prof.David Bowtell, a pioneer of array technology); theHoward Florey Institute; and other commercialcompanies. Prof. Coppel’s research interests include themolecular biology of malaria antigens and malariavaccine development. Bioinformatics research inMelbourne is being carried out also at the VictorianPartnership for Advanced Computing (VPAC) and theLudwig Institute for Cancer Research.
The University of Adelaide hosts the MicroarrayAnalysis Group (MAG) directed by Dr. Patty Solomon.Its primary aims are to provide advice on thestatistical design and analysis of microarray experimentsspecific to the local context; to provide access tostate-of-the-art image processing and data analysissoftware; and to collaborate with national andinternational groups working on microarray informatics.
Concerning bioinformatics in Tasmania, the stategovernment has recognized the growing commercialand academic research potential of this field withfinancial support for the setting up of the TasmanianBioinformatics Center of Excellence (with Dr. MichelleAllan as its CEO).
The bioinformatics research community in
Australia has been fortunate in having one of
the leading researchers on the international
stage in the field, Prof. Terry Speed
(University of California Berkeley), now
spending six months each year at the Walter
& Eliza Hall Institute (WEHI) in Melbourne.
QUT has identified bioinformatics as a
strategic area for research and education.
Its Faculty of Information Technology has
created a research concentration in
bioinformatics.
apbn.v7n3.ls.2 28/1/03, 5:28 pm83
84 APBN • Vol. 7 • No. 3 • 2003
www.asiabiotech.com
Tim Littlejohn Michael Poidinger
Mark Ragan Yi-Ping Phoebe Chen
Kevin Burrage Ross Coppel
Some of Australia Bioinformaticians
Bioinformatics research in Australia is also takingplace in many of the Cooperative Research Centers(CRCs), particularly those that come under the umbrellaof the Biotechnology Education and training program.For example, there is the Cooperative Research Centerfor the Discovery of Genes for Common HumanDiseases, which actively pursues bioinformaticsresearch.
Mention should also be made of (i) The AustralianGenome Research Facility (AGRF) directed by Prof.Mattick at UQ (with a Melbourne branch located atWEHI), which provides an engine for large scale geneticdiscovery by Australian research organizations andindustry ; (ii) BioLateral Pty. Ltd. which has providedtraining programs across the spectrum of bioinformaticproblems (molecular modeling, microarray analysis,data management, programming); and (iii) TheAustralian Biotechnology Association (AusBioTech),which supports regular bioinformatics related events atthe various branches throughout Australia, including theannual AusBioTech conference, which brings togetherscientists from industry and academia.
This year two international conferences onbioinformatics are to be held. Firstly, there is the FirstAsia Pacific Bioinformatics Conference, to be held atAdelaide within Australia Computer Science Week(February 4 – 7, 2003). The Asia-Pacific BioinformaticsConference series, of which Dr. Phoebe Chen is afounder, is to be an annual forum for exploring research,development and novel applications of bioinformatics.The second conference is the 11th InternationalConference on Intelligent Systems for Molecular Biology(ISMB 2003) to be held in Brisbane (June 29 – July 3).This conference is sponsored by the International Societyfor Computational Biology and is one of the majorconferences in bioinformatics.
References
The First Asia-Pacific Bioinformatics Conference http://
www.fit.qut.edu.au/~chenp/APBC2003.
The 11th International Conference on Intelligent Systems for Molecular
Biology http://www.iscb.org/ismb2003/index.shtml
Littlejohn, T. (2000): Bioinformatics in Australia. Bioinformatics
16, 849 – 850.
Acknowledgments
The authors would like to thank Ms. Jess Mar (European
Bioinformatics Institute (formerly of UQ)) for her assistance in the
preparation of this article.
Georg Weiller Goff McLanchian
The Victorian Bioinformatics Consortium
(VBC) is directed by Prof. Ross Coppel. Prof.
Coppel’s research interests include the
molecular biology of malaria antigens and
malaria vaccine development.
The Center for Bioinformation Science at the
Australian National University (ANU), co-
directed by Prof. Sue Wilson and Prof. Simon
Easteel, collaborates extensively with groups
within the ANU and outside.
85APBN • Vol. 7 • No. 3 • 2003
his book contains articles written by experts on a wide range of topics that are associated with the
analysis and management of biological information at the molecular level. It contains chapters on RNA and
protein structure analysis, DNA computing, sequence mapping, genome comparison, gene expression data
mining, metabolic network modeling, and phyloinformatics.
The important work of some representative researchers in bioinformatics is brought together for the first time
in one volume. The topic is treated in depth and is related to, where applicable, other emerging technologies
such as data mining and visualization. The goal of the book is to introduce readers to the principle techniques
of bioinformatics in the hope that they will build on them to make new discoveries of their own.
Readership: Molecular biologists who rely on computers and mathematical scientists with interests in biology.
266pp • Feb 2003 • 981-238-257-7 • US$38 •␣ £26
COMPUTATIONAL BIOLOGY ANDGENOME INFORMATICSedited by Jason T L Wang (New Jersey Institute of Technology, USA),
Contents: Exploring RNA Intermediate
Conformations with the Massively Parallel Genetic
Algorithm; Introduction to Self-Assembling DNA
Nanostructures for Computation and
Nanofabrication; Mapping Sequence to Rice FPC;
Graph Theoretic Sequence Clustering Algorithms
and their Applications to Genome Comparison; The
Protein Information Resource for Functional
Genomics and Proteomics; High-Grade Ore for Data
Mining in 3D Structures; Protein Classification: A
Geometric Hashing Approach; Interrelated
T
For more information, please contact your nearest World Scientific office:USA office: 1060 Main Street, Suite 202, River Edge, NJ 07661, USA Toll-free Fax: 1 888 977 2665
Toll-free Tel: 1 800 227 7562 E-mail:[email protected] office: 57 Shelton Street, Covent Garden, London WC2H 9HE, UK Fax: +44 (0)20 7836 2020
Tel: +44 (0)20 7836 0888 E-mail:[email protected] office: Farrer Road, P O Box 128, Singapore 912805
Fax: +65 6467 7667 Tel: +65 6466 5775 E-mail:[email protected]
World ScientificAn International Publisher
Home Page:www.worldscientific.com
86 APBN • Vol. 7 • No. 3 • 2003
www.asiabiotech.com
The Status ofFormalizedBioinformatics
Abstract
This review describes the current state ofbioinformatics education in Australia, outlining theaward and non-award courses offered by AustralianUniversities and centers.
Keywords: Bioinformatic degree; Australia.
1 Introduction
Bioinformatics is a new, under developed andunder resourced field in Australia. Whilst there are anumber of centers with a focus on bioinformaticsresearch, including the Victorian BioinformaticsConsortium at the University of Melbourne and MonashUniversity, the Institute for Molecular Biosciences (IMB)at the University of Queensland, The BioinformaticCenter of Excellence in Tasmania, the Center forBioInformation Science (CBIS) at the Australian NationalUniversity and the Sydney University BiologicalInformatics and Technology Center (SUBIT), the amountof research and number of qualified bioinformaticiansin Australia remains small, compared with othercountries.
However, in the past five years there has been anincrease in the number of bioinformatics degreesappearing in Australia. Compared to the US markets,there is a serious lack of postgraduate degrees inAustralia with only two universities (University ofSydney and Curtin University) providing postgraduatedegrees. As of yet there have been no graduations fromthese as of December 2002.
Note that in the past ten years most universities inAustralia have incorporated some practicalbioinformatics into their molecular biology andbiotechnology teaching, many using the resources ofthe Australian National Genomic Information Center(ANGIS, see later). In addition, several other universitiesalso teach bioinformatics within their current Bachelorof Science/Bachelor of Biotechnology degree structure.They allow students to major in bioinformatics but donot offer Bioinformatics as a degree in its own right.These courses will not be covered in this article.
2 Australian Degrees in Bioinformatics
2.1 Undergraduate Degrees
In 2003 there will be nine Australian Universitiesthat will be providing specified Bioinformatics degrees.As of 2002 only two (University of Sydney and La TrobeUniversity) have produced graduates. Of the remainderthree will be taking applications for the first time in 2003(Macquarie University, University of SouthernQueensland and University of Western Australia).
The content of these degrees differs from course tocourse but there are a few underlying similarities (seeTable 1). The courses can be roughly divided into twostreams; a degree that produces bioinformaticsprogrammers and a stream that produces bioinformaticstechnicians. The former includes the degrees that havethe major emphasis on computer science, mathematicsand statistics while the latter is more biological inorientation.
Bioinformatics, with its emphasis on computerscience, mathematics and statistics, had not beenconsidered a suitable candidate for distance educationdue to the molecular biology component. Also theuniversities that had so far produced the Bioinformaticsdegrees tend not to have strength in the area of distanceeducation. However, in 2003 the University of SouthernQueensland will launch is Bachelor of Bioinformaticsdegree that can be taken by distance education withcompulsory residential schools in the semester break.
Bioinformatics is a new, under developed and
under resourced field in Australia. Whilst
there are a number of centers with a focus
on bioinformatics research, the amount of
research and number of qualified
bioinformaticians in Australia remains small,
compared with other countries.
87APBN • Vol. 7 • No. 3 • 2003
in AustraliaEducation
Michael Poidinger and Sonia CattleyAustralian National Genomic Information Service(ANGIS), B19, University of Sydney, Australia.
2.2 Postgraduate Degrees
Despite the number of undergraduate degrees onoffer, only two of the nine universities have establisheda post graduate degree. The University of Sydney hasset up a Graduate Certificate, Graduate Diploma,Coursework Masters degree combination that has beenrunning since August 2002. These post graduatecoursework degrees are directed at both workingscientists who need retraining in bioinformatics andcomputer scientists who wish to be training in biologyto work as bioinformaticians. A Graduate Certificate inbioinformatics has been available at Curtin Universityfor several years, however, there have been no graduatesas yet.
2.3 Award Courses
2.3.1 ANGIS
ANGIS has been training working scientists in theapplication of currently available bioinformatics
programs for 12 years. Courses are given in databasesearching, applied bioinformatics and the use of theANGIS bioinformatics interfaces. The aim of thesecourses is to train applied bioinformaticians and notcomputer programmers. Courses are held at least oncea year in Sydney, Melbourne, Brisbane and Adelaide.
2.3.2 Biolateral
Biolateral is a Sydney based company that offersintensive courses in bioinformatics application andtheory. These courses include training in computerprogramming, and the analysis of data from newtechnologies such as microarrays.
References
Additional information about these degrees can be found at http://
www.angis.org.au/new/education/study.html along with links to the
individual university course information sites.
88 APBN • Vol. 7 • No. 3 • 2003
www.asiabiotech.com
in SingaporeBioinformatics
Limsoon WongInstitute for Infocomm Research21 Heng Mui Keng Terrace, Singapore 119613
1 Summary
Singapore seeks to be an international center forthe biomedical sciences and its related industries.Bioinformatics is seen as an important ingredient in thisambition. We provide in this short report a briefoverview of bioinformatics in Singapore. We coveraspects such as training (Section 3), research (Section4), and commercialization (Section 5). We alsointroduce some of the main centers of activities, as wellas some of the bioinformaticists in these centers.
2 Background
As the Singapore government is the main driver todevelop the biomedical sector into a new pillar of theSingapore economy, most of the main organizations thatare currently involved in bioinformatics research anddevelopment in Singapore are government-fundedinstitutions. Before we get into the details, it is useful tolay out these main organizations.
