Volume 15, issue 1, December 2014
423 articles in this issue
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APP: an Automated Proteomics Pipeline for the analysis of mass spectrometry data based on multiple open access tools
Authors (first, second and last of 4)
- Erik K Malm
- Vaibhav Srivastava
- Vincent Bulone
- Content type: Software
- Open Access
- Published: 30 December 2014
- Article: 441
This is part of 1 collection: -
FogBank: a single cell segmentation across multiple cell lines and image modalities
Authors (first, second and last of 6)
- Joe Chalfoun
- Michael Majurski
- Mary Brady
- Content type: Research article
- Open Access
- Published: 30 December 2014
- Article: 431
This is part of 1 collection: -
WEBnm@ v2.0: Web server and services for comparing protein flexibility
Authors (first, second and last of 8)
- Sandhya P Tiwari
- Edvin Fuglebakk
- Nathalie Reuter
- Content type: Software
- Open Access
- Published: 30 December 2014
- Article: 427
This is part of 1 collection: -
A framework for feature extraction from hospital medical data with applications in risk prediction
Authors (first, second and last of 8)
- Truyen Tran
- Wei Luo
- Svetha Venkatesh
- Content type: Research article
- Open Access
- Published: 30 December 2014
- Article: 425
This is part of 1 collection: -
BitTorious: global controlled genomics data publication, research and archiving via BitTorrent extensions
Authors
- Preston V Lee
- Valentin Dinu
- Content type: Software
- Open Access
- Published: 21 December 2014
- Article: 424
This is part of 1 collection: -
Prediction of plant pre-microRNAs and their microRNAs in genome-scale sequences using structure-sequence features and support vector machine
Authors (first, second and last of 4)
- Jun Meng
- Dong Liu
- Yushi Luan
- Content type: Methodology article
- Open Access
- Published: 30 December 2014
- Article: 423
This is part of 1 collection: -
An integrated network visualization framework towards metabolic engineering applications
Authors
- Alberto Noronha
- Paulo Vilaça
- Miguel Rocha
- Content type: Software
- Open Access
- Published: 30 December 2014
- Article: 420
This is part of 1 collection: -
Prediction of piRNAs using transposon interaction and a support vector machine
Authors (first, second and last of 7)
- Kai Wang
- Chun Liang
- Fei Li
- Content type: Methodology article
- Open Access
- Published: 30 December 2014
- Article: 419
This is part of 1 collection: -
JRC GMO-Matrix: a web application to support Genetically Modified Organisms detection strategies
Authors (first, second and last of 7)
- Alexandre Angers-Loustau
- Mauro Petrillo
- Joachim Kreysa
- Content type: Database
- Open Access
- Published: 30 December 2014
- Article: 417
This is part of 1 collection: -
Unique features of apicoplast DNA gyrases from Toxoplasma gondii and Plasmodium falciparum
Authors (first, second and last of 4)
- Soshichiro Nagano
- Ting-Yu Lin
- Jonathan Gardiner Heddle
- Content type: Research article
- Open Access
- Published: 19 December 2014
- Article: 416
This is part of 1 collection: -
Interactive visual exploration of overlapping similar structures for three-dimensional microscope images
Authors (first, second and last of 7)
- Megumi Nakao
- Shintaro Takemoto
- Tetsuya Matsuda
- Content type: Research article
- Open Access
- Published: 19 December 2014
- Article: 415
This is part of 1 collection: -
EPMLR: sequence-based linear B-cell epitope prediction method using multiple linear regression
Authors
- Yao Lian
- Meng Ge
- Xian-Ming Pan
- Content type: Research article
- Open Access
- Published: 19 December 2014
- Article: 414
This is part of 1 collection: -
Identification of metabolites from 2D 1H-13C HSQC NMR using peak correlation plots
Authors (first, second and last of 7)
- Tommy Öman
- May-Britt Tessem
- Trygve Andreassen
- Content type: Methodology article
- Open Access
- Published: 16 December 2014
- Article: 413
This is part of 1 collection: -
Mammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs
Authors
- Anagha Joshi
- Content type: Research article
- Open Access
- Published: 30 December 2014
- Article: 412
This is part of 1 collection: -
Predicting breast cancer using an expression values weighted clinical classifier
Authors (first, second and last of 4)
- Minta Thomas
- Kris De Brabanter
- Bart De Moor
- Content type: Methodology Article
- Open Access
- Published: 31 December 2014
- Article: 411
This is part of 1 collection: -
Identifying target processes for microbial electrosynthesis by elementary mode analysis
Authors
- Frauke Kracke
- Jens O Krömer
- Content type: Research article
- Open Access
- Published: 30 December 2014
- Article: 410
