Volume 28, Number 1, January 2012 Discovery Note - Systems Biology
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journals/bioinformatics/ChenGLL12 Yang Chen ,
Jin Gu ,
Dan Li ,
Shao Li :
Time-course network analysis reveals TNF-α can promote G1 /S transition of cell cycle in vascular endothelial cells.
1-4
Original Papers - Genome Analysis
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journals/bioinformatics/ZhaoTY12 Yongan Zhao ,
Haixu Tang ,
Yuzhen Ye :
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data.
125-126
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journals/bioinformatics/DassiMRMTCQ12 Letters to the Editor - Genome Analysis
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Volume 28, Number 2, January 2012 Original Papers - Genome Analysis
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journals/bioinformatics/DingBROTZHHMCAS12 Jiarui Ding ,
Ali Bashashati ,
Andrew Roth ,
Arusha Oloumi ,
Kane Tse ,
Thomas Zeng ,
Gholamreza Haffari ,
Martin Hirst ,
Marco A. Marra ,
Anne Condon ,
Sam Aparicio ,
Sohrab P. Shah :
Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data.
167-175
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journals/bioinformatics/RamirezLA12 Applications Note - Genome Analysis
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journals/bioinformatics/AsmannMHBLCSDHNLZKKK12 Yan W. Asmann ,
Sumit Middha ,
Asif Hossain ,
Saurabh Baheti ,
Ying Li ,
High-Seng Chai ,
Zhifu Sun ,
Patrick H. Duffy ,
Ahmed A. Hadad ,
Asha Nair ,
Xiaoyu Liu ,
Yuji Zhang ,
Eric W. Klee ,
Krishna R. Kalari ,
Jean-Pierre Kocher :
TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data.
277-278
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journals/bioinformatics/GattoL12 Laurent Gatto ,
Kathryn S. Lilley :
MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation.
288-289
Systems Biology
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Volume 28, Number 3, February 2012 Discovery Note - Systems Biology
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journals/bioinformatics/LiuN12 Wei Liu ,
Mahesan Niranjan :
Gaussian process modelling for bicoid mRNA regulation in spatio-temporal Bicoid profile.
366-372
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journals/bioinformatics/KarnovskyWHTSLSSJBAO12 Alla Karnovsky ,
Terry E. Weymouth ,
Tim Hull ,
V. Glenn Tarcea ,
Giovanni Scardoni ,
Carlo Laudanna ,
Maureen A. Sartor ,
Kathleen A. Stringer ,
H. V. Jagadish ,
Charles F. Burant ,
Brian D. Athey ,
Gilbert S. Omenn :
Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data.
373-380
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Volume 28, Number 4, February 2012 Discovery Note - Genome Analysis
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Volume 28, Number 5, March 2012 Discovery Note - Phylogenetics
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journals/bioinformatics/LatyshevaJPCB12 Original Papers - Genome Analysis
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journals/bioinformatics/EmdeSWSVKHR12 Sequence Analysis
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journals/bioinformatics/MorkH12 Søren Mørk ,
Ian Holmes :
Evaluating bacterial gene-finding HMM structures as probabilistic logic programs.
636-642
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journals/bioinformatics/Komurov12 Kakajan Komurov :
Modeling community-wide molecular networks of multicellular systems.
694-700
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journals/bioinformatics/ChenCHLLYOTC12 Data and Text Mining
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journals/bioinformatics/SengerGEDPFMG12 Applications Note - Genome Analysis
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journals/bioinformatics/Chen12 Gary K. Chen :
A scalable and portable framework for massively parallel variable selection in genetic association studies.
719-720
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journals/bioinformatics/HongRPLJKYBPRCYLKLKS12 Dongwan Hong ,
Arang Rhie ,
Sung-Soo Park ,
Jongkeun Lee ,
Young Seok Ju ,
Sujung Kim ,
Saet-Byeol Yu ,
Thomas Bleazard ,
Hyun Seok Park ,
Hwanseok Rhee ,
Hyonyong Chong ,
Kap-Seok Yang ,
Yeon-Su Lee ,
In-Hoo Kim ,
Jin Soo Lee ,
Jong-Il Kim ,
Jeong-Sun Seo :
FX: an RNA-Seq analysis tool on the cloud.
