Subject: Bioinformatics Table of Contents for 1 January 2020 ------=_Part_1275200852.1579219556362 Content-Type: text/plain;charset=UTF-8 Oxford Academic *** Bioinformatics *** Volume 36, Issue 1, 1 January 2020 Read this issue (https://academic.oup.com/bioinformatics/issue/36/1) ------------------------------ Discover high impact research in Bioinformatics Explore our collection of highly cited articles from Bioinformatics. These articles are freely available until the end of 2019. Read now ------------------------------ ============================= ORIGINAL PAPERS ============================Cloud bursting galaxy: federated identity and access management Vahid Jalili, Enis Afgan, James Taylor, Jeremy Goecks (https://academic.oup.com/bioinformatics/article/36/1/1/5514039) MRLR: unraveling high-resolution meiotic recombination by linked reads Peng Xu, Timothy Kennell, Jr., Min Gao, Robert P Kimberly, Zechen Chong (https://academic.oup.com/bioinformatics/article/36/1/10/5520436) Bayesian GWAS with Structured and Non-Local Priors Adam Kaplan, Eric F Lock, Mark Fiecas (https://academic.oup.com/bioinformatics/article/36/1/17/5522013) DepthFinder: a tool to determine the optimal read depth for reduced-representation sequencing Davoud Torkamaneh, Jérôme Laroche, Brian Boyle, François Belzile (https://academic.oup.com/bioinformatics/article/36/1/26/5512354) arcasHLA: high-resolution HLA typing from RNAseq Rose Orenbuch, Ioan Filip, Devon Comito, Jeffrey Shaman, Itsik Pe'er (https://academic.oup.com/bioinformatics/article/36/1/33/5512361) Protein contact prediction using metagenome sequence data and residual neural networks Qi Wu, Zhenling Peng, Ivan Anishchenko, Qian Cong, David Baker (https://academic.oup.com/bioinformatics/article/36/1/41/5512356) sefOri: selecting the best-engineered sequence features to predict DNA replication origins Chenwei Lou, Jian Zhao, Ruoyao Shi, Qian Wang, Wenyang Zhou (https://academic.oup.com/bioinformatics/article/36/1/49/5520948) DeepMito: accurate prediction of protein sub-mitochondrial localization using convolutional neural networks Castrense Savojardo, Niccolò Bruciaferri, Giacomo Tartari, Pier Luigi Martelli, Rita Casadio (https://academic.oup.com/bioinformatics/article/36/1/56/5520945) Simultaneous prediction of multiple outcomes using revised stacking algorithms Li Xing, Mary L Lesperance, Xuekui Zhang (https://academic.oup.com/bioinformatics/article/36/1/65/5526872) circDeep: deep learning approach for circular RNA classification from other long non-coding RNA Mohamed Chaabane, Robert M Williams, Austin T Stephens, Juw Won Park (https://academic.oup.com/bioinformatics/article/36/1/73/5527751) DeePaC: predicting pathogenic potential of novel DNA with reverse-complement neural networks Jakub M Bartoszewicz, Anja Seidel, Robert Rentzsch, Bernhard Y Renard (https://academic.oup.com/bioinformatics/article/36/1/81/5531656) QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction Fabian Sievers, Desmond G Higgins (https://academic.oup.com/bioinformatics/article/36/1/90/5530966) P3DOCK: a protein--RNA docking webserver based on template-based and template-free docking Jinfang Zheng, Xu Hong, Juan Xie, Xiaoxue Tong, Shiyong Liu (https://academic.oup.com/bioinformatics/article/36/1/96/5512355) Sequence alignment using machine learning for accurate template-based protein structure prediction Shuichiro Makigaki, Takashi Ishida (https://academic.oup.com/bioinformatics/article/36/1/104/5514048) iScore: a novel graph kernel-based function for scoring protein--protein docking models Cunliang Geng, Yong Jung, Nicolas Renaud, Vasant Honavar, Alexandre M J J Bonvin (https://academic.oup.com/bioinformatics/article/36/1/112/5519113) Positive multistate protein design Jelena Vucinic, David Simoncini, Manon Ruffini, Sophie Barbe, Thomas Schiex (https://academic.oup.com/bioinformatics/article/36/1/122/5519117) iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures Jiyao Wang, Philippe Youkharibache, Dachuan Zhang, Christopher J Lanczycki, Renata C Geer (https://academic.oup.com/bioinformatics/article/36/1/131/5520951) Increasing the efficiency and accuracy of the ABACUS protein sequence design method Peng Xiong, Xiuhong Hu, Bin Huang, Jiahai Zhang, Quan Chen (https://academic.oup.com/bioinformatics/article/36/1/136/5523181) MaNGA: a novel multi-niche multi-objective genetic algorithm for QSAR modelling Angela Serra, Serli nlü, Paola Festa, Vittorio Fortino, Dario Greco (https://academic.oup.com/bioinformatics/article/36/1/145/5522367) A helical lock and key model of polyproline II conformation with SH3 Tomer Meirson, David Bomze, Liron Kahlon, Hava Gil-Henn, Abraham O Samson (https://academic.oup.com/bioinformatics/article/36/1/154/5524599) Towards accurate high-throughput ligand affinity prediction by exploiting structural ensembles, docking metrics and ligand similarity Melanie Schneider, Jean-Luc Pons, William Bourguet, Gilles Labesse (https://academic.oup.com/bioinformatics/article/36/1/160/5539694) A dynamic programing approach to integrate gene expression data and network information for pathway model generation Yuexu Jiang, Yanchun Liang, Duolin Wang, Dong Xu, Trupti Joshi (https://academic.oup.com/bioinformatics/article/36/1/169/5511838) An empirical Bayesian ranking method, with applications to high throughput biology John Ferguson, Joseph Chang (https://academic.oup.com/bioinformatics/article/36/1/177/5514040) Genetic cooperativity in multi-layer networks implicates cell survival and senescence in the striatum of Huntington's disease mice synchronous to symptoms Erwan Bigan, Satish Sasidharan Nair, François-Xavier Lejeune, Hélissande Fragnaud, Frédéric Parmentier (https://academic.oup.com/bioinformatics/article/36/1/186/5522008) Inference of differential gene regulatory networks based on gene expression and genetic perturbation data Xin Zhou, Xiaodong Cai (https://academic.oup.com/bioinformatics/article/36/1/197/5526871) MiTPeptideDB: a proteogenomic resource for the discovery of novel peptides Elizabeth Guruceaga, Alba Garin-Muga, Victor Segura (https://academic.oup.com/bioinformatics/article/36/1/205/5523846) Mycorrhiza: genotype assignment using phylogenetic networks Jeremy Georges-Filteau, Richard C Hamelin, Mathieu Blanchette (https://academic.oup.com/bioinformatics/article/36/1/212/5514044) Estimation of population genetic parameters using an EM algorithm and sequence data from experimental evolution populations Yasuhiro Kojima, Hirotaka Matsumoto, Hisanori Kiryu (https://academic.oup.com/bioinformatics/article/36/1/221/5520943) Reversible jump MCMC for multi-model inference in Metabolic Flux Analysis Axel Theorell, Katharina Nöh (https://academic.oup.com/bioinformatics/article/36/1/232/5520434) Modelling cancer progression using Mutual Hazard Networks Rudolf Schill, Stefan Solbrig, Tilo Wettig, Rainer Spang (https://academic.oup.com/bioinformatics/article/36/1/241/5524604) Scaling tree-based automated machine learning to biomedical big data with a feature set selector Trang T Le, Weixuan Fu, Jason H Moore (https://academic.oup.com/bioinformatics/article/36/1/250/5511404) GMSimpute: a generalized two-step Lasso approach to impute missing values in label-free mass spectrum analysis Qian Li, Kate Fisher, Wenjun Meng, Bin Fang, Eric Welsh (https://academic.oup.com/bioinformatics/article/36/1/257/5519114) CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision Alexander Junge, Lars Juhl Jensen (https://academic.oup.com/bioinformatics/article/36/1/264/5519116) Deep learning on chaos game representation for proteins Hannah F Löchel, Dominic Eger, Theodor Sperlea, Dominik Heider (https://academic.oup.com/bioinformatics/article/36/1/272/5521624) Towards reliable named entity recognition in the biomedical domain John M Giorgi, Gary D Bader (https://academic.oup.com/bioinformatics/article/36/1/280/5520946) Deep representation learning for domain adaptable classification of infrared spectral imaging data Arne P Raulf, Joshua Butke, Claus Küpper, Frederik Großerueschkamp, Klaus Gerwert (https://academic.oup.com/bioinformatics/article/36/1/287/5521621) HUNER: improving biomedical NER with pretraining Leon Weber, Jannes Münchmeyer, Tim Rocktäschel, Maryam Habibi, Ulf Leser (https://academic.oup.com/bioinformatics/article/36/1/295/5523847) Isoform function prediction based on bi-random walks on a heterogeneous network Guoxian Yu, Keyao Wang, Carlotta Domeniconi, Maozu Guo, Jun Wang (https://academic.oup.com/bioinformatics/article/36/1/303/5524603) Cooler: scalable storage for Hi-C data and other genomically labeled arrays Nezar Abdennur, Leonid A Mirny (https://academic.oup.com/bioinformatics/article/36/1/311/5530598) A sequential algorithm to detect diffusion switching along intracellular particle trajectories Vincent Briane, Myriam Vimond, Cesar Augusto Valades-Cruz, Antoine Salomon, Christian Wunder (https://academic.oup.com/bioinformatics/article/36/1/317/5520435) GENOME ANALYSIS ------------------------------ Cloud bursting galaxy: federated identity and access management Vahid Jalili, Enis Afgan, James Taylor, Jeremy Goecks (https://academic.oup.com/bioinformatics/article/36/1/1/5514039) MRLR: unraveling high-resolution meiotic recombination by linked reads Peng Xu, Timothy Kennell, Jr., Min Gao, Robert P Kimberly, Zechen Chong (https://academic.oup.com/bioinformatics/article/36/1/10/5520436) Bayesian GWAS with Structured and Non-Local Priors Adam Kaplan, Eric F Lock, Mark Fiecas (https://academic.oup.com/bioinformatics/article/36/1/17/5522013) SEQUENCE ANALYSIS ------------------------------ DepthFinder: a tool to determine the optimal read depth for reduced-representation sequencing Davoud Torkamaneh, Jérôme Laroche, Brian Boyle, François Belzile (https://academic.oup.com/bioinformatics/article/36/1/26/5512354) arcasHLA: high-resolution HLA typing from RNAseq Rose Orenbuch, Ioan Filip, Devon Comito, Jeffrey Shaman, Itsik Pe'er (https://academic.oup.com/bioinformatics/article/36/1/33/5512361) Protein contact prediction using metagenome sequence data and residual neural networks Qi Wu, Zhenling Peng, Ivan Anishchenko, Qian Cong, David Baker (https://academic.oup.com/bioinformatics/article/36/1/41/5512356) sefOri: selecting the best-engineered sequence features to predict DNA replication origins Chenwei Lou, Jian Zhao, Ruoyao Shi, Qian Wang, Wenyang Zhou (https://academic.oup.com/bioinformatics/article/36/1/49/5520948) DeepMito: accurate prediction of protein sub-mitochondrial localization using convolutional neural networks Castrense Savojardo, Niccolò Bruciaferri, Giacomo Tartari, Pier Luigi Martelli, Rita Casadio (https://academic.oup.com/bioinformatics/article/36/1/56/5520945) Simultaneous prediction of multiple outcomes using revised stacking algorithms Li Xing, Mary L Lesperance, Xuekui Zhang (https://academic.oup.com/bioinformatics/article/36/1/65/5526872) circDeep: deep learning approach for circular RNA classification from other long non-coding RNA Mohamed Chaabane, Robert M Williams, Austin T Stephens, Juw Won Park (https://academic.oup.com/bioinformatics/article/36/1/73/5527751) DeePaC: predicting pathogenic potential of novel DNA with reverse-complement neural networks Jakub M Bartoszewicz, Anja Seidel, Robert Rentzsch, Bernhard Y Renard (https://academic.oup.com/bioinformatics/article/36/1/81/5531656) QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction Fabian Sievers, Desmond G Higgins (https://academic.oup.com/bioinformatics/article/36/1/90/5530966) STRUCTURAL BIOINFORMATICS ------------------------------ P3DOCK: a protein--RNA docking webserver based on template-based and template-free docking Jinfang Zheng, Xu Hong, Juan Xie, Xiaoxue Tong, Shiyong Liu (https://academic.oup.com/bioinformatics/article/36/1/96/5512355) Sequence alignment using machine learning for accurate template-based protein structure prediction Shuichiro Makigaki, Takashi Ishida (https://academic.oup.com/bioinformatics/article/36/1/104/5514048) iScore: a novel graph kernel-based function for scoring protein--protein docking models Cunliang Geng, Yong Jung, Nicolas Renaud, Vasant Honavar, Alexandre M J J Bonvin (https://academic.oup.com/bioinformatics/article/36/1/112/5519113) Positive multistate protein design Jelena Vucinic, David Simoncini, Manon Ruffini, Sophie Barbe, Thomas Schiex (https://academic.oup.com/bioinformatics/article/36/1/122/5519117) iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures Jiyao Wang, Philippe Youkharibache, Dachuan Zhang, Christopher J Lanczycki, Renata C Geer (https://academic.oup.com/bioinformatics/article/36/1/131/5520951) Increasing the efficiency and accuracy of the ABACUS protein sequence design method Peng Xiong, Xiuhong Hu, Bin Huang, Jiahai Zhang, Quan Chen (https://academic.oup.com/bioinformatics/article/36/1/136/5523181) MaNGA: a novel multi-niche multi-objective genetic algorithm for QSAR modelling Angela Serra, Serli nlü, Paola Festa, Vittorio Fortino, Dario Greco (https://academic.oup.com/bioinformatics/article/36/1/145/5522367) A helical lock and key model of polyproline II conformation with SH3 Tomer Meirson, David Bomze, Liron Kahlon, Hava Gil-Henn, Abraham O Samson (https://academic.oup.com/bioinformatics/article/36/1/154/5524599) Towards accurate high-throughput ligand affinity prediction by exploiting structural ensembles, docking metrics and ligand similarity Melanie Schneider, Jean-Luc Pons, William Bourguet, Gilles Labesse (https://academic.oup.com/bioinformatics/article/36/1/160/5539694) GENE EXPRESSION ------------------------------ A dynamic programing approach to integrate gene expression data and network information for pathway model generation Yuexu Jiang, Yanchun Liang, Duolin Wang, Dong Xu, Trupti Joshi (https://academic.oup.com/bioinformatics/article/36/1/169/5511838) An empirical Bayesian ranking method, with applications to high throughput biology John Ferguson, Joseph Chang (https://academic.oup.com/bioinformatics/article/36/1/177/5514040) Genetic cooperativity in multi-layer networks implicates cell survival and senescence in the striatum of Huntington's disease mice synchronous to symptoms Erwan Bigan, Satish Sasidharan Nair, François-Xavier Lejeune, Hélissande Fragnaud, Frédéric Parmentier (https://academic.oup.com/bioinformatics/article/36/1/186/5522008) Inference of differential gene regulatory networks based on gene expression and genetic perturbation data Xin Zhou, Xiaodong Cai (https://academic.oup.com/bioinformatics/article/36/1/197/5526871) MiTPeptideDB: a proteogenomic resource for the discovery of novel peptides Elizabeth Guruceaga, Alba Garin-Muga, Victor Segura (https://academic.oup.com/bioinformatics/article/36/1/205/5523846) GENETICS AND POPULATION ANALYSIS ------------------------------ Mycorrhiza: genotype assignment using phylogenetic networks Jeremy Georges-Filteau, Richard C Hamelin, Mathieu Blanchette (https://academic.oup.com/bioinformatics/article/36/1/212/5514044) Estimation of population genetic parameters using an EM algorithm and sequence data from experimental evolution populations Yasuhiro Kojima, Hirotaka Matsumoto, Hisanori Kiryu (https://academic.oup.com/bioinformatics/article/36/1/221/5520943) SYSTEMS BIOLOGY ------------------------------ Reversible jump MCMC for multi-model inference in Metabolic Flux Analysis Axel Theorell, Katharina Nöh (https://academic.oup.com/bioinformatics/article/36/1/232/5520434) Modelling cancer progression using Mutual Hazard Networks Rudolf Schill, Stefan Solbrig, Tilo Wettig, Rainer Spang (https://academic.oup.com/bioinformatics/article/36/1/241/5524604) DATA AND TEXT MINING ------------------------------ Scaling tree-based automated machine learning to biomedical big data with a feature set selector Trang T Le, Weixuan Fu, Jason H Moore (https://academic.oup.com/bioinformatics/article/36/1/250/5511404) GMSimpute: a generalized two-step Lasso approach to impute missing values in label-free mass spectrum analysis Qian Li, Kate Fisher, Wenjun Meng, Bin Fang, Eric Welsh (https://academic.oup.com/bioinformatics/article/36/1/257/5519114) CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision Alexander Junge, Lars Juhl Jensen (https://academic.oup.com/bioinformatics/article/36/1/264/5519116) Deep learning on chaos game representation for proteins Hannah F Löchel, Dominic Eger, Theodor Sperlea, Dominik Heider (https://academic.oup.com/bioinformatics/article/36/1/272/5521624) Towards reliable named entity recognition in the biomedical domain John M Giorgi, Gary D Bader (https://academic.oup.com/bioinformatics/article/36/1/280/5520946) Deep representation learning for domain adaptable classification of infrared spectral imaging data Arne P Raulf, Joshua Butke, Claus Küpper, Frederik Großerueschkamp, Klaus Gerwert (https://academic.oup.com/bioinformatics/article/36/1/287/5521621) HUNER: improving biomedical NER with pretraining Leon Weber, Jannes Münchmeyer, Tim Rocktäschel, Maryam Habibi, Ulf Leser (https://academic.oup.com/bioinformatics/article/36/1/295/5523847) Isoform function prediction based on bi-random walks on a heterogeneous network Guoxian Yu, Keyao Wang, Carlotta Domeniconi, Maozu Guo, Jun Wang (https://academic.oup.com/bioinformatics/article/36/1/303/5524603) Cooler: scalable storage for Hi-C data and other genomically labeled arrays Nezar Abdennur, Leonid A Mirny (https://academic.oup.com/bioinformatics/article/36/1/311/5530598) BIOIMAGE INFORMATICS ------------------------------ A sequential algorithm to detect diffusion switching along intracellular particle trajectories Vincent Briane, Myriam Vimond, Cesar Augusto Valades-Cruz, Antoine Salomon, Christian Wunder (https://academic.oup.com/bioinformatics/article/36/1/317/5520435) ============================= ERRATUM ============================Adaptive boosting-based computational model for predicting potential miRNA-disease associations Yan Zhao, Xing Chen, Jun Yin (https://academic.oup.com/bioinformatics/article/36/1/330/5522958) Unsubscribe (http://cp20.com/unsubscribe) Manage email alerts 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Our Privacy Policy (http://global.oup.com/privacy) sets out how Oxford University Press handles your personal information. The content of this email is protected by copyright. Oxford University Press This email is intended for bionet@evol.mcmaster.ca. ------=_Part_1275200852.1579219556362 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Discover high impact research in Bioinformatics
 
Explore our collection of highly cited articles from Bioinformatics. These articles are freely available until the end of 2019.
Read now
 
 
 
 
 
 
Bioinformatics  
Volume 36 Issue 1
 
1 January 2020
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Cloud bursting galaxy: federated identity and access management border= 
 
Vahid Jalili; Enis Afgan; James Taylor; Jeremy Goecks
 
 
MRLR: unraveling high-resolution meiotic recombination by linked reads 
 
Peng Xu; Timothy Kennell, Jr.; Min Gao ; Robert P Kimberly; Zechen Chong
 
 
Bayesian GWAS with Structured and Non-Local Priors 
 
Adam Kaplan; Eric F Lock; Mark Fiecas
 
 
 
SEQUENCE ANALYSIS
 
 
 
DepthFinder: a tool to determine the optimal read depth for reduced-representation sequencing 
 
Davoud Torkamaneh; Jérôme Laroche; Brian Boyle ; François Belzile
 
 
arcasHLA: high-resolution HLA typing from RNAseq border=  
 
Rose Orenbuch; Ioan Filip; Devon Comito ; Jeffrey Shaman; Itsik Pe'er ...
 
 
Protein contact prediction using metagenome sequence data and residual neural networks 
 
Qi Wu; Zhenling Peng; Ivan Anishchenko ; Qian Cong; David Baker ...
 
 
sefOri: selecting the best-engineered sequence features to predict DNA replication origins 
 
Chenwei Lou; Jian Zhao; Ruoyao Shi ; Qian Wang; Wenyang Zhou ...
 
 
DeepMito: accurate prediction of protein sub-mitochondrial localization using convolutional neural networks border= 
 
Castrense Savojardo ; Niccolò Bruciaferri; Giacomo Tartari; Pier Luigi Martelli; Rita Casadio
 
 
Simultaneous prediction of multiple outcomes using revised stacking algorithms 
 
Li Xing; Mary L Lesperance; Xuekui Zhang
 
 
circDeep: deep learning approach for circular RNA classification from other long non-coding RNA border= 
 
Mohamed Chaabane ; Robert M Williams; Austin T Stephens; Juw Won Park
 
 
DeePaC: predicting pathogenic potential of novel DNA with reverse-complement neural networks 
 
Jakub M Bartoszewicz; Anja Seidel; Robert Rentzsch ; Bernhard Y Renard
 
 
QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction border= 
 
Fabian Sievers ; Desmond G Higgins
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
P3DOCK: a protein'RNA docking webserver based on template-based and template-free docking 
 
Jinfang Zheng; Xu Hong; Juan Xie ; Xiaoxue Tong; Shiyong Liu
 
 
Sequence alignment using machine learning for accurate template-based protein structure prediction 
 
Shuichiro Makigaki; Takashi Ishida
 
 
iScore: a novel graph kernel-based function for scoring protein'protein docking models border= 
 
Cunliang Geng ; Yong Jung; Nicolas Renaud; Vasant Honavar; Alexandre M J J Bonvin ...
 
 
Positive multistate protein design 
 
Jelena Vucinic; David Simoncini; Manon Ruffini ; Sophie Barbe; Thomas Schiex
 
 
iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures 
 
Jiyao Wang; Philippe Youkharibache; Dachuan Zhang ; Christopher J Lanczycki; Renata C Geer ...
 
 
Increasing the efficiency and accuracy of the ABACUS protein sequence design method 
 
Peng Xiong; Xiuhong Hu; Bin Huang ; Jiahai Zhang; Quan Chen ...
 
