Subject: Bioinformatics Table of Contents for 15 December 2018 ------=_Part_398359451.1544807755214 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_398359451.1544807755214 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Bioinformatics  
Volume 34 Issue 24
 
15 December 2018
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
AA9int: SNP interaction pattern search using non-hierarchical additive model set 
 
Hui-Yi Lin; Po-Yu Huang; Dung-Tsa Chen; Heng-Yuan Tung ; Thomas A Sellers ...
 
 
GIFT: Guided and Interpretable Factorization for Tensors with an application to large-scale multi-platform cancer analysis border= 
 
Jungwoo Lee ; Sejoon Oh; Lee Sael
 
 
Prediction of human-Bacillus anthracis protein'protein interactions using multi-layer neural network border=  
 
Ibrahim Ahmed; Peter Witbooi; Alan Christoffels
 
 
snpAD: an ancient DNA genotype caller border= 
 
Kay Prüfer
 
 
BMC3C: binning metagenomic contigs using codon usage, sequence composition and read coverage 
 
Guoxian Yu; Yuan Jiang; Jun Wang; Hao Zhang ; Haiwei Luo
 
 
 
SEQUENCE ANALYSIS
 
 
 
SpliceRover: interpretable convolutional neural networks for improved splice site prediction 
 
Jasper Zuallaert; Fréderic Godin; Mijung Kim; Arne Soete; Yvan Saeys ...
 
 
Practical dynamic de Bruijn graphs 
 
Victoria G Crawford; Alan Kuhnle; Christina Boucher; Rayan Chikhi ; Travis Gagie
 
 
iLoc-lncRNA: predict the subcellular location of lncRNAs by incorporating octamer composition into general PseKNC 
 
Zhen-Dong Su; Yan Huang; Zhao-Yue Zhang; Ya-Wei Zhao ; Dong Wang ...
 
 
appreci8: a pipeline for precise variant calling integrating 8 tools border=  
 
Sarah Sandmann; Mohsen Karimi; Aniek O de Graaf ; Christian Rohde; Stefanie Göllner ...
 
 
Hybrid correction of highly noisy long reads using a variable-order de Bruijn graph 
 
Pierre Morisse; Thierry Lecroq; Arnaud Lefebvre
 
 
Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome 
 
Fuyi Li; Chen Li; Tatiana T Marquez-Lago; André Leier; Tatsuya Akutsu ...
 
 
 
GENE EXPRESSION
 
 
 
LncmiRSRN: identification and analysis of long non-coding RNA related miRNA sponge regulatory network in human cancer 
 
Junpeng Zhang; Lin Liu; Jiuyong Li; Thuc Duy Le
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Comparing complex variants in family trios border=  
 
Berke Ç Topta┼č; Goran Rakocevic; Péter Kómár ; Deniz Kural
 
 
 
SYSTEMS BIOLOGY
 
 
 
Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints 
 
Siu H J Chan; Lin Wang; Satyakam Dash; Costas D Maranas
 
 
Predicting miRNA'disease association based on inductive matrix completion 
 
Xing Chen; Lei Wang; Jia Qu; Na-Na Guan ; Jian-Qiang Li
 
 
Hierarchical optimization for the efficient parametrization of ODE models border=  
 
Carolin Loos; Sabrina Krause; Jan Hasenauer
 
 
 
DATA AND TEXT MINING
 
 
 
HUME: large-scale detection of causal genetic factors of adverse drug reactions 
 
Mehrdad Mansouri; Bowei Yuan; Colin J D Ross; Bruce C Carleton ; Martin Ester
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
MetaPOAP: presence or absence of metabolic pathways in metagenome-assembled genomes 
 
Lewis M Ward; Patrick M Shih; Woodward W Fischer
 
 
GATK PathSeq: a customizable computational tool for the discovery and identification of microbial sequences in libraries from eukaryotic hosts border= 
 
Mark A Walker ; Chandra Sekhar Pedamallu; Akinyemi I Ojesina; Susan Bullman; Ted Sharpe ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
SOPanG: online text searching over a pan-genome 
 
Aleksander Cisłak; Szymon Grabowski; Jan Holub
 
 
MrBait: universal identification and design of targeted-enrichment capture probes 
 
Tyler K Chafin; Marlis R Douglas; Michael E Douglas
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
RiboSketch: versatile visualization of multi-stranded RNA and DNA secondary structure 
 
Jacob S Lu; Eckart Bindewald; Wojciech K Kasprzak; Bruce A Shapiro
 
 
Noise peak filtering in multi-dimensional NMR spectra using convolutional neural networks 
 
Naohiro Kobayashi; Yoshikazu Hattori; Takashi Nagata; Shoko Shinya ; Peter Güntert ...
 
 
 
GENE EXPRESSION
 
 
 
runibic: a Bioconductor package for parallel row-based biclustering of gene expression data 
 
Patryk Orzechowski; Artur Pa┼"szczyk; Xiuzhen Huang; Jason H Moore
 
 
iS-CellR: a user-friendly tool for analyzing and visualizing single-cell RNA sequencing data border=  
 
Mitulkumar V Patel
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
PopViz: a webserver for visualizing minor allele frequencies and damage prediction scores of human genetic variations 
 
Peng Zhang; Benedetta Bigio; Franck Rapaport; Shen-Ying Zhang; Jean-Laurent Casanova ...
 
 
pyseer: a comprehensive tool for microbial pangenome-wide association studies border=  
 
John A Lees; Marco Galardini; Stephen D Bentley ; Jeffrey N Weiser; Jukka Corander
 
 
 
SYSTEMS BIOLOGY
 
 
 
MetaboAnalystR: an R package for flexible and reproducible analysis of metabolomics data border= 
 
Jasmine Chong; Jianguo Xia
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
Database of evidence for precision oncology portal 
 
Sam Q Sun; R Jay Mashl; Sohini Sengupta; Adam D Scott ; Weihua Wang ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
SCIP: a single-cell image processor toolbox 
 
Leonardo Martins; Ramakanth Neeli-Venkata; Samuel M D Oliveira; Antti Häkkinen ; Andre S Ribeiro ...
 
 
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