Subject: Bioinformatics Table of Contents for 15 October 2019 ------=_Part_1858985462.1571444014167 Content-Type: text/plain;charset=UTF-8 Oxford Academic *** {Bioinformatics} *** Volume 35, Issue 20, 15 October 2019 Read this issue (https://academic.oup.com/bioinformatics/issue/35/20) ------------------------------ 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 ------------------------------ ============================= REVIEW ============================ SEQUENCE ANALYSIS ------------------------------ EPIP: a novel approach for condition-specific enhancer--promoter interaction prediction Amlan Talukder, Samaneh Saadat, Xiaoman Li, Haiyan Hu (https://academic.oup.com/bioinformatics/article/35/20/3877/5549495) ============================= DISCOVERY NOTE ============================ SEQUENCE ANALYSIS ------------------------------ Sub-dominant principal components inform new vaccine targets for HIV Gag Syed Faraz Ahmed, Ahmed A Quadeer, David Morales-Jimenez, Matthew R McKay (https://academic.oup.com/bioinformatics/article/35/20/3884/5524601) ============================= ORIGINAL PAPERS ============================Multiresolution correction of GC bias and application to identification of copy number alterations Ho Jang, Hyunju Lee (https://academic.oup.com/bioinformatics/article/35/20/3890/5378704) Dissecting differential signals in high-throughput data from complex tissues Ziyi Li, Zhijin Wu, Peng Jin, Hao Wu (https://academic.oup.com/bioinformatics/article/35/20/3898/5418952) ORE identifies extreme expression effects enriched for rare variants F Richter, G E Hoffman, K B Manheimer, N Patel, A J Sharp (https://academic.oup.com/bioinformatics/article/35/20/3906/5418790) ERVcaller: identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data Xun Chen, Dawei Li (https://academic.oup.com/bioinformatics/article/35/20/3913/5416145) Discovery of tandem and interspersed segmental duplications using high-throughput sequencing Arda Soylev, Thong Minh Le, Hajar Amini, Can Alkan, Fereydoun Hormozdiari (https://academic.oup.com/bioinformatics/article/35/20/3923/5425335) Stable H3K4me3 is associated with transcription initiation during early embryo development Xin Huang, Xudong Gao, Wanying Li, Shuai Jiang, Ruijiang Li (https://academic.oup.com/bioinformatics/article/35/20/3931/5376516) Neural networks with circular filters enable data efficient inference of sequence motifs Christopher F Blum, Markus Kollmann (https://academic.oup.com/bioinformatics/article/35/20/3937/5421163) SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing Dennis C Wylie, Hans A Hofmann, Boris V Zemelman (https://academic.oup.com/bioinformatics/article/35/20/3944/5418797) FLAS: fast and high-throughput algorithm for PacBio long-read self-correction Ergude Bao, Fei Xie, Changjin Song, Dandan Song (https://academic.oup.com/bioinformatics/article/35/20/3953/5416141) ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization John Yin, Chao Zhang, Siavash Mirarab (https://academic.oup.com/bioinformatics/article/35/20/3961/5418955) Protein multiple alignments: sequence-based versus structure-based programs Mathilde Carpentier, Jacques Chomilier (https://academic.oup.com/bioinformatics/article/35/20/3970/5426703) SCL: a lattice-based approach to infer 3D chromosome structures from single-cell Hi-C data Hao Zhu, Zheng Wang (https://academic.oup.com/bioinformatics/article/35/20/3981/5378702) Classical scoring functions for docking are unable to exploit large volumes of structural and interaction data Hongjian Li, Jiangjun Peng, Pavel Sidorov, Yee Leung, Kwong-Sak Leung (https://academic.oup.com/bioinformatics/article/35/20/3989/5380764) Significance tests for analyzing gene expression data with small sample sizes Insha Ullah, Sudhir Paul, Zhenjie Hong, You-Gan Wang (https://academic.oup.com/bioinformatics/article/35/20/3996/5381541) Developing