Volume 13, issue 1, December 2012
337 articles in this issue
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Copy number variation signature to predict human ancestry
Authors (first, second and last of 4)
- Melissa Pronold
- Marzieh Vali
- Shahab Asgharzadeh
- Content type: Methodology article
- Open Access
- Published: 27 December 2012
- Article: 336
This is part of 1 collection: -
Unlocking the potential of publicly available microarray data using inSilicoDb and inSilicoMerging R/Bioconductor packages
Authors (first, second and last of 11)
- Jonatan Taminau
- Stijn Meganck
- Ann Nowé
- Content type: Software
- Open Access
- Published: 24 December 2012
- Article: 335
This is part of 1 collection: -
Protein interface classification by evolutionary analysis
Authors (first, second and last of 4)
- Jose M Duarte
- Adam Srebniak
- Guido Capitani
- Content type: Research article
- Open Access
- Published: 22 December 2012
- Article: 334
This is part of 1 collection: -
RNAmap2D – calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures
Authors (first, second and last of 4)
- Michal J Pietal
- Natalia Szostak
- Janusz M Bujnicki
- Content type: Software
- Open Access
- Published: 21 December 2012
- Article: 333
This is part of 1 collection: -
CYPSI: a structure-based interface for cytochrome P450s and ligands in Arabidopsis thaliana
Authors
- Gaihua Zhang
- Yijing Zhang
- Zhen Su
- Content type: Database
- Open Access
- Published: 20 December 2012
- Article: 332
This is part of 1 collection: -
Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study
Authors (first, second and last of 7)
- Lei Sun
- Zhihua Zhang
- Hui Liu
- Content type: Research article
- Open Access
- Published: 13 December 2012
- Article: 331
This is part of 1 collection: -
Fast detection of de novo copy number variants from SNP arrays for case-parent trios
Authors (first, second and last of 6)
- Robert B Scharpf
- Terri H Beaty
- Ingo Ruczinski
- Content type: Methodology article
- Open Access
- Published: 12 December 2012
- Article: 330
This is part of 1 collection: -
Generalization of the normal-exponential model: exploration of a more accurate parametrisation for the signal distribution on Illumina BeadArrays
Authors
- Sandra Plancade
- Yves Rozenholc
- Eiliv Lund
- Content type: Research article
- Open Access
- Published: 11 December 2012
- Article: 329
This is part of 1 collection: -
Comparison of co-expression measures: mutual information, correlation, and model based indices
Authors
- Lin Song
- Peter Langfelder
- Steve Horvath
- Content type: Research article
- Open Access
- Published: 09 December 2012
- Article: 328
This is part of 1 collection: -
Improving stability and understandability of genotype-phenotype mapping in Saccharomyces using regularized variable selection in L-PLS regression
Authors (first, second and last of 4)
- Tahir Mehmood
- Jonas Warringer
- Solve Sæbø
- Content type: Research article
- Open Access
- Published: 08 December 2012
- Article: 327
This is part of 1 collection: -
A computational pipeline for the development of multi-marker bio-signature panels and ensemble classifiers
Authors (first, second and last of 11)
- Oliver P Günther
- Virginia Chen
- Raymond T Ng
- Content type: Methodology article
- Open Access
- Published: 08 December 2012
- Article: 326
This is part of 1 collection: -
A novel approach for biomarker selection and the integration of repeated measures experiments from two assays
Authors (first, second and last of 4)
- Benoit Liquet
- Kim-Anh Lê Cao
- Rodolphe Thiébaut
- Content type: Methodology article
- Open Access
- Published: 06 December 2012
- Article: 325
This is part of 1 collection: -
Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework
Authors (first, second and last of 8)
- Steven Lewis
- Attila Csordas
- John Boyle
- Content type: Software
- Open Access
- Published: 05 December 2012
- Article: 324
This is part of 1 collection: -
Flexible and efficient genome tiling design with penalized uniqueness score
Authors (first, second and last of 4)
- Yang Du
- Eduard Murani
- Klaus Wimmers
- Content type: Methodology article
- Open Access
- Published: 05 December 2012
- Article: 323
This is part of 1 collection: -
Finding quasi-modules of human and viral miRNAs: a case study of human cytomegalovirus (HCMV)
Authors (first, second and last of 6)
- Isana Veksler-Lublinsky
- Yonat Shemer-Avni
- Michal Ziv-Ukelson
- Content type: Research article
- Open Access
- Published: 03 December 2012
- Article: 322
This is part of 1 collection: -
Learning virulent proteins from integrated query networks
