Subject: Bioinformatics Table of Contents for 1 February 2020 ------=_Part_933242651.1581364055606 Content-Type: text/plain;charset=UTF-8 Oxford Academic *** Bioinformatics *** Volume 36, Issue 3, 1 February 2020 Read this issue (https://academic.oup.com/bioinformatics/issue/36/3) ------------------------------ 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 ============================A powerful and flexible weighted distance-based method incorporating interactions between DNA methylation and environmental factors on health outcomes Ya Wang, Min Qian, Deliang Tang, Julie Herbstman, Frederica Perera (https://academic.oup.com/bioinformatics/article/36/3/653/5553097) pWGBSSimla: a profile-based whole-genome bisulfite sequencing data simulator incorporating methylation QTLs, allele-specific methylations and differentially methylated regions Ren-Hua Chung, Chen-Yu Kang (https://academic.oup.com/bioinformatics/article/36/3/660/5545541) Accurate loop calling for 3D genomic data with cLoops Yaqiang Cao, Zhaoxiong Chen, Xingwei Chen, Daosheng Ai, Guoyu Chen (https://academic.oup.com/bioinformatics/article/36/3/666/5553098) Partition: a surjective mapping approach for dimensionality reduction Joshua Millstein, Francesca Battaglin, Malcolm Barrett, Shu Cao, Wu Zhang (https://academic.oup.com/bioinformatics/article/36/3/676/5554652) Fast and accurate correction of optical mapping data via spaced seeds Leena Salmela, Kingshuk Mukherjee, Simon J Puglisi, Martin D Muggli, Christina Boucher (https://academic.oup.com/bioinformatics/article/36/3/682/5559485) Regulatory annotation of genomic intervals based on tissue-specific expression QTLs Tianlei Xu, Peng Jin, Zhaohui S Qin (https://academic.oup.com/bioinformatics/article/36/3/690/5555289) Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API Thomas Desvignes, Phillipe Loher, Karen Eilbeck, Jeffery Ma, Gianvito Urgese (https://academic.oup.com/bioinformatics/article/36/3/698/5556118) PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins Yanju Zhang, Sha Yu, Ruopeng Xie, Jiahui Li, André Leier (https://academic.oup.com/bioinformatics/article/36/3/704/5545087) neoepiscope improves neoepitope prediction with multivariant phasing Mary A Wood, Austin Nguyen, Adam J Struck, Kyle Ellrott, Abhinav Nellore (https://academic.oup.com/bioinformatics/article/36/3/713/5551338) Improved representation of sequence bloom trees Robert S Harris, Paul Medvedev (https://academic.oup.com/bioinformatics/article/36/3/721/5553093) Accurate estimation of microbial sequence diversity with Distanced Timothy J Hackmann (https://academic.oup.com/bioinformatics/article/36/3/728/5556106) ChaperISM: improved chaperone binding prediction using position-independent scoring matrices M B B Gutierres, C B C Bonorino, M M Rigo (https://academic.oup.com/bioinformatics/article/36/3/735/5555810) Accurate and efficient cell lineage tree inference from noisy single cell data: the maximum likelihood perfect phylogeny approach Yufeng Wu (https://academic.oup.com/bioinformatics/article/36/3/742/5555811) Integrating ab initio and template-based algorithms for protein'protein complex structure prediction Sweta Vangaveti, Thom Vreven, Yang Zhang, Zhiping Weng (https://academic.oup.com/bioinformatics/article/36/3/751/5545093) Learning from the ligand: using ligand-based features to improve binding affinity prediction Fergus Boyles, Charlotte M Deane, Garrett M Morris (https://academic.oup.com/bioinformatics/article/36/3/758/5554651) Automatic local resolution-based sharpening of cryo-EM maps Erney Ramírez-Aportela, Jose Luis Vilas, Alisa