Subject: Bioinformatics Table of Contents for 01 January 2018 ------=_Part_1944060623.1513966332785 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/ljxlu-d41kr9-63so3tc3/) [[BannerToken]] [[AlertTitleToken]] [[SelfServeTextToken]] [[FirstAdvertisingToken]] [[TOCMainToken]] Unsubscribe (http://click.skem1.com/form?ljxlu--ply5-63so3tc3&sl=tq&t=5)Manage email alerts (http://click.skem1.com/click/ljxlu-d41kra-63so3tc3/) 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/ljxlu-d41krb-63so3tc4/) [[BottomAdvertisingToken]] This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_1944060623.1513966332785 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Bioinformatics  
Volume 34 Issue 1
 
01 January 2018
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development 
 
Karolina Elżbieta Kaczor-Urbanowicz; Yong Kim; Feng Li; Timur Galeev; Rob R Kitchen ...
 
 
Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data border= 
 
Sha Joe Zhu ; Jacob Almagro-Garcia; Gil McVean
 
 
Enhanced guide-RNA design and targeting analysis for precise CRISPR genome editing of single and consortia of industrially relevant and non-model organisms 
 
Brian J Mendoza; Cong T Trinh
 
 
 
SEQUENCE ANALYSIS
 
 
 
ReMILO: reference assisted misassembly detection algorithm using short and long reads 
 
Ergude Bao; Changjin Song; Lingxiao Lan
 
 
iPromoter-2L: a two-layer predictor for identifying promoters and their types by multi-window-based PseKNC  
 
Bin Liu; Fan Yang; De-Shuang Huang ; Kuo-Chen Chou
 
 
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
In silico structural modeling of multiple epigenetic marks on DNA 
 
Konrad Krawczyk; Samuel Demharter; Bernhard Knapp; Charlotte M Deane; Peter Minary
 
 
LightDock: a new multi-scale approach to protein'protein docking 
 
Brian Jiménez-García; Jorge Roel-Touris ; Miguel Romero-Durana; Miquel Vidal; Daniel Jiménez-González ...
 
 
 
GENE EXPRESSION
 
 
 
SparseIso: a novel Bayesian approach to identify alternatively spliced isoforms from RNA-seq data 
 
Xu Shi; Xiao Wang; Tian-Li Wang ; Leena Hilakivi-Clarke; Robert Clarke ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
A nonparametric significance test for sampled networks border=  
 
Andrew Elliott; Elizabeth Leicht; Alan Whitmore ; Gesine Reinert; Felix Reed-Tsochas
 
 
 
DATA AND TEXT MINING
 
 
 
Orthologue chemical space and its influence on target prediction border=  
 
Lewis H Mervin; Krishna C Bulusu; Leen Kalash ; Avid M Afzal; Fredrik Svensson ...
 
 
 
 
tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine 
 
Chih-Hsuan Wei ; Lon Phan; Juliana Feltz; Rama Maiti; Tim Hefferon ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Morphologically constrained and data informed cell segmentation of budding yeast 
 
Elco Bakker ; Peter S Swain; Matthew M Crane
 
 
Three-dimensional cardiovascular imaging-genetics: a mass univariate framework border= 
 
Carlo Biffi; Antonio de Marvao; Mark I Attard; Timothy J W Dawes ; Nicola Whiffin ...
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
4D nucleome Analysis Toolbox: analysis of Hi-C data with abnormal karyotype and time series capabilities 
 
Laura Seaman; Indika Rajapakse
 
 
NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis border= 
 
Jochen Singer; Hans-Joachim Ruscheweyh; Ariane L Hofmann; Thomas Thurnherr; Franziska Singer ...
 
 
CSAR: a contig scaffolding tool using algebraic rearrangements 
 
Kun-Tze Chen ; Chia-Liang Liu; Shang-Hao Huang; Hsin-Ting Shen; Yi-Kung Shieh ...
 
 
biospear: an R package for biomarker selection in penalized Cox regression 
 
Nils Ternès; Federico Rotolo; Stefan Michiels
 
 
 
SEQUENCE ANALYSIS
 
 
 
Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples border= 
 
Christopher Wilks; Phani Gaddipati; Abhinav Nellore; Ben Langmead
 
 
CRISPR-RT: a web application for designing CRISPR-C2c2 crRNA with improved target specificity 
 
Houxiang Zhu; Emily Richmond; Chun Liang
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
NavMol 3.0: enabling the representation of metabolic reactions by blind users 
 
Yuri Binev ; Daniela Peixoto; Florbela Pereira; Ian Rodrigues; Sofia Cavaco ...
 
 
Mobi 2.0: an improved method to define intrinsic disorder, mobility and linear binding regions in protein structures  
 
Damiano Piovesan; Silvio C E Tosatto
 
 
 
SYSTEMS BIOLOGY
 
 
 
PySCeSToolbox: a collection of metabolic pathway analysis tools 
 
Carl D Christensen ; Jan-Hendrik S Hofmeyr; Johann M Rohwer
 
 
Interactive network visualization in Jupyter notebooks: visJS2jupyter 
 
Sara Brin Rosenthal; Julia Len; Mikayla Webster; Aaron Gary; Amanda Birmingham ...
 
 
 
DATA AND TEXT MINING
 
 
 
Kfits: a software framework for fitting and cleaning outliers in kinetic measurements 
 
Oded Rimon; Dana Reichmann
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
An automated tool for obtaining QSAR-ready series of compounds using semantic web technologies 
 
Oriol López-Massaguer; Ferran Sanz; Manuel Pastor
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Irys Extract border= 
 
Rani Arielly; Yuval Ebenstein
 
 
SMLocalizer, a GPU accelerated ImageJ plugin for single molecule localization microscopy border= 
 
Kristoffer Bernhem; Hjalmar Brismar
 
 
SPECIAL ISSUE: RECOMB-SEQ/RECOMB-CCB/RECOMB-CG
 
 
 
 
GENE EXPRESSION
 
 
 
DIMM-SC: a Dirichlet mixture model for clustering droplet-based single cell transcriptomic data 
 
Zhe Sun; Ting Wang; Ke Deng ; Xiao-Feng Wang; Robert Lafyatis ...
 
 
 
GENOME ANALYSIS
 
 
 
Faucet: streaming de novo assembly graph construction border=  
 
Roye Rozov; Gil Goldshlager; Eran Halperin ; Ron Shamir
 
 
 
SEQUENCE ANALYSIS
 
 
 
An accurate algorithm for the detection of DNA fragments from dilution pool sequencing experiments 
 
Vikas Bansal
 
 
QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data 
 
Pavel Skums ; Alex Zelikovsky; Rahul Singh; Walker Gussler; Zoya Dimitrova ...
 
 
A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures  
 
Xinan Liu; Ye Yu; Jinpeng Liu ; Corrine F Elliott; Chen Qian ...
 
 
CORRIGENDUM
 
 
 
QVZ: lossy compression of quality values 
 
Greg Malysa; Mikel Hernaez; Idoia Ochoa ; Milind Rao; Karthik Ganesan ...
 
 
ERRATUM
 
 
 
The systematic analysis of ultraconserved genomic regions in the budding yeast 
 
Zhi-Kai Yang; Feng Gao
 
 
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