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Bioinformatics, Volume 27
Volume 27, Number 1, January 2011
- Qianchuan He
, Dan-Yu Lin:
A variable selection method for genome-wide association studies. 1-8 - Maria Elena Sana, Maria Iascone
, Daniela Marchetti, Jeffrey J. T. Palatini
, Marco Galasso
, Stefano Volinia
:
GAMES identifies and annotates mutations in next-generation sequencing projects. 9-13 - Dong Seon Kim, Yoonsoo Hahn
:
Identification of human-specific transcript variants induced by DNA insertions in the human genome. 14-21
- Monzoorul Haque Mohammed, Tarini Shankar Ghosh, Nitin Kumar Singh, Sharmila S. Mande:
SPHINX - an algorithm for taxonomic binning of metagenomic sequences. 22-30 - Yuheng Li, Nicholas Chia, Mario Lauria
, Ralf Bundschuh
:
A performance enhanced PSI-BLAST based on hybrid alignment. 31-37
- Jaime Huerta-Cepas
, Toni Gabaldón
:
Assigning duplication events to relative temporal scales in genome-wide studies. 38-45
- R. Dustin Schaeffer
, Amanda L. Jonsson, Andrew M. Simms, Valerie Daggett:
Generation of a consensus protein domain dictionary. 46-54 - Chandrajit L. Bajaj, Rezaul Alam Chowdhury, Muhibur Rasheed:
A dynamic data structure for flexible molecular maintenance and informatics. 55-62
- Haimao Zhan, Xin Chen, Shizhong Xu:
A stochastic expectation and maximization algorithm for detecting quantitative trait-associated genes. 63-69 - Johannes M. Freudenberg
, Siva Sivaganesan, Mukta Phatak, Kaustubh Shinde, Mario Medvedovic:
Generalized random set framework for functional enrichment analysis using primary genomics datasets. 70-77 - Sunghee Oh
, Dongwan D. Kang, Guy N. Brock
, George C. Tseng:
Biological impact of missing-value imputation on downstream analyses of gene expression profiles. 78-86 - Vanya Van Belle, Kristiaan Pelckmans, Sabine Van Huffel, Johan A. K. Suykens
:
Improved performance on high-dimensional survival data by application of Survival-SVM. 87-94
- Peilin Jia, Siyuan Zheng
, Jirong Long
, Wei Zheng, Zhongming Zhao:
dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks. 95-102
- Nidhal Bouaynaya, Roman Shterenberg, Dan Schonfeld:
Inverse perturbation for optimal intervention in gene regulatory networks. 103-110 - Guy Geva, Roded Sharan:
Identification of protein complexes from co-immunoprecipitation data. 111-117
- Shi 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. 118-126
- Gail L. Rosen
, Erin R. Reichenberger, Aaron M. Rosenfeld:
NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads. 127-129
- Timo Lassmann
, Yoshihide Hayashizaki, Carsten O. Daub
:
SAMStat: monitoring biases in next generation sequencing data. 130-131
- Jean-Christophe Gelly
, Alexandre G. de Brevern
:
Protein Peeling 3D: new tools for analyzing protein structures. 132-133
- Ryan Abo, Stacey Knight
, Alun Thomas
, Nicola J. Camp:
Automated construction and testing of multi-locus gene-gene associations. 134-136
- Fernando García-Alcalde
, Federico García-López, Joaquín Dopazo
, Ana Conesa
:
Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data. 137-139 - Laurin A. J. Mueller, Karl G. Kugler, Andreas Dander, Armin Graber, Matthias Dehmer:
QuACN: an R package for analyzing complex biological networks quantitatively. 140-141 - Ronan M. T. Fleming
, Ines Thiele
:
von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models. 142-143
- Paul Martin
, Anne Barton
, Stephen Eyre
:
ASSIMILATOR: a new tool to inform selection of associated genetic variants for functional studies. 144-146
Volume 27, Number 2, January 2011
- Dong Dong, Xiaojian Shao
, Zhaolei Zhang:
Differential effects of chromatin regulators and transcription factors on gene regulation: a nucleosomal perspective. 147-152 - Giuseppe Narzisi
, Bud Mishra:
Scoring-and-unfolding trimmed tree assembler: concepts, constructs and comparisons. 153-160 - Vito M. R. Muggeo, Giada Adelfio
:
Efficient change point detection for genomic sequences of continuous measurements. 161-166
- Pramila Nuwantha Ariyaratne, Wing-Kin Sung
:
PE-Assembler: de novo assembler using short paired-end reads. 167-174 - Ahrim Youn, Richard Simon:
Identifying cancer driver genes in tumor genome sequencing studies. 175-181 - Panagiotis D. Vouzis, Nikolaos V. Sahinidis
:
GPU-BLAST: using graphics processors to accelerate protein sequence alignment. 182-188 - Sanchit Misra, Ankit Agrawal
, Wei-keng Liao
, Alok N. Choudhary:
Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing. 189-195 - Fabio Gori
, Gianluigi Folino
, Mike S. M. Jetten, Elena Marchiori:
MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks. 196-203
- Tobias Hamp, Fabian Birzele, Fabian Buchwald, Stefan Kramer:
Improving structure alignment-based prediction of SCOP families using Vorolign Kernels. 204-210 - Stefan E. Seemann, Andreas S. Richter
, Tanja Gesell
, Rolf Backofen, Jan Gorodkin
:
PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences. 211-219
- Gregory Riddick, Hua Song, Susie Ahn, Jennifer Walling, Diego Borges-Rivera
, Wei Zhang, Howard A. Fine:
Predicting in vitro drug sensitivity using Random Forests. 220-224 - Hong-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. 225-231
- Darong Lai, Xinyi Yang, Gang Wu, Yuanhua Liu, Christine Nardini
:
Inference of gene networks - application to Bifidobacterium. 232-237 - Holger Fröhlich
, Paurush Praveen
, Achim Tresch:
Fast and efficient dynamic nested effects models. 238-244 - Tae-Hwan Kim, Junil Kim
, Pat Heslop-Harrison
, Kwang-Hyun Cho:
Evolutionary design principles and functional characteristics based on kingdom-specific network motifs. 245-251 - Isabel 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. 252-258
- Quoc-Chinh Bui, Sophia Katrenko
, Peter M. A. Sloot:
A hybrid approach to extract protein-protein interactions. 259-265
- Qing 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. 266-267 - Valentina Boeva
, Andrei Yu. 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. 268-269 - Simon J. van Heeringen
, Gert Jan C. Veenstra
:
GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments. 270-271 - Ryan Koehler, Hadar Issac, Nicole Cloonan
, Sean M. Grimmond
:
The uniqueome: a mappability resource for short-tag sequencing. 272-274
- Paulo C. Carvalho, Juliana S. G. Fischer, Jonas Perales, John R. Yates III, Valmir Carneiro Barbosa
, Elias Bareinboim:
Analyzing marginal cases in differential shotgun proteomics. 275-276 - Emese 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. 277-278 - Stephanie Kehr
, Sebastian Bartschat, Peter F. Stadler
, Hakim Tafer
:
PLEXY: efficient target prediction for box C/D snoRNAs. 279-280
- Lukas 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. 281-283
- Nicholas A. Davis, Ahwan Pandey, Brett A. McKinney:
Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS. 284-285 - Rebecca Rooke
, Guojun Yang:
TE Displayer for post-genomic analysis of transposable elements. 286-287
- Matthias Vigelius, Aidan Lane, Bernd Meyer:
Accelerating reaction-diffusion simulations with general-purpose graphics processing units. 288-290
Volume 27, Number 3, February 2011
- Lucian Ilie
, Farideh Fazayeli, Silvana Ilie:
HiTEC: accurate error correction in high-throughput sequencing data. 295-302 - Lars Halvor Gidskehaug, Matthew Kent, Ben J. Hayes
, Sigbjørn Lien:
Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array. 303-310 - Haitao Jiang, Binhai Zhu, Daming Zhu:
Algorithms for sorting unsigned linear genomes by the DCJ operations. 311-316
- Peter Menzel
, Peter F. Stadler
, Jan Gorodkin
:
maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences. 317-325 - Leonard 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. 326-333 - Samuel V. Angiuoli
, Steven L. Salzberg
:
Mugsy: fast multiple alignment of closely related whole genomes. 334-342
- Pascal Benkert
, Marco Biasini, Torsten Schwede
:
Toward the estimation of the absolute quality of individual protein structure models. 343-350 - Hongbo Zhu, M. Teresa Pisabarro
:
MSPocket: an orientation-independent algorithm for the detection of ligand binding pockets. 351-358
- Vinícius 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. 359-367 - António dos Anjos
, Anders L. B. Møller, Bjarne Kjær Ersbøll
, Christine Finnie
, Hamid Reza Shahbazkia
:
New approach for segmentation and quantification of two-dimensional gel electrophoresis images. 368-375
- Todd A. Gibson, Debra Goldberg:
Improving evolutionary models of protein interaction networks. 376-382 - Xiaojian Shao
, Chris Soon Heng 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. 383-390 - Yongsoo 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. 391-398 - Ming 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. 399-404 - Gábor Iván, Vince Grolmusz
:
When the Web meets the cell: using personalized PageRank for analyzing protein interaction networks. 405-407
- Emily 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. 408-415
- Vijay Garla, Yong Kong
, Sebastian Szpakowski, Michael Krauthammer
:
MU2A - reconciling the genome and transcriptome to determine the effects of base substitutions. 416-418 - Philippe Lamy, Carsten Wiuf
, Torben F. Ørntoft, Claus L. Andersen
:
Rseg - an R package to optimize segmentation of SNP array data. 419-420
- Shao-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. 421-422
- Daniel Aioanei, Marco Brucale
, Bruno Samorì:
