Subject: Bioinformatics Table of Contents for 15 July 2017 Oxford Academic
 
 
 
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New issue alert
 
Bioinformatics  
Volume 33 Issue 14
 
15 July 2017
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
swga: a primer design toolkit for selective whole genome amplification border= 
 
Erik L. Clarke; Sesh A. Sundararaman; Stephanie N. Seifert; Frederic D. Bushman ; Beatrice H. Hahn ...
 
 
Tagging SNP-set selection with maximum information based on linkage disequilibrium structure in genome-wide association studies 
 
Shudong Wang ; Sicheng He; Fayou Yuan; Xinjie Zhu
 
 
 
SEQUENCE ANALYSIS
 
 
 
Pseudoalignment for metagenomic read assignment 
 
L. Schaeffer; H. Pimentel; N. Bray ; P. Melsted; L. Pachter
 
 
RNAscClust
: clustering RNA sequences using structure conservation and graph based motifs border=
 
 
Milad Miladi; Alexander Junge; Fabrizio Costa; Stefan E. Seemann ; Jakob Hull Havgaard ...
 
 
Computational modeling of in vivo and in vitro protein-DNA interactions by multiple instance learning 
 
Zhen Gao ; Jianhua Ruan
 
 
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
A network model predicts the intensity of residue-protein thermal coupling 
 
Luciano Censoni; Heloisa dos Santos Muniz; Leandro Mart├şnez
 
 
Fast, clash-free RNA conformational morphing using molecular junctions 
 
Am├ęlie H├ęliou; Dominik Budday; Rasmus Fonseca; Henry van den Bedem
 
 
 
GENE EXPRESSION
 
 
 
QRank: a novel quantile regression tool for eQTL discovery 
 
Xiaoyu Song ; Gen Li; Zhenwei Zhou; Xianling Wang; Iuliana Ionita-Laza ...
 
 
Quantifying circular RNA expression from RNA-seq data using model-based framework 
 
Musheng Li; Xueying Xie; Jing Zhou; Mengying Sheng ; Xiaofeng Yin ...
 
 
Meta-analytic framework for liquid association 
 
Lin Wang ; Silvia Liu; Ying Ding; Shin-sheng Yuan; Yen-Yi Ho ...
 
 
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Fast admixture analysis and population tree estimation for SNP and NGS data 
 
Jade Yu Cheng; Thomas Mailund; Rasmus Nielsen
 
 
 
SYSTEMS BIOLOGY
 
 
 
SANA: simulated annealing far outperforms many other search algorithms for biological network alignment 
 
Nil Mamano ; Wayne B. Hayes
 
 
Stepwise inference of likely dynamic flux distributions from metabolic time series data 
 
Mojdeh Faraji ; Eberhard O. Voit
 
 
VCNet: vector-based gene co-expression network construction and its application to RNA-seq data 
 
Zengmiao Wang ; Huaying Fang; Nelson Leung-Sang Tang; Minghua Deng
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Morphologically constrained spectral unmixing by dictionary learning for multiplex fluorescence microscopy 
 
Murad Megjhani; Pedro Correa de Sampaio ; Julienne Leigh Carstens; Raghu Kalluri; Badrinath Roysam
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
DNA Compass: a secure, client-side site for navigating personal genetic information border= 
 
Charles Curnin ; Assaf Gordon; Yaniv Erlich
 
 
Dynamix: dynamic visualization by automatic selection of informative tracks from hundreds of genomic datasets border= 
 
Matthias Monfort; Eileen E. M. Furlong; Charles Girardot
 
 
SynMap2 and SynMap3D: web-based whole-genome synteny browsers 
 
Asher Haug-Baltzell; Sean A. Stephens; Sean Davey; Carlos E. Scheidegger; Eric Lyons
 
 
HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps border= 
 
Koon-Kiu Yan; Galip G├╝rkan Yard─▒mc─▒; Chengfei Yan; William S. Noble; Mark Gerstein
 
 
GenomeScope: fast reference-free genome profiling from short reads 
 
Gregory W. Vurture; Fritz J. Sedlazeck ; Maria Nattestad; Charles J. Underwood; Han Fang ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
ResistoMap'online visualization of human gut microbiota antibiotic resistome border= 
 
Konstantin S. Yarygin; Boris A. Kovarsky ; Tatyana S. Bibikova; Damir S. Melnikov; Alexander V. Tyakht ...
 
 
poRe GUIs for parallel and real-time processing of MinION sequence data border= 
 
Robert D. Stewart; Mick Watson
 
 
ConKit: a python interface to contact predictions border= 
 
Felix Simkovic; Jens M. H. Thomas; Daniel J. Rigden
 
 
Aozan: an automated post-sequencing data-processing pipeline  
 
Sandrine Perrin; Cyril Firmo; Sophie Lemoine ; St├ęphane Le Crom; Laurent Jourdren
 
 
 
PHYLOGENETICS
 
 
 
DLTree: efficient and accurate phylogeny reconstruction using the dynamical language method 
 
Qi Wu; Zu-Guo Yu; Jianyi Yang
 
 
 
GENE EXPRESSION
 
 
 
rMATS-DVR: rMATS discovery of differential variants in RNA 
 
Jinkai Wang ; Yang Pan; Shihao Shen; Lan Lin; Yi Xing
 
 
The RNASeq-er API'a gateway to systematically updated analysis of public RNA-seq data border= 
 
Robert Petryszak; Nuno A. Fonseca ; Anja F├╝llgrabe; Laura Huerta; Maria Keays ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution 
 
Thomas O. McDonald; Franziska Michor
 
 
Constructing linkage maps in the genomics era with MapDisto 2.0  
 
Christopher Heffelfinger; Christopher A. Fragoso; Mathias Lorieux
 
 
 
SYSTEMS BIOLOGY
 
 
 
MaBoSS 2.0: an environment for stochastic Boolean modeling 
 
Gautier Stoll ; Barth├ęl├ęmy Caron; Eric Viara; Aur├ęlien Dugourd; Andrei Zinovyev ...
 
 
SmartR: an open-source platform for interactive visual analytics for translational research data border= 
 
Sascha Herzinger; Wei Gu ; Venkata Satagopam; Serge Eifes; Kavita Rege ...
 
 
Estimating gene regulatory networks with pandaR border= 
 
Daniel Schlauch; Joseph N. Paulson; Albert Young; Kimberly Glass ; John Quackenbush
 
 
MetCCS predictor: a web server for predicting collision cross-section values of metabolites in ion mobility-mass spectrometry based metabolomics 
 
Zhiwei Zhou ; Xin Xiong; Zheng-Jiang Zhu
 
 
PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data 
 
Istemi Bahceci; Ugur Dogrusoz; Konnor C. La; ├ zg├╝n Babur; Jianjiong Gao ...
 
 
 
DATA AND TEXT MINING
 
 
 
HLA-MA: simple yet powerful matching of samples using HLA typing results 
 
Clemens Messerschmidt; Manuel Holtgrewe; Dieter Beule
 
 
MESSAGE FROM THE ISCB
 
 
 
Message from the ISCB: 2017 ISCB Innovator Award Given to Aviv Regev 
 
Christiana N. Fogg; Diane E. Kovats; Bonnie Berger
 
 
Message from the ISCB: 2017 ISCB Accomplishment by a Senior Scientist Award Given to Pavel Pevzner 
 
Christiana N. Fogg; Diane E. Kovats ; Bonnie Berger
 
 
Message from the ISCB: 2017 ISCB Overton Prize Awarded to Christoph Bock 
 
Christiana N. Fogg ; Diane E. Kovats; Bonnie Berger
 
 
Message from the ISCB: 2017 Outstanding Contributions to ISCB Award Given to Fran Lewitter 
 
Christiana N. Fogg; Diane E. Kovats; Bonnie Berger
 
 
ISMB/ECCB 2017: THE 25TH ANNUAL CONFERENCE INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY HELD JOINTLY WITH THE 16TH ANNUAL EUROPEAN CONFERENCE ON COMPUTATIONAL BIOLOGY, PRAGUE, CZECH REPUBLIC, JULY 21'25, 2017
 
 
 
 
ISMB/ECCB 2017 PROCEEDINGS
 
 
 
ISMB/ECCB 2017 proceedings border= 
 
Niko Beerenwinkel; Yana Bromberg
 
 
 
ISMB/ECCB 2017 PROCEEDINGS PAPERS COMMITTEE
 
 
 
ISMB/ECCB 2017 PROCEEDINGS PAPERS COMMITTEE border= 
 
 
 
 
3DSIG
 
 
 
CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions border= 
 
Mark A. Hallen; Bruce R. Donald
 
 
Deep learning-based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms border= 
 
Min Xu; Xiaoqi Chai; Hariank Muthakana; Xiaodan Liang ; Ge Yang ...
 
 
Large-scale structure prediction by improved contact predictions and model quality assessment border= 
 
Mirco Michel; David Men├ęndez Hurtado; Karolis Uziela; Arne Elofsson
 
 
SnapDock'template-based docking by Geometric Hashing border= 
 
Michael Estrin; Haim J. Wolfson
 
 
 
BIO-ONTOLOGIES
 
 
 
Deep learning with word embeddings improves biomedical named entity recognition border= 
 
Maryam Habibi; Leon Weber; Mariana Neves; David Luis Wiegandt; Ulf Leser
 
 
BIOSSES: a semantic sentence similarity estimation system for the biomedical domain border= 
 
Gizem So─čanc─▒o─člu ; Hakime ├ zt├╝rk; Arzucan ├ zg├╝r
 
 
 
CAMDA
 
 
 
Rectified factor networks for biclustering of omics data border= 
 
Djork-Arn├ę Clevert; Thomas Unterthiner; Gundula Povysil; Sepp Hochreiter
 
 
Applying meta-analysis to genotype-tissue expression data from multiple tissues to identify eQTLs and increase the number of eGenes border= 
 
Dat Duong ; Lisa Gai; Sagi Snir; Eun Yong Kang; Buhm Han ...
 
 
 
FUNCTION
 
 
 
Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference border= 
 
Cl├ęment-Marie Train; Natasha M. Glover; Gaston H. Gonnet; Adrian M. Altenhoff; Christophe Dessimoz
 
 
DextMP: deep dive into text for predicting moonlighting proteins border= 
 
Ishita K. Khan ; Mansurul Bhuiyan; Daisuke Kihara
 
 
 
HITSEQ
 
 
 
Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding border=  
 
Xu Min; Wanwen Zeng; Ning Chen ; Ting Chen; Rui Jiang
 
 
HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington's epigenetic landscape border= 
 
Jing Guo; Jie Zheng
 
 
Improving the performance of minimizers and winnowing schemes border= 
 
Guillaume Mar├žais; David Pellow; Daniel Bork; Yaron Orenstein ; Ron Shamir ...
 
 
Modelling haplotypes with respect to reference cohort variation graphs border= 
 
Yohei Rosen; Jordan Eizenga; Benedict Paten
 
 
Abundance estimation and differential testing on strain level in metagenomics data border= 
 
Martina Fischer; Benjamin Strauch; Bernhard Y. Renard
 
 
deBGR: an efficient and near-exact representation of the weighted de Bruijn graph border= 
 
Prashant Pandey; Michael A. Bender ; Rob Johnson; Rob Patro
 
 
Improved data-driven likelihood factorizations for transcript abundance estimation border= 
 
Mohsen Zakeri; Avi Srivastava; Fatemeh Almodaresi; Rob Patro
 
 
Tumor phylogeny inference using tree-constrained importance sampling border= 
 
Gryte Satas; Benjamin J. Raphael
 
 
Discovery and genotyping of novel sequence insertions in many sequenced individuals border= 
 
P─▒nar Kavak ; Yen-Yi Lin; Ibrahim Numanagi─ç; Hossein Asghari; Tunga G├╝ng├Âr ...
 
 
 
NETBIO
 
 
 
Incorporating interaction networks into the determination of functionally related hit genes in genomic experiments with Markov random fields border= 
 
Sean Robinson; Jaakko Nevalainen; Guillaume Pinna; Anna Campalans; J. Pablo Radicella ...
 
 
Alignment of dynamic networks border= 
 
V. Vijayan ; D. Critchlow; T. Milenkovi─ç
 
 
Predicting multicellular function through multi-layer tissue networks border= 
 
Marinka Zitnik; Jure Leskovec
 
 
A new method to study the change of miRNA'mRNA interactions due to environmental exposures border= 
 
Francesca Petralia; Vasily N. Aushev; Kalpana Gopalakrishnan; Maya Kappil ; Nyan W. Khin ...
 
 
Multiple network-constrained regressions expand insights into influenza vaccination responses border= 
 
Stefan Avey; Subhasis Mohanty; Jean Wilson; Heidi Zapata; Samit R. Joshi ...
 
 
Image-based spatiotemporal causality inference for protein signaling networks border= 
 
Xiongtao Ruan ; Christoph W├╝lfing; Robert F. Murphy
 
 
 
REGGEN
 
 
 
Denoising genome-wide histone ChIP-seq with convolutional neural networks border= 
 
Pang Wei Koh; Emma Pierson; Anshul Kundaje
 
 
TITER: predicting translation initiation sites by deep learning border= 
 
Sai Zhang; Hailin Hu ; Tao Jiang; Lei Zhang; Jianyang Zeng
 
 
Direct AUC optimization of regulatory motifs border= 
 
Lin Zhu; Hong-Bo Zhang; De-Shuang Huang
 
 
Exploiting sequence-based features for predicting enhancer'promoter interactions border= 
 
Yang Yang; Ruochi Zhang ; Shashank Singh; Jian Ma
 
 
miniMDS: 3D structural inference from high-resolution Hi-C data border= 
 
Lila Rieber; Shaun Mahony
 
 
 
RNA
 
 
 
DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields border= 
 
Mingfu Shao; Jianzhu Ma; Sheng Wang
 
 
Integrative deep models for alternative splicing border= 
 
Anupama Jha; Matthew R. Gazzara ; Yoseph Barash
 
 
Efficient approximations of RNA kinetics landscape using non-redundant sampling border= 
 
Juraj Mich├ílik; H├ęl├Ęne Touzet; Yann Ponty
 
 
 
SYSMOD
 
 
 
A scalable moment-closure approximation for large-scale biochemical reaction networks border= 
 
Atefeh Kazeroonian; Fabian J. Theis ; Jan Hasenauer
 
 
Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data border= 
 
Eugenio Cinquemani; Val├ęrie Laroute; Muriel Cocaign-Bousquet; Hidde de Jong; Delphine Ropers
 
 
popFBA: tackling intratumour heterogeneity with Flux Balance Analysis border= 
 
Chiara Damiani ; Marzia Di Filippo; Dario Pescini; Davide Maspero; Riccardo Colombo ...
 
 
Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems border= 
 
Dennis Pischel; Kai Sundmacher ; Robert J. Flassig
 
 
 
TRANSMED
 
 
 
Association testing of bisulfite-sequencing methylation data via a Laplace approximation border= 
 
Omer Weissbrod; Elior Rahmani; Regev Schweiger; Saharon Rosset ; Eran Halperin
 
 
Molecular signatures that can be transferred across different omics platforms border= 
 
M. Altenbuchinger; P. Schwarzfischer; T. Rehberg; J. Reinders; Ch. W. Kohler ...
 
 
Identification of associations between genotypes and longitudinal phenotypes via temporally-constrained group sparse canonical correlation analysis border= 
 
Xiaoke Hao; Chanxiu Li; Jingwen Yan; Xiaohui Yao; Shannon L. Risacher ...
 
 
Predicting phenotypes from microarrays using amplified, initially marginal, eigenvector regression border= 
 
Lei Ding; Daniel J. McDonald
 
 
Systematic identification of feature combinations for predicting drug response with Bayesian multi-view multi-task linear regression border= 
 
Muhammad Ammad-ud-din; Suleiman A. Khan; Krister Wennerberg; Tero Aittokallio
 
 
 
VARI
 
 
 
Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes border= 
 
Yoichiro Nakatani; Aoife McLysaght
 
 
Increasing the power of meta-analysis of genome-wide association studies to detect heterogeneous effects border= 
 
C. H. Lee ; E. Eskin; B. Han
 
 
When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants border= 
 
Kymberleigh A. Pagel; Vikas Pejaver; Guan Ning Lin; Hyun-Jun Nam ; Matthew Mort ...
 
 
 
AUTHOR INDEX
 
 
 
Author Index border= 
 
 
 
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