 
MaNGA: a novel multi-niche multi-objective genetic algorithm for QSAR modelling 
 
Angela Serra; Serli Önlü; Paola Festa ; Vittorio Fortino; Dario Greco
 
 
A helical lock and key model of polyproline II conformation with SH3 
 
Tomer Meirson; David Bomze; Liron Kahlon ; Hava Gil-Henn; Abraham O Samson
 
 
Towards accurate high-throughput ligand affinity prediction by exploiting structural ensembles, docking metrics and ligand similarity border= 
 
Melanie Schneider ; Jean-Luc Pons; William Bourguet; Gilles Labesse
 
 
 
GENE EXPRESSION
 
 
 
A dynamic programing approach to integrate gene expression data and network information for pathway model generation 
 
Yuexu Jiang; Yanchun Liang; Duolin Wang ; Dong Xu; Trupti Joshi
 
 
An empirical Bayesian ranking method, with applications to high throughput biology 
 
John Ferguson; Joseph Chang
 
 
Genetic cooperativity in multi-layer networks implicates cell survival and senescence in the striatum of Huntington's disease mice synchronous to symptoms border= 
 
Erwan Bigan ; Satish Sasidharan Nair; François-Xavier Lejeune; Hélissande Fragnaud; Frédéric Parmentier ...
 
 
Inference of differential gene regulatory networks based on gene expression and genetic perturbation data 
 
Xin Zhou; Xiaodong Cai
 
 
MiTPeptideDB: a proteogenomic resource for the discovery of novel peptides 
 
Elizabeth Guruceaga; Alba Garin-Muga; Victor Segura
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Mycorrhiza: genotype assignment using phylogenetic networks 
 
Jeremy Georges-Filteau; Richard C Hamelin; Mathieu Blanchette
 
 
Estimation of population genetic parameters using an EM algorithm and sequence data from experimental evolution populations 
 
Yasuhiro Kojima; Hirotaka Matsumoto; Hisanori Kiryu
 
 
 
SYSTEMS BIOLOGY
 
 
 
Reversible jump MCMC for multi-model inference in Metabolic Flux Analysis 
 
Axel Theorell; Katharina Nöh
 
 
Modelling cancer progression using Mutual Hazard Networks border=  
 
Rudolf Schill; Stefan Solbrig; Tilo Wettig; Rainer Spang
 
 
 
DATA AND TEXT MINING
 
 
 
Scaling tree-based automated machine learning to biomedical big data with a feature set selector border= 
 
Trang T Le ; Weixuan Fu; Jason H Moore
 
 
GMSimpute: a generalized two-step Lasso approach to impute missing values in label-free mass spectrum analysis border= 
 
Qian Li ; Kate Fisher; Wenjun Meng; Bin Fang; Eric Welsh ...
 
 
CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision border= 
 
Alexander Junge ; Lars Juhl Jensen
 
 
Deep learning on chaos game representation for proteins 
 
Hannah F Löchel; Dominic Eger; Theodor Sperlea ; Dominik Heider
 
 
Towards reliable named entity recognition in the biomedical domain border= 
 
John M Giorgi ; Gary D Bader
 
 
Deep representation learning for domain adaptable classification of infrared spectral imaging data 
 
Arne P Raulf; Joshua Butke; Claus Küpper ; Frederik Großerueschkamp; Klaus Gerwert ...
 
 
HUNER: improving biomedical NER with pretraining 
 
Leon Weber; Jannes Münchmeyer; Tim Rocktäschel ; Maryam Habibi; Ulf Leser
 
 
Isoform function prediction based on bi-random walks on a heterogeneous network 
 
Guoxian Yu; Keyao Wang; Carlotta Domeniconi ; Maozu Guo; Jun Wang
 
 
Cooler: scalable storage for Hi-C data and other genomically labeled arrays 
 
Nezar Abdennur; Leonid A Mirny
 
 
 
BIOIMAGE INFORMATICS
 
 
 
A sequential algorithm to detect diffusion switching along intracellular particle trajectories 
 
Vincent Briane; Myriam Vimond; Cesar Augusto Valades-Cruz ; Antoine Salomon; Christian Wunder ...
 
 
 
ERRATUM
 
 
 
Adaptive boosting-based computational model for predicting potential miRNA-disease associations 
 
Yan Zhao; Xing Chen; Jun Yin
 
 
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