structural profile matrices for protein secondary structure and solvent accessibility prediction Zafer Aydin, Nuh Azginoglu, Halil Ibrahim Bilgin, Mete Celik (https://academic.oup.com/bioinformatics/article/35/20/4004/5425326) Probabilistic count matrix factorization for single cell expression data analysis Ghislain Durif, Laurent Modolo, Jeff E Mold, Sophie Lambert-Lacroix, Franck Picard (https://academic.oup.com/bioinformatics/article/35/20/4011/5378703) maTE: discovering expressed interactions between microRNAs and their targets Malik Yousef, Loai Abdallah, Jens Allmer (https://academic.oup.com/bioinformatics/article/35/20/4020/5416143) Simultaneous clustering of multiview biomedical data using manifold optimization Yun Yu, Lei-Hong Zhang, Shuqin Zhang (https://academic.oup.com/bioinformatics/article/35/20/4029/5421162) SummaryAUC: a tool for evaluating the performance of polygenic risk prediction models in validation datasets with only summary level statistics Lei Song, Aiyi Liu, Jianxin Shi, P V Gejman, A R Sanders (https://academic.oup.com/bioinformatics/article/35/20/4038/5419857) Modelling GĂ-E with historical weather information improves genomic prediction in new environments Jussi Gillberg, Pekka Marttinen, Hiroshi Mamitsuka, Samuel Kaski (https://academic.oup.com/bioinformatics/article/35/20/4045/5448861) SodaPop: a forward simulation suite for the evolutionary dynamics of asexual populations on protein fitness landscapes Louis Gauthier, RĂ©micia Di Franco, Adrian W R Serohijos (https://academic.oup.com/bioinformatics/article/35/20/4053/5380769) CyTOFmerge: integrating mass cytometry data across multiple panels Tamim Abdelaal, Thomas Höllt, Vincent van Unen, Boudewijn P F Lelieveldt, Frits Koning (https://academic.oup.com/bioinformatics/article/35/20/4063/5381543) Simulation-assisted machine learning Timo M Deist, Andrew Patti, Zhaoqi Wang, David Krane, Taylor Sorenson (https://academic.oup.com/bioinformatics/article/35/20/4072/5418953) Enhanced Waddington landscape model with cell--cell communication can explain molecular mechanisms of self-organization Hosein Fooladi, Parsa Moradi, Ali Sharifi-Zarchi, Babak Hosein Khalaj (https://academic.oup.com/bioinformatics/article/35/20/4081/5418791) CliqueMS: a computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network Oriol Senan, Antoni Aguilar-Mogas, Miriam Navarro, Jordi Capellades, Luke Noon (https://academic.oup.com/bioinformatics/article/35/20/4089/5418951) Differential proteostatic regulation of insoluble and abundant proteins Reshmi Ramakrishnan, Bert Houben, Frederic Rousseau, Joost Schymkowitz (https://academic.oup.com/bioinformatics/article/35/20/4098/5418794) Drug repositioning through integration of prior knowledge and projections of drugs and diseases Ping Xuan, Yangkun Cao, Tiangang Zhang, Xiao Wang, Shuxiang Pan (https://academic.oup.com/bioinformatics/article/35/20/4108/5378700) Compressed filesystem for managing large genome collections Gonzalo Navarro, VĂ­ctor SepĂşlveda, Mauricio MarĂ­n, SenĂ©n González (https://academic.oup.com/bioinformatics/article/35/20/4120/5384493) Health assistant: answering your questions anytime from biomedical literature Zan-Xia Jin, Bo-Wen Zhang, Fan Fang, Le-Le Zhang, Xu-Cheng Yin (https://academic.oup.com/bioinformatics/article/35/20/4129/5384491) SPRINT-Gly: predicting N- and O-linked glycosylation sites of human and mouse proteins by using sequence and predicted structural properties Ghazaleh Taherzadeh, Abdollah Dehzangi, Maryam Golchin, Yaoqi Zhou, Matthew P Campbell (https://academic.oup.com/bioinformatics/article/35/20/4140/5418954) BrAPI---an application programming interface for plant breeding applications Peter Selby, Rafael Abbeloos, Jan Erik Backlund, Martin Basterrechea Salido, Guillaume Bauchet (https://academic.oup.com/bioinformatics/article/35/20/4147/5418796) GENOME ANALYSIS ------------------------------ Multiresolution correction of GC bias and application to identification of copy number alterations Ho Jang, Hyunju Lee (https://academic.oup.com/bioinformatics/article/35/20/3890/5378704) Dissecting differential signals in high-throughput data from complex tissues Ziyi Li, Zhijin Wu, Peng Jin, Hao Wu (https://academic.oup.com/bioinformatics/article/35/20/3898/5418952) ORE identifies extreme expression effects enriched for rare variants F Richter, G E Hoffman, K B Manheimer, N Patel, A J Sharp (https://academic.oup.com/bioinformatics/article/35/20/3906/5418790) ERVcaller: identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data Xun Chen, Dawei Li (https://academic.oup.com/bioinformatics/article/35/20/3913/5416145) Discovery of tandem and interspersed segmental duplications using high-throughput sequencing Arda Soylev, Thong Minh Le, Hajar Amini, Can Alkan, Fereydoun Hormozdiari (https://academic.oup.com/bioinformatics/article/35/20/3923/5425335) Stable H3K4me3 is associated with transcription initiation during early embryo development Xin Huang, Xudong Gao, Wanying Li, Shuai Jiang, Ruijiang Li (https://academic.oup.com/bioinformatics/article/35/20/3931/5376516) SEQUENCE ANALYSIS ------------------------------ Neural networks with circular filters enable data efficient inference of sequence motifs Christopher F Blum, Markus Kollmann (https://academic.oup.com/bioinformatics/article/35/20/3937/5421163) SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing Dennis C Wylie, Hans A Hofmann, Boris V Zemelman (https://academic.oup.com/bioinformatics/article/35/20/3944/5418797) FLAS: fast and high-throughput algorithm for PacBio long-read self-correction Ergude Bao, Fei Xie, Changjin Song, Dandan Song (https://academic.oup.com/bioinformatics/article/35/20/3953/5416141) PHYLOGENETICS ------------------------------ ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization John Yin, Chao Zhang, Siavash Mirarab (https://academic.oup.com/bioinformatics/article/35/20/3961/5418955) STRUCTURAL BIOINFORMATICS ------------------------------ Protein multiple alignments: sequence-based versus structure-based programs Mathilde Carpentier, Jacques Chomilier (https://academic.oup.com/bioinformatics/article/35/20/3970/5426703) SCL: a lattice-based approach to infer 3D chromosome structures from single-cell Hi-C data Hao Zhu, Zheng Wang (https://academic.oup.com/bioinformatics/article/35/20/3981/5378702) Classical scoring functions for docking are unable to exploit large volumes of structural and interaction data Hongjian Li, Jiangjun Peng, Pavel Sidorov, Yee Leung, Kwong-Sak Leung (https://academic.oup.com/bioinformatics/article/35/20/3989/5380764) Significance tests for analyzing gene expression data with small sample sizes Insha Ullah, Sudhir Paul, Zhenjie Hong, You-Gan Wang (https://academic.oup.com/bioinformatics/article/35/20/3996/5381541) Developing structural profile matrices for protein secondary structure and solvent accessibility prediction Zafer Aydin, Nuh Azginoglu, Halil Ibrahim Bilgin, Mete Celik (https://academic.oup.com/bioinformatics/article/35/20/4004/5425326) GENE EXPRESSION ------------------------------ Probabilistic count matrix factorization for single cell expression data analysis Ghislain Durif, Laurent Modolo, Jeff E Mold, Sophie Lambert-Lacroix, Franck Picard (https://academic.oup.com/bioinformatics/article/35/20/4011/5378703) maTE: discovering expressed interactions between microRNAs and their targets Malik Yousef, Loai Abdallah, Jens Allmer (https://academic.oup.com/bioinformatics/article/35/20/4020/5416143) Simultaneous clustering of multiview biomedical data using manifold optimization Yun Yu, Lei-Hong Zhang, Shuqin Zhang (https://academic.oup.com/bioinformatics/article/35/20/4029/5421162) GENETICS AND POPULATION ANALYSIS ------------------------------ SummaryAUC: a tool for evaluating the