Glukhova, Roberto Melero, Pablo Conesa (https://academic.oup.com/bioinformatics/article/36/3/765/5554698) ECHO: an application for detection and analysis of oscillators identifies metabolic regulation on genome-wide circadian output Hannah De los Santos, Emily J Collins, Catherine Mann, April W Sagan, Meaghan S Jankowski (https://academic.oup.com/bioinformatics/article/36/3/773/5544107) Using multiple measurements of tissue to estimate subject- and cell-type-specific gene expression Jiebiao Wang, Bernie Devlin, Kathryn Roeder (https://academic.oup.com/bioinformatics/article/36/3/782/5545976) scHinter: imputing dropout events for single-cell RNA-seq data with limited sample size Pengchao Ye, Wenbin Ye, Congting Ye, Shuchao Li, Lishan Ye (https://academic.oup.com/bioinformatics/article/36/3/789/5544928) NExUS: Bayesian simultaneous network estimation across unequal sample sizes Priyam Das, Christine B Peterson, Kim-Anh Do, Rehan Akbani, Veerabhadran Baladandayuthapani (https://academic.oup.com/bioinformatics/article/36/3/798/5555873) Alternating EM algorithm for a bilinear model in isoform quantification from RNA-seq data Wenjiang Deng, Tian Mou, Krishna R Kalari, Nifang Niu, Liewei Wang (https://academic.oup.com/bioinformatics/article/36/3/805/5545974) DeepCOP: deep learning-based approach to predict gene regulating effects of small molecules Godwin Woo, Michael Fernandez, Michael Hsing, Nathan A Lack, Ayse Derya Cavga (https://academic.oup.com/bioinformatics/article/36/3/813/5554893) Tissue-specific deconvolution of immune cell composition by integrating bulk and single-cell transcriptomes Ziyi Chen, Chengyang Ji, Qin Shen, Wei Liu, F Xiao-Feng Qin (https://academic.oup.com/bioinformatics/article/36/3/819/5554701) A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data J Víctor Moreno-Mayar, Thorfinn Sand Korneliussen, Jyoti Dalal, Gabriel Renaud, Anders Albrechtsen (https://academic.oup.com/bioinformatics/article/36/3/828/5554699) A latent unknown clustering integrating multi-omics data (LUCID) with phenotypic traits Cheng Peng, Jun Wang, Isaac Asante, Stan Louie, Ran Jin (https://academic.oup.com/bioinformatics/article/36/3/842/5556107) Graph convolution for predicting associations between miRNA and drug resistance Yu-an Huang, Pengwei Hu, Keith C C Chan, Zhu-Hong You (https://academic.oup.com/bioinformatics/article/36/3/851/5545546) Machine learning empowers phosphoproteome prediction in cancers Hongyang Li, Yuanfang Guan (https://academic.oup.com/bioinformatics/article/36/3/859/5549493) Gene relevance based on multiple evidences in complex networks Noemi Di Nanni, Matteo Gnocchi, Marco Moscatelli, Luciano Milanesi, Ettore Mosca (https://academic.oup.com/bioinformatics/article/36/3/865/5553095) MEXCOwalk: mutual exclusion and coverage based random walk to identify cancer modules Rafsan Ahmed, Ilyes Baali, Cesim Erten, Evis Hoxha, Hilal Kazan (https://academic.oup.com/bioinformatics/article/36/3/872/5552148) A Gaussian process-based definition reveals new and bona fide genetic interactions compared to a multiplicative model in the Gram-negative Escherichia coli Ashwani Kumar, Ali Hosseinnia, Alla Gagarinova, Sadhna Phanse, Sunyoung Kim (https://academic.oup.com/bioinformatics/article/36/3/880/5555290) Genome-phenome explorer (GePhEx): a tool for the visualization and interpretation of phenotypic relationships supported by genetic evidence Xavier Farré, Nino Spataro, Frederic Haziza, Jordi Rambla, Arcadi Navarro (https://academic.oup.com/bioinformatics/article/36/3/890/5545092) PIRD: Pan Immune Repertoire Database Wei Zhang, Longlong