721-723
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journals/bioinformatics/MakarovOCLBY12 Gene Expression
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journals/bioinformatics/ChittendenHTMAGSBNQH12 Thomas W. Chittenden ,
Eleanor Howe ,
Jennifer M. Taylor ,
Jessica C. Mar ,
Martin J. Aryee ,
Harold Gómez ,
Razvan Sultana ,
John C. Braisted ,
Sarita J. Nair ,
John Quackenbush ,
Chris Holmes :
nEASE: a method for gene ontology subclassification of high-throughput gene expression data.
726-728
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journals/bioinformatics/WangYHSHAJSL12 Systems Biology
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journals/bioinformatics/CarrB12 Rogan Carr ,
Elhanan Borenstein :
NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment.
734-735
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journals/bioinformatics/SpoelMC12
Volume 28, Number 6, March 2012 Original Papers - Genome Analysis
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journals/bioinformatics/LiG12 Yihan Li ,
Debashis Ghosh :
Assumption weighting for incorporating heterogeneity into meta-analysis of genomic data.
807-814
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journals/bioinformatics/LiuWWLYLWYCZLL12 Chi-Man Liu ,
Thomas K. F. Wong ,
Edward Wu ,
Ruibang Luo ,
Siu-Ming Yiu ,
Yingrui Li ,
Bingqiang Wang ,
Chang Yu ,
Xiaowen Chu ,
Kaiyong Zhao ,
Ruiqiang Li ,
Tak Wah Lam :
SOAP3: ultra-fast GPU-based parallel alignment tool for short reads.
878-879
Structural Bioinformatics
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journals/bioinformatics/ChojnowskiBB12 Gene Expression
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journals/bioinformatics/PiroozniaWAVTHGPZ12 Letter to the Editor Genome Analysis
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journals/bioinformatics/DessimozGRSH12 Corrigendum Genome Analysis
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journals/bioinformatics/KohaneV12a
Volume 28, Number 7, April 2012 Original Papers - Sequence Analysis
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journals/bioinformatics/RothDMCHGBHTOMAS12 Andrew Roth ,
Jiarui Ding ,
Ryan D. Morin ,
Anamaria Crisan ,
Gavin Ha ,
Ryan Giuliany ,
Ali Bashashati ,
Martin Hirst ,
Gulisa Turashvili ,
Arusha Oloumi ,
Marco A. Marra ,
Sam Aparicio ,
Sohrab P. Shah :
JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data.
907-913
Structural Bioinformatics
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journals/bioinformatics/LiuAJG12 Gene Expression
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journals/bioinformatics/KawaguchiIHHMOSST12 Genetics and Population Analysis
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journals/bioinformatics/ZhiWLZ12 Systems Biology
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journals/bioinformatics/HemertD12 export record as
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journals/bioinformatics/ZhaoL12 Shiwen Zhao ,
Shao Li :
A co-module approach for elucidating drug-disease associations and revealing their molecular basis.
955-961
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journals/bioinformatics/HeRWM12 Feng He ,
Jie Ren ,
Wei Wang ,
Jun Ma :
Evaluating the Drosophila Bicoid morphogen gradient system through dissecting the noise in transcriptional bursts.
970-975
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journals/bioinformatics/NaamatiFBL12 Data and Text Mining
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journals/bioinformatics/NiknejadCPRBR12 Applications Note Genome Analysis
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journals/bioinformatics/SunLZECVH12 Sequence Analysis
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journals/bioinformatics/ChiN12 Sang-Mun Chi ,
Dougu Nam :
WegoLoc: accurate prediction of protein subcellular localization using weighted Gene Ontology terms.
1028-1030
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journals/bioinformatics/BonnalAGGMMMPRSSSVWWKP12 Raoul J. P. Bonnal ,
Jan Aerts ,
George Githinji ,
Naohisa Goto ,
Daniel MacLean ,
Chase A. Miller ,
Hiroyuki Mishima ,
Massimiliano Pagani ,
Ricardo Ramirez-Gonzalez ,
Geert Smant ,
Francesco Strozzi ,
Rob Syme ,
Rutger A. Vos ,
Trevor J. Wennblom ,
Ben J. Woodcroft ,
Toshiaki Katayama ,
Pjotr Prins :
Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics.
1035-1037
Structural Bioinformatics
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journals/bioinformatics/BungeWBFCA12 Systems Biology
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journals/bioinformatics/GuignonDABGPCRB12
Volume 28, Number 8, April 2012 Editorial
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journals/bioinformatics/PengBVW12 Discovery Note - Genome Analysis
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journals/bioinformatics/RitchieGR12 Original Papers - Genome Analysis
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journals/bioinformatics/BeckBBUPW12 Sequence Analysis
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journals/bioinformatics/Galinsky12 Vitaly L. Galinsky :
YOABS: yet other aligner of biological sequences - an efficient linearly scaling nucleotide aligner.
1070-1077
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journals/bioinformatics/SchulzZVB12 Structural Bioinformatics
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journals/bioinformatics/KiryuA12 Hisanori Kiryu ,
Kiyoshi Asai :
Rchange: algorithms for computing energy changes of RNA secondary structures in response to base mutations.
1093-1101
Gene Expression
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journals/bioinformatics/Chang12 Jeffrey T. Chang :
Deriving transcriptional programs and functional processes from gene expression databases.
1122-1129
Systems Biology
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journals/bioinformatics/VanlierTHR12a Data and Text Mining
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journals/bioinformatics/KimKWZ12 Applications Note - Genome Analysis
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journals/bioinformatics/ZhaoS12 Xiaobei Zhao ,
Albin Sandelin :
GMD: measuring the distance between histograms with applications on high-throughput sequencing reads.
1164-1165
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journals/bioinformatics/SteissLSP12 Phylogenetics
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journals/bioinformatics/BhaduriQLUK12 Genetics and Population Analysis
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journals/bioinformatics/GautierV12 Mathieu Gautier ,
Renaud Vitalis :
rehh : an R package to detect footprints of selection in genome-wide SNP data from haplotype structure.
1176-1177
Systems Biology
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journals/bioinformatics/Adams12 Richard R. Adams :
SED-ED, a workflow editor for computational biology experiments written in SED-ML.
1180-1181
Data and Text Mining
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journals/bioinformatics/HuangLLHM12 Databases and Ontologies
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journals/bioinformatics/SacconeQJ12
Volume 28, Number 9, May 2012 Review - Systems Biology
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journals/bioinformatics/MeyerHRNSSBCRPS12 Pablo Meyer ,
Julia Hoeng ,
John Jeremy Rice ,
Raquel Norel ,
Jörg Sprengel ,
Katrin Stolle ,
Thomas Bonk ,
Stephanie Corthesy ,
Ajay K. Royyuru ,
Manuel C. Peitsch ,
Gustavo Stolovitzky :
Industrial methodology for process verification in research (IMPROVER): toward systems biology verification.
1193-1201
Original Papers - Phylogenetics
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journals/bioinformatics/HajirasoulihaSJVS12 Structural Bioinformatics
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journals/bioinformatics/MatherHT12 Systems Biology
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journals/bioinformatics/YuanXXBL12 Data and Text Mining
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journals/bioinformatics/CamposMLOR12 Databases and Ontologies
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journals/bioinformatics/Osumi-SutherlandRMNRJA12 Applications Note - Genome Analysis
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journals/bioinformatics/SeokXGDX12 Sequence Analysis
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journals/bioinformatics/PopendorfS12 Structural Bioinformatics
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journals/bioinformatics/HospitalAFCOG12 Genetics and Population Analysis
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journals/bioinformatics/ReppellBZ12 Systems Biology
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journals/bioinformatics/StreifSRBF12 Data and Text Mining
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journals/bioinformatics/MillardLSP12 Corrigendum - Data and Text Mining
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journals/bioinformatics/StamoulisB12
Volume 28, Number 10, May 2012 Discovery Notes - Structural Bioinformatics
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journals/bioinformatics/ReboulMWD12 Databases and Ontologies
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journals/bioinformatics/JoshiCFCLMSPSWH12 Hiren J. Joshi ,
Katy M. Christiansen ,
Joffrey Fitz ,
Jun Cao ,
Anna Lipzen ,
Joel Martin ,
A. Michelle Smith-Moritz ,
Len A. Pennacchio ,
Wendy S. Schackwitz ,
Detlef Weigel ,
Joshua L. Heazlewood :
1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions.
1303-1306
Original Papers - Genome Analysis
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journals/bioinformatics/LiLATDRTHCG12 Sequence Analysis
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journals/bioinformatics/SunB12 Structural Bioinformatics
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journals/bioinformatics/PangZKS12 Gene Expression
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journals/bioinformatics/Shabalin12 Andrey A. Shabalin :
Matrix eQTL: ultra fast eQTL analysis via large matrix operations.