performance of polygenic risk prediction models in validation datasets with only summary level statistics Lei Song, Aiyi Liu, Jianxin Shi, P V Gejman, A R Sanders (https://academic.oup.com/bioinformatics/article/35/20/4038/5419857) Modelling GĂ-E with historical weather information improves genomic prediction in new environments Jussi Gillberg, Pekka Marttinen, Hiroshi Mamitsuka, Samuel Kaski (https://academic.oup.com/bioinformatics/article/35/20/4045/5448861) SYSTEMS BIOLOGY ------------------------------ SodaPop: a forward simulation suite for the evolutionary dynamics of asexual populations on protein fitness landscapes Louis Gauthier, RĂ©micia Di Franco, Adrian W R Serohijos (https://academic.oup.com/bioinformatics/article/35/20/4053/5380769) CyTOFmerge: integrating mass cytometry data across multiple panels Tamim Abdelaal, Thomas Höllt, Vincent van Unen, Boudewijn P F Lelieveldt, Frits Koning (https://academic.oup.com/bioinformatics/article/35/20/4063/5381543) Simulation-assisted machine learning Timo M Deist, Andrew Patti, Zhaoqi Wang, David Krane, Taylor Sorenson (https://academic.oup.com/bioinformatics/article/35/20/4072/5418953) Enhanced Waddington landscape model with cell--cell communication can explain molecular mechanisms of self-organization Hosein Fooladi, Parsa Moradi, Ali Sharifi-Zarchi, Babak Hosein Khalaj (https://academic.oup.com/bioinformatics/article/35/20/4081/5418791) CliqueMS: a computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network Oriol Senan, Antoni Aguilar-Mogas, Miriam Navarro, Jordi Capellades, Luke Noon (https://academic.oup.com/bioinformatics/article/35/20/4089/5418951) Differential proteostatic regulation of insoluble and abundant proteins Reshmi Ramakrishnan, Bert Houben, Frederic Rousseau, Joost Schymkowitz (https://academic.oup.com/bioinformatics/article/35/20/4098/5418794) DATA AND TEXT MINING ------------------------------ Drug repositioning through integration of prior knowledge and projections of drugs and diseases Ping Xuan, Yangkun Cao, Tiangang Zhang, Xiao Wang, Shuxiang Pan (https://academic.oup.com/bioinformatics/article/35/20/4108/5378700) Compressed filesystem for managing large genome collections Gonzalo Navarro, VĂ­ctor SepĂşlveda, Mauricio MarĂ­n, SenĂ©n González (https://academic.oup.com/bioinformatics/article/35/20/4120/5384493) Health assistant: answering your questions anytime from biomedical literature Zan-Xia Jin, Bo-Wen Zhang, Fan Fang, Le-Le Zhang, Xu-Cheng Yin (https://academic.oup.com/bioinformatics/article/35/20/4129/5384491) SPRINT-Gly: predicting N- and O-linked glycosylation sites of human and mouse proteins by using sequence and predicted structural properties Ghazaleh Taherzadeh, Abdollah Dehzangi, Maryam Golchin, Yaoqi Zhou, Matthew P Campbell (https://academic.oup.com/bioinformatics/article/35/20/4140/5418954) DATABASES AND ONTOLOGIES ------------------------------ BrAPI---an application programming interface for plant breeding applications Peter Selby, Rafael Abbeloos, Jan Erik Backlund, Martin Basterrechea Salido, Guillaume Bauchet (https://academic.oup.com/bioinformatics/article/35/20/4147/5418796) ============================= APPLICATIONS NOTES ============================ppsPCP: a plant presence/absence variants scanner and pan-genome construction pipeline Muhammad Tahir Ul Qamar, Xitong Zhu, Feng Xing, Ling-Ling Chen (https://academic.oup.com/bioinformatics/article/35/20/4156/5372683) ScanNeo: identifying indel-derived neoantigens using RNA-Seq data Ting-You Wang, Li Wang, Sk Kayum Alam, Luke H Hoeppner, Rendong Yang (https://academic.oup.com/bioinformatics/article/35/20/4159/5384488) GToTree: a user-friendly workflow for phylogenomics Michael D Lee (https://academic.oup.com/bioinformatics/article/35/20/4162/5378708) Lemon: a framework for rapidly mining structural information from the Protein Data Bank Jonathan Fine, Gaurav Chopra (https://academic.oup.com/bioinformatics/article/35/20/4165/5380765) FoldX 5.0: working with RNA, small molecules and a new graphical interface Javier Delgado, Leandro G Radusky, Damiano Cianferoni, Luis Serrano (https://academic.oup.com/bioinformatics/article/35/20/4168/5381539) CABS-dock standalone: a toolbox for flexible protein--peptide docking Mateusz Kurcinski, Maciej Pawel Ciemny, Tymoteusz Oleniecki, Aleksander Kuriata, Aleksandra E Badaczewska-Dawid (https://academic.oup.com/bioinformatics/article/35/20/4170/5378705) Holistic optimization of an RNA-seq workflow for multi-threaded environments Ling-Hong Hung, Wes Lloyd, Radhika Agumbe Sridhar, Saranya Devi Athmalingam Ravishankar, Yuguang Xiong (https://academic.oup.com/bioinformatics/article/35/20/4173/5374759) Pinetree: a step-wise gene expression simulator with codon-specific translation rates Benjamin R Jack, Claus O Wilke (https://academic.oup.com/bioinformatics/article/35/20/4176/5421510) PleioNet: a web-based visualization tool for exploring pleiotropy across complex traits X Raymond Gao, Hua Huang (https://academic.oup.com/bioinformatics/article/35/20/4179/5378706) ECOGEMS: efficient compression and retrieve of SNP data of 2058 rice accessions with integer sparse matrices Wen Yao, Fangfang Huang, Xuehai Zhang, Jihua Tang (https://academic.oup.com/bioinformatics/article/35/20/4181/5380768) PedigreeNet: a web-based pedigree viewer for biological databases Bremen L Braun, David A Schott, John L Portwood, Carson M Andorf, Taner Z Sen (https://academic.oup.com/bioinformatics/article/35/20/4184/5418795) CytoBackBone: an algorithm for merging of phenotypic information from different cytometric profiles Adrien Leite Pereira, Olivier Lambotte, Roger Le Grand, Antonio Cosma, Nicolas Tchitchek (https://academic.oup.com/bioinformatics/article/35/20/4187/5418792) GladiaTOX: GLobal Assessment of Dose-IndicAtor in TOXicology Vincenzo Belcastro, Stephane Cano, Diego Marescotti, Stefano Acali, Carine Poussin (https://academic.oup.com/bioinformatics/article/35/20/4190/5380766) PgpRules: a decision tree based prediction server for P-glycoprotein substrates and inhibitors Pei-Hua Wang, Yi-Shu Tu, Yufeng J Tseng (https://academic.oup.com/bioinformatics/article/35/20/4193/5421161) onlineFDR: an R package to control the false discovery rate for growing data repositories David S Robertson, Jan Wildenhain, Adel Javanmard, Natasha A Karp (https://academic.oup.com/bioinformatics/article/35/20/4196/5380770) TISIDB: an integrated repository portal for tumor--immune system interactions Beibei Ru, Ching Ngar Wong, Yin Tong, Jia Yi Zhong, Sophia Shek Wa Zhong (https://academic.oup.com/bioinformatics/article/35/20/4200/5418799) The TMCrys server for supporting crystallization of transmembrane proteins Julia K Varga, Gábor E Tusnády (https://academic.oup.com/bioinformatics/article/35/20/4203/5355054) GENOME ANALYSIS ------------------------------ ppsPCP: a plant presence/absence variants scanner and pan-genome construction pipeline Muhammad Tahir Ul Qamar, Xitong Zhu, Feng Xing, Ling-Ling Chen (https://academic.oup.com/bioinformatics/article/35/20/4156/5372683) ScanNeo: identifying indel-derived neoantigens using RNA-Seq data Ting-You Wang, Li Wang, Sk Kayum Alam, Luke H Hoeppner, Rendong Yang (https://academic.oup.com/bioinformatics/article/35/20/4159/5384488) PHYLOGENETICS ------------------------------ GToTree: a user-friendly workflow for phylogenomics Michael D Lee (https://academic.oup.com/bioinformatics/article/35/20/4162/5378708) STRUCTURAL BIOINFORMATICS ------------------------------ Lemon: a framework for rapidly mining structural information from the Protein Data Bank Jonathan Fine, Gaurav Chopra (https://academic.oup.com/bioinformatics/article/35/20/4165/5380765) FoldX 5.0: working with RNA, small molecules and a new graphical interface Javier Delgado, Leandro G Radusky, Damiano Cianferoni, Luis Serrano (https://academic.oup.com/bioinformatics/article/35/20/4168/5381539) CABS-dock standalone: a toolbox for flexible protein--peptide docking Mateusz Kurcinski, Maciej Pawel Ciemny, Tymoteusz Oleniecki, Aleksander Kuriata, Aleksandra E Badaczewska-Dawid (https://academic.oup.com/bioinformatics/article/35/20/4170/5378705) GENE EXPRESSION ------------------------------ Holistic optimization of an RNA-seq workflow for multi-threaded environments Ling-Hong Hung, Wes Lloyd, Radhika Agumbe Sridhar, Saranya Devi Athmalingam Ravishankar, Yuguang Xiong (https://academic.oup.com/bioinformatics/article/35/20/4173/5374759) Pinetree: a step-wise gene expression simulator with codon-specific translation rates Benjamin R Jack, Claus O Wilke (https://academic.oup.com/bioinformatics/article/35/20/4176/5421510) GENETICS AND POPULATION ANALYSIS ------------------------------ PleioNet: a web-based visualization tool for exploring pleiotropy across complex traits X Raymond Gao, Hua Huang (https://academic.oup.com/bioinformatics/article/35/20/4179/5378706) ECOGEMS: efficient compression and retrieve of SNP data of 2058 rice accessions with integer sparse matrices Wen Yao, Fangfang Huang, Xuehai Zhang, Jihua Tang (https://academic.oup.com/bioinformatics/article/35/20/4181/5380768) PedigreeNet: a web-based pedigree viewer for biological databases Bremen L Braun, David A Schott, John L Portwood, Carson M Andorf, Taner Z Sen (https://academic.oup.com/bioinformatics/article/35/20/4184/5418795) SYSTEMS BIOLOGY ------------------------------ CytoBackBone: an algorithm for merging of phenotypic information from different cytometric profiles Adrien Leite Pereira, Olivier Lambotte, Roger Le Grand, Antonio Cosma, Nicolas Tchitchek (https://academic.oup.com/bioinformatics/article/35/20/4187/5418792) DATA AND TEXT MINING ------------------------------ GladiaTOX: GLobal Assessment of Dose-IndicAtor in TOXicology Vincenzo Belcastro, Stephane Cano, Diego Marescotti, Stefano Acali, Carine Poussin (https://academic.oup.com/bioinformatics/article/35/20/4190/5380766) PgpRules: a decision tree based prediction server for P-glycoprotein substrates and inhibitors Pei-Hua Wang, Yi-Shu Tu, Yufeng J Tseng (https://academic.oup.com/bioinformatics/article/35/20/4193/5421161) DATABASES AND ONTOLOGIES ------------------------------ onlineFDR: an R package to control the false discovery rate for growing data repositories David S Robertson, Jan Wildenhain, Adel Javanmard, Natasha A Karp (https://academic.oup.com/bioinformatics/article/35/20/4196/5380770) TISIDB: an integrated repository portal for tumor--immune system interactions Beibei Ru, Ching Ngar Wong, Yin Tong, Jia Yi Zhong, Sophia Shek Wa Zhong (https://academic.oup.com/bioinformatics/article/35/20/4200/5418799) STRUCTURAL GENOMICS ------------------------------ The TMCrys server for supporting crystallization of transmembrane proteins Julia K Varga, Gábor E Tusnády (https://academic.oup.com/bioinformatics/article/35/20/4203/5355054) ============================= CORRIGENDA ============================relax: the analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data SĂ©bastien Morin, Troels E Linnet, Mathilde Lescanne, Paul Schanda, Gary S Thompson (https://academic.oup.com/bioinformatics/article/35/20/4205/5510533) Corrigendum to: A new cis-acting regulatory element driving gene expression in the zebrafish pineal gland Shahar Alon, Eli Eisenberg, Jasmine Jacob-Hirsch, Gideon Rechavi, Gad Vatine (https://academic.oup.com/bioinformatics/article/35/20/4206/5491599) 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, OX2 6DP, UK. 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_1858985462.1571444014167 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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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.
Read now
 
 
 
 
 
 
Bioinformatics  
Volume 35 Issue 20
 
15 October 2019
 
button-issue.png
 
 
REVIEW
 
 
 
 
SEQUENCE ANALYSIS
 
 
 
EPIP: a novel approach for condition-specific enhancer'promoter interaction prediction 
 
Amlan Talukder; Samaneh Saadat; Xiaoman Li ; Haiyan Hu
 
 
 
DISCOVERY NOTE
 
 
 
 
SEQUENCE ANALYSIS
 
 
 
Sub-dominant principal components inform new vaccine targets for HIV Gag 
 
Syed Faraz Ahmed; Ahmed A Quadeer; David Morales-Jimenez ; Matthew R McKay
 
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Multiresolution correction of GC bias and application to identification of copy number alterations 
 
Ho Jang; Hyunju Lee
 
 
Dissecting differential signals in high-throughput data from complex tissues 
 
Ziyi Li; Zhijin Wu; Peng Jin ; Hao Wu
 
 
ORE identifies extreme expression effects enriched for rare variants 
 
F Richter; G E Hoffman; K B Manheimer ; N Patel; A J Sharp ...
 
 
ERVcaller: identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data 
 
Xun Chen; Dawei Li
 
 
Discovery of tandem and interspersed segmental duplications using high-throughput sequencing 
 
Arda Soylev; Thong Minh Le; Hajar Amini ; Can Alkan; Fereydoun Hormozdiari
 
 
Stable H3K4me3 is associated with transcription initiation during early embryo development 
 
Xin Huang; Xudong Gao; Wanying Li ; Shuai Jiang; Ruijiang Li ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
Neural networks with circular filters enable data efficient inference of sequence motifs border= 
 
Christopher F Blum ; Markus Kollmann
 
 
SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing 
 
Dennis C Wylie; Hans A Hofmann; Boris V Zemelman
 
 
FLAS: fast and high-throughput algorithm for PacBio long-read self-correction 
 
Ergude Bao; Fei Xie; Changjin Song ; Dandan Song
 
 
 
PHYLOGENETICS
 
 
 
ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization 
 
John Yin; Chao Zhang; Siavash Mirarab
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Protein multiple alignments: sequence-based versus structure-based programs 
 
Mathilde Carpentier; Jacques Chomilier
 
 
SCL: a lattice-based approach to infer 3D chromosome structures from single-cell Hi-C data border= 
 
Hao Zhu ; Zheng Wang
 
 
Classical scoring functions for docking are unable to exploit large volumes of structural and interaction data 
 
Hongjian Li; Jiangjun Peng; Pavel Sidorov ; Yee Leung; Kwong-Sak Leung ...
 
 
Significance tests for analyzing gene expression data with small sample sizes 
 
Insha Ullah; Sudhir Paul; Zhenjie Hong ; You-Gan Wang
 
 
Developing structural profile matrices for protein secondary structure and solvent accessibility prediction 
 
Zafer Aydin; Nuh Azginoglu; Halil Ibrahim Bilgin ; Mete Celik
 
 
 
GENE EXPRESSION
 
 
 
Probabilistic count matrix factorization for single cell expression data analysis 
 
Ghislain Durif; Laurent Modolo; Jeff E Mold ; Sophie Lambert-Lacroix; Franck Picard
 
 
maTE: discovering expressed interactions between microRNAs and their targets 
 
Malik Yousef; Loai Abdallah; Jens Allmer
 
 
Simultaneous clustering of multiview biomedical data using manifold optimization 
 
Yun Yu; Lei-Hong Zhang; Shuqin Zhang
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
SummaryAUC: a tool for evaluating the performance of polygenic risk prediction models in validation datasets with only summary level statistics  
 
Lei Song; Aiyi Liu; Jianxin Shi ; P V Gejman; A R Sanders ...
 
 
Modelling G × E with historical weather information improves genomic prediction in new environments border= 
 
Jussi Gillberg ; Pekka Marttinen; Hiroshi Mamitsuka; Samuel Kaski
 
 
 
SYSTEMS BIOLOGY
 
 
 
SodaPop: a forward simulation suite for the evolutionary dynamics of asexual populations on protein fitness landscapes 
 
Louis Gauthier; Rémicia Di Franco; Adrian W R Serohijos
 
 
CyTOFmerge: integrating mass cytometry data across multiple panels border= 
 
Tamim Abdelaal ; Thomas Höllt; Vincent van Unen; Boudewijn P F Lelieveldt; Frits Koning ...
 
 
Simulation-assisted machine learning border=  
 
Timo M Deist; Andrew Patti; Zhaoqi Wang ; David Krane; Taylor Sorenson ...
 
 
Enhanced Waddington landscape model with cell'cell communication can explain molecular mechanisms of self-organization 
 
Hosein Fooladi; Parsa Moradi; Ali Sharifi-Zarchi ; Babak Hosein Khalaj
 
 
CliqueMS: a computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network border= 
 
Oriol Senan ; Antoni Aguilar-Mogas; Miriam Navarro; Jordi Capellades; Luke Noon ...
 
 
Differential proteostatic regulation of insoluble and abundant proteins border= 
 
Reshmi Ramakrishnan ; Bert Houben; Frederic Rousseau; Joost Schymkowitz
 
 
 
DATA AND TEXT MINING
 
 
 
Drug repositioning through integration of prior knowledge and projections of drugs and diseases 
 
Ping Xuan; Yangkun Cao; Tiangang Zhang ; Xiao Wang; Shuxiang Pan ...
 
 
Compressed filesystem for managing large genome collections 
 
Gonzalo Navarro; Víctor Sepúlveda; Mauricio Marín ; Senén González
 
 
Health assistant: answering your questions anytime from biomedical literature 
 
Zan-Xia Jin; Bo-Wen Zhang; Fan Fang ; Le-Le Zhang; Xu-Cheng Yin
 
 
SPRINT-Gly: predicting N- and O-linked glycosylation sites of human and mouse proteins by using sequence and predicted structural properties 
 
Ghazaleh Taherzadeh; Abdollah Dehzangi; Maryam Golchin ; Yaoqi Zhou; Matthew P Campbell
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
BrAPI'an application programming interface for plant breeding applications border= 
 
Peter Selby ; Rafael Abbeloos; Jan Erik Backlund; Martin Basterrechea Salido; Guillaume Bauchet ...
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
ppsPCP: a plant presence/absence variants scanner and pan-genome construction pipeline 
 
Muhammad Tahir Ul Qamar; Xitong Zhu; Feng Xing ; Ling-Ling Chen
 
 
ScanNeo: identifying indel-derived neoantigens using RNA-Seq data 
 
Ting-You Wang; Li Wang; Sk Kayum Alam ; Luke H Hoeppner; Rendong Yang
 
 
 
PHYLOGENETICS
 
 
 
GToTree: a user-friendly workflow for phylogenomics border= 
 
Michael D Lee
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Lemon: a framework for rapidly mining structural information from the Protein Data Bank border= 
 
Jonathan Fine ; Gaurav Chopra
 
 
FoldX 5.0: working with RNA, small molecules and a new graphical interface border= 
 
Javier Delgado ; Leandro G Radusky; Damiano Cianferoni; Luis Serrano
 
 
CABS-dock standalone: a toolbox for flexible protein'peptide docking border= 
 
Mateusz Kurcinski ; Maciej Pawel Ciemny; Tymoteusz Oleniecki; Aleksander Kuriata; Aleksandra E Badaczewska-Dawid ...
 
 
 
GENE EXPRESSION
 
 
 
Holistic optimization of an RNA-seq workflow for multi-threaded environments 
 
Ling-Hong Hung; Wes Lloyd; Radhika Agumbe Sridhar ; Saranya Devi Athmalingam Ravishankar; Yuguang Xiong ...
 
 
Pinetree: a step-wise gene expression simulator with codon-specific translation rates 
 
Benjamin R Jack; Claus O Wilke
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
PleioNet: a web-based visualization tool for exploring pleiotropy across complex traits 
 
X Raymond Gao; Hua Huang
 
 
ECOGEMS: efficient compression and retrieve of SNP data of 2058 rice accessions with integer sparse matrices 
 
Wen Yao; Fangfang Huang; Xuehai Zhang ; Jihua Tang
 
 
PedigreeNet: a web-based pedigree viewer for biological databases 
 
Bremen L Braun; David A Schott; John L Portwood ; Carson M Andorf; Taner Z Sen
 
 
 
SYSTEMS BIOLOGY
 
 
 
CytoBackBone: an algorithm for merging of phenotypic information from different cytometric profiles border= 
 
Adrien Leite Pereira ; Olivier Lambotte; Roger Le Grand; Antonio Cosma; Nicolas Tchitchek
 
 
 
DATA AND TEXT MINING
 
 
 
GladiaTOX: GLobal Assessment of Dose-IndicAtor in TOXicology border= 
 
Vincenzo Belcastro ; Stephane Cano; Diego Marescotti; Stefano Acali; Carine Poussin ...
 
 
PgpRules: a decision tree based prediction server for P-glycoprotein substrates and inhibitors 
 
Pei-Hua Wang; Yi-Shu Tu; Yufeng J Tseng
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
onlineFDR: an R package to control the false discovery rate for growing data repositories border= 
 
David S Robertson ; Jan Wildenhain; Adel Javanmard; Natasha A Karp
 
 
TISIDB: an integrated repository portal for tumor'immune system interactions 
 
Beibei Ru; Ching Ngar Wong; Yin Tong ; Jia Yi Zhong; Sophia Shek Wa Zhong ...
 
 
 
STRUCTURAL GENOMICS
 
 
 
The TMCrys server for supporting crystallization of transmembrane proteins border= 
 
Julia K Varga ; Gábor E Tusnády
 
 
 
CORRIGENDA
 
 
 
relax: the analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data border= 
 
Sébastien Morin ; Troels E Linnet; Mathilde Lescanne; Paul Schanda; Gary S Thompson ...
 
 
Corrigendum to: A new cis-acting regulatory element driving gene expression in the zebrafish pineal gland 
 
Shahar Alon; Eli Eisenberg; Jasmine Jacob-Hirsch ; Gideon Rechavi; Gad Vatine ...
 
 
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