Wang, Ke Liu, Xiaofeng Wei, Kai Yang (https://academic.oup.com/bioinformatics/article/36/3/897/5543102) MeLAD: an integrated resource for metalloenzyme-ligand associations Gen Li, Yu Su, Yu-Hang Yan, Jia-Yi Peng, Qing-Qing Dai (https://academic.oup.com/bioinformatics/article/36/3/904/5554465) Semi-blind sparse affine spectral unmixing of autofluorescence-contaminated micrographs Blair J Rossetti, Steven A Wilbert, Jessica L Mark Welch, Gary G Borisy, James G Nagy (https://academic.oup.com/bioinformatics/article/36/3/910/5556289) GENOME ANALYSIS ------------------------------ A powerful and flexible weighted distance-based method incorporating interactions between DNA methylation and environmental factors on health outcomes Ya Wang, Min Qian, Deliang Tang, Julie Herbstman, Frederica Perera (https://academic.oup.com/bioinformatics/article/36/3/653/5553097) pWGBSSimla: a profile-based whole-genome bisulfite sequencing data simulator incorporating methylation QTLs, allele-specific methylations and differentially methylated regions Ren-Hua Chung, Chen-Yu Kang (https://academic.oup.com/bioinformatics/article/36/3/660/5545541) Accurate loop calling for 3D genomic data with cLoops Yaqiang Cao, Zhaoxiong Chen, Xingwei Chen, Daosheng Ai, Guoyu Chen (https://academic.oup.com/bioinformatics/article/36/3/666/5553098) Partition: a surjective mapping approach for dimensionality reduction Joshua Millstein, Francesca Battaglin, Malcolm Barrett, Shu Cao, Wu Zhang (https://academic.oup.com/bioinformatics/article/36/3/676/5554652) Fast and accurate correction of optical mapping data via spaced seeds Leena Salmela, Kingshuk Mukherjee, Simon J Puglisi, Martin D Muggli, Christina Boucher (https://academic.oup.com/bioinformatics/article/36/3/682/5559485) Regulatory annotation of genomic intervals based on tissue-specific expression QTLs Tianlei Xu, Peng Jin, Zhaohui S Qin (https://academic.oup.com/bioinformatics/article/36/3/690/5555289) Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API Thomas Desvignes, Phillipe Loher, Karen Eilbeck, Jeffery Ma, Gianvito Urgese (https://academic.oup.com/bioinformatics/article/36/3/698/5556118) SEQUENCE ANALYSIS ------------------------------ PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins Yanju Zhang, Sha Yu, Ruopeng Xie, Jiahui Li, André Leier (https://academic.oup.com/bioinformatics/article/36/3/704/5545087) neoepiscope improves neoepitope prediction with multivariant phasing Mary A Wood, Austin Nguyen, Adam J Struck, Kyle Ellrott, Abhinav Nellore (https://academic.oup.com/bioinformatics/article/36/3/713/5551338) Improved representation of sequence bloom trees Robert S Harris, Paul Medvedev (https://academic.oup.com/bioinformatics/article/36/3/721/5553093) Accurate estimation of microbial sequence diversity with Distanced Timothy J Hackmann (https://academic.oup.com/bioinformatics/article/36/3/728/5556106) ChaperISM: improved chaperone binding prediction using position-independent scoring matrices M B B Gutierres, C B C Bonorino, M M Rigo (https://academic.oup.com/bioinformatics/article/36/3/735/5555810) PHYLOGENETICS ------------------------------ Accurate and efficient cell lineage tree inference from noisy single cell data: the maximum likelihood perfect phylogeny approach Yufeng Wu (https://academic.oup.com/bioinformatics/article/36/3/742/5555811) STRUCTURAL BIOINFORMATICS ------------------------------ Integrating ab initio and template-based algorithms for protein'protein complex structure prediction Sweta Vangaveti, Thom Vreven, Yang Zhang, Zhiping Weng (https://academic.oup.com/bioinformatics/article/36/3/751/5545093) Learning from the ligand: using ligand-based features to improve binding affinity prediction Fergus Boyles, Charlotte M Deane, Garrett M Morris (https://academic.oup.com/bioinformatics/article/36/3/758/5554651) Automatic local resolution-based sharpening of cryo-EM maps Erney Ramírez-Aportela, Jose Luis Vilas, Alisa Glukhova, Roberto Melero, Pablo Conesa (https://academic.oup.com/bioinformatics/article/36/3/765/5554698) GENE EXPRESSION ------------------------------ ECHO: an application for detection and analysis of oscillators identifies metabolic regulation on genome-wide circadian output Hannah De los Santos, Emily J Collins, Catherine Mann, April W Sagan, Meaghan S Jankowski (https://academic.oup.com/bioinformatics/article/36/3/773/5544107) Using multiple measurements of tissue to estimate subject- and cell-type-specific gene expression Jiebiao Wang, Bernie Devlin, Kathryn Roeder (https://academic.oup.com/bioinformatics/article/36/3/782/5545976) scHinter: imputing dropout events for single-cell RNA-seq data with limited sample size Pengchao Ye, Wenbin Ye, Congting Ye, Shuchao Li, Lishan Ye (https://academic.oup.com/bioinformatics/article/36/3/789/5544928) NExUS: Bayesian simultaneous network estimation across unequal sample sizes Priyam Das, Christine B Peterson, Kim-Anh Do, Rehan Akbani, Veerabhadran Baladandayuthapani (https://academic.oup.com/bioinformatics/article/36/3/798/5555873) Alternating EM algorithm for a bilinear model in isoform quantification from RNA-seq data Wenjiang Deng, Tian Mou, Krishna R Kalari, Nifang Niu, Liewei Wang (https://academic.oup.com/bioinformatics/article/36/3/805/5545974) DeepCOP: deep learning-based approach to predict gene regulating effects of small molecules Godwin Woo, Michael Fernandez, Michael Hsing, Nathan A Lack, Ayse Derya Cavga (https://academic.oup.com/bioinformatics/article/36/3/813/5554893) Tissue-specific deconvolution of immune cell composition by integrating bulk and single-cell transcriptomes Ziyi Chen, Chengyang Ji, Qin Shen, Wei Liu, F Xiao-Feng Qin (https://academic.oup.com/bioinformatics/article/36/3/819/5554701) GENETICS AND POPULATION ANALYSIS ------------------------------ A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data J Víctor Moreno-Mayar, Thorfinn Sand Korneliussen, Jyoti Dalal, Gabriel Renaud, Anders Albrechtsen (https://academic.oup.com/bioinformatics/article/36/3/828/5554699) A latent unknown clustering integrating multi-omics data (LUCID) with phenotypic traits Cheng Peng, Jun Wang, Isaac Asante, Stan Louie, Ran Jin (https://academic.oup.com/bioinformatics/article/36/3/842/5556107) SYSTEMS BIOLOGY ------------------------------ Graph convolution for predicting associations between miRNA and drug resistance Yu-an Huang, Pengwei Hu, Keith C C Chan, Zhu-Hong You (https://academic.oup.com/bioinformatics/article/36/3/851/5545546) Machine learning empowers phosphoproteome prediction in cancers Hongyang Li, Yuanfang Guan (https://academic.oup.com/bioinformatics/article/36/3/859/5549493) Gene relevance based on multiple evidences in complex networks Noemi Di Nanni, Matteo Gnocchi, Marco Moscatelli, Luciano Milanesi, Ettore Mosca (https://academic.oup.com/bioinformatics/article/36/3/865/5553095) MEXCOwalk: mutual exclusion and coverage based random walk to identify cancer modules Rafsan Ahmed, Ilyes Baali, Cesim Erten, Evis Hoxha, Hilal Kazan (https://academic.oup.com/bioinformatics/article/36/3/872/5552148) A Gaussian process-based definition reveals new and bona fide genetic interactions compared to a multiplicative model in the Gram-negative