Subject: Bioinformatics Table of Contents for 15 November 2019 ------=_Part_1844286541.1574020582239 Content-Type: text/plain;charset=UTF-8 Oxford Academic *** {Bioinformatics} *** Volume 35, Issue 22, 1 November 2019 Read this issue (https://academic.oup.com/bioinformatics/issue/35/22) ------------------------------ 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 ============================PHANOTATE: a novel approach to gene identification in phage genomes Katelyn McNair, Carol Zhou, Elizabeth A Dinsdale, Brian Souza, Robert A Edwards (https://academic.oup.com/bioinformatics/article/35/22/4537/5480131) Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference Taro Matsutani, Yuki Ueno, Tsukasa Fukunaga, Michiaki Hamada (https://academic.oup.com/bioinformatics/article/35/22/4543/5472341) Automatic curation of large comparative animal MicroRNA datasets Ali M Yazbeck, Peter F Stadler, Kifah Tout, Jörg Fallmann (https://academic.oup.com/bioinformatics/article/35/22/4553/5472340) Fast detection of maximal exact matches via fixed sampling of query K-mers and Bloom filtering of index K-mers Yuansheng Liu, Leo Yu Zhang, Jinyan Li (https://academic.oup.com/bioinformatics/article/35/22/4560/5474908) Identification of differentially expressed gene sets using the Generalized Berk--Jones statistic Sheila M Gaynor, Ryan Sun, Xihong Lin, John Quackenbush (https://academic.oup.com/bioinformatics/article/35/22/4568/5486401) DeepPASTA: deep neural network based polyadenylation site analysis Ashraful Arefeen, Xinshu Xiao, Tao Jiang (https://academic.oup.com/bioinformatics/article/35/22/4577/5480129) DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning Peng Ni, Neng Huang, Zhi Zhang, De-Peng Wang, Fan Liang (https://academic.oup.com/bioinformatics/article/35/22/4586/5474907) A new statistic for efficient detection of repetitive sequences Sijie Chen, Yixin Chen, Fengzhu Sun, Michael S Waterman, Xuegong Zhang (https://academic.oup.com/bioinformatics/article/35/22/4596/5472337) A framework for space-efficient variable-order Markov models Fabio Cunial, Jarno Alanko, Djamal Belazzougui (https://academic.oup.com/bioinformatics/article/35/22/4607/5475595) Computational identification of prion-like RNA-binding proteins that form liquid phase-separated condensates Gabriele Orlando, Daniele Raimondi, Francesco Tabaro, Francesco Codicè, Yves Moreau (https://academic.oup.com/bioinformatics/article/35/22/4617/5474906) BHap: a novel approach for bacterial haplotype reconstruction Xin Li, Samaneh Saadat, Haiyan Hu, Xiaoman Li (https://academic.oup.com/bioinformatics/article/35/22/4624/5475598) ProSampler: an ultrafast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery Yang Li, Pengyu Ni, Shaoqiang Zhang, Guojun Li, Zhengchang Su (https://academic.oup.com/bioinformatics/article/35/22/4632/5487382) Develop machine learning-based regression predictive models for engineering protein solubility Xi Han, Xiaonan Wang, Kang Zhou (https://academic.oup.com/bioinformatics/article/35/22/4640/5481956) ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks Yang Li, Jun Hu, Chengxin Zhang, Dong-Jun Yu, Yang Zhang (https://academic.oup.com/bioinformatics/article/35/22/4647/5487385) A decision-theoretic approach to the evaluation of machine learning algorithms in computational drug discovery Oliver P Watson, Isidro Cortes-Ciriano, Aimee R Taylor, James A Watson (https://academic.oup.com/bioinformatics/article/35/22/4656/5487387) Dynamical important residue network (DIRN): network inference via conformational change Quan Li, Ray Luo, Hai-Feng Chen (https://academic.oup.com/bioinformatics/article/35/22/4664/5481960) Hybrid analysis of gene dynamics predicts context-specific expression and offers regulatory insights Justin D Finkle, Neda Bagheri (https://academic.oup.com/bioinformatics/article/35/22/4671/5474904) Cell-level somatic mutation detection from single-cell RNA sequencing Trung Nghia Vu, Ha-Nam Nguyen, Stefano Calza, Krishna R Kalari, Liewei Wang (https://academic.oup.com/bioinformatics/article/35/22/4679/5480302) scMatch: a single-cell gene expression profile annotation tool using reference datasets Rui Hou, Elena Denisenko, Alistair R R Forrest (https://academic.oup.com/bioinformatics/article/35/22/4688/5480299) LAmbDA: label ambiguous domain adaptation dataset integration reduces batch effects and improves subtype detection Travis S Johnson, Tongxin Wang, Zhi Huang, Christina Y Yu, Yi Wu (https://academic.oup.com/bioinformatics/article/35/22/4696/5481958) Continuous-state HMMs for modeling time-series single-cell RNA-Seq data Chieh Lin, Ziv Bar-Joseph (https://academic.oup.com/bioinformatics/article/35/22/4707/5481957) NGSEP3: accurate variant calling across species and sequencing protocols Daniel Tello, Juanita Gil, Cristian D Loaiza, John J Riascos, Nicolás Cardozo (https://academic.oup.com/bioinformatics/article/35/22/4716/5480128) Multi-SNP mediation intersection-union test Wujuan Zhong, Cassandra N Spracklen, Karen L Mohlke, Xiaojing Zheng, Jason Fine (https://academic.oup.com/bioinformatics/article/35/22/4724/5480134) Adaptive boosting-based computational model for predicting potential miRNA-disease associations Yan Zhao, Xing Chen, Jun Yin (https://academic.oup.com/bioinformatics/article/35/22/4730/5481952) Graph-based data integration from bioactive peptide databases of pharmaceutical interest: toward an organized collection enabling visual network analysis Longendri Aguilera-Mendoza, Yovani Marrero-Ponce, Jesus A Beltran, Roberto Tellez Ibarra, Hugo A Guillen-Ramirez (https://academic.oup.com/bioinformatics/article/35/22/4739/5474901) Another look at matrix correlations Ahmad Borzou, Razie Yousefi, Rovshan G Sadygov (https://academic.oup.com/bioinformatics/article/35/22/4748/5480130) GENOME ANALYSIS ------------------------------ PHANOTATE: a novel approach to gene identification in phage genomes Katelyn McNair, Carol Zhou, Elizabeth A Dinsdale, Brian Souza, Robert A Edwards (https://academic.oup.com/bioinformatics/article/35/22/4537/5480131) Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference Taro Matsutani, Yuki Ueno, Tsukasa Fukunaga, Michiaki Hamada (https://academic.oup.com/bioinformatics/article/35/22/4543/5472341) Automatic curation of large comparative animal MicroRNA datasets Ali M Yazbeck, Peter F Stadler, Kifah Tout, Jörg Fallmann (https://academic.oup.com/bioinformatics/article/35/22/4553/5472340) Fast detection of maximal exact matches via fixed sampling of query K-mers and Bloom filtering of index K-mers Yuansheng Liu, Leo Yu Zhang, Jinyan Li (https://academic.oup.com/bioinformatics/article/35/22/4560/5474908) Identification of differentially expressed gene sets using the Generalized Berk--Jones statistic Sheila M Gaynor, Ryan Sun, Xihong Lin, John Quackenbush (https://academic.oup.com/bioinformatics/article/35/22/4568/5486401) DeepPASTA: deep neural network based polyadenylation site analysis Ashraful Arefeen, Xinshu Xiao, Tao Jiang (https://academic.oup.com/bioinformatics/article/35/22/4577/5480129) DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning Peng Ni, Neng Huang, Zhi Zhang, De-Peng Wang, Fan Liang (https://academic.oup.com/bioinformatics/article/35/22/4586/5474907) SEQUENCE ANALYSIS ------------------------------ A new statistic for efficient detection of repetitive sequences Sijie Chen, Yixin Chen, Fengzhu Sun, Michael S Waterman, Xuegong Zhang (https://academic.oup.com/bioinformatics/article/35/22/4596/5472337) A framework for space-efficient variable-order Markov models Fabio Cunial, Jarno Alanko, Djamal Belazzougui (https://academic.oup.com/bioinformatics/article/35/22/4607/5475595) Computational identification of prion-like RNA-binding proteins that form liquid phase-separated condensates Gabriele Orlando, Daniele Raimondi, Francesco Tabaro, Francesco Codicè, Yves Moreau (https://academic.oup.com/bioinformatics/article/35/22/4617/5474906) BHap: a novel approach for bacterial haplotype reconstruction Xin Li, Samaneh Saadat, Haiyan Hu, Xiaoman Li (https://academic.oup.com/bioinformatics/article/35/22/4624/5475598) ProSampler: an ultrafast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery Yang Li, Pengyu Ni, Shaoqiang Zhang, Guojun Li, Zhengchang Su (https://academic.oup.com/bioinformatics/article/35/22/4632/5487382) Develop machine learning-based regression predictive models for engineering protein solubility Xi Han, Xiaonan Wang, Kang Zhou (https://academic.oup.com/bioinformatics/article/35/22/4640/5481956) STRUCTURAL BIOINFORMATICS ------------------------------ ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks Yang Li, Jun Hu, Chengxin Zhang, Dong-Jun Yu, Yang Zhang (https://academic.oup.com/bioinformatics/article/35/22/4647/5487385) A decision-theoretic approach to the evaluation of machine learning algorithms in computational drug discovery Oliver P Watson, Isidro Cortes-Ciriano, Aimee R Taylor, James A Watson (https://academic.oup.com/bioinformatics/article/35/22/4656/5487387) Dynamical important residue network (DIRN): network inference via conformational change Quan Li, Ray Luo, Hai-Feng Chen (https://academic.oup.com/bioinformatics/article/35/22/4664/5481960) GENE EXPRESSION ------------------------------ Hybrid analysis of gene dynamics predicts context-specific expression and offers regulatory insights Justin D Finkle, Neda Bagheri (https://academic.oup.com/bioinformatics/article/35/22/4671/5474904) Cell-level somatic mutation detection from single-cell RNA sequencing Trung Nghia Vu, Ha-Nam Nguyen, Stefano Calza, Krishna R Kalari, Liewei Wang (https://academic.oup.com/bioinformatics/article/35/22/4679/5480302) scMatch: a single-cell gene expression profile annotation tool using reference datasets Rui Hou, Elena Denisenko, Alistair R R Forrest (https://academic.oup.com/bioinformatics/article/35/22/4688/5480299) LAmbDA: label ambiguous domain adaptation dataset integration reduces batch effects and improves subtype detection Travis S Johnson, Tongxin Wang, Zhi Huang, Christina Y Yu, Yi Wu (https://academic.oup.com/bioinformatics/article/35/22/4696/5481958) Continuous-state HMMs for modeling time-series single-cell RNA-Seq data Chieh Lin, Ziv Bar-Joseph (https://academic.oup.com/bioinformatics/article/35/22/4707/5481957) GENETICS AND POPULATION ANALYSIS ------------------------------ NGSEP3: accurate variant calling across species and sequencing protocols Daniel Tello, Juanita Gil, Cristian D Loaiza, John J Riascos, Nicolás Cardozo (https://academic.oup.com/bioinformatics/article/35/22/4716/5480128) SYSTEMS BIOLOGY ------------------------------ Multi-SNP mediation intersection-union test Wujuan Zhong, Cassandra N Spracklen, Karen L Mohlke, Xiaojing Zheng, Jason Fine (https://academic.oup.com/bioinformatics/article/35/22/4724/5480134) Adaptive boosting-based computational model for predicting potential miRNA-disease associations Yan Zhao, Xing Chen, Jun Yin (https://academic.oup.com/bioinformatics/article/35/22/4730/5481952) DATA AND TEXT MINING ------------------------------ Graph-based data integration from bioactive peptide databases of pharmaceutical interest: toward an organized collection enabling visual network analysis Longendri Aguilera-Mendoza, Yovani Marrero-Ponce, Jesus A Beltran, Roberto Tellez Ibarra, Hugo A Guillen-Ramirez (https://academic.oup.com/bioinformatics/article/35/22/4739/5474901) Another look at matrix correlations Ahmad Borzou, Razie Yousefi, Rovshan G Sadygov (https://academic.oup.com/bioinformatics/article/35/22/4748/5480130) ============================= APPLICATIONS NOTES ============================ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions Egor Dolzhenko, Viraj Deshpande, Felix Schlesinger, Peter Krusche, Roman Petrovski (https://academic.oup.com/bioinformatics/article/35/22/4754/5499079) snakePipes: facilitating flexible, scalable and integrative epigenomic analysis Vivek Bhardwaj, Steffen Heyne, Katarzyna Sikora, Leily Rabbani, Michael Rauer (https://academic.oup.com/bioinformatics/article/35/22/4757/5499080) RBPSponge: genome-wide identification of lncRNAs that sponge RBPs Saber HafezQorani, Aissa Houdjedj, Mehmet Arici, Abdesselam Said, Hilal Kazan (https://academic.oup.com/bioinformatics/article/35/22/4760/5509522) Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data Jonathan Cairns, William R Orchard, Valeriya Malysheva, Mikhail Spivakov (https://academic.oup.com/bioinformatics/article/35/22/4764/5514042) eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data Charles E Breeze, Alex P Reynolds, Jenny van Dongen, Ian Dunham, John Lazar (https://academic.oup.com/bioinformatics/article/35/22/4767/5510552) Nanopype: a modular and scalable nanopore data processing pipeline Pay Giesselmann, Sara Hetzel, Franz-Josef Müller, Alexander Meissner, Helene Kretzmer (https://academic.oup.com/bioinformatics/article/35/22/4770/5514474) capC-MAP: software for analysis of Capture-C data Adam Buckle, Nick Gilbert, Davide Marenduzzo, Chris A Brackley (https://academic.oup.com/bioinformatics/article/35/22/4773/5512362) Testing clonal relatedness of two tumors from the same patient based on their mutational profiles: update of the Clonality R package Audrey Mauguen, Venkatraman E Seshan, Colin B Begg, Irina Ostrovnaya (https://academic.oup.com/bioinformatics/article/35/22/4776/5518921) GeneNoteBook, a collaborative notebook for comparative genomics Rens Holmer, Robin van Velzen, Rene Geurts, Ton Bisseling, Dick de Ridder (https://academic.oup.com/bioinformatics/article/35/22/4779/5519115) svtools: population-scale analysis of structural variation David E Larson, Haley J Abel, Colby Chiang, Abhijit Badve, Indraniel Das (https://academic.oup.com/bioinformatics/article/35/22/4782/5520944) OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers Claudia Arnedo-Pac, Loris Mularoni, Ferran Muiños, Abel Gonzalez-Perez, Nuria Lopez-Bigas (https://academic.oup.com/bioinformatics/article/35/22/4788/5522012) GTShark: genotype compression in large projects Sebastian Deorowicz, Agnieszka Danek (https://academic.oup.com/bioinformatics/article/35/22/4791/5521623) SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions Qingzhen Hou, Paul F G De Geest, Christian J Griffioen, Sanne Abeln, Jaap Heringa (https://academic.oup.com/bioinformatics/article/35/22/4794/5497259) Seq2Feature: a comprehensive web-based feature extraction tool Rahul Nikam, M Michael Gromiha (https://academic.oup.com/bioinformatics/article/35/22/4797/5499130) NX4: a web-based visualization of large multiple sequence alignments A Solano-Roman, C Cruz-Castillo, D Offenhuber, A Colubri (https://academic.oup.com/bioinformatics/article/35/22/4800/5510560) VCF/Plotein: visualization and prioritization of genomic variants from human exome sequencing projects Raul Ossio, O Isaac Garcia-Salinas, Diego Said Anaya-Mancilla, Jair S Garcia-Sotelo, Luis A Aguilar (https://academic.oup.com/bioinformatics/article/35/22/4803/5510555) BAMixChecker: an automated checkup tool for matched sample pairs in NGS cohort Hein Chun, Sangwoo Kim (https://academic.oup.com/bioinformatics/article/35/22/4806/5514045) Noise-cancelling repeat finder: uncovering tandem repeats in error-prone long-read sequencing data Robert S Harris, Monika Cechova, Kateryna D Makova (https://academic.oup.com/bioinformatics/article/35/22/4809/5530597) DepLogo: visualizing sequence dependencies in R Jan Grau, Martin Nettling, Jens Keilwagen (https://academic.oup.com/bioinformatics/article/35/22/4812/5521622) RERconverge: an R package for associating evolutionary rates with convergent traits Amanda Kowalczyk, Wynn K Meyer, Raghavendran Partha, Weiguang Mao, Nathan L Clark (https://academic.oup.com/bioinformatics/article/35/22/4815/5514536) iTUPA: an online automated application to perform Topographic-Unit Parsimony Analysis Muhsen Hammoud, Charles Morphy D Santos, Joao Paulo Gois (https://academic.oup.com/bioinformatics/article/35/22/4818/5514049) PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes Brian Jiménez-García, Katarina Elez, Panagiotis I Koukos, Alexandre Mjj Bonvin, Anna Vangone (https://academic.oup.com/bioinformatics/article/35/22/4821/5505420) WDSPdb: an updated resource for WD40 proteins Jing Ma, Ke An, Jing-Bo Zhou, Nuo-Si Wu, Yang Wang (https://academic.oup.com/bioinformatics/article/35/22/4824/5510551) EnImpute: imputing dropout events in single-cell RNA-sequencing data via ensemble learning Xiao-Fei Zhang, Le Ou-Yang, Shuo Yang, Xing-Ming Zhao, Xiaohua Hu (https://academic.oup.com/bioinformatics/article/35/22/4827/5498284) SIGN: similarity identification in gene expression Seyed Ali Madani Tonekaboni, Venkata Satya Kumar Manem, Nehme El-Hachem, Benjamin Haibe-Kains (https://academic.oup.com/bioinformatics/article/35/22/4830/5518919) DEUS: an R package for accurate small RNA profiling based on differential expression of unique sequences Tim Jeske, Peter Huypens, Laura Stirm, Selina Höckele, Christine M Wurmser (https://academic.oup.com/bioinformatics/article/35/22/4834/5522007) RAISS: robust and accurate imputation from summary statistics Hanna Julienne, Huwenbo Shi, Bogdan Pasaniuc, Hugues Aschard (https://academic.oup.com/bioinformatics/article/35/22/4837/5512360) RAbHIT: R Antibody Haplotype Inference Tool Ayelet Peres, Moriah Gidoni, Pazit Polak, Gur Yaari (https://academic.oup.com/bioinformatics/article/35/22/4840/5512357) SCANVIS: a tool for SCoring, ANnotating and VISualizing splice junctions Phaedra Agius, Heather Geiger, Nicolas Robine (https://academic.oup.com/bioinformatics/article/35/22/4843/5514043) vulcanSpot: a tool to prioritize therapeutic vulnerabilities in cancer Javier Perales-Patón, Tomás Di Domenico, Coral Fustero-Torre, Elena Piñeiro-Yáñez, Carlos Carretero-Puche (https://academic.oup.com/bioinformatics/article/35/22/4846/5512479) MetOSite: an integrated resource for the study of methionine residues sulfoxidation Héctor Valverde, Francisco R Cantón, Juan Carlos Aledo (https://academic.oup.com/bioinformatics/article/35/22/4849/5514041) PhenoScanner V2: an expanded tool for searching human genotype--phenotype associations Mihir A Kamat, James A Blackshaw, Robin Young, Praveen Surendran, Stephen Burgess (https://academic.oup.com/bioinformatics/article/35/22/4851/5522366) VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations James D Stephenson, Roman A Laskowski, Andrew Nightingale, Matthew E Hurles, Janet M Thornton (https://academic.oup.com/bioinformatics/article/35/22/4854/5514476) Sequencing data discovery with MetaSeek Adrienne Hoarfrost, Nick Brown, C Titus Brown, Carol Arnosti (https://academic.oup.com/bioinformatics/article/35/22/4857/5521620) Deep fusion of contextual and object-based representations for delineation of multiple nuclear phenotypes Mina Khoshdeli, Garrett Winkelmaier, Bahram Parvin (https://academic.oup.com/bioinformatics/article/35/22/4860/5499132) GENOME ANALYSIS ------------------------------ ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions Egor Dolzhenko, Viraj Deshpande, Felix Schlesinger, Peter Krusche, Roman Petrovski (https://academic.oup.com/bioinformatics/article/35/22/4754/5499079) snakePipes: facilitating flexible, scalable and integrative epigenomic analysis Vivek Bhardwaj, Steffen Heyne, Katarzyna Sikora, Leily Rabbani, Michael Rauer (https://academic.oup.com/bioinformatics/article/35/22/4757/5499080) RBPSponge: genome-wide identification of lncRNAs that sponge RBPs Saber HafezQorani, Aissa Houdjedj, Mehmet Arici, Abdesselam Said, Hilal Kazan (https://academic.oup.com/bioinformatics/article/35/22/4760/5509522) Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data Jonathan Cairns, William R Orchard, Valeriya Malysheva, Mikhail Spivakov (https://academic.oup.com/bioinformatics/article/35/22/4764/5514042) eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data Charles E Breeze, Alex P Reynolds, Jenny van Dongen, Ian Dunham, John Lazar (https://academic.oup.com/bioinformatics/article/35/22/4767/5510552) Nanopype: a modular and scalable nanopore data processing pipeline Pay Giesselmann, Sara Hetzel, Franz-Josef Müller, Alexander Meissner, Helene Kretzmer (https://academic.oup.com/bioinformatics/article/35/22/4770/5514474) capC-MAP: software for analysis of Capture-C data Adam Buckle, Nick Gilbert, Davide Marenduzzo, Chris A Brackley (https://academic.oup.com/bioinformatics/article/35/22/4773/5512362) Testing clonal relatedness of two tumors from the same patient based on their mutational profiles: update of the Clonality R package Audrey Mauguen, Venkatraman E Seshan, Colin B Begg, Irina Ostrovnaya (https://academic.oup.com/bioinformatics/article/35/22/4776/5518921) GeneNoteBook, a collaborative notebook for comparative genomics Rens Holmer, Robin van Velzen, Rene Geurts, Ton Bisseling, Dick de Ridder (https://academic.oup.com/bioinformatics/article/35/22/4779/5519115) svtools: population-scale analysis of structural variation David E Larson, Haley J Abel, Colby Chiang, Abhijit Badve, Indraniel Das (https://academic.oup.com/bioinformatics/article/35/22/4782/5520944) OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers Claudia Arnedo-Pac, Loris Mularoni, Ferran Muiños, Abel Gonzalez-Perez, Nuria Lopez-Bigas (https://academic.oup.com/bioinformatics/article/35/22/4788/5522012) GTShark: genotype compression in large projects Sebastian Deorowicz, Agnieszka Danek (https://academic.oup.com/bioinformatics/article/35/22/4791/5521623) SEQUENCE ANALYSIS ------------------------------ SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions Qingzhen Hou, Paul F G De Geest, Christian J Griffioen, Sanne Abeln, Jaap Heringa (https://academic.oup.com/bioinformatics/article/35/22/4794/5497259) Seq2Feature: a comprehensive web-based feature extraction tool Rahul Nikam, M Michael Gromiha (https://academic.oup.com/bioinformatics/article/35/22/4797/5499130) NX4: a web-based visualization of large multiple sequence alignments A Solano-Roman, C Cruz-Castillo, D Offenhuber, A Colubri (https://academic.oup.com/bioinformatics/article/35/22/4800/5510560) VCF/Plotein: visualization and prioritization of genomic variants from human exome sequencing projects Raul Ossio, O Isaac Garcia-Salinas, Diego Said Anaya-Mancilla, Jair S Garcia-Sotelo, Luis A Aguilar (https://academic.oup.com/bioinformatics/article/35/22/4803/5510555) BAMixChecker: an automated checkup tool for matched sample pairs in NGS cohort Hein Chun, Sangwoo Kim (https://academic.oup.com/bioinformatics/article/35/22/4806/5514045) Noise-cancelling repeat finder: uncovering tandem repeats in error-prone long-read sequencing data Robert S Harris, Monika Cechova, Kateryna D Makova (https://academic.oup.com/bioinformatics/article/35/22/4809/5530597) DepLogo: visualizing sequence dependencies in R Jan Grau, Martin Nettling, Jens Keilwagen (https://academic.oup.com/bioinformatics/article/35/22/4812/5521622) PHYLOGENETICS ------------------------------ RERconverge: an R package for associating evolutionary rates with convergent traits Amanda Kowalczyk, Wynn K Meyer, Raghavendran Partha, Weiguang Mao, Nathan L Clark (https://academic.oup.com/bioinformatics/article/35/22/4815/5514536) iTUPA: an online automated application to perform Topographic-Unit Parsimony Analysis Muhsen Hammoud, Charles Morphy D Santos, Joao Paulo Gois (https://academic.oup.com/bioinformatics/article/35/22/4818/5514049) STRUCTURAL BIOINFORMATICS ------------------------------ PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes Brian Jiménez-García, Katarina Elez, Panagiotis I Koukos, Alexandre Mjj Bonvin, Anna Vangone (https://academic.oup.com/bioinformatics/article/35/22/4821/5505420) WDSPdb: an updated resource for WD40 proteins Jing Ma, Ke An, Jing-Bo Zhou, Nuo-Si Wu, Yang Wang (https://academic.oup.com/bioinformatics/article/35/22/4824/5510551) GENE EXPRESSION ------------------------------ EnImpute: imputing dropout events in single-cell RNA-sequencing data via ensemble learning Xiao-Fei Zhang, Le Ou-Yang, Shuo Yang, Xing-Ming Zhao, Xiaohua Hu (https://academic.oup.com/bioinformatics/article/35/22/4827/5498284) SIGN: similarity identification in gene expression Seyed Ali Madani Tonekaboni, Venkata Satya Kumar Manem, Nehme El-Hachem, Benjamin Haibe-Kains (https://academic.oup.com/bioinformatics/article/35/22/4830/5518919) DEUS: an R package for accurate small RNA profiling based on differential expression of unique sequences Tim Jeske, Peter Huypens, Laura Stirm, Selina Höckele, Christine M Wurmser (https://academic.oup.com/bioinformatics/article/35/22/4834/5522007) GENETICS AND POPULATION ANALYSIS ------------------------------ RAISS: robust and accurate imputation from summary statistics Hanna Julienne, Huwenbo Shi, Bogdan Pasaniuc, Hugues Aschard (https://academic.oup.com/bioinformatics/article/35/22/4837/5512360) RAbHIT: R Antibody Haplotype Inference Tool Ayelet Peres, Moriah Gidoni, Pazit Polak, Gur Yaari (https://academic.oup.com/bioinformatics/article/35/22/4840/5512357) SYSTEMS BIOLOGY ------------------------------ SCANVIS: a tool for SCoring, ANnotating and VISualizing splice junctions Phaedra Agius, Heather Geiger, Nicolas Robine (https://academic.oup.com/bioinformatics/article/35/22/4843/5514043) vulcanSpot: a tool to prioritize therapeutic vulnerabilities in cancer Javier Perales-Patón, Tomás Di Domenico, Coral Fustero-Torre, Elena Piñeiro-Yáñez, Carlos Carretero-Puche (https://academic.oup.com/bioinformatics/article/35/22/4846/5512479) DATABASES AND ONTOLOGIES ------------------------------ MetOSite: an integrated resource for the study of methionine residues sulfoxidation Héctor Valverde, Francisco R Cantón, Juan Carlos Aledo (https://academic.oup.com/bioinformatics/article/35/22/4849/5514041) PhenoScanner V2: an expanded tool for searching human genotype--phenotype associations Mihir A Kamat, James A Blackshaw, Robin Young, Praveen Surendran, Stephen Burgess (https://academic.oup.com/bioinformatics/article/35/22/4851/5522366) VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations James D Stephenson, Roman A Laskowski, Andrew Nightingale, Matthew E Hurles, Janet M Thornton (https://academic.oup.com/bioinformatics/article/35/22/4854/5514476) Sequencing data discovery with MetaSeek Adrienne Hoarfrost, Nick Brown, C Titus Brown, Carol Arnosti (https://academic.oup.com/bioinformatics/article/35/22/4857/5521620) BIOIMAGE INFORMATICS ------------------------------ Deep fusion of contextual and object-based representations for delineation of multiple nuclear phenotypes Mina Khoshdeli, Garrett Winkelmaier, Bahram Parvin (https://academic.oup.com/bioinformatics/article/35/22/4860/5499132) ============================= LETTER TO THE EDITOR ============================ STRUCTURAL BIOINFORMATICS ------------------------------ AlphaFold at CASP13 Mohammed AlQuraishi (https://academic.oup.com/bioinformatics/article/35/22/4862/5497249) Unsubscribe (http://cp20.com/unsubscribe) Manage email alerts (https://academic.oup.com/my-account/email-alerts) Written requests to unsubscribe can be sent to: Journals Marketing, Oxford University Press, Great Clarendon Street, Oxford, 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New issue alert
 
 
 
 
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.
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Bioinformatics  
Volume 35 Issue 22
 
15 November 2019
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
PHANOTATE: a novel approach to gene identification in phage genomes border= 
 
Katelyn McNair ; Carol Zhou; Elizabeth A Dinsdale; Brian Souza; Robert A Edwards
 
 
Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference border= 
 
Taro Matsutani ; Yuki Ueno; Tsukasa Fukunaga; Michiaki Hamada
 
 
Automatic curation of large comparative animal MicroRNA datasets 
 
Ali M Yazbeck; Peter F Stadler; Kifah Tout ; Jörg Fallmann
 
 
Fast detection of maximal exact matches via fixed sampling of query K-mers and Bloom filtering of index K-mers 
 
Yuansheng Liu; Leo Yu Zhang; Jinyan Li
 
 
Identification of differentially expressed gene sets using the Generalized Berk'Jones statistic 
 
Sheila M Gaynor; Ryan Sun; Xihong Lin ; John Quackenbush
 
 
DeepPASTA: deep neural network based polyadenylation site analysis 
 
Ashraful Arefeen; Xinshu Xiao; Tao Jiang
 
 
DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning 
 
Peng Ni; Neng Huang; Zhi Zhang ; De-Peng Wang; Fan Liang ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
A new statistic for efficient detection of repetitive sequences 
 
Sijie Chen; Yixin Chen; Fengzhu Sun ; Michael S Waterman; Xuegong Zhang
 
 
A framework for space-efficient variable-order Markov models 
 
Fabio Cunial; Jarno Alanko; Djamal Belazzougui
 
 
Computational identification of prion-like RNA-binding proteins that form liquid phase-separated condensates 
 
Gabriele Orlando; Daniele Raimondi; Francesco Tabaro ; Francesco Codicè; Yves Moreau ...
 
 
BHap: a novel approach for bacterial haplotype reconstruction 
 
Xin Li; Samaneh Saadat; Haiyan Hu ; Xiaoman Li
 
 
ProSampler: an ultrafast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery 
 
Yang Li; Pengyu Ni; Shaoqiang Zhang ; Guojun Li; Zhengchang Su
 
 
Develop machine learning-based regression predictive models for engineering protein solubility 
 
Xi Han; Xiaonan Wang; Kang Zhou
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks 
 
Yang Li; Jun Hu; Chengxin Zhang ; Dong-Jun Yu; Yang Zhang
 
 
A decision-theoretic approach to the evaluation of machine learning algorithms in computational drug discovery border= 
 
Oliver P Watson ; Isidro Cortes-Ciriano; Aimee R Taylor; James A Watson
 
 
Dynamical important residue network (DIRN): network inference via conformational change 
 
Quan Li; Ray Luo; Hai-Feng Chen
 
 
 
GENE EXPRESSION
 
 
 
Hybrid analysis of gene dynamics predicts context-specific expression and offers regulatory insights border= 
 
Justin D Finkle ; Neda Bagheri
 
 
Cell-level somatic mutation detection from single-cell RNA sequencing border= 
 
Trung Nghia Vu ; Ha-Nam Nguyen; Stefano Calza; Krishna R Kalari; Liewei Wang ...
 
 
scMatch: a single-cell gene expression profile annotation tool using reference datasets border= 
 
Rui Hou ; Elena Denisenko; Alistair R R Forrest
 
 
LAmbDA: label ambiguous domain adaptation dataset integration reduces batch effects and improves subtype detection 
 
Travis S Johnson; Tongxin Wang; Zhi Huang ; Christina Y Yu; Yi Wu ...
 
 
Continuous-state HMMs for modeling time-series single-cell RNA-Seq data 
 
Chieh Lin; Ziv Bar-Joseph
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
NGSEP3: accurate variant calling across species and sequencing protocols border= 
 
Daniel Tello ; Juanita Gil; Cristian D Loaiza; John J Riascos; Nicolás Cardozo ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
Multi-SNP mediation intersection-union test 
 
Wujuan Zhong; Cassandra N Spracklen; Karen L Mohlke ; Xiaojing Zheng; Jason Fine ...
 
 
Adaptive boosting-based computational model for predicting potential miRNA-disease associations 
 
Yan Zhao; Xing Chen; Jun Yin
 
 
 
DATA AND TEXT MINING
 
 
 
Graph-based data integration from bioactive peptide databases of pharmaceutical interest: toward an organized collection enabling visual network analysis  
 
Longendri Aguilera-Mendoza; Yovani Marrero-Ponce; Jesus A Beltran; Roberto Tellez Ibarra; Hugo A Guillen-Ramirez ...
 
 
Another look at matrix correlations 
 
Ahmad Borzou; Razie Yousefi; Rovshan G Sadygov
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions border= 
 
Egor Dolzhenko ; Viraj Deshpande; Felix Schlesinger; Peter Krusche; Roman Petrovski ...
 
 
snakePipes: facilitating flexible, scalable and integrative epigenomic analysis border= 
 
Vivek Bhardwaj ; Steffen Heyne; Katarzyna Sikora; Leily Rabbani; Michael Rauer ...
 
 
RBPSponge: genome-wide identification of lncRNAs that sponge RBPs 
 
Saber HafezQorani; Aissa Houdjedj; Mehmet Arici ; Abdesselam Said; Hilal Kazan
 
 
Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data border= 
 
Jonathan Cairns ; William R Orchard; Valeriya Malysheva; Mikhail Spivakov
 
 
eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data border= 
 
Charles E Breeze ; Alex P Reynolds; Jenny van Dongen; Ian Dunham; John Lazar ...
 
 
Nanopype: a modular and scalable nanopore data processing pipeline 
 
Pay Giesselmann; Sara Hetzel; Franz-Josef Müller ; Alexander Meissner; Helene Kretzmer
 
 
capC-MAP: software for analysis of Capture-C data 
 
Adam Buckle; Nick Gilbert; Davide Marenduzzo ; Chris A Brackley
 
 
Testing clonal relatedness of two tumors from the same patient based on their mutational profiles: update of the Clonality R package 
 
Audrey Mauguen; Venkatraman E Seshan; Colin B Begg ; Irina Ostrovnaya
 
 
GeneNoteBook, a collaborative notebook for comparative genomics border= 
 
Rens Holmer; Robin van Velzen; Rene Geurts; Ton Bisseling; Dick de Ridder ...
 
 
svtools: population-scale analysis of structural variation border=  
 
David E Larson; Haley J Abel; Colby Chiang; Abhijit Badve; Indraniel Das ...
 
 
OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers border= 
 
Claudia Arnedo-Pac ; Loris Mularoni; Ferran Muiños; Abel Gonzalez-Perez; Nuria Lopez-Bigas
 
 
GTShark: genotype compression in large projects 
 
Sebastian Deorowicz; Agnieszka Danek
 
 
 
SEQUENCE ANALYSIS
 
 
 
SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions 
 
Qingzhen Hou; Paul F G De Geest; Christian J Griffioen ; Sanne Abeln; Jaap Heringa ...
 
 
Seq2Feature: a comprehensive web-based feature extraction tool 
 
Rahul Nikam; M Michael Gromiha
 
 
NX4: a web-based visualization of large multiple sequence alignments 
 
A Solano-Roman; C Cruz-Castillo; D Offenhuber ; A Colubri
 
 
VCF/Plotein: visualization and prioritization of genomic variants from human exome sequencing projects border= 
 
Raul Ossio ; O Isaac Garcia-Salinas; Diego Said Anaya-Mancilla; Jair S Garcia-Sotelo; Luis A Aguilar ...
 
 
BAMixChecker: an automated checkup tool for matched sample pairs in NGS cohort border= 
 
Hein Chun ; Sangwoo Kim
 
 
Noise-cancelling repeat finder: uncovering tandem repeats in error-prone long-read sequencing data border= 
 
Robert S Harris ; Monika Cechova; Kateryna D Makova
 
 
DepLogo: visualizing sequence dependencies in R 
 
Jan Grau; Martin Nettling; Jens Keilwagen
 
 
 
PHYLOGENETICS
 
 
 
RERconverge: an R package for associating evolutionary rates with convergent traits 
 
Amanda Kowalczyk; Wynn K Meyer; Raghavendran Partha ; Weiguang Mao; Nathan L Clark ...
 
 
iTUPA: an online automated application to perform Topographic-Unit Parsimony Analysis 
 
Muhsen Hammoud; Charles Morphy D Santos; João Paulo Gois
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes 
 
Brian Jiménez-García; Katarina Elez; Panagiotis I Koukos ; Alexandre Mjj Bonvin; Anna Vangone
 
 
WDSPdb: an updated resource for WD40 proteins border=  
 
Jing Ma; Ke An; Jing-Bo Zhou ; Nuo-Si Wu; Yang Wang ...
 
 
 
GENE EXPRESSION
 
 
 
EnImpute: imputing dropout events in single-cell RNA-sequencing data via ensemble learning 
 
Xiao-Fei Zhang; Le Ou-Yang; Shuo Yang ; Xing-Ming Zhao; Xiaohua Hu ...
 
 
SIGN: similarity identification in gene expression 
 
Seyed Ali Madani Tonekaboni; Venkata Satya Kumar Manem; Nehme El-Hachem ; Benjamin Haibe-Kains
 
 
DEUS: an R package for accurate small RNA profiling based on differential expression of unique sequences border= 
 
Tim Jeske ; Peter Huypens; Laura Stirm; Selina Höckele; Christine M Wurmser ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
RAISS: robust and accurate imputation from summary statistics 
 
Hanna Julienne; Huwenbo Shi; Bogdan Pasaniuc ; Hugues Aschard
 
 
RAbHIT: R Antibody Haplotype Inference Tool 
 
Ayelet Peres; Moriah Gidoni; Pazit Polak ; Gur Yaari
 
 
 
SYSTEMS BIOLOGY
 
 
 
SCANVIS: a tool for SCoring, ANnotating and VISualizing splice junctions 
 
Phaedra Agius; Heather Geiger; Nicolas Robine
 
 
vulcanSpot: a tool to prioritize therapeutic vulnerabilities in cancer border= 
 
Javier Perales-Patón ; Tomás Di Domenico; Coral Fustero-Torre; Elena Piñeiro-Yáñez; Carlos Carretero-Puche ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
MetOSite: an integrated resource for the study of methionine residues sulfoxidation 
 
Héctor Valverde; Francisco R Cantón; Juan Carlos Aledo
 
 
PhenoScanner V2: an expanded tool for searching human genotype'phenotype associations border= 
 
Mihir A Kamat ; James A Blackshaw; Robin Young; Praveen Surendran; Stephen Burgess ...
 
 
VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations border= 
 
James D Stephenson ; Roman A Laskowski; Andrew Nightingale; Matthew E Hurles; Janet M Thornton
 
 
Sequencing data discovery with MetaSeek 
 
Adrienne Hoarfrost; Nick Brown; C Titus Brown ; Carol Arnosti
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Deep fusion of contextual and object-based representations for delineation of multiple nuclear phenotypes 
 
Mina Khoshdeli; Garrett Winkelmaier; Bahram Parvin
 
 
 
LETTER TO THE EDITOR
 
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
AlphaFold at CASP13 
 
Mohammed AlQuraishi
 
 
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