Authors
- Eithon Cadag
- Peter Tarczy-Hornoch
- Peter J Myler
- Content type: Methodology article
- Open Access
- Published: 02 December 2012
- Article: 321
This is part of 1 collection: -
Multiple-platform data integration method with application to combined analysis of microarray and proteomic data
Authors (first, second and last of 6)
- Shicheng Wu
- Yawen Xu
- Xin Gao
- Content type: Methodology article
- Open Access
- Published: 02 December 2012
- Article: 320
This is part of 1 collection: -
SNPEVG: a graphical tool for GWAS graphing with mouse clicks
Authors
- Shengwen Wang
- Daniel Dvorkin
- Yang Da
- Content type: Software
- Open Access
- Published: 30 November 2012
- Article: 319
This is part of 1 collection: -
On the contributions of topological features to transcriptional regulatory network robustness
Authors
- Faiyaz Al Zamal
- Derek Ruths
- Content type: Research article
- Open Access
- Published: 30 November 2012
- Article: 318
This is part of 1 collection: -
A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs
Authors (first, second and last of 4)
- Phillip Seitzer
- Elizabeth G Wilbanks
- Marc T Facciotti
- Content type: Research article
- Open Access
- Published: 27 November 2012
- Article: 317
This is part of 1 collection: -
TeraStitcher - A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images
Authors
- Alessandro Bria
- Giulio Iannello
- Content type: Software
- Open Access
- Published: 27 November 2012
- Article: 316
This is part of 1 collection: -
CloudMan as a platform for tool, data, and analysis distribution
Authors
- Enis Afgan
- Brad Chapman
- James Taylor
- Content type: Software
- Open Access
- Published: 27 November 2012
- Article: 315
This is part of 1 collection: -
Local functional descriptors for surface comparison based binding prediction
Authors
- Gregory M Cipriano
- N George Phillips Jr
- Michael Gleicher
- Content type: Research article
- Open Access
- Published: 24 November 2012
- Article: 314
This is part of 1 collection: -
EpicCapo: epitope prediction using combined information of amino acid pairwise contact potentials and HLA-peptide contact site information
Authors (first, second and last of 10)
- Thammakorn Saethang
- Osamu Hirose
- Kenji Satou
- Content type: Research article
- Open Access
- Published: 24 November 2012
- Article: 313
This is part of 1 collection: -
Core Hunter II: fast core subset selection based on multiple genetic diversity measures using Mixed Replica search
Authors (first, second and last of 4)
- Herman De Beukelaer
- Petr Smýkal
- Veerle Fack
- Content type: Research article
- Open Access
- Published: 23 November 2012
- Article: 312
This is part of 1 collection: -
Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools
Authors (first, second and last of 7)
- Susan C Tilton
- Tamara L Tal
- Katrina M Waters
- Content type: Software
- Open Access
- Published: 23 November 2012
- Article: 311
This is part of 1 collection: -
Automatic design of decision-tree induction algorithms tailored to flexible-receptor docking data
Authors (first, second and last of 7)
- Rodrigo C Barros
- Ana T Winck
- Osmar Norberto de Souza
- Content type: Research article
- Open Access
- Published: 21 November 2012
- Article: 310
This is part of 1 collection: -
An assessment on epitope prediction methods for protozoa genomes
Authors (first, second and last of 7)
- Daniela M Resende
- Antônio M Rezende
- Jeronimo C Ruiz
- Content type: Research article
- Open Access
- Published: 21 November 2012
- Article: 309
This is part of 1 collection: -
Estimating relative abundances of proteins from shotgun proteomics data
Authors (first, second and last of 6)
- Sean McIlwain
- Michael Mathews
- William Stafford Noble
- Content type: Software
- Open Access
- Published: 19 November 2012
- Article: 308
This is part of 1 collection: -
Multiple graph regularized protein domain ranking
Authors
- Jim Jing-Yan Wang
- Halima Bensmail
- Xin Gao
- Content type: Methodology article
- Open Access
- Published: 19 November 2012
- Article: 307
This is part of 1 collection: -
Gains of ubiquitylation sites in highly conserved proteins in the human lineage
Authors
- Dong Seon Kim
- Yoonsoo Hahn
- Content type: Research article
- Open Access
- Published: 17 November 2012
- Article: 306
This is part of 1 collection: -
Copy Number Variation detection from 1000 Genomes project exon capture sequencing data
Authors (first, second and last of 7)
- Jiantao Wu
- Krzysztof R Grzeda
- Gabor T Marth
- Content type: Methodology article
- Open Access
- Published: 17 November 2012
- Article: 305
This is part of 1 collection: -
Improving protein coreference resolution by simple semantic classification
Authors (first, second and last of 5)
- Ngan Nguyen
- Jin-Dong Kim
- Junichi Tsujii
- Content type: Research article
- Open Access
- Published: 17 November 2012
- Article: 304
This is part of 1 collection: -
Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model
Authors (first, second and last of 6)
- Kristof De Beuf
- Joachim De Schrijver
- Lieven Clement
- Content type: Methodology article
- Open Access
- Published: 15 November 2012
- Article: 303
This is part of 1 collection: -
PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides
Authors
- Anita Sarkar
- Serge Pérez
- Content type: Database
- Open Access
- Published: 14 November 2012
- Article: 302
This is part of 1 collection: -
NRE: a tool for exploring neutral loci in the human genome
Authors
- Leonardo Arbiza
- Elaine Zhong
- Alon Keinan
- Content type: Software
- Open Access
- Published: 14 November 2012
- Article: 301
This is part of 1 collection: -
Clustering of time-course gene expression profiles using normal mixture models with autoregressive random effects
Authors
- Kui Wang
- Shu Kay Ng
- Geoffrey J McLachlan
- Content type: Methodology article
- Open Access
- Published: 14 November 2012
- Article: 300
This is part of 1 collection: -
Human-specific protein isoforms produced by novel splice sites in the human genome after the human-chimpanzee divergence
Authors
- Dong Seon Kim
- Yoonsoo Hahn
- Content type: Research article
- Open Access
- Published: 13 November 2012
- Article: 299
This is part of 1 collection: -
Improving accuracy for cancer classification with a new algorithm for genes selection
Authors (first, second and last of 5)
- Hongyan Zhang
- Haiyan Wang
- Zheming Yuan
- Content type: Methodology article
- Open Access
- Published: 13 November 2012
- Article: 298
This is part of 1 collection: -
Oculus: faster sequence alignment by streaming read compression
Authors
- Brendan A Veeneman
- Matthew K Iyer
- Arul M Chinnaiyan
- Content type: Software
- Open Access
- Published: 13 November 2012
- Article: 297
This is part of 1 collection: -
Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation
Authors (first, second and last of 6)
- Daniel Wüstner
- Lukasz M Solanko
- Michael A Lomholt
- Content type: Methodology article
- Open Access
- Published: 13 November 2012
- Article: 296
This is part of 1 collection: -
iMS2Flux– a high–throughput processing tool for stable isotope labeled mass spectrometric data used for metabolic flux analysis
Authors (first, second and last of 6)
- C Hart Poskar
- Jan Huege
- Björn H Junker
- Content type: Software
- Open Access
- Published: 12 November 2012
- Article: 295
This is part of 1 collection: -
Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction
Authors
- Antonio Mora
- Ian M Donaldson
- Content type: Research article
- Open Access
- Published: 12 November 2012
- Article: 294
This is part of 1 collection: -
The tree alignment problem
Authors
- Andrés Varón
- Ward C Wheeler
- Content type: Research article
- Open Access
- Published: 09 November 2012
- Article: 293
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Effective inter-residue contact definitions for accurate protein fold recognition
Authors
- Chao Yuan
- Hao Chen
- Daisuke Kihara
- Content type: Research article
- Open Access
- Published: 09 November 2012
- Article: 292
This is part of 1 collection: -
Isotope pattern deconvolution for peptide mass spectrometry by non-negative least squares/least absolute deviation template matching
Authors (first, second and last of 7)
- Martin Slawski
- Rene Hussong
- Matthias Hein
- Content type: Methodology article
- Open Access
- Published: 08 November 2012
- Article: 291
This is part of 1 collection: -
mGOASVM: Multi-label protein subcellular localization based on gene ontology and support vector machines
Authors
- Shibiao Wan
- Man-Wai Mak
- Sun-Yuan Kung
- Content type: Methodology article
- Open Access
- Published: 06 November 2012
- Article: 290
This is part of 1 collection: -
The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement
Authors
- Marcin Pawlowski
- Janusz M Bujnicki
- Content type: Research article
- Open Access
- Published: 05 November 2012
- Article: 289
This is part of 1 collection: -
PAnalyzer: A software tool for protein inference in shotgun proteomics
Authors (first, second and last of 6)
- Gorka Prieto
- Kerman Aloria
- Rune Matthiesen
- Content type: Software
- Open Access
- Published: 05 November 2012
- Article: 288
This is part of 1 collection: