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Volume 33, Issue 14
15 July 2017
ISSN 1367-4803
EISSN 1460-2059

ORIGINAL PAPERS

GENOME ANALYSIS

swga: a primer design toolkit for selective whole genome amplification
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
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 Martínez
Fast, clash-free RNA conformational morphing using molecular junctions
Amélie Héliou; 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
Charles Curnin; Assaf Gordon; Yaniv Erlich
Dynamix: dynamic visualization by automatic selection of informative tracks from hundreds of genomic datasets
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
Koon-Kiu Yan; Galip Gürkan Yardımcı; 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
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
Robert D. Stewart; Mick Watson
ConKit: a python interface to contact predictions
Felix Simkovic; Jens M. H. Thomas; Daniel J. Rigden
Aozan: an automated post-sequencing data-processing pipeline
Sandrine Perrin; Cyril Firmo; Sophie Lemoine; Stéphane 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
Robert Petryszak; Nuno A. Fonseca; Anja Füllgrabe; 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; Barthélémy Caron; Eric Viara; Aurélien Dugourd; Andrei Zinovyev ...
SmartR: an open-source platform for interactive visual analytics for translational research data
Sascha Herzinger; Wei Gu; Venkata Satagopam; Serge Eifes; Kavita Rege ...
Estimating gene regulatory networks with pandaR
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; Özgün 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
Niko Beerenwinkel; Yana Bromberg

ISMB/ECCB 2017 PROCEEDINGS PAPERS COMMITTEE

ISMB/ECCB 2017 PROCEEDINGS PAPERS COMMITTEE

3DSIG

CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions
Mark A. Hallen; Bruce R. Donald
Deep learning-based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms
Min Xu; Xiaoqi Chai; Hariank Muthakana; Xiaodan Liang; Ge Yang ...
Large-scale structure prediction by improved contact predictions and model quality assessment
Mirco Michel; David Menéndez Hurtado; Karolis Uziela; Arne Elofsson
SnapDock—template-based docking by Geometric Hashing
Michael Estrin; Haim J. Wolfson

BIO-ONTOLOGIES

Deep learning with word embeddings improves biomedical named entity recognition
Maryam Habibi; Leon Weber; Mariana Neves; David Luis Wiegandt; Ulf Leser
BIOSSES: a semantic sentence similarity estimation system for the biomedical domain
Gizem Soğancıoğlu; Hakime Öztürk; Arzucan Özgür

CAMDA

Rectified factor networks for biclustering of omics data
Djork-Arné 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
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
Clément-Marie Train; Natasha M. Glover; Gaston H. Gonnet; Adrian M. Altenhoff; Christophe Dessimoz
DextMP: deep dive into text for predicting moonlighting proteins
Ishita K. Khan; Mansurul Bhuiyan; Daisuke Kihara

HITSEQ

Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding
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
Jing Guo; Jie Zheng
Improving the performance of minimizers and winnowing schemes
Guillaume Marçais; David Pellow; Daniel Bork; Yaron Orenstein; Ron Shamir ...
Modelling haplotypes with respect to reference cohort variation graphs
Yohei Rosen; Jordan Eizenga; Benedict Paten
Abundance estimation and differential testing on strain level in metagenomics data
Martina Fischer; Benjamin Strauch; Bernhard Y. Renard
deBGR: an efficient and near-exact representation of the weighted de Bruijn graph
Prashant Pandey; Michael A. Bender; Rob Johnson; Rob Patro
Improved data-driven likelihood factorizations for transcript abundance estimation
Mohsen Zakeri; Avi Srivastava; Fatemeh Almodaresi; Rob Patro
Tumor phylogeny inference using tree-constrained importance sampling
Gryte Satas; Benjamin J. Raphael
Discovery and genotyping of novel sequence insertions in many sequenced individuals
Pınar Kavak; Yen-Yi Lin; Ibrahim Numanagić; Hossein Asghari; Tunga Güngör ...

NETBIO

Incorporating interaction networks into the determination of functionally related hit genes in genomic experiments with Markov random fields
Sean Robinson; Jaakko Nevalainen; Guillaume Pinna; Anna Campalans; J. Pablo Radicella ...
Alignment of dynamic networks
V. Vijayan; D. Critchlow; T. Milenković
Predicting multicellular function through multi-layer tissue networks
Marinka Zitnik; Jure Leskovec
A new method to study the change of miRNA–mRNA interactions due to environmental exposures
Francesca Petralia; Vasily N. Aushev; Kalpana Gopalakrishnan; Maya Kappil; Nyan W. Khin ...
Multiple network-constrained regressions expand insights into influenza vaccination responses
Stefan Avey; Subhasis Mohanty; Jean Wilson; Heidi Zapata; Samit R. Joshi ...
Image-based spatiotemporal causality inference for protein signaling networks
Xiongtao Ruan; Christoph Wülfing; Robert F. Murphy

REGGEN

Denoising genome-wide histone ChIP-seq with convolutional neural networks
Pang Wei Koh; Emma Pierson; Anshul Kundaje
TITER: predicting translation initiation sites by deep learning
Sai Zhang; Hailin Hu; Tao Jiang; Lei Zhang; Jianyang Zeng
Direct AUC optimization of regulatory motifs
Lin Zhu; Hong-Bo Zhang; De-Shuang Huang
Exploiting sequence-based features for predicting enhancer–promoter interactions
Yang Yang; Ruochi Zhang; Shashank Singh; Jian Ma
miniMDS: 3D structural inference from high-resolution Hi-C data
Lila Rieber; Shaun Mahony

RNA

DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields
Mingfu Shao; Jianzhu Ma; Sheng Wang
Integrative deep models for alternative splicing
Anupama Jha; Matthew R. Gazzara; Yoseph Barash
Efficient approximations of RNA kinetics landscape using non-redundant sampling
Juraj Michálik; Hélène Touzet; Yann Ponty

SYSMOD

A scalable moment-closure approximation for large-scale biochemical reaction networks
Atefeh Kazeroonian; Fabian J. Theis; Jan Hasenauer
Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data
Eugenio Cinquemani; Valérie Laroute; Muriel Cocaign-Bousquet; Hidde de Jong; Delphine Ropers
popFBA: tackling intratumour heterogeneity with Flux Balance Analysis
Chiara Damiani; Marzia Di Filippo; Dario Pescini; Davide Maspero; Riccardo Colombo ...
Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems
Dennis Pischel; Kai Sundmacher; Robert J. Flassig

TRANSMED

Association testing of bisulfite-sequencing methylation data via a Laplace approximation
Omer Weissbrod; Elior Rahmani; Regev Schweiger; Saharon Rosset; Eran Halperin
Molecular signatures that can be transferred across different omics platforms
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
Xiaoke Hao; Chanxiu Li; Jingwen Yan; Xiaohui Yao; Shannon L. Risacher ...
Predicting phenotypes from microarrays using amplified, initially marginal, eigenvector regression
Lei Ding; Daniel J. McDonald
Systematic identification of feature combinations for predicting drug response with Bayesian multi-view multi-task linear regression
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
Yoichiro Nakatani; Aoife McLysaght
Increasing the power of meta-analysis of genome-wide association studies to detect heterogeneous effects
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
Kymberleigh A. Pagel; Vikas Pejaver; Guan Ning Lin; Hyun-Jun Nam; Matthew Mort ...

AUTHOR INDEX

Author Index
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  • Online ISSN 1460-2059
  • Print ISSN 1367-4803
  • Copyright © 2017 Oxford University Press

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