Subject: Bioinformatics Table of Contents for 1 November 2019 ------=_Part_1827250050.1572739768245 Content-Type: text/plain;charset=UTF-8 Oxford Academic *** {Bioinformatics} *** Volume 35, Issue 21, 1 November 2019 Read this issue (https://academic.oup.com/bioinformatics/issue/35/21) ------------------------------ 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 ============================TORMES: an automated pipeline for whole bacterial genome analysis Narciso M Quijada, David Rodríguez-Lázaro, Jose María Eiros, Marta Hernández (https://academic.oup.com/bioinformatics/article/35/21/4207/5430930) Nano-GLADIATOR: real-time detection of copy number alterations from nanopore sequencing data Alberto Magi, Davide Bolognini, Niccoló Bartalucci, Alessandra Mingrino, Roberto Semeraro (https://academic.oup.com/bioinformatics/article/35/21/4213/5428178) HiCNN: a very deep convolutional neural network to better enhance the resolution of Hi-C data Tong Liu, Zheng Wang (https://academic.oup.com/bioinformatics/article/35/21/4222/5436129) SolidBin: improving metagenome binning with semi-supervised normalized cut Ziye Wang, Zhengyang Wang, Yang Young Lu, Fengzhu Sun, Shanfeng Zhu (https://academic.oup.com/bioinformatics/article/35/21/4229/5448864) Graph analysis of fragmented long-read bacterial genome assemblies Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré (https://academic.oup.com/bioinformatics/article/35/21/4239/5421164) A Bayesian model integration for mutation calling through data partitioning Takuya Moriyama, Seiya Imoto, Shuto Hayashi, Yuichi Shiraishi, Satoru Miyano (https://academic.oup.com/bioinformatics/article/35/21/4247/5423180) Shouji: a fast and efficient pre-alignment filter for sequence alignment Mohammed Alser, Hasan Hassan, Akash Kumar, Onur Mutlu, Can Alkan (https://academic.oup.com/bioinformatics/article/35/21/4255/5421509) scRNAss: a single-cell RNA-seq assembler via imputing dropouts and combing junctions Juntao Liu, Xiangyu Liu, Xianwen Ren, Guojun Li (https://academic.oup.com/bioinformatics/article/35/21/4264/5429354) PEPred-Suite: improved and robust prediction of therapeutic peptides using adaptive feature representation learning Leyi Wei, Chen Zhou, Ran Su, Quan Zou (https://academic.oup.com/bioinformatics/article/35/21/4272/5474905) Overlap graph-based generation of haplotigs for diploids and polyploids Jasmijn A Baaijens, Alexander Schönhuth (https://academic.oup.com/bioinformatics/article/35/21/4281/5474903) Accounting for ambiguity in ancestral sequence reconstruction A Oliva, S Pulicani, V Lefort, L Bréhélin, O Gascuel (https://academic.oup.com/bioinformatics/article/35/21/4290/5448860) Determining parameters for non-linear models of multi-loop free energy change Max Ward, Hongying Sun, Amitava Datta, Michael Wise, David H Mathews (https://academic.oup.com/bioinformatics/article/35/21/4298/5421512) Assessing reproducibility of matrix factorization methods in independent transcriptomes Laura Cantini, Ulykbek Kairov, Aurélien de Reyniès, Emmanuel Barillot, François Radvanyi (https://academic.oup.com/bioinformatics/article/35/21/4307/5426054) Performance of gene expression analyses using de novo assembled transcripts in polyploid species Ling-Yun Chen, Diego F Morales-Briones, Courtney N Passow, Ya Yang (https://academic.oup.com/bioinformatics/article/35/21/4314/5545975) Kinpute: using identity by descent to improve genotype imputation Mark Abney, Aisha ElSherbiny (https://academic.oup.com/bioinformatics/article/35/21/4321/5421157) A coordinate descent approach for sparse Bayesian learning in high dimensional QTL mapping and genome-wide association studies Meiyue Wang, Shizhong Xu (https://academic.oup.com/bioinformatics/article/35/21/4327/5436130) Unsupervised discovery of phenotype-specific multi-omics networks W Jenny Shi, Yonghua Zhuang, Pamela H Russell, Brian D Hobbs, Margaret M Parker (https://academic.oup.com/bioinformatics/article/35/21/4336/5430928) Genome-wide identification of the essential protein-coding genes and long non-coding RNAs for human pan-cancer Yuwei Zhang, Yang Tao, Huihui Ji, Wei Li, Xingli Guo (https://academic.oup.com/bioinformatics/article/35/21/4344/5421514) rMTA: robust metabolic transformation analysis Luis V Valcárcel, Verónica Torrano, Luis Tobalina, Arkaitz Carracedo, Francisco J Planes (https://academic.oup.com/bioinformatics/article/35/21/4350/5421511) ASICS: an R package for a whole analysis workflow of 1D 1H NMR spectra Gaëlle Lefort, Laurence Liaubet, Cécile Canlet, Patrick Tardivel, Marie-Christine Père (https://academic.oup.com/bioinformatics/article/35/21/4356/5448862) A learning-based framework for miRNA-disease association identification using neural networks Jiajie Peng, Weiwei Hui, Qianqian Li, Bolin Chen, Jianye Hao (https://academic.oup.com/bioinformatics/article/35/21/4364/5448859) Open Agile text mining for bioinformatics: the PubAnnotation ecosystem Jin-Dong Kim, Yue Wang, Toyofumi Fujiwara, Shujiro Okuda, Tiffany J Callahan (https://academic.oup.com/bioinformatics/article/35/21/4372/5425327) Figure and caption extraction from biomedical documents Pengyuan Li, Xiangying Jiang, Hagit Shatkay (https://academic.oup.com/bioinformatics/article/35/21/4381/5428177) GENOME ANALYSIS ------------------------------ TORMES: an automated pipeline for whole bacterial genome analysis Narciso M Quijada, David Rodríguez-Lázaro, Jose María Eiros, Marta Hernández (https://academic.oup.com/bioinformatics/article/35/21/4207/5430930) Nano-GLADIATOR: real-time detection of copy number alterations from nanopore sequencing data Alberto Magi, Davide Bolognini, Niccoló Bartalucci, Alessandra Mingrino, Roberto Semeraro (https://academic.oup.com/bioinformatics/article/35/21/4213/5428178) HiCNN: a very deep convolutional neural network to better enhance the resolution of Hi-C data Tong Liu, Zheng Wang (https://academic.oup.com/bioinformatics/article/35/21/4222/5436129) SolidBin: improving metagenome binning with semi-supervised normalized cut Ziye Wang, Zhengyang Wang, Yang Young Lu, Fengzhu Sun, Shanfeng Zhu (https://academic.oup.com/bioinformatics/article/35/21/4229/5448864) SEQUENCE ANALYSIS ------------------------------ Graph analysis of fragmented long-read bacterial genome assemblies Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré (https://academic.oup.com/bioinformatics/article/35/21/4239/5421164) A Bayesian model integration for mutation calling through data partitioning Takuya Moriyama, Seiya Imoto, Shuto Hayashi, Yuichi Shiraishi, Satoru Miyano (https://academic.oup.com/bioinformatics/article/35/21/4247/5423180) Shouji: a fast and efficient pre-alignment filter for sequence alignment Mohammed Alser, Hasan Hassan, Akash Kumar, Onur Mutlu, Can Alkan (https://academic.oup.com/bioinformatics/article/35/21/4255/5421509) scRNAss: a single-cell RNA-seq assembler via imputing dropouts and combing junctions Juntao Liu, Xiangyu Liu, Xianwen Ren, Guojun Li (https://academic.oup.com/bioinformatics/article/35/21/4264/5429354) PEPred-Suite: improved and robust prediction of therapeutic peptides using adaptive feature representation learning Leyi Wei, Chen Zhou, Ran Su, Quan Zou (https://academic.oup.com/bioinformatics/article/35/21/4272/5474905) Overlap graph-based generation of haplotigs for diploids and polyploids Jasmijn A Baaijens, Alexander Schönhuth (https://academic.oup.com/bioinformatics/article/35/21/4281/5474903) PHYLOGENETICS ------------------------------ Accounting for ambiguity in ancestral sequence reconstruction A Oliva, S Pulicani, V Lefort, L Bréhélin, O Gascuel (https://academic.oup.com/bioinformatics/article/35/21/4290/5448860) STRUCTURAL BIOINFORMATICS ------------------------------ Determining parameters for non-linear models of multi-loop free energy change Max Ward, Hongying Sun, Amitava Datta, Michael Wise, David H Mathews (https://academic.oup.com/bioinformatics/article/35/21/4298/5421512) GENE EXPRESSION ------------------------------ Assessing reproducibility of matrix factorization methods in independent transcriptomes Laura Cantini, Ulykbek Kairov, Aurélien de Reyniès, Emmanuel Barillot, François Radvanyi (https://academic.oup.com/bioinformatics/article/35/21/4307/5426054) Performance of gene expression analyses using de novo assembled transcripts in polyploid species Ling-Yun Chen, Diego F Morales-Briones, Courtney N Passow, Ya Yang (https://academic.oup.com/bioinformatics/article/35/21/4314/5545975) GENETICS AND POPULATION ANALYSIS ------------------------------ Kinpute: using identity by descent to improve genotype imputation Mark Abney, Aisha ElSherbiny (https://academic.oup.com/bioinformatics/article/35/21/4321/5421157) A coordinate descent approach for sparse Bayesian learning in high dimensional QTL mapping and genome-wide association studies Meiyue Wang, Shizhong Xu (https://academic.oup.com/bioinformatics/article/35/21/4327/5436130) SYSTEMS BIOLOGY ------------------------------ Unsupervised discovery of phenotype-specific multi-omics networks W Jenny Shi, Yonghua Zhuang, Pamela H Russell, Brian D Hobbs, Margaret M Parker (https://academic.oup.com/bioinformatics/article/35/21/4336/5430928) Genome-wide identification of the essential protein-coding genes and long non-coding RNAs for human pan-cancer Yuwei Zhang, Yang Tao, Huihui Ji, Wei Li, Xingli Guo (https://academic.oup.com/bioinformatics/article/35/21/4344/5421514) rMTA: robust metabolic transformation analysis Luis V Valcárcel, Verónica Torrano, Luis Tobalina, Arkaitz Carracedo, Francisco J Planes (https://academic.oup.com/bioinformatics/article/35/21/4350/5421511) ASICS: an R package for a whole analysis workflow of 1D 1H NMR spectra Gaëlle Lefort, Laurence Liaubet, Cécile Canlet, Patrick Tardivel, Marie-Christine Père (https://academic.oup.com/bioinformatics/article/35/21/4356/5448862) A learning-based framework for miRNA-disease association identification using neural networks Jiajie Peng, Weiwei Hui, Qianqian Li, Bolin Chen, Jianye Hao (https://academic.oup.com/bioinformatics/article/35/21/4364/5448859) DATA AND TEXT MINING ------------------------------ Open Agile text mining for bioinformatics: the PubAnnotation ecosystem Jin-Dong Kim, Yue Wang, Toyofumi Fujiwara, Shujiro Okuda, Tiffany J Callahan (https://academic.oup.com/bioinformatics/article/35/21/4372/5425327) Figure and caption extraction from biomedical documents Pengyuan Li, Xiangying Jiang, Hagit Shatkay (https://academic.oup.com/bioinformatics/article/35/21/4381/5428177) ============================= APPLICATIONS NOTES ============================GenomeWarp: an alignment-based variant coordinate transformation Cory Y McLean, Yeongwoo Hwang, Ryan Poplin, Mark A DePristo (https://academic.oup.com/bioinformatics/article/35/21/4389/5420550) epic2 efficiently finds diffuse domains in ChIP-seq data Endre Bakken Stovner, Pål Sætrom (https://academic.oup.com/bioinformatics/article/35/21/4392/5421513) HLA*LA---HLA typing from linearly projected graph alignments Alexander T Dilthey, Alexander J Mentzer, Raphael Carapito, Clare Cutland, Nezih Cereb (https://academic.oup.com/bioinformatics/article/35/21/4394/5426702) Structural variant analysis for linked-read sequencing data with gemtools S U Greer, H P Ji (https://academic.oup.com/bioinformatics/article/35/21/4397/5426055) IntronDB: a database for eukaryotic intron features Dapeng Wang (https://academic.oup.com/bioinformatics/article/35/21/4400/5428179) multiPhATE: bioinformatics pipeline for functional annotation of phage isolates Carol L Ecale Zhou, Stephanie Malfatti, Jeffrey Kimbrel, Casandra Philipson, Katelyn McNair (https://academic.oup.com/bioinformatics/article/35/21/4402/5488969) Spliceogen: an integrative, scalable tool for the discovery of splice-altering variants Steven Monger, Michael Troup, Eddie Ip, Sally L Dunwoodie, Eleni Giannoulatou (https://academic.oup.com/bioinformatics/article/35/21/4405/5472338) Identifying centromeric satellites with dna-brnn Heng Li (https://academic.oup.com/bioinformatics/article/35/21/4408/5466455) icHET: interactive visualization of cytoplasmic heteroplasmy Vinhthuy Phan, Diem-Trang Pham, Caroline Melton, Adam J Ramsey, Bernie J Daigle, Jr. (https://academic.oup.com/bioinformatics/article/35/21/4411/5481955) Graphical data mining of cancer mechanisms with SEMA Mustafa Solmaz, Adam Lane, Bilal Gonen, Ogulsheker Akmamedova, Mehmet H Gunes (https://academic.oup.com/bioinformatics/article/35/21/4413/5487380) gpart: human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks Sun Ah Kim, Myriam Brossard, Delnaz Roshandel, Andrew D Paterson, Shelley B Bull (https://academic.oup.com/bioinformatics/article/35/21/4419/5487391) G-OnRamp: a Galaxy-based platform for collaborative annotation of eukaryotic genomes Yating Liu, Luke Sargent, Wilson Leung, Sarah C R Elgin, Jeremy Goecks (https://academic.oup.com/bioinformatics/article/35/21/4422/5487392) Tibanna: software for scalable execution of portable pipelines on the cloud Soohyun Lee, Jeremy Johnson, Carl Vitzthum, Koray Kırlı, Burak H Alver (https://academic.oup.com/bioinformatics/article/35/21/4424/5488124) Hayai-Annotation Plants: an ultra-fast and comprehensive functional gene annotation system in plants Andrea Ghelfi, Kenta Shirasawa, Hideki Hirakawa, Sachiko Isobe (https://academic.oup.com/bioinformatics/article/35/21/4427/5489908) ntEdit: scalable genome sequence polishing René L Warren, Lauren Coombe, Hamid Mohamadi, Jessica Zhang, Barry Jaquish (https://academic.oup.com/bioinformatics/article/35/21/4430/5490204) TPES: tumor purity estimation from SNVs Alessio Locallo, Davide Prandi, Tarcisio Fedrizzi, Francesca Demichelis (https://academic.oup.com/bioinformatics/article/35/21/4433/5490858) HyAsP, a greedy tool for plasmids identification Robert Müller, Cedric Chauve (https://academic.oup.com/bioinformatics/article/35/21/4436/5497247) SPar-K: a method to partition NGS signal data Romain Groux, Philipp Bucher (https://academic.oup.com/bioinformatics/article/35/21/4440/5497248) simuG: a general-purpose genome simulator Jia-Xing Yue, Gianni Liti (https://academic.oup.com/bioinformatics/article/35/21/4442/5497256) PyPore: a python toolbox for nanopore sequencing data handling Roberto Semeraro, Alberto Magi (https://academic.oup.com/bioinformatics/article/35/21/4445/5472339) ORCA: a comprehensive bioinformatics container environment for education and research Shaun D Jackman, Tatyana Mozgacheva, Susie Chen, Brendan O'Huiginn, Lance Bailey (https://academic.oup.com/bioinformatics/article/35/21/4448/5475597) Cram-JS: reference-based decompression in node and the browser Robert Buels, Shihab Dider, Colin Diesh, James Robinson, Ian Holmes (https://academic.oup.com/bioinformatics/article/35/21/4451/5490857) RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference Alexey M Kozlov, Diego Darriba, Tomáš Flouri, Benoit Morel, Alexandros Stamatakis (https://academic.oup.com/bioinformatics/article/35/21/4453/5487384) parMATT: parallel multiple alignment of protein 3D-structures with translations and twists for distributed-memory systems Maksim V Shegay, Dmitry A Suplatov, Nina N Popova, Vytas K Švedas, Vladimir V Voevodin (https://academic.oup.com/bioinformatics/article/35/21/4456/5421160) RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA Sha Gong, Chengxin Zhang, Yang Zhang (https://academic.oup.com/bioinformatics/article/35/21/4459/5480133) epiTAD: a web application for visualizing chromosome conformation capture data in the context of genetic epidemiology Jordan H Creed, Garrick Aden-Buie, Alvaro N Monteiro, Travis A Gerke (https://academic.oup.com/bioinformatics/article/35/21/4462/5490859) FusionLearn: a biomarker selection algorithm on cross-platform data Xin Gao, Yuan Zhong (https://academic.oup.com/bioinformatics/article/35/21/4465/5421175) IsoformSwitchAnalyzeR: analysis of changes in genome-wide patterns of alternative splicing and its functional consequences Kristoffer Vitting-Seerup, Albin Sandelin (https://academic.oup.com/bioinformatics/article/35/21/4469/5466456) The barcode, UMI, set format and BUStools Páll Melsted, Vasilis Ntranos, Lior Pachter (https://academic.oup.com/bioinformatics/article/35/21/4472/5487510) 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/35/21/4474/5497255) Variant Score Ranker---a web application for intuitive missense variant prioritization Juanjiangmeng Du, Monica Sudarsanam, Eduardo Pérez-Palma, Andrea Ganna, Laurent Francioli (https://academic.oup.com/bioinformatics/article/35/21/4478/5480132) SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal Mathias Currat, Miguel Arenas, Claudio S Quilodràn, Laurent Excoffier, Nicolas Ray (https://academic.oup.com/bioinformatics/article/35/21/4480/5488121) IsoCor: isotope correction for high-resolution MS labeling experiments Pierre Millard, Baudoin Delépine, Matthieu Guionnet, Maud Heuillet, Floriant Bellvert (https://academic.oup.com/bioinformatics/article/35/21/4484/5418798) RTNsurvival: an R/Bioconductor package for regulatory network survival analysis Clarice S Groeneveld, Vinicius S Chagas, Steven J M Jones, A Gordon Robertson, Bruce A J Ponder (https://academic.oup.com/bioinformatics/article/35/21/4488/5421508) The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein--protein interaction and signalling networks Bence gg, Andrea Császár, Máté Szalay-Bek', Dániel V Veres, Réka Mizsei (https://academic.oup.com/bioinformatics/article/35/21/4490/5475596) clustermq enables efficient parallelization of genomic analyses Michael Schubert (https://academic.oup.com/bioinformatics/article/35/21/4493/5499081) MINERVA API and plugins: opening molecular network analysis and visualization to the community David Hoksza, Piotr Gawron, Marek Ostaszewski, Ewa Smula, Reinhard Schneider (https://academic.oup.com/bioinformatics/article/35/21/4496/5480127) sbgntikz---a TikZ library to draw SBGN maps Adrien Rougny (https://academic.oup.com/bioinformatics/article/35/21/4499/5487386) INDRA-IPM: interactive pathway modeling using natural language with automated assembly Petar V Todorov, Benjamin M Gyori, John A Bachman, Peter K Sorger (https://academic.oup.com/bioinformatics/article/35/21/4501/5487381) PathFXweb: a web application for identifying drug safety and efficacy phenotypes Jennifer L Wilson, Mike Wong, Ajinkya Chalke, Nicholas Stepanov, Dragutin Petkovic (https://academic.oup.com/bioinformatics/article/35/21/4504/5494700) Lipid Mini-On: mining and ontology tool for enrichment analysis of lipidomic data Geremy Clair, Sarah Reehl, Kelly G Stratton, Matthew E Monroe, Malak M Tfaily (https://academic.oup.com/bioinformatics/article/35/21/4507/5448863) TractaViewer: a genome-wide tool for preliminary assessment of therapeutic target druggability Neil Pearson, Karim Malki, David Evans, Lewis Vidler, Cara Ruble (https://academic.oup.com/bioinformatics/article/35/21/4509/5487388) Entrezpy: a Python library to dynamically interact with the NCBI Entrez databases Jan P Buchmann, Edward C Holmes (https://academic.oup.com/bioinformatics/article/35/21/4511/5488119) PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model Benjamin S Glicksberg, Boris Oskotsky, Phyllis M Thangaraj, Nicholas Giangreco, Marcus A Badgeley (https://academic.oup.com/bioinformatics/article/35/21/4515/5520433) FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization Youssef Darzi, Yuta Yamate, Takuji Yamada (https://academic.oup.com/bioinformatics/article/35/21/4519/5475599) Biomedical image augmentation using Augmentor Marcus D Bloice, Peter M Roth, Andreas Holzinger (https://academic.oup.com/bioinformatics/article/35/21/4522/5466454) YeastSpotter: accurate and parameter-free web segmentation for microscopy images of yeast cells Alex X Lu, Taraneh Zarin, Ian S Hsu, Alan M Moses (https://academic.oup.com/bioinformatics/article/35/21/4525/5490207) MyelinJ: an ImageJ macro for high throughput analysis of myelinating cultures Michael J Whitehead, George A McCanney, Hugh J Willison, Susan C Barnett (https://academic.oup.com/bioinformatics/article/35/21/4528/5490206) CytoPacq: a web-interface for simulating multi-dimensional cell imaging David Wiesner, David Svoboda, Martin Maška, Michal Kozubek (https://academic.oup.com/bioinformatics/article/35/21/4531/5494701) GENOME ANALYSIS ------------------------------ GenomeWarp: an alignment-based variant coordinate transformation Cory Y McLean, Yeongwoo Hwang, Ryan Poplin, Mark A DePristo (https://academic.oup.com/bioinformatics/article/35/21/4389/5420550) epic2 efficiently finds diffuse domains in ChIP-seq data Endre Bakken Stovner, Pål Sætrom (https://academic.oup.com/bioinformatics/article/35/21/4392/5421513) HLA*LA---HLA typing from linearly projected graph alignments Alexander T Dilthey, Alexander J Mentzer, Raphael Carapito, Clare Cutland, Nezih Cereb (https://academic.oup.com/bioinformatics/article/35/21/4394/5426702) Structural variant analysis for linked-read sequencing data with gemtools S U Greer, H P Ji (https://academic.oup.com/bioinformatics/article/35/21/4397/5426055) IntronDB: a database for eukaryotic intron features Dapeng Wang (https://academic.oup.com/bioinformatics/article/35/21/4400/5428179) multiPhATE: bioinformatics pipeline for functional annotation of phage isolates Carol L Ecale Zhou, Stephanie Malfatti, Jeffrey Kimbrel, Casandra Philipson, Katelyn McNair (https://academic.oup.com/bioinformatics/article/35/21/4402/5488969) Spliceogen: an integrative, scalable tool for the discovery of splice-altering variants Steven Monger, Michael Troup, Eddie Ip, Sally L Dunwoodie, Eleni Giannoulatou (https://academic.oup.com/bioinformatics/article/35/21/4405/5472338) Identifying centromeric satellites with dna-brnn Heng Li (https://academic.oup.com/bioinformatics/article/35/21/4408/5466455) icHET: interactive visualization of cytoplasmic heteroplasmy Vinhthuy Phan, Diem-Trang Pham, Caroline Melton, Adam J Ramsey, Bernie J Daigle, Jr. (https://academic.oup.com/bioinformatics/article/35/21/4411/5481955) Graphical data mining of cancer mechanisms with SEMA Mustafa Solmaz, Adam Lane, Bilal Gonen, Ogulsheker Akmamedova, Mehmet H Gunes (https://academic.oup.com/bioinformatics/article/35/21/4413/5487380) gpart: human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks Sun Ah Kim, Myriam Brossard, Delnaz Roshandel, Andrew D Paterson, Shelley B Bull (https://academic.oup.com/bioinformatics/article/35/21/4419/5487391) G-OnRamp: a Galaxy-based platform for collaborative annotation of eukaryotic genomes Yating Liu, Luke Sargent, Wilson Leung, Sarah C R Elgin, Jeremy Goecks (https://academic.oup.com/bioinformatics/article/35/21/4422/5487392) Tibanna: software for scalable execution of portable pipelines on the cloud Soohyun Lee, Jeremy Johnson, Carl Vitzthum, Koray Kırlı, Burak H Alver (https://academic.oup.com/bioinformatics/article/35/21/4424/5488124) Hayai-Annotation Plants: an ultra-fast and comprehensive functional gene annotation system in plants Andrea Ghelfi, Kenta Shirasawa, Hideki Hirakawa, Sachiko Isobe (https://academic.oup.com/bioinformatics/article/35/21/4427/5489908) ntEdit: scalable genome sequence polishing René L Warren, Lauren Coombe, Hamid Mohamadi, Jessica Zhang, Barry Jaquish (https://academic.oup.com/bioinformatics/article/35/21/4430/5490204) TPES: tumor purity estimation from SNVs Alessio Locallo, Davide Prandi, Tarcisio Fedrizzi, Francesca Demichelis (https://academic.oup.com/bioinformatics/article/35/21/4433/5490858) HyAsP, a greedy tool for plasmids identification Robert Müller, Cedric Chauve (https://academic.oup.com/bioinformatics/article/35/21/4436/5497247) SPar-K: a method to partition NGS signal data Romain Groux, Philipp Bucher (https://academic.oup.com/bioinformatics/article/35/21/4440/5497248) simuG: a general-purpose genome simulator Jia-Xing Yue, Gianni Liti (https://academic.oup.com/bioinformatics/article/35/21/4442/5497256) SEQUENCE ANALYSIS ------------------------------ PyPore: a python toolbox for nanopore sequencing data handling Roberto Semeraro, Alberto Magi (https://academic.oup.com/bioinformatics/article/35/21/4445/5472339) ORCA: a comprehensive bioinformatics container environment for education and research Shaun D Jackman, Tatyana Mozgacheva, Susie Chen, Brendan O'Huiginn, Lance Bailey (https://academic.oup.com/bioinformatics/article/35/21/4448/5475597) Cram-JS: reference-based decompression in node and the browser Robert Buels, Shihab Dider, Colin Diesh, James Robinson, Ian Holmes (https://academic.oup.com/bioinformatics/article/35/21/4451/5490857) PHYLOGENETICS ------------------------------ RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference Alexey M Kozlov, Diego Darriba, Tomáš Flouri, Benoit Morel, Alexandros Stamatakis (https://academic.oup.com/bioinformatics/article/35/21/4453/5487384) STRUCTURAL BIOINFORMATICS ------------------------------ parMATT: parallel multiple alignment of protein 3D-structures with translations and twists for distributed-memory systems Maksim V Shegay, Dmitry A Suplatov, Nina N Popova, Vytas K Švedas, Vladimir V Voevodin (https://academic.oup.com/bioinformatics/article/35/21/4456/5421160) RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA Sha Gong, Chengxin Zhang, Yang Zhang (https://academic.oup.com/bioinformatics/article/35/21/4459/5480133) epiTAD: a web application for visualizing chromosome conformation capture data in the context of genetic epidemiology Jordan H Creed, Garrick Aden-Buie, Alvaro N Monteiro, Travis A Gerke (https://academic.oup.com/bioinformatics/article/35/21/4462/5490859) GENE EXPRESSION ------------------------------ FusionLearn: a biomarker selection algorithm on cross-platform data Xin Gao, Yuan Zhong (https://academic.oup.com/bioinformatics/article/35/21/4465/5421175) IsoformSwitchAnalyzeR: analysis of changes in genome-wide patterns of alternative splicing and its functional consequences Kristoffer Vitting-Seerup, Albin Sandelin (https://academic.oup.com/bioinformatics/article/35/21/4469/5466456) The barcode, UMI, set format and BUStools Páll Melsted, Vasilis Ntranos, Lior Pachter (https://academic.oup.com/bioinformatics/article/35/21/4472/5487510) 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/35/21/4474/5497255) GENETICS AND POPULATION ANALYSIS ------------------------------ Variant Score Ranker---a web application for intuitive missense variant prioritization Juanjiangmeng Du, Monica Sudarsanam, Eduardo Pérez-Palma, Andrea Ganna, Laurent Francioli (https://academic.oup.com/bioinformatics/article/35/21/4478/5480132) SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal Mathias Currat, Miguel Arenas, Claudio S Quilodràn, Laurent Excoffier, Nicolas Ray (https://academic.oup.com/bioinformatics/article/35/21/4480/5488121) SYSTEMS BIOLOGY ------------------------------ IsoCor: isotope correction for high-resolution MS labeling experiments Pierre Millard, Baudoin Delépine, Matthieu Guionnet, Maud Heuillet, Floriant Bellvert (https://academic.oup.com/bioinformatics/article/35/21/4484/5418798) RTNsurvival: an R/Bioconductor package for regulatory network survival analysis Clarice S Groeneveld, Vinicius S Chagas, Steven J M Jones, A Gordon Robertson, Bruce A J Ponder (https://academic.oup.com/bioinformatics/article/35/21/4488/5421508) The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein--protein interaction and signalling networks Bence gg, Andrea Császár, Máté Szalay-Bek', Dániel V Veres, Réka Mizsei (https://academic.oup.com/bioinformatics/article/35/21/4490/5475596) clustermq enables efficient parallelization of genomic analyses Michael Schubert (https://academic.oup.com/bioinformatics/article/35/21/4493/5499081) MINERVA API and plugins: opening molecular network analysis and visualization to the community David Hoksza, Piotr Gawron, Marek Ostaszewski, Ewa Smula, Reinhard Schneider (https://academic.oup.com/bioinformatics/article/35/21/4496/5480127) sbgntikz---a TikZ library to draw SBGN maps Adrien Rougny (https://academic.oup.com/bioinformatics/article/35/21/4499/5487386) INDRA-IPM: interactive pathway modeling using natural language with automated assembly Petar V Todorov, Benjamin M Gyori, John A Bachman, Peter K Sorger (https://academic.oup.com/bioinformatics/article/35/21/4501/5487381) PathFXweb: a web application for identifying drug safety and efficacy phenotypes Jennifer L Wilson, Mike Wong, Ajinkya Chalke, Nicholas Stepanov, Dragutin Petkovic (https://academic.oup.com/bioinformatics/article/35/21/4504/5494700) DATA AND TEXT MINING ------------------------------ Lipid Mini-On: mining and ontology tool for enrichment analysis of lipidomic data Geremy Clair, Sarah Reehl, Kelly G Stratton, Matthew E Monroe, Malak M Tfaily (https://academic.oup.com/bioinformatics/article/35/21/4507/5448863) TractaViewer: a genome-wide tool for preliminary assessment of therapeutic target druggability Neil Pearson, Karim Malki, David Evans, Lewis Vidler, Cara Ruble (https://academic.oup.com/bioinformatics/article/35/21/4509/5487388) Entrezpy: a Python library to dynamically interact with the NCBI Entrez databases Jan P Buchmann, Edward C Holmes (https://academic.oup.com/bioinformatics/article/35/21/4511/5488119) PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model Benjamin S Glicksberg, Boris Oskotsky, Phyllis M Thangaraj, Nicholas Giangreco, Marcus A Badgeley (https://academic.oup.com/bioinformatics/article/35/21/4515/5520433) DATABASES AND ONTOLOGIES ------------------------------ FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization Youssef Darzi, Yuta Yamate, Takuji Yamada (https://academic.oup.com/bioinformatics/article/35/21/4519/5475599) BIOIMAGE INFORMATICS ------------------------------ Biomedical image augmentation using Augmentor Marcus D Bloice, Peter M Roth, Andreas Holzinger (https://academic.oup.com/bioinformatics/article/35/21/4522/5466454) YeastSpotter: accurate and parameter-free web segmentation for microscopy images of yeast cells Alex X Lu, Taraneh Zarin, Ian S Hsu, Alan M Moses (https://academic.oup.com/bioinformatics/article/35/21/4525/5490207) MyelinJ: an ImageJ macro for high throughput analysis of myelinating cultures Michael J Whitehead, George A McCanney, Hugh J Willison, Susan C Barnett (https://academic.oup.com/bioinformatics/article/35/21/4528/5490206) CytoPacq: a web-interface for simulating multi-dimensional cell imaging David Wiesner, David Svoboda, Martin Maška, Michal Kozubek (https://academic.oup.com/bioinformatics/article/35/21/4531/5494701) ============================= CORRIGENDA ============================Haplotype assembly of autotetraploid potato using integer linear programing Enrico Siragusa, Niina Haiminen, Richard Finkers, Richard Visser, Laxmi Parida (https://academic.oup.com/bioinformatics/article/35/21/4534/5529342) 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/35/21/4535/5536356) 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/35/21/4536/5544340) 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.biology.mcmaster.ca. ------=_Part_1827250050.1572739768245 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.
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Bioinformatics  
Volume 35 Issue 21
 
1 November 2019
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
TORMES: an automated pipeline for whole bacterial genome analysis 
 
Narciso M Quijada; David Rodríguez-Lázaro; Jose María Eiros ; Marta Hernández
 
 
Nano-GLADIATOR: real-time detection of copy number alterations from nanopore sequencing data 
 
Alberto Magi; Davide Bolognini; Niccoló Bartalucci ; Alessandra Mingrino; Roberto Semeraro ...
 
 
HiCNN: a very deep convolutional neural network to better enhance the resolution of Hi-C data border= 
 
Tong Liu ; Zheng Wang
 
 
SolidBin: improving metagenome binning with semi-supervised normalized cut 
 
Ziye Wang; Zhengyang Wang; Yang Young Lu ; Fengzhu Sun; Shanfeng Zhu
 
 
 
SEQUENCE ANALYSIS
 
 
 
Graph analysis of fragmented long-read bacterial genome assemblies 
 
Pierre Marijon; Rayan Chikhi; Jean-Stéphane Varré
 
 
A Bayesian model integration for mutation calling through data partitioning border= 
 
Takuya Moriyama ; Seiya Imoto; Shuto Hayashi; Yuichi Shiraishi; Satoru Miyano ...
 
 
Shouji: a fast and efficient pre-alignment filter for sequence alignment 
 
Mohammed Alser; Hasan Hassan; Akash Kumar ; Onur Mutlu; Can Alkan
 
 
scRNAss: a single-cell RNA-seq assembler via imputing dropouts and combing junctions 
 
Juntao Liu; Xiangyu Liu; Xianwen Ren ; Guojun Li
 
 
PEPred-Suite: improved and robust prediction of therapeutic peptides using adaptive feature representation learning 
 
Leyi Wei; Chen Zhou; Ran Su ; Quan Zou
 
 
Overlap graph-based generation of haplotigs for diploids and polyploids 
 
Jasmijn A Baaijens; Alexander Schönhuth
 
 
 
PHYLOGENETICS
 
 
 
Accounting for ambiguity in ancestral sequence reconstruction 
 
A Oliva; S Pulicani; V Lefort ; L Bréhélin; O Gascuel ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Determining parameters for non-linear models of multi-loop free energy change 
 
Max Ward; Hongying Sun; Amitava Datta ; Michael Wise; David H Mathews
 
 
 
GENE EXPRESSION
 
 
 
Assessing reproducibility of matrix factorization methods in independent transcriptomes border= 
 
Laura Cantini ; Ulykbek Kairov; Aurélien de Reyniès; Emmanuel Barillot; François Radvanyi ...
 
 
Performance of gene expression analyses using de novo assembled transcripts in polyploid species 
 
Ling-Yun Chen; Diego F Morales-Briones; Courtney N Passow ; Ya Yang
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Kinpute: using identity by descent to improve genotype imputation 
 
Mark Abney; Aisha ElSherbiny
 
 
A coordinate descent approach for sparse Bayesian learning in high dimensional QTL mapping and genome-wide association studies 
 
Meiyue Wang; Shizhong Xu
 
 
 
SYSTEMS BIOLOGY
 
 
 
Unsupervised discovery of phenotype-specific multi-omics networks 
 
W Jenny Shi; Yonghua Zhuang; Pamela H Russell ; Brian D Hobbs; Margaret M Parker ...
 
 
Genome-wide identification of the essential protein-coding genes and long non-coding RNAs for human pan-cancer 
 
Yuwei Zhang; Yang Tao; Huihui Ji ; Wei Li; Xingli Guo ...
 
 
rMTA: robust metabolic transformation analysis 
 
Luis V Valcárcel; Verónica Torrano; Luis Tobalina ; Arkaitz Carracedo; Francisco J Planes
 
 
ASICS: an R package for a whole analysis workflow of 1D 1H NMR spectra 
 
Gaëlle Lefort; Laurence Liaubet; Cécile Canlet ; Patrick Tardivel; Marie-Christine Père ...
 
 
A learning-based framework for miRNA-disease association identification using neural networks 
 
Jiajie Peng; Weiwei Hui; Qianqian Li ; Bolin Chen; Jianye Hao ...
 
 
 
DATA AND TEXT MINING
 
 
 
Open Agile text mining for bioinformatics: the PubAnnotation ecosystem border= 
 
Jin-Dong Kim ; Yue Wang; Toyofumi Fujiwara; Shujiro Okuda; Tiffany J Callahan ...
 
 
Figure and caption extraction from biomedical documents border=  
 
Pengyuan Li; Xiangying Jiang; Hagit Shatkay
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
GenomeWarp: an alignment-based variant coordinate transformation border= 
 
Cory Y McLean ; Yeongwoo Hwang; Ryan Poplin; Mark A DePristo
 
 
epic2 efficiently finds diffuse domains in ChIP-seq data 
 
Endre Bakken Stovner; Pål Sætrom
 
 
HLA*LA'HLA typing from linearly projected graph alignments border=  
 
Alexander T Dilthey; Alexander J Mentzer; Raphael Carapito; Clare Cutland; Nezih Cereb ...
 
 
Structural variant analysis for linked-read sequencing data with gemtools 
 
S U Greer; H P Ji
 
 
IntronDB: a database for eukaryotic intron features 
 
Dapeng Wang
 
 
multiPhATE: bioinformatics pipeline for functional annotation of phage isolates border= 
 
Carol L Ecale Zhou ; Stephanie Malfatti; Jeffrey Kimbrel; Casandra Philipson; Katelyn McNair ...
 
 
Spliceogen: an integrative, scalable tool for the discovery of splice-altering variants 
 
Steven Monger; Michael Troup; Eddie Ip ; Sally L Dunwoodie; Eleni Giannoulatou
 
 
Identifying centromeric satellites with dna-brnn 
 
Heng Li
 
 
icHET: interactive visualization of cytoplasmic heteroplasmy 
 
Vinhthuy Phan; Diem-Trang Pham; Caroline Melton ; Adam J Ramsey; Bernie J Daigle, Jr. ...
 
 
Graphical data mining of cancer mechanisms with SEMA border=  
 
Mustafa Solmaz; Adam Lane; Bilal Gonen ; Ogulsheker Akmamedova; Mehmet H Gunes ...
 
 
gpart: human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks border= 
 
Sun Ah Kim ; Myriam Brossard; Delnaz Roshandel; Andrew D Paterson; Shelley B Bull ...
 
 
G-OnRamp: a Galaxy-based platform for collaborative annotation of eukaryotic genomes border= 
 
Yating Liu ; Luke Sargent; Wilson Leung; Sarah C R Elgin; Jeremy Goecks
 
 
Tibanna: software for scalable execution of portable pipelines on the cloud 
 
Soohyun Lee; Jeremy Johnson; Carl Vitzthum ; Koray Kırlı; Burak H Alver ...
 
 
Hayai-Annotation Plants: an ultra-fast and comprehensive functional gene annotation system in plants border= 
 
Andrea Ghelfi ; Kenta Shirasawa; Hideki Hirakawa; Sachiko Isobe
 
 
ntEdit: scalable genome sequence polishing border=  
 
René L Warren; Lauren Coombe; Hamid Mohamadi; Jessica Zhang; Barry Jaquish ...
 
 
TPES: tumor purity estimation from SNVs 
 
Alessio Locallo; Davide Prandi; Tarcisio Fedrizzi ; Francesca Demichelis
 
 
HyAsP, a greedy tool for plasmids identification 
 
Robert Müller; Cedric Chauve
 
 
SPar-K: a method to partition NGS signal data 
 
Romain Groux; Philipp Bucher
 
 
simuG: a general-purpose genome simulator border=  
 
Jia-Xing Yue; Gianni Liti
 
 
 
SEQUENCE ANALYSIS
 
 
 
PyPore: a python toolbox for nanopore sequencing data handling 
 
Roberto Semeraro; Alberto Magi
 
 
ORCA: a comprehensive bioinformatics container environment for education and research border= 
 
Shaun D Jackman ; Tatyana Mozgacheva; Susie Chen; Brendan O'Huiginn; Lance Bailey ...
 