There are two large universities in Singapore,namely the National University of Singapore (NUS) andthe Nanyang Technological University (NTU). The NUShas a longer history in bioinformatics and biomedicaltraining and research, while the NTU did not have alife science school until recently. Both universities arein the process of stepping up their bioinformatics trainingand research programs.
The Agency for Science Technology &Research (A*STAR) is the major provider ofscience and technology research funding inSingapore, and manages all the nationalresearch institutes in Singapore. Several of thesenational research institutes have bioinformaticsand related activities, including theBioinformatics Institute (BII), the GenomeInstitute of Singapore (GIS), the Institute ofMolecular & Cell Biology (IMCB), the Institute
of High Performance Computing (IHPC), and theInstitute for Infocomm Research (I2R).
The I2 R has the longest history in this field, andthough the amount of its resources devoted tobioinformatics is small, it accounts for a lion’s share ofSingapore’s output in bioinformatics research. The BIIand GIS are newly set up entities and are expected tobecome Singapore’s main centers of bioinformatics andhigh throughput biology research.
Besides the organizations above, there are anumber of polytechnics, hospital-associated researchcenters, as well as commercial entities that haveactivities relating to bioinformatics.
In the remaining sections of this report, we willsurvey the bioinformatics activities of all of these publicand private organizations.
3 Training Programs
There are four major university-level bioinformaticstraining programs in Singapore. The first and oldestprogram is the S* Life Science Informatics Alliance, anorganization involving Karolinska Institutet, NUS,Stanford University, UC San Diego, University ofSydney, University of Uppsala, and University ofWestern Cape. This is a global alliance to provide aglobal, unified bioinformatics learning environment
89APBN • Vol. 7 • No. 3 • 2003
made up of modular courses in the disciplines ofgenomics, bioinformatics, and medical informatics. Themodules are assembled from selected lectures from theseven universities involved and are offered throughdistance learning. The main driver of this Alliance inSingapore is Shoba Ranganathan and Tin-Wee Tan inthe NUS. Shoba also organizes a bioinformatics modulein the NUS Department of Biochemistry that is aimedat biology and biochemistry majors.
The second program is a full-time MSc-level courseorganized by the BII in partnership with the NUS. Thisis a two-year course. It was started in 2002 and has asmall but selective enrolment. A distinctive quality ofthe BII program is that it has a very active literaturereview and journal club series. The program is lead byGunaretnam Rajagopal, director of the BII.
The third program is a part-time MSc-level courseto be launched in 2003 in the NTU. It is also a two-yearcourse. The course co-ordinator is Chee-Keong Kwoh.The renowned bioinformaticist Ming Li, of the Universityof Waterloo, is the external examiner of this course.
The last program is not yet a full program. Itcurrently comprises a couple of very goodbioinformatics modules, viz. combinatorial methods inbioinformatics and computation foundation inbioinformatics, offered to undergraduates at the Schoolof Computing in the NUS. These two modules weremounted in 2002 after the arrival of Ken Sung at theschool.
4 Research Projects
The NUS currently has several pockets ofbioinformatics activities. In the Department ofBiochemistry, Shoba Ranganathan and Tin-Wee Tanare active in Asia-Pacific Bioinformatics Network,a non-profit and non-governmental organizationthat promotes bioinformatics awareness and educationin the Asia-Pacific region. Their group has done curationand research in alternate splicing, databases forstructural biology, assignment of function based on 3Dstructural model (Ranganathan 2001), etc. In theDepartment of Computational Science, Yuzong Chenhas been working on computer-aided drug design anddynamics of biomolecules. In the Department ofMathematics, there are also several researchers whohave made interesting contributions to bioinformatics.Particularly notable is Kwok-Pui Choi and LouxinZhang’s recent theoretical work on spaced seeds, whichis an idea that can significantly improve the efficiencyand sensitivity of sequence homology search.
The NUS School of Computing did not have anyactivity in bioinformatics until this year. Besides KenSung, there are now several other researchers in theschool with an interest in this field: Gabriel Ciobanu isinterested in the logical modeling of protein interaction;Roland Yap, Tzu-Yun Leong, Wynne Hsu, and Mong-LiLee are interested in medical data analysis; andBeng-Chin Ooi and Kian-Lee Tan are interested inindexing of genomic and protein sequences (Ooi, Pang,Wang, Wong & Yu 2002).
The NTU has started its BioInformatics ResearchCenter (BIRC) in 2002. The key members of the BIRCinclude Jagath C. Rajapakse — who is an experiencedresearcher in neural networks and medical imaging,Chee-Keong Kwoh — who is an expert in probabilisticinference and medical imaging, and K. C. Lun — whois well-known in the medical informatics world. Theresearch interests of BIRC covers a very broad spectrum,such as computational genomics, functional genomics,structural genomics, molecular imaging, and medicalinformatics.
The NTU School of Mechanical & ProductionEngineering also has a small team of bioinformaticsresearchers. The most experienced amongst them isMeena Sakharkar, who earned the first bioinformaticsPhD awarded by the NUS. She has done excellentcuration work on introns and exons (Sakharkar,Kangueane, Woon, Tan, Kolatkar, Long & de Souza2000, Sakharkar, Tan & de Souza 2001). Besides thiswork, her group are also exploring peptide vaccinedesign and protein-protein interaction.
The BII was set up in 2001 to encourage, develop,and support trained expertise in bioinformatics toadvance biomedical research and development inSingapore. It currently has skeletal research groups insystems biology, structural & functional genomics,computational genomics, medical genomics, anddistributed computing. The key researchers areGunaretnam Rajagopal — who has significantexperience in supercomputing techniques for modelingcomplex systems, Pawan Dhar, Kuo-Bin Li, and AdrianMondry. The BII scientific advisory board has manyluminaries in the bioinformatics world, includingMichael S. Waterman, Leroy E. Hood, and John Wooley.
The GIS is Singapore’s flagship in genomic sciences.The bioinformatics works conducted in GIS are largelyin support of various biological research projects in GIS.The key bioinformatics researchers in GIS are PhilipLong — who is well-known in the machine learning
90 APBN • Vol. 7 • No. 3 • 2003
www.asiabiotech.com
field, Prasanna Kolatkar — who is an expert in proteincrystal structures, and Lin Kui — who is an excellentbioinformaticist. It is also worth noting that, David J.Lipman, a luminary of the bioinformatics field, sits onthe GIS scientific advisory board. An important recentbioinformatics project at the GIS was the design anddevelopment of a S. pombe genome-wide ORFmicroarray. This is one of the few S. pombe microarraysthat are being used in the studies of global geneexpression patterns and their regulation. Another recentproject was a study of cellular responses to estrogens.Here, bioinformatics was used to identifydirect targets of estrogen receptors. This projecthas successfully produced over 100 earlyestrogen-responsive genes with putative estrogenresponse elements, which was a five-fold increase overthe 20 or so known estrogen-responsive genes withestrogen response elements. A third project was thestudy of gene expression of hepatocellular carcinoma.Bioinformatics was used to examine the variationin gene expression patterns in paired samplesof hepatocellular carcinoma tumour tissues andnon-tumour counterparts. A significant on-goingbioinformatics effort at the GIS is the development of aprotein-protein interactions database to help betterunderstand the intricate relationships between theindividual proteins within different genomes.
The IMCB’s recent main bioinformatics activitieswere centered on its Fugu project. Its informatics team,lead by Elia Stupka, was the work horse that annotatedand analyzed the draft Fugu genome sequence (Aparicioet al. 2002).
The IHPC does not have a bioinformatics group.However, its computational chemistry group, lead byWu Ping, does have some bioinformatics capabilities,especially in the protein structure and modeling aspects.An interesting project of this group in 1998 was a studyof prostate cancer where prognosis was made based onchemical data from hair samples of patients.
I2R currently has the most active bioinformaticsresearchers in Singapore — after all, it was the firstorganization to conduct bioinformatics research in asignificant way in Singapore. The key bioinformaticsresearchers in I2R are Vladimir B. Bajic — who hascreated an extremely accurate human transcription startsite prediction system, Vladimir Brusic — who is apioneer in immunoinformatics research, Jinyan Li —who has made innovative contributions to dataminingtechnology research with his idea of emerging patterns,
See-Kiong Ng — who wrote the key genotypingautomation software that was used by DeCODE togenotype the Icelandic population, and LimsoonWong — who conducted the first piece of bioinformaticsresearch in Singapore back in 1994. The group’sresearch also benefits from the participation of LouxinZhang of the NUS Department of Mathematics — whois an expert in sequence analysis and phylogenyreconstruction algorithms, and Christian Schoenbachof RIKEN Japan — who is a member of the FANTOM02core team.
As mentioned earlier, the first piece ofbioinformatics research in Singapore was conducted in1994 in I2R. It was the development of the Kleisli querysystem for the integration and manipulation of datasources that are highly heterogeneous, highly complex,and geographically dispersed. Amongst the firstproblems the system was applied to was the so-called“impossible” biological data integration problemsidentified by the US Department of Energy at that time(DOE 1993). This was one of the earliest and mostgeneral data integration system for biology (Buneman,Davidson, Hart, Overton & Wong 1995, Wong 2002).The system was subsequently licensed in 1998 togeneticXchange of Menlo Park for commercialization,see http://www. geneticxchange.com.
This project was followed by the FIMM project in1996 which focused on curation of informationpertaining to human functional immunology(Schoenbach, Koh, Sheng, Wong & Brusic 2000), andon development of methods for recognizingimmunogenic peptides from antigens (Brusic &Zeleznikow 1999, Brusic, Petrovsky, Zhang & Bajic2002). This project was a pioneer of the field that hasnow come to be known as immunoinformatics(Petrovsky & Brusic 2002). The group has madesuccessful epitope predictions in several disease areassuch as IDDM, melanoma, HIV, Malaria, renaltransplantation, just to name a few.
By around end of 1998, the I2R group becamesufficiently experienced and launched several majorprojects in the subsequent years aiming at post-genomeknowledge discovery problems. The earliest amongstthese later projects was the PIES project which wasstarted in 1998 to use natural language processingtechniques to extract protein interaction informationfrom scientific literature (Ng & Wong 1999). The groupalso started the literature datamining track in the PacificSymposium on Biocomputing series and organized thetrack for three years until 2002, when this topic wasfinally recognized as an important challenge(Hirschman, Park, Tsujii, Wong & Wu 2002). A prototype
91APBN • Vol. 7 • No. 3 • 2003
of PIES was licensed in 2001 to Molecular Connectionsin Bangalore as the backbone of its curation system,see http://www.molecularconnections.com.
Following PIES, the Dragon project was started in2000 to analyze and predict gene features in genomicDNAs. By late 2001, the project has delivered initialsuccess — its human transcription start site recognizeris currently the most accurate in the world by asignificant margin (Bajic, Chong, Seah & Brusic 2002).It has recently been licensed to BioBase of Germany tobe integrated into their TRANSPLORER product in 2003,see http://www.biobase.de.
Most recently, the I2R group has also embarked ona project to develop technologies for analyzing clinicaldata, including gene expression and proteomic data. Adriving interest of this project is the research on newdatamining and classification algorithms that are bothhighly accurate and highly comprehensible. Most of theinitial ideas are based on the concept of emergingpatterns (Li & Wong 2002a) and have delivered someinitial successes (Li & Wong 2002b, Yeoh et al. 2002).
Besides these projects, the I2R group is also busyin analysing a specific group of zinc finger proteins, incurating information on action of toxins on ion channels,and in algorithms and methodologies for various aspectsof post-genome knowledge discoveries, especially thosepertaining to protein interactions.
5 Commercial Sector Activities
In the commercial sector, the most notable is theNational Cancer Center, where Patrick Tan is leadingthe OmniArray Research Group. This group investigatesthe influence of genetic differences on the developmentof certain cancer diseases. The group has made goodprogress in the use of cDNA microarray technology andin the management and analysis of microarray data (Ooi& Tan 2003).
Another organization is the Lilly Systems BiologyResearch Center managed by Santosh Mishra, a veryseasoned bioinformaticist. The Lilly Systems BiologyResearch Center is a subsidiary of Eli Lilly and Company.The center is to deliver innovative computational toolsto help identify novel drug targets and elucidate drugmechanisms.
On a smaller scale are start-up companies such asKooPrime, Helixense, Agenica, and several others.KooPrime is a spin-out from the NUS and specializesin laboratory information management and automation.Helixense is marketing a data integration platform calledgRNA that they developed in-house. Agenica is a jointventure between Mitsui and the National Cancer Centerto develop a molecular gene expression database forhuman breast cancer.
6 Closing Remarks
We would like to close this report by a few briefremarks on the history and progress of bioinformaticsin Singapore.
As early as 1991 or 1992, there was already alimited amount of bioinformatics activities in Singaporethat were championed by Tin-Wee Tan. However, theseactivities were mostly about mirroring of data collectionsand standard sequence searching applications.
The nature of bioinformatics activities in Singaporebegan to take on a more research-oriented characterwhen Limsoon Wong started work on the Kleisli querysystem in 1994. This work generated significant interestsfrom several large international pharmaceuticalcompanies.
This helped convinced the Singapore EconomicDevelopment Board to provide the funding in 1996 tostart a Bioinformatics Center in the NUS as a jointcollaboration between the support services of Tin-Weeat the NUS and the research of Limsoon at the I2R (thenknown as the Institute of Systems Science). The resourcesof this Bioinformatics Center allowed several talented
In the commercial sector, the most notable
is the National Cancer Center, where Patrick
Tan is leading the OmniArray Research
Group. The group has made good progress
in the use of cDNA microarray technology
and in the management and analysis of
microarray data (Ooi & Tan 2003).
An important recent bioinformatics
project at the GIS was the design and
development of a S. pombe genome-
wide ORF microarray. This is one of the
few S. pombe microarrays that are
being used in the studies of global gene
expression patterns and their
regulation.
92 APBN • Vol. 7 • No. 3 • 2003
www.asiabiotech.com
researchers to be recruited and nurtured into full-fledgedbioinformaticists. Some of them have already beenmentioned earlier: Louxin Zhang, Prasanna Kolatkar,Meena Sakharkar, Vladimir Brusic, Kui Lin, ShobaRanganathan, and several others.
By 2000, the potential of bioinformatics in modernbiomedical research and high-throughput biologicalinvestigations has been fully recognized. Therefore,A*STAR initiated significant new funding to encourageand support research and development in this area. TheGIS was established as the flagship for high-throughputgenomic research in Singapore. A year later, the BII wasestablished to drive bioinformatics training and research.Both the NUS and the NTU also responded byestablishing proper degree programs in bioinformaticsin 2002 and 2003.
Today, as described in the main sections of thereport, we see considerable bioinformatics activities inSingapore. We can therefore expect increased vibrancein this field in Singapore in the near future.
References
Aparicio, S. et al. (2002): Whole-genome shotgun assembly and
analysis of the genome of fugu rubripes, Science 297(5585),
1301 – 1310.
Bajic, V., Chong, A., Seah, S. & Brusic, V. (2002): Intelligent
system for vertebrate promoter recognition, IEEE Intelligent Systems
17(4), 64 – 70.
Brusic, V., Petrovsky, N., Zhang, G. & Bajic, V. (2002): Prediction of
promiscuous peptides that bind HLA class I molecules, Immunology
and Cell Biology 80, 280 – 285.
Brusic, V. & Zeleznikow, J. (1999): Computational binding assays
of antigenic peptides, Letters in Peptide Science 6, 313 – 324.
Buneman, P., Davidson, S., Hart, K., Overton, C. & Wong, L. (1995):
A data transformation system for biological data sources, Proceedings
of International Conference on Very Large Data Bases, Zurich,
Switzerland, 21, 158 – 169.
Dept. of Energy (1993): DOE Informatics Summit Meeting
Report, available at http://www.ornl.gov/hgmis/publicat/miscpubs/
bioinfo/ contents.html.
Hirschman, L., Park, J. C., Tsujii, J., Wong, L. & Wu, C. H. (2002):
Accomplishments and challenges in literature data mining for
biology, Bioinformatics 18, 1553 – 1561.
Li, J. & Wong, L. (2002a): Geography of differences between
two classes of data, Proceedings of European Conference on
Principles of Data Mining and Knowledge Discovery, Helsinki,
Finland, 6, 325 – 337.
Li, J. & Wong, L. (2002b): Identifying good diagnostic genes or
gene groups from gene expression data by using the concept of
emerging patterns, Bionformatics 18, 725 – 734.
Ng, S.-K. & Wong, M. (1999): Toward routine automatic pathway
discovery from on-line scientific text abstracts, Genomic Informatics
10, 104 – 112.
Ooi, B. C., Pang, H. H., Wang, H., Wong, L. & Yu, C. (2002): Fast
filter-and-refine algorithms for subsequence selection, Proceedings
of International Data Engineering and Applications Symposium,
Edmonton, Canada, 6, 243 – 254.
Ooi, C. & Tan, P. (2003): Genetic algorithms applied to multi-class
prediction for the analysis of gene expression data, Bioinformatics
19, 37 – 44.
Petrovsky, N. & Brusic, V. (2002): Computational immunology: The
coming of age, Immunology and Cell Biology 80, 248 – 254.
Ranganathan, S. (2001): Molecular modeling on the web,
Biotechniques 30, 50 – 52.
Sakharkar, M., kangueane, P., Woon, T., Tan, T. W., Kolatkar, P., Long,
M. & de souza, S. (2000): IE-Kb: intron-exon knowledge base,
Bioinformatics 17, 671 – 675.
Sakharkar, M., Tan, T. W. & de Souza, S. (2001): Generation of a
database containing discordant intron positions in eukaryotic genes
(MIDB), Bioinformatics 17, 671 – 675.
Schoenbach, C., Koh, J. Sheng, X., Wong, L. & Brusic, V. (2000):
FIMM, a database of functional molecular immunology, Nucleic Acids
Research 28(1), 222 – 224.
Wong, L. (2002): Technologies for integrating biological data, Briefings
in Bioinformatics 3(4), 389 – 404.
Yeoh, E.-J. et al. (2002): Classification, subtype discovery, and
prediction of outcome in pediatric acute lymphoblastic leukemia by
gene expression profiling, Cancer Cell 1, 133 – 143.
The nature of bioinformatics activities in
Singapore began to take on a more research-
oriented character when Limsoon Wong
started work on the Kleisli query system in
1994. This work generated significant
interests from several large international
pharmaceutical companies.
93APBN • Vol. 7 • No. 3 • 2003
Bioinformatics Service,Research and Education at CBI
Jingchu LuoCollege of Life Sciences, National Laboratory of Protein Engineering and Plant Genetic Engineering
Center of Bioinformatics, Peking University, Beijing 100871, [email protected]
Abstract
Bioinformatics plays an important role for in theresearch and development of the life science andbiotechnology. This paper intends to give an overviewof the activities of bioinformatics service, research andeducation at the Center of Bioinformatics, PekingUniversity; the national node of the European MolecularBiology Network and the Asia Pacific BioinformaticsNetwork.
Keywords: Bioinformatics; EMBnet; APBioNet.
1 Introduction
It has been only 12 years since the term“bioinformatics” started to appear in biomedicaljournals, according to the text search against thePubMed database (Benson, et al. 1990). Only threepapers related to this topic were found in 1993, but thisnumber increased to 988 in 2002. A simple Googlesearch (1 Jan 2003) using the keyword “bioinformatics”returned 999 000 entries of which 486 000 pages werein English. Needless to say the rapid growth ofbioinformatics is due to the rapid growth of the internet,which in turn, is a reflection of the rapid growth ofinformation science, during the last decade of the 20thcentury. The genome projects, especially the modelorganisms including human and mouse, pour sequencedata into databases accessible over the internet. DNAchip technology and proteome research make thebiological resource even more complex andcomprehensive.
Computational approaches in biological sciencecan be traced back to the early 1970s as indicated byMount (2000) in his book. The work by pioneers ofbiocomputing, such as the PAM scoring matrixconstructed by Dayhoff, the sequence alignmentalgorithms developed by Needleman-Wunsch and
Smith-Waterman, the DNA sequence database initiatedby Goad and the database search tools contributed byLipman and Pearson have been the basis of, and arestill major resources for the current research,development and application in bioinformatics.
The database of 3D structures of proteins (PDB)started to collect atomic co-ordinates of proteinmolecules 25 years ago (Bernstein et al. 1977). TheChou-Fasman and GOR methods of protein secondarystructure prediction, and the efforts to analyse andclassify, the attempt to predict and design protein 3Dstructures can also be dated to late 1970s (Sternberg1978, Lifson 1979).
Driven by the huge amount of data and theavailability of the information highway, a new paradigmshift has been emerged in the life sciences (Gilbert1991). However, the diversity and complexity of thebiological data make it difficult for biologists to accessthe information (Stein 2002). Integration of softwaretools and databases is in great demand in currentbioinformatics research and development (Chichurel2002).
The diversity and complexity of the
biological data make it difficult for
biologists to access the information
(Stein 2002). Integration of software
tools and databases is in great
demand in current bioinformatics
research and development (Chichurel
2002).
94 APBN • Vol. 7 • No. 3 • 2003
www.asiabiotech.com
2.1 Service
CBI provides bioinformatics resources for domesticusers, which include both databases and software tools.More than 140 databases such as the DNA and proteinsequences and structures, genome and sequence-relatedmapping, mutation and literature reference databaseshave been installed in the database query system SRS(http://srs.pku.edu.cn). Mirrors of dozens of sites suchas ExPASy, GoldenPath, ENSEMBL, GDB, RGD (RatGenome Database), S-Star (Bioinformatics onlineeducation), have been set up to make access easy fordomestic users. Other bioinformatics information, suchas description of software tools, user manuals,documents and workshop presentations were also putonline either in English or in Chinese. A local BLASTserver and the sequence analysis GUI JEMBOSS areopen to the public through the internet. A moleculardesign platform is accessible for local users. All thepublic databases and programs can be downloaded viathe CBI FTP server.
2.2 Research
In addition to the bioinformatics service, CBI carriesout bioinformatics research and development. Thehuman proteome annotation system has been set upand the protein annotation knowledge database wasconstructed (http://pak.cbi.pku.edu.cn). Prediction ofsecreted proteins from the human proteome andconstruction of the secreted protein database have beencompleted. Specialist database information systems forthe protein neurotoxin database, rice dwarf virus andChina’s ethnic genome diversity have been constructed.Databases of protein loop classification and proteindomain assignment have been developed incollaboration with UK scientists. Cytomer, a relationaldatabase of gene regulation and expression at the tissueand cell specific level, was constructed collaborativelywith German bioinformaticians (Wingendar et al. 2001).A prokaryotic genome assembly assistant system (Yu etal. 2002) and a microbe genome annotation platformwere developed. Jupdate, a Java interface for the
In April 1999, 41 senior Chinese scientists weregathering at the First Forum of the Core Sciences in the21st Century organized by the Natural ScienceFoundation of China (NSFC). As implied by the title ofthis Forum, “Information science in the life science”,both Chinese scientists and funding agencies hadrecognized the importance of bioinformatics forbiological research and biotechnology development. InApril 2000 the first Chinese bioinformatics conferencewas held in Beijing, following a workshop “Life Sciencein the Internet Times”. Research in computationalbiology in China can be tracked to late 1980s (Zhang1989). Scientists in several universities and academicinstitutions started to work on computer analysis of DNAand protein sequences, as well as protein modeling anddesign. Computer programs such as the sequenceanalysis package GoldKey were also developed.Application of computational tools to molecular biologyhas been used to help with experimental data analysis.
2 Activities
The European Molecular Biology Network(EMBnet, http://www.embnet.org) was formed in 1988by European scientists and is an internationalorganization for bioinformatics service, research andeducation. In 1996 the Center of Bioinformatics atPeking University (CBI, http://www.cbi.pku.edu.cn)joined EMBnet and became the national nodeof China. Together with colleagues in the AsiaPacific rim, CBI has also been actively workingin the Asia Pacific Bioinformatics Network(APBioNet, http://www.apbionet.org). With support fromthe Ministry of Science and Technology, the Ministry ofEducation, the China Education and Research Network(CERNET, http://www.cernet.edu.cn) and the varioushelp from EMBnet colleagues, CBI has been playing asignificant role in bioinformatics service, research andeducation.
Research in computational biology in China
can be tracked to late 1980s (Zhang
1989). Scientists in several universities
and academic institutions started to work
on computer analysis of DNA and protein
sequences, as well as protein modeling
and design. Application of computational
tools to molecular biology has been used
to help with experimental data analysis.
Other bioinformatics information, such as
description of software tools, user
manuals, documents and workshop
presentations were also put online either
in English or in Chinese.
95APBN • Vol. 7 • No. 3 • 2003
automatic updating and maintaining of biologicaldatabases is being tested. Based on the idea that “halfday on the web saves you half month in the lab”, anintegrated bioinformatics platform WebLab is beingdeveloped. Projects of algorithm development, genomesequence analysis, structure prediction, moleculardesign and drug discovery are all activefields (Wang etal. 2002).
2.3 Education
CBI is playing a leading role in bioinformaticseducation and training in China. Both Ph.D. and MScprograms for bioinformatics and biocomputing havebeen started to meet the need of this fast growing field(Pearson 2001). A practical course “Application ofbioinformatics to molecular biology” has been runningfor graduate students of biology, medicine andagriculture at the College of Life Sciences and theMedical School of Peking University, as well as ChinaAgricultural University and China Academy ofAgricultural Sciences. Various seminars, workshops andcourses on bioinformatics and biocomputing have beenorganized during the past five years. Bioinformaticsexperts were invited to give lectures and to help withhands-on practice for participants not only frommainland China, but also from Hong Kong, Taiwan andThailand. Text books were edited or translated (Luo etal. 2002).
3 Future Direction
It is now well recognized by both the domesticand international bioinformatics communities that CBIhas been playing an important role in providingbioinformatics services, carrying on research andtraining bioinformatics talents in China. Nevertheless,CBI is still in its infancy. We are keen to learnexperiences of, seek assistance from and exchange ideaswith bioinformatics and biocomputing experts from allover the world.
References
Benson, D., Boguski, M., Lipman, D., Ostell J. (1990): The National
Center for Biotechnology Information. Genomics 6(3), 389 – 91.
Bernstein, F. C., Koetzle, T. F., Williams , G. J., Meyer, E. F. Jr., Brice,
M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., Tasumi, M (1977):
The Protein Data Bank: a computer-based archival file for
macromolecular structures. J Mol Biol 112(3), 535 – 542.
Chen, X., Wang ,L.Q., Huang, Y., Qiu, P., Murgolo, N.J., Greene,
J.R., Wu, C.H., Jiang, Y. (2002): IRE_FINDER — Computational Search
of Iron Response Element in Human and Mouse UTRs. Acta
Biochimica et Biophysica Sinica 34(6), 743 – 747.
Chichurel, M. (2002): Bioinformatics: bringing it all together. Nature
419(6908), 751 – 755
Gilbert, W. (1991): Towards a paradigm shift in biology. Nature,
349(10), 99.
Lifson, S. and Sander, C. (1979): Antiparallel and parallel beta-strands
differ in amino acid residue preferences, Nature. 282(5734),
109 – 111.
Luo, J., et al (2002): Introduction to bioinformatics (Chinese translation)
(eds. Attwood T. and Parry-Smith, D.), Beijing, Peking Univ. Press.
Mount, D. (200): Bioinformatics — Sequence and Genome Analysis,
New York, CSHL Press.
Pearson, W.R. (2001): Training for bioinformatics and computational
biology. Bioinformatics 17(9), 761 – 762.
Stein, L. (2002): Creating a bioinformatics nation. Nature. 417(6885),
119 – 120.
Sternberg, M.J. and Thornton, J.M. (1978): Prediction of protein
structure from amino acid sequence. Nature 271(5640), 15 – 20.
Wang, X.Y., Shi, X.L., Hao, B.L. (2002): The transfer RNA genes in
Oryza sativa L. ssp. indica, Science in China, 45, 504 – 511.
Wingender, E., Chen, X., Fricke, E., Geffers, R., Hehl, R., Liebich, I.,
Krull, M., Matys, V., Michael, H., Ohnhauser, R., Pruss, M., Schacherer,
F., Thiele, S., Urbach, S. (2001): The TRANSFAC system on gene
expression regulation. Nucleic Acids Res 29(1), 281 – 283.
Yu, Z., Li, T., Zhao, J.D. and Luo, J.C. (2002): PGAAS: a prokaryotic
genome assembly assistant system. Bioinformatics 18(5), 661 – 665.
Zhang C.T., Zhou G.F. (1989): Analysis of sequences of twist angles
in DNA double helix. Int J Biol Macromol 11(3), 165 – 168.
In addition to the bioinformatics service,
CBI carries out bioinformatics research and
development. Specialist database
information systems for the protein
neurotoxin database, rice dwarf virus and
China’s ethnic genome diversity have been
constructed.
In China, CBI is playing a leading role in
bioinformatics education and training,
offering both Ph.D. and MSc programs for
bioinformatics and biocomputing to meet the
growing demand.
95APBN • Vol. 7 • No. 3 • 2003
automatic updating and maintaining of biologicaldatabases is being tested. Based on the idea that “halfday on the web saves you half month in the lab”, anintegrated bioinformatics platform WebLab is beingdeveloped. Projects of algorithm development, genomesequence analysis, structure prediction, moleculardesign and drug discovery are all activefields (Wang etal. 2002).
2.3 Education
CBI is playing a leading role in bioinformaticseducation and training in China. Both Ph.D. and MScprograms for bioinformatics and biocomputing havebeen started to meet the need of this fast growing field(Pearson 2001). A practical course “Application ofbioinformatics to molecular biology” has been runningfor graduate students of biology, medicine andagriculture at the College of Life Sciences and theMedical School of Peking University, as well as ChinaAgricultural University and China Academy ofAgricultural Sciences. Various seminars, workshops andcourses on bioinformatics and biocomputing have beenorganized during the past five years. Bioinformaticsexperts were invited to give lectures and to help withhands-on practice for participants not only frommainland China, but also from Hong Kong, Taiwan andThailand. Text books were edited or translated (Luo etal. 2002).
3 Future Direction
It is now well recognized by both the domesticand international bioinformatics communities that CBIhas been playing an important role in providingbioinformatics services, carrying on research andtraining bioinformatics talents in China. Nevertheless,CBI is still in its infancy. We are keen to learnexperiences of, seek assistance from and exchange ideaswith bioinformatics and biocomputing experts from allover the world.
References
Benson, D., Boguski, M., Lipman, D., Ostell J. (1990): The National
Center for Biotechnology Information. Genomics 6(3), 389 – 91.
Bernstein, F. C., Koetzle, T. F., Williams , G. J., Meyer, E. F. Jr., Brice,
M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., Tasumi, M (1977):
The Protein Data Bank: a computer-based archival file for
macromolecular structures. J Mol Biol 112(3), 535 – 542.
Chen, X., Wang ,L.Q., Huang, Y., Qiu, P., Murgolo, N.J., Greene,
J.R., Wu, C.H., Jiang, Y. (2002): IRE_FINDER — Computational Search
of Iron Response Element in Human and Mouse UTRs. Acta
Biochimica et Biophysica Sinica 34(6), 743 – 747.
Chichurel, M. (2002): Bioinformatics: bringing it all together. Nature
419(6908), 751 – 755
Gilbert, W. (1991): Towards a paradigm shift in biology. Nature,
349(10), 99.
Lifson, S. and Sander, C. (1979): Antiparallel and parallel beta-strands
differ in amino acid residue preferences, Nature. 282(5734),
109 – 111.
Luo, J., et al (2002): Introduction to bioinformatics (Chinese translation)
(eds. Attwood T. and Parry-Smith, D.), Beijing, Peking Univ. Press.
Mount, D. (200): Bioinformatics — Sequence and Genome Analysis,
New York, CSHL Press.
Pearson, W.R. (2001): Training for bioinformatics and computational
biology. Bioinformatics 17(9), 761 – 762.
Stein, L. (2002): Creating a bioinformatics nation. Nature. 417(6885),
119 – 120.
Sternberg, M.J. and Thornton, J.M. (1978): Prediction of protein
structure from amino acid sequence. Nature 271(5640), 15 – 20.
Wang, X.Y., Shi, X.L., Hao, B.L. (2002): The transfer RNA genes in
Oryza sativa L. ssp. indica, Science in China, 45, 504 – 511.
Wingender, E., Chen, X., Fricke, E., Geffers, R., Hehl, R., Liebich, I.,
Krull, M., Matys, V., Michael, H., Ohnhauser, R., Pruss, M., Schacherer,
F., Thiele, S., Urbach, S. (2001): The TRANSFAC system on gene
expression regulation. Nucleic Acids Res 29(1), 281 – 283.
Yu, Z., Li, T., Zhao, J.D. and Luo, J.C. (2002): PGAAS: a prokaryotic
genome assembly assistant system. Bioinformatics 18(5), 661 – 665.
Zhang C.T., Zhou G.F. (1989): Analysis of sequences of twist angles
in DNA double helix. Int J Biol Macromol 11(3), 165 – 168.
In addition to the bioinformatics service,
CBI carries out bioinformatics research and
development. Specialist database
information systems for the protein
neurotoxin database, rice dwarf virus and
China’s ethnic genome diversity have been
constructed.
In China, CBI is playing a leading role in
bioinformatics education and training,
offering both Ph.D. and MSc programs for
bioinformatics and biocomputing to meet the
growing demand.
