Subject: Bioinformatics Table of Contents for 15 June 2018 ------=_Part_269946010.1529257941131 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_269946010.1529257941131 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Bioinformatics  
Volume 34 Issue 12
 
15 June 2018
 
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DISCOVERY NOTE
 
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Evolutionary relationship between the cysteine and histidine rich domains (CHORDs) and Btk-type zinc fingers 
 
Gurmeet Kaur; Srikrishna Subramanian
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
HPViewer: sensitive and specific genotyping of human papillomavirus in metagenomic DNA 
 
Yuhan Hao; Liying Yang; Antonio Galvao Neto; Milan R Amin; Dervla Kelly ...
 
 
EPS-LASSO: test for high-dimensional regression under extreme phenotype sampling of continuous traits 
 
Chao Xu; Jian Fang; Hui Shen; Yu-Ping Wang; Hong-Wen Deng
 
 
Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants border= 
 
Zhihui Luo; Xinping Fan; Yao Su; Yu S Huang
 
 
Progressive approach for SNP calling and haplotype assembly using single molecular sequencing data 
 
Fei Guo; Dan Wang; Lusheng Wang
 
 
 
 
 
SEQUENCE ANALYSIS
 
 
 
BAUM: improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach 
 
Anqi Wang; Zhanyu Wang ; Zheng Li; Lei M Li
 
 
O-GlcNAcPRED-II: an integrated classification algorithm for identifying O-GlcNAcylation sites based on fuzzy undersampling and a K-means PCA oversampling technique 
 
Cangzhi Jia; Yun Zuo; Quan Zou
 
 
A low-complexity add-on score for protein remote homology search with COMER 
 
Mindaugas Margelevičius
 
 
HIITE: HIV-1 incidence and infection time estimator 
 
Sung Yong Park; Tanzy M T Love; Shivankur Kapoor; Ha Youn Lee
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
pepKalc: scalable and comprehensive calculation of electrostatic interactions in random coil polypeptides 
 
Kamil Tamiola; Ruud M Scheek ; Pieter van der Meulen; Frans A A Mulder
 
 
 
 
Novel overlapping subgraph clustering for the detection of antigen epitopes 
 
Liang Zhao ; Shaogui Wu; Jiawen Jiang; Wencui Li; Jie Luo ...
 
 
 
GENE EXPRESSION
 
 
 
Spectral clustering based on learning similarity matrix 
 
Seyoung Park ; Hongyu Zhao
 
 
scEpath: energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data border= 
 
Suoqin Jin; Adam L MacLean; Tao Peng; Qing Nie
 
 
 
SYSTEMS BIOLOGY
 
 
 
PhenoRank: reducing study bias in gene prioritization through simulation border= 
 
Alex J Cornish; Alessia David; Michael J E Sternberg
 
 
ChemDistiller: an engine for metabolite annotation in mass spectrometry border= 
 
Ivan Laponogov; Noureddin Sadawi; Dieter Galea; Reza Mirnezami; Kirill A Veselkov
 
 
 
DATA AND TEXT MINING
 
 
 
Towards self-learning based hypotheses generation in biomedical text domain 
 
Vishrawas Gopalakrishnan; Kishlay Jha; Guangxu Xun; Hung Q Ngo ; Aidong Zhang
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
TOXsIgN: a cross-species repository for toxicogenomic signatures 
 
Thomas A Darde; Pierre Gaudriault; Rémi Beranger; Clément Lancien; Annaëlle Caillarec-Joly ...
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
TSAPA: identification of tissue-specific alternative polyadenylation sites in plants 
 
Guoli Ji; Moliang Chen; Wenbin Ye; Sheng Zhu; Congting Ye ...
 
 
Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny 
 
Eugene Urrutia; Hao Chen ; Zilu Zhou; Nancy R Zhang; Yuchao Jiang
 
 
GCevobase: an evolution-based database for GC content in eukaryotic genomes 
 
Dapeng Wang
 
 
 
SEQUENCE ANALYSIS
 
 
 
Kpax3: Bayesian bi-clustering of large sequence datasets border= 
 
Alberto Pessia; Jukka Corander
 
 
GCPred: a web tool for guanylyl cyclase functional centre prediction from amino acid sequence 
 
Nuo Xu; Dongfang Fu; Shiang Li; Yuxuan Wang ; Aloysius Wong
 
 
 
GENE EXPRESSION
 
 
 
INfORM: Inference of NetwOrk Response Modules border= 
 
Veer Singh Marwah; Pia Anneli Sofia Kinaret; Angela Serra; Giovanni Scala ; Antti Lauerma ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Improving SNP prioritization and pleiotropic architecture estimation by incorporating prior knowledge using graph-GPA 
 
Hang J Kim; Zhenning Yu; Andrew Lawson; Hongyu Zhao ; Dongjun Chung
 
 
omicsPrint: detection of data linkage errors in multiple omics studies 
 
Maarten van Iterson ; Davy Cats; Paul Hop; Bastiaan T Heijmans
 
 
KMgene: a unified R package for gene-based association analysis for complex traits border= 
 
Qi Yan; Zhou Fang; Wei Chen
 
 
 
SYSTEMS BIOLOGY
 
 
 
GEMMER: GEnome-wide tool for Multi-scale Modeling data Extraction and Representation for Saccharomyces cerevisiae border= 
 
Thierry D G A Mondeel; Frédéric Crémazy; Matteo Barberis
 
 
L1000FWD: fireworks visualization of drug-induced transcriptomic signatures 
 
Zichen Wang; Alexander Lachmann; Alexandra B Keenan; Avi Ma'ayan
 
 
Selenzyme: enzyme selection tool for pathway design border= 
 
Pablo Carbonell ; Jerry Wong; Neil Swainston; Eriko Takano; Nicholas J Turner ...
 
 
ssbio: a Python framework for structural systems biology 
 
Nathan Mih; Elizabeth Brunk; Ke Chen; Edward Catoiu; Anand Sastry ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
AbDesigner3D: a structure-guided tool for peptide-based antibody production 
 
Thammakorn Saethang; Kenneth Hodge; Ingorn Kimkong; D Michael Payne; Mark A Knepper ...
 
 
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