Subject: Bioinformatics Table of Contents for 1 June 2017 Oxford Academic
 
 
 
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New issue alert
 
Bioinformatics  
Volume 33 Issue 11
 
1 June 2017
 
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DISCOVERY NOTE
 
 
 
 
GENE EXPRESSION
 
 
 
Genome-wide analysis of DNA methylation profiles in a senescence-accelerated mouse prone 8 brain using whole-genome bisulfite sequencing 
 
Shuai Zhang; Chunxia Qin; Guoqiong Cao; Limin Guo; Chengqiang Feng ...
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
chainCleaner improves genome alignment specificity and sensitivity 
 
Hernando G. Suarez; Bjoern E. Langer; Pradnya Ladde; Michael Hiller
 
 
Hierarchical sets: analyzing pangenome structure through scalable set visualizations border= 
 
Thomas Lin Pedersen
 
 
 
SEQUENCE ANALYSIS
 
 
 
Evolutionary design of multiple genes encoding the same protein 
 
Goro Terai ; Satoshi Kamegai; Akito Taneda; Kiyoshi Asai
 
 
Supporting precision medicine by data mining across multi-disciplines: an integrative approach for generating comprehensive linkages between single nucleotide variants (SNVs) and drug-binding sites 
 
Amrita Roy Choudhury; Tiejun Cheng; Lon Phan; Stephen H. Bryant ; Yanli Wang
 
 
 
 
 
PHYLOGENETICS
 
 
 
Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo border= 
 
P. Kapli; S. Lutteropp; J. Zhang; K. Kobert ; P. Pavlidis ...
 
 
Unrealistic phylogenetic trees may improve phylogenetic footprinting border= 
 
Martin Nettling; Hendrik Treutler; Jesus Cerquides; Ivo Grosse
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Classification of RNA structure change by ėgazing' at experimental data border= 
 
Chanin Tolson Woods; Alain Laederach
 
 
ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model 
 
Castrense Savojardo; Piero Fariselli; Pier Luigi Martelli; Rita Casadio
 
 
Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins 
 
Wei Tian; Meishan Lin; Hammad Naveed ; Jie Liang
 
 
 
 
 
GENE EXPRESSION
 
 
 
FIT: statistical modeling tool for transcriptome dynamics under fluctuating field conditions border= 
 
Koji Iwayama; Yuri Aisaka; Natsumaro Kutsuna; Atsushi J. Nagano
 
 
 
SYSTEMS BIOLOGY
 
 
 
Identification of protein complexes by integrating multiple alignment of protein interaction networks 
 
Cheng-Yu Ma ; Yi-Ping Phoebe Chen; Bonnie Berger; Chung-Shou Liao
 
 
Automated cell type discovery and classification through knowledge transfer border= 
 
Hao-Chih Lee; Roman Kosoy; Christine E. Becker; Joel T. Dudley ; Brian A. Kidd
 
 
 
DATA AND TEXT MINING
 
 
 
NSSRF: global network similarity search with subgraph signatures and its applications 
 
Jiao Zhang; Sam Kwong; Yuheng Jia; Ka-Chun Wong
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Quantification of fibrous spatial point patterns from single-molecule localization microscopy (SMLM) data 
 
Ruby Peters ; Marta Benthem Mu√Īiz; Juliette Griffi√©; David J. Williamson; George W. Ashdown ...
 
 
Extracting morphologies from third harmonic generation images of structurally normal human brain tissue 
 
Zhiqing Zhang; Nikolay V. Kuzmin; Marie Louise Groot ; Jan C. de Munck
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
A comprehensive quality control workflow for paired tumor-normal NGS experiments 
 
Christopher M. Schroeder; Franz J. Hilke; Markus W. Löffler; Michael Bitzer ; Florian Lenz ...
 
 
ANAQUIN: a software toolkit for the analysis of spike-in controls for next generation sequencing 
 
Ted Wong ; Ira W. Deveson; Simon A. Hardwick; Tim R. Mercer
 
 
LOCUST: a custom sequence locus typer for classifying microbial isolates 
 
Lauren M. Brinkac; Erin Beck; Jason Inman; Pratap Venepally ; Derrick E. Fouts ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
aRNApipe: a balanced, efficient and distributed pipeline for processing RNA-seq data in high-performance computing environments border= 
 
Arnald Alonso; Brittany N. Lasseigne; Kelly Williams; Josh Nielsen ; Ryne C. Ramaker ...
 
 
MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data border= 
 
B. Fosso; M. Santamaria; M. D'Antonio; D. Lovero; G. Corrado ...
 
 
H(O)TA: estimation of DNA methylation and hydroxylation levels and efficiencies from time course data 
 
Charalampos Kyriakopoulos; Pascal Giehr ; Verena Wolf
 
 
 
GENE EXPRESSION
 
 
 
Riborex: fast and flexible identification of differential translation from Ribo-seq data 
 
Wenzheng Li; Weili Wang; Philip J. Uren; Luiz O. F. Penalva; Andrew D. Smith
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
admixturegraph: an R package for admixture graph manipulation and fitting border= 
 
Kalle Leppälä; Svend V. Nielsen; Thomas Mailund
 
 
 
SYSTEMS BIOLOGY
 
 
 
CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models border= 
 
Hulda S. Haraldsdóttir; Ben Cousins ; Ines Thiele; Ronan M.T. Fleming; Santosh Vempala
 
 
 
DATA AND TEXT MINING
 
 
 
LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data 
 
Jennifer E. Kyle; Kevin L. Crowell; Cameron P. Casey; Grant M. Fujimoto; Sangtae Kim ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
Ligandbook: an online repository for small and drug-like molecule force field parameters border= 
 
Jan DomaŇ"ski; Oliver Beckstein ; Bogdan I. Iorga
 
 
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