Subject: Bioinformatics Table of Contents for 01 February 2018 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Bioinformatics  
Volume 34 Issue 3
 
01 February 2018
 
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DISCOVERY NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
The systematic analysis of ultraconserved genomic regions in the budding yeast 
 
Zhi-Kai Yang; Feng Gao
 
 
 
GENE EXPRESSION
 
 
 
ZCCHC17 is a master regulator of synaptic gene expression in Alzheimer's disease 
 
Zeljko Tomljanovic; Mitesh Patel; William Shin; Andrea Califano ; Andrew F Teich
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing border= 
 
Tarmo Äijö; Christian L Müller; Richard Bonneau
 
 
CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data 
 
Weilong Guo; Ping Zhu ; Matteo Pellegrini; Michael Q Zhang; Xiangfeng Wang ...
 
 
A new haplotype block detection method for dense genome sequencing data based on interval graph modeling of clusters of highly correlated SNPs 
 
Sun Ah Kim; Chang-Sung Cho; Suh-Ryung Kim; Shelley B Bull ; Yun Joo Yoo
 
 
 
 
Tumor origin detection with tissue-specific miRNA and DNA methylation markers 
 
Wei Tang ; Shixiang Wan; Zhen Yang; Andrew E Teschendorff; Quan Zou
 
 
 
SEQUENCE ANALYSIS
 
 
 
SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data 
 
Paul D Blischak ; Laura S Kubatko; Andrea D Wolfe
 
 
FMtree: a fast locating algorithm of FM-indexes for genomic data 
 
Haoyu Cheng; Ming Wu; Yun Xu
 
 
AQUa: an adaptive framework for compression of sequencing quality scores with random access functionality 
 
Tom Paridaens; Glenn Van Wallendael; Wesley De Neve; Peter Lambert
 
 
MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota 
 
Evgenii I Olekhnovich; Artem T Vasilyev; Vladimir I Ulyantsev; Elena S Kostryukova; Alexander V Tyakht
 
 
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
A comprehensive assessment of long intrinsic protein disorder from the DisProt database 
 
Marco Necci; Damiano Piovesan; Zsuzsanna Dosztányi; Peter Tompa ; Silvio C E Tosatto
 
 
RRDB: a comprehensive and non-redundant benchmark for RNA'RNA docking and scoring 
 
Yumeng Yan ; Sheng-You Huang
 
 
Protein'protein interaction specificity is captured by contact preferences and interface composition border= 
 
Francesca Nadalin; Alessandra Carbone
 
 
GradDock: rapid simulation and tailored ranking functions for peptide-MHC Class I docking 
 
Hyun-Ho Kyeong; Yoonjoo Choi; Hak-Sung Kim
 
 
Structure-based prediction of protein' peptide binding regions using Random Forest 
 
Ghazaleh Taherzadeh; Yaoqi Zhou; Alan Wee-Chung Liew; Yuedong Yang
 
 
 
GENE EXPRESSION
 
 
 
High dimensional classification with combined adaptive sparse PLS and logistic regression 
 
Ghislain Durif ; Laurent Modolo; Jakob Michaelsson; Jeff E Mold; Sophie Lambert-Lacroix ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
Integrating splice-isoform expression into genome-scale models characterizes breast cancer metabolism 
 
Claudio Angione
 
 
Genome-scale fluxes predicted under the guidance of enzyme abundance using a novel hyper-cube shrink algorithm 
 
Zhengwei Xie; Tianyu Zhang ; Qi Ouyang
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
FATHMM-XF: accurate prediction of pathogenic point mutations via extended features border= 
 
Mark F Rogers; Hashem A Shihab; Matthew Mort ; David N Cooper; Tom R Gaunt ...
 
 
Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses 
 
Fabiano B Menegidio; Daniela L Jabes; Regina Costa de Oliveira; Luiz R Nunes
 
 
Canvas SPW: calling de novo copy number variants in pedigrees 
 
Sergii Ivakhno; Eric Roller; Camilla Colombo; Philip Tedder; Anthony J Cox
 
 
Identification of cancer driver genes in focal genomic aberrations from whole-exome sequencing data 
 
Ho Jang ; Hyunju Lee
 
 
MALDIrppa: quality control and robust analysis for mass spectrometry data 
 
Javier Palarea-Albaladejo ; Kevin Mclean; Frank Wright; David G E Smith
 
 
 
GENE EXPRESSION
 
 
 
Identification and visualization of differential isoform expression in RNA-seq time series border= 
 
María José Nueda; Jordi Martorell-Marugan; Cristina Martí; Sonia Tarazona; Ana Conesa
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Novel features and enhancements in BioBin, a tool for the biologically inspired binning and association analysis of rare variants border= 
 
Anna O Basile ; Marta Byrska-Bishop; John Wallace; Alexander T Frase; Marylyn D Ritchie
 
 
 
SYSTEMS BIOLOGY
 
 
 
graphkernels: R and Python packages for graph comparison border= 
 
Mahito Sugiyama; M Elisabetta Ghisu; Felipe Llinares-López; Karsten Borgwardt
 
 
 
DATA AND TEXT MINING
 
 
 
diffuStats: an R package to compute diffusion-based scores on biological networks 
 
Sergio Picart-Armada ; Wesley K Thompson; Alfonso Buil; Alexandre Perera-Lluna
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
DIBS: a repository of disordered binding sites mediating interactions with ordered proteins border= 
 
Eva Schad; Erzsébet Fichó ; Rita Pancsa; István Simon; Zsuzsanna Dosztányi ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
DiversePathsJ: diverse shortest paths for bioimage analysis border= 
 
Virginie Uhlmann; Carsten Haubold ; Fred A Hamprecht; Michael Unser
 
 
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