Subject: Bioinformatics Table of Contents for 1 September 2019 ------=_Part_864674301.1567966053139 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_864674301.1567966053139 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Bioinformatics  
Volume 35 Issue 17
 
1 September 2019
 
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DISCOVERY NOTE
 
 
 
 
GENOME ANALYSIS
 
 
 
Identifying residues that determine palmitoylation using association rule mining 
 
Bandana Kumari; Ravindra Kumar; Manish Kumar
 
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
An accurate and powerful method for copy number variation detection 
 
Feifei Xiao; Xizhi Luo; Ning Hao; Yue S Niu ; Xiangjun Xiao ...
 
 
A simple convolutional neural network for prediction of enhancer'promoter interactions with DNA sequence data 
 
Zhong Zhuang; Xiaotong Shen; Wei Pan
 
 
SVIM: structural variant identification using mapped long reads border= 
 
David Heller; Martin Vingron
 
 
multiHiCcompare: joint normalization and comparative analysis of complex Hi-C experiments 
 
John C Stansfield; Kellen G Cresswell; Mikhail G Dozmorov
 
 
Inferring clonal heterogeneity in cancer using SNP arrays and whole genome sequencing 
 
Mark R Zucker; Lynne V Abruzzo; Carmen D Herling; Lynn L Barron ; Michael J Keating ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
MSC: a metagenomic sequence classification algorithm 
 
Subrata Saha; Jethro Johnson; Soumitra Pal; George M Weinstock ; Sanguthevar Rajasekaran
 
 
TOPAS: network-based structural alignment of RNA sequences 
 
Chun-Chi Chen; Hyundoo Jeong; Xiaoning Qian; Byung-Jun Yoon
 
 
Characterization and identification of long non-coding RNAs based on feature relationship 
 
Guangyu Wang; Hongyan Yin; Boyang Li; Chunlei Yu ; Fan Wang ...
 
 
MULTiPly: a novel multi-layer predictor for discovering general and specific types of promoters 
 
Meng Zhang; Fuyi Li; Tatiana T Marquez-Lago; André Leier ; Cunshuo Fan ...
 
 
Improved indel detection in DNA and RNA via realignment with ABRA2 border=  
 
Lisle E Mose; Charles M Perou; Joel S Parker
 
 
OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs border=  
 
Zachary Sethna; Yuval Elhanati; Curtis G Callan, Jr ; Aleksandra M Walczak; Thierry Mora
 
 
Protein fold recognition based on multi-view modeling 
 
Ke Yan; Xiaozhao Fang; Yong Xu; Bin Liu
 
 
Best-first search guided multistage mass spectrometry-based glycan identification 
 
Yaojun Wang; Dongbo Bu; Chuncui Huang; Hui Wang ; Jinyu Zhou ...
 
 
 
PHYLOGENETICS
 
 
 
Tracing the ancestry of operons in bacteria 
 
Huy N Nguyen; Ashish Jain; Oliver Eulenstein; Iddo Friedberg
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Statistical force-field for structural modeling using chemical cross-linking/mass spectrometry distance constraints 
 
Allan J R Ferrari; Fabio C Gozzo; Leandro Martínez
 
 
KORP: knowledge-based 6D potential for fast protein and loop modeling 
 
José Ramón López-Blanco; Pablo Chacón
 
 
AllerCatPro'prediction of protein allergenicity potential from the protein sequence border=  
 
Sebastian Maurer-Stroh; Nora L Krutz; Petra S Kern ; Vithiagaran Gunalan; Minh N Nguyen ...
 
 
 
GENE EXPRESSION
 
 
 
Large-scale analysis of human gene expression variability associates highly variable drug targets with lower drug effectiveness and safety border= 
 
Eyal Simonovsky ; Ronen Schuster; Esti Yeger-Lotem
 
 
ClusterMap: compare multiple single cell RNA-Seq datasets across different experimental conditions 
 
Xin Gao; Deqing Hu; Madelaine Gogol; Hua Li
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
PopCluster: an algorithm to identify genetic variants with ethnicity-dependent effects 
 
Anastasia Gurinovich; Harold Bae; John J Farrell ; Stacy L Andersen; Stefano Monti ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays 
 
Amrit Singh; Casey P Shannon; Benoît Gautier ; Florian Rohart; Michaël Vacher ...
 
 
Characterizing and ranking computed metabolic engineering strategies border=  
 
Philipp Schneider; Steffen Klamt
 
 
Benchmark problems for dynamic modeling of intracellular processes border=  
 
Helge Hass; Carolin Loos; Elba Raimúndez-Álvarez ; Jens Timmer; Jan Hasenauer ...
 
 
COmplexome Profiling ALignment (COPAL) reveals remodeling of mitochondrial protein complexes in Barth syndrome border=  
 
Joeri Van Strien; Sergio Guerrero-Castillo; Iliana A Chatzispyrou ; Riekelt H Houtkooper; Ulrich Brandt ...
 
 
A network of networks approach for modeling interconnected brain tissue-specific networks border=  
 
Hideko Kawakubo; Yusuke Matsui; Itaru Kushima ; Norio Ozaki; Teppei Shimamura
 
 
Benchmarking time-series data discretization on inference methods 
 
Yuezhe Li; Tiffany Jann; Paola Vera-Licona
 
 
 
DATA AND TEXT MINING
 
 
 
Comparison of statistical algorithms for daily syndromic surveillance aberration detection border= 
 
Angela Noufaily; Roger A Morbey ; Felipe J Colón-González; Alex J Elliot; Gillian E Smith ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
The interplay between microRNA and alternative splicing of linear and circular RNAs in eleven plant species 
 
Huiyuan Wang; Huihui Wang; Hangxiao Zhang; Sheng Liu; Yongsheng Wang ...
 
 
CMEP: a database for circulating microRNA expression profiling 
 
Jian-Rong Li; Chun-Yip Tong; Tsai-Jung Sung; Ting-Yu Kang ; Xianghong Jasmine Zhou ...
 
 
The ReproGenomics Viewer: a multi-omics and cross-species resource compatible with single-cell studies for the reproductive science community 
 
Thomas A Darde; Estelle Lecluze; Aurélie Lardenois ; Isabelle Stévant; Nathan Alary ...
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
Ordino: a visual cancer analysis tool for ranking and exploring genes, cell lines and tissue samples border= 
 
Marc Streit; Samuel Gratzl; Holger Stitz; Andreas Wernitznig; Thomas Zichner ...
 
 
Sstack: an R package for stacking with applications to scenarios involving sequential addition of samples and features 
 
Kevin Matlock; Raziur Rahman; Souparno Ghosh; Ranadip Pal
 
 
Crisflash: open-source software to generate CRISPR guide RNAs against genomes annotated with individual variation border=  
 
Adrien L S Jacquin; Duncan T Odom; Margus Lukk
 
 
PSiTE: a Phylogeny guided Simulator for Tumor Evolution 
 
Hechuan Yang; Bingxin Lu; Lan Huong Lai; Abner Herbert Lim ; Jacob Josiah Santiago Alvarez ...
 
 
ensembldb: an R package to create and use Ensembl-based annotation resources border=  
 
Johannes Rainer; Laurent Gatto; Christian X Weichenberger
 
 
Varanto: variant enrichment analysis and annotation 
 
Oskari Timonen; Mikko Särkkä; Tibor Fülöp; Anton Mattsson ; Juha Kekäläinen ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
SMuRF: portable and accurate ensemble prediction of somatic mutations border=  
 
Weitai Huang; Yu Amanda Guo; Karthik Muthukumar ; Probhonjon Baruah; Mei Mei Chang ...
 
 
SRG extractor: a skinny reference genome approach for reduced-representation sequencing 
 
Davoud Torkamaneh; Jérôme Laroche; Istvan Rajcan; François Belzile
 
 
 
PHYLOGENETICS
 
 
 
AQUAPONY: visualization and interpretation of phylogeographic information on phylogenetic trees 
 
Bastien Cazaux; Guillaume Castel; Eric Rivals
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
PyLink: a PyMOL plugin to identify links 
 
Aleksandra M Gierut; Pawel Dabrowski-Tumanski; Wanda Niemyska; Kenneth C Millett ; Joanna I Sulkowska
 
 
TopoLink: evaluation of structural models using chemical crosslinking distance constraints 
 
Allan J R Ferrari; Milan A Clasen; Louise Kurt; Paulo C Carvalho ; Fabio C Gozzo ...
 
 
Deuteros: software for rapid analysis and visualization of data from differential hydrogen deuterium exchange-mass spectrometry border= 
 
Andy M C Lau ; Zainab Ahdash; Chloe Martens; Argyris Politis
 
 
SMARTCyp 3.0: enhanced cytochrome P450 site-of-metabolism prediction server 
 
Lars Olsen; Marco Montefiori; Khanhvi Phuc Tran; Flemming Steen Jørgensen
 
 
 
GENE EXPRESSION
 
 
 
Streamlined analysis of LINCS L1000 data with the slinky package for R 
 
Eric J Kort; Stefan Jovinge
 
 
METACLUSTER'an R package for context-specific expression analysis of metabolic gene clusters 
 
Michael Banf; Kangmei Zhao; Seung Y Rhee
 
 
EBIC: an open source software for high-dimensional and big data analyses 
 
Patryk Orzechowski; Jason H Moore
 
 
DiffNetFDR: differential network analysis with false discovery rate control 
 
Xiao-Fei Zhang; Le Ou-Yang; Shuo Yang; Xiaohua Hu ; Hong Yan
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
KASPspoon: an in vitro and in silico PCR analysis tool for high-throughput SNP genotyping border= 
 
Alsamman M Alsamman; Shafik D Ibrahim ; Aladdin Hamwieh
 
 
A web application and service for imputing and visualizing missense variant effect maps border=  
 
Yingzhou Wu; Jochen Weile; Atina G Cote ; Song Sun; Jennifer Knapp ...
 
 
admixr'R package for reproducible analyses using ADMIXTOOLS border=  
 
Martin Petr; Benjamin Vernot; Janet Kelso
 
 
 
SYSTEMS BIOLOGY
 
 
 
CluMSID: an R package for similarity-based clustering of tandem mass spectra to aid feature annotation in metabolomics 
 
Tobias Depke; Raimo Franke; Mark Brönstrup
 
 
 
DATA AND TEXT MINING
 
 
 
RIscoper: a tool for RNA'RNA interaction extraction from the literature 
 
Yang Zhang; Tianyuan Liu; Liqun Chen; Jinxurong Yang ; Jiayi Yin ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
queryMed: Semantic Web functions for linking pharmacological and medical knowledge to data 
 
Y Rivault; O Dameron; N Le Meur
 
 
InterMineR: an R package for InterMine databases border= 
 
Konstantinos A Kyritsis; Bing Wang; Julie Sullivan ; Rachel Lyne; Gos Micklem
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Efficient implementation of convolutional neural networks in the data processing of two-photon in vivo imaging border= 
 
Yangzhen Wang; Feng Su ; Shanshan Wang; Chaojuan Yang; Yonglu Tian ...
 
 
 
LETTER TO THE EDITOR
 
 
 
 
GENOME ANALYSIS
 
 
 
Functional data analysis for computational biology 
 
Marzia A Cremona; Hongyan Xu; Kateryna D Makova; Matthew Reimherr ; Francesca Chiaromonte ...
 
 
 
CORRIGENDA
 
 
 
GlycanAnalyzer: software for automated interpretation of N -glycan profiles after exoglycosidase digestions border= 
 
Ian Walsh; Terry Nguyen-Khuong ; Katherine Wongtrakul-Kish; Shi Jie Tay; Daniel Chew ...
 
 
Expanded functionality, increased accuracy, and enhanced speed in the de novo genotyping-by-sequencing pipeline GBS-SNP-CROP border= 
 
Arthur T O Melo; Iago Hale
 
 
Inferring clonal heterogeneity in cancer using SNP arrays and whole genome sequencing 
 
Mark R Zucker; Lynne V Abruzzo; Carmen D Herling; Lynn L Barron ; Michael J Keating ...
 
 
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