Journal: Bioinformatics

Volume 27, Issue 9

1195 -- 1200Tomas W. Fitzgerald, Lee D. Larcombe, Solena Le Scouarnec, Stephen Clayton, Diana Rajan, Nigel P. Carter, Richard Redon. aCGH.Spline - an R package for aCGH dye bias normalization
1201 -- 1206Jie Huang, Andrew D. Johnson, Christopher J. O Donnell. PRIMe: a method for characterization and evaluation of pleiotropic regions from multiple genome-wide association studies
1207 -- 1214António M. Costa, José A. Tenreiro Machado, Maria Dulce Quelhas. Histogram-based DNA analysis for the visualization of chromosome, genome and species information
1215 -- 1223Christoph J. Thieme, Lydia Gramzow, Dajana Lobbes, Günter Theißen. SplamiR - prediction of spliced miRNAs in plants
1224 -- 1230Andrea Pierleoni, Pier Luigi Martelli, Rita Casadio. MemLoci: predicting subcellular localization of membrane proteins in eukaryotes
1231 -- 1238Celine Vens, Marie-Noëlle Rosso, Etienne G. J. Danchin. Identifying discriminative classification-based motifs in biological sequences
1239 -- 1246Ahmed M. Mehdi, Muhammad Shoaib B. Sehgal, Bostjan Kobe, Timothy L. Bailey, Mikael Bodén. A probabilistic model of nuclear import of proteins
1247 -- 1254Liisa Heikkinen, Mikko Kolehmainen, Garry Wong. Prediction of microRNA targets in ::::Caenorhabditis elegans:::: using a self-organizing map
1255 -- 1261Jianfu Zhou, Xiaoguang Liu, Douglas S. Stones, Qiang Xie, Gang Wang. MrBayes on a Graphics Processing Unit
1262 -- 1268Wei Zhao, Meng Xu, Zhi Liang, Bo Ding, Liwen Niu, Haiyan Liu, Maikun Teng. Structure-based ::::de novo:::: prediction of zinc-binding sites in proteins of unknown function
1269 -- 1276Jangsun Baek, Geoffrey J. McLachlan. Mixtures of common ::::t::::-factor analyzers for clustering high-dimensional microarray data
1277 -- 1283Hafiz Muhammad Shahzad Asif, Guido Sanguinetti. Large-scale learning of combinatorial transcriptional dynamics from gene expression
1284 -- 1289Qianqian Zhu, Jeffrey C. Miecznikowski, Marc S. Halfon. A wholly defined Agilent microarray spike-in dataset
1290 -- 1298Haisu Ma, Eric E. Schadt, Lee M. Kaplan, Hongyu Zhao. COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method
1299 -- 1306Jochen Weile, Matthew R. Pocock, Simon J. Cockell, Phillip W. Lord, James M. Dewar, Eva-Maria Holstein, Darren J. Wilkinson, David A. Lydall, Jennifer Hallinan, Anil Wipat. Customizable views on semantically integrated networks for systems biology
1307 -- 1308Micha Bayer, Iain Milne, Gordon Stephen, Paul Shaw, Linda Cardle, Frank Wright, David Marshall. Comparative visualization of genetic and physical maps with Strudel
1309 -- 1310Ling Sing Yung, Can Yang, Xiang Wan, Weichuan Yu. GBOOST: a GPU-based tool for detecting gene-gene interactions in genome-wide case control studies
1311 -- 1312Ernesto Picardi, Mattia D Antonio, Danilo Carrabino, Tiziana Castrignanò, Graziano Pesole. ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments
1313 -- 1315Matteo Cereda, Manuela Sironi, Matteo Cavalleri, Uberto Pozzoli. GeCo++: a C++ library for genomic features computation and annotation in the presence of variants
1316 -- 1317Manuela Hummel, Sarah Bonnin, Ernesto Lowy, Guglielmo Roma. TEQC: an R package for quality control in target capture experiments
1318 -- 1319Andrzej Zielezinski, Wojciech M. Karlowski. Agos - a universal web tool for GW Argonaute-binding domain prediction
1320 -- 1321Teong Han Chew, Kwee Hong Joyce-Tan, Farizuwana Akma, Mohd Shahir Shamsir. birgHPC: creating instant computing clusters for bioinformatics and molecular dynamics
1322 -- 1323Aron Hennerdal, Arne Elofsson. Rapid membrane protein topology prediction
1324 -- 1326Jamel Meslamani, Didier Rognan, Esther Kellenberger. sc-PDB: a database for identifying variations and multiplicity of druggable binding sites in proteins
1327 -- 1329David Shirvanyants, Anastassia N. Alexandrova, Nikolay V. Dokholyan. Rigid substructure search
1330 -- 1331Amy L. Olex, Jacquelyn S. Fetrow. SC:::2:::ATmd: a tool for integration of the figure of merit with cluster analysis for gene expression data
1332 -- 1334Laurent Excoffier, Matthieu Foll. fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios
1335 -- 1336Tiago Antao, Ian M. Hastings. ogaraK: a population genetics simulator for malaria
1337 -- 1338Asad Naeem, Andrew P. French, Darren M. Wells, Tony P. Pridmore. High-throughput feature counting and measurement of roots
1339 -- 1340Arnald Alonso, Antonio Julià, Antoni Beltran, Maria Vinaixa, Marta Díaz, Lourdes Ibañez, Xavier Correig, Sara Marsal. AStream: an R package for annotating LC/MS metabolomic data
1341 -- 1342Björn A. Grüning, Christian Senger, Anika Erxleben, Stephan Flemming, Stefan Günther. Compounds In Literature (CIL): screening for compounds and relatives in PubMed
1343 -- 1344Catherine A. Hayes, Niclas G. Karlsson, Weston B. Struwe, Frédérique Lisacek, Pauline M. Rudd, Nicolle H. Packer, Matthew P. Campbell. UniCarb-DB: a database resource for glycomic discovery

Volume 27, Issue 8

1045 -- 1051Zhengkui Wang, Yue Wang, Kian-Lee Tan, Limsoon Wong, Divyakant Agrawal. ::::eCEO::::: an efficient Cloud Epistasis cOmputing model in genome-wide association study
1052 -- 1060Eitan Halper-Stromberg, Laurence Frelin, Ingo Ruczinski, Robert B. Scharpf, Chunfa Jie, Benilton Carvalho, Haiping Hao, Kurt N. Hetrick, Anne Jedlicka, Amanda Dziedzic, Kim Doheny, Alan F. Scott, Steve Baylin, Jonathan Pevsner, Forrest Spencer, Rafael A. Irizarry. Performance assessment of copy number microarray platforms using a spike-in experiment
1061 -- 1067David Koslicki. Topological entropy of DNA sequences
1068 -- 1075Marcus Kinsella, Olivier Harismendy, Masakazu Nakano, Kelly A. Frazer, Vineet Bafna. Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs
1076 -- 1085Christian M. Reidys, Fenix W. D. Huang, Jørgen E. Andersen, Robert C. Penner, Peter F. Stadler, Markus E. Nebel. Topology and prediction of RNA pseudoknots
1086 -- 1093Emidio Capriotti, Tomás Norambuena, Marc A. Martí-Renom, Francisco Melo. All-atom knowledge-based potential for RNA structure prediction and assessment
1094 -- 1100Jessica C. Mar, Christine A. Wells, John Quackenbush. Defining an informativeness metric for clustering gene expression data
1101 -- 1107Liangxiu Han, Jano I. van Hemert, Richard A. Baldock. Automatically identifying and annotating mouse embryo gene expression patterns
1108 -- 1112Marie Brown, David C. Wedge, Royston Goodacre, Douglas B. Kell, Philip N. Baker, Louise C. Kenny, Mamas A. Mamas, Ludwig Neyses, Warwick B. Dunn. Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets
1113 -- 1120Duc-Hau Le, Yung-Keun Kwon. The effects of feedback loops on disease comorbidity in human signaling networks
1121 -- 1127Thanet Praneenararat, Toshihisa Takagi, Wataru Iwasaki. Interactive, multiscale navigation of large and complicated biological networks
1128 -- 1134Victor Spirin, Alexander Shpunt, Jan Seebacher, Marc Gentzel, Andrej Shevchenko, Steven Gygi, Shamil R. Sunyaev. Assigning spectrum-specific ::::P::::-values to protein identifications by mass spectrometry
1135 -- 1142Andrew D. Fox, Benjamin J. Hescott, Anselm Blumer, Donna K. Slonim. Connectedness of PPI network neighborhoods identifies regulatory hub proteins
1143 -- 1149Jung-Hsien Chiang, Heng-Hui Liu, Yi-Ting Huang. Condensing biomedical journal texts through paragraph ranking
1150 -- 1151Marcela Dávila López, Tore Samuelsson. eGOB: eukaryotic Gene Order Browser
1152 -- 1154Justin Jee, Joel S. Rozowsky, Kevin Y. Yip, Lucas Lochovsky, Robert Bjornson, Guoneng Zhong, Zhengdong D. Zhang, Yutao Fu, Jie Wang, Zhiping Weng, Mark Gerstein. ACT: aggregation and correlation toolbox for analyses of genome tracks
1155 -- 1156Anthony P. Fejes, Alireza Hadj Khodabakhshi, Inanç Birol, Steven J. M. Jones. Human variation database: an open-source database template for genomic discovery
1157 -- 1158Heng Li. Improving SNP discovery by base alignment quality
1159 -- 1161William A. Walters, J. Gregory Caporaso, Christian L. Lauber, Donna Berg-Lyons, Noah Fierer, Rob Knight. PrimerProspector: ::::de novo:::: design and taxonomic analysis of barcoded polymerase chain reaction primers
1162 -- 1163Hans-Ulrich Klein, Christoph Bartenhagen, Alexander Kohlmann, Vera Grossmann, Christian Ruckert, Torsten Haferlach, Martin Dugas. R453Plus1Toolbox: an R/Bioconductor package for analyzing Roche 454 Sequencing data
1164 -- 1165Diego Darriba, Guillermo L. Taboada, Ramon Doallo, David Posada. ProtTest 3: fast selection of best-fit models of protein evolution
1166 -- 1167Marc Kirchner, Buote Xu, Hanno Steen, Judith A. J. Steen. libfbi: a C++ implementation for fast box intersection and application to sparse mass spectrometry data
1168 -- 1169Haleh Yasrebi. SurvJamda: an R package to predict patients' survival and risk assessment using joint analysis of microarray gene expression data
1170 -- 1171Guido Klingbeil, Radek Erban, Mike Giles, Philip K. Maini. STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB
1172 -- 1173Yoshinori Tamada, Rui Yamaguchi, Seiya Imoto, Osamu Hirose, Ryo Yoshida, Masao Nagasaki, Satoru Miyano. SiGN-SSM: open source parallel software for estimating gene networks with state space models
1174 -- 1175George C. Linderman, Vishal N. Patel, Mark R. Chance, Gürkan Bebek. BiC: a web server for calculating bimodality of coexpression between gene and protein networks
1176 -- 1178Isthiaq Ahmad, Frank Suits, Berend Hoekman, Morris A. Swertz, Heorhiy Byelas, Martijn Dijkstra, Rob W. W. Hooft, Dmitry Katsubo, Bas van Breukelen, Rainer Bischoff 0003, Peter Horvatovich. A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data
1179 -- 1180Lee Kamentsky, Thouis R. Jones, Adam Fraser, Mark-Anthony Bray, David J. Logan, Katherine L. Madden, Vebjorn Ljosa, Curtis Rueden, Kevin W. Eliceiri, Anne E. Carpenter. Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software
1181 -- 1182Ruth Dannenfelser, Alexander Lachmann, Mariola Szenk, Avi Ma ayan. FNV: light-weight flash-based network and pathway viewer
1183 -- 1184Michael Specht, Sebastian Kuhlgert, Christian Fufezan, Michael Hippler. Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows
1185 -- 1186Simon Kocbek, Rune Sætre, Gregor Stiglic, Jin-Dong Kim, Igor Pernek, Yoshimasa Tsuruoka, Peter Kokol, Sophia Ananiadou, Jun-ichi Tsujii. AGRA: analysis of gene ranking algorithms
1187 -- 1189Bryan Brancotte, Anne Biton, Isabelle Bernard-Pierrot, François Radvanyi, Fabien Reyal, Sarah Cohen Boulakia. Gene List significance at-a-glance with GeneValorization
1190 -- 1191Hongzhan Huang, Peter B. McGarvey, Baris E. Suzek, Raja Mazumder, Jian Zhang, Yongxing Chen, Cathy H. Wu. A comprehensive protein-centric ID mapping service for molecular data integration
1192 -- 1193Javed Mohammed Khan, Harish Reddy Cheruku, Joo Chuan Tong, Shoba Ranganathan. MPID-T2: a database for sequence-structure-function analyses of pMHC and TR/pMHC structures
1194 -- 0Meïli C. Baragatti, Denys Pommeret. Comments on 'Bayesian variable selection for disease classification using gene expression data'

Volume 27, Issue 7

895 -- 898K. J. Siddle, Judith A. Goodship, Bernard Keavney, Mauro F. Santibanez-Koref. Bases adjacent to mononucleotide repeats show an increased single nucleotide polymorphism frequency in the human genome
899 -- 902Katja Luck, Gilles Travé. Phage display can select over-hydrophobic sequences that may impair prediction of natural domain-peptide interactions
903 -- 911Burkhard Linke, Robert Giegerich, Alexander Goesmann. Conveyor: a workflow engine for bioinformatic analyses
912 -- 918Grace S. Shieh, Shurong Zheng, Richard A. Johnson, Yi-Feng Chang, Kunio Shimizu, Chia-Chang Wang, Sen-Lin Tang. Modeling and comparing the organization of circular genomes
919 -- 924Stefan Götz, Roland Arnold, Patricia Sebastián-León, Samuel Martín-Rodríguez, Patrick Tischler, Marc-André Jehl, Joaquín Dopazo, Thomas Rattei, Ana Conesa. B2G-FAR, a species-centered GO annotation repository
925 -- 932Ilona Kifer, Ruth Nussinov, Haim J. Wolfson. GOSSIP: a method for fast and accurate global alignment of protein structures
933 -- 938James W. Shirley, Sereyvathana Ty, Shin-ichiro Takebayashi, Xiuwen Liu, David M. Gilbert. FISH Finder: a high-throughput tool for analyzing FISH images
939 -- 945Francois Berenger, Yong Zhou, Rojan Shrestha, Kam Y. J. Zhang. Entropy-accelerated exact clustering of protein decoys
946 -- 952Christoph Hafemeister, Ivan G. Costa, Alexander Schönhuth, Alexander Schliep. Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions
953 -- 960Florian Klinglmueller, Thomas Tuechler, Martin Posch. Cross-platform comparison of microarray data using order restricted inference
961 -- 967Tomasz Konopka. Automated analysis of biological oscillator models using mode decomposition
968 -- 972Alexander T. Dilthey, Loukas Moutsianas, Stephen Leslie, Gil McVean. HLA*IMP - an integrated framework for imputing classical HLA alleles from SNP genotypes
973 -- 979Goksel Misirli, Jennifer Hallinan, Tommy Yu, James R. Lawson, Sarala M. Wimalaratne, Mike T. Cooling, Anil Wipat. Model annotation for synthetic biology: automating model to nucleotide sequence conversion
980 -- 986Maximilian Haeussler, Martin Gerner, Casey M. Bergman. Annotating genes and genomes with DNA sequences extracted from biomedical articles
987 -- 993Björn Voss, Michael Hanselmann, Bernhard Y. Renard, Martin S. Lindner, Ullrich Köthe, Marc Kirchner, Fred A. Hamprecht. SIMA: Simultaneous Multiple Alignment of LC/MS Peak Lists
994 -- 1000Sach Mukherjee, Steven M. Hill. Network clustering: probing biological heterogeneity by sparse graphical models
1001 -- 1008Robert Hoehndorf, Michel Dumontier, Anika Oellrich, Sarala M. Wimalaratne, Dietrich Rebholz-Schuhmann, Paul Schofield, Georgios V. Gkoutos. A common layer of interoperability for biomedical ontologies based on OWL EL
1009 -- 1010Mitchell J. Sullivan, Nicola K. Petty, Scott A. Beatson. Easyfig: a genome comparison visualizer
1011 -- 1012Matei David, Misko Dzamba, Dan Lister, Lucian Ilie, Michael Brudno. SHRiMP2: Sensitive yet Practical Short Read Mapping
1013 -- 1014Francesco Strozzi, Jan Aerts. A Ruby API to query the Ensembl database for genomic features
1015 -- 1016Brent S. Pedersen, Haibao Tang, Michael Freeling. Gobe: an interactive, web-based tool for comparative genomic visualization
1017 -- 1018Charles E. Grant, Timothy L. Bailey, William Stafford Noble. FIMO: scanning for occurrences of a given motif
1019 -- 1020Zachary Dwight, Robert Palais, Carl T. Wittwer. uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application
1021 -- 1022Gerd Neudert, Gerhard Klebe. fconv: format conversion, manipulation and feature computation of molecular data
1023 -- 1025Rendong Yang, Chen Zhang, Zhen Su. LSPR: an integrated periodicity detection algorithm for unevenly sampled temporal microarray data
1026 -- 1027Antti Honkela, Pei Gao, Jonatan Ropponen, Magnus Rattray, Neil D. Lawrence. tigre: Transcription factor inference through gaussian process reconstruction of expression for bioconductor
1028 -- 1029Zhike Zi. SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models
1030 -- 1031Michael E. Smoot, Keiichiro Ono, Trey Ideker, Steven Maere. PiNGO: a Cytoscape plugin to find candidate genes in biological networks
1032 -- 1033Minlie Huang, Jingchen Liu, Xiaoyan Zhu. GeneTUKit: a software for document-level gene normalization
1034 -- 1035Annekathrin Bartsch, Boyke Bunk, Isam Haddad, Johannes Klein, Richard Münch, Thorsten Johl, Uwe Kärst, Lothar Jänsch, Dieter Jahn, Ida Retter. GeneReporter - sequence-based document retrieval and annotation
1036 -- 1038Bai Zhang, Ye Tian, Lu Jin, Huai Li, Ie-Ming Shih, Subha Madhavan, Robert Clarke, Eric P. Hoffman, Jianhua Xuan, Leena Hilakivi-Clarke, Yue Wang. DDN: a caBIG:::®::: analytical tool for differential network analysis
1039 -- 1040Kamil Tamiola, Frans A. A. Mulder. ncIDP-assign: a SPARKY extension for the effective NMR assignment of intrinsically disordered proteins
1041 -- 1042Ketil Malde. Flower: extracting information from pyrosequencing data
1043 -- 1044Andrew G. Winter, Jan Wildenhain, Mike Tyers. BioGRID REST Service, BiogridPlugin2 and BioGRID WebGraph: new tools for access to interaction data at BioGRID

Volume 27, Issue 6

745 -- 748Wai-ki Yip, Christoph Lange. Quantitative trait prediction based on genetic marker-array data, a simulation study
749 -- 756Jan Fostier, Sebastian Proost, Bart Dhoedt, Yvan Saeys, Piet Demeester, Yves Van de Peer, Klaas Vandepoele. A greedy, graph-based algorithm for the alignment of multiple homologous gene lists
757 -- 763Oliver Keller, Martin Kollmar, Mario Stanke, Stephan Waack. A novel hybrid gene prediction method employing protein multiple sequence alignments
764 -- 770Guillaume Marçais, Carl Kingsford. A fast, lock-free approach for efficient parallel counting of occurrences of ::::k::::-mers
771 -- 776Yi Zhang, Xianhui Wang, Le Kang. A ::::k::::-mer scheme to predict piRNAs and characterize locust piRNAs
777 -- 784Yejun Wang, Qing Zhang, Ming-an Sun, Dianjing Guo. High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles
785 -- 790Yang Cao, Lin Song, Zhichao Miao, Yun Hu, Liqing Tian, Taijiao Jiang. Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation
791 -- 796Guy Tsafnat, Jaron Schaeffer, Andrew Clayphan, Jonathan R. Iredell, Sally R. Partridge, Enrico W. Coiera. Computational inference of grammars for larger-than-gene structures from annotated gene sequences
797 -- 806Clement Chung, Jian Liu, Andrew Emili, Brendan J. Frey. Computational refinement of post-translational modifications predicted from tandem mass spectrometry
807 -- 814Alexandra Posekany, K. Felsenstein, P. Sykacek. Biological assessment of robust noise models in microarray data analysis
815 -- 821V. M. Lourenço, Ana M. Pires, M. Kirst. Robust linear regression methods in association studies
822 -- 828Rick Twee-Hee Ong, Xuanyao Liu, Wan-Ting Poh, Xueling Sim, Kee Seng Chia, Yik-Ying Teo. A method for identifying haplotypes carrying the causative allele in positive natural selection and genome-wide association studies
829 -- 836Christian Rödelsperger, Peter Krawitz, Sebastian Bauer, Jochen Hecht, Abigail W. Bigham, Michael Bamshad, Birgit Jonske de Condor, Michal R. Schweiger, Peter N. Robinson. Identity-by-descent filtering of exome sequence data for disease-gene identification in autosomal recessive disorders
837 -- 843Tianqi Zhu, Yucheng Hu, Zhi-Ming Ma, De-Xing Zhang, Tiejun Li, Ziheng Yang. Efficient simulation under a population genetics model of carcinogenesis
844 -- 852Stuart R. Jefferys, Morgan C. Giddings. Baking a mass-spectrometry data PIE with McMC and simulated annealing: predicting protein post-translational modifications from integrated top-down and bottom-up data
853 -- 859Lin Hou, Lin Wang, Minping Qian, Dong Li, Chao Tang, Yunping Zhu, Minghua Deng, Fangting Li. Modular analysis of the probabilistic genetic interaction network
860 -- 862Sebastian Deorowicz, Szymon Grabowski. Compression of DNA sequence reads in FASTQ format
863 -- 864Robert Schmieder, Robert Edwards. Quality control and preprocessing of metagenomic datasets
865 -- 866Michael Edmonson, Jinghui Zhang, Chunhua Yan, Richard P. Finney, Daoud M. Meerzaman, Kenneth H. Buetow. Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format
867 -- 869Angela Goncalves, Andrew Tikhonov, Alvis Brazma, Misha Kapushesky. A pipeline for RNA-seq data processing and quality assessment
870 -- 871Qiang Song, Andrew D. Smith. Identifying dispersed epigenomic domains from ChIP-Seq data
872 -- 873Andrew T. Magis, John C. Earls, Youn-Hee Ko, James A. Eddy, Nathan D. Price. Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup
874 -- 876Yanxiang Zhou, Juliane Liepe, Xia Sheng, Michael P. H. Stumpf, Chris Barnes. GPU accelerated biochemical network simulation
877 -- 878Xuejian Xiong, Hongyan Song, Tuan On, Lucas Lochovsky, Nicholas J. Provart, John Parkinson. PhyloPro: a web-based tool for the generation and visualization of phylogenetic profiles across Eukarya
879 -- 880Xin Wang, Camille Terfve, John C. Rose, Florian Markowetz. HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens
881 -- 882Matthieu Vignes, Juliette Blanchet, Damien Leroux, Florence Forbes. SpaCEM:::3:::: a software for biological module detection when data is incomplete, high dimensional and dependent
883 -- 884Yanqi Hao, Anna Merkoulovitch, James Vlasblom, Shuye Pu, Andrei L. Turinsky, Denitza Roudeva, Brian Turner, Jack Greenblatt, Shoshana J. Wodak. OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms
885 -- 886Francesca Chignola, Silvia Mari, Tim J. Stevens, Rasmus H. Fogh, Valeria Mannella, Wayne Boucher, Giovanna Musco. The CCPN Metabolomics Project: a fast protocol for metabolite identification by 2D-NMR
887 -- 888Riku Louhimo, Sampsa Hautaniemi. CNAmet: an R package for integrating copy number, methylation and expression data
889 -- 890Thomas A. Down, Matias Piipari, Tim J. P. Hubbard. Dalliance: interactive genome viewing on the web
891 -- 893Mark Y. Tong, Christopher A. Cassa, Isaac S. Kohane. Automated validation of genetic variants from large databases: ensuring that variant references refer to the same genomic locations

Volume 27, Issue 5

595 -- 603Alexej Abyzov, Mark Gerstein. AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision
604 -- 610Christopher Oldmeadow, Jonathan M. Keith. Model selection in Bayesian segmentation of multiple DNA alignments
611 -- 618Xiaolin Hao, Rui Jiang, Ting Chen. Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering
619 -- 625Anna Katharina Dehof, Alexander Rurainski, Quang Bao Anh Bui, Sebastian Böcker, Hans-Peter Lenhof, Andreas Hildebrandt. Automated bond order assignment as an optimization problem
626 -- 632Zhenjiang Xu, David H. Mathews. Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences
633 -- 640Ryung S. Kim, Juan Lin. Multi-level mixed effects models for bead arrays
641 -- 648Eric Dugat-Bony, Mohieddine Missaoui, Eric Peyretaillade, Corinne Biderre-Petit, Ourdia Bouzid, Christophe Gouinaud, David R. C. Hill, Pierre Peyret. HiSpOD: probe design for functional DNA microarrays
649 -- 654Xiujie Chen, Jiankai Xu, Bangqing Huang, Jin Li, Xin Wu, Ling Ma, Xiaodong Jia, Xiusen Bian, Fujian Tan, Lei Liu, Sheng Chen, Xia Li. A sub-pathway-based approach for identifying drug response principal network
655 -- 661Yosef Prat, Menachem Fromer, Nathan Linial, Michal Linial. Recovering key biological constituents through sparse representation of gene expression
662 -- 669Liyan Gao, Zhide Fang, Kui Zhang, Degui Zhi, Xiangqin Cui. Length bias correction for RNA-seq data in gene set analyses
670 -- 677Xuexia Wang, Xiaofeng Zhu, Huaizhen Qin, Richard S. Cooper, Warren J. Ewens, Chun Li, Mingyao Li. Adjustment for local ancestry in genetic association analysis of admixed populations
678 -- 685Vonn Walter, Andrew B. Nobel, Fred A. Wright. DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors
686 -- 692Lily Wang, Peilin Jia, Russell D. Wolfinger, Xi Chen, Britney L. Grayson, Thomas M. Aune, Zhongming Zhao. An efficient hierarchical generalized linear mixed model for pathway analysis of genome-wide association studies
693 -- 699Marco Grzegorczyk, Dirk Husmeier. Improvements in the reconstruction of time-varying gene regulatory networks: dynamic programming and regularization by information sharing among genes
700 -- 706Hung Xuan Ta, Patrik Koskinen, Liisa Holm. A novel method for assigning functional linkages to proteins using enhanced phylogenetic trees
707 -- 712Feng Feng, Ana Paula Sales, Thomas B. Kepler. A Bayesian approach for estimating calibration curves and unknown concentrations in immunoassays
713 -- 714Jonathan M. Cairns, Christiana Spyrou, Rory Stark, Mike L. Smith, Andy G. Lynch, Simon Tavaré. BayesPeak - an R package for analysing ChIP-seq data
715 -- 717Lakshmi Kuttippurathu, Michael Hsing, Yongchao Liu, Bertil Schmidt, Douglas L. Maskell, Kyungjoon Lee, Aibin He, William T. Pu, Sek Won Kong. CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments
718 -- 719Heng Li. Tabix: fast retrieval of sequence features from generic TAB-delimited files
720 -- 722Troy B. Hawkins, Jessica Dantzer, Brandon Peters, Mary Dinauer, Keithanne Mockaitis, Sean D. Mooney, Kenneth Cornetta. Identifying viral integration sites using SeqMap 2.0
723 -- 724Kliment Olechnovic, Mindaugas Margelevicius, Ceslovas Venclovas. Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure
725 -- 726Daniel Baron, Audrey Bihouée, Raluca Teusan, Emeric Dubois, Frédérique Savagner, Marja Steenman, Rémi Houlgatte, Gérard Ramstein. MADGene: retrieval and processing of gene identifier lists for the analysis of heterogeneous microarray datasets
727 -- 729Bevan Emma Huang, Andrew W. George. R/mpMap: a computational platform for the genetic analysis of multiparent recombinant inbred lines
730 -- 731Monica Chagoyen, Florencio Pazos. MBRole: enrichment analysis of metabolomic data
732 -- 733Francois Ribalet, David M. Schruth, E. Virginia Armbrust. flowPhyto: enabling automated analysis of microscopic algae from continuous flow cytometric data
734 -- 735Chuan Hock Koh, Masao Nagasaki, Ayumu Saito, Chen Li 0007, Limsoon Wong, Satoru Miyano. MIRACH: efficient model checker for quantitative biological pathway models
736 -- 738Guoqiang Yu, Huai Li, Sook S. Ha, Ie-Ming Shih, Robert Clarke, Eric P. Hoffman, Subha Madhavan, Jianhua Xuan, Yue Joseph Wang. PUGSVM: a caBIG:::TM::: analytical tool for multiclass gene selection and predictive classification
739 -- 740Ming Li, Shuo Chen, Joan Zhang, Heidi Chen, Yu Shyr. Wave-spec: a preprocessing package for mass spectrometry data
741 -- 742Mark R. Southern, Patrick R. Griffin. A Java API for working with PubChem datasets
743 -- 744Tommy Yu, Catherine M. Lloyd, David P. Nickerson, Mike T. Cooling, Andrew K. Miller, Alan Garny, Jonna R. Terkildsen, James R. Lawson, Randall Britten, Peter J. Hunter, Poul M. F. Nielsen. The Physiome Model Repository 2

Volume 27, Issue 4

441 -- 448Melissa S. Cline, Rachel Karchin. Using bioinformatics to predict the functional impact of SNVs
449 -- 455Bernhard Haubold, Floyd A. Reed, Peter Pfaffelhuber. Alignment-free estimation of nucleotide diversity
456 -- 463Andrew X. Li, Manja Marz, Jing Qin, Christian M. Reidys. RNA-RNA interaction prediction based on multiple sequence alignments
464 -- 470Kana Shimizu, Koji Tsuda. SlideSort: all pairs similarity search for short reads
471 -- 478Tak-Ming Chan, Ka Chun Wong, Kin-Hong Lee, Man Hon Wong, Chi-Kong Lau, Stephen Kwok-Wing Tsui, Kwong-Sak Leung. Discovering approximate-associated sequence patterns for protein-DNA interactions
479 -- 486Thomas C. Conway, Andrew J. Bromage. Succinct data structures for assembling large genomes
487 -- 494Teppei Ebina, Hiroyuki Toh, Yutaka Kuroda. DROP: an SVM domain linker predictor trained with optimal features selected by random forest
495 -- 501Francesco C. Stingo, Marina Vannucci. Variable selection for discriminant analysis with Markov random field priors for the analysis of microarray data
502 -- 508Zhengpeng Wu, Xi Wang, Xuegong Zhang. Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq
509 -- 515Sangsoon Woo, Jeffrey T. Leek, John D. Storey. A computationally efficient modular optimal discovery procedure
516 -- 523Jiahan Li, Kiranmoy Das, Guifang Fu, Runze Li, Rongling Wu. The Bayesian lasso for genome-wide association studies
524 -- 533Frank-Michael Schleif, T. Riemer, U. Börner, L. Schnapka-Hille, M. Cross. Genetic algorithm for shift-uncertainty correction in 1-D NMR-based metabolite identifications and quantifications
534 -- 540Alberto Rezola, Luis F. de Figueiredo, M. Brock, Jon Pey, Adam Podhorski, Christoph Wittmann, Stefan Schuster, Alexander Bockmayr, Francisco J. Planes. Exploring metabolic pathways in genome-scale networks via generating flux modes
541 -- 547Paul A. Jensen, Jason A. Papin. Functional integration of a metabolic network model and expression data without arbitrary thresholding
548 -- 555Ritwik Layek, Aniruddha Datta, Michael L. Bittner, Edward R. Dougherty. Cancer therapy design based on pathway logic
556 -- 563Wessel N. van Wieringen, Aad van der Vaart. Statistical analysis of the cancer cell s molecular entropy using high-throughput data
564 -- 571Hang Xiao, Ying Li, Jiulin Du, Axel Mosig. ::::Ct3d: :::: tracking microglia motility in 3D using a novel cosegmentation approach
572 -- 577Jürgen Hartler, Martin Trötzmüller, Chandramohan Chitraju, Friedrich Spener, Harald C. Köfeler, Gerhard G. Thallinger. Lipid Data Analyzer: unattended identification and quantitation of lipids in LC-MS data
578 -- 579Marten Boetzer, Christiaan V. Henkel, Hans J. Jansen, Derek Butler, Walter Pirovano. Scaffolding pre-assembled contigs using SSPACE
580 -- 581David L. A. Wood, Qinying Xu, John V. Pearson, Nicole Cloonan, Sean M. Grimmond. X-MATE: a flexible system for mapping short read data
582 -- 583Jose Ignacio Agulleiro Baldo, José-Jesús Fernández. Fast tomographic reconstruction on multicore computers
584 -- 586Clive G. Bowsher. Automated analysis of information processing, kinetic independence and modular architecture in biochemical networks using MIDIA
587 -- 588Leonardo Bottolo, Marc Chadeau-Hyam, David I. Hastie, Sarah R. Langley, Enrico Petretto, Laurence Tiret, David Tregouet, Sylvia Richardson. ::::ESS::::++: a C++ objected-oriented algorithm for Bayesian stochastic search model exploration
589 -- 591Mikhail Gostev, Julio Fernandez-Banet, Johan Rung, Joern Dietrich, Inga Prokopenko, Samuli Ripatti, Mark I. McCarthy, Alvis Brazma, Maria Krestyaninova. SAIL - a software system for sample and phenotype availability across biobanks and cohorts

Volume 27, Issue 3

295 -- 302Lucian Ilie, Farideh Fazayeli, Silvana Ilie. HiTEC: accurate error correction in high-throughput sequencing data
303 -- 310Lars Halvor Gidskehaug, Matthew Kent, Ben J. Hayes, Sigbjørn Lien. Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array
311 -- 316Haitao Jiang, Binhai Zhu, Daming Zhu. Algorithms for sorting unsigned linear genomes by the DCJ operations
317 -- 325Peter Menzel, Peter F. Stadler, Jan Gorodkin. maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences
326 -- 333Leonard Apeltsin, John H. Morris, Patricia C. Babbitt, Thomas E. Ferrin. Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution
334 -- 342Samuel V. Angiuoli, Steven L. Salzberg. Mugsy: fast multiple alignment of closely related whole genomes
343 -- 350Pascal Benkert, Marco Biasini, Torsten Schwede. Toward the estimation of the absolute quality of individual protein structure models
351 -- 358Hongbo Zhu, M. Teresa Pisabarro. MSPocket: an orientation-independent algorithm for the detection of ligand binding pockets
359 -- 367Vinícius Bonato, Veerabhadran Baladandayuthapani, Bradley M. Broom, Erik P. Sulman, Kenneth D. Aldape, Kim-Anh Do. Bayesian ensemble methods for survival prediction in gene expression data
368 -- 375António dos Anjos, Anders L. B. Møller, Bjarne K. Ersbøll, Christine Finnie, Hamid Shahbazkia. New approach for segmentation and quantification of two-dimensional gel electrophoresis images
376 -- 382Todd A. Gibson, Debra Goldberg. Improving evolutionary models of protein interaction networks
383 -- 390Xiaojian Shao, Chris S. H. Tan, Courtney Voss, Shawn S. C. Li, Naiyang Deng, Gary D. Bader. A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequence
391 -- 398YongSoo Kim, Taek-Kyun Kim, Yungu Kim, Jiho Yoo, Sungyong You, Inyoul Y. Lee, George Carlson, Leroy Hood, Seungjin Choi, Daehee Hwang. Principal network analysis: identification of subnetworks representing major dynamics using gene expression data
399 -- 404Ming Zhou, Xiliang Zheng, Jin Wang, Shaojun Dong. Non-destructive biocomputing security system based on gas-controlled biofuel cell and potentially used for intelligent medical diagnostics
405 -- 407Gábor Iván, Vince Grolmusz. When the Web meets the cell: using personalized PageRank for analyzing protein interaction networks
408 -- 415Emily Doughty, Attila Kertész-Farkas, Olivier Bodenreider, Gary Thompson, Asa Adadey, Thomas A. Peterson, Maricel G. Kann. Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature
416 -- 418Vijay Garla, Yong Kong, Sebastian Szpakowski, Michael Krauthammer. MU2A - reconciling the genome and transcriptome to determine the effects of base substitutions
419 -- 420Philippe Lamy, Carsten Wiuf, Torben F. Ørntoft, Claus L. Andersen. Rseg - an R package to optimize segmentation of SNP array data
421 -- 422Shao-Ke Lou, Bing Ni, Leung-Yau Lo, Stephen Kwok-Wing Tsui, Ting-Fung Chan, Kwong-Sak Leung. ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping
423 -- 425Daniel Aioanei, Marco Brucale, Bruno Samorì. Open source platform for the execution and analysis of mechanical refolding experiments
426 -- 427Per Larsson, Marcin J. Skwark, Björn Wallner, Arne Elofsson. Improved predictions by Pcons.net using multiple templates
428 -- 430Xun Lan, Russell Bonneville, Jeff Apostolos, Wangcheng Wu, Victor X. Jin. W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data
431 -- 432Michael E. Smoot, Keiichiro Ono, Johannes Ruscheinski, Peng-Liang Wang, Trey Ideker. Cytoscape 2.8: new features for data integration and network visualization
433 -- 434Albert Gevorgyan, Michael E. Bushell, Claudio Avignone-Rossa, Andrzej M. Kierzek. SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks
435 -- 436M. Miquel, I. López-Ribera, M. Ràmia, Sònia Casillas, Antonio Barbadilla, C. M. Vicient. MASISH: a database for gene expression in maize seeds
437 -- 438Y. Wayne Huang, Adam P. Arkin, John-Marc Chandonia. WIST: toolkit for rapid, customized LIMS development
439 -- 0Daniel F. Schwarz, Inke R. König, Andreas Ziegler. On safari to Random Jungle: a fast implementation of Random Forests for high-dimensional data

Volume 27, Issue 24

3331 -- 3332Lars Juhl Jensen, Alex Bateman. The rise and fall of supervised machine learning techniques
3333 -- 3340Sonja Althammer, Juan González-Vallinas, Cecilia Ballaré, Miguel Beato, Eduardo Eyras. Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data
3341 -- 3347Tse-Yi Wang, Chien-Hao Su, Huai-Kuang Tsai. MetaRank: a rank conversion scheme for comparative analysis of microbial community compositions
3348 -- 3355Scott Hazelhurst, Zsuzsanna Lipták. KABOOM! A new suffix array based algorithm for clustering expression data
3356 -- 3363Xugang Ye, Guoli Wang, Stephen F. Altschul. An assessment of substitution scores for protein profile-profile comparison
3364 -- 3370Mahmoud ElHefnawi, Nafisa Hassan, Mona Kamar, Rania Siam, Anna Lisa Remoli, Iman El-Azab, Osama AlAidy, Giulia Marsili, Marco Sgarbanti. The design of optimal therapeutic small interfering RNA molecules targeting diverse strains of influenza A virus
3371 -- 3378Qian Cong, Lisa N. Kinch, Jimin Pei, Shuoyong Shi, Vyacheslav N. Grishin, Wenlin Li, Nick V. Grishin. An automatic method for CASP9 free modeling structure prediction assessment
3379 -- 3384Yunqi Li, Yaping Fang, Jianwen Fang. Predicting residue-residue contacts using random forest models
3385 -- 3391Carsten Kemena, Jean-François Taly, Jens Kleinjung, Cédric Notredame. STRIKE: evaluation of protein MSAs using a single 3D structure
3392 -- 3398Robbie P. Joosten, Krista Joosten, Serge X. Cohen, Gert Vriend, Anastassis Perrakis. Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank
3399 -- 3406Levi Waldron, Melania Pintilie, Ming-Sound Tsao, Frances A. Shepherd, Curtis Huttenhower, Igor Jurisica. Optimized application of penalized regression methods to diverse genomic data
3407 -- 3414Mattia Zampieri, Giuseppe Legname, Daniel Segrè, Claudio Altafini. A system-level approach for deciphering the transcriptional response to prion infection
3415 -- 3422Nicholas E. Newell. Cascade detection for the extraction of localized sequence features; specificity results for HIV-1 protease and structure-function results for the Schellman loop
3423 -- 3424Ryan K. Dale, Brent S. Pedersen, Aaron R. Quinlan. Pybedtools: a flexible Python library for manipulating genomic datasets and annotations
3425 -- 3426Oksana Riba-Grognuz, Laurent Keller, Laurent Falquet, Ioannis Xenarios, Yannick Wurm. de novo genome assemblies
3427 -- 3429Marcelo Rivas-Astroza, Dan Xie, Xiaoyi Cao, Sheng Zhong. Mapping personal functional data to personal genomes
3430 -- 3431Douglas M. Fowler, Carlos L. Araya, Wayne Gerard, Stanley Fields. Enrich: software for analysis of protein function by enrichment and depletion of variants
3432 -- 3434Yang Zhou, Wubin Qu, Yiming Lu, Yanchun Zhang, Xiaolei Wang, Dongsheng Zhao, Yi Yang, Chenggang Zhang. VizPrimer: a web server for visualized PCR primer design based on known gene structure
3435 -- 3436Robert Kofler, Ram Vinay Pandey, Christian Schlötterer. PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)
3437 -- 3438Huaiyu Mi, Anushya Muruganujan, Emek Demir, Yukiko Matsuoka, Akira Funahashi, Hiroaki Kitano, Paul D. Thomas. BioPAX support in CellDesigner
3439 -- 3440Kamil Fijorek, Damian Fijorek, Barbara Wisniowska, Sebastian Polak. BDTcomparator: a program for comparing binary classifiers

Volume 27, Issue 23

3221 -- 3227Chao Cheng, Renqiang Min, Mark Gerstein. TIP: A probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles
3228 -- 3234Jin Zhang, Yufeng Wu. SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data
3235 -- 3241Geir Kjetil Sandve, Egil Ferkingstad, Ståle Nygård. Sequential Monte Carlo multiple testing
3242 -- 3249Zhenqiu Liu, William Hsiao, Brandi L. Cantarel, Elliott Franco Drábek, Claire Fraser-Liggett. Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data
3250 -- 3258Siavash Mirarab, Tandy Warnow. FASTSP: linear time calculation of alignment accuracy
3259 -- 3265Leena Salmela, Veli Mäkinen, Niko Välimäki, Johannes Ylinen, Esko Ukkonen. Fast scaffolding with small independent mixed integer programs
3266 -- 3275Minmei Hou, Ping Yao, Angela Antonou, Mitrick A. Johns. Pico-inplace-inversions between human and chimpanzee
3276 -- 3285Peter Schmidtke, Axel Bidon-Chanal, F. Javier Luque, Xavier Barril. MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories
3286 -- 3292Gilad Wainreb, Lior Wolf, Haim Ashkenazy, Yves Dehouck, Nir Ben-Tal. Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site
3293 -- 3299Shuiwang Ji. Computational network analysis of the anatomical and genetic organizations in the mouse brain
3300 -- 3305A. Sofia Silva, Shona H. Wood, Sipko van Dam, Sven Berres, Anne McArdle, João Pedro de Magalhães. Gathering insights on disease etiology from gene expression profiles of healthy tissues
3306 -- 3312Aurélie Névéol, W. John Wilbur, Zhiyong Lu. Extraction of data deposition statements from the literature: a method for automatically tracking research results
3313 -- 3314Michal Wozniak, Limsoon Wong, Jerzy Tiuryn. CAMBerVis: visualization software to support comparative analysis of multiple bacterial strains
3315 -- 3316Alex Stivala, Michael Wybrow, Anthony Wirth, James C. Whisstock, Peter J. Stuckey. Automatic generation of protein structure cartoons with Pro-origami
3317 -- 3318Jesse M. Engreitz, Rong Chen, Alexander A. Morgan, Joel Dudley, Rohan Mallelwar, Atul J. Butte. ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression
3319 -- 3320Sudhir Kumar, Charlotte Konikoff, Bernard Van Emden, Christopher Busick, Kailah T. Davis, Shuiwang Ji, Lin-Wei Wu, Hector Ramos, Thomas Brody, Sethuraman Panchanathan, Jieping Ye, Timothy L. Karr, Kristyn Gerold, Michael McCutchan, Stuart J. Newfeld. Drosophila embryogenesis
3321 -- 3322Donglin Huang, Yiling Huang, Youhuang Bai, Dijun Chen, Ralf Hofestädt, Christian Klukas, Ming Chen 0005. MyBioNet: interactively visualize, edit and merge biological networks on the Web
3323 -- 3324Jonathan Blakes, Jamie Twycross, Francisco José Romero-Campero, Natalio Krasnogor. in silico modelling platform for Systems and Synthetic Biology
3325 -- 3326Assaf Gottlieb, Oded Magger, Igor Berman, Eytan Ruppin, Roded Sharan. PRINCIPLE: a tool for associating genes with diseases via network propagation
3327 -- 3328Nikolas Papanikolaou, Evangelos Pafilis, Stavros Nikolaou, Christos A. Ouzounis, Ioannis Iliopoulos, Vassilis J. Promponas. BioTextQuest: a web-based biomedical text mining suite for concept discovery
3329 -- 3330Qingqing Yang, Chengxiang Qiu, Jie Yang, Qing Wu, Qinghua Cui. miREnvironment Database: providing a bridge for microRNAs, environmental factors and phenotypes

Volume 27, Issue 22

3079 -- 3084Kai Wang, Rasmus Wernersson, Søren Brunak. The strength of intron donor splice sites in human genes displays a bell-shaped pattern
3085 -- 3092Michiaki Hamada, Edward Wijaya, Martin C. Frith, Kiyoshi Asai. Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection
3093 -- 3101Naama Elefant, Yael Altuvia, Hanah Margalit. A wide repertoire of miRNA binding sites: prediction and functional implications
3102 -- 3109Diana L. Kolbe, Sean R. Eddy. Fast filtering for RNA homology search
3110 -- 3116Ivan Kalev, Michael Habeck. HHfrag: HMM-based fragment detection using HHpred
3117 -- 3122Zhichao Miao, Yang Cao, Taijiao Jiang. RASP: rapid modeling of protein side chain conformations
3123 -- 3128Castrense Savojardo, Piero Fariselli, Rita Casadio. Improving the detection of transmembrane β-barrel chains with N-to-1 extreme learning machines
3129 -- 3134Kevin K. Dobbin, Stephanie Cooke. Lower confidence bounds for prediction accuracy in high dimensions via AROHIL Monte Carlo
3135 -- 3141Christopher Minas, Simon J. Waddell, Giovanni Montana. Distance-based differential analysis of gene curves
3142 -- 3148Yu-cheng Liu, Chun-Pei Cheng, Vincent S. Tseng. Discovering relational-based association rules with multiple minimum supports on microarray datasets
3149 -- 3157Joana P. Gonçalves, Alexandre P. Francisco, Nuno P. Mira, Miguel C. Teixeira, Isabel Sá-Correia, Arlindo L. Oliveira, Sara C. Madeira. TFRank: network-based prioritization of regulatory associations underlying transcriptional responses
3158 -- 3165Ruiqi Wang, Kaihui Liu, Luonan Chen, Kazuyuki Aihara. cis-inhibition in Notch signaling
3166 -- 3172Anna Goldenberg, Sara Mostafavi, Gerald Quon, Paul C. Boutros, Quaid Morris. Unsupervised detection of genes of influence in lung cancer using biological networks
3173 -- 3178Qiang Huang, Ling-Yun Wu, Xiang-Sun Zhang. An efficient network querying method based on conditional random fields
3179 -- 3185Yufan Guo, Anna Korhonen, Ilona Silins, Ulla Stenius. Weakly supervised learning of information structure of scientific abstracts - is it accurate enough to benefit real-world tasks in biomedicine?
3186 -- 3192Solange Delagenière, Patrice Brenchereau, Ludovic Launer, Alun W. Ashton, Ricardo Leal, Stéphanie Veyrier, José Gabadinho, Elspeth J. Gordon, Samuel D. Jones, Karl Erik Levik, Seán M. McSweeney, Stéphanie Monaco, Max Nanao, Darren Spruce, Olof Svensson, Martin A. Walsh, Gordon A. Leonard. ISPyB: an information management system for synchrotron macromolecular crystallography
3193 -- 3199Nico Adams, Robert Hoehndorf, Georgios V. Gkoutos, Gesine Hansen, Christian Hennig. PIDO: the primary immunodeficiency disease ontology
3200 -- 3201Pierre Lindenbaum, Solena Le Scouarnec, Vincent Portero, Richard Redon. Knime4Bio: a set of custom nodes for the interpretation of next-generation sequencing data with KNIME
3202 -- 3203Lorena Pantano, Xavier Estivill, Eulalia Martí. A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome
3204 -- 3205Jonatan Taminau, David Steenhoff, Alain Coletta, Stijn Meganck, Cosmin Lazar, Virginie de Schaetzen, Robin Duque, Colin Molter, Hugues Bersini, Ann Nowé, David Y. Weiss Solís. inSilicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO
3206 -- 3208Markus S. Schröder, Aedín C. Culhane, John Quackenbush, Benjamin Haibe-Kains. survcomp: an R/Bioconductor package for performance assessment and comparison of survival models
3209 -- 3210Eleanor Howe, Raktim Sinha, Daniel Schlauch, John Quackenbush. RNA-Seq analysis in MeV
3211 -- 3213Matthew R. Lakin, Simon Youssef, Filippo Polo, Stephen Emmott, Andrew Phillips. Visual DSD: a design and analysis tool for DNA strand displacement systems
3214 -- 3215Zeqiang Ma, David L. Tabb, Joseph Burden, Matthew Chambers, Matthew B. Cox, Michael J. Cantrell, Amy-Joan L. Ham, Michael D. Litton, Michael R. Oreto, William C. Schultz, Scott M. Sobecki, Tina Y. Tsui, Gregory R. Wernke, Daniel C. Liebler. Supporting tool suite for production proteomics
3216 -- 3217Gustavo Glusman, Juan Caballero, Denise E. Mauldin, Leroy Hood, Jared C. Roach. Kaviar: an accessible system for testing SNV novelty
3218 -- 3219Meng-Pin Weng, Ben-Yang Liao. Drosophila phenotype enrichment analysis for insect functional genomics

Volume 27, Issue 21

2927 -- 2935Brett Trost, Anthony J. Kusalik. Computational prediction of eukaryotic phosphorylation sites
2936 -- 2943Yue Wang, Guimei Liu, Mengling Feng, Limsoon Wong. An empirical comparison of several recent epistatic interaction detection methods
2944 -- 2948Chaitanya A. Athale, Hemangi Chaudhari. Escherichia coli
2949 -- 2956Sandro Morganella, Stefano Maria Pagnotta, Michele Ceccarelli. Finding recurrent copy number alterations preserving within-sample homogeneity
2957 -- 2963Tanja Magoc, Steven L. Salzberg. FLASH: fast length adjustment of short reads to improve genome assemblies
2964 -- 2971Sergey Koren, Todd J. Treangen, Mihai Pop. Bambus 2: scaffolding metagenomes
2972 -- 2978Shu Yang, Hari Krishna Yalamanchili, Xinran Li, Kwok-Ming Yao, Pak Chung Sham, Michael Q. Zhang, Junwen Wang. Correlated evolution of transcription factors and their binding sites
2979 -- 2986Sebastian Deorowicz, Szymon Grabowski. Robust relative compression of genomes with random access
2987 -- 2993Heng Li. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
2994 -- 3001Yuan Li, Shaojie Zhang. Finding stable local optimal RNA secondary structures
3002 -- 3009Iain H. Moal, Rudi Agius, Paul A. Bates. Protein-protein binding affinity prediction on a diverse set of structures
3010 -- 3016Jie Wu, Martin Akerman, Shuying Sun, W. Richard McCombie, Adrian R. Krainer, Michael Q. Zhang. SpliceTrap: a method to quantify alternative splicing under single cellular conditions
3017 -- 3023Mingguang Shi, Bing Zhang 0003. Semi-supervised learning improves gene expression-based prediction of cancer recurrence
3024 -- 3028Yungki Park, Edward M. Marcotte. Revisiting the negative example sampling problem for predicting protein-protein interactions
3029 -- 3035Genevera I. Allen, Mirjana Maletic-Savatic. Sparse non-negative generalized PCA with applications to metabolomics
3036 -- 3043Twan van Laarhoven, Sander B. Nabuurs, Elena Marchiori. Gaussian interaction profile kernels for predicting drug-target interaction
3044 -- 3049Bin Chen, Kevin J. McConnell, Nikil Wale, David J. Wild, Eric M. Gifford. Comparing bioassay response and similarity ensemble approaches to probing protein pharmacology
3050 -- 3055X. G. Zhao, W. Dai, Y. Li, L. Tian. AUC-based biomarker ensemble with an application on gene scores predicting low bone mineral density
3056 -- 3064Chao Sima, Ulisses Braga-Neto, Edward R. Dougherty. High-dimensional bolstered error estimation
3065 -- 3066Huat Chye Lim, Marcel E. Curlin, John E. Mittler. HIV Therapy Simulator: a graphical user interface for comparing the effectiveness of novel therapy regimens
3067 -- 3069Meg Pirrung, Ryan Kennedy, J. Gregory Caporaso, Jesse Stombaugh, Doug Wendel, Rob Knight. TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata
3070 -- 3071Thibaut Jombart, Ismaïl Ahmed. adegenet 1.3-1: new tools for the analysis of genome-wide SNP data
3072 -- 3073Ananth Kalyanaraman, William R. Cannon, Benjamin Latt, Douglas J. Baxter. MapReduce implementation of a hybrid spectral library-database search method for large-scale peptide identification
3074 -- 3075Simon Roux, Michaël Faubladier, Antoine Mahul, Nils Paulhe, Aurélien Bernard, Didier Debroas, François Enault. Metavir: a web server dedicated to virome analysis
3076 -- 3077Wenming Zhao, Wanfei Liu, Dongmei Tian, Bixia Tang, Yanqing Wang, Caixia Yu, Rujiao Li, Yunchao Ling, Jiayan Wu, Shuhui Song, Songnian Hu. wapRNA: a web-based application for the processing of RNA sequences

Volume 27, Issue 20

2775 -- 2781Xiaohua Douglas Zhang, Francesca Santini, Raul Lacson, Shane D. Marine, Qian Wu, Luca Benetti, Ruojing Yang, Alex McCampbell, Joel P. Berger, Dawn M. Toolan, Erica M. Stec, Daniel J. Holder, Keith A. Soper, Joseph F. Heyse, Marc Ferrer. cSSMD: assessing collective activity for addressing off-target effects in genome-scale RNA interference screens
2782 -- 2789Lucía Spangenberg, Florian Battke, Martí Graña, Kay Nieselt, Hugo Naya. Identifying associations between amino acid changes and meta information in alignments
2790 -- 2796Matthew Ruffalo, Thomas LaFramboise, Mehmet Koyutürk. Comparative analysis of algorithms for next-generation sequencing read alignment
2797 -- 2805Tilo Eißler, Christopher P. Hodges, Harald Meier. PTPan - overcoming memory limitations in oligonucleotide string matching for primer/probe design
2806 -- 2811Eugen Fazius, Vladimir Shelest, Ekaterina Shelest. SiTaR: a novel tool for transcription factor binding site prediction
2812 -- 2819Catherine Mooney, Yong-hong Wang, Gianluca Pollastri. SCLpred: protein subcellular localization prediction by N-to-1 neural networks
2820 -- 2827Anisah W. Ghoorah, Marie-Dominique Devignes, Malika Smaïl-Tabbone, David W. Ritchie. Spatial clustering of protein binding sites for template based protein docking
2828 -- 2835Ying Shen, Hau-San Wong, Shaohong Zhang, Zhiwen Yu. Feature-based 3D motif filtering for ribosomal RNA
2836 -- 2842Elad Donsky, Haim J. Wolfson. PepCrawler: a fast RRT-based algorithm for high-resolution refinement and binding affinity estimation of peptide inhibitors
2843 -- 2850José Ramón López-Blanco, José Ignacio Garzón, Pablo Chacón. iMod: multipurpose normal mode analysis in internal coordinates
2851 -- 2858Zhengyu Ouyang, Mingzhou Song, Robert Güth, Thomas Ha, Matt Larouche, Daniel Goldowitz. Conserved and differential gene interactions in dynamical biological systems
2859 -- 2865Pushpike Jayantha Thilakarathne, Lieven Clement, Dan Lin 0004, Ziv Shkedy, Adetayo Kasim, Willem Talloen, Matthias Versele, Geert Verbeke. ® peptide array data: an application to an oncology experiment
2866 -- 2872Melissa M. Matzke, Katrina M. Waters, Thomas O. Metz, Jon M. Jacobs, Amy C. Sims, Ralph S. Baric, Joel G. Pounds, Bobbie-Jo M. Webb-Robertson. Improved quality control processing of peptide-centric LC-MS proteomics data
2873 -- 2879Andrea Ocone, Guido Sanguinetti. Reconstructing transcription factor activities in hierarchical transcription network motifs
2880 -- 2887Barak Markus, Ohad S. Birk, Dan Geiger. Integration of SNP genotyping confidence scores in IBD inference
2888 -- 2894Anthony R. Soltis, Jeffrey J. Saucerman. Robustness portraits of diverse biological networks conserved despite order-of-magnitude parameter uncertainty
2895 -- 2902Lei Qu, Fuhui Long, Xiao Liu, Stuart K. Kim, Eugene W. Myers, Hanchuan Peng. C.elegans
2903 -- 2904Matthew K. Iyer, Arul M. Chinnaiyan, Christopher A. Maher. ChimeraScan: a tool for identifying chimeric transcription in sequencing data
2905 -- 2906Arnaud Despalins, Souhir Marsit, Jacques Oberto. Absynte: a web tool to analyze the evolution of orthologous archaeal and bacterial gene clusters
2907 -- 2909Bernd Jagla, Bernd Wiswedel, Jean-Yves Coppée. Extending KNIME for next-generation sequencing data analysis
2910 -- 2912Filip Bielejec, Andrew Rambaut, Marc A. Suchard, Philippe Lemey. SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics
2913 -- 2914Shide Liang, Dandan Zheng, Chi Zhang, Daron M. Standley. Fast and accurate prediction of protein side-chain conformations
2915 -- 2916Anna Vangone, Raffaele Spinelli, Vittorio Scarano, Luigi Cavallo, Romina Oliva. COCOMAPS: a web application to analyze and visualize contacts at the interface of biomolecular complexes
2917 -- 2918Atanas Kamburov, Rachel Cavill, Timothy M. D. Ebbels, Ralf Herwig, Hector C. Keun. Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA
2919 -- 2920Jike Cui, Todd F. DeLuca, Jae-Yoon Jung, Dennis P. Wall. Detecting biological network organization and functional gene orthologs
2921 -- 2923Rui-Ru Ji, Nathan O. Siemers, Ming Lei, Liang Schweizer, Robert E. Bruccoleri. SDRS - an algorithm for analyzing large-scale dose-response data
2924 -- 2925Christina M. Bergey. Alu insertions for use in primate phylogeny and population genetics

Volume 27, Issue 2

147 -- 152Dong Dong, Xiaojian Shao, Zhaolei Zhang. Differential effects of chromatin regulators and transcription factors on gene regulation: a nucleosomal perspective
153 -- 160Giuseppe Narzisi, Bud Mishra. Scoring-and-unfolding trimmed tree assembler: concepts, constructs and comparisons
161 -- 166Vito M. R. Muggeo, Giada Adelfio. Efficient change point detection for genomic sequences of continuous measurements
175 -- 181Ahrim Youn, Richard Simon. Identifying cancer driver genes in tumor genome sequencing studies
182 -- 188Panagiotis D. Vouzis, Nikolaos V. Sahinidis. GPU-BLAST: using graphics processors to accelerate protein sequence alignment
189 -- 195Sanchit Misra, Ankit Agrawal, Wei-keng Liao, Alok N. Choudhary. Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing
196 -- 203Fabio Gori, Gianluigi Folino, Mike S. M. Jetten, Elena Marchiori. MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks
204 -- 210Tobias Hamp, Fabian Birzele, Fabian Buchwald, Stefan Kramer. Improving structure alignment-based prediction of SCOP families using Vorolign Kernels
211 -- 219Stefan E. Seemann, Andreas S. Richter, Tanja Gesell, Rolf Backofen, Jan Gorodkin. PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences
220 -- 224Gregory Riddick, Hua Song, Susie Ahn, Jennifer Walling, Diego Borges-Rivera, Wei Zhang, Howard A. Fine. Predicting ::::in vitro:::: drug sensitivity using Random Forests
225 -- 231Hong-Qiang Wang, Lindsey K. Tuominen, Chung-Jui Tsai. SLIM: a sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures
232 -- 237Darong Lai, Xinyi Yang, Gang Wu, Yuanhua Liu, Christine Nardini. Inference of gene networks - application to ::::Bifidobacterium::::
238 -- 244Holger Fröhlich, Paurush Praveen, Achim Tresch. Fast and efficient dynamic nested effects models
245 -- 251Tae-Hwan Kim, Junil Kim, Pat Heslop-Harrison, Kwang-Hyun Cho. Evolutionary design principles and functional characteristics based on kingdom-specific network motifs
252 -- 258Isabel A. Nepomuceno-Chamorro, Francisco Azuaje, Yvan Devaux, Petr V. Nazarov, Arnaud Muller, Jesús S. Aguilar-Ruiz, Daniel R. Wagner. Prognostic transcriptional association networks: a new supervised approach based on regression trees
259 -- 265Quoc-Chinh Bui, Sophia Katrenko, Peter M. A. Sloot. A hybrid approach to extract protein-protein interactions
266 -- 267Qing Yu, Elizabeth M. Ryan, Todd M. Allen, Bruce W. Birren, Matthew R. Henn, Niall J. Lennon. PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes
268 -- 269Valentina Boeva, Andrei Zinovyev, Kevin Bleakley, Jean-Philippe Vert, Isabelle Janoueix-Lerosey, Olivier Delattre, Emmanuel Barillot. Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization
270 -- 271Simon J. van Heeringen, Gert Jan C. Veenstra. de novo motif prediction pipeline for ChIP-sequencing experiments
272 -- 274Ryan Koehler, Hadar Issac, Nicole Cloonan, Sean M. Grimmond. The uniqueome: a mappability resource for short-tag sequencing
275 -- 276Paulo C. Carvalho, Juliana S. G. Fischer, Jonas Perales, John R. Yates III, Valmir C. Barbosa, Elias Bareinboim. Analyzing marginal cases in differential shotgun proteomics
277 -- 278Emese Meglécz, Sylvain Piry, Erick Desmarais, Maxime Galan, André Gilles, Emmanuel Guivier, Nicolas Pech, Jean-François Martin. SESAME (SEquence Sorter & AMplicon Explorer): genotyping based on high-throughput multiplex amplicon sequencing
279 -- 280Stephanie Kehr, Sebastian Bartschat, Peter F. Stadler, Hakim Tafer. PLEXY: efficient target prediction for box C/D snoRNAs
281 -- 283Lukas Habegger, Andrea Sboner, Tara A. Gianoulis, Joel S. Rozowsky, Ashish Agarwal, Michael Snyder, Mark Gerstein. RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries
284 -- 285Nicholas A. Davis, Ahwan Pandey, Brett A. McKinney. Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS
286 -- 287Rebecca Rooke, Guojun Yang. TE Displayer for post-genomic analysis of transposable elements
288 -- 290Matthias Vigelius, Aidan Lane, Bernd Meyer. Accelerating reaction-diffusion simulations with general-purpose graphics processing units

