:facetid:toc:\"db/journals/bib/bib13.bht\"OK:facetid:toc:db/journals/bib/bib13.bhtJeffrey D. AllenSiling WangMin Chen 0014Luc GirardJohn D. MinnaYang XieGuanghua XiaoProbe mapping across multiple microarray platforms.Briefings Bioinform.135547-5542012Journal Articlesclosedjournals/bib/AllenWCGMXX1210.1093/BIB/BBR076https://doi.org/10.1093/bib/bbr076https://dblp.org/rec/journals/bib/AllenWCGMXX12URL#4279590Russ B. AltmanEditorial: Current progress in Bioinformatics 2012.Briefings Bioinform.134393-3942012Journal Articlesclosedjournals/bib/Altman1210.1093/BIB/BBS042https://doi.org/10.1093/bib/bbs042https://dblp.org/rec/journals/bib/Altman12URL#4279591Gürkan BebekMehmet KoyutürkNathan D. Price 0001Mark R. ChanceNetwork biology methods integrating biological data for translational science.Briefings Bioinform.134446-4592012Journal Articlesclosedjournals/bib/BebekKPC1210.1093/BIB/BBR075https://doi.org/10.1093/bib/bbr075https://dblp.org/rec/journals/bib/BebekKPC12URL#4279592Alfonso Benítez-PáezSonia Cárdenas-BritoAndrés J. GutiérrezA practical guide for the computational selection of residues to be experimentally characterized in protein families.Briefings Bioinform.133329-3362012Journal Articlesclosedjournals/bib/Benitez-PaezCG1210.1093/BIB/BBR052https://doi.org/10.1093/bib/bbr052https://dblp.org/rec/journals/bib/Benitez-PaezCG12URL#4279593Daniel P. BerrarPeter A. FlachCaveats and pitfalls of ROC analysis in clinical microarray research (and how to avoid them).Briefings Bioinform.13183-972012Journal Articlesclosedjournals/bib/BerrarF1210.1093/BIB/BBR008https://doi.org/10.1093/bib/bbr008https://dblp.org/rec/journals/bib/BerrarF12URL#4279594Elhanan BorensteinComputational systems biology and in silico modeling of the human microbiome.Briefings Bioinform.136769-7802012Journal Articlesclosedjournals/bib/Borenstein1210.1093/BIB/BBS022https://doi.org/10.1093/bib/bbs022https://dblp.org/rec/journals/bib/Borenstein12URL#4279595Anne-Laure BoulesteixAndreas Bender 0001Justo Lorenzo BermejoCarolin StroblRandom forest Gini importance favours SNPs with large minor allele frequency: impact, sources and recommendations.Briefings Bioinform.133292-3042012Journal Articlesclosedjournals/bib/BoulesteixBBS1210.1093/BIB/BBR053https://doi.org/10.1093/bib/bbr053https://dblp.org/rec/journals/bib/BoulesteixBBS12URL#4279596Emidio CapriottiNathan L. NehrtMaricel G. KannYana BrombergBioinformatics for personal genome interpretation.Briefings Bioinform.134495-5122012Journal Articlesclosedjournals/bib/CapriottiNKB1210.1093/BIB/BBR070https://doi.org/10.1093/bib/bbr070https://dblp.org/rec/journals/bib/CapriottiNKB12URL#4279597Matthew CollisonRobert P. HirtAnil WipatSirintra NakjangPhilippe SanseauJames R. BrownData mining the human gut microbiota for therapeutic targets.Briefings Bioinform.136751-7682012Journal Articlesclosedjournals/bib/CollisonHWNSB1210.1093/BIB/BBS002https://doi.org/10.1093/bib/bbs002https://dblp.org/rec/journals/bib/CollisonHWNSB12URL#4279598Johannes DrögeAlice Carolyn McHardyTaxonomic binning of metagenome samples generated by next-generation sequencing technologies.Briefings Bioinform.136646-6552012Journal Articlesclosedjournals/bib/DrogeM1210.1093/BIB/BBS031https://doi.org/10.1093/bib/bbs031https://dblp.org/rec/journals/bib/DrogeM12URL#4279599Caroline DurrantMorris A. SwertzRudi AlbertsDanny ArendsSteffen MöllerRichard MottPjotr PrinsK. Joeri van der VeldeRitsert C. JansenKlaus SchughartBioinformatics tools and database resources for systems genetics analysis in mice - a short review and an evaluation of future needs.Briefings Bioinform.132135-1422012Journal Articlesclosedjournals/bib/DurrantSAAMMPVJS1210.1093/BIB/BBR026https://doi.org/10.1093/bib/bbr026https://dblp.org/rec/journals/bib/DurrantSAAMMPVJS12URL#4279600Julien DutheilDetecting coevolving positions in a molecule: why and how to account for phylogeny.Briefings Bioinform.132228-2432012Journal Articlesclosedjournals/bib/Dutheil1210.1093/BIB/BBR048https://doi.org/10.1093/bib/bbr048https://dblp.org/rec/journals/bib/Dutheil12URL#4279601Alberto FaroDaniela GiordanoConcetto SpampinatoCombining literature text mining with microarray data: advances for system biology modeling.Briefings Bioinform.13161-822012Journal Articlesclosedjournals/bib/FaroGS1210.1093/BIB/BBR018https://doi.org/10.1093/bib/bbr018https://dblp.org/rec/journals/bib/FaroGS12URL#4279602Carlotta De FilippoMatteo RamazzottiPaolo FontanaDuccio CavalieriBioinformatic approaches for functional annotation and pathway inference in metagenomics data.Briefings Bioinform.136696-7102012Journal Articlesclosedjournals/bib/FilippoRFC1210.1093/BIB/BBS070https://doi.org/10.1093/bib/bbs070https://dblp.org/rec/journals/bib/FilippoRFC12URL#4279603Francesca FinotelloEnrico LavezzoPaolo FontanaDenis PeruzzoAlessandro AlbieroLuisa BarzonMarco FaldaBarbara Di CamilloStefano ToppoComparative analysis of algorithms for whole-genome assembly of pyrosequencing data.Briefings Bioinform.133269-2802012Journal Articlesclosedjournals/bib/FinotelloLFPABFCT1210.1093/BIB/BBR063https://doi.org/10.1093/bib/bbr063https://dblp.org/rec/journals/bib/FinotelloLFPABFCT12URL#4279604Samuel FloresJulie BernauerSeokmin ShinRuhong ZhouXuhui HuangMultiscale modeling of macromolecular biosystems.Briefings Bioinform.134395-4052012Journal Articlesclosedjournals/bib/FloresBSZH1210.1093/BIB/BBR077https://doi.org/10.1093/bib/bbr077https://dblp.org/rec/journals/bib/FloresBSZH12URL#4279605James A. FosterJohn BungeJack A. GilbertJason H. MooreMeasuring the microbiome: perspectives on advances in DNA-based techniques for exploring microbial life.Briefings Bioinform.134420-4292012Journal Articlesclosedjournals/bib/FosterBGM1210.1093/BIB/BBR080https://doi.org/10.1093/bib/bbr080https://dblp.org/rec/journals/bib/FosterBGM12URL#4279606Pietro Hiram GuzziMarco MinaConcettina GuerraMario CannataroSemantic similarity analysis of protein data: assessment with biological features and issues.Briefings Bioinform.135569-5852012Journal Articlesclosedjournals/bib/GuzziMGC1210.1093/BIB/BBR066https://doi.org/10.1093/bib/bbr066https://dblp.org/rec/journals/bib/GuzziMGC12URL#4279607Udo HahnKevin Bretonnel CohenYael GartenNigam H. ShahMining the pharmacogenomics literature - a survey of the state of the art.Briefings Bioinform.134460-4942012Journal Articlesclosedjournals/bib/HahnCGS1210.1093/BIB/BBS018https://doi.org/10.1093/bib/bbs018https://dblp.org/rec/journals/bib/HahnCGS12URL#4279608Norman HuangParantu K. ShahCheng LiLessons from a decade of integrating cancer copy number alterations with gene expression profiles.Briefings Bioinform.133305-3162012Journal Articlesclosedjournals/bib/HuangSL1210.1093/BIB/BBR056https://doi.org/10.1093/bib/bbr056https://dblp.org/rec/journals/bib/HuangSL12URL#4279609Ting HuangJingjing WangWeichuan YuZengyou HeProtein inference: a review.Briefings Bioinform.135586-6142012Journal Articlesclosedjournals/bib/HuangWYH1210.1093/BIB/BBS004https://doi.org/10.1093/bib/bbs004https://dblp.org/rec/journals/bib/HuangWYH12URL#4279610Jui-Hung HungTun-Hsiang YangZhenjun HuZhiping WengCharles DeLisiGene set enrichment analysis: performance evaluation and usage guidelines.Briefings Bioinform.133281-2912012Journal Articlesclosedjournals/bib/HungYHWD1210.1093/BIB/BBR049https://doi.org/10.1093/bib/bbr049https://dblp.org/rec/journals/bib/HungYHWD12URL#4279611Chris I. HunterAlex L. MitchellPhilip JonesCraig McAnullaSebastien PesseatMaxim ScheremetjewSarah HunterMetagenomic analysis: the challenge of the data bonanza.Briefings Bioinform.136743-7462012Journal Articlesclosedjournals/bib/HunterMJMPSH1210.1093/BIB/BBS020https://doi.org/10.1093/bib/bbs020https://dblp.org/rec/journals/bib/HunterMJMPSH12URL#4279612Shin KawanoHiromasa OnoToshihisa TakagiHidemasa BonoTutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV.Briefings Bioinform.132258-2682012Journal Articlesclosedjournals/bib/KawanoOTB1210.1093/BIB/BBR039https://doi.org/10.1093/bib/bbr039https://dblp.org/rec/journals/bib/KawanoOTB12URL#4279613Sarah A. KillcoyneJeremy HandcockThomas RobinsonEric W. DeutschJohn BoyleInterfaces to PeptideAtlas: a case study of standard data access systems.Briefings Bioinform.135615-6262012Journal Articlesclosedjournals/bib/KillcoyneHRDB1210.1093/BIB/BBR067https://doi.org/10.1093/bib/bbr067https://dblp.org/rec/journals/bib/KillcoyneHRDB12URL#4279614André KoschmiederKarin ZimmermannSilke TrißlThomas StoltmannUlf LeserTools for managing and analyzing microarray data.Briefings Bioinform.13146-602012Journal Articlesclosedjournals/bib/KoschmiederZTSL1210.1093/BIB/BBR010https://doi.org/10.1093/bib/bbr010https://dblp.org/rec/journals/bib/KoschmiederZTSL12URL#4279615Martin KrzywinskiInanç BirolSteven J. M. JonesMarco A. MarraHive plots - rational approach to visualizing networks.Briefings Bioinform.135627-6442012Journal Articlesclosedjournals/bib/KrzywinskiBJM1210.1093/BIB/BBR069https://doi.org/10.1093/bib/bbr069https://dblp.org/rec/journals/bib/KrzywinskiBJM12URL#4279616Weizhong Li 0002Limin FuBeifang NiuSitao WuJohn C. WooleyUltrafast clustering algorithms for metagenomic sequence analysis.Briefings Bioinform.136656-6682012Journal Articlesclosedjournals/bib/LiFNWW1210.1093/BIB/BBS035https://doi.org/10.1093/bib/bbs035https://dblp.org/rec/journals/bib/LiFNWW12URL#4279617Xia Li 0004Wei Jiang 0023Wei LiBaofeng LianShuyuan WangMingzhi LiaoXiaowen ChenYanqiu WangYingli LvShiyuan WangLei YangDissection of human MiRNA regulatory influence to subpathway.Briefings Bioinform.132175-1862012Journal Articlesclosedjournals/bib/LiJLLWLCWLWY1210.1093/BIB/BBR043https://doi.org/10.1093/bib/bbr043https://dblp.org/rec/journals/bib/LiJLLWLCWLWY12URL#4279618Sharmila S. MandeMonzoorul Haque MohammedTarini Shankar GhoshClassification of metagenomic sequences: methods and challenges.Briefings Bioinform.136669-6812012Journal Articlesclosedjournals/bib/MandeMG1210.1093/BIB/BBS054https://doi.org/10.1093/bib/bbs054https://dblp.org/rec/journals/bib/MandeMG12URL#4279619Matthew N. McCallAnthony AlmudevarAffymetrix GeneChip microarray preprocessing for multivariate analyses.Briefings Bioinform.135536-5462012Journal Articlesclosedjournals/bib/McCallA1210.1093/BIB/BBR072https://doi.org/10.1093/bib/bbr072https://dblp.org/rec/journals/bib/McCallA12URL#4279620Raphaël MouradChristine SinoquetPhilippe Leray 0001Probabilistic graphical models for genetic association studies.Briefings Bioinform.13120-332012Journal Articlesclosedjournals/bib/MouradSL1210.1093/BIB/BBR015https://doi.org/10.1093/bib/bbr015https://dblp.org/rec/journals/bib/MouradSL12URL#4279621Ahmed Ragab NabhanIndra Neil SarkarThe impact of taxon sampling on phylogenetic inference: a review of two decades of controversy.Briefings Bioinform.131122-1342012Journal Articlesclosedjournals/bib/NabhanS1210.1093/BIB/BBR014https://doi.org/10.1093/bib/bbr014https://dblp.org/rec/journals/bib/NabhanS12URL#4279622Catherine Ngom-BruCaroline BarrettoGut microbiota: methodological aspects to describe taxonomy and functionality.Briefings Bioinform.136747-7502012Journal Articlesclosedjournals/bib/Ngom-BruB1210.1093/BIB/BBS019https://doi.org/10.1093/bib/bbs019https://dblp.org/rec/journals/bib/Ngom-BruB12URL#4279623Marc-Alexandre NolinMichel DumontierFrançois BelleauJacques CorbeilBuilding an HIV data mashup using Bio2RDF.Briefings Bioinform.13198-1062012Journal Articlesclosedjournals/bib/NolinDBC1210.1093/BIB/BBR003https://doi.org/10.1093/bib/bbr003https://dblp.org/rec/journals/bib/NolinDBC12URL#4279624Tulika PrakashTodd D. TaylorFunctional assignment of metagenomic data: challenges and applications.Briefings Bioinform.136711-7272012Journal Articlesclosedjournals/bib/PrakashT1210.1093/BIB/BBS033https://doi.org/10.1093/bib/bbs033https://dblp.org/rec/journals/bib/PrakashT12URL#4279625Chang F. QuoChanchala KaddiJohn H. PhanAmin ZollanvariMingqing XuMay D. WangGil AlterovitzReverse engineering biomolecular systems using -omic data: challenges, progress and opportunities.Briefings Bioinform.134430-4452012Journal Articlesclosedjournals/bib/QuoKPZXWA1210.1093/BIB/BBS026https://doi.org/10.1093/bib/bbs026https://dblp.org/rec/journals/bib/QuoKPZXWA12URL#4279626Kristian RotherWojciech PotrzebowskiTomasz PutonMagdalena RotherEwa WywialJanusz M. BujnickiA toolbox for developing bioinformatics software.Briefings Bioinform.132244-2572012Journal Articlesclosedjournals/bib/RotherPPRWB1210.1093/BIB/BBR035https://doi.org/10.1093/bib/bbr035https://dblp.org/rec/journals/bib/RotherPPRWB12URL#4279627Monica SantamariaBruno FossoArianna ConsiglioGiorgio De CaroGiorgio GrilloFlavio LicciulliSabino LiuniMarinella MarzanoDaniel Alonso-AlemanyGabriel ValienteGraziano PesoleReference databases for taxonomic assignment in metagenomics.Briefings Bioinform.136682-6952012Journal Articlesclosedjournals/bib/SantamariaFCCGLLMAVP1210.1093/BIB/BBS036https://doi.org/10.1093/bib/bbs036https://dblp.org/rec/journals/bib/SantamariaFCCGLLMAVP12URL#4279628Rebekka SchlatterNicole PhilippiGaby WangorschRobert PickOliver SawodnyChristoph BornerJens TimmerMichael EdererThomas DandekarIntegration of Boolean models exemplified on hepatocyte signal transduction.Briefings Bioinform.133365-3762012Journal Articlesclosedjournals/bib/SchlatterPWPSBTED1210.1093/BIB/BBR065https://doi.org/10.1093/bib/bbr065https://dblp.org/rec/journals/bib/SchlatterPWPSBTED12URL#4279629Maria Victoria SchneiderPeter WalterMarie-Claude BlatterJames WatsonMichelle D. BrazasKristian RotherAidan BuddAllegra ViaCelia W. G. van GelderJoachim JacobPedro L. FernandesTommi H. NyrönenJavier De Las RivasThomas BlicherRafael C. JiménezJane E. LovelandJennifer McDowallPhilip JonesBrendan W. VaughanRodrigo LopezTeresa K. AttwoodCatherine BrooksbankBioinformatics Training Network (BTN): a community resource for bioinformatics trainers.Briefings Bioinform.133383-3892012Journal Articlesclosedjournals/bib/SchneiderWBWBRBVGJFNRBJLMJVLAB1210.1093/BIB/BBR064https://doi.org/10.1093/bib/bbr064https://dblp.org/rec/journals/bib/SchneiderWBWBRBVGJFNRBJLMJVLAB12URL#4279630Andrew A. ShelenkovEugene V. KorotkovLEPSCAN - a web server for searching latent periodicity in DNA sequences.Briefings Bioinform.132143-1492012Journal Articlesclosedjournals/bib/ShelenkovK1210.1093/BIB/BBR044https://doi.org/10.1093/bib/bbr044https://dblp.org/rec/journals/bib/ShelenkovK12URL#4279631Li Shen 0001Principles of Computational Modeling in NeuroscienceDavid Sterratt, Bruce Graham, Andrew Gillies and David Willshaw.Briefings Bioinform.133390-3922012Journal Articlesclosedjournals/bib/Shen1210.1093/BIB/BBS003https://doi.org/10.1093/bib/bbs003https://dblp.org/rec/journals/bib/Shen12URL#4279632Age K. SmildeMarieke E. TimmermanMargriet M. W. B. HendriksJeroen J. JansenHuub C. J. HoefslootGeneric framework for high-dimensional fixed-effects ANOVA.Briefings Bioinform.135524-5352012Journal Articlesclosedjournals/bib/SmildeTHJH1210.1093/BIB/BBR071https://doi.org/10.1093/bib/bbr071https://dblp.org/rec/journals/bib/SmildeTHJH12URL#4279633Kristel Van SteenTravelling the world of gene-gene interactions.Briefings Bioinform.1311-192012Journal Articlesclosedjournals/bib/Steen1210.1093/BIB/BBR012https://doi.org/10.1093/bib/bbr012https://dblp.org/rec/journals/bib/Steen12URL#4279634Yijun SunYunpeng CaiSusan M. HuseRob Knight 0001William G. FarmerieXiaoyu WangVolker MaiA large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis.Briefings Bioinform.131107-1212012Journal Articlesclosedjournals/bib/SunCHKFWM1210.1093/BIB/BBR009https://doi.org/10.1093/bib/bbr009https://dblp.org/rec/journals/bib/SunCHKFWM12URL#4279635Hanno TeelingFrank Oliver GlöcknerCurrent opportunities and challenges in microbial metagenome analysis - a bioinformatic perspective.Briefings Bioinform.136728-7422012Journal Articlesclosedjournals/bib/TeelingG1210.1093/BIB/BBS039https://doi.org/10.1093/bib/bbs039https://dblp.org/rec/journals/bib/TeelingG12URL#4279636Vladimir B. TeifKarsten RippeCalculating transcription factor binding maps for chromatin.Briefings Bioinform.132187-2012012Journal Articlesclosedjournals/bib/TeifR1210.1093/BIB/BBR037https://doi.org/10.1093/bib/bbr037https://dblp.org/rec/journals/bib/TeifR12URL#4279637Gabriel ValienteGraziano PesoleEditorial.Briefings Bioinform.1366452012Journal Articlesclosedjournals/bib/ValienteP1210.1093/BIB/BBS079https://doi.org/10.1093/bib/bbs079https://dblp.org/rec/journals/bib/ValienteP12URL#4279638Juan Wang 0018Zhi-xin LiChengxiang QiuDong WangQinghua CuiThe relationship between rational drug design and drug side effects.Briefings Bioinform.133377-3822012Journal Articlesclosedjournals/bib/WangLQWC1210.1093/BIB/BBR061https://doi.org/10.1093/bib/bbr061https://dblp.org/rec/journals/bib/WangLQWC12URL#4279639Chenguang WangZhong WangDaniel R. ProwsRongling WuA computational framework for the inheritance pattern of genomic imprinting for complex traits.Briefings Bioinform.13134-452012Journal Articlesclosedjournals/bib/WangWPW1210.1093/BIB/BBR023https://doi.org/10.1093/bib/bbr023https://dblp.org/rec/journals/bib/WangWPW12URL#4279640Yakun WangMeng XuZhong WangMing TaoJunjia ZhuLi Wang 0021Runze LiScott A. BerceliRongling WuHow to cluster gene expression dynamics in response to environmental signals.Briefings Bioinform.132162-1742012Journal Articlesclosedjournals/bib/WangXWTZWLBW1210.1093/BIB/BBR032https://doi.org/10.1093/bib/bbr032https://dblp.org/rec/journals/bib/WangXWTZWLBW12URL#4279641Jinlian WangYuji ZhangCatalin MarianHabtom W. RessomIdentification of aberrant pathways and network activities from high-throughput data.Briefings Bioinform.134406-4192012Journal Articlesclosedjournals/bib/WangZMR1210.1093/BIB/BBS001https://doi.org/10.1093/bib/bbs001https://dblp.org/rec/journals/bib/WangZMR12URL#4279642Jing Wang 0004Xianxiao ZhouJing Zhu 0004Yunyan GuWenyuan ZhaoJinfeng ZouZheng Guo 0002GO-function: deriving biologically relevant functions from statistically significant functions.Briefings Bioinform.132216-2272012Journal Articlesclosedjournals/bib/WangZZGZZG1210.1093/BIB/BBR041https://doi.org/10.1093/bib/bbr041https://dblp.org/rec/journals/bib/WangZZGZZG12URL#4279643Elisabeth WongBrittany A. BaurSaad QuaderChun-Hsi HuangBiological network motif detection: principles and practice.Briefings Bioinform.132202-2152012Journal Articlesclosedjournals/bib/WongBQH1210.1093/BIB/BBR033https://doi.org/10.1093/bib/bbr033https://dblp.org/rec/journals/bib/WongBQH12URL#4279644Ming WuChristina ChanLearning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression data.Briefings Bioinform.132150-1612012Journal Articlesclosedjournals/bib/WuC1210.1093/BIB/BBR029https://doi.org/10.1093/bib/bbr029https://dblp.org/rec/journals/bib/WuC12URL#4279645Runqing YangXin WangYuehua CuiBayesian inference for genomic imprinting underlying developmental characteristics.Briefings Bioinform.135555-5682012Journal Articlesclosedjournals/bib/YangWC1210.1093/BIB/BBR079https://doi.org/10.1093/bib/bbr079https://dblp.org/rec/journals/bib/YangWC12URL#4279646Tao YuJialiang Li 0001Shuangge MaAdjusting confounders in ranking biomarkers: a model-based ROC approach.Briefings Bioinform.135513-5232012Journal Articlesclosedjournals/bib/YuLM1210.1093/BIB/BBS008https://doi.org/10.1093/bib/bbs008https://dblp.org/rec/journals/bib/YuLM12URL#4279647Lianming ZhangKeiko UdakaHiroshi MamitsukaShanfeng ZhuToward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools.Briefings Bioinform.133350-3642012Journal Articlesclosedjournals/bib/ZhangUMZ1210.1093/BIB/BBR060https://doi.org/10.1093/bib/bbr060https://dblp.org/rec/journals/bib/ZhangUMZ12URL#4279648Xiyang ZhaoChunfa TongXiaoming PangZhong WangYunqian GuoFang DuRongling WuFunctional mapping of ontogeny in flowering plants.Briefings Bioinform.133317-3282012Journal Articlesclosedjournals/bib/ZhaoTPWGDW1210.1093/BIB/BBR054https://doi.org/10.1093/bib/bbr054https://dblp.org/rec/journals/bib/ZhaoTPWGDW12URL#4279649David duVerleHiroshi MamitsukaA review of statistical methods for prediction of proteolytic cleavage.Briefings Bioinform.133337-3492012Journal Articlesclosedjournals/bib/duVerleM1210.1093/BIB/BBR059https://doi.org/10.1093/bib/bbr059https://dblp.org/rec/journals/bib/duVerleM12URL#4279650