Subject: Bioinformatics Table of Contents for 15 June 2017 Oxford Academic
 
 
 
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New issue alert
 
Bioinformatics  
Volume 33 Issue 12
 
15 June 2017
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
HIPred: an integrative approach to predicting haploinsufficient genes border= 
 
Hashem A. Shihab; Mark F. Rogers; Colin Campbell; Tom R. Gaunt
 
 
Accurate prediction of human essential genes using only nucleotide composition and association information 
 
Feng-Biao Guo; Chuan Dong; Hong-Li Hua; Shuo Liu; Hao Luo ...
 
 
pETM: a penalized Exponential Tilt Model for analysis of correlated high-dimensional DNA methylation data 
 
Hokeun Sun; Ya Wang; Yong Chen; Yun Li; Shuang Wang
 
 
 
SEQUENCE ANALYSIS
 
 
 
PhosphoPICK-SNP: quantifying the effect of amino acid variants on protein phosphorylation 
 
Ralph Patrick ; Bostjan Kobe; Kim-Anh Lê Cao; Mikael Bodén
 
 
Kollector: transcript-informed, targeted de novo assembly of gene loci border= 
 
Erdi Kucuk; Justin Chu; Benjamin P. Vandervalk; S. Austin Hammond ; René L. Warren ...
 
 
 
 
 
PHYLOGENETICS
 
 
 
STELLS2: fast and accurate coalescent-based maximum likelihood inference of species trees from gene tree topologies 
 
Jingwen Pei; Yufeng Wu
 
 
Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST 
 
Guy Baele; Philippe Lemey; Andrew Rambaut; Marc A. Suchard
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
IRaPPA: information retrieval based integration of biophysical models for protein assembly selection border= 
 
Iain H. Moal; Didier Barradas-Bautista; Brian Jiménez-García; Mieczyslaw Torchala; Arjan van der Velde ...
 
 
Statistical database analysis of the role of loop dynamics for protein'protein complex formation and allostery 
 
Yina Gu; Da-Wei Li ; Rafael Brüschweiler
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Genome-wide genetic heterogeneity discovery with categorical covariates border= 
 
Felipe Llinares-López; Laetitia Papaxanthos; Dean Bodenham; Damian Roqueiro ; COPDGene Investigators ...
 
 
 
 
 
SYSTEMS BIOLOGY
 
 
 
AptRank: an adaptive PageRank model for protein function prediction on   bi-relational graphs 
 
Biaobin Jiang; Kyle Kloster; David F. Gleich; Michael Gribskov
 
 
RelExplain'integrating data and networks to explain biological processes 
 
Evi Berchtold; Gergely Csaba; Ralf Zimmer
 
 
Benchmarking substrate-based kinase activity inference using phosphoproteomic data border= 
 
Claudia Hernandez-Armenta; David Ochoa ; Emanuel Gonçalves; Julio Saez-Rodriguez; Pedro Beltrao
 
 
 
DATA AND TEXT MINING
 
 
 
nala : text mining natural language mutation mentions border= 
 
Juan Miguel Cejuela; Aleksandar Bojchevski ; Carsten Uhlig; Rustem Bekmukhametov; Sanjeev Kumar Karn ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Bayesian network'response regression 
 
Lu Wang; Daniele Durante; Rex E. Jung ; David B. Dunson
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
cyvcf2: fast, flexible variant analysis with Python border= 
 
Brent S. Pedersen; Aaron R. Quinlan
 
 
GLINT: a user-friendly toolset for the analysis of high-throughput DNA-methylation array data 
 
Elior Rahmani; Reut Yedidim; Liat Shenhav; Regev Schweiger ; Omer Weissbrod ...
 
 
Binning_refiner: improving genome bins through the combination of different binning programs 
 
Wei-Zhi Song ; Torsten Thomas
 
 
Simulome: a genome sequence and variant simulator border= 
 
Adam Price; Cynthia Gibas
 
 
 
SEQUENCE ANALYSIS
 
 
 
Dscam1 web server: online prediction of Dscam1 self- and hetero-affinity 
 
Simone Marini; Nelson Nazzicari; Filippo Biscarini; Guang-Zhong Wang
 
 
cooccurNet: an R package for co-occurrence network construction and analysis 
 
Yuanqiang Zou; Zhiqiang Wu; Lizong Deng ; Aiping Wu; Fan Wu ...
 
 
DiagnoProt: a tool for discovery of new molecules by mass spectrometry 
 
André R.F. Silva; Diogo B. Lima; Alejandro Leyva; Rosario Duran; Carlos Batthyany ...
 
 
 
PHYLOGENETICS
 
 
 
Phyx: phylogenetic tools for unix border= 
 
Joseph W. Brown; Joseph F. Walker; Stephen A. Smith
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
FELLS: fast estimator of latent local structure 
 
Damiano Piovesan; Ian Walsh; Giovanni Minervini ; Silvio C.E. Tosatto
 
 
 
GENE EXPRESSION
 
 
 
PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF 
 
Genevieve L. Stein-O'Brien; Jacob L. Carey; Wai Shing Lee; Michael Considine; Alexander V. Favorov ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
MBV: a method to solve sample mislabeling and detect technical bias in large combined genotype and sequencing assay datasets 
 
Alexandre Fort; Nikolaos I. Panousis; Marco Garieri; Stylianos E. Antonarakis; Tuuli Lappalainen ...
 
 
OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations border= 
 
Ramon Diaz-Uriarte
 
 
VALORATE: fast and accurate log-rank test in balanced and unbalanced comparisons of survival curves and cancer genomics 
 
Victor Treviño; Jose Tamez-Pena
 
 
 
SYSTEMS BIOLOGY
 
 
 
sfinx: an R package for the elimination of false positives from affinity purification'mass spectrometry datasets 
 
Kevin Titeca ; Pieter Meysman; Kris Laukens; Lennart Martens; Jan Tavernier ...
 
 
PMAnalyzer: a new web interface for bacterial growth curve analysis border= 
 
Daniel A. Cuevas; Robert A. Edwards
 
 
 
BIOIMAGE INFORMATICS
 
 
 
MotifNet: a web-server for network motif analysis 
 
Ilan Y. Smoly ; Eugene Lerman; Michal Ziv-Ukelson; Esti Yeger-Lotem
 
 
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