Subject: Bioinformatics Table of Contents for 15 May 2017 Oxford Academic
 
 
 
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New issue alert
 
Bioinformatics  
Volume 33 Issue 10
 
15 May 2017
 
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DISCOVERY NOTE
 
 
 
 
GENOME ANALYSIS
 
 
 
LncRNA/DNA binding analysis reveals losses and gains and lineage specificity of genomic imprinting in mammals 
 
Haihua Liu; Xiaoxiao Shang; Hao Zhu
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE 
 
William H. Majoros; Michael S. Campbell; Carson Holt; Erin K. DeNardo; Doreen Ware ...
 
 
Large-scale 16S gene assembly using metagenomics shotgun sequences 
 
Feng Zeng; Zicheng Wang; Ying Wang; Jizhong Zhou ; Ting Chen
 
 
 
SEQUENCE ANALYSIS
 
 
 
Computational prediction of species-specific malonylation sites via enhanced characteristic strategy 
 
Li-Na Wang; Shao-Ping Shi; Hao-Dong Xu; Ping-Ping Wen; Jian-Ding Qiu
 
 
AFRESh: an adaptive framework for compression of reads and assembled sequences with random access functionality 
 
Tom Paridaens; Glenn Van Wallendael; Wesley De Neve; Peter Lambert
 
 
 
 
PALADIN: protein alignment for functional profiling whole metagenome shotgun data border= 
 
Anthony Westbrook; Jordan Ramsdell; Taruna Schuelke; Louisa Normington; R. Daniel Bergeron ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Seeing the trees through the forest: sequence-based homo- and heteromeric protein-protein interaction sites prediction using random forest 
 
Qingzhen Hou; Paul F. G. De Geest; Wim F. Vranken; Jaap Heringa; K. Anton Feenstra
 
 
A DNA intercalation methodology for an efficient prediction of ligand binding pose and energetics 
 
Anjali Soni; Pooja Khurana ; Tanya Singh; B. Jayaram
 
 
Correlated mutations select misfolded from properly folded proteins 
 
P.P. Wozniak; G. Vriend; M. Kotulska
 
 
 
GENE EXPRESSION
 
 
 
Powerful differential expression analysis incorporating network topology for next-generation sequencing data 
 
Malathi S.I. Dona; Luke A. Prendergast; Suresh Mathivanan; Shivakumar Keerthikumar; Agus Salim
 
 
 
 
DeuteRater: a tool for quantifying peptide isotope precision and kinetic proteomics 
 
Bradley C. Naylor; Michael T. Porter ; Elise Wilson; Adam Herring; Spencer Lofthouse ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
GWAR: robust analysis and meta-analysis of genome-wide association studies 
 
Niki L. Dimou; Konstantinos D. Tsirigos; Arne Elofsson ; Pantelis G. Bagos
 
 
 
SYSTEMS BIOLOGY
 
 
 
Inference of cellular level signaling networks using single-cell gene expression data in Caenorhabditis elegans reveals mechanisms of cell fate specification 
 
Xiao-Tai Huang; Yuan Zhu; Lai Hang Leanne Chan; Zhongying Zhao ; Hong Yan
 
 
SigMod: an exact and efficient method to identify a strongly interconnected disease-associated module in a gene network 
 
Yuanlong Liu ; Myriam Brossard; Damian Roqueiro; Patricia Margaritte-Jeannin; Chloé Sarnowski ...
 
 
Sparse network modeling and metscape-based visualization methods for the analysis of large-scale metabolomics data  
 
Sumanta Basu; William Duren; Charles R. Evans ; Charles F. Burant; George Michailidis ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
miRmine: a database of human miRNA expression profiles 
 
Bharat Panwar; Gilbert S. Omenn; Yuanfang Guan
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
Introducing COCOS: codon consequence scanner for annotating reading frame changes induced by stop-lost and frame shift variants border= 
 
Mariusz Butkiewicz; Jonathan L. Haines; William S. Bush
 
 
MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other transcriptomic sites 
 
Anthony O. Olarerin-George; Samie R. Jaffrey
 
 
KNIME4NGS: a comprehensive toolbox for next generation sequencing analysis 
 
Maximilian Hastreiter; Tim Jeske; Jonathan Hoser; Michael Kluge ; Kaarin Ahomaa ...
 
 
ASCIIGenome: a command line genome browser for console terminals border= 
 
Dario Beraldi
 
 
annoPeak: a web application to annotate and visualize peaks from ChIP-seq/ChIP-exo-seq 
 
Xing Tang ; Arunima Srivastava; Huayang Liu; Raghu Machiraju; Kun Huang ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
Better diagnostic signatures from RNAseq data through use of auxiliary co-data 
 
Putri W. Novianti ; Barbara C. Snoek; Saskia M. Wilting; Mark A. van de Wiel
 
 
FASTdoop: a versatile and efficient library for the input of FASTA and FASTQ files for MapReduce Hadoop bioinformatics applications 
 
Umberto Ferraro Petrillo; Gianluca Roscigno; Giuseppe Cattaneo; Raffaele Giancarlo
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
ProQ3D: improved model quality assessments using deep learning 
 
Karolis Uziela ; David Menéndez Hurtado; Nanjiang Shu; Björn Wallner; Arne Elofsson
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
VCF-kit: assorted utilities for the variant call format border= 
 
Daniel E. Cook; Erik C. Andersen
 
 
 
SYSTEMS BIOLOGY
 
 
 
NetLand: quantitative modeling and visualization of Waddington's epigenetic landscape using probabilistic potential border=  
 
Jing Guo; Feng Lin; Xiaomeng Zhang ; Vivek Tanavde; Jie Zheng
 
 
 
DATA AND TEXT MINING
 
 
 
ėCOV'COP' allows to detect CNVs responsible for inherited diseases among amplicons sequencing data 
 
P. Derouault; B. Parfait; R. Moulinas; C.-C. Barrot ; F. Sturtz ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
The JWS online simulation database 
 
Martin Peters; Johann J. Eicher; David D. van Niekerk; Dagmar Waltemath; Jacky L. Snoep
 
 
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