Subject: Bioinformatics Table of Contents for 15 December 2019 ------=_Part_644184369.1579024595483 Content-Type: text/plain;charset=UTF-8 Oxford Academic *** Bioinformatics *** Volume 35, Issue 24, 15 December 2019 Read this issue (https://academic.oup.com/bioinformatics/issue/35/24) ------------------------------ 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 ============================MTTFsite: cross-cell type TF binding site prediction by using multi-task learning Jiyun Zhou, Qin Lu, Lin Gui, Ruifeng Xu, Yunfei Long (https://academic.oup.com/bioinformatics/article/35/24/5067/5510558) New algorithms for detecting multi-effect and multi-way epistatic interactions Javad Ansarifar, Lizhi Wang (https://academic.oup.com/bioinformatics/article/35/24/5078/5511839) Full-length de novo viral quasispecies assembly through variation graph construction Jasmijn A Baaijens, Bastiaan Van der Roest, Johannes Köster, Leen Stougie, Alexander Schönhuth (https://academic.oup.com/bioinformatics/article/35/24/5086/5506652) deconvSeq: deconvolution of cell mixture distribution in sequencing data Rose Du, Vince Carey, Scott T Weiss (https://academic.oup.com/bioinformatics/article/35/24/5095/5506629) DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data Albert Y Xue, Angela M Yu, Julius B Lucks, Neda Bagheri (https://academic.oup.com/bioinformatics/article/35/24/5103/5544638) DeepSymmetry: using 3D convolutional networks for identification of tandem repeats and internal symmetries in protein structures Guillaume Pagès, Sergei Grudinin (https://academic.oup.com/bioinformatics/article/35/24/5113/5510549) AutoDock CrankPep: combining folding and docking to predict protein--peptide complexes Yuqi Zhang, Michel F Sanner (https://academic.oup.com/bioinformatics/article/35/24/5121/5510553) DNN-Dom: predicting protein domain boundary from sequence alone by deep neural network Qiang Shi, Weiya Chen, Siqi Huang, Fanglin Jin, Yinghao Dong (https://academic.oup.com/bioinformatics/article/35/24/5128/5514047) Path2Surv: Pathway/gene set-based survival analysis using multiple kernel learning Onur Dereli, Ceyda Oğuz, Mehmet Gönen (https://academic.oup.com/bioinformatics/article/35/24/5137/5506626) Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms Joanna Zyla, Michal Marczyk, Teresa Domaszewska, Stefan H E Kaufmann, Joanna Polanska (https://academic.oup.com/bioinformatics/article/35/24/5146/5511403) DECENT: differential expression with capture efficiency adjustmeNT for single-cell RNA-seq data Chengzhong Ye, Terence P Speed, Agus Salim (https://academic.oup.com/bioinformatics/article/35/24/5155/5514046) Assessing concordance among human, in silico predictions and functional assays on genetic variant classification Jiaqi Luo, Tianliangwen Zhou, Xiaobin You, Yi Zi, Xiaoting Li (https://academic.oup.com/bioinformatics/article/35/24/5163/5505418) ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification Lara Schneider, Tim Kehl, Kristina Thedinga, Nadja Liddy Grammes, Christina Backes (https://academic.oup.com/bioinformatics/article/35/24/5171/5481954) Identification of disease-associated loci using machine learning for genotype and network data integration Luis G Leal, Alessia David, Marjo-Riita Jarvelin, Sylvain Sebert, Minna Männikkö (https://academic.oup.com/bioinformatics/article/35/24/5182/5487393) deepDR: a network-based deep learning approach to in silico drug repositioning Xiangxiang Zeng, Siyi Zhu, Xiangrong Liu, Yadi Zhou, Ruth Nussinov (https://academic.oup.com/bioinformatics/article/35/24/5191/5497253) Smart computational exploration of stochastic gene regulatory network models using human-in-the-loop semi-supervised learning Fredrik Wrede, Andreas Hellander (https://academic.oup.com/bioinformatics/article/35/24/5199/5505421) CNet: a multi-omics approach to detecting clinically associated, combinatory genomic signatures Peilin Jia, Guangsheng Pei, Zhongming Zhao (https://academic.oup.com/bioinformatics/article/35/24/5207/5505417) A scalable method for parameter identification in kinetic models of metabolism using steady-state data Shyam Srinivasan, William R Cluett, Radhakrishnan Mahadevan (https://academic.oup.com/bioinformatics/article/35/24/5216/5514038) Graphlet Laplacians for topology-function and topology-disease relationships Sam F L Windels, Noël Malod-Dognin, Nataša Pržulj (https://academic.oup.com/bioinformatics/article/35/24/5226/5514477) Deep learning of the back-splicing code for circular RNA formation Jun Wang, Liangjiang Wang (https://academic.oup.com/bioinformatics/article/35/24/5235/5488122) Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions Ana S C. Silva, Robbin Bouwmeester, Lennart Martens, Sven Degroeve (https://academic.oup.com/bioinformatics/article/35/24/5243/5488123) ReSimNet: drug response similarity prediction using Siamese neural networks Minji Jeon, Donghyeon Park, Jinhyuk Lee, Hwisang Jeon, Miyoung Ko (https://academic.oup.com/bioinformatics/article/35/24/5249/5497254) Improving data splitting for classification applications in spectrochemical analyses employing a random-mutation Kennard-Stone algorithm approach Camilo L M Morais, Marfran C D Santos, Kássio M G Lima, Francis L Martin (https://academic.oup.com/bioinformatics/article/35/24/5257/5497250) A fully computational and reasonable representation for karyotypes Jennifer D Warrender, Anthony V Moorman, Phillip Lord (https://academic.oup.com/bioinformatics/article/35/24/5264/5522010) Incorporating spatial--anatomical similarity into the VGWAS framework for AD biomarker detection Meiyan Huang, Yuwei Yu, Wei Yang, Qianjin Feng (https://academic.oup.com/bioinformatics/article/35/24/5271/5490205) ARMBIS: accurate and robust matching of brain image sequences from multiple modal imaging techniques Qi Shen, Goayu Xiao, Yingwei Zheng, Jie Wang, Yue Liu (https://academic.oup.com/bioinformatics/article/35/24/5281/5494698) NRStitcher: non-rigid stitching of terapixel-scale volumetric images Arttu Miettinen, Ioannis Vogiatzis Oikonomidis, Anne Bonnin, Marco Stampanoni (https://academic.oup.com/bioinformatics/article/35/24/5290/5497257) Genome analysis ------------------------------ MTTFsite: cross-cell type TF binding site prediction by using multi-task learning Jiyun Zhou, Qin Lu, Lin Gui, Ruifeng Xu, Yunfei Long (https://academic.oup.com/bioinformatics/article/35/24/5067/5510558) New algorithms for detecting multi-effect and multi-way epistatic interactions Javad Ansarifar, Lizhi Wang (https://academic.oup.com/bioinformatics/article/35/24/5078/5511839) Sequence analysis ------------------------------ Full-length de novo viral quasispecies assembly through variation graph construction Jasmijn A Baaijens, Bastiaan Van der Roest, Johannes Köster, Leen Stougie, Alexander Schönhuth (https://academic.oup.com/bioinformatics/article/35/24/5086/5506652) deconvSeq: deconvolution of cell mixture distribution in sequencing data Rose Du, Vince Carey, Scott T Weiss (https://academic.oup.com/bioinformatics/article/35/24/5095/5506629) Structural bioinformatics ------------------------------ DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data Albert Y Xue, Angela M Yu, Julius B Lucks, Neda Bagheri (https://academic.oup.com/bioinformatics/article/35/24/5103/5544638) DeepSymmetry: using 3D convolutional networks for identification of tandem repeats and internal symmetries in protein structures Guillaume Pagès, Sergei Grudinin (https://academic.oup.com/bioinformatics/article/35/24/5113/5510549) AutoDock CrankPep: combining folding and docking to predict protein--peptide complexes Yuqi Zhang, Michel F Sanner (https://academic.oup.com/bioinformatics/article/35/24/5121/5510553) DNN-Dom: predicting protein domain boundary from sequence alone by deep neural network Qiang Shi, Weiya Chen, Siqi Huang, Fanglin Jin, Yinghao Dong (https://academic.oup.com/bioinformatics/article/35/24/5128/5514047) Gene expression ------------------------------ Path2Surv: Pathway/gene set-based survival analysis using multiple kernel learning Onur Dereli, Ceyda Oğuz, Mehmet Gönen (https://academic.oup.com/bioinformatics/article/35/24/5137/5506626) Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms Joanna Zyla, Michal Marczyk, Teresa Domaszewska, Stefan H E Kaufmann, Joanna Polanska (https://academic.oup.com/bioinformatics/article/35/24/5146/5511403) DECENT: differential expression with capture efficiency adjustmeNT for single-cell RNA-seq data Chengzhong Ye, Terence P Speed, Agus Salim (https://academic.oup.com/bioinformatics/article/35/24/5155/5514046) Genetics and population analysis ------------------------------ Assessing concordance among human, in silico predictions and functional assays on genetic variant classification Jiaqi Luo, Tianliangwen Zhou, Xiaobin You, Yi Zi, Xiaoting Li (https://academic.oup.com/bioinformatics/article/35/24/5163/5505418) Systems biology ------------------------------ ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification Lara Schneider, Tim Kehl, Kristina Thedinga, Nadja Liddy Grammes, Christina Backes (https://academic.oup.com/bioinformatics/article/35/24/5171/5481954) Identification of disease-associated loci using machine learning for genotype and network data integration Luis G Leal, Alessia David, Marjo-Riita Jarvelin, Sylvain Sebert, Minna Männikkö (https://academic.oup.com/bioinformatics/article/35/24/5182/5487393) deepDR: a network-based deep learning approach to in silico drug repositioning Xiangxiang Zeng, Siyi Zhu, Xiangrong Liu, Yadi Zhou, Ruth Nussinov (https://academic.oup.com/bioinformatics/article/35/24/5191/5497253) Smart computational exploration of stochastic gene regulatory network models using human-in-the-loop semi-supervised learning Fredrik Wrede, Andreas Hellander (https://academic.oup.com/bioinformatics/article/35/24/5199/5505421) CNet: a multi-omics approach to detecting clinically associated, combinatory genomic signatures Peilin Jia, Guangsheng Pei, Zhongming Zhao (https://academic.oup.com/bioinformatics/article/35/24/5207/5505417) A scalable method for parameter identification in kinetic models of metabolism using steady-state data Shyam Srinivasan, William R Cluett, Radhakrishnan Mahadevan (https://academic.oup.com/bioinformatics/article/35/24/5216/5514038) Graphlet Laplacians for topology-function and topology-disease relationships Sam F L Windels, Noël Malod-Dognin, Nataša Pržulj (https://academic.oup.com/bioinformatics/article/35/24/5226/5514477) Data and text mining ------------------------------ Deep learning of the back-splicing code for circular RNA formation Jun Wang, Liangjiang Wang (https://academic.oup.com/bioinformatics/article/35/24/5235/5488122) Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions Ana S C. Silva, Robbin Bouwmeester, Lennart Martens, Sven Degroeve (https://academic.oup.com/bioinformatics/article/35/24/5243/5488123) ReSimNet: drug response similarity prediction using Siamese neural networks Minji Jeon, Donghyeon Park, Jinhyuk Lee, Hwisang Jeon, Miyoung Ko (https://academic.oup.com/bioinformatics/article/35/24/5249/5497254) Improving data splitting for classification applications in spectrochemical analyses employing a random-mutation Kennard-Stone algorithm approach Camilo L M Morais, Marfran C D Santos, Kássio M G Lima, Francis L Martin (https://academic.oup.com/bioinformatics/article/35/24/5257/5497250) Databases and ontologies ------------------------------ A fully computational and reasonable representation for karyotypes Jennifer D Warrender, Anthony V Moorman, Phillip Lord (https://academic.oup.com/bioinformatics/article/35/24/5264/5522010) Bioimage informatics ------------------------------ Incorporating spatial--anatomical similarity into the VGWAS framework for AD biomarker detection Meiyan Huang, Yuwei Yu, Wei Yang, Qianjin Feng (https://academic.oup.com/bioinformatics/article/35/24/5271/5490205) ARMBIS: accurate and robust matching of brain image sequences from multiple modal imaging techniques Qi Shen, Goayu Xiao, Yingwei Zheng, Jie Wang, Yue Liu (https://academic.oup.com/bioinformatics/article/35/24/5281/5494698) NRStitcher: non-rigid stitching of terapixel-scale volumetric images Arttu Miettinen, Ioannis Vogiatzis Oikonomidis, Anne Bonnin, Marco Stampanoni (https://academic.oup.com/bioinformatics/article/35/24/5290/5497257) ============================= APPLICATIONS NOTES ============================MEpurity: estimating tumor purity using DNA methylation data Bowen Liu, Xiaofei Yang, Tingjie Wang, Jiadong Lin, Yongyong Kang (https://academic.oup.com/bioinformatics/article/35/24/5298/5531131) Predicting promoters in phage genomes using PhagePromoter Marta Sampaio, Miguel Rocha, Hugo Oliveira, Oscar Dias (https://academic.oup.com/bioinformatics/article/35/24/5301/5540317) geneCo: a visualized comparative genomic method to analyze multiple genome structures Jaehee Jung, Jong Im Kim, Gangman Yi (https://academic.oup.com/bioinformatics/article/35/24/5303/5539862) scRNABatchQC: multi-samples quality control for single cell RNA-seq data Qi Liu, Quanhu Sheng, Jie Ping, Marisol Adelina Ramirez, Ken S Lau (https://academic.oup.com/bioinformatics/article/35/24/5306/5542946) JUCHMME: a Java Utility for Class Hidden Markov Models and Extensions for biological sequence analysis Ioannis A Tamposis, Konstantinos D Tsirigos, Margarita C Theodoropoulou, Panagiota I Kontou, Georgios N Tsaousis (https://academic.oup.com/bioinformatics/article/35/24/5309/5524600) PTM-Logo: a program for generation of sequence logos based on position-specific background amino-acid probabilities Thammakorn Saethang, Kenneth Hodge, Chin-Rang Yang, Yue Zhao, Ingorn Kimkong (https://academic.oup.com/bioinformatics/article/35/24/5313/5535597) Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit Maurits J J Dijkstra, Atze J van der Ploeg, K Anton Feenstra, Wan J Fokkink, Sanne Abeln (https://academic.oup.com/bioinformatics/article/35/24/5315/5542395) Sequence tube maps: making graph genomes intuitive to commuters Wolfgang Beyer, Adam M Novak, Glenn Hickey, Jeffrey Chan, Vanessa Tan (https://academic.oup.com/bioinformatics/article/35/24/5318/5542397) MCMCtreeR: functions to prepare MCMCtree analyses and visualize posterior ages on trees Mark N Puttick (https://academic.oup.com/bioinformatics/article/35/24/5321/5530964) TCR3d: The T cell receptor structural repertoire database Ragul Gowthaman, Brian G Pierce (https://academic.oup.com/bioinformatics/article/35/24/5323/5523179) Benchmarking fold detection by DaliLite v.5 Liisa Holm (https://academic.oup.com/bioinformatics/article/35/24/5326/5526869) DDT - Drug Discovery Tool: a fast and intuitive graphics user interface for docking and molecular dynamics analysis Simone Aureli, Daniele Di Marino, Stefano Raniolo, Vittorio Limongelli (https://academic.oup.com/bioinformatics/article/35/24/5328/5532220) HDX-Viewer: interactive 3D visualization of hydrogen--deuterium exchange data David Bouyssié, Jean Lesne, Marie Locard-Paulet, Renaud Albigot, Odile Burlet-Schiltz (https://academic.oup.com/bioinformatics/article/35/24/5331/5530164) VeriNA3d: an R package for nucleic acids data mining Diego Gallego, Leonardo Darré, Pablo D Dans, Modesto Orozco (https://academic.oup.com/bioinformatics/article/35/24/5334/5529936) diSTruct v1.0: generating biomolecular structures from distance constraints Oskar Taubert, Ines Reinartz, Henning Meyerhenke, Alexander Schug (https://academic.oup.com/bioinformatics/article/35/24/5337/5536876) TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets Laura Puente-Santamaria, Wyeth W Wasserman, Luis del Peso (https://academic.oup.com/bioinformatics/article/35/24/5339/5538988) CaPSSA: visual evaluation of cancer biomarker genes for patient stratification and survival analysis using mutation and expression data Yeongjun Jang, Jihae Seo, Insu Jang, Byungwook Lee, Sun Kim (https://academic.oup.com/bioinformatics/article/35/24/5341/5522011) Comprehensive study of the exposome and omic data using rexposome Bioconductor Packages Carles Hernandez-Ferrer, Gregory A Wellenius, Ibon Tamayo, Xavier Basagaña, Jordi Sunyer (https://academic.oup.com/bioinformatics/article/35/24/5344/5523848) Genetic association testing using the GENESIS R/Bioconductor package Stephanie M Gogarten, Tamar Sofer, Han Chen, Chaoyu Yu, Jennifer A Brody (https://academic.oup.com/bioinformatics/article/35/24/5346/5536872) amplimap: a versatile tool to process and analyze targeted NGS data Nils Koelling, Marie Bernkopf, Eduardo Calpena, Geoffrey J Maher, Kerry A Miller (https://academic.oup.com/bioinformatics/article/35/24/5349/5539690) MPRAscore: robust and non-parametric analysis of massively parallel reporter assays Abhishek Niroula, Ram Ajore, Björn Nilsson (https://academic.oup.com/bioinformatics/article/35/24/5351/5540322) KinomeX: a web application for predicting kinome-wide polypharmacology effect of small molecules Zhaojun Li, Xutong Li, Xiaohong Liu, Zunyun Fu, Zhaoping Xiong (https://academic.oup.com/bioinformatics/article/35/24/5354/5522009) RTNduals: an R/Bioconductor package for analysis of co-regulation and inference of dual regulons Vinicius S Chagas, Clarice S Groeneveld, Kelin G Oliveira, Sheyla Trefflich, Rodrigo C de Almeida (https://academic.oup.com/bioinformatics/article/35/24/5357/5524602) The nPYc-Toolbox, a Python module for the pre-processing, quality-control and analysis of metabolic profiling datasets Caroline J Sands, Arnaud M Wolfer, Gonçalo D S Correia, Noureddin Sadawi, Arfan Ahmed (https://academic.oup.com/bioinformatics/article/35/24/5359/5539689) CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models Vítor Vieira, Miguel Rocha (https://academic.oup.com/bioinformatics/article/35/24/5361/5540319) BLANT---fast graphlet sampling tool Sridevi Maharaj, Brennan Tracy, Wayne B Hayes (https://academic.oup.com/bioinformatics/article/35/24/5363/5542947) CytoGPS: a web-enabled karyotype analysis tool for cytogenetics Zachary B Abrams, Lin Zhang, Lynne V Abruzzo, Nyla A Heerema, Suli Li (https://academic.oup.com/bioinformatics/article/35/24/5365/5526870) The NEW ESID online database network Raphael Scheible, Stephan Rusch, David Guzman, Nizar Mahlaoui, Stephan Ehl (https://academic.oup.com/bioinformatics/article/35/24/5367/5526873) VariantQC: a visual quality control report for variant evaluation Melissa Y Yan, Betsy Ferguson, Benjamin N Bimber (https://academic.oup.com/bioinformatics/article/35/24/5370/5532508) SquiggleKit: a toolkit for manipulating nanopore signal data James M Ferguson, Martin A Smith (https://academic.oup.com/bioinformatics/article/35/24/5372/5537108) DISPOT: a simple knowledge-based protein domain interaction statistical potential Oleksandr Narykov, Dmytro Bogatov, Dmitry Korkin (https://academic.oup.com/bioinformatics/article/35/24/5374/5539863) PyMethylProcess---convenient high-throughput preprocessing workflow for DNA methylation data Joshua J Levy, Alexander J Titus, Lucas A Salas, Brock C Christensen (https://academic.oup.com/bioinformatics/article/35/24/5379/5542385) ROBOKOP: an abstraction layer and user interface for knowledge graphs to support question answering Kenneth Morton, Patrick Wang, Chris Bizon, Steven Cox, James Balhoff (https://academic.oup.com/bioinformatics/article/35/24/5382/5549494) Interactive exploration of heterogeneous biological networks with Biomine Explorer Vid Podpečan, Živa Ramšak, Kristina Gruden, Hannu Toivonen, Nada Lavrač (https://academic.oup.com/bioinformatics/article/35/24/5385/5522368) ValTrendsDB: bringing Protein Data Bank validation information closer to the user Vladimír Horský, Veronika Bendová, Dominik Toušek, Jaroslav Koča, Radka Svobodová (https://academic.oup.com/bioinformatics/article/35/24/5389/5526874) sAOP: linking chemical stressors to adverse outcomes pathway networks Alejandro Aguayo-Orozco, Karine Audouze, Troels Siggaard, Robert Barouki, Søren Brunak (https://academic.oup.com/bioinformatics/article/35/24/5391/5536875) Hydra image processor: 5-D GPU image analysis library with MATLAB and python wrappers Eric Wait, Mark Winter, Andrew R Cohen (https://academic.oup.com/bioinformatics/article/35/24/5393/5523180) Genome analysis ------------------------------ MEpurity: estimating tumor purity using DNA methylation data Bowen Liu, Xiaofei Yang, Tingjie Wang, Jiadong Lin, Yongyong Kang (https://academic.oup.com/bioinformatics/article/35/24/5298/5531131) Predicting promoters in phage genomes using PhagePromoter Marta Sampaio, Miguel Rocha, Hugo Oliveira, Oscar Dias (https://academic.oup.com/bioinformatics/article/35/24/5301/5540317) geneCo: a visualized comparative genomic method to analyze multiple genome structures Jaehee Jung, Jong Im Kim, Gangman Yi (https://academic.oup.com/bioinformatics/article/35/24/5303/5539862) scRNABatchQC: multi-samples quality control for single cell RNA-seq data Qi Liu, Quanhu Sheng, Jie Ping, Marisol Adelina Ramirez, Ken S Lau (https://academic.oup.com/bioinformatics/article/35/24/5306/5542946) Sequence analysis ------------------------------ JUCHMME: a Java Utility for Class Hidden Markov Models and Extensions for biological sequence analysis Ioannis A Tamposis, Konstantinos D Tsirigos, Margarita C Theodoropoulou, Panagiota I Kontou, Georgios N Tsaousis (https://academic.oup.com/bioinformatics/article/35/24/5309/5524600) PTM-Logo: a program for generation of sequence logos based on position-specific background amino-acid probabilities Thammakorn Saethang, Kenneth Hodge, Chin-Rang Yang, Yue Zhao, Ingorn Kimkong (https://academic.oup.com/bioinformatics/article/35/24/5313/5535597) Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit Maurits J J Dijkstra, Atze J van der Ploeg, K Anton Feenstra, Wan J Fokkink, Sanne Abeln (https://academic.oup.com/bioinformatics/article/35/24/5315/5542395) Sequence tube maps: making graph genomes intuitive to commuters Wolfgang Beyer, Adam M Novak, Glenn Hickey, Jeffrey Chan, Vanessa Tan (https://academic.oup.com/bioinformatics/article/35/24/5318/5542397) Phylogenetics ------------------------------ MCMCtreeR: functions to prepare MCMCtree analyses and visualize posterior ages on trees Mark N Puttick (https://academic.oup.com/bioinformatics/article/35/24/5321/5530964) Structural bioinformatics ------------------------------ TCR3d: The T cell receptor structural repertoire database Ragul Gowthaman, Brian G Pierce (https://academic.oup.com/bioinformatics/article/35/24/5323/5523179) Benchmarking fold detection by DaliLite v.5 Liisa Holm (https://academic.oup.com/bioinformatics/article/35/24/5326/5526869) DDT - Drug Discovery Tool: a fast and intuitive graphics user interface for docking and molecular dynamics analysis Simone Aureli, Daniele Di Marino, Stefano Raniolo, Vittorio Limongelli (https://academic.oup.com/bioinformatics/article/35/24/5328/5532220) HDX-Viewer: interactive 3D visualization of hydrogen--deuterium exchange data David Bouyssié, Jean Lesne, Marie Locard-Paulet, Renaud Albigot, Odile Burlet-Schiltz (https://academic.oup.com/bioinformatics/article/35/24/5331/5530164) VeriNA3d: an R package for nucleic acids data mining Diego Gallego, Leonardo Darré, Pablo D Dans, Modesto Orozco (https://academic.oup.com/bioinformatics/article/35/24/5334/5529936) diSTruct v1.0: generating biomolecular structures from distance constraints Oskar Taubert, Ines Reinartz, Henning Meyerhenke, Alexander Schug (https://academic.oup.com/bioinformatics/article/35/24/5337/5536876) Gene expression ------------------------------ TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets Laura Puente-Santamaria, Wyeth W Wasserman, Luis del Peso (https://academic.oup.com/bioinformatics/article/35/24/5339/5538988) Genetics and population analysis ------------------------------ CaPSSA: visual evaluation of cancer biomarker genes for patient stratification and survival analysis using mutation and expression data Yeongjun Jang, Jihae Seo, Insu Jang, Byungwook Lee, Sun Kim (https://academic.oup.com/bioinformatics/article/35/24/5341/5522011) Comprehensive study of the exposome and omic data using rexposome Bioconductor Packages Carles Hernandez-Ferrer, Gregory A Wellenius, Ibon Tamayo, Xavier Basagaña, Jordi Sunyer (https://academic.oup.com/bioinformatics/article/35/24/5344/5523848) Genetic association testing using the GENESIS R/Bioconductor package Stephanie M Gogarten, Tamar Sofer, Han Chen, Chaoyu Yu, Jennifer A Brody (https://academic.oup.com/bioinformatics/article/35/24/5346/5536872) amplimap: a versatile tool to process and analyze targeted NGS data Nils Koelling, Marie Bernkopf, Eduardo Calpena, Geoffrey J Maher, Kerry A Miller (https://academic.oup.com/bioinformatics/article/35/24/5349/5539690) MPRAscore: robust and non-parametric analysis of massively parallel reporter assays Abhishek Niroula, Ram Ajore, Björn Nilsson (https://academic.oup.com/bioinformatics/article/35/24/5351/5540322) Systems biology ------------------------------ KinomeX: a web application for predicting kinome-wide polypharmacology effect of small molecules Zhaojun Li, Xutong Li, Xiaohong Liu, Zunyun Fu, Zhaoping Xiong (https://academic.oup.com/bioinformatics/article/35/24/5354/5522009) RTNduals: an R/Bioconductor package for analysis of co-regulation and inference of dual regulons Vinicius S Chagas, Clarice S Groeneveld, Kelin G Oliveira, Sheyla Trefflich, Rodrigo C de Almeida (https://academic.oup.com/bioinformatics/article/35/24/5357/5524602) The nPYc-Toolbox, a Python module for the pre-processing, quality-control and analysis of metabolic profiling datasets Caroline J Sands, Arnaud M Wolfer, Gonçalo D S Correia, Noureddin Sadawi, Arfan Ahmed (https://academic.oup.com/bioinformatics/article/35/24/5359/5539689) CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models Vítor Vieira, Miguel Rocha (https://academic.oup.com/bioinformatics/article/35/24/5361/5540319) BLANT---fast graphlet sampling tool Sridevi Maharaj, Brennan Tracy, Wayne B Hayes (https://academic.oup.com/bioinformatics/article/35/24/5363/5542947) Data and text mining ------------------------------ CytoGPS: a web-enabled karyotype analysis tool for cytogenetics Zachary B Abrams, Lin Zhang, Lynne V Abruzzo, Nyla A Heerema, Suli Li (https://academic.oup.com/bioinformatics/article/35/24/5365/5526870) The NEW ESID online database network Raphael Scheible, Stephan Rusch, David Guzman, Nizar Mahlaoui, Stephan Ehl (https://academic.oup.com/bioinformatics/article/35/24/5367/5526873) VariantQC: a visual quality control report for variant evaluation Melissa Y Yan, Betsy Ferguson, Benjamin N Bimber (https://academic.oup.com/bioinformatics/article/35/24/5370/5532508) SquiggleKit: a toolkit for manipulating nanopore signal data James M Ferguson, Martin A Smith (https://academic.oup.com/bioinformatics/article/35/24/5372/5537108) DISPOT: a simple knowledge-based protein domain interaction statistical potential Oleksandr Narykov, Dmytro Bogatov, Dmitry Korkin (https://academic.oup.com/bioinformatics/article/35/24/5374/5539863) PyMethylProcess---convenient high-throughput preprocessing workflow for DNA methylation data Joshua J Levy, Alexander J Titus, Lucas A Salas, Brock C Christensen (https://academic.oup.com/bioinformatics/article/35/24/5379/5542385) ROBOKOP: an abstraction layer and user interface for knowledge graphs to support question answering Kenneth Morton, Patrick Wang, Chris Bizon, Steven Cox, James Balhoff (https://academic.oup.com/bioinformatics/article/35/24/5382/5549494) Databases and ontologies ------------------------------ Interactive exploration of heterogeneous biological networks with Biomine Explorer Vid Podpečan, Živa Ramšak, Kristina Gruden, Hannu Toivonen, Nada Lavrač (https://academic.oup.com/bioinformatics/article/35/24/5385/5522368) ValTrendsDB: bringing Protein Data Bank validation information closer to the user Vladimír Horský, Veronika Bendová, Dominik Toušek, Jaroslav Koča, Radka Svobodová (https://academic.oup.com/bioinformatics/article/35/24/5389/5526874) sAOP: linking chemical stressors to adverse outcomes pathway networks Alejandro Aguayo-Orozco, Karine Audouze, Troels Siggaard, Robert Barouki, Søren Brunak (https://academic.oup.com/bioinformatics/article/35/24/5391/5536875) Bioimage informatics ------------------------------ Hydra image processor: 5-D GPU image analysis library with MATLAB and python wrappers Eric Wait, Mark Winter, Andrew R Cohen (https://academic.oup.com/bioinformatics/article/35/24/5393/5523180) ============================= CORRIGENDA ============================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/35/24/5396/5542645) MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome Anjun Ma, Minxuan Sun, Adam McDermaid, Bingqiang Liu, Qin Ma (https://academic.oup.com/bioinformatics/article/35/24/5397/5580590) 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_644184369.1579024595483 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 24
 
15 December 2019
 
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ORIGINAL PAPERS
 
 
 
 
Genome analysis
 
 
 
MTTFsite: cross-cell type TF binding site prediction by using multi-task learning border= 
 
Jiyun Zhou ; Qin Lu; Lin Gui; Ruifeng Xu; Yunfei Long ...
 
 
New algorithms for detecting multi-effect and multi-way epistatic interactions 
 
Javad Ansarifar; Lizhi Wang
 
 
 
Sequence analysis
 
 
 
Full-length de novo viral quasispecies assembly through variation graph construction 
 
Jasmijn A Baaijens; Bastiaan Van der Roest; Johannes Köster ; Leen Stougie; Alexander Schönhuth
 
 
deconvSeq: deconvolution of cell mixture distribution in sequencing data 
 
Rose Du; Vince Carey; Scott T Weiss
 
 
 
Structural bioinformatics
 
 
 
DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data border= 
 
Albert Y Xue ; Angela M Yu; Julius B Lucks; Neda Bagheri
 
 
DeepSymmetry: using 3D convolutional networks for identification of tandem repeats and internal symmetries in protein structures 
 
Guillaume Pagès; Sergei Grudinin
 
 
AutoDock CrankPep: combining folding and docking to predict protein'peptide complexes 
 
Yuqi Zhang; Michel F Sanner
 
 
DNN-Dom: predicting protein domain boundary from sequence alone by deep neural network 
 
Qiang Shi; Weiya Chen; Siqi Huang ; Fanglin Jin; Yinghao Dong ...
 
 
 
Gene expression
 
 
 
Path2Surv: Pathway/gene set-based survival analysis using multiple kernel learning 
 
Onur Dereli; Ceyda Oğuz; Mehmet Gönen
 
 
Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms border= 
 
Joanna Zyla ; Michal Marczyk; Teresa Domaszewska; Stefan H E Kaufmann; Joanna Polanska ...
 