Volume 27, Issue 19

2621 -- 2624Ivan V. Kulakovskiy, A. A. Belostotsky, Artem S. Kasianov, Natalie G. Esipova, Yulia A. Medvedeva, I. A. Eliseeva, Vsevolod Makeev. A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites
2625 -- 2632Mengyuan Xu, Clarice R. Weinberg, David M. Umbach, Leping Li. coMOTIF: a mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq Data
2633 -- 2640Darshan Singh, Christian F. Orellana, Yin Hu, Corbin D. Jones, Yufeng Liu, Derek Y. Chiang, Jinze Liu, Jan F. Prins. FDM: a graph-based statistical method to detect differential transcription using RNA-seq data
2641 -- 2647He Quan Sun, Malcolm Yoke-Hean Low, Wen-Jing Hsu, Ching-Wai Tan, Jagath C. Rajapakse. Tree-structured algorithm for long weak motif discovery
2648 -- 2654Jarupon Fah Sathirapongsasuti, Hane Lee, Basil A. J. Horst, Georg Brunner, Alistair J. Cochran, Scott Binder, John Quackenbush, Stanley F. Nelson. Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV
2655 -- 2663Daniel Gaston, Edward Susko, Andrew J. Roger. A phylogenetic mixture model for the identification of functionally divergent protein residues
2664 -- 2671Aïda Ouangraoua, Eric Tannier, Cedric Chauve. Reconstructing the architecture of the ancestral amniote genome
2672 -- 2678Yi-Hui Zhou, Kai Xia, Fred A. Wright. A powerful and flexible approach to the analysis of RNA sequence count data
2679 -- 2685Yinyin Yuan, Oscar M. Rueda, Christina Curtis, Florian Markowetz. Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer
2686 -- 2691Zheng Li, Ping Li, Arun Krishnan, Jingdong Liu. Large-scale dynamic gene regulatory network inference combining differential equation models with local dynamic Bayesian network analysis
2692 -- 2699TaeHyun Hwang, Wei Zhang 0032, Maoqiang Xie, Jinfeng Liu, Rui Kuang. Inferring disease and gene set associations with rank coherence in networks
2700 -- 2706Chih-Hung Wu, Hsiao-Ching Lee, Bor-Sen Chen. Robust synthetic gene network design via library-based search method
2707 -- 2713Orland R. Gonzalez, Ralf Zimmer. Contextual analysis of RNAi-based functional screens using interaction networks
2714 -- 2720Jarno Mäkelä, Heikki Huttunen, Meenakshisundaram Kandhavelu, Olli Yli-Harja, Andre S. Ribeiro. Escherichia coli
2721 -- 2729Nona Naderi, Thomas Kappler, Christopher J. O. Baker, René Witte. OrganismTagger: detection, normalization and grounding of organism entities in biomedical documents
2730 -- 2737Xinglong Wang, Iain McKendrick, Ian Barrett, Ian Dix, Tim French, Jun'ichi Tsujii, Sophia Ananiadou. Automatic extraction of angiogenesis bioprocess from text
2738 -- 2745Domingo S. Rodríguez-Baena, Antonio J. Pérez-Pulido, Jesús S. Aguilar-Ruiz. A biclustering algorithm for extracting bit-patterns from binary datasets
2746 -- 2753Elizabeth Rossin, Tsung I. Lin, Hsiu J. Ho, Steven J. Mentzer, Saumyadipta Pyne. A framework for analytical characterization of monoclonal antibodies based on reactivity profiles in different tissues
2754 -- 2755Ricardo Ramirez-Gonzalez, Mario Caccamo, Daniel MacLean. Gee Fu: a sequence version and web-services database tool for genomic assembly, genome feature and NGS data
2756 -- 2757Aaron E. Darling, Andrew J. Tritt, Jonathan A. Eisen, Marc T. Facciotti. Mauve Assembly Metrics
2758 -- 2760Cuong Cao Dang, Vincent Lefort, Le Sy Vinh, Si Quang Le, Olivier Gascuel. ReplacementMatrix: a web server for maximum-likelihood estimation of amino acid replacement rate matrices
2761 -- 2762Georg Basler, Zoran Nikoloski. JMassBalance: mass-balanced randomization and analysis of metabolic networks
2763 -- 2764Christoph Gille, Katrin Hübner, Andreas Hoppe, Hermann-Georg Holzhütter. Metannogen: annotation of biological reaction networks
2765 -- 2766Nguyen Xuan Vinh, Madhu Chetty, Ross L. Coppel, Pramod P. Wangikar. GlobalMIT: learning globally optimal dynamic bayesian network with the mutual information test criterion
2767 -- 2768Duc-Hau Le, Yung-Keun Kwon. NetDS: a Cytoscape plugin to analyze the robustness of dynamics and feedforward/feedback loop structures of biological networks
2769 -- 2771Jörg Hakenberg, Martin Gerner, Maximilian Haeussler, Illés Solt, Conrad Plake, Michael Schroeder, Graciela Gonzalez, Goran Nenadic, Casey M. Bergman. The GNAT library for local and remote gene mention normalization
2772 -- 2773Yoona Kim, Steven Bark, Vivian Hook, Nuno Bandeira. NeuroPedia: neuropeptide database and spectral library

Volume 27, Issue 18

2473 -- 2477Adrian Schröder, Johannes Wollnik, Clemens Wrzodek, Andreas Dräger, Michael Bonin, Oliver Burk, Maria Thomas, Wolfgang E. Thasler, Ulrich M. Zanger, Andreas Zell. Inferring statin-induced gene regulatory relationships in primary human hepatocytes
2478 -- 2485Luciana Ferrer, Alexander Glennon Shearer, Peter D. Karp. Discovering novel subsystems using comparative genomics
2486 -- 2493Donglai Wei, Lauren V. Alpert, Charles E. Lawrence. RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences
2494 -- 2501Dong Seon Kim, Yoonsoo Hahn. Identification of novel phosphorylation modification sites in human proteins that originated after the human-chimpanzee divergence
2502 -- 2509Ergude Bao, Tao Jiang, Isgouhi Kaloshian, Thomas Girke. SEED: efficient clustering of next-generation sequences
2510 -- 2517Matej Lexa, Tomás Martínek, Ivana Burgetova, Daniel Kopecek, Marie Brázdová. A dynamic programming algorithm for identification of triplex-forming sequences
2518 -- 2528Gregory R. Grant, Michael H. Farkas, Angel D. Pizarro, Nicholas F. Lahens, Jonathan Schug, Brian P. Brunk, Christian J. Stoeckert Jr., John B. Hogenesch, Eric A. Pierce. Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
2529 -- 2536Qian Liu, Steven C. H. Hoi, Chinh T. T. Su, Zhenhua Li, Chee Keong Kwoh, Limsoon Wong, Jinyan Li. Structural analysis of the hot spots in the binding between H1N1 HA and the 2D1 antibody: do mutations of H1N1 from 1918 to 2009 affect much on this binding?
2537 -- 2545Sheng Wang, Jian Peng 0001, Jinbo Xu. Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling
2546 -- 2553Lan Zagar, Francesca Mulas, Silvia Garagna, Maurizio Zuccotti, Riccardo Bellazzi, Blaz Zupan. Stage prediction of embryonic stem cell differentiation from genome-wide expression data
2554 -- 2562Hui Yuan Xiong, Yoseph Barash, Brendan J. Frey. Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context
2563 -- 2570Inka J. Appel, Wolfram Gronwald, Rainer Spang. Estimating classification probabilities in high-dimensional diagnostic studies
2571 -- 2577Fan Xia, Ji-Yuan Zhou, Wing Kam Fung. A powerful approach for association analysis incorporating imprinting effects
2578 -- 2585Can Yang, Xiaowei Zhou, Xiang Wan, Qiang Yang, Hong Xue, Weichuan Yu. Identifying disease-associated SNP clusters via contiguous outlier detection
2586 -- 2594Hong-Jie Dai, Yen-Ching Chang, Richard Tzong-Han Tsai, Wen-Lian Hsu. Integration of gene normalization stages and co-reference resolution using a Markov logic network
2595 -- 2597Igor Lukashin, Pavel S. Novichkov, Dario Boffelli, Alex R. Paciorkowski, Simon Minovitsky, Song Yang, Inna Dubchak. VISTA Region Viewer (RViewer) - a computational system for prioritizing genomic intervals for biomedical studies
2598 -- 2600Ying Wang, Gaurang Mehta, Rajiv Mayani, Jingxi Lu, Tade Souaiaia, Yangho Chen, Andrew P. Clark, Hee Jae Yoon, Lin Wan, Oleg V. Evgrafov, James A. Knowles, Ewa Deelman, Ting Chen. RseqFlow: workflows for RNA-Seq data analysis
2601 -- 2602Kristian Cibulskis, Aaron McKenna, Tim Fennell, Eric Banks, Mark A. DePristo, Gad Getz. ContEst: estimating cross-contamination of human samples in next-generation sequencing data
2603 -- 2604Marc J. Lajeunesse. phyloMeta: a program for phylogenetic comparative analyses with meta-analysis
2605 -- 2606David Fournier, Miguel A. Andrade-Navarro. PDBpaint, a visualization webservice to tag protein structures with sequence annotations
2607 -- 2609Li Chen, Tsung-Han Chan, Peter L. Choyke, Elizabeth M. C. Hillman, Chong-Yung Chi, Zaver M. Bhujwalla, Ge Wang, Sean S. Wang, Zsolt Szabo, Yue Joseph Wang. in vivo dynamic contrast-enhanced imaging of complex tissues
2610 -- 2611Oana Chis, Julio R. Banga, Eva Balsa-Canto. GenSSI: a software toolbox for structural identifiability analysis of biological models
2612 -- 2613Florian Battke, Stephan Symons, Alexander Herbig, Kay Nieselt. GaggleBridge: collaborative data analysis
2614 -- 2615Xiaozeng Yang, Lei Li. miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants
2616 -- 2617Jose M. Villaveces, Rafael C. Jimenez, Leyla J. Garcia, Gustavo A. Salazar, Bernat Gel, Nicola J. Mulder, Maria Jesus Martin, Alexander García Castro, Henning Hermjakob. Dasty3, a WEB framework for DAS
2618 -- 2619Jacek Sroka, Lukasz Krupa, Andrzej M. Kierzek, Jerzy Tyszkiewicz. Taverna workbench

Volume 27, Issue 17

2325 -- 2329Adam Roberts, Harold Pimentel, Cole Trapnell, Lior Pachter. Identification of novel transcripts in annotated genomes using RNA-Seq
2330 -- 2337Fabian Menges, Giuseppe Narzisi, Bud Mishra. TotalReCaller: improved accuracy and performance via integrated alignment and base-calling
2338 -- 2345Catherine Stamoulis, Rebecca A. Betensky. A novel signal processing approach for the detection of copy number variations in the human genome
2346 -- 2353Hisanori Kiryu. Sufficient statistics and expectation maximization algorithms in phylogenetic tree models
2354 -- 2360Robert C. McLeay, Chris J. Leat, Timothy L. Bailey. Tissue-specific prediction of directly regulated genes
2361 -- 2367Peter Huggins, Shan Zhong, Idit Shiff, Rachel Beckerman, Oleg Laptenko, Carol Prives, Marcel H. Schulz, Itamar Simon, Ziv Bar-Joseph. DECOD: fast and accurate discriminative DNA motif finding
2368 -- 2375Alexander Goncearenco, Igor N. Berezovsky. Computational reconstruction of primordial prototypes of elementary functional loops in modern proteins
2376 -- 2383Miguel Rojas-Chertó, Piotr T. Kasper, Egon L. Willighagen, Rob J. Vreeken, Thomas Hankemeier, Theo H. Reijmers. Elemental composition determination based on MS:::::::n:::::::
2384 -- 2390Ivano Bertini, David A. Case, Lucio Ferella, Andrea Giachetti, Antonio Rosato. A Grid-enabled web portal for NMR structure refinement with AMBER
2391 -- 2398Mikhail Jiline, Stan Matwin, Marcel Turcotte. Annotation concept synthesis and enrichment analysis: a logic-based approach to the interpretation of high-throughput experiments
2399 -- 2405Yuichi Shiraishi, Mariko Okada-Hatakeyama, Satoru Miyano. A rank-based statistical test for measuring synergistic effects between two gene sets
2406 -- 2413Yiming Lu, Yang Zhou, Wubin Qu, Minghua Deng, Chenggang Zhang. A Lasso regression model for the construction of microRNA-target regulatory networks
2414 -- 2421Tiago J. S. Lopes, Martin Schaefer, Jason Shoemaker, Yukiko Matsuoka, Jean-Fred Fontaine, Gabriele Neumann, Miguel A. Andrade-Navarro, Yoshihiro Kawaoka, Hiroaki Kitano. Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases
2422 -- 2425Alan Tan, Ben W. Tripp, Denise Daley. BRISK - research-oriented storage kit for biology-related data
2426 -- 2428Daniel Blankenberg, James Taylor, Anton Nekrutenko, The Galaxy Team. Making whole genome multiple alignments usable for biologists
2429 -- 2430Mitchell J. Brittnacher, Christine Fong, H. S. Hayden, M. A. Jacobs, Matthew Radey, Laurence Rohmer. PGAT: a multistrain analysis resource for microbial genomes
2431 -- 2432Matthew Z. DeMaere, Federico M. Lauro, Torsten Thomas, Sheree Yau, Ricardo Cavicchioli. Simple high-throughput annotation pipeline (SHAP)
2433 -- 2434Lucian Ilie, Silvana Ilie, Anahita Mansouri Bigvand. SpEED: fast computation of sensitive spaced seeds
2435 -- 2436Brent Pedersen, Tzung-Fu Hsieh, Christian Ibarra, Robert L. Fischer. MethylCoder: software pipeline for bisulfite-treated sequences
2437 -- 2438Jonathan M. Eastman, C. E. Timothy Paine, Olivier J. Hardy. spacodiR: structuring of phylogenetic diversity in ecological communities
2439 -- 2440Martin Ryberg, R. Henrik Nilsson, P. Brandon Matheny. DivBayes and SubT: exploring species diversification using Bayesian statistics
2441 -- 2442Magdalena Rother, Kaja Milanowska, Tomasz Puton, Jaroslaw Jeleniewicz, Kristian Rother, Janusz M. Bujnicki. ModeRNA server: an online tool for modeling RNA 3D structures
2443 -- 2445J. Y. Semegni, M. Wamalwa, R. Gaujoux, G. W. Harkins, A. Gray, D. P. Martin. NASP: a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments
2446 -- 2447Francesco Ferrari, Aldo Solari, Cristina Battaglia, Silvio Bicciato. ::::PREDA::::: an R-package to identify regional variations in genomic data
2448 -- 2450Asif Javed, Marc Pybus, Marta Melé, Filippo Utro, Jaume Bertranpetit, Francesc Calafell, Laxmi Parida. IRiS: Construction of ARG networks at genomic scales
2451 -- 2452Jan Bot, Marcel J. T. Reinders. CytoscapeRPC: a plugin to create, modify and query Cytoscape networks from scripting languages
2453 -- 2454Mark Longair, Dean A. Baker, J. Douglas Armstrong. Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes
2455 -- 2456Jianguo Xia, Igor Sinelnikov, David S. Wishart. MetATT: a web-based metabolomics tool for analyzing time-series and two-factor datasets
2457 -- 2458Kevin R. Sanft, Sheng Wu, Min Roh, Jin Fu, Rone Kwei Lim, Linda R. Petzold. StochKit2: software for discrete stochastic simulation of biochemical systems with events
2459 -- 2462Andrea Pinna, Nicola Soranzo, Ina Hoeschele, Alberto de la Fuente. Simulating systems genetics data with SysGenSIM
2463 -- 2464Ulrich Bodenhofer, Andreas Kothmeier, Sepp Hochreiter. APCluster: an R package for affinity propagation clustering
2465 -- 2467Qian-Nan Hu, Zhe Deng, Huanan Hu, Dong-Sheng Cao, Yi-Zeng Liang. RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity
2468 -- 2470Natalja Kurbatova, Tomasz Adamusiak, Pavel Kurnosov, Morris A. Swertz, Misha Kapushesky. ontoCAT: an R package for ontology traversal and search
2471 -- 2472Euna Jeong, Masao Nagasaki, Emi Ikeda, Yayoi Sekiya, Ayumu Saito, Satoru Miyano. CSO validator: improving manual curation workflow for biological pathways

