简介：AsthetopologicalpropertiesofeachspotinDNAmicroarrayimagesmayvaryfromoneanother,weemployedgranulometriestounderstandtheshape-sizecontentcontributedduetoasignificantintensityvaluewithinaspot.Analysiswasperformedonthemicroarrayimagethatconsistedof240spotsbyusingconceptsfrommathematicalmorphology.Inordertofindoutindicesforeachspotandtofurtherclassifythem,weadoptedmorphologicalmultiscaleopenings,whichprovidedmicroarraysatmultiplescales.Successiveopenedmicroarraysweresubtractedtoidentifytheprotrusionsthatweresmallerthanthesizeofstructuringelement.Spot-wisedetails,intermsofprobabilityoftheseobservedprotrusions,werecomputedbyplacingaregularlyspacedgridonmicroarraysuchthateachspotwascenteredineachgrid.Basedontheprobabilityofsizedistributionfunctionsoftheseprotrusionsisolatedateachlevel,weestimatedthemeansizeandtextureindexforeachspot.Withthesecharacteristics,weclassifiedthespotsinamicroarrayimageintobrightanddullcategoriesthroughpatternspectrumandshape-sizecomplexitymeasures.Thesesegregatedspotscanbecomparedwiththoseofhybridizationlevels.

简介：The2004SoutheastAsiaTsunamikillednearly5,400peopleinSouthernThailand,includingforeigntouristsandlocalresidents.TorecoverDNAevidenceasmuchaspossiblefromtheseriouslydecomposedbodies,weexploredproceduresofsamplepreparationfrombothboneandtoothsamplesaswellasbothmitochondrialandnuclearmarkers.DespitehavingfailedtorecoverenoughDNAfornuclearmarkertyping,wesucceededinobtainingfullyinformativeresultsformitochondrialmarkers(HV1andHV2)from258toothsampleswithasuccessrateof51%(258/507).UsinganorganicDNAextractionmethodcoupledwithanultrafiltrationstep,weobtained16STR(including13CODISloci,onesexdiscriminationlocus,andtwoIdentifilerloci)profilesfor834sampleswithasuccessrateof79%(834/1,062).Inaddition,bycomparingtheallelicfrequenciesbetweenthetypedsamplesasagroupandotherindexpopulations,weconcludethattheThaitsunamivictimsareacombinedgroupofseveralpopulations.Ourresultsprovidevaluableevidenceandprotocolsforthefutureforensicpractice.

简介：DNA聚合酶III是为DNA的复制负责的五eubacterialDNA聚合酶之一双。在DNA聚合酶III核心酶的十个子单元之中，高山哈子单元两个都为polymerizing催化反应DNA海滨。在这研究，我们提取了高山的genomic序列哈从159的子单元定序eubacterial染色体，并且执行了基于顺序的种系发生、结构的分析。我们发现所有eubacterial染色体有至少一座高山哈子单元，哪个形式homodimers或heterodimers。种系发生并且领域高山的结构的分析以及拷贝数字变化哈在每个细菌的子单元显示高山的分类哈子单元进四个基本的组：polC，dnaE1，dnaE2，和dnaE3。这个分类具有在染色体作文分析的本质。我们也巩固了命名惯例在基因注解避免进一步的混乱。

简介：DNAbarcodingisapowerfulapproachforcharacterizingspeciesoforganisms,especiallythosewithalmostidenticalmorphologicalfeatures,therebyhelpingtotoestablishphylogeneticrelationshipsandrevealevolutionaryhistories.Inthisstudy,wechosea648-bpsegmentofthemitochondrialgene,cytochromecoxidasesubunit1(COI),asastandardbarcoderegiontoestablishphylogeneticrelation-shipsamongbrineshrimp(Artemia)speciesfrommajorhabitatsaroundtheworldandfurtherfocusedonthebiodiversityofArtemiaspeciesinChina,especiallyintheTibetanPlateau.SamplesfromfivemajorsaltlakesoftheTibetanPlateaulocatedataltitudesover4,000mshowedcleardifferencesfromotherArtemiapop-ulationsinChina.Wealsoobservedtwoconsistentaminoacidchanges,153A/Vand183L/F,intheCOIgenebetweenthehighandlowaltitudespeciesinChina.Moreover,indelsintheCOIsequencewereidentifiedincystandadultsamplesuniquetotheCoQenpopulationfromtheTibetanPlateau,demonstratingtheneedforadditionalinvestigationsofthemitochondrialgenomeamongTibetanArtemiapopulations.

简介：Arraycomparativegenomichybridization(CGH)hasbeenpopularlyusedforanalyzingDNAcopynumbervariationsindiseaseslikecancer.Inthisstudy,weinvestigated82sporadicsamplesfrom49breastcancerpatientsusing1-MbresolutionbacterialartificialchromosomeCGHarrays.Anumberofhighlyfrequentgenomicaberrationswerediscovered,whichmayactas'drivers'oftumorprogression.Meanwhile,thegenomicprofilesoffour'normal'breasttissuesamplestakenatleast2cmawayfromtheprimarytumorsiteswerealsofoundtohavesomegenomicaberrationsthatrecurredwithhighfrequencyintheprimarytumors,whichmayhaveimportantimplicationsforclinicaltherapy.Additionally,weperformedclasscomparisonandclasspredictionforvariousclinicopathologicalparameters,andalistofcharacteristicgenomicaberrationsassociatedwithdifferentclinicopathologicalphenotypeswascompiled.Ourstudyprovidescluesforfurtherinvestigationsoftheunderlyingmechanismsofbreastcarcinogenesis.

简介：DNAsequencescanbetreatedasfinite-lengthsymbolstringsoverafour-letteralphabet(A,C,T,G).Asauniversalandcomputablecomplexitymeasure,LZcomplexityisvalidtodescribethecomplexityofDNAsequences.Inthisstudy,aconceptofconditionalLZcomplexitybetweentwosequencesisproposedaccordingtotheprincipleofLZcomplexitymeasure.AnLZcomplexitydistancemetricbetweentwononnullsequencesisdefinedbyutilizingconditionalLZcomplexity.BasedonLZcomplexitydistance,aphylogenetictreeof26speciesofplacentalmammals(Eutheria)withthreeoutgroupspecieswasreconstructedfromtheircompletemitochondrialgenomes.Onthedebatethatwhichtwoofthethreemaingroupsofplacentalmammals,namelyPrimates,Ferungulates,andRodents,aremorecloselyrelated,thephylogenetictreereconstructedbasedonLZcomplexitydistancesupportsthesuggestionthatPrimatesandFerungulatesaremorecloselyrelated.

简介：AninteractivetooltovisualizetheK-stringcompositionoflongDNAsequencesincludingbacterialcompletegenomesisdescribed.Itisespeciallyusefulforexploringshortpalindromicstructuresinthesequences.TheSeeDNAprogramrunsonRedHatLinuxwithGTK+support.Itdisplaystwo-dimensional(2D)orone-dimensional(1D)histogramsoftheK-stringdistributionofagivensequenceand/oritsrandomizedcounterpart.ItisalsocapableofshowingthedifferenceofK-stringdistributionsbetweentwosequences.TheCsourcecodeusingtheGTK+packageisfreelyavailable.

简介：Accurateidentificationofprotein-codingregions(exons)inDNAsequenceshasbeenachallengingtaskinbioinformatics.Particularlythecodingregionshavea3-baseperiodicity,whichformsthebasisofallexonidentificationmethods.Manysignalprocessingtoolsandtechniqueshavebeenappliedsuccessfullyfortheidentificationtaskbutstillimprovementinthisdirectionisneeded.Inthispaper,wehaveintroducedanewpromisingmodel-independenttime-frequencyfilteringtechniquebasedonS-transformforaccurateidentificationofthecodingregions.TheS-transformisapowerfullineartime-frequencyrepresentationusefulforfilteringintime-frequencydomain.Thepotentialoftheproposedtechniquehasbeenassessedthroughsimulationstudyandtheresultsobtainedhavebeencomparedwiththeexistingmethodsusingstandarddatasets.Thecomparativestudydemonstratesthattheproposedmethodoutperformsitscounterpartsinidentifyingthecodingregions.

简介：Computationalanalysisisessentialfortransformingthemassesofmicroarraydataintoamechanisticunderstandingofcancer.Herewepresentamethodforfindinggenefunctionalmodulesofcancerfrommicroarraydataandhaveappliedittocoloncancer.First,acoloncancergenenetworkandanormalcolontissuegenenetworkwereconstructedusingcorrelationsbetweenthegenes.Thenthemodulesthattendedtohaveahomogeneousfunctionalcompositionwereidentifiedbysplit-tingupthenetwork.Analysisofbothnetworksrevealedthattheyarescale-free.Comparisonofthegenefunctionalmodulesforcoloncancerandnormaltissuesshowedthatthemodules’functionschangedwiththeirstructures.

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：在染色体为特定的DNA目标设计锌手指蛋白质主题在染色体工程的领域里是批评的。我们为为绑在特定的目标DNA地点的C2H2锌手指预言识别helices开发了一个计算方法。这预言用锌手指蛋白质和他们的目标DNA三位字节的彻底的数据集基于人工的神经网络。用户们能为也要预言在的二或三根锌手指选择选择一模块化或为输入DNA顺序的synergistic时尚。这个方法将为对为几个生物、生物医学的应用程序设计特定的锌手指抄写因素和锌手指核酸酶感兴趣的研究人员是珍贵的。网工具ZiF预言在http://web.iitd.ac.in/sundar/zifpredict/在网上是可得到的。