 
DECENT: differential expression with capture efficiency adjustmeNT for single-cell RNA-seq data border= 
 
Chengzhong Ye ; Terence P Speed; Agus Salim
 
 
 
Genetics and population analysis
 
 
 
Assessing concordance among human, in silico predictions and functional assays on genetic variant classification 
 
Jiaqi Luo; Tianliangwen Zhou; Xiaobin You ; Yi Zi; Xiaoting Li ...
 
 
 
Systems biology
 
 
 
ClinOmicsTrailbc : a visual analytics tool for breast cancer treatment stratification border= 
 
Lara Schneider ; Tim Kehl; Kristina Thedinga; Nadja Liddy Grammes; Christina Backes ...
 
 
Identification of disease-associated loci using machine learning for genotype and network data integration border= 
 
Luis G Leal ; Alessia David; Marjo-Riita Jarvelin; Sylvain Sebert; Minna Männikkö ...
 
 
deepDR: a network-based deep learning approach to in silico drug repositioning 
 
Xiangxiang Zeng; Siyi Zhu; Xiangrong Liu ; Yadi Zhou; Ruth Nussinov ...
 
 
Smart computational exploration of stochastic gene regulatory network models using human-in-the-loop semi-supervised learning 
 
Fredrik Wrede; Andreas Hellander
 
 
CNet: a multi-omics approach to detecting clinically associated, combinatory genomic signatures 
 
Peilin Jia; Guangsheng Pei; Zhongming Zhao
 
 
A scalable method for parameter identification in kinetic models of metabolism using steady-state data 
 
Shyam Srinivasan; William R Cluett; Radhakrishnan Mahadevan
 
 
Graphlet Laplacians for topology-function and topology-disease relationships 
 
Sam F L Windels; Noël Malod-Dognin; Nataša Pržulj
 
 
 
Data and text mining
 
 
 
Deep learning of the back-splicing code for circular RNA formation 
 
Jun Wang; Liangjiang Wang
 
 
Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions 
 
Ana S C. Silva; Robbin Bouwmeester; Lennart Martens ; Sven Degroeve
 
 
ReSimNet: drug response similarity prediction using Siamese neural networks 
 
Minji Jeon; Donghyeon Park; Jinhyuk Lee ; Hwisang Jeon; Miyoung Ko ...
 
 
Improving data splitting for classification applications in spectrochemical analyses employing a random-mutation Kennard-Stone algorithm approach border= 
 
Camilo L M Morais ; Marfran C D Santos; Kássio M G Lima; Francis L Martin
 
 
 
Databases and ontologies
 
 
 
A fully computational and reasonable representation for karyotypes border= 
 
Jennifer D Warrender ; Anthony V Moorman; Phillip Lord
 
 
 
Bioimage informatics
 
 
 
Incorporating spatial'anatomical similarity into the VGWAS framework for AD biomarker detection 
 
Meiyan Huang; Yuwei Yu; Wei Yang ; Qianjin Feng
 
 
ARMBIS: accurate and robust matching of brain image sequences from multiple modal imaging techniques 
 
Qi Shen; Goayu Xiao; Yingwei Zheng ; Jie Wang; Yue Liu ...
 
 
NRStitcher: non-rigid stitching of terapixel-scale volumetric images 
 
Arttu Miettinen; Ioannis Vogiatzis Oikonomidis; Anne Bonnin ; Marco Stampanoni
 
 
 
APPLICATIONS NOTES
 
 
 
 
Genome analysis
 
 
 
MEpurity: estimating tumor purity using DNA methylation data 
 
Bowen Liu; Xiaofei Yang; Tingjie Wang ; Jiadong Lin; Yongyong Kang ...
 
 
Predicting promoters in phage genomes using PhagePromoter 
 
Marta Sampaio; Miguel Rocha; Hugo Oliveira ; Oscar Dias
 
 
geneCo: a visualized comparative genomic method to analyze multiple genome structures border= 
 
Jaehee Jung ; Jong Im Kim; Gangman Yi
 
 
scRNABatchQC: multi-samples quality control for single cell RNA-seq data border= 
 
Qi Liu ; Quanhu Sheng; Jie Ping; Marisol Adelina Ramirez; Ken S Lau ...
 
 
 
Sequence analysis
 
 
 
JUCHMME: a Java Utility for Class Hidden Markov Models and Extensions for biological sequence analysis 
 
Ioannis A Tamposis; Konstantinos D Tsirigos; Margarita C Theodoropoulou ; Panagiota I Kontou; Georgios N Tsaousis ...
 
 
PTM-Logo: a program for generation of sequence logos based on position-specific background amino-acid probabilities 
 
Thammakorn Saethang; Kenneth Hodge; Chin-Rang Yang ; Yue Zhao; Ingorn Kimkong ...
 
 
Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit border= 
 
Maurits J J Dijkstra ; Atze J van der Ploeg; K Anton Feenstra; Wan J Fokkink; Sanne Abeln ...
 
 
Sequence tube maps: making graph genomes intuitive to commuters border= 
 
Wolfgang Beyer ; Adam M Novak; Glenn Hickey; Jeffrey Chan; Vanessa Tan ...
 
 
 
Phylogenetics
 
 
 
MCMCtreeR: functions to prepare MCMCtree analyses and visualize posterior ages on trees 
 
Mark N Puttick
 
 
 
Structural bioinformatics
 
 
 
TCR3d: The T cell receptor structural repertoire database border= 
 
Ragul Gowthaman; Brian G Pierce
 
 
Benchmarking fold detection by DaliLite v.5 
 
Liisa Holm
 
 
DDT - Drug Discovery Tool: a fast and intuitive graphics user interface for docking and molecular dynamics analysis border= 
 
Simone Aureli ; Daniele Di Marino; Stefano Raniolo; Vittorio Limongelli
 
 
HDX-Viewer: interactive 3D visualization of hydrogen'deuterium exchange data border= 
 
David Bouyssié ; Jean Lesne; Marie Locard-Paulet; Renaud Albigot; Odile Burlet-Schiltz ...
 
 
VeriNA3d: an R package for nucleic acids data mining 
 
Diego Gallego; Leonardo Darré; Pablo D Dans ; Modesto Orozco
 
 
diSTruct v1.0: generating biomolecular structures from distance constraints 
 
Oskar Taubert; Ines Reinartz; Henning Meyerhenke ; Alexander Schug
 
 
 
Gene expression
 
 
 
TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets 
 
Laura Puente-Santamaria; Wyeth W Wasserman; Luis del Peso
 
 
 
Genetics and population analysis
 
 
 
CaPSSA: visual evaluation of cancer biomarker genes for patient stratification and survival analysis using mutation and expression data  
 
Yeongjun Jang; Jihae Seo; Insu Jang ; Byungwook Lee; Sun Kim ...
 
 
Comprehensive study of the exposome and omic data using rexposome Bioconductor Packages 
 
Carles Hernandez-Ferrer; Gregory A Wellenius; Ibon Tamayo ; Xavier Basagaña; Jordi Sunyer ...
 
 
Genetic association testing using the GENESIS R/Bioconductor package 
 
Stephanie M Gogarten; Tamar Sofer; Han Chen ; Chaoyu Yu; Jennifer A Brody ...
 
 
amplimap: a versatile tool to process and analyze targeted NGS data border= 
 
Nils Koelling ; Marie Bernkopf; Eduardo Calpena; Geoffrey J Maher; Kerry A Miller ...
 
 
MPRAscore: robust and non-parametric analysis of massively parallel reporter assays 
 
Abhishek Niroula; Ram Ajore; Björn Nilsson
 
 
 
Systems biology
 
 
 
KinomeX: a web application for predicting kinome-wide polypharmacology effect of small molecules 
 
Zhaojun Li; Xutong Li; Xiaohong Liu ; Zunyun Fu; Zhaoping Xiong ...
 
 
RTNduals: an R/Bioconductor package for analysis of co-regulation and inference of dual regulons 
 
Vinicius S Chagas; Clarice S Groeneveld; Kelin G Oliveira ; Sheyla Trefflich; Rodrigo C de Almeida ...
 
 
The nPYc-Toolbox, a Python module for the pre-processing, quality-control and analysis of metabolic profiling datasets border= 
 
Caroline J Sands ; Arnaud M Wolfer; Gonçalo D S Correia; Noureddin Sadawi; Arfan Ahmed ...
 
 
CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models 
 
Vítor Vieira; Miguel Rocha
 
 
BLANT'fast graphlet sampling tool 
 
Sridevi Maharaj; Brennan Tracy; Wayne B Hayes
 
 
 
Data and text mining
 
 
 
CytoGPS: a web-enabled karyotype analysis tool for cytogenetics border= 
 
Zachary B Abrams ; Lin Zhang; Lynne V Abruzzo; Nyla A Heerema; Suli Li ...
 
 
The NEW ESID online database network 
 
Raphael Scheible; Stephan Rusch; David Guzman ; Nizar Mahlaoui; Stephan Ehl ...
 
 
VariantQC: a visual quality control report for variant evaluation 
 
Melissa Y Yan; Betsy Ferguson; Benjamin N Bimber
 
 
SquiggleKit: a toolkit for manipulating nanopore signal data border= 
 
James M Ferguson ; Martin A Smith
 
 
DISPOT: a simple knowledge-based protein domain interaction statistical potential border= 
 
Oleksandr Narykov ; Dmytro Bogatov; Dmitry Korkin
 
 
PyMethylProcess'convenient high-throughput preprocessing workflow for DNA methylation data 
 
Joshua J Levy; Alexander J Titus; Lucas A Salas ; Brock C Christensen
 
 
ROBOKOP: an abstraction layer and user interface for knowledge graphs to support question answering border= 
 
Kenneth Morton ; Patrick Wang; Chris Bizon; Steven Cox; James Balhoff ...
 
 
 
Databases and ontologies
 
 
 
Interactive exploration of heterogeneous biological networks with Biomine Explorer border= 
 
Vid Podpečan ; Živa Ramšak; Kristina Gruden; Hannu Toivonen; Nada Lavrač
 
 
ValTrendsDB: bringing Protein Data Bank validation information closer to the user border= 
 
Vladimír Horský ; Veronika Bendová; Dominik Toušek; Jaroslav Koča; Radka Svobodová
 
 
sAOP: linking chemical stressors to adverse outcomes pathway networks border= 
 
Alejandro Aguayo-Orozco ; Karine Audouze; Troels Siggaard; Robert Barouki; Søren Brunak ...
 
 
 
Bioimage informatics
 
 
 
Hydra image processor: 5-D GPU image analysis library with MATLAB and python wrappers 
 
Eric Wait; Mark Winter; Andrew R Cohen
 
 
 
CORRIGENDA
 
 
 
OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers border= 
 
Claudia Arnedo-Pac ; Loris Mularoni; Ferran Muiños; Abel Gonzalez-Perez; Nuria Lopez-Bigas
 
 
MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome 
 
Anjun Ma; Minxuan Sun; Adam McDermaid ; Bingqiang Liu; Qin Ma
 
 
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