Volume 27, Issue 16

2173 -- 2180Danni Yu, John Danku, Ivan Baxter, Sungjin Kim, Olena K. Vatamaniuk, David E. Salt, Olga Vitek. Noise reduction in genome-wide perturbation screens using linear mixed-effect models
2181 -- 2186L. F. Stead, I. C. Wood, David R. Westhead. KvSNP: accurately predicting the effect of genetic variants in voltage-gated potassium channels
2187 -- 2193Eva-Maria Willing, Margarete Hoffmann, Juliane D. Klein, Detlef Weigel, Christine Dreyer. Paired-end RAD-seq for ::::de novo:::: assembly and marker design without available reference
2194 -- 2200Robert C. Edgar, Brian J. Haas, Jose C. Clemente, Christopher Quince, Rob Knight. UCHIME improves sensitivity and speed of chimera detection
2201 -- 2208Yong-Min Lao, Lan Xiao, Zhi-Wei Ye, Jian-guo Jiang, Shi-Shui Zhou. ::::In silico:::: analysis of phytoene synthase and its promoter reveals hints for regulation mechanisms of carotenogenesis in ::::Duanliella bardawil::::
2209 -- 2215Pradeep Kota, Feng Ding, Srinivas Ramachandran, Nikolay V. Dokholyan. Gaia: automated quality assessment of protein structure models
2216 -- 2223Seymour Knowles-Barley, Nancy J. Butcher, Ian A. Meinertzhagen, J. Douglas Armstrong. Biologically inspired EM image alignment and neural reconstruction
2224 -- 2230Castrense Savojardo, Piero Fariselli, Monther Alhamdoosh, Pier Luigi Martelli, Andrea Pierleoni, Rita Casadio. Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization
2231 -- 2238Matthias Maneck, Alexandra Schrader, Dieter Kube, Rainer Spang. Genomic data integration using guided clustering
2239 -- 2247Tobias Bauer, Roland Eils, Rainer König. RIP: the regulatory interaction predictor - a machine learning-based approach for predicting target genes of transcription factors
2248 -- 2255Stephan Symons, Kay Nieselt. MGV: a generic graph viewer for comparative omics data
2256 -- 2262Siu Hung Joshua Chan, Ping Ji. Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks
2263 -- 2270Thomas Schaffter, Daniel Marbach, Dario Floreano. GeneNetWeaver: ::::in silico:::: benchmark generation and performance profiling of network inference methods
2271 -- 2278Sanjay Joshua Swamidass, Bradley T. Calhoun, Joshua A. Bittker, Nicole E. Bodycombe, Paul A. Clemons. Enhancing the rate of scaffold discovery with diversity-oriented prioritization
2279 -- 2287Timothy Driscoll, Joseph L. Gabbard, Chunhong Mao, Oral Dalay, Maulik Shukla, Clark C. Freifeld, Anne Gatewood Hoen, John S. Brownstein, Bruno W. S. Sobral. Integration and visualization of host-pathogen data related to infectious diseases
2288 -- 2295Carissa G. Fonseca, Michael Backhaus, David A. Bluemke, Randall Britten, Jae Do Chung, Brett R. Cowan, Ivo D. Dinov, J. Paul Finn, Peter J. Hunter, Alan H. Kadish, Daniel C. Lee, Joao A. C. Lima, Pau Medrano-Gracia, Kalyanam Shivkumar, Avan Suinesiaputra, Wenchao Tao, Alistair A. Young. The Cardiac Atlas Project - an imaging database for computational modeling and statistical atlases of the heart
2296 -- 2297Yurong Xin, Yongchao Ge, Fatemeh G. Haghighi. Methyl-Analyzer - whole genome DNA methylation profiling
2298 -- 2299Chien-Hao Su, Ming-Tsung Hsu, Tse-Yi Wang, Sufeng Chiang, Jen-Hao Cheng, Francis C. Weng, Cheng-Yan Kao, Daryi Wang, Huai-Kuang Tsai. MetaABC - an integrated metagenomics platform for data adjustment, binning and clustering
2300 -- 2301Jason R. Grant, Adriano S. Arantes, Xiaoping Liao, Paul Stothard. In-depth annotation of SNPs arising from resequencing projects using NGS-SNP
2302 -- 2303Xinyi Liu, Xubo Su, Fei Wang, Zhimin Huang, Qi Wang, Zhen Li, Ruina Zhang, Lifang Wu, Yi Pan, Yingyi Chen, Hanyi Zhuang, Guoqiang Chen, Ting Shi, Jian Zhang. ODORactor: a web server for deciphering olfactory coding
2304 -- 2305Zhan Su, Jonathan Marchini, Peter Donnelly. HAPGEN2: simulation of multiple disease SNPs
2309 -- 2310Hamid Bolouri, Rajiv Dulepet, Michael Angerman. Menu-driven cloud computing and resource sharing for R and Bioconductor
2311 -- 2313Eva Balsa-Canto, Julio R. Banga. AMIGO, a toolbox for advanced model identification in systems biology using global optimization
2314 -- 2315Clemens Wrzodek, Andreas Dräger, Andreas Zell. KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats
2316 -- 2318Raphael B. M. Aggio, Silas Granato Villas-Bôas, Katya Ruggiero. Metab: an R package for high-throughput analysis of metabolomics data generated by GC-MS
2319 -- 2320Jialiang Huang, Yi Liu, Wei Zhang, Hong Yu, Jing-Dong J. Han. eResponseNet: a package prioritizing candidate disease genes through cellular pathways
2321 -- 2322Kai J. Kohlhoff, Marc H. Sosnick, William T. Hsu, Vijay S. Pande, Russ B. Altman. CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms
2323 -- 0Guy Haskin Fernald, Emidio Capriotti, Roxana Daneshjou, Konrad J. Karczewski, Russ B. Altman. Bioinformatics challenges for personalized medicine

Volume 27, Issue 15

2027 -- 2030Ofer Isakov, Shira Modai, Noam Shomron. Pathogen detection using short-RNA deep sequencing subtraction and assembly
2031 -- 2037Yong Lin, Jian Li, Hui Shen, Lei Zhang, Christopher J. Papasian, Hong-Wen Deng. Comparative studies of ::::de novo:::: assembly tools for next-generation sequencing technologies
2038 -- 2046Adam B. Olshen, Henrik Bengtsson, Pierre Neuvial, Paul T. Spellman, Richard A. Olshen, Venkatraman E. Seshan. Parent-specific copy number in paired tumor-normal studies using circular binary segmentation
2047 -- 2053Vikas Bansal, Ondrej Libiger. A probabilistic method for the detection and genotyping of small indels from population-scale sequence data
2054 -- 2061Rui Yan, Paul C. Boutros, Igor Jurisica. A tree-based approach for motif discovery and sequence classification
2062 -- 2067Shu-An Chen, Yu-Yen Ou, Tzong-Yi Lee, M. Michael Gromiha. Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties
2068 -- 2075Simon A. Berger, Alexandros Stamatakis. Aligning short reads to reference alignments and trees
2076 -- 2082Yuedong Yang, Eshel Faraggi, Huiying Zhao, Yaoqi Zhou. Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates
2083 -- 2088Zengming Zhang, Yu Li, Biaoyang Lin, Michael Schroeder, Bingding Huang. Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction
2089 -- 2097Martin Sill, Sebastian Kaiser, Axel Benner, Annette Kopp-Schneider. Robust biclustering by sparse singular value decomposition incorporating stability selection
2098 -- 2103Stan Pounds, Cuilan Lani Gao, Robert A. Johnson, Karen D. Wright, Helen Poppleton, David Finkelstein, Sarah E. S. Leary, Richard J. Gilbertson. A procedure to statistically evaluate agreement of differential expression for cross-species genomics
2104 -- 2111Harm-Jan Westra, Ritsert C. Jansen, Rudolf S. N. Fehrmann, Gerard J. te Meerman, David van Heel, Cisca Wijmenga, Lude Franke. MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects
2112 -- 2118Todd L. Edwards, Zhuo Song, Chun Li. Enriching targeted sequencing experiments for rare disease alleles
2119 -- 2126Shujie Ma, Lijian Yang, Roberto Romero, Yuehua Cui. Varying coefficient model for gene-environment interaction: a non-linear look
2127 -- 2133Luca Beltrame, Enrica Calura, Razvan R. Popovici, Lisa Rizzetto, Damariz Rivero Guedez, Michele Donato, Chiara Romualdi, Sorin Draghici, Duccio Cavalieri. The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways
2134 -- 2140Oleg Paliy, Brent D. Foy. Mathematical modeling of 16S ribosomal DNA amplification reveals optimal conditions for the interrogation of complex microbial communities with phylogenetic microarrays
2141 -- 2143Rong She, Jeffrey Shih-Chieh Chu, Bora Uyar, Jun Wang, Ke Wang, Nansheng Chen. genBlastG: using BLAST searches to build homologous gene models
2144 -- 2146Joseph K. Pickrell, Daniel J. Gaffney, Yoav Gilad, Jonathan K. Pritchard. False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions
2147 -- 2148Wing Chung Wong, Dewey Kim, Hannah Carter, Mark Diekhans, Michael C. Ryan, Rachel Karchin. CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer
2149 -- 2150Oscar Flores, Modesto Orozco. nucleR: a package for non-parametric nucleosome positioning
2151 -- 2152Thomas K. F. Wong, Kwok-Lung Wan, Bay-Yuan Hsu, Brenda W. Y. Cheung, Wing-Kai Hon, Tak Wah Lam, Siu-Ming Yiu. RNASAlign: RNA Structural Alignment System
2153 -- 2155Aurelien Ginolhac, Morten Rasmussen, M. Thomas P. Gilbert, Eske Willerslev, Ludovic Orlando. mapDamage: testing for damage patterns in ancient DNA sequences
2156 -- 2158Petr Danecek, Adam Auton, Gonçalo R. Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert E. Handsaker, Gerton Lunter, Gabor T. Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin. The variant call format and VCFtools
2159 -- 2160Luca Pireddu, Simone Leo, Gianluigi Zanetti. SEAL: a distributed short read mapping and duplicate removal tool
2161 -- 2162Mark Moll, Drew H. Bryant, Lydia E. Kavraki. The LabelHash Server and Tools for substructure-based functional annotation
2163 -- 2164Abdullah Kahraman, Lars Malmström, Ruedi Aebersold. Xwalk: computing and visualizing distances in cross-linking experiments
2165 -- 2166Augustin Luna, Margot Sunshine, Martijn P. van Iersel, Mirit I. Aladjem, Kurt W. Kohn. PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs)
2167 -- 2168Andreas Dräger, Nicolas Rodriguez, Marine Dumousseau, Alexander Dörr, Clemens Wrzodek, Nicolas Le Novère, Andreas Zell, Michael Hucka. JSBML: a flexible Java library for working with SBML
2169 -- 2170Xin-Yuan Song, Zhao-Hua Lu. Response to Comments on Bayesian variable selection for disease classification using gene expression data
2171 -- 0Susanne Balzer, Ketil Malde, Anders Lanzén, Animesh Sharma, Inge Jonassen. Characteristics of 454 pyrosequencing data - enabling realistic simulation with flowsim

Volume 27, Issue 14

1885 -- 1888Luis Sánchez-Pulido, Chris P. Ponting. Cdc45: the missing RecJ ortholog in eukaryotes?
1889 -- 1893Julien Lajugie, Eric E. Bouhassira. GenPlay, a multipurpose genome analyzer and browser
1894 -- 1900Dominic Rose, Michael Hiller, Katharina Schutt, Jörg Hackermüller, Rolf Backofen, Peter F. Stadler. Computational discovery of human coding and non-coding transcripts with conserved splice sites
1908 -- 1914Craig T. Armstrong, Thomas L. Vincent, Peter J. Green, Derek N. Woolfson. SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences
1915 -- 1921Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan. Sensitive and fast mapping of di-base encoded reads
1922 -- 1928Huanying Ge, Kejun Liu, Todd Juan, Fang Fang, Matthew Newman, Wolfgang Hoeck. FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution
1929 -- 1933Bas E. Dutilh, Rasa Jurgelenaite, Radek Szklarczyk, Sacha A. F. T. van Hijum, Harry R. Harhangi, Markus Schmid, Bart de Wild, Kees-Jan Françoijs, Henk Stunnenberg, Marc Strous, Mike S. M. Jetten, Huub J. M. Op den Camp, Martijn A. Huynen. FACIL: Fast and Accurate Genetic Code Inference and Logo
1934 -- 1940Hakim Tafer, Fabian Amman, Florian Eggenhofer, Peter F. Stadler, Ivo L. Hofacker. Fast accessibility-based prediction of RNA-RNA interactions
1941 -- 1947Haim Ashkenazy, Ron Unger, Yossef Kliger. Hidden conformations in protein structures
1948 -- 1956Riet De Smet, Kathleen Marchal. An ensemble biclustering approach for querying gene expression compendia with experimental lists
1957 -- 1963Wanding Zhou, Luay Nakhleh. The strength of chemical linkage as a criterion for pruning metabolic graphs
1964 -- 1970Gengjie Jia, Gregory Stephanopoulos, Rudiyanto Gunawan. Parameter estimation of kinetic models from metabolic profiles: two-phase dynamic decoupling method
1971 -- 1978Ales Maver, Borut Peterlin. Positional integratomic approach in identification of genomic candidate regions for Parkinson s disease
1979 -- 1985Maurice Berk, Timothy M. D. Ebbels, Giovanni Montana. A statistical framework for biomarker discovery in metabolomic time course data
1986 -- 1994Laura Tolosi, Thomas Lengauer. Classification with correlated features: unreliability of feature ranking and solutions
1995 -- 1997Yufeng Shen, Ruijie Song, Itsik Pe er. Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association
1998 -- 2000Dongliang Ge, Elizabeth K. Ruzzo, Kevin V. Shianna, Min He, Kimberly Pelak, Erin L. Heinzen, Anna C. Need, Elizabeth T. Cirulli, Jessica M. Maia, Samuel P. Dickson, Mingfu Zhu, Abanish Singh, Andrew S. Allen, David B. Goldstein. SVA: software for annotating and visualizing sequenced human genomes
2001 -- 2002Peter V. Troshin, James B. Procter, Geoffrey J. Barton. Java bioinformatics analysis web services for multiple sequence alignment - JABAWS: MSA
2003 -- 2005Alberto J. M. Martin, Michele Vidotto, Filippo Boscariol, Tomàs Di Domenico, Ian Walsh, Silvio C. E. Tosatto. RING: networking interacting residues, evolutionary information and energetics in protein structures
2006 -- 2008Chunfa Tong, Zhong Wang, Bo Zhang, Jisen Shi, Rongling Wu. 3FunMap: full-sib family functional mapping of dynamic traits
2009 -- 2010Stefan Gretar Thorleifsson, Ines Thiele. rBioNet: A COBRA toolbox extension for ::::r::::econstructing high-quality ::::bio::::chemical ::::net::::works
2011 -- 2012Alex T. Kalinka, Pavel Tomancak. linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type
2013 -- 2014Nicolas Rapin, Ole Lund, Filippo Castiglione. Immune system simulation online
2015 -- 2017Supawadee Ingsriswang, Sunai Yokwai, Duangdao Wichadakul. LinkinPath: from sequence to interconnected pathway
2018 -- 2020David Lagorce, Julien Maupetit, Jonathan B. Baell, Olivier Sperandio, Pierre Tufféry, Maria A. Miteva, Hervé Galons, Bruno O. Villoutreix. The FAF-Drugs2 server: a multistep engine to prepare electronic chemical compound collections
2021 -- 2022Katy Wolstencroft, Stuart Owen, Matthew Horridge, Olga Krebs, Wolfgang Mueller, Jacky L. Snoep, Franco du Preez, Carole A. Goble. RightField: embedding ontology annotation in spreadsheets
2023 -- 2024Sudhir Kumar, S. Blair Hedges. TimeTree2: species divergence times on the iPhone
2025 -- 2026Jonathan D. Wren. Question answering systems in biology and medicine - the time is now

Volume 27, Issue 13

7 -- 14Denis C. Bauer, Kai Willadsen, Fabian A. Buske, Kim-Anh Lê Cao, Timothy L. Bailey, Graham Dellaire, Mikael Bodén. Sorting the nuclear proteome
15 -- 23Jamie R. Hill, Sebastian Kelm, Jiye Shi, Charlotte M. Deane. Environment specific substitution tables improve membrane protein alignment
24 -- 33Marcin J. Mizianty, Lukasz A. Kurgan. Sequence-based prediction of protein crystallization, purification and production propensity
34 -- 42Charles W. O Donnell, Jérôme Waldispühl, Mieszko Lis, Randal Halfmann, Srinivas Devadas, Susan Lindquist, Bonnie Berger. A method for probing the mutational landscape of amyloid structure
43 -- 51Arun Siddharth Konagurthu, Lloyd Allison, Peter J. Stuckey, Arthur M. Lesk. Piecewise linear approximation of protein structures using the principle of minimum message length
52 -- 60Andrej J. Savol, Virginia M. Burger, Pratul K. Agarwal, Arvind Ramanathan, Chakra Chennubhotla. QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin
61 -- 68S. Shivashankar, S. Srivathsan, B. Ravindran, Ashish V. Tendulkar. Multi-view methods for protein structure comparison using latent dirichlet allocation
69 -- 76Min Xu, Martin Beck, Frank Alber. Template-free detection of macromolecular complexes in cryo electron tomograms
77 -- 84André Altmann, Peter Weber, Carina Quast, Monika Rex-Haffner, Elisabeth B. Binder, Bertram Müller-Myhsok. vipR: variant identification in pooled DNA using R
85 -- 93Kengo Sato, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu, Kiyoshi Asai. IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming
94 -- 101Yu Peng, Henry C. M. Leung, Siu-Ming Yiu, Francis Y. L. Chin. Meta-IDBA: a ::::de Novo:::: assembler for metagenomic data
102 -- 110Zhiyong Wang, Jinbo Xu. A conditional random fields method for RNA sequence-structure relationship modeling and conformation sampling
111 -- 119Yoshimasa Tsuruoka, Makoto Miwa, Kaisei Hamamoto, Jun-ichi Tsujii, Sophia Ananiadou. Discovering and visualizing indirect associations between biomedical concepts
120 -- 128Sanmitra Bhattacharya, Viet Ha-Thuc, Padmini Srinivasan. MeSH: a window into full text for document summarization
129 -- 136Christian Höner zu Siederdissen, Stephan H. F. Bernhart, Peter F. Stadler, Ivo L. Hofacker. A folding algorithm for extended RNA secondary structures
137 -- 141Paul Medvedev, Eric Scott, Boyko Kakaradov, Pavel A. Pevzner. Error correction of high-throughput sequencing datasets with non-uniform coverage
142 -- 148Regev Schweiger, Michal Linial, Nathan Linial. Generative probabilistic models for protein-protein interaction networks - the biclique perspective
149 -- 158Günhan Gülsoy, Tamer Kahveci. RINQ: Reference-based Indexing for Network Queries
159 -- 166Zhipeng Xie, Chee Keong Kwoh, Xiaoli Li, Min Wu. Construction of co-complex score matrix for protein complex prediction from AP-MS data
167 -- 176Yong Chen, Tao Jiang, Rui Jiang. Uncover disease genes by maximizing information flow in the phenome-interactome network
177 -- 185Noa Novershtern, Aviv Regev, Nir Friedman. Physical Module Networks: an integrative approach for reconstructing transcription regulation
186 -- 195Sara Berthoumieux, Matteo Brilli, Hidde de Jong, Daniel Kahn, Eugenio Cinquemani. Identification of metabolic network models from incomplete high-throughput datasets
196 -- 204Ankur P. Parikh, Wei Wu, Ross E. Curtis, Eric P. Xing. TREEGL: reverse engineering tree-evolving gene networks underlying developing biological lineages
205 -- 213Phuong Dao, Kendric Wang, Colin Collins, Martin Ester, Anna Lapuk, Süleyman Cenk Sahinalp. Optimally discriminative subnetwork markers predict response to chemotherapy
214 -- 221Tony Kam-Thong, Benno Pütz, Nazanin Karbalai, Bertram Müller-Myhsok, Karsten M. Borgwardt. Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs
222 -- 229Jing Li, Benjamin Horstman, Yixuan Chen. Detecting epistatic effects in association studies at a genomic level based on an ensemble approach
230 -- 238Theodore Alexandrov, Jan Hendrik Kobarg. Efficient spatial segmentation of large imaging mass spectrometry datasets with spatially aware clustering
239 -- 247Hanchuan Peng, Fuhui Long, Gene Myers. Automatic 3D neuron tracing using all-path pruning
248 -- 256Celine Scornavacca, Franziska Zickmann, Daniel H. Huson. Tanglegrams for rooted phylogenetic trees and networks
257 -- 265Haris Gavranovic, Cedric Chauve, Jérôme Salse, Eric Tannier. Mapping ancestral genomes with massive gene loss: A matrix sandwich problem
266 -- 274Javad Sadri, Abdoulaye Baniré Diallo, Mathieu Blanchette. Predicting site-specific human selective pressure using evolutionary signatures
275 -- 282Michael F. Lin, Irwin Jungreis, Manolis Kellis. PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions
283 -- 287Nicola Bonzanni, Nianshu Zhang, Stephen G. Oliver, Jasmin Fisher. The role of proteosome-mediated proteolysis in modulating potentially harmful transcription factor activity in ::::Saccharomyces cerevisiae::::
288 -- 294Nicholas A. Furlotte, Hyun Min Kang, Chun Ye, Eleazar Eskin. Mixed-model coexpression: calculating gene coexpression while accounting for expression heterogeneity
295 -- 303Michael B. Mayhew, Joshua W. Robinson, Boyoun Jung, Steven B. Haase, Alexander J. Hartemink. A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments
304 -- 309Susanne Balzer, Ketil Malde, Inge Jonassen. Systematic exploration of error sources in pyrosequencing flowgram data
310 -- 316Guangxu Jin, Hong Zhao, Xiaobo Zhou, Stephen T. C. Wong. An enhanced Petri-net model to predict synergistic effects of pairwise drug combinations from gene microarray data
317 -- 323David Golan, Saharon Rosset. Accurate estimation of heritability in genome wide studies using random effects models
324 -- 332Suyash Shringarpure, Daegun Won, Eric P. Xing. StructHDP: automatic inference of number of clusters and population structure from admixed genotype data
333 -- 341Sofia Kyriazopoulou-Panagiotopoulou, Dorna Kashef Haghighi, Sarah J. Aerni, Andreas Sundquist, Sivan Bercovici, Serafim Batzoglou. Reconstruction of genealogical relationships with applications to Phase III of HapMap
342 -- 348Limin Li, Barbara Rakitsch, Karsten M. Borgwardt. ccSVM: correcting Support Vector Machines for confounding factors in biological data classification
349 -- 356Filipe Santana, Daniel Schober, Zulma Medeiros, Fred Freitas, Stefan Schulz. Ontology patterns for tabular representations of biomedical knowledge on neglected tropical diseases
357 -- 365Henning Redestig, Ivan G. Costa. Detection and interpretation of metabolite-transcript coresponses using combined profiling data
366 -- 373Ludwig Geistlinger, Gergely Csaba, Robert Küffner, Nicola J. Mulder, Ralf Zimmer. From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems
374 -- 382Edoardo M. Airoldi, Katherine A. Heller, Ricardo Silva. Small sets of interacting proteins suggest functional linkage mechanisms via Bayesian analogical reasoning
383 -- 391Pawel P. Labaj, Germán G. Leparc, Bryan E. Linggi, Lye Meng Markillie, H. Steven Wiley, David P. Kreil. Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling
392 -- 400Julia Sivriver, Naomi Habib, Nir Friedman. An integrative clustering and modeling algorithm for dynamical gene expression data
401 -- 409Shihua Zhang, Qingjiao Li, Juan Liu, Xianghong Jasmine Zhou. A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules
1741 -- 1748Guy Haskin Fernald, Emidio Capriotti, Roxana Daneshjou, Konrad J. Karczewski, Russ B. Altman. Genome Analysis
1749 -- 1753Yong E. Zhang, Maria D. Vibranovski, Benjamin H. Krinsky, Manyuan Long. A cautionary note for retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes
1754 -- 1757Roberto Chignola, Vladislav Vyshemirsky, Marcello Farina, Alessio Del Fabbro, Edoardo Milotti. Modular model of TNFα cytotoxicity
1758 -- 1764Zhiming Dai, Xianhua Dai, Qian Xiang. Genome-wide DNA sequence polymorphisms facilitate nucleosome positioning in yeast
1765 -- 1771Josue Samayoa, Fitnat H. Yildiz, Kevin Karplus. Identification of prokaryotic small proteins using a comparative genomic approach
1772 -- 1779Qiwei Li, Xiaodan Fan, Tong Liang, Shuo-Yen Robert Li. An MCMC algorithm for detecting short adjacent repeats shared by multiple sequences
1780 -- 1787Tzong-Yi Lee, Zong-Qing Lin, Sheng-Jen Hsieh, Neil Arvin Bretaña, Cheng-Tsung Lu. Exploiting maximal dependence decomposition to identify conserved motifs from a group of aligned signal sequences
1788 -- 1797Hisanori Kiryu, Goro Terai, Osamu Imamura, Hiroyuki Yoneyama, Kenji Suzuki, Kiyoshi Asai. A detailed investigation of accessibilities around target sites of siRNAs and miRNAs
1798 -- 1805Sungroh Yoon, Jinkyu Kim, Justine Hum, Hanjoo Kim, Seunghyun Park, Wipapat Kladwang, Rhiju Das. HiTRACE: high-throughput robust analysis for capillary electrophoresis
1806 -- 1813Ferenc Zsila, Zsolt Bikadi, David Malik, Peter Hari, Imre Pechan, Attila Bérces, Eszter Hazai. Evaluation of drug-human serum albumin binding interactions with support vector machine aided online automated docking
1814 -- 1821Tingjun Hou, Youyong Li, Wei Wang. Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy
1822 -- 1831Lori A. Dalton, Edward R. Dougherty. Application of the Bayesian MMSE estimator for classification error to gene expression microarray data
1832 -- 1838Sushmita Roy, Margaret Werner-Washburne, Terran Lane. A multiple network learning approach to capture system-wide condition-specific responses
1839 -- 1845Hendrik Rohn, Christian Klukas, Falk Schreiber. Creating views on integrated multidomain data
1846 -- 1853Jaegyoon Ahn, Youngmi Yoon, Chihyun Park, Eunji Shin, Sanghyun Park. Integrative gene network construction for predicting a set of complementary prostate cancer genes
1854 -- 1859Charles Jackson, Estelle Glory-Afshar, Robert F. Murphy, Jelena Kovacevic. Model building and intelligent acquisition with application to protein subcellular location classification
1860 -- 1866Jesse Gillis, Paul Pavlidis. The role of indirect connections in gene networks in predicting function
1867 -- 1868Clifford A. Meyer, Housheng H. He, Myles Brown, X. Shirley Liu. BINOCh: binding inference from nucleosome occupancy changes
1869 -- 1870Brian Walenz, Liliana Florea. Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing
1871 -- 1872Fernando Muñiz-Fernandez, Angel Carreño-Torres, Carlos Morcillo-Suarez, Arcadi Navarro. Genome-wide association studies pipeline (GWASpi): a desktop application for genome-wide SNP analysis and management
1873 -- 1875Hariklia Eleftherohorinou, Johanna C. Andersson-Assarsson, Robin G. Walters, Julia S. El-Sayed Moustafa, Lachlan J. M. Coin, Peter Jacobson, Lena M. S. Carlsson, Alexandra I. F. Blakemore, Philippe Froguel, Andrew J. Walley, Mario Falchi. famCNV: copy number variant association for quantitative traits in families
1876 -- 1877Gabriele Sales, Chiara Romualdi. ::::parmigene:::: - a parallel R package for mutual information estimation and gene network reconstruction
1878 -- 1879Matti Kankainen, Peddinti V. Gopalacharyulu, Liisa Holm, Matej Oresic. MPEA - metabolite pathway enrichment analysis
1880 -- 1881Ross E. Curtis, Amos Yuen, Le Song, Anuj Goyal, Eric P. Xing. TVNViewer: An interactive visualization tool for exploring networks that change over time or space
1882 -- 1883Sebastian Bauer, Peter N. Robinson, Julien Gagneur. Model-based gene set analysis for Bioconductor

Volume 27, Issue 12

1595 -- 1602Michael C. Wendl, John W. Wallis, Ling Lin, Cyriac Kandoth, Elaine R. Mardis, Richard K. Wilson, Li Ding. PathScan: a tool for discerning mutational significance in groups of putative cancer genes
1603 -- 1609Emi Tanaka, Timothy L. Bailey, Charles E. Grant, William Stafford Noble, Uri Keich. Improved similarity scores for comparing motifs
1610 -- 1617Justin Bedo, Adam Kowalczyk. Genome annotation test with validation on transcription start site and ChIP-Seq for Pol-II binding data
1618 -- 1624Peter Meinicke, Kathrin Petra Aßhauer, Thomas Lingner. Mixture models for analysis of the taxonomic composition of metagenomes
1625 -- 1629Matteo Floris, Domenico Raimondo, Guido Leoni, Massimiliano Orsini, Paolo Marcatili, Anna Tramontano. MAISTAS: a tool for automatic structural evaluation of alternative splicing products
1630 -- 1636Ali Abdul-Gader, Andrew John Miles, B. A. Wallace. A reference dataset for the analyses of membrane protein secondary structures and transmembrane residues using circular dichroism spectroscopy
1637 -- 1644Cheng Zheng, Shucha Zhang, Susanne Ragg, Daniel Raftery, Olga Vitek. Identification and quantification of metabolites in :::1:::H NMR spectra by Bayesian model selection
1645 -- 1652Michael Seifert, Marc Strickert, Alexander Schliep, Ivo Grosse. Exploiting prior knowledge and gene distances in the analysis of tumor expression profiles with extended Hidden Markov Models
1653 -- 1659Timothy L. Bailey. DREME: motif discovery in transcription factor ChIP-seq data
1660 -- 1666Seongho Kim, Aiqin Fang, Bing Wang, Jaesik Jeong, Xiang Zhang. An optimal peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using mixture similarity measure
1667 -- 1674Senol Isci, Cengizhan Ozturk, Jon Jones, Hasan H. Otu. Pathway analysis of high-throughput biological data within a Bayesian network framework
1675 -- 1683Mohammadmahdi R. Yousefi, Jianping Hua, Edward R. Dougherty. Multiple-rule bias in the comparison of classification rules
1684 -- 1690Olga Ivchenko, Erfan Younesi, Mohammad Shahid, Antje Wolf, Bernd Müller, Martin Hofmann-Apitius. PLIO: an ontology for formal description of protein-ligand interactions
1691 -- 1692Derek W. Barnett, Erik K. Garrison, Aaron R. Quinlan, Michael Strömberg, Gabor T. Marth. BamTools: a C++ API and toolkit for analyzing and managing BAM files
1693 -- 1695Camille Sabbah, Gildas Mazo, Caroline Paccard, Fabien Reyal, Philippe Hupé. SMETHILLIUM: spatial normalization METHod for ILLumina InfinIUM HumanMethylation BeadChip
1696 -- 1697Philip Machanick, Timothy L. Bailey. MEME-ChIP: motif analysis of large DNA datasets
1698 -- 1699Irina Ostrovnaya, Venkatraman E. Seshan, Adam B. Olshen, Colin B. Begg. Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles
1700 -- 1701Daniel Beck, Matt Settles, James A. Foster. OTUbase: an R infrastructure package for operational taxonomic unit data
1702 -- 1703Nanjiang Shu, Arne Elofsson. KalignP: Improved multiple sequence alignments using position specific gap penalties in Kalign2
1704 -- 1705Beifang Niu, Zhengwei Zhu, LiMin Fu, Sitao Wu, Weizhong Li. FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes
1706 -- 1707Jesse Stombaugh, Jeremy Widmann, Daniel McDonald, Rob Knight. Boulder ALignment Editor (ALE): a web-based RNA alignment tool
1708 -- 1710Yang Li, Jeremy Chien, David I. Smith, Jian Ma. FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq
1711 -- 1712Joost J. J. van Durme, Javier Delgado, Francois Stricher, Luis Serrano, Joost Schymkowitz, Frederic Rousseau. A graphical interface for the FoldX forcefield
1713 -- 1714Fabien Mareuil, Christophe Blanchet, Therese E. Malliavin, Michael Nilges. Grid computing for improving conformational sampling in NMR structure calculation
1715 -- 1716Zheng Wang, Jesse Eickholt, Jianlin Cheng. APOLLO: a quality assessment service for single and multiple protein models
1717 -- 1718Tiago Antao, Mark A. Beaumont. Mcheza: a workbench to detect selection using dominant markers
1719 -- 1720Ola Spjuth, Martin Eklund, Maris Lapinsh, Muhammad Junaid, Jarl E. S. Wikberg. Services for prediction of drug susceptibility for HIV proteases and reverse transcriptases at the HIV drug research centre
1721 -- 1722Wen Xu, Adam M. Smith, James R. Faeder, G. Elisabeta Marai. RuleBender: a visual interface for rule-based modeling
1723 -- 1724Shashank Agarwal, Hong Yu. Figure summarizer browser extensions for PubMed Central
1725 -- 1726Joachim von Eichborn, Philip E. Bourne, Robert Preissner. Cobweb: a Java applet for network exploration and visualisation
1727 -- 1728Woonghee Lee, Jin Hae Kim, William M. Westler, John L. Markley. PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination
1729 -- 1730Vlad Popovici, Eva Budinska, Mauro Delorenzi. Rgtsp: a generalized top scoring pairs package for class prediction
1731 -- 1733Kangseok Kim, Wonil Kim, Sunshin Kim. ReMark: an automatic program for clustering orthologs flexibly combining a Recursive and a Markov clustering algorithms
1734 -- 1735Dominic S. Lütjohann, Asmi H. Shah, Michael P. Christen, Florian Richter, Karsten Knese, Urban Liebel. Sciencenet - towards a global search and share engine for all scientific knowledge
1736 -- 1738Ashok Reddy Dinasarapu, Brian Saunders, Iley Ozerlat, Kenan Azam, Shankar Subramaniam. Signaling gateway molecule pages - a data model perspective
1739 -- 1740Arthur Liberzon, Aravind Subramanian, Reid Pinchback, Helga Thorvaldsdóttir, Pablo Tamayo, Jill P. Mesirov. Molecular signatures database (MSigDB) 3.0

Volume 27, Issue 11

1455 -- 1461Leena Salmela, Jan Schröder. Correcting errors in short reads by multiple alignments
1462 -- 1465Gibran Hemani, Athanasios Theocharidis, Wenhua Wei, Chris S. Haley. EpiGPU: exhaustive pairwise epistasis scans parallelized on consumer level graphics cards
1466 -- 1472Mirjana Domazet-Loso, Bernhard Haubold. Alignment-free detection of local similarity among viral and bacterial genomes
1473 -- 1480Guoqiang Yu, Bai Zhang, G. Steven Bova, Jianfeng Xu, Ie-Ming Shih, Yue Wang. BACOM: ::::in silico:::: detection of genomic deletion types and correction of normal cell contamination in copy number data
1481 -- 1488Andrew McPherson, Chunxiao Wu, Iman Hajirasouliha, Fereydoun Hormozdiari, Faraz Hach, Anna Lapuk, Stanislav Volik, Sohrab Shah, Colin Collins, Süleyman Cenk Sahinalp. Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data
1489 -- 1495Henry C. M. Leung, Siu-Ming Yiu, Bin Yang, Yu Peng, Yi Wang, Zhihua Liu, Jing-Chi Chen, Junjie Qin, Ruiqiang Li, Francis Y. L. Chin. A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio
1496 -- 1505Andrew E. Teschendorff, Joanna Zhuang, Martin Widschwendter. Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies
1506 -- 1512Bin Wang, Xiao Feng Wang, Yaguang Xi. Normalizing bead-based microRNA expression data: a measurement error model-based approach
1513 -- 1520Dan He, Farhad Hormozdiari, Nicholas A. Furlotte, Eleazar Eskin. Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions
1521 -- 1528Qianghu Wang, Jie Sun, Meng Zhou, Haixiu Yang, Yan Li, Xiang Li, Sali Lv, Xia Li, Yixue Li. A novel network-based method for measuring the functional relationship between gene sets
1529 -- 1536Markus Maucher, Barbara Kracher, Michael Kühl, Hans A. Kestler. Inferring Boolean network structure via correlation
1537 -- 1545Fangping Mu, Clifford J. Unkefer, Pat J. Unkefer, William S. Hlavacek. Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds
1546 -- 1554Kai Christian Bader, Christian Grothoff, Harald Meier. Comprehensive and relaxed search for oligonucleotide signatures in hierarchically clustered sequence datasets
1555 -- 1561Teo Shu Mei, Yudi Pawitan, Vikrant Kumar, Anbupalam Thalamuthu, Mark Seielstad, Kee Seng Chia, Agus Salim. Multi-platform segmentation for joint detection of copy number variants
1562 -- 1568Ward Blondé, Vladimir Mironov, Aravind Venkatesan, Erick Antezana, Bernard De Baets, Martin Kuiper. Reasoning with bio-ontologies: using relational closure rules to enable practical querying
1569 -- 1570Cenny Taslim, Tim Hui-Ming Huang, Shili Lin. DIME: R-package for identifying differential ChIP-seq based on an ensemble of mixture models
1571 -- 1572Felix Krueger, Simon R. Andrews. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
1573 -- 1574Corinna Vehlow, Henning Stehr, Matthias Winkelmann, Jose M. Duarte, Lars Petzold, Juliane Dinse, Michael Lappe. CMView: Interactive contact map visualization and analysis
1575 -- 1577Ahmet Bakan, Lidio M. Meireles, Ivet Bahar. ::::ProDy::::: Protein Dynamics Inferred from Theory and Experiments
1578 -- 1580Tian Xia, John L. Van Hemert, Julie A. Dickerson. CytoModeler: a tool for bridging large-scale network analysis and dynamic quantitative modeling
1581 -- 1582Deguo Xia, Haoran Zheng, Zhiqiang Liu, Guisheng Li, Jinlong Li, Jiong Hong, Kai Zhao. MRSD: a web server for Metabolic Route Search and Design
1583 -- 1584Ahmet Emre Aladag, Cesim Erten, Melih Sözdinler. Reliability-Oriented bioinformatic networks visualization
1585 -- 1586Ambarish Biswas, Raghuraj Rao, Shivshankar Umashankar, Kalyan C. Mynampati, Sheela Reuben, Gauri Parab, Sanjay Swarup. datPAV - an online processing, analysis and visualization tool for exploratory investigation of experimental data
1587 -- 1588Pieter Audenaert, Thomas Van Parys, Florian Brondel, Mario Pickavet, Piet Demeester, Yves Van de Peer, Tom Michoel. CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks
1589 -- 1590Soumya Raychaudhuri. VIZ-GRAIL: visualizing functional connections across disease loci
1591 -- 1593Masao Nagasaki, Ayumu Saito, André Fujita, Georg Tremmel, Kazuko Ueno, Emi Ikeda, Euna Jeong, Satoru Miyano. Systems biology model repository for macrophage pathway simulation

Volume 27, Issue 10

1345 -- 0Olli-P. Kallioniemi, Lodewyk Wessels, Alfonso Valencia. On the organization of bioinformatics core services in biology-based research institutes
1346 -- 1350Daniel C. Ellwanger, Florian A. Büttner, Hans-Werner Mewes, Volker Stümpflen. The sufficient minimal set of miRNA seed types
1351 -- 1358Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jörn Kalinowski, Jens Stoye, Alexander Goesmann. Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming
1359 -- 1367W. Timothy J. White, Barbara R. Holland. Faster exact maximum parsimony search with XMP
1368 -- 1376Ping Xuan, Maozu Guo, Xiaoyan Liu, Yangchao Huang, Wenbin Li, Yufei Huang. ::::PlantMiRNAPred::::: efficient classification of real and pseudo plant pre-miRNAs
1377 -- 1383Klaus Jung, Benjamin Becker, Edgar Brunner, Tim Beißbarth. Comparison of global tests for functional gene sets in two-group designs and selection of potentially effect-causing genes
1384 -- 1389Erdal Cosgun, Nita A. Limdi, Christine W. Duarte. High-dimensional pharmacogenetic prediction of a continuous trait using machine learning techniques with application to warfarin dose prediction in African Americans
1390 -- 1396Oleksii Kuchaiev, Natasa Przulj. Integrative network alignment reveals large regions of global network similarity in yeast and human
1397 -- 1403Georg Basler, Oliver Ebenhöh, Joachim Selbig, Zoran Nikoloski. Mass-balanced randomization of metabolic networks
1404 -- 1412Martial Sankar, Karen S. Osmont, Jakub Rolcik, Bojan Gujas, Danuse Tarkowska, Miroslav Strnad, Ioannis Xenarios, Christian S. Hardtke. A qualitative continuous model of cellular auxin and brassinosteroid signaling and their crosstalk
1413 -- 1421Christophe Bécavin, Nicolas Tchitchek, Colette Mintsa-Eya, Annick Lesne, Arndt Benecke. Improving the efficiency of multidimensional scaling in the analysis of high-dimensional data using singular value decomposition
1422 -- 1428Hei-Chia Wang, Yi-Hsiu Chen, Hung-Yu Kao, Shaw-Jenq Tsai. Inference of transcriptional regulatory network by bootstrapping patterns
1429 -- 1435Lauren Becnel Boyd, Scott P. Hunicke-Smith, Grace A. Stafford, Elaine T. Freund, Michele Ehlman, Uma Chandran, Robert Dennis, Anna T. Fernandez, Stephen Goldstein, David Steffen, Benjamin Tycko, Juli D. Klemm. The caBIG® Life Science Business Architecture Model
1436 -- 1437Yuanwei Zhang, Yifan Yang, Huan Zhang, Xiaohua Jiang, Bo Xu, Yu Xue, Yunxia Cao, Qian Zhai, Yong Zhai, Mingqing Xu, Howard J. Cooke, Qinghua Shi. Prediction of novel pre-microRNAs with high accuracy through boosting and SVM
1438 -- 1439Timothy Nugent, Sean Ward, David T. Jones. The MEMPACK alpha-helical transmembrane protein structure prediction server
1440 -- 1441Ola Larsson, Nahum Sonenberg, Robert Nadon. ::::anota::::: analysis of differential translation in genome-wide studies
1442 -- 1443Marc Johannes, Holger Fröhlich, Holger Sültmann, Tim Beißbarth. pathClass: an R-package for integration of pathway knowledge into support vector machines for biomarker discovery
1444 -- 1446Xinan Yang, Jianrong Li, Younghee Lee, Yves A. Lussier. ::::GO-Module::::: functional synthesis and improved interpretation of Gene Ontology patterns
1447 -- 1448Li Chen, George Wu, Hongkai Ji. hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data

Volume 27, Issue 1

1 -- 8Qianchuan He, Dan-Yu Lin. A variable selection method for genome-wide association studies
9 -- 13Maria Elena Sana, Maria Iascone, Daniela Marchetti, Jeff Palatini, Marco Galasso, Stefano Volinia. GAMES identifies and annotates mutations in next-generation sequencing projects
14 -- 21Dong Seon Kim, Yoonsoo Hahn. Identification of human-specific transcript variants induced by DNA insertions in the human genome
22 -- 30Monzoorul Haque Mohammed, Tarini Shankar Ghosh, Nitin Kumar Singh, Sharmila S. Mande. SPHINX - an algorithm for taxonomic binning of metagenomic sequences
31 -- 37Yuheng Li, Nicholas Chia, Mario Lauria, Ralf Bundschuh. A performance enhanced PSI-BLAST based on hybrid alignment
38 -- 45Jaime Huerta-Cepas, Toni Gabaldón. Assigning duplication events to relative temporal scales in genome-wide studies
46 -- 54R. Dustin Schaeffer, Amanda L. Jonsson, Andrew M. Simms, Valerie Daggett. Generation of a consensus protein domain dictionary
55 -- 62Chandrajit L. Bajaj, Rezaul Alam Chowdhury, Muhibur Rasheed. A dynamic data structure for flexible molecular maintenance and informatics
63 -- 69Haimao Zhan, Xin Chen, Shizhong Xu. A stochastic expectation and maximization algorithm for detecting quantitative trait-associated genes
70 -- 77Johannes M. Freudenberg, Siva Sivaganesan, Mukta Phatak, Kaustubh Shinde, Mario Medvedovic. Generalized random set framework for functional enrichment analysis using primary genomics datasets
78 -- 86Sunghee Oh, Dongwan D. Kang, Guy N. Brock, George C. Tseng. Biological impact of missing-value imputation on downstream analyses of gene expression profiles
87 -- 94Vanya Van Belle, Kristiaan Pelckmans, Sabine Van Huffel, Johan A. K. Suykens. Improved performance on high-dimensional survival data by application of Survival-SVM
95 -- 102Peilin Jia, SiYuan Zheng, Jirong Long, Wei Zheng, Zhongming Zhao. dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks
103 -- 110Nidhal Bouaynaya, Roman Shterenberg, Dan Schonfeld. Inverse perturbation for optimal intervention in gene regulatory networks
111 -- 117Guy Geva, Roded Sharan. Identification of protein complexes from co-immunoprecipitation data
118 -- 126Shi Yu, Xinhai Liu, Léon-Charles Tranchevent, Wolfgang Glänzel, Johan A. K. Suykens, Bart De Moor, Yves Moreau. Optimized data fusion for K-means Laplacian clustering
127 -- 129Gail L. Rosen, Erin R. Reichenberger, Aaron M. Rosenfeld. NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads
130 -- 131Timo Lassmann, Yoshihide Hayashizaki, Carsten O. Daub. SAMStat: monitoring biases in next generation sequencing data
132 -- 133Jean-Christophe Gelly, Alexandre G. de Brevern. Protein Peeling 3D: new tools for analyzing protein structures
134 -- 136Ryan Abo, Stacey Knight, Alun Thomas, Nicola J. Camp. Automated construction and testing of multi-locus gene-gene associations
137 -- 139Fernando García-Alcalde, Federico García-López, Joaquín Dopazo, Ana Conesa. Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data
140 -- 141Laurin A. J. Mueller, Karl G. Kugler, Andreas Dander, Armin Graber, Matthias Dehmer. QuACN: an R package for analyzing complex biological networks quantitatively
142 -- 143Ronan M. T. Fleming, Ines Thiele. von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models
144 -- 146Paul Martin, Anne Barton, Stephen Eyre. ASSIMILATOR: a new tool to inform selection of associated genetic variants for functional studies