Subject: Bioinformatics Table of Contents for 01 August 2018 ------=_Part_902743680.1532888573254 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_902743680.1532888573254 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Bioinformatics  
Volume 34 Issue 15
 
01 August 2018
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
TAPAS: tool for alternative polyadenylation site analysis 
 
Ashraful Arefeen; Juntao Liu; Xinshu Xiao; Tao Jiang
 
 
Repeat-aware evaluation of scaffolding tools 
 
Igor Mandric; Sergey Knyazev; Alex Zelikovsky
 
 
A Bayesian framework for multiple trait colocalization from summary association statistics 
 
Claudia Giambartolomei; Jimmy Zhenli Liu ; Wen Zhang; Mads Hauberg; Huwenbo Shi ...
 
 
Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors 
 
Jiawei Wang; Bingjiao Yang; André Leier; Tatiana T Marquez-Lago ; Morihiro Hayashida ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
Integrating long-range connectivity information into de Bruijn graphs border= 
 
Isaac Turner; Kiran V Garimella; Zamin Iqbal; Gil McVean
 
 
ADPredict: ADP-ribosylation site prediction based on physicochemical and structural descriptors border= 
 
Matteo Lo Monte; Candida Manelfi ; Marica Gemei; Daniela Corda; Andrea Rosario Beccari
 
 
SCOTCH: subtype A coreceptor tropism classification in HIV-1 
 
Hannah F Löchel; Mona Riemenschneider; Dmitrij Frishman; Dominik Heider
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Cost function network-based design of protein'protein interactions: predicting changes in binding affinity 
 
Clément Viricel ; Simon de Givry; Thomas Schiex; Sophie Barbe
 
 
NMRNet: a deep learning approach to automated peak picking of protein NMR spectra 
 
Piotr Klukowski; Michał Augoff; Maciej Zięba; Maciej Drwal ; Adam Gonczarek ...
 
 
CoABind: a novel algorithm for Coenzyme A (CoA)- and CoA derivatives-binding residues prediction 
 
Qiaozhen Meng ; Zhenling Peng; Jianyi Yang
 
 
DeepSol: a deep learning framework for sequence-based protein solubility prediction 
 
Sameer Khurana; Reda Rawi; Khalid Kunji; Gwo-Yu Chuang; Halima Bensmail ...
 
 
 
DATA AND TEXT MINING
 
 
 
A global network of biomedical relationships derived from text border= 
 
Bethany Percha ; Russ B Altman
 
 
A new method for the high-precision assessment of tumor changes in response to treatment border= 
 
P D Tar; N A Thacker; M Babur; Y Watson; S Cheung ...
 
 
Mitigating the adverse impact of batch effects in sample pattern detection 
 
Teng Fei; Tengjiao Zhang ; Weiyang Shi; Tianwei Yu
 
 
Learned protein embeddings for machine learning 
 
Kevin K Yang; Zachary Wu; Claire N Bedbrook; Frances H Arnold
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
MIRA: an R package for DNA methylation-based inference of regulatory activity border=  
 
John T Lawson; Eleni M Tomazou; Christoph Bock ; Nathan C Sheffield
 
 
EPIC-CoGe: managing and analyzing genomic data border= 
 
Andrew D L Nelson; Asher K Haug-Baltzell; Sean Davey; Brian D Gregory; Eric Lyons
 
 
METHCOMP: a special purpose compression platform for DNA methylation data 
 
Jianhao Peng; Olgica Milenkovic ; Idoia Ochoa
 
 
EWAS: epigenome-wide association study software 2.0 border= 
 
Jing Xu; Linna Zhao; Di Liu; Simeng Hu; Xiuling Song ...
 
 
accuMUlate: a mutation caller designed for mutation accumulation experiments 
 
David J Winter; Steven H Wu ; Abigail A Howell; Ricardo B R Azevedo; Rebecca A Zufall ...
 
 
AGORA: organellar genome annotation from the amino acid and nucleotide references 
 
Jaehee Jung; Jong Im Kim; Young-Sik Jeong; Gangman Yi
 
 
 
SEQUENCE ANALYSIS
 
 
 
esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis border= 
 
Zheng Wei ; Wei Zhang; Huan Fang; Yanda Li; Xiaowo Wang
 
 
NanoPack: visualizing and processing long-read sequencing data border= 
 
Wouter De Coster; Svenn D'Hert ; Darrin T Schultz; Marc Cruts; Christine Van Broeckhoven
 
 
SCRAM: a pipeline for fast index-free small RNA read alignment and visualization 
 
Stephen J Fletcher; Mikael Boden; Neena Mitter; Bernard J Carroll
 
 
Arioc: GPU-accelerated alignment of short bisulfite-treated reads 
 
Richard Wilton; Xin Li ; Andrew P Feinberg; Alexander S Szalay
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
CMV: visualization for RNA and protein family models and their comparisons border= 
 
Florian Eggenhofer; Ivo L Hofacker; Rolf Backofen; Christian Höner zu Siederdissen
 
 
REStLESS: automated translation of glycan sequences from residue-based notation to SMILES and atomic coordinates 
 
Ivan Yu Chernyshov ; Philip V Toukach
 
 
 
GENE EXPRESSION
 
 
 
Design tools for MPRA experiments 
 
Andrew R Ghazi ; Edward S Chen; David M Henke; Namrata Madan; Leonard C Edelstein ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
SPV: a JavaScript Signaling Pathway Visualizer border= 
 
Alberto Calderone; Gianni Cesareni
 
 
 
DATA AND TEXT MINING
 
 
 
ddPCRclust: an R package and Shiny app for automated analysis of multiplexed ddPCR data border= 
 
Benedikt G Brink ; Justin Meskas; Ryan R Brinkman
 
 
SimPhospho: a software tool enabling confident phosphosite assignment border= 
 
Veronika Suni; Tomi Suomi; Tomoya Tsubosaka; Susumu Y Imanishi ; Laura L Elo ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
MetaboCraft: building a Minecraft plugin for metabolomics border= 
 
Anargyros Megalios; Rónán Daly; Karl Burgess
 
 
 
BIOIMAGE INFORMATICS
 
 
 
QuimP: analyzing transmembrane signalling in highly deformable cells border= 
 
Piotr Baniukiewicz; Sharon Collier; Till Bretschneider
 
 
LETTER TO THE EDITOR
 
 
 
 
DATA AND TEXT MINING
 
 
 
Data mining of effect sizes from PubMed abstracts: a cross-study conceptual replication  
 
Paul Monsarrat; Jean-Noel Vergnes
 
 
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