简介：ThispaperexaminesrecentdevelopmentsandapplicationsofHiddenMarkovModels(HMMs)tovariousproblemsincomputationalbiology,includingmultiplesequencealignment,homologydetection,proteinsequencesclassification,andgenomicannotation.

简介：Althoughvariousgenomeprojectshaveprovidedusenormousstaticsequenceinformation,understandingofthesophisticatedbiologycontinuestorequireintegratingthecomputationalmodeling,systemanalysis,technologydevelopmentforexperiments,andquantitativeexperimentsalltogethertoanalyzethebiologyarchitectureonvariouslevels,whichisjusttheoriginofsystemsbiologysubject.Thisreviewdiscussestheobject,itscharacteristics,andresearchattentionsinsystemsbiology,andsummarizestheanalysismethods,experimentaltechnologies,researchdevelopments,andsooninthefourkeyfieldsofsystemsbiology-systemicstructures,dynamics,controlmethods,anddesignprinciples.

简介：Ascientificdreamproposedsome20yearsagohasbeenrealized-thecompletionoftheDNAsequencefortheHumanGenomeProject(HGP)in2004.Asaresult,anentirelynewfieldofbiologicalresearchhasarisen:genomebiologyorgenomicsiscelebratedforitsunprecedentedscale,intrinsicallydigitaloutput,andsystematicapproachtogettingallthedata.Itssequel,theHapMapProject,willreachfruitionlaterthisyear.Theseprojectsestablishednewprecedentsforinternationalcollaborationsandopendataaccess.

简介：TheChina-UKSystemsBiologyWorkshop2005washeldduringJune20-21intheNationalScienceParkofZhejiangUniversity,Hangzhou,China.ItwasorganizedbytheInstituteofBioinformatics,ZhejiangUniversity,andwasinitiatedbyProf.Dr.JunZhu(ZhejiangUniversity)andProf.Dr.JohnFindlay(UniversityofLeeds,UK).TheworkshopwaspartoftheprogramcalledUK-ChinaPartnersinScience,aone-yearcampaignthatwasinitiatedbytheBritishgovernmenttoexploremorecollaborationsbetweenUKandChinaonscienceandtechnology.Itwasattendedalsobyarepresentativeofthisprogram,Mr.FrankYuan,seniorscience&innovationofficer.Theideaoftheworkshopwastobringtogetherexpertswithspecialistsinsystemsbiologyinordertopromotethe"naturalpartnership"betweenscientistsfromthetwocountries.Themostimportantitemsofsystemsbiologyconsideredattheworkshopwere:(1)Newtechnologiesandadvancesinsystemsbiology;(2)Researchdevelopmentsingenomicsandproteomics;(3)Newmethodologiesandsoftwareincomputationalbiology;(4)ResearchcollaborationonsystemsbiologybetweenChinaandUK.

简介：MicroRNAs(miRNAs)areendogenouslyexpressednon-codingRNAsof20-24nucleotides,whichpost-transcriptionallyregulategeneexpressioninplantsandanimals.RecentlyithasbeenrecognizedthatmiRNAscompriseoneoftheabundantgenefamiliesinmulticellularspecies,andtheirregulatoryfunctionsinvariousbiologicalprocessesarewidelyspread.Therehasbeenasurgeintheresearchactivitiesinthisfieldinthepastfewyears.Fromtheverybeginning,computationalmethodshavebeenutilizedasindispensabletools,andmanydiscoverieshavebeenobtainedthroughcombinationofexperimentalandcomputationalapproaches.Inthisreview,bothbiologicalandcomputationalaspectsofmiRNAwillbediscussed.AbriefhistoryofthediscoveryofmiRNAanddiscussionofmicroarrayapplicationsinmiRNAresearcharealsoincluded.

简介：U7smallnuclearRNA(snRNA)sequenceshavebeendescribedonlyforahandfulofanimalspeciesinthepast.Herewedescribeacomputationalsearchforfunc-tionalU7snRNAgenesthroughoutvertebratesincludingtheupstreamsequenceelementscharacteristicforsnRNAstranscribedbypolymeraseⅡ.Basedontheresultsofthissearch,wediscussthehighvariabilityofU7snRNAsinbothse-quenceandstructure,andreportonanattempttofindU7snRNAsequencesinbasaldeuterostomesandnon-drosophilidsinsectgenomesbasedonacombinationofsequence,structure,andpromoterfeatures.Duetotheextremelyshortse-quenceandthehighvariabilityinbothsequenceandstructure,nounambiguouscandidateswerefound.TheseresultscastdoubtonputativeU7homologsinevenmoredistantorganismsthatarereportedinthemostrecentreleaseoftheRfamdatabase.

简介：Withthedevelopmentofgenomesequencingformanyorganisms,moreandmorerawsequencesneedtobeannotated.Genepredictionbycomputationalmethodsforfindingthelocationofproteincodingregionsisoneoftheessentialissuesinbioinformatics.Twoclassesofmethodsaregenerallyadopted:similaritybasedsearchesandabinitioprediction.Here,wereviewthedevelopmentofgenepredictionmethods,summarizethemeasuresforevaluatingpredictorquality,highlightopenproblemsinthisarea,anddiscussfutureresearchdirections.

简介：生物信息的途径补充了试验性的努力到inventorize植物miRNA目标。我们执行了产生通常认为的miRNA的一张全面的表的transcriptome指向的米饭(Oryzasativa)的全球计算分析。我们的预言(684个唯一的抄本)证明米饭miRNAs调停包括抄写(41%)的多样的功能的规定，催化作用(28%)，绑定(18%)，和transporter活动(11%)。在预言的目标之中，61.7%点击在编码区域，将近72%目标让独居的miRNA撞击。学习预言了通常认为地调整象压力反应，催化作用，和绑定一样的函数的34miRNAs的超过70个新奇目标。非常，目标的一半(55%)在O之间被保存，这被观察。sativaindica和O。sativa装饰用的梨树。31个miRNA家庭的成员被发现拥有在米饭之间并且至少的保存目标另外的草家庭成员之一。大约44%唯一的目标在二个不一样的miRNA预言算法之间是普通的。跨种类的保存和算法的一致的如此的程度在在这研究预言的米饭miRNA目标的表授与信心。

简介：尽管有它对疟疾的功效，在Artemisiaannua的artemisinin的相对低的收益(0.01%-0.8%)是到这药的商品化的严肃的限制。由外长、内长的因素的artemisinin和它的规定的biosynthetic小径的更好的理解是必要的改进artemisinin产量。增加的证据证明了microRNAs(miRNAs)在各种各样的生物过程起多重作用。在这研究，我们对表示顺序标签(EST)从Arabidopsis和米饭使用了以前已知的miRNAsA的数据库。annua将在A寻找潜在的miRNAs和他们的目标。annua。六潜在的miRNAs的一个总数被预言，它属于miR414和miR1310家庭。而且，八潜在的目标基因在这种被识别。在他们之中，七基因编码在artemisinin生合成起重要作用的蛋白质，包括HMG-CoAreductase(HMGR)，amorpha-4,11-dienesynthase(广告)，farnesyl焦磷酸盐synthase(FPS)和细胞色素P450。另外，为通常认为的AINTEGUMENTA编码的基因，涉及信号transduction和开发，也作为目标之一被预言。这在silico学习是第一显示miRNAs指向编码涉及artemisinin生合成的酶的基因，它可以帮助在A理解artemisinin生合成的调停miRNA的规定。annua。

简介：MicroRNAs(miRNAs)是小non-protein-codingpost-transcriptional的一个最新识别的班在工厂和动物的规章的RNA。有Ambros实验公式和另外的结构的特征标准过滤器的为表示顺序的基于的搜索标注的计算相同(EST)的使用是向从茶和其染色体还没被定序的另外的工厂种类的保存miRNAs的发现和隔离的合适的联合。在现在的学习，我们爆炸了茶(山茶sinensis)的数据库寻找潜在的miRNAs的EST，用以前已知的植物miRNAs。第一次，从四个家庭的四候选人miRNAs在茶被识别。用最新识别的miRNA序列，30潜在的目标基因的一个总数为11个miRNA家庭被识别；6这些预言的目标基因编码抄写因素(20%)，16目标基因看起来在多样的生理的进程(53%)起作用，8目标基因有假想或未知的函数(27%)。这些调查结果更加拓宽在茶理解miRNA的功能的范围。

简介：植物蛋白质蛋白质相互作用网络没被大规模实验识别了。以便更好在米饭理解蛋白质相互作用，预言的米饭Interactome网络(PRIN；http://bis.zju.edu.cn/prin/)介绍76,585个预言的相互作用包含5,049米饭蛋白质。在印射米饭的genomic特征以后(去注解，subcellular本地化预言，和基因表示)，我们发现一个注解得好、生物学上重要的网络是足够富有的在高顺序的生物系统以内捕获许多重要功能的连接，例如小径和生物进程。而且，我们作为例子拿了疯盒子的包含域的蛋白质和生理节奏的节奏发信号小径证明功能的蛋白质建筑群和生物小径能有效地在我们的预言的网络被扩展。在PRIN的扩展分子的网络更加改进了这些分析的能力集成存在知识并且提供新奇卓见进基因和基因网络的功能和协作。

简介：陷阱，SLD5的heterotetramer，PSF1，PSF2，和PSF3蛋白质，一个新兴的染色质因素被认出涉及开始和DNA复制的延伸步。尽管酵母和Xenopus陷阱基因很好被记录，他们在更高的优核质的orthologous基因充分没被描绘。在这研究，我们报导genomic结构和哺乳动物的陷阱基因的transcriptional规定。浆液刺激在人的房间增加了GINSmRNA层次。用通常认为的陷阱倡导者序列的记者基因试金表明哺乳动物的陷阱的表示被17beta-Estradiol-stimulated雌激素受体高山调整哈，并且人的PSF3充当对抄写因素E2F1应答的基因。这研究的目标是介绍当前的数据以便在哺乳动物的房间在陷阱基因规定和函数的领域里鼓励进一步的工作。

简介：miRNAsarenon-codingsmallRNAsthatinvolvediversebiologicalprocesses.Untilnow,littleisknownabouttheirrolesinplantdroughtresistance.Physcomitrellapatensishighlytoleranttodrought;however,itisnotclearaboutthebasicbiologyofthetraitsthatcontributeP.patensthisimportantcharacter.Inthiswork,wediscovered16droughtstress-associatedmiRNA(DsAmR)familiesinP.patensthroughcomputationalanalysis.DuetothepossiblediscrepancyofexpressionperiodsandtissuedistributionsbetweenpotentialDsAmRsandtheirtargetinggenes,andtheexistenceoffalsepositiveresultsincomputationalidentification,thepredictionresultsshouldbeexaminedwithfurtherexperimentalvalidation.WealsoconstructedanmiRNAco-regulationnetwork,andidentifiedtwonetworkhubs,miR902a-5pandmiR414,whichmayplayimportantrolesinregulatingdrought-resistancetraits.Wedistributedourresultsthroughanonlinedatabasenamedppt-miRBase,whichcanbeaccessedathttp://bioinfor.cnu.edu.cn/ppt_miRBase/index.php.OurmethodsinfindingDsAmRandmiRNAco-regulationnetworkshowedanewdirectionforidentifyingmiRNAfunctions.

简介：Leishmaniaisassociatedwithabroadspectrumofdiseases,rangingfromsimplecutaneoustoinvasivevisceralleishmaniasis.Here,thesequencesoftencysteineproteasesoftypesA,BandCofLeishmaniamajorwereobtainedfromGeneDBdatabase.PredictionofMHCclassIepitopesofthesecysteineproteaseswasperformedbyNetCTLprogramversion1.2.Inaddition,byusingBcePredserver,differentstructuralpropertiesoftheproteinswerepredictedtofindouttheirpotentialBcellepitopes.Accordingtothiscomputationalanalysis,nineregionswerepredictedasBcellepitopes.Theresultsprovideusefulinformationfordesigningpeptide-basedvaccines.