Open source platform for the execution and analysis of mechanical refolding experiments. 423-425 - Per Larsson, Marcin J. Skwark
, Björn Wallner
, Arne Elofsson
:
Improved predictions by Pcons.net using multiple templates. 426-427
- Xun 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. 428-430
- Michael E. Smoot, Keiichiro Ono, Johannes Ruscheinski, Peng-Liang Wang, Trey Ideker
:
Cytoscape 2.8: new features for data integration and network visualization. 431-432 - Albert 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. 433-434
- Miquel Miquel, I. López-Ribera, Miquel Ràmia, Sònia Casillas
, Antonio Barbadilla
, Carlos M. Vicient
:
MASISH: a database for gene expression in maize seeds. 435-436 - Y. Wayne Huang, Adam P. Arkin, John-Marc Chandonia
:
WIST: toolkit for rapid, customized LIMS development. 437-438
- Daniel F. Schwarz, Inke R. König
, Andreas Ziegler
:
On safari to Random Jungle: a fast implementation of Random Forests for high-dimensional data. 439
Volume 27, Number 4, February 2011
- Melissa S. Cline, Rachel Karchin
:
Using bioinformatics to predict the functional impact of SNVs. 441-448
- Bernhard Haubold, Floyd A. Reed
, Peter Pfaffelhuber:
Alignment-free estimation of nucleotide diversity. 449-455
- Andrew X. Li, Manja Marz
, Jing Qin
, Christian M. Reidys:
RNA-RNA interaction prediction based on multiple sequence alignments. 456-463 - Kana Shimizu
, Koji Tsuda:
SlideSort: all pairs similarity search for short reads. 464-470 - Tak-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. 471-478 - Thomas C. Conway, Andrew J. Bromage:
Succinct data structures for assembling large genomes. 479-486
- Teppei Ebina
, Hiroyuki Toh, Yutaka Kuroda:
DROP: an SVM domain linker predictor trained with optimal features selected by random forest. 487-494
- Francesco C. Stingo
, Marina Vannucci:
Variable selection for discriminant analysis with Markov random field priors for the analysis of microarray data. 495-501 - Zhengpeng Wu, Xi Wang
, Xuegong Zhang:
Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq. 502-508 - Sangsoon Woo, Jeffrey T. Leek
, John D. Storey
:
A computationally efficient modular optimal discovery procedure. 509-515
- Jiahan Li, Kiranmoy Das, Guifang Fu
, Runze Li
, Rongling Wu:
The Bayesian lasso for genome-wide association studies. 516-523
- Frank-Michael Schleif
, T. Riemer, U. Börner, L. Schnapka-Hille, Michael Cross
:
Genetic algorithm for shift-uncertainty correction in 1-D NMR-based metabolite identifications and quantifications. 524-533 - Alberto Rezola
, Luis F. de Figueiredo, Matthias 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. 534-540 - Paul A. Jensen, Jason A. Papin
:
Functional integration of a metabolic network model and expression data without arbitrary thresholding. 541-547 - Ritwik Layek, Aniruddha Datta, Michael L. Bittner, Edward R. Dougherty:
Cancer therapy design based on pathway logic. 548-555 - Wessel N. van Wieringen
, Aad van der Vaart:
Statistical analysis of the cancer cell's molecular entropy using high-throughput data. 556-563
- Hang Xiao, Ying Li
, Jiulin Du, Axel Mosig
:
Ct3d: tracking microglia motility in 3D using a novel cosegmentation approach. 564-571 - Jürgen 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. 572-577
- Marten Boetzer, Christiaan V. Henkel
, Hans J. Jansen
, Derek Butler, Walter Pirovano
:
Scaffolding pre-assembled contigs using SSPACE. 578-579
- David L. A. Wood, Qinying Xu, John V. Pearson
, Nicole Cloonan
, Sean M. Grimmond
:
X-MATE: a flexible system for mapping short read data. 580-581
- Jose Ignacio Agulleiro Baldo, José-Jesús Fernández:
Fast tomographic reconstruction on multicore computers. 582-583
- Clive G. Bowsher:
Automated analysis of information processing, kinetic independence and modular architecture in biochemical networks using MIDIA. 584-586
- Leonardo 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. 587-588
- Mikhail 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. 589-591
- Klaus Peter Schliep:
phangorn: phylogenetic analysis in R. 592-593
Volume 27, Number 5, March 2011
- Alexej Abyzov
, Mark Gerstein:
AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision. 595-603 - Christopher Oldmeadow
, Jonathan M. Keith
:
Model selection in Bayesian segmentation of multiple DNA alignments. 604-610
- Xiaolin Hao, Rui Jiang
, Ting Chen:
Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering. 611-618
- Anna Katharina Dehof, Alexander Rurainski, Quang Bao Anh Bui, Sebastian Böcker
, Hans-Peter Lenhof, Andreas Hildebrandt
:
Automated bond order assignment as an optimization problem. 619-625 - Zhenjiang Xu
, David H. Mathews:
Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences. 626-632