Escherichia coli Ashwani Kumar, Ali Hosseinnia, Alla Gagarinova, Sadhna Phanse, Sunyoung Kim (https://academic.oup.com/bioinformatics/article/36/3/880/5555290) DATA AND TEXT MINING ------------------------------ Genome-phenome explorer (GePhEx): a tool for the visualization and interpretation of phenotypic relationships supported by genetic evidence Xavier Farré, Nino Spataro, Frederic Haziza, Jordi Rambla, Arcadi Navarro (https://academic.oup.com/bioinformatics/article/36/3/890/5545092) DATABASES AND ONTOLOGIES ------------------------------ PIRD: Pan Immune Repertoire Database Wei Zhang, Longlong Wang, Ke Liu, Xiaofeng Wei, Kai Yang (https://academic.oup.com/bioinformatics/article/36/3/897/5543102) MeLAD: an integrated resource for metalloenzyme-ligand associations Gen Li, Yu Su, Yu-Hang Yan, Jia-Yi Peng, Qing-Qing Dai (https://academic.oup.com/bioinformatics/article/36/3/904/5554465) BIOIMAGE INFORMATICS ------------------------------ Semi-blind sparse affine spectral unmixing of autofluorescence-contaminated micrographs Blair J Rossetti, Steven A Wilbert, Jessica L Mark Welch, Gary G Borisy, James G Nagy (https://academic.oup.com/bioinformatics/article/36/3/910/5556289) ============================= APPLICATIONS NOTE ============================PyRanges: efficient comparison of genomic intervals in Python Endre Bakken Stovner, Pål Sætrom (https://academic.oup.com/bioinformatics/article/36/3/918/5543103) MultiGuideScan: a multi-processing tool for designing CRISPR guide RNA libraries Tao Li, Shaokai Wang, Feng Luo, Fang-Xiang Wu, Jianxin Wang (https://academic.oup.com/bioinformatics/article/36/3/920/5544268) MsPAC: a tool for haplotype-phased structural variant detection Oscar L Rodriguez, Anna Ritz, Andrew J Sharp, Ali Bashir (https://academic.oup.com/bioinformatics/article/36/3/922/5545544) CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies Hrant Hovhannisyan, Ahmed Hafez, Carlos Llorens, Toni Gabaldón (https://academic.oup.com/bioinformatics/article/36/3/925/5544929) G3viz: an R package to interactively visualize genetic mutation data using a lollipop-diagram Xin Guo, Bo Zhang, Wenqi Zeng, Shuting Zhao, Dongliang Ge (https://academic.oup.com/bioinformatics/article/36/3/928/5545091) RICOPILI: Rapid Imputation for COnsortias PIpeLIne Max Lam, Swapnil Awasthi, Hunna J Watson, Jackie Goldstein, Georgia Panagiotaropoulou (https://academic.oup.com/bioinformatics/article/36/3/930/5545088) Tersect: a set theoretical utility for exploring sequence variant data Tomasz J Kurowski, Fady Mohareb (https://academic.oup.com/bioinformatics/article/36/3/934/5544926) miComplete: weighted quality evaluation of assembled microbial genomes Eric Hugoson, Wai Tin Lam, Lionel Guy (https://academic.oup.com/bioinformatics/article/36/3/936/5553089) HiLight-PTM: an online application to aid matching peptide pairs with isotopically labelled PTMs Harry J Whitwell, Peter DiMaggio, Jr (https://academic.oup.com/bioinformatics/article/36/3/938/5551339) CROSSalive: a web server for predicting the in vivo structure of RNA molecules Riccardo Delli Ponti, Alexandros Armaos, Andrea Vandelli, Gian Gaetano Tartaglia (https://academic.oup.com/bioinformatics/article/36/3/940/5555809) DDAP: docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases Tingyang Li, Ashootosh Tripathi, Fengan Yu, David H Sherman, Arvind Rao (https://academic.oup.com/bioinformatics/article/36/3/942/5559484) StrainHub: a phylogenetic tool to construct pathogen transmission networks Adriano de Bernardi Schneider, Colby T Ford, Reilly Hostager, John Williams, Michael Cioce (https://academic.oup.com/bioinformatics/article/36/3/945/5550625) Protein Homeostasis Database: protein quality control in E.coli Reshmi Ramakrishnan, Bert Houben, ukasz Kreft, Alexander Botzki, Joost Schymkowitz (https://academic.oup.com/bioinformatics/article/36/3/948/5544931) LightDock goes information-driven Jorge Roel-Touris, Alexandre M J J Bonvin, Brian Jiménez-García (https://academic.oup.com/bioinformatics/article/36/3/950/5550626) Knot_pull'python package for biopolymer smoothing and knot detection Aleksandra I Jarmolinska, Anna Gambin, Joanna I Sulkowska (https://academic.oup.com/bioinformatics/article/36/3/953/5550333) MEPSAnd: minimum energy path surface analysis over n-dimensional surfaces Iñigo Marcos-Alcalde, Eduardo López-Viñas, Paulino Gómez-Puertas (https://academic.oup.com/bioinformatics/article/36/3/956/5550624) CRDS: Consensus Reverse Docking System for target fishing Aeri Lee, Dongsup Kim (https://academic.oup.com/bioinformatics/article/36/3/959/5552149) pCRM1exportome: database of predicted CRM1-dependent Nuclear Export Signal (NES) motifs in cancer-related genes Yoonji Lee, Jordan M Baumhardt, Jimin Pei, Yuh Min Chook, Nick V Grishin (https://academic.oup.com/bioinformatics/article/36/3/961/5553090) BBKNN: fast batch alignment of single cell transcriptomes Krzysztof Pola"ski, Matthew D Young, Zhichao Miao, Kerstin B Meyer, Sarah A Teichmann (https://academic.oup.com/bioinformatics/article/36/3/964/5545955) baerhunter: an R package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data A Ozuna, D Liberto, R M Joyce, K B Arnvig, I Nobeli (https://academic.oup.com/bioinformatics/article/36/3/966/5550627) NACHO: an R package for quality control of NanoString nCounter data Mickaël Canouil, Gerard A Bouland, Amélie Bonnefond, Philippe Froguel, Leen M 't Hart (https://academic.oup.com/bioinformatics/article/36/3/970/5553566) CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes Vinicius da Silva, Marcel Ramos, Martien Groenen, Richard Crooijmans, Anna Johansson (https://academic.oup.com/bioinformatics/article/36/3/972/5544927) U-PASS: unified power analysis and forensics for qualitative traits in genetic association studies Zheng Gao, Jonathan Terhorst, Cristopher V Van Hout, Stilian Stoev (https://academic.oup.com/bioinformatics/article/36/3/974/5545977) EasyModel: user-friendly tool for building and analysis of simple mathematical models in systems biology Jordi Bartolome, Rui Alves, Francesc Solsona, Ivan Teixido (https://academic.oup.com/bioinformatics/article/36/3/976/5554697) AntiHIV-Pred: web-resource for in silico prediction of anti-HIV/AIDS activity Leonid Stolbov, Dmitry Druzhilovskiy, Anastasia Rudik, Dmitry Filimonov, Vladimir Poroikov (https://academic.oup.com/bioinformatics/article/36/3/978/5550623) KRAB ZNF explorer'the online tool for the exploration of the transcriptomic profiles of KRAB-ZNF factors in The Cancer Genome Atlas Rafał Cylwa, Kornel Kiełczewski, Marta Machnik, Urszula Oleksiewicz, Przemysław Biecek (https://academic.oup.com/bioinformatics/article/36/3/980/5544925) COMBAT-TB-NeoDB: fostering tuberculosis research through integrative analysis using graph database technologies Thoba Lose, Peter van Heusden, Alan Christoffels (https://academic.oup.com/bioinformatics/article/36/3/982/5554700) GENOME ANALYSIS ------------------------------ PyRanges: efficient comparison of genomic intervals in Python Endre Bakken Stovner, Pål Sætrom (https://academic.oup.com/bioinformatics/article/36/3/918/5543103) MultiGuideScan: a multi-processing tool for designing CRISPR guide RNA libraries Tao Li, Shaokai Wang, Feng Luo, Fang-Xiang Wu, Jianxin Wang (https://academic.oup.com/bioinformatics/article/36/3/920/5544268) MsPAC: a tool for haplotype-phased structural variant detection Oscar L Rodriguez, Anna Ritz, Andrew J Sharp, Ali Bashir (https://academic.oup.com/bioinformatics/article/36/3/922/5545544) CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies Hrant Hovhannisyan, Ahmed Hafez, Carlos Llorens, Toni Gabaldón (https://academic.oup.com/bioinformatics/article/36/3/925/5544929) G3viz: an R package to interactively visualize genetic mutation data using a lollipop-diagram Xin Guo, Bo Zhang, Wenqi Zeng, Shuting Zhao, Dongliang Ge (https://academic.oup.com/bioinformatics/article/36/3/928/5545091) RICOPILI: Rapid Imputation for COnsortias PIpeLIne Max Lam, Swapnil Awasthi, Hunna J Watson, Jackie Goldstein, Georgia Panagiotaropoulou (https://academic.oup.com/bioinformatics/article/36/3/930/5545088) Tersect: a set theoretical utility for exploring sequence variant data Tomasz J Kurowski, Fady Mohareb (https://academic.oup.com/bioinformatics/article/36/3/934/5544926) miComplete: weighted quality evaluation of assembled microbial genomes Eric Hugoson, Wai Tin Lam, Lionel Guy (https://academic.oup.com/bioinformatics/article/36/3/936/5553089) SEQUENCE ANALYSIS ------------------------------ HiLight-PTM: an online application to aid matching peptide pairs with isotopically labelled PTMs Harry J Whitwell, Peter DiMaggio, Jr (https://academic.oup.com/bioinformatics/article/36/3/938/5551339) CROSSalive: a web server for predicting the in vivo structure of RNA molecules Riccardo Delli Ponti, Alexandros Armaos, Andrea Vandelli, Gian Gaetano Tartaglia (https://academic.oup.com/bioinformatics/article/36/3/940/5555809) DDAP: docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases Tingyang Li, Ashootosh Tripathi, Fengan Yu, David H Sherman, Arvind Rao (https://academic.oup.com/bioinformatics/article/36/3/942/5559484) PHYLOGENETICS ------------------------------ StrainHub: a phylogenetic tool to construct pathogen transmission networks Adriano de Bernardi Schneider, Colby T Ford, Reilly Hostager, John Williams, Michael Cioce (https://academic.oup.com/bioinformatics/article/36/3/945/5550625) STRUCTURAL BIOINFORMATICS ------------------------------ Protein Homeostasis Database: protein quality control in E.coli Reshmi Ramakrishnan, Bert Houben, ukasz Kreft, Alexander Botzki, Joost Schymkowitz (https://academic.oup.com/bioinformatics/article/36/3/948/5544931) LightDock goes information-driven Jorge Roel-Touris, Alexandre M J J Bonvin, Brian Jiménez-García (https://academic.oup.com/bioinformatics/article/36/3/950/5550626) Knot_pull'python package for biopolymer smoothing and knot detection Aleksandra I Jarmolinska, Anna Gambin, Joanna I Sulkowska (https://academic.oup.com/bioinformatics/article/36/3/953/5550333) MEPSAnd: minimum energy path surface analysis over n-dimensional surfaces Iñigo Marcos-Alcalde, Eduardo López-Viñas, Paulino Gómez-Puertas (https://academic.oup.com/bioinformatics/article/36/3/956/5550624) CRDS: Consensus Reverse Docking System for target fishing Aeri Lee, Dongsup Kim (https://academic.oup.com/bioinformatics/article/36/3/959/5552149) pCRM1exportome: database of predicted CRM1-dependent Nuclear Export Signal (NES) motifs in cancer-related genes Yoonji Lee, Jordan M Baumhardt, Jimin Pei, Yuh Min Chook, Nick V Grishin (https://academic.oup.com/bioinformatics/article/36/3/961/5553090) GENE EXPRESSION ------------------------------ BBKNN: fast batch alignment of single cell transcriptomes Krzysztof Pola"ski, Matthew D Young, Zhichao Miao, Kerstin B Meyer, Sarah A Teichmann (https://academic.oup.com/bioinformatics/article/36/3/964/5545955) baerhunter: an R package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data A Ozuna, D Liberto, R M Joyce, K B Arnvig, I Nobeli (https://academic.oup.com/bioinformatics/article/36/3/966/5550627) NACHO: an R package for quality control of NanoString nCounter data Mickaël Canouil, Gerard A Bouland, Amélie Bonnefond, Philippe Froguel, Leen M 't Hart (https://academic.oup.com/bioinformatics/article/36/3/970/5553566) GENETICS AND POPULATION ANALYSIS ------------------------------ CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes Vinicius da Silva, Marcel Ramos, Martien Groenen, Richard Crooijmans, Anna Johansson (https://academic.oup.com/bioinformatics/article/36/3/972/5544927) U-PASS: unified power analysis and forensics for qualitative traits in genetic association studies Zheng Gao, Jonathan Terhorst, Cristopher V Van Hout, Stilian Stoev (https://academic.oup.com/bioinformatics/article/36/3/974/5545977) SYSTEMS BIOLOGY ------------------------------ EasyModel: user-friendly tool for building and analysis of simple mathematical models in systems biology Jordi Bartolome, Rui Alves, Francesc Solsona, Ivan Teixido (https://academic.oup.com/bioinformatics/article/36/3/976/5554697) DATA AND TEXT MINING ------------------------------ AntiHIV-Pred: web-resource for in silico prediction of anti-HIV/AIDS activity Leonid Stolbov, Dmitry Druzhilovskiy, Anastasia Rudik, Dmitry Filimonov, Vladimir Poroikov (https://academic.oup.com/bioinformatics/article/36/3/978/5550623) DATABASES AND ONTOLOGIES ------------------------------ KRAB ZNF explorer'the online tool for the exploration of the transcriptomic profiles of KRAB-ZNF factors in The Cancer Genome Atlas Rafał Cylwa, Kornel Kiełczewski, Marta Machnik, Urszula Oleksiewicz, Przemysław Biecek (https://academic.oup.com/bioinformatics/article/36/3/980/5544925) COMBAT-TB-NeoDB: fostering tuberculosis research through integrative analysis using graph database technologies Thoba Lose, Peter van Heusden, Alan Christoffels (https://academic.oup.com/bioinformatics/article/36/3/982/5554700) 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_933242651.1581364055606 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 36 Issue 3
 
1 February 2020
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
A powerful and flexible weighted distance-based method incorporating interactions between DNA methylation and environmental factors on health outcomes  
 
Ya Wang; Min Qian; Deliang Tang ; Julie Herbstman; Frederica Perera ...
 
 
pWGBSSimla: a profile-based whole-genome bisulfite sequencing data simulator incorporating methylation QTLs, allele-specific methylations and differentially methylated regions  
 
Ren-Hua Chung; Chen-Yu Kang
 
 
Accurate loop calling for 3D genomic data with cLoops 
 
Yaqiang Cao; Zhaoxiong Chen; Xingwei Chen ; Daosheng Ai; Guoyu Chen ...
 
 
Partition: a surjective mapping approach for dimensionality reduction 
 
Joshua Millstein; Francesca Battaglin; Malcolm Barrett ; Shu Cao; Wu Zhang ...
 
 
Fast and accurate correction of optical mapping data via spaced seeds border= 
 
Leena Salmela ; Kingshuk Mukherjee; Simon J Puglisi; Martin D Muggli; Christina Boucher
 
 
Regulatory annotation of genomic intervals based on tissue-specific expression QTLs 
 
Tianlei Xu; Peng Jin; Zhaohui S Qin
 
 
Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API 
 
Thomas Desvignes; Phillipe Loher; Karen Eilbeck ; Jeffery Ma; Gianvito Urgese ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins 