Subject: Bioinformatics Table of Contents for 15 December 2017 ------=_Part_698012202.1513278755318 Content-Type: text/plain;charset=UTF-8 Oxford Academic [[HeaderAdvertisingToken]] https://silverchair.emailcampaigns.net/media/50/509735/OUP/oxford_logo.jpg?g72331686458 (http://click.skem1.com/click/ldkf4-d0lwab-66q6ox34/) [[BannerToken]] [[AlertTitleToken]] [[SelfServeTextToken]] [[FirstAdvertisingToken]] [[TOCMainToken]] Unsubscribe (http://click.skem1.com/form?ldkf4--ply5-66q6ox33&sl=tq&t=5)Manage email alerts (http://click.skem1.com/click/ldkf4-d0lwac-66q6ox35/) Written requests to unsubscribe can be sent to: Journals Marketing, Oxford University Press, Great Clarendon Street, Oxford, OX2 6DP, UK. The content of this email is protected by copyright. https://silverchair.emailcampaigns.net/media/50/509735/OUP/oxforde_university.jpg?g72331733632 (http://click.skem1.com/click/ldkf4-d0lwad-66q6ox36/) [[BottomAdvertisingToken]] This email is intended for bionet@evol.mcmaster.ca. ------=_Part_698012202.1513278755318 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Bioinformatics  
Volume 33 Issue 24
 
15 December 2017
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
HaploForge: a comprehensive pedigree drawing and haplotype visualization web application 
 
Mehmet Tekman; Alan Medlar; Monika Mozere; Robert Kleta; Horia Stanescu
 
 
LLR: a latent low-rank approach to colocalizing genetic risk variants in multiple GWAS 
 
Jin Liu; Xiang Wan ; Chaolong Wang; Chao Yang; Xiaowei Zhou ...
 
 
Genome-wide association studies using a penalized moving-window regression 
 
Minli Bao; Kai Wang
 
 
FIRE: functional inference of genetic variants that regulate gene expression 
 
Nilah M Ioannidis; Joe R Davis; Marianne K DeGorter; Nicholas B Larson; Shannon K McDonnell ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
SVM-dependent pairwise HMM: an application to protein pairwise alignments 
 
Gabriele Orlando ; Daniele Raimondi; Taushif Khan; Tom Lenaerts; Wim F Vranken
 
 
 
 
MusiteDeep: a deep-learning framework for general and kinase-specific phosphorylation site prediction 
 
Duolin Wang; Shuai Zeng; Chunhui Xu; Wangren Qiu ; Yanchun Liang ...
 
 
RUCS: rapid identification of PCR primers for unique core sequences border= 
 
Martin Christen Frølund Thomsen; Henrik Hasman; Henrik Westh; Hülya Kaya; Ole Lund
 
 
Kmer-SSR: a fast and exhaustive SSR search algorithm border= 
 
Brandon D Pickett ; Justin B Miller; Perry G Ridge
 
 
An improved compound Poisson model for the number of motif hits in DNA sequences border= 
 
Wolfgang Kopp; Martin Vingron
 
 
 
PHYLOGENETICS
 
 
 
Comparison of methods for phylogenetic B-cell lineage inference using time-resolved antibody repertoire simulations (AbSim) 
 
Alexander Yermanos; Victor Greiff ; Nike Julia Krautler; Ulrike Menzel; Andreas Dounas ...
 
 
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
FOLD: a method to optimize power in meta-analysis of genetic association studies with overlapping subjects border= 
 
Emma E Kim; Seunghoon Lee ; Cue Hyunkyu Lee; Hyunjung Oh; Kyuyoung Song ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
Predicting novel metabolic pathways through subgraph mining 
 
Aravind Sankar; Sayan Ranu; Karthik Raman
 
 
HiDi: an efficient reverse engineering schema for large-scale dynamic regulatory network reconstruction using adaptive differentiation 
 
Yue Deng; Hector Zenil; Jesper Tegnér; Narsis A Kiani
 
 
 
DATA AND TEXT MINING
 
 
 
Cancer Hallmarks Analytics Tool (CHAT): a text mining approach to organize and evaluate scientific literature on cancer border= 
 
Simon Baker; Imran Ali; Ilona Silins; Sampo Pyysalo; Yufan Guo ...
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
ChAMP: updated methylation analysis pipeline for Illumina BeadChips border= 
 
Yuan Tian ; Tiffany J Morris; Amy P Webster; Zhen Yang; Stephan Beck ...
 
 
CESAR 2.0 substantially improves speed and accuracy of comparative gene annotation 
 
Virag Sharma; Peter Schwede; Michael Hiller
 
 
Real-time demultiplexing Nanopore barcoded sequencing data with npBarcode  
 
Son Hoang Nguyen; Tania P S Duarte; Lachlan J M Coin ; Minh Duc Cao
 
 
 
SEQUENCE ANALYSIS
 
 
 
ALIGNSEC: viewing protein secondary structure predictions within large multiple sequence alignments 
 
Gilbert Deléage
 
 
 
PHYLOGENETICS
 
 
 
PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context border= 
 
Pieter Libin; Ewout Vanden Eynden; Francesca Incardona; Ann Nowé ; Antonia Bezenchek ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
AlloSigMA: allosteric signaling and mutation analysis server 
 
Enrico Guarnera; Zhen Wah Tan; Zejun Zheng; Igor N Berezovsky
 
 
Integrative structural and dynamical biology with PLUMED-ISDB 
 
Massimiliano Bonomi; Carlo Camilloni
 
 
 
GENE EXPRESSION
 
 
 
clustComp, a bioconductor package for the comparison of clustering results border= 
 
Aurora Torrente; Alvis Brazma
 
 
 
DATA AND TEXT MINING
 
 
 
psygenet2r: a R/Bioconductor package for the analysis of psychiatric disease genes border= 
 
Alba Gutiérrez-Sacristán; Carles Hernández-Ferrer; Juan R González; Laura I Furlong
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
PiMP my metabolome: an integrated, web-based tool for LC-MS metabolomics data border= 
 
Yoann Gloaguen; Fraser Morton; Rónán Daly; Ross Gurden ; Simon Rogers ...
 
 
ncDR: a comprehensive resource of non-coding RNAs involved in drug resistance 
 
Enyu Dai ; Feng Yang; Jing Wang; Xu Zhou; Qian Song ...
 
 
Enabling reproducible real-time quantitative PCR research: the RDML package 
 
Stefan Rödiger; MichaƂ Burdukiewicz; Andrej-Nikolai Spiess ; Konstantin Blagodatskikh
 
 
SPECIAL ISSUE: HITSEQ
 
 
 
 
GENOME ANALYSIS
 
 
 
Genotyping inversions and tandem duplications 
 
Jana Ebler; Alexander Schönhuth; Tobias Marschall
 
 
 
SEQUENCE ANALYSIS
 
 
 
TwoPaCo: an efficient algorithm to build the compacted de Bruijn graph from many complete genomes 
 
Ilia Minkin ; Son Pham; Paul Medvedev
 
 
Rail-RNA: scalable analysis of RNA-seq splicing and coverage 
 
Abhinav Nellore; Leonardo Collado-Torres; Andrew E Jaffe; José Alquicira-Hernández; Christopher Wilks ...
 
 
popSTR: population-scale detection of STR variants  
 
Snædís Kristmundsdóttir; Brynja D Sigurpálsdóttir; Birte Kehr ; Bjarni V Halldórsson
 
 
CORRIGENDA
 
 
 
DeepLoc: prediction of protein subcellular localization using deep learning 
 
Jose Juan Almagro Armenteros; Casper Kaae Sønderby; Søren Kaae Sønderby; Henrik Nielsen ; Ole Winther
 
 
iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data 
 
Riccardo Panero ; Antonio Rinaldi; Domenico Memoli; Giovanni Nassa; Maria Ravo ...
 
 
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