1353-1358
Genetics and Population Analysis
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journals/bioinformatics/BaranPSTGERCFARBH12 Yael Baran ,
Bogdan Pasaniuc ,
Sriram Sankararaman ,
Dara G. Torgerson ,
Christopher Gignoux ,
Celeste Eng ,
William Rodriguez-Cintron ,
Rocio Chapela ,
Jean G. Ford ,
Pedro C. Avila ,
Jose Rodriguez-Santana ,
Esteban Gonzàlez Burchard ,
Eran Halperin :
Fast and accurate inference of local ancestry in Latino populations.
1359-1367
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journals/bioinformatics/SunW12 Hokeun Sun ,
Shuang Wang :
Penalized logistic regression for high-dimensional DNA methylation data with case-control studies.
1368-1375
Systems Biology
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journals/bioinformatics/KuffnerPTWZ12 Databases and Ontologies
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journals/bioinformatics/SparkesC12 Andrew Sparkes ,
Amanda Clare :
AutoLabDB: a substantial open source database schema to support a high-throughput automated laboratory.
1390-1397
Applications Note - Genome Analysis
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journals/bioinformatics/FawalSDM12 Structural Bioinformatics
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journals/bioinformatics/ComoglioR12 Data and Text Mining
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journals/bioinformatics/WangYY12 Databases and Ontologies
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journals/bioinformatics/QinZGTLWWCSDHLLZL12 Bo Qin ,
Meng Zhou ,
Ying Ge ,
Len Taing ,
Tao Liu ,
Qian Wang ,
Su Wang ,
Junsheng Chen ,
Lingling Shen ,
Xikun Duan ,
Sheng'en Hu ,
Wei Li ,
Henry Long ,
Yong Zhang ,
X. Shirley Liu :
CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human.
1411-1412
Corrigendum - Databases and Ontologies
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journals/bioinformatics/FengSK12
Volume 28, Number 11, June 2012 Hitseq Papers - Genome Analysis
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journals/bioinformatics/CoxBJR12 Sequence Analysis
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journals/bioinformatics/GritsenkoNRR12 Original Papers - Genome Analysis
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journals/bioinformatics/LaiDLDZ12 Structural Bioinformatics
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journals/bioinformatics/OzenneBSHJSBCB12 Gene Expression
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journals/bioinformatics/TeschendorffW12 Systems Biology
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journals/bioinformatics/LiuN12a Xin Liu ,
Mahesan Niranjan :
State and parameter estimation of the heat shock response system using Kalman and particle filters.
1501-1507
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journals/bioinformatics/ZabetA12a Applications Note - Genome Analysis
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journals/bioinformatics/PejaverARBCLLBKBK12 Vikas Rao Pejaver ,
Jaehyun An ,
SungMin Rhee ,
Ankita Bhan ,
Jeong-Hyeon Choi ,
Boshu Liu ,
Heewook Lee ,
Pamela J. Brown ,
David Kysela ,
Yves V. Brun ,
Sun Kim :
GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis.
1527-1529
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journals/bioinformatics/DeLucaLSFNWRWG12 Sequence Analysis
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journals/bioinformatics/HuYSLLLCMZLYBLF12 Xuesong Hu ,
Jianying Yuan ,
Yujian Shi ,
Jianliang Lu ,
Binghang Liu ,
Zhenyu Li ,
Yanxiang Chen ,
Desheng Mu ,
Hao Zhang ,
Nan Li ,
Zhen Yue ,
Fan Bai ,
Heng Li ,
Wei Fan :
pIRS: Profile-based Illumina pair-end reads simulator.
1533-1535
Phylogenetics
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journals/bioinformatics/PopescuHP12 Structural Bioinformatics
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journals/bioinformatics/PihanCGD12 Gene Expression
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journals/bioinformatics/WaggottCYWLB12 Systems Biology
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journals/bioinformatics/SzederkenyiBA12 Databases and Ontologies
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journals/bioinformatics/GaoLZ12 Genetics and Population Analysis
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journals/bioinformatics/StanhopeA12 Stephen A. Stanhope ,
Mark Abney :
GLOGS: a fast and powerful method for GWAS of binary traits with risk covariates in related populations.
1553-1554
Volume 28, Number 12, June 2012 ISMB 2012
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journals/bioinformatics/X12 ISMB 2012 Committee.
2-6
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journals/bioinformatics/PatelCB12 Chirag J. Patel ,
Rong Chen ,
Atul J. Butte :
Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease.
121-126
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journals/bioinformatics/LeeX12 Seunghak Lee ,
Eric P. Xing :
Leveraging input and output structures for joint mapping of epistatic and marginal eQTLs.
137-146