 
Cram-JS: reference-based decompression in node and the browser 
 
Robert Buels; Shihab Dider; Colin Diesh ; James Robinson; Ian Holmes
 
 
 
PHYLOGENETICS
 
 
 
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference border= 
 
Alexey M Kozlov ; Diego Darriba; Tomáš Flouri; Benoit Morel; Alexandros Stamatakis
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
parMATT: parallel multiple alignment of protein 3D-structures with translations and twists for distributed-memory systems 
 
Maksim V Shegay; Dmitry A Suplatov; Nina N Popova ; Vytas K Švedas; Vladimir V Voevodin
 
 
RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA 
 
Sha Gong; Chengxin Zhang; Yang Zhang
 
 
epiTAD: a web application for visualizing chromosome conformation capture data in the context of genetic epidemiology 
 
Jordan H Creed; Garrick Aden-Buie; Alvaro N Monteiro ; Travis A Gerke
 
 
 
GENE EXPRESSION
 
 
 
FusionLearn: a biomarker selection algorithm on cross-platform data 
 
Xin Gao; Yuan Zhong
 
 
IsoformSwitchAnalyzeR: analysis of changes in genome-wide patterns of alternative splicing and its functional consequences 
 
Kristoffer Vitting-Seerup; Albin Sandelin
 
 
The barcode, UMI, set format and BUStools 
 
Páll Melsted; Vasilis Ntranos; Lior Pachter
 
 
MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome 
 
Anjun Ma; Minxuan Sun; Adam McDermaid ; Bingqiang Liu; Qin Ma
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Variant Score Ranker'a web application for intuitive missense variant prioritization 
 
Juanjiangmeng Du; Monica Sudarsanam; Eduardo Pérez-Palma ; Andrea Ganna; Laurent Francioli ...
 
 
SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal border= 
 
Mathias Currat ; Miguel Arenas; Claudio S Quilodràn; Laurent Excoffier; Nicolas Ray
 
 
 
SYSTEMS BIOLOGY
 
 
 
IsoCor: isotope correction for high-resolution MS labeling experiments 
 
Pierre Millard; Baudoin Delépine; Matthieu Guionnet ; Maud Heuillet; Floriant Bellvert ...
 
 
RTNsurvival: an R/Bioconductor package for regulatory network survival analysis 
 
Clarice S Groeneveld; Vinicius S Chagas; Steven J M Jones ; A Gordon Robertson; Bruce A J Ponder ...
 
 
The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein'protein interaction and signalling networks border= 
 
Bence Ágg ; Andrea Császár; Máté Szalay-Bek'; Dániel V Veres; Réka Mizsei ...
 
 
clustermq enables efficient parallelization of genomic analyses border= 
 
Michael Schubert
 
 
MINERVA API and plugins: opening molecular network analysis and visualization to the community border= 
 
David Hoksza ; Piotr Gawron; Marek Ostaszewski; Ewa Smula; Reinhard Schneider
 
 
sbgntikz'a TikZ library to draw SBGN maps 
 
Adrien Rougny
 
 
INDRA-IPM: interactive pathway modeling using natural language with automated assembly border= 
 
Petar V Todorov ; Benjamin M Gyori; John A Bachman; Peter K Sorger
 
 
PathFXweb: a web application for identifying drug safety and efficacy phenotypes border= 
 
Jennifer L Wilson ; Mike Wong; Ajinkya Chalke; Nicholas Stepanov; Dragutin Petkovic ...
 
 
 
DATA AND TEXT MINING
 
 
 
Lipid Mini-On: mining and ontology tool for enrichment analysis of lipidomic data 
 
Geremy Clair; Sarah Reehl; Kelly G Stratton ; Matthew E Monroe; Malak M Tfaily ...
 
 
TractaViewer: a genome-wide tool for preliminary assessment of therapeutic target druggability 
 
Neil Pearson; Karim Malki; David Evans ; Lewis Vidler; Cara Ruble ...
 
 
Entrezpy: a Python library to dynamically interact with the NCBI Entrez databases border= 
 
Jan P Buchmann ; Edward C Holmes
 
 
PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model border= 
 
Benjamin S Glicksberg ; Boris Oskotsky; Phyllis M Thangaraj; Nicholas Giangreco; Marcus A Badgeley ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization border= 
 
Youssef Darzi ; Yuta Yamate; Takuji Yamada
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Biomedical image augmentation using Augmentor 
 
Marcus D Bloice; Peter M Roth; Andreas Holzinger
 
 
YeastSpotter: accurate and parameter-free web segmentation for microscopy images of yeast cells border= 
 
Alex X Lu ; Taraneh Zarin; Ian S Hsu; Alan M Moses
 
 
MyelinJ: an ImageJ macro for high throughput analysis of myelinating cultures border= 
 
Michael J Whitehead ; George A McCanney; Hugh J Willison; Susan C Barnett
 
 
CytoPacq: a web-interface for simulating multi-dimensional cell imaging border= 
 
David Wiesner ; David Svoboda; Martin Maška; Michal Kozubek
 
 
 
CORRIGENDA
 
 
 
Haplotype assembly of autotetraploid potato using integer linear programing border= 
 
Enrico Siragusa ; Niina Haiminen; Richard Finkers; Richard Visser; Laxmi Parida
 
 
PgpRules: a decision tree based prediction server for P-glycoprotein substrates and inhibitors 
 
Pei-Hua Wang; Yi-Shu Tu; Yufeng J Tseng
 
 
Nanopype: a modular and scalable nanopore data processing pipeline 
 
Pay Giesselmann; Sara Hetzel; Franz-Josef Müller ; Alexander Meissner; Helene Kretzmer
 
 
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