This is part of 1 collection: -
DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis
Authors
- Jose A Gomez
- Kai Höffner
- Paul I Barton
- Content type: Software
- Open Access
- Published: 18 December 2014
- Article: 409
This is part of 1 collection: -
Kiwi: a tool for integration and visualization of network topology and gene-set analysis
Authors
- Leif Väremo
- Francesco Gatto
- Jens Nielsen
- Content type: Software
- Open Access
- Published: 11 December 2014
- Article: 408
This is part of 1 collection: -
A statistical approach to quantification of genetically modified organisms (GMO) using frequency distributions
Authors
- Lars Gerdes
- Ulrich Busch
- Sven Pecoraro
- Content type: Research article
- Open Access
- Published: 14 December 2014
- Article: 407
This is part of 1 collection: -
CLAST: CUDA implemented large-scale alignment search tool
Authors (first, second and last of 5)
- Masahiro Yano
- Hiroshi Mori
- Ken Kurokawa
- Content type: Software
- Open Access
- Published: 11 December 2014
- Article: 406
This is part of 1 collection: -
Methodology for the inference of gene function from phenotype data
Authors (first, second and last of 4)
- Joao A Ascensao
- Mary E Dolan
- Judith A Blake
- Content type: Methodology article
- Open Access
- Published: 12 December 2014
- Article: 405
This is part of 1 collection: -
ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs
Authors (first, second and last of 7)
- Christina Otto
- Mathias Möhl
- Sebastian Will
- Content type: Research Article
- Open Access
- Published: 31 December 2014
- Article: 404
This is part of 1 collection: -
QUDeX-MS: hydrogen/deuterium exchange calculation for mass spectra with resolved isotopic fine structure
Authors
- Joseph P Salisbury
- Qian Liu
- Jeffrey N Agar
- Content type: Software
- Open Access
- Published: 11 December 2014
- Article: 403
This is part of 1 collection: -
MCMC implementation of the optimal Bayesian classifier for non-Gaussian models: model-based RNA-Seq classification
Authors
- Jason M Knight
- Ivan Ivanov
- Edward R Dougherty
- Content type: Research Article
- Open Access
- Published: 10 December 2014
- Article: 401
This is part of 1 collection: -
Exact reconstruction of gene regulatory networks using compressive sensing
Authors
- Young Hwan Chang
- Joe W Gray
- Claire J Tomlin
- Content type: Research Article
- Open Access
- Published: 14 December 2014
- Article: 400
This is part of 1 collection: -
Integrating protein structural dynamics and evolutionary analysis with Bio3D
Authors (first, second and last of 4)
- Lars Skjærven
- Xin-Qiu Yao
- Barry J Grant
- Content type: Software
- Open Access
- Published: 10 December 2014
- Article: 399
This is part of 1 collection: -
solGS: a web-based tool for genomic selection
Authors (first, second and last of 9)
- Isaak Y Tecle
- Jeremy D Edwards
- Lukas A Mueller
- Content type: Software
- Open Access
- Published: 14 December 2014
- Article: 398
This is part of 1 collection: -
Comparative evaluation of gene set analysis approaches for RNA-Seq data
Authors
- Yasir Rahmatallah
- Frank Emmert-Streib
- Galina Glazko
- Content type: Methodology article
- Open Access
- Published: 05 December 2014
- Article: 397
This is part of 1 collection: -
Pathomx: an interactive workflow-based tool for the analysis of metabolomic data
Authors
- Martin A Fitzpatrick
- Catherine M McGrath
- Stephen P Young
- Content type: Software
- Open Access
- Published: 10 December 2014
- Article: 396
This is part of 1 collection: -
CompareSVM: supervised, Support Vector Machine (SVM) inference of gene regularity networks
Authors (first, second and last of 4)
- Zeeshan Gillani
- Muhammad Sajid Hamid Akash
- Ming Chen
- Content type: Research article
- Open Access
- Published: 30 November 2014
- Article: 395
This is part of 1 collection: -
MPAgenomics: an R package for multi-patient analysis of genomic markers
Authors (first, second and last of 6)
- Quentin Grimonprez
- Alain Celisse
- Guillemette Marot
- Content type: Software
- Open Access
- Published: 14 December 2014
- Article: 394
This is part of 1 collection: -
Computational prediction of protein interactions related to the invasion of erythrocytes by malarial parasites
Authors (first, second and last of 9)
- Xuewu Liu
- Yuxiao Huang
- Ya Zhao
- Content type: Research article
- Open Access
- Published: 30 November 2014
- Article: 393
This is part of 1 collection: -
Meta-eQTL: a tool set for flexible eQTL meta-analysis
Authors (first, second and last of 4)
- Antonio Fabio Di Narzo
- Haoxiang Cheng
- Ke Hao
- Content type: Software
- Open Access
- Published: 28 November 2014
- Article: 392
This is part of 1 collection: -
SPoRE: a mathematical model to predict double strand breaks and axis protein sites in meiosis
Authors
- Raphaël Champeimont
- Alessandra Carbone
- Content type: Methodology Article
- Open Access
- Published: 11 December 2014
- Article: 391
This is part of 1 collection: -
Pathway activity inference for multiclass disease classification through a mathematical programming optimisation framework
Authors (first, second and last of 4)
- Lingjian Yang
- Chrysanthi Ainali
- Lazaros G Papageorgiou
- Content type: Research article
- Open Access
- Published: 05 December 2014
- Article: 390
This is part of 1 collection: -
VTBuilder: a tool for the assembly of multi isoform transcriptomes
Authors (first, second and last of 5)
- John Archer
- Gareth Whiteley
- Simon C Wagstaff
- Content type: Software
- Open Access
- Published: 03 December 2014
- Article: 389
This is part of 1 collection: -
Linear-time computation of minimal absent words using suffix array
Authors (first, second and last of 4)
- Carl Barton
- Alice Heliou
- Solon P Pissis
- Content type: Research article
- Open Access
- Published: 20 December 2014
- Article: 388
This is part of 1 collection: -
Gene network inference using continuous time Bayesian networks: a comparative study and application to Th17 cell differentiation
Authors (first, second and last of 4)
- Enzo Acerbi
- Teresa Zelante
- Fabio Stella
- Content type: Research Article
- Open Access
- Published: 11 December 2014
- Article: 387
This is part of 1 collection: -
Finding gene regulatory network candidates using the gene expression knowledge base
Authors (first, second and last of 7)
- Aravind Venkatesan
- Sushil Tripathi
- Martin Kuiper
- Content type: Research article
- Open Access
- Published: 10 December 2014
- Article: 386
This is part of 1 collection: -
Comparison of classification methods that combine clinical data and high-dimensional mass spectrometry data
Authors (first, second and last of 6)
- Caroline Truntzer
- Elise Mostacci
- Hervé Cardot
- Content type: Research Article
- Open Access
- Published: 29 November 2014
- Article: 385
This is part of 1 collection: -
AKE - the Accelerated k-mer Exploration web-tool for rapid taxonomic classification and visualization
Authors
- Daniel Langenkämper
- Alexander Goesmann
- Tim Wilhelm Nattkemper
- Content type: Methodology Article
- Open Access
- Published: 13 December 2014
- Article: 384
This is part of 1 collection: -
Efficient prediction of human protein-protein interactions at a global scale
Authors (first, second and last of 19)
- Andrew Schoenrock
- Bahram Samanfar
- Ashkan Golshani
- Content type: Research article
- Open Access
- Published: 10 December 2014
- Article: 383
This is part of 1 collection: -
Masking as an effective quality control method for next-generation sequencing data analysis
Authors
- Sajung Yun
- Sijung Yun
- Content type: Methodology article
- Open Access
- Published: 13 December 2014
- Article: 382
This is part of 1 collection: -
CAR: contig assembly of prokaryotic draft genomes using rearrangements
Authors (first, second and last of 4)
- Chin Lung Lu
- Kun-Tze Chen
- Hsien-Tai Chiu
- Content type: Software
- Open Access
- Published: 28 November 2014
- Article: 381
This is part of 1 collection: -
Computational approach for calculating the probability of eukaryotic translation initiation from ribo-seq data that takes into account leaky scanning
Authors
- Audrey M Michel
- Dmitry E Andreev
- Pavel V Baranov
- Content type: Methodology article
- Open Access
- Published: 21 November 2014
- Article: 380
This is part of 1 collection: -
Anatomy of enzyme channels
Authors (first, second and last of 8)
- Lukáš Pravda
- Karel Berka
- Michal Otyepka
- Content type: Research article
- Open Access
- Published: 18 November 2014
- Article: 379
This is part of 1 collection: -
A meta-learning approach for B-cell conformational epitope prediction
Authors (first, second and last of 5)
- Yuh-Jyh Hu
- Shun-Chien Lin
- Shun-Ning You
- Content type: Methodology article
- Open Access
- Published: 18 November 2014
- Article: 378
This is part of 1 collection: -
TE-Tracker: systematic identification of transposition events through whole-genome resequencing
Authors (first, second and last of 14)
- Arthur Gilly
- Mathilde Etcheverry
- Jean-Marc Aury
- Content type: Methodology article
- Open Access
- Published: 19 November 2014
- Article: 377
This is part of 1 collection: -
A simple peak detection and label-free quantitation algorithm for chromatography-mass spectrometry
Authors (first, second and last of 13)
- Ken Aoshima
- Kentaro Takahashi
- Yoshiya Oda
- Content type: Methodology article
- Open Access
- Published: 25 November 2014
- Article: 376
This is part of 1 collection: