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ORCIDBioinformatics, Volume 28
Volume 28, Number 1, January 2012
- Yang Chen, Jin Gu
, Dan Li, Shao Li:
Time-course network analysis reveals TNF-α can promote G1/S transition of cell cycle in vascular endothelial cells. 1-4
- Minzhu Xie, Jing Li, Tao Jiang:
Detecting genome-wide epistases based on the clustering of relatively frequent items. 5-12
- Guohui Yao, Liang Ye, Hongyu Gao, Patrick Minx, Wesley C. Warren, George M. Weinstock:
Graph accordance of next-generation sequence assemblies. 13-16 - David Langenberger, Sachin Pundhir, Claus Thorn Ekstrøm, Peter F. Stadler, Steve Hoffmann, Jan Gorodkin:
deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns. 17-24 - Natsuhiro Ichinose, Tetsushi Yada, Osamu Gotoh:
Large-scale motif discovery using DNA Gray code and equiprobable oligomers. 25-31 - Dapeng Li, Tonghua Li, Peisheng Cong, Wenwei Xiong, Jiangming Sun:
A novel structural position-specific scoring matrix for the prediction of protein secondary structures. 32-39 - Arief Gusnanto, Henry M. Wood, Yudi Pawitan, Pamela Rabbitts, Stefano Berri:
Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data. 40-47
- Ryan M. Ames, Daniel Money, Vikramsinh P. Ghatge, Simon Whelan, Simon C. Lovell:
Determining the evolutionary history of gene families. 48-55
- Gabriel Cuéllar-Partida, Fabian A. Buske, Robert C. McLeay, Tom Whitington, William Stafford Noble, Timothy L. Bailey:
Epigenetic priors for identifying active transcription factor binding sites. 56-62 - Ming Hu, Yu Zhu, Jeremy M. G. Taylor, Jun S. Liu, Zhaohui S. Qin:
Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq. 63-68
- Stefan Maetschke, Martin Simonsen, Melissa J. Davis, Mark A. Ragan:
Gene Ontology-driven inference of protein-protein interactions using inducers. 69-75 - Nicola Soranzo, Fahimeh Ramezani, Giovanni Iacono, Claudio Altafini:
Decompositions of large-scale biological systems based on dynamical properties. 76-83 - Emmanuelle Becker, Benoît Robisson, Charles E. Chapple, Alain Guénoche, Marie-Christine Brun:
Multifunctional proteins revealed by overlapping clustering in protein interaction network. 84-90 - Muhammad Tahir, Asifullah Khan, Abdul Majid:
Protein subcellular localization of fluorescence imagery using spatial and transform domain features. 91-97 - Xiujun Zhang, Xing-Ming Zhao, Kun He, Le Lu, Yongwei Cao, Jingdong Liu, Jin-Kao Hao, Zhi-Ping Liu, Luonan Chen:
Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information. 98-104 - Edward Y. Chen, Huilei Xu, Simon Gordonov, Maribel P. Lim, Matthew H. Perkins, Avi Ma'ayan:
Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. 105-111
- Daniel J. Stekhoven, Peter Bühlmann:
MissForest - non-parametric missing value imputation for mixed-type data. 112-118
- Xavier Rafael Palou, Michael P. Schroeder, Núria López-Bigas:
SVGMap: configurable image browser for experimental data. 119-120 - Kun Liang, Sündüz Keles:
Detecting differential binding of transcription factors with ChIP-seq. 121-122 - Francesco Vezzi, Cristian Del Fabbro, Alexandru I. Tomescu, Alberto Policriti:
rNA: a fast and accurate short reads numerical aligner. 123-124
- Yongan Zhao, Haixu Tang, Yuzhen Ye:
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. 125-126 - Manal Kalkatawi, Farania Rangkuti, Michael Schramm, Boris R. Jankovic, Allan Kamau, Rajesh Chowdhary, John A. C. Archer, Vladimir B. Bajic:
Dragon PolyA Spotter: predictor of poly(A) motifs within human genomic DNA sequences. 127-129 - Marc Torrent, Paolo Di Tommaso, David Pulido, Victòria M. Nogués, Cédric Notredame, Ester Boix, David Andreu:
AMPA: an automated web server for prediction of protein antimicrobial regions. 130-131 - Mattia C. F. Prosperi, Marco Salemi:
QuRe: software for viral quasispecies reconstruction from next-generation sequencing data. 132-133
- Céline Bellenguez, Amy Strange, Colin Freeman, Peter Donnelly, Chris C. A. Spencer:
A robust clustering algorithm for identifying problematic samples in genome-wide association studies. 134-135
- Brian Pratt, J. Jeffry Howbert, Natalie I. Tasman, Erik J. Nilsson:
MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services. 136-137 - Walter Georgescu, John P. Wikswo, Vito Quaranta:
CellAnimation: an open source MATLAB framework for microscopy assays. 138-139
- Stephanie A. Canny, Yasel Cruz, Mark R. Southern, Patrick R. Griffin:
PubChem promiscuity: a web resource for gathering compound promiscuity data from PubChem. 140-141
- Erik Dassi, A. Malossini, Angela Re, Tommaso Mazza, Toma Tebaldi, Luigi Caputi, Alessandro Quattrone:
AURA: Atlas of UTR Regulatory Activity. 142-144
- Xiang Wan, Can Yang, Weichuan Yu:
Comments on 'An empirical comparison of several recent epistatic interaction detection methods'. 145-146
- Yue Wang, Guimei Liu, Mengling Feng, Limsoon Wong:
Response: an empirical comparison of several recent epistatic interaction detection methods. 147-148
- Marie 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. 149 - Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan:
Sensitive and fast mapping of di-base encoded reads. 150
Volume 28, Number 2, January 2012
- Gerard Wong, Christopher Leckie, Adam Kowalczyk:
FSR: feature set reduction for scalable and accurate multi-class cancer subtype classification based on copy number. 151-159 - David R. Riley, Samuel V. Angiuoli, Jonathan Crabtree, Julie C. Dunning Hotopp, Hervé Tettelin:
Using Sybil for interactive comparative genomics of microbes on the web. 160-166
- Jiarui Ding, Ali Bashashati, Andrew Roth, Arusha Oloumi, Kane Tse, Thomas Zeng, Gholamreza Haffari, Martin Hirst, Marco A. Marra, Anne Condon, Sam Aparicio, Sohrab P. Shah:
Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data. 167-175 - Yi-Fei Huang, Geoffrey Brian Golding:
Inferring sequence regions under functional divergence in duplicate genes. 176-183 - David T. Jones, Daniel W. A. Buchan, Domenico Cozzetto, Massimiliano Pontil:
PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. 184-190
- Benjamin Albrecht, Céline Scornavacca, Alberto Cenci, Daniel H. Huson:
Fast computation of minimum hybridization networks. 191-197
- Anna Philips, Kaja Milanowska, Grzegorz Lach, Michal J. Boniecki, Kristian Rother, Janusz M. Bujnicki:
MetalionRNA: computational predictor of metal-binding sites in RNA structures. 198-205
- Mark Maienschein-Cline, Jie Zhou, Kevin P. White, Roger Sciammas, Aaron R. Dinner:
Discovering transcription factor regulatory targets using gene expression and binding data. 206-213 - Geert Geeven, Ronald E. van Kesteren, August B. Smit, Mathisca C. M. de Gunst:
Identification of context-specific gene regulatory networks with GEMULA - gene expression modeling using LAsso. 214-221 - Bettina Grün, Theresa Scharl, Friedrich Leisch:
Modelling time course gene expression data with finite mixtures of linear additive models. 222-228
- Hua Wang, Feiping Nie, Heng Huang, Sungeun Kim, Kwangsik Nho, Shannon L. Risacher, Andrew J. Saykin, Li Shen:
Identifying quantitative trait loci via group-sparse multitask regression and feature selection: an imaging genetics study of the ADNI cohort. 229-237
- Jose L. Rubio-Guivernau, Vasily Gurchenkov, Miguel A. Luengo-Oroz, Louise Duloquin, Paul Bourgine, Andrés Santos, Nadine Peyriéras, María J. Ledesma-Carbayo:
Wavelet-based image fusion in multi-view three-dimensional microscopy. 238-245
- José Caldas, Nils Gehlenborg, Eeva Kettunen, Ali Faisal, Mikko Rönty, Andrew G. Nicholson, Sakari Knuutila, Alvis Brazma, Samuel Kaski:
Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma. 246-253 - Nathan Harmston, Wendy Filsell, Michael P. H. Stumpf:
Which species is it? Species-driven gene name disambiguation using random walks over a mixture of adjacency matrices. 254-260 - Jean-Philippe Carralot, Arnaud Ogier, Annette Boese, Auguste Genovesio, Priscille Brodin, Peter Sommer, Thierry Dorval:
A novel specific edge effect correction method for RNA interference screenings. 261-268
- Fidel Ramírez, Glenn Lawyer, Mario Albrecht:
Novel search method for the discovery of functional relationships. 269-276
- Yan W. Asmann, Sumit Middha, Asif Hossain, Saurabh Baheti, Ying Li, High-Seng Chai, Zhifu Sun, Patrick H. Duffy, Ahmed A. Hadad, Asha A. Nair, Xiaoyu Liu, Yuji Zhang, Eric W. Klee, Krishna R. Kalari, Jean-Pierre A. Kocher:
TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. 277-278 - Pablo Librado, Filipe G. Vieira, Julio Rozas:
BadiRate: estimating family turnover rates by likelihood-based methods. 279-281 - Aristotelis Tsirigos, Niina Haiminen, Erhan Bilal, Filippo Utro:
GenomicTools: a computational platform for developing high-throughput analytics in genomics. 282-283
- R. W. W. Brouwer, M. C. G. N. van den Hout, Frank G. Grosveld, Wilfred F. J. van IJcken:
NARWHAL, a primary analysis pipeline for NGS data. 284-285
- Chi-Ho Ngan, David R. Hall, Brandon S. Zerbe, Laurie E. Grove, Dima Kozakov, Sandor Vajda:
FTSite: high accuracy detection of ligand binding sites on unbound protein structures. 286-287
- Laurent Gatto, Kathryn S. Lilley:
MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation. 288-289
- Christopher W. Whelan, M. Kemal Sönmez:
Computing graphlet signatures of network nodes and motifs in Cytoscape with GraphletCounter. 290-291 - Dominique F. Chu, Nicolae Radu Zabet, Tobias von der Haar:
A novel and versatile computational tool to model translation. 292-293 - Lu Zhang, Shengchang Gu, Yuan Liu, Bingqiang Wang, Francisco Azuaje:
Gene set analysis in the cloud. 294-295
- Nigel F. Reuel, Peter Bojo, Jingqing Zhang, Ardemis A. Boghossian, Jin-Ho Ahn, Jong-Ho Kim, Michael S. Strano:
NoRSE: noise reduction and state evaluator for high-frequency single event traces. 296-297 - Heidi E. L. Lischer, Laurent Excoffier:
PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs. 298-299
- Christian M. Reidys, Fenix W. D. Huang, Jørgen E. Andersen, Robert C. Penner, Peter F. Stadler, Markus E. Nebel:
Addendum: topology and prediction of RNA pseudoknots. 300
Volume 28, Number 3, February 2012
- Xin Wei, Ann F. Hoffman, Shannon M. Hamilton, Qing Xiang, Yang He, W. Venus So, Sung-Sau So, David Mark:
A simple statistical test to infer the causality of target/phenotype correlation from small molecule phenotypic screens. 301-305
- Olga Shevchuk, Louisa Roselius, Gabriele Günther, Johannes Klein, Dieter Jahn, Michael Steinert, Richard Münch:
InFiRe - a novel computational method for the identification of insertion sites in transposon mutagenized bacterial genomes. 306-310
- David E. Larson, Christopher C. Harris, Ken Chen, Daniel C. Koboldt, Travis E. Abbott, David J. Dooling, Timothy J. Ley, Elaine R. Mardis, Richard K. Wilson, Li Ding:
SomaticSniper: identification of somatic point mutations in whole genome sequencing data. 311-317 - Antonio Marco, Sam Griffiths-Jones:
Detection of microRNAs in color space. 318-323
- Ryotaro Koike, Motonori Ota:
SCPC: a method to structurally compare protein complexes. 324-330 - Ke Chen, Marcin J. Mizianty, Lukasz A. Kurgan:
Prediction and analysis of nucleotide-binding residues using sequence and sequence-derived structural descriptors. 331-341 - Valdete M. Gonçalves-Almeida, Douglas E. V. Pires, Raquel Cardoso de Melo Minardi, Carlos Henrique da Silveira, Wagner Meira Jr., Marcelo M. Santoro:
HydroPaCe: understanding and predicting cross-inhibition in serine proteases through hydrophobic patch centroids. 342-349 - J. W. Heal, J. E. Jimenez-Roldan, Stephen A. Wells, R. B. Freedman, Rudolf A. Römer:
Inhibition of HIV-1 protease: the rigidity perspective. 350-357
- Gengxin Li, Joel Gelernter, Henry R. Kranzler, Hongyu Zhao:
M3: an improved SNP calling algorithm for Illumina BeadArray data. 358-365
- Wei Liu, Mahesan Niranjan:
Gaussian process modelling for bicoid mRNA regulation in spatio-temporal Bicoid profile. 366-372 - Alla Karnovsky, Terry E. Weymouth, Tim Hull, V. Glenn Tarcea, Giovanni Scardoni, Carlo Laudanna, Maureen A. Sartor, Kathleen A. Stringer, H. V. Jagadish, Charles F. Burant, Brian D. Athey, Gilbert S. Omenn:
Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data. 373-380 - Kathrin Ballerstein, Axel von Kamp, Steffen Klamt, Utz-Uwe Haus:
Minimal cut sets in a metabolic network are elementary modes in a dual network. 381-387 - Mario Latendresse, Markus Krummenacker, Miles Trupp, Peter D. Karp:
Construction and completion of flux balance models from pathway databases. 388-396
- Natalia Jiménez-Lozano, Joan Segura, José Ramón Macías, Juanjo Vega, José María Carazo:
Integrating human and murine anatomical gene expression data for improved comparisons. 397-402 - Yupeng Wang, Sandeep J. Joseph, Xinyu Liu, Michael Kelley, Romdhane Rekaya:
SNPxGE2: a database for human SNP-coexpression associations. 403-410 - Nestor Milyaev, David Osumi-Sutherland, Simon Reeve, Nicholas Burton, Richard A. Baldock, J. Douglas Armstrong:
The Virtual Fly Brain browser and query interface. 411-415
- Yongbing Zhao, Jiayan Wu, Junhui Yang, Shixiang Sun, Jing-Fa Xiao, Jun Yu:
PGAP: pan-genomes analysis pipeline. 416-418 - Mikhail G. Dozmorov, Lukas R. Cara, Cory B. Giles, Jonathan D. Wren:
GenomeRunner: automating genome exploration. 419-420 - F. Anthony San Lucas, Gao T. Wang, Paul Scheet, Bo Peng:
Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools. 421-422 - Valentina Boeva, Tatiana G. Popova, Kevin Bleakley, Pierre Chiche, Julie Cappo, Gudrun Schleiermacher, Isabelle Janoueix-Lerosey, Olivier Delattre, Emmanuel Barillot:
Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. 423-425
- Carlos Prieto, Carlos García-Estrada, Diego Lorenzana, Juan Francisco Martín:
NRPSsp: non-ribosomal peptide synthase substrate predictor. 426-427 - Benjamin Kreck, George Marnellos, Julia Richter, Felix Krueger, Reiner Siebert, Andre Franke:
B-SOLANA: an approach for the analysis of two-base encoding bisulfite sequencing data. 428-429 - Yuanxin Xi, Christoph Bock, Fabian Müller, Deqiang Sun, Alexander Meissner, Wei Li:
RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing. 430-432 - Robert Schmieder, Yan Wei Lim, Robert A. Edwards:
Identification and removal of ribosomal RNA sequences from metatranscriptomes. 433-435 - Antonio Gonzalez, Jesse Stombaugh, Christian L. Lauber, Noah Fierer, Rob Knight:
SitePainter: a tool for exploring biogeographical patterns. 436-438
- Conan K. Wang, Saroja K. Weeratunga, Chris M. Pacheco, Andreas Hofmann:
DMAN: a Java tool for analysis of multi-well differential scanning fluorimetry experiments. 439-440 - Julia T. Philip, Charles H. Pence, Holly V. Goodson:
MTBindingSim: simulate protein binding to microtubules. 441-443
- Christian Fuchsberger, Daniel Taliun, Peter P. Pramstaller, Cristian Pattaro:
GWAtoolbox: an R package for fast quality control and handling of genome-wide association studies meta-analysis data. 444-445
- Enrico Glaab, Reinhard Schneider:
PathVar: analysis of gene and protein expression variance in cellular pathways using microarray data. 446-447
- Sarala M. Wimalaratne, Pierre Grenon, Robert Hoehndorf, Georgios V. Gkoutos, Bernard de Bono:
An infrastructure for ontology-based information systems in biomedicine: RICORDO case study. 448-450 - Kai Xia, Andrey A. Shabalin, Shunping Huang, Vered Madar, Yi-Hui Zhou, Wei Wang, Fei Zou, Wei Sun, Patrick F. Sullivan, Fred A. Wright:
seeQTL: a searchable database for human eQTLs. 451-452
Volume 28, Number 4, February 2012
- Wilson Wen Bin Goh, Hirotaka Oikawa, Judy Chia Ghee Sng, Marek J. Sergot, Limsoon Wong:
The role of miRNAs in complex formation and control. 453-456
- Thomas J. Hardcastle, Krystyna A. Kelly, David C. Baulcombe:
Identifying small interfering RNA loci from high-throughput sequencing data. 457-463 - Tim Carver, Simon R. Harris, Matthew Berriman, Julian Parkhill, Jacqueline A. McQuillan:
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. 464-469 - Alberto Magi, Lorenzo Tattini, Tommaso Pippucci, Francesca Torricelli, Matteo Benelli:
Read count approach for DNA copy number variants detection. 470-478
- Yanju Zhang, Eric-Wubbo Lameijer, Peter A. C. 't Hoen, Zemin Ning, P. Eline Slagboom, Kai Ye:
PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data. 479-486 - Phil Arnold, Ionas Erb, Mikhail Pachkov, Nacho Molina, Erik van Nimwegen:
MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences. 487-494 - Benjamin P. Blackburne, Simon Whelan:
Measuring the distance between multiple sequence alignments. 495-502
- Ian Walsh, Alberto J. M. Martin, Tomás Di Domenico, Silvio C. E. Tosatto:
ESpritz: accurate and fast prediction of protein disorder. 503-509 - Tim Harder, Mikael Borg, Wouter Boomsma, Peter Røgen, Thomas Hamelryck:
Fast large-scale clustering of protein structures using Gauss integrals. 510-515 - Sikander Hayat, Arne Elofsson:
BOCTOPUS: improved topology prediction of transmembrane β barrel proteins. 516-522 - Sudhakar Sahoo, Andreas Alexander Albrecht:
Approximating the set of local minima in partial RNA folding landscapes. 523-530
- Tiejun Tong, Liang Chen, Hongyu Zhao:
Improved mean estimation and its application to diagonal discriminant analysis. 531-537 - Isaac S. Kohane, Vladimir I. Valtchinov:
Quantifying the white blood cell transcriptome as an accessible window to the multiorgan transcriptome. 538-545
- Lipi R. Acharya, Thair Judeh, Guangdi Wang, Dongxiao Zhu:
Optimal structural inference of signaling pathways from unordered and overlapping gene sets. 546-556 - Thomas Handorf, Edda Klipp:
Modeling mechanistic biological networks: An advanced Boolean approach. 557-563
- Youting Sun, Jianqiu Zhang, Ulisses M. Braga-Neto, Edward R. Dougherty:
BPDA2d - a 2D global optimization-based Bayesian peptide detection algorithm for liquid chromatograph-mass spectrometry. 564-572 - Raivo Kolde, Sven Laur, Priit Adler, Jaak Vilo:
Robust rank aggregation for gene list integration and meta-analysis. 573-580
- Leila Taher, Leelavati Narlikar, Ivan Ovcharenko:
CLARE: Cracking the LAnguage of Regulatory Elements. 581-583
- Thilo Muth, Juan A. García-Martín, Antonio Rausell, David de Juan, Alfonso Valencia, Florencio Pazos:
JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. 584-586 - Jinyan Huang, V. Renault, J. Sengenès, Nizar Touleimat, S. Michel,