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ORCIDBioinformatics, Volume 25
Volume 25, Number 1, January 2009
- Francesca Diella, Sophie Chabanis-Davidson, Katja Luck, Claudia Chica
, Chenna Ramu, Claus Nerlov, Toby J. Gibson:
KEPE - a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors. 1-5
- Nawar Malhis, Yaron S. N. Butterfield, Martin Ester, Steven J. M. Jones:
Slider - maximum use of probability information for alignment of short sequence reads and SNP detection. 6-13 - Anna M. Ritz, Gregory Shakhnarovich, Arthur R. Salomon, Benjamin J. Raphael:
Discovery of phosphorylation motif mixtures in phosphoproteomics data. 14-21 - Anton V. Persikov, Robert Osada, Mona Singh:
Predicting DNA recognition by Cys2His2 zinc finger proteins. 22-29 - Jiansheng Wu, Hongde Liu, Xueye Duan, Yan Ding, Hongtao Wu, Yunfei Bai, Xiao Sun:
Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature. 30-35
- Chikara Furusawa, Naoaki Ono, Shingo Suzuki, Tomoharu Agata, Hiroshi Shimizu, Tetsuya Yomo:
Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays. 36-41 - A. Marie Fitch, M. Beatrix Jones:
Shortest path analysis using partial correlations for classifying gene functions from gene expression data. 42-47 - Adam L. Asare, Zhong Gao, Vincent J. Carey, Richard Wang, Vicki Seyfert-Margolis:
Power enhancement via multivariate outlier testing with gene expression arrays. 48-53
- James A. Koziol, Anne C. Feng, Zhenyu Jia, Yipeng Wang, Seven Goodison, Michael McClelland, Dan Mercola:
The wisdom of the commons: ensemble tree classifiers for prostate cancer prognosis. 54-60 - Ling-Yun Wu, Xiaobo Zhou, Fuhai Li, Xiaorong Yang, Chung-Che Chang, Stephen T. C. Wong:
Conditional random pattern algorithm for LOH inference and segmentation. 61-67 - Sharlee Climer, Gerold Jäger, Alan R. Templeton, Weixiong Zhang:
How frugal is mother nature with haplotypes? 68-74
- Adi L. Tarca, Sorin Draghici, Purvesh Khatri, Sonia S. Hassan, Pooja Mittal, Jung-Sun Kim, Chong Jai Kim, Juan Pedro Kusanovic, Roberto Romero:
A novel signaling pathway impact analysis. 75-82 - Hao Zhang, Claus Lundegaard, Morten Nielsen:
Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods. 83-89 - Ross P. Carlson:
Decomposition of complex microbial behaviors into resource-based stress responses. 90-97 - Xuebing Wu, Qifang Liu, Rui Jiang:
Align human interactome with phenome to identify causative genes and networks underlying disease families. 98-104 - Jingkai Yu, Russell L. Finley Jr.:
Combining multiple positive training sets to generate confidence scores for protein-protein interactions. 105-111
- Rachel Cavill, Hector C. Keun, Elaine Holmes, John C. Lindon, Jeremy K. Nicholson, Timothy M. D. Ebbels:
Genetic algorithms for simultaneous variable and sample selection in metabonomics. 112-118
- Tim J. Carver, Nick R. Thomson, Alan J. Bleasby, Matthew Berriman, Julian Parkhill:
DNAPlotter: circular and linear interactive genome visualization. 119-120
- Iain Melvin, Jason Weston, Christina S. Leslie, William Stafford Noble:
RANKPROP: a web server for protein remote homology detection. 121-122 - Gang-Qing Hu, Xiaobin Zheng, Huaiqiu Zhu, Zhen-Su She:
Prediction of translation initiation site for microbial genomes with TriTISA. 123-125
- Iain Milne, Dominik Lindner, Micha Bayer, Dirk Husmeier, Gráinne McGuire, David F. Marshall, Frank Wright:
TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. 126-127
- G. Golfier, Sophie Lemoine, A. van Miltenberg, A. Bendjoudi, J. Rossier, Stéphane Le Crom, Marie-Claude Potier:
Selection of oligonucleotides for whole-genome microarrays with semi-automatic update. 128-129 - Charles Addo-Quaye, Webb Miller, Michael J. Axtell:
CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. 130-131
- Manuel A. R. Ferreira, Shaun Purcell:
A multivariate test of association. 132-133 - Christine Herold, Tim Becker:
Genetic association analysis with FAMHAP: a major program update. 134-136
- Jing Gao, Alexander S. Ade, V. Glenn Tarcea, Terry E. Weymouth, Barbara R. Mirel, H. V. Jagadish, David J. States:
Integrating and annotating the interactome using the MiMI plugin for cytoscape. 137-138 - Rutger W. W. Brouwer, Sacha A. F. T. van Hijum, Oscar P. Kuipers:
MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context. 139-140
- Brigitte Waegele, Irmtraud Dunger-Kaltenbach, Gisela Fobo, Corinna Montrone, Hans-Werner Mewes, Andreas Ruepp:
CRONOS: the cross-reference navigation server. 141-143
- Clare Sansom:
ISMB 2008 conference report. 144-146
- Anne Kupczok, Arndt von Haeseler:
Comment on 'A congruence index for testing topological similarity between trees'. 147-149 - Damien M. de Vienne, Tatiana Giraud, Olivier C. Martin:
In response to comment on 'A congruence index for testing topological similarity between trees'. 150-151
- Luis F. de Figueiredo, Stefan Schuster, Christoph Kaleta, David A. Fell:
Can sugars be produced from fatty acids? A test case for pathway analysis tools. 152-158
Volume 25, Number 2, January 2009
- Alex Bateman, Robert D. Finn, Peter J. Sims, Therese Wiedmer, Andreas Biegert, Johannes Söding:
Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors. 159-162
- Richard S. P. Horler, Andrew Butcher, Nikitas Papangelopoulos, Peter D. Ashton, Gavin H. Thomas:
EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations. 163-166
- Xiaohui Xie, Paul Rigor, Pierre Baldi:
MotifMap: a human genome-wide map of candidate regulatory motif sites. 167-174
- William H. Majoros, Uwe Ohler:
Complexity reduction in context-dependent DNA substitution models. 175-182 - Shijie Zhang, Wei Su, Jiong Yang:
ARCS-Motif: discovering correlated motifs from unaligned biological sequences. 183-189
- Yufeng Wu:
A practical method for exact computation of subtree prune and regraft distance. 190-196 - Alex Webb, John M. Hancock, Christopher C. Holmes:
Phylogenetic inference under recombination using Bayesian stochastic topology selection. 197-203
- Ganesan Pugalenthi, E. Ke Tang, Ponnuthurai N. Suganthan, Saikat Chakrabarti:
Identification of structurally conserved residues of proteins in absence of structural homologs using neural network ensemble. 204-210
- Maureen A. Sartor, George D. Leikauf, Mario Medvedovic:
LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data. 211-217 - Sebastian Böcker, Matthias C. Letzel, Zsuzsanna Lipták, Anton Pervukhin:
SIRIUS: decomposing isotope patterns for metabolite identification. 218-224
- Filip Van Nieuwerburgh, Els Goetghebeur, Mado Vandewoestyne, Dieter Deforce:
Impact of allelic dropout on evidential value of forensic DNA profiles using RMNE. 225-229 - Saliha Yilmaz, Philippe Jonveaux, Cedric Bicep, Laurent Pierron, Malika Smaïl-Tabbone, Marie-Dominique Devignes:
Gene-disease relationship discovery based on model-driven data integration and database view definition. 230-236 - Lina Chen, Liangcai Zhang, Yan Zhao, Liangde Xu, Yukui Shang, Qian Wang, Wan Li, Hong Wang, Xia Li:
Prioritizing risk pathways: a novel association approach to searching for disease pathways fusing SNPs and pathways. 237-242
- Kevin Y. Yip, Mark Gerstein:
Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions. 243-250 - Donald A. Barkauskas, Hyun Joo An, Scott R. Kronewitter, Maria Lorna de Leoz, Helen K. Chew, Ralph W. de Vere White, Gary S. Leiserowitz, Suzanne Miyamoto, Carlito B. Lebrilla, David M. Rocke:
Detecting glycan cancer biomarkers in serum samples using MALDI FT-ICR mass spectrometry data. 251-257
- Gavin Brelstaff, Manuele Bicego, Nicola Culeddu, Matilde Chessa:
Bag of Peaks: interpretation of NMR spectrometry. 258-264 - Sach Mukherjee, Steven Pelech, Richard M. Neve, Wen-Lin Kuo, Safiyyah Ziyad, Paul T. Spellman, Joe W. Gray, Terence P. Speed:
Sparse combinatorial inference with an application in cancer biology. 265-271
- Nobutaka Kitamura, Kouhei Akazawa, Akinori Miyashita, Ryozo Kuwano, Shin-ichi Toyabe, Junichiro Nakamura, Norihito Nakamura, Tatsuhiko Sato, M. Aminul Hoque:
Programs for calculating the statistical powers of detecting susceptibility genes in case-control studies based on multistage designs. 272-273
- Scott Christley, Yiming Lu, Chen Li, Xiaohui Xie:
Human genomes as email attachments. 274-275
- Wubin Qu, Zhiyong Shen, Dongsheng Zhao, Yi Yang, Chenggang Zhang:
MFEprimer: multiple factor evaluation of the specificity of PCR primers. 276-278 - Tim F. Rayner, Faisal Ibne Rezwan, Margus Lukk, Xiangqun Zheng Bradley, Anna Farne, Ele Holloway, James Malone, Eleanor Williams, Helen E. Parkinson:
MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB. 279-280
- Oliver S. P. Davis, Robert Plomin, Leonard C. Schalkwyk:
The SNPMaP package for R: a framework for genome-wide association using DNA pooling on microarrays. 281-283 - Wei Chen, Liming Liang, Gonçalo R. Abecasis:
GWAS GUI: graphical browser for the results of whole-genome association studies with high-dimensional phenotypes. 284-285
- Bartek Wilczynski, Norbert Dojer:
BNFinder: exact and efficient method for learning Bayesian networks. 286-287
- Seth Carbon, Amelia Ireland, Christopher J. Mungall, Shengqiang Shu, Brad Marshall, Suzanna Lewis:
AmiGO: online access to ontology and annotation data. 288-289
Volume 25, Number 3, February 2009
- Bogumil Kaczkowski, Elfar Torarinsson, Kristin Reiche, Jakob Hull Havgaard, Peter F. Stadler, Jan Gorodkin:
Structural profiles of human miRNA families from pairwise clustering. 291-294
- Benedict Paten, Javier Herrero, Kathryn Beal, Ewan Birney:
Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. 295-301 - Denise Y. F. Mak, Gary Benson:
All hits all the time: parameter-free calculation of spaced seed sensitivity. 302-308
- Jumamurat R. Bayjanov, Michiel Wels, Marjo Starrenburg, Johan E. T. van Hylckama Vlieg, Roland J. Siezen, Douwe Molenaar:
PanCGH: a genotype-calling algorithm for pangenome CGH data. 309-314
- Stan Pounds, Cheng Cheng, Charles Mullighan, Susana C. Raimondi, Sheila Shurtleff, James R. Downing:
Reference alignment of SNP microarray signals for copy number analysis of tumors. 315-321 - Krzysztof Wabnik, Torgeir R. Hvidsten, Anna M. Kedzierska, Jelle Van Leene, Geert De Jaeger, Gerrit T. S. Beemster, Henryk Jan Komorowski, Martin T. R. Kuiper:
Gene expression trends and protein features effectively complement each other in gene function prediction. 322-330 - KunHong Liu, Chun-Gui Xu:
A genetic programming-based approach to the classification of multiclass microarray datasets. 331-337
- Junghyun Namkung, Kyunga Kim, Sung-Gon Yi, Wonil Chung, Min-Seok Kwon, Taesung Park:
New evaluation measures for multifactor dimensionality reduction classifiers in gene-gene interaction analysis. 338-345
- Ekaterina M. Myasnikova, Svetlana Surkova, Lena Panok, Maria Samsonova, John Reinitz:
Estimation of errors introduced by confocal imaging into the data on segmentation gene expression in Drosophila. 346-352 - Mahesh Yaragatti, Ted Sandler, Lyle H. Ungar:
A predictive model for identifying mini-regulatory modules in the mouse genome. 353-357 - Hu Li, Choong Yong Ung, Xiao Hua Ma, Bao Wen Li, Boon Chuan Low, Zhi Wei Cao, Yu Zong Chen:
Simulation of crosstalk between small GTPase RhoA and EGFR-ERK signaling pathway via MEKK1. 358-364 - David Goldberg, Marshall W. Bern, Simon J. North, Stuart M. Haslam, Anne Dell:
Glycan family analysis for deducing N-glycan topology from single MS. 365-371 - Hailiang Huang, Joel S. Bader:
Precision and recall estimates for two-hybrid screens. 372-378
- Anthony Y. C. Kuk, Han Zhang, Yaning Yang:
Computationally feasible estimation of haplotype frequencies from pooled DNA with and without Hardy-Weinberg equilibrium. 379-386 - Je-Gun Joung, Zhangjun Fei:
Identification of microRNA regulatory modules in Arabidopsis via a probabilistic graphical model. 387-393 - Yusuke Miyao, Kenji Sagae, Rune Sætre, Takuya Matsuzaki, Jun'ichi Tsujii:
Evaluating contributions of natural language parsers to protein-protein interaction extraction. 394-400 - Age K. Smilde, Henk A. L. Kiers, S. Bijlsma, C. M. Rubingh, M. J. van Erk:
Matrix correlations for high-dimensional data: the modified RV-coefficient. 401-405
- Davide Bolchini, Anthony Finkelstein, Vito Perrone, Sylvia Nagl:
Better bioinformatics through usability analysis. 406-412
- Christopher Reynolds, David Damerell, Susan Jones:
ProtorP: a protein-protein interaction analysis server. 413-414
- Audrey Kauffmann, Robert Gentleman, Wolfgang Huber:
arrayQualityMetrics - a bioconductor package for quality assessment of microarray data. 415-416
- Julien Chiquet, Alexander Smith, Gilles Grasseau, Catherine Matias, Christophe Ambroise:
SIMoNe: Statistical Inference for MOdular NEtworks. 417-418 - Martino Barenco, E. Papouli, Sonia H. Shah, Daniel Brewer, Crispin J. Miller, Michael Hubank:
rHVDM: an R package to predict the activity and targets of a transcription factor. 419-420
Volume 25, Number 4, February 2009
- Robert P. Guralnick, Andrew W. Hill:
Biodiversity informatics: automated approaches for documenting global biodiversity patterns and processes. 421-428
- Alex Bateman, John Quackenbush:
Editorial. 429
- Fuxiao Xin, Meng Li, Curtis Balch, Michael Thomson, Meiyun Fan, Yunlong Liu, Scott M. Hammond, Sun Kim, Kenneth P. Nephew:
Computational analysis of microRNA profiles and their target genes suggests significant involvement in breast cancer antiestrogen resistance. 430-434
- Helge G. Roider, Thomas Manke, Sean O'Keeffe, Martin Vingron, Stefan A. Haas:
PASTAA: identifying transcription factors associated with sets of co-regulated genes. 435-442
- Norman E. Davey, Denis C. Shields, Richard J. Edwards:
Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery. 443-450 - Tala Bakheet, Andrew J. Doig:
Properties and identification of human protein drug targets. 451-457 - René L. Warren, Brad H. Nelson, Robert A. Holt:
Profiling model T-cell metagenomes with short reads. 458-464 - Michiaki Hamada, Hisanori Kiryu, Kengo Sato, Toutai Mituyama, Kiyoshi Asai:
Prediction of RNA secondary structure using generalized centroid estimators. 465-473
- Dirk Stratmann, Carine van Heijenoort, Eric Guittet:
NOEnet-Use of NOE networks for NMR resonance assignment of proteins with known 3D structure. 474-481
- Daniel M. Gatti, Andrey A. Shabalin, Tieu-Chong Lam, Fred A. Wright, Ivan Rusyn, Andrew B. Nobel:
FastMap: Fast eQTL mapping in homozygous populations. 482-489 - Anagha Joshi, Riet De Smet, Kathleen Marchal, Yves Van de Peer, Tom Michoel:
Module networks revisited: computational assessment and prioritization of model predictions. 490-496
- Mingyao Li, Kai Wang, Struan F. A. Grant, Hakon Hakonarson, Chun Li:
ATOM: a powerful gene-based association test by combining optimally weighted markers. 497-503 - Can Yang, Zengyou He, Xiang Wan, Qiang Yang, Hong Xue, Weichuan Yu:
SNPHarvester: a filtering-based approach for detecting epistatic interactions in genome-wide association studies. 504-511
- Simon Rogers, Richard A. Scheltema, Mark A. Girolami, Rainer Breitling:
Probabilistic assignment of formulas to mass peaks in metabolomics experiments. 512-518 - Oliver Kotte, Matthias Heinemann:
A divide-and-conquer approach to analyze underdetermined biochemical models. 519-525
- Bai Zhang, Huai Li, Rebecca B. Riggins, Ming Zhan, Jianhua Xuan, Zhen Zhang, Eric P. Hoffman, Robert Clarke, Yue Joseph Wang:
Differential dependency network analysis to identify condition-specific topological changes in biological networks. 526-532
- Sascha Steinbiss, Gordon Gremme, Christin Schärfer, Malte Mader, Stefan Kurtz:
AnnotationSketch: a genome annotation drawing library. 533-534 - Michael S. Barker, Katrina M. Dlugosch, A. Chaitanya C. Reddy, Sarah N. Amyotte, Loren H. Rieseberg:
SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses. 535-536
- Jeremy M. Brown, Robert ElDabaje:
PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy. 537-538
- Benjamin M. Bulheller, Jonathan D. Hirst:
DichroCalc - circular and linear dichroism online. 539-540
- Daniel M. Gatti, Myroslav Sypa, Ivan Rusyn, Fred A. Wright, William T. Barry:
SAFEGUI: resampling-based tests of categorical significance in gene expression data made easy. 541-542 - Ryosuke R. Ishiwata, Masaki S. Morioka, Soichi Ogishima, Hiroshi Tanaka:
BioCichlid: central dogma-based 3D visualization system of time-course microarray data on a hierarchical biological network. 543-544 - Qihao Qi, Yingdong Zhao, Ming-Chung Li, Richard M. Simon:
Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools. 545-547 - Edward Ryder, H. Spriggs, E. Drummond, Daniel St Johnston, Steven Russell:
The Flannotator - a gene and protein expression annotation tool for Drosophila melanogaster. 548-549 - Evert-Jan Blom, Jos B. T. M. Roerdink, Oscar P. Kuipers, Sacha A. F. T. van Hijum:
MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data. 550-551
- Gilles Guillot, Matthieu Foll:
Correcting for ascertainment bias in the inference of population structure. 552-554
- Uma Mudunuri, Anney Che, Ming Yi, Robert M. Stephens:
bioDBnet: the biological database network. 555-556 - Jeff Heard, William Kaufmann, Xiaojun Guan:
A novel method for large tree visualization. 557-558
Volume 25, Number 5, March 2009
- Shahar Alon, Eli Eisenberg, Jasmine Jacob-Hirsch, Gideon Rechavi, Gad Vatine, Reiko Toyama, Steven L. Coon, David C. Klein, Yoav Gothilf:
A new cis-acting regulatory element driving gene expression in the zebrafish pineal gland. 559-562
- Shamim Ahmed, Ayumu Saito, Miho Suzuki, Naoto Nemoto, Koichi Nishigaki:
Host-parasite relations of bacteria and phages can be unveiled by Oligostickiness, a measure of relaxed sequence similarity. 563-570 - Xu Ling, Xin He, Dong Xin:
Detecting gene clusters under evolutionary constraint in a large number of genomes. 571-577 - Leila Taher, Ivan Ovcharenko:
Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements. 578-584
- Xue-wen Chen, Jong Cheol Jeong:
Sequence-based prediction of protein interaction sites with an integrative method. 585-591
- Fuxia Cheng, Stefanie Hartmann, Mayetri Gupta, Joseph G. Ibrahim, Todd J. Vision:
A hierarchical model for incomplete alignments in phylogenetic inference. 592-598