Subject: Bioinformatics Table of Contents for 15 February 2018 Oxford Academic
 
 
 
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Bioinformatics  
Volume 34 Issue 4
 
15 February 2018
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Genome-wide pre-miRNA discovery from few labeled examples 
 
C Yones; G Stegmayer; D H Milone; Cenk Sahinalp
 
 
findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies  
 
Hequan Sun; Jia Ding; Mathieu Piednoël ; Korbinian Schneeberger; Inanc Birol
 
 
Compression of genomic sequencing reads via hash-based reordering: algorithm and analysis 
 
Shubham Chandak; Kedar Tatwawadi; Tsachy Weissman; Inanc Birol
 
 
 
SEQUENCE ANALYSIS
 
 
 
Squeakr: an exact and approximate k-mer counting system 
 
Prashant Pandey ; Michael A Bender; Rob Johnson; Rob Patro; Bonnie Berger
 
 
Beyond similarity assessment: selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm border= 
 
Taikai Takeda ; Michiaki Hamada; John Hancock
 
 
 
 
MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes 
 
Pierre Pericard ; Yoann Dufresne; Loïc Couderc; Samuel Blanquart; Hélène Touzet ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures border= 
 
Manuel Alejandro Marín-López; Joan Planas-Iglesias; Joaquim Aguirre-Plans; Jaume Bonet; Javier Garcia-Garcia ...
 
 
BetaSerpentine: a bioinformatics tool for reconstruction of amyloid structures 
 
Stanislav A Bondarev; Olga V Bondareva ; Galina A Zhouravleva; Andrey V Kajava; Alfonso Valencia
 
 
ThreaDNA: predicting DNA mechanics' contribution to sequence selectivity of proteins along whole genomes 
 
Jasmin Cevost; Cédric Vaillant; Sam Meyer; Burkhard Rost
 
 
 
GENE EXPRESSION
 
 
 
Generalized correlation measure using count statistics for gene expression data with ordered samples 
 
Y X Rachel Wang ; Ke Liu; Elizabeth Theusch; Jerome I Rotter; Marisa W Medina ...
 
 
 
 
Robust and sparse correlation matrix estimation for the analysis of high-dimensional genomics data 
 
Angela Serra; Pietro Coretto; Michele Fratello; Roberto Tagliaferri ; Oliver Stegle
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Applying family analyses to electronic health records to facilitate genetic research 
 
Xiayuan Huang; Robert C Elston; Guilherme J Rosa; John Mayer; Zhan Ye ...
 
 
An omnibus test for differential distribution analysis of microbiome sequencing data 
 
Jun Chen; Emily King ; Rebecca Deek; Zhi Wei; Yue Yu ...
 
 
 
DATA AND TEXT MINING
 
 
 
A collaborative filtering-based approach to biomedical knowledge discovery 
 
Jake Lever; Sitanshu Gakkhar; Michael Gottlieb ; Tahereh Rashnavadi; Santina Lin ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier border= 
 
Maxat Kulmanov; Mohammed Asif Khan; Robert Hoehndorf; Jonathan Wren
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
Segway 2.0: Gaussian mixture models and minibatch training border= 
 
Rachel C W Chan; Maxwell W Libbrecht ; Eric G Roberts; Jeffrey A Bilmes; William Stafford Noble ...
 
 
diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data border= 
 
Caleb A Lareau; Martin J Aryee; Bonnie Berger
 
 
HiCapTools: a software suite for probe design and proximity detection for targeted chromosome conformation capture applications 
 
Anandashankar Anil; Rapolas Spalinskas ; Örjan Åkerborg; Pelin Sahlén; Bonnie Berger
 
 
SAGE2: parallel human genome assembly 
 
Michael Molnar; Ehsan Haghshenas; Lucian Ilie; Inanc Birol
 
 
Krait: an ultrafast tool for genome-wide survey of microsatellites and primer design 
 
Lianming Du; Chi Zhang; Qin Liu ; Xiuyue Zhang; Bisong Yue ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy 
 
Jiangning Song; Fuyi Li; André Leier; Tatiana T Marquez-Lago ; Tatsuya Akutsu ...
 
 
CLIFinder: identification of LINE-1 chimeric transcripts in RNA-seq data 
 
Marie-Elisa Pinson ; Romain Pogorelcnik; Franck Court; Philippe Arnaud; Catherine Vaurs-Barrière ...
 
 
 
GENE EXPRESSION
 
 
 
Towards unified quality verification of synthetic count data with countsimQC border= 
 
Charlotte Soneson; Mark D Robinson; Ziv Bar-Joseph
 
 
 
PROTEOMICS
 
 
 
Phosphonormalizer: an R package for normalization of MS-based label-free phosphoproteomics 
 
Sohrab Saraei; Tomi Suomi; Otto Kauko ; Laura L Elo; Oliver Stegle
 
 
 
SYSTEMS BIOLOGY
 
 
 
PyDREAM: high-dimensional parameter inference for biological models in python border=  
 
Erin M Shockley; Jasper A Vrugt; Carlos F Lopez ; Alfonso Valencia
 
 
UC2 search: using unique connectivity of uncharged compounds for metabolite annotation by database searching in mass spectrometry-based metabolomics border= 
 
Nozomu Sakurai; Takafumi Narise; Joon-Soo Sim; Chang-Muk Lee; Chiaki Ikeda ...
 
 
xMWAS: a data-driven integration and differential network analysis tool 
 
Karan Uppal; Chunyu Ma ; Young-Mi Go; Dean P Jones; Jonathan Wren
 
 
PyBEL: a computational framework for Biological Expression Language border= 
 
Charles Tapley Hoyt; Andrej Konotopez; Christian Ebeling; Jonathan Wren
 
 
PESTO: Parameter EStimation TOolbox border= 
 
Paul Stapor ; Daniel Weindl; Benjamin Ballnus; Sabine Hug; Carolin Loos ...
 
 
 
DATA AND TEXT MINING
 
 
 
ViewBS: a powerful toolkit for visualization of high-throughput bisulfite sequencing data border= 
 
Xiaosan Huang; Shaoling Zhang; Kongqing Li; Jyothi Thimmapuram; Shaojun Xie ...
 
 
ROSC-Pred: web-service for rodent organ-specific carcinogenicity prediction 
 
Alexey Lagunin; Anastasia Rudik ; Dmitry Druzhilovsky; Dmitry Filimonov; Vladimir Poroikov ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
OncomiR : an online resource for exploring pan-cancer microRNA dysregulation 
 
Nathan W Wong; Yuhao Chen; Shuai Chen ; Xiaowei Wang; Alfonso Valencia
 
 
ndexr'an R package to interface with the network data exchange 
 
Florian Auer; Zaynab Hammoud; Alexandr Ishkin; Dexter Pratt; Trey Ideker ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
SliceMap: an algorithm for automated brain region annotation 
 
Michaël Barbier; Astrid Bottelbergs; Rony Nuydens; Andreas Ebneth; Winnok H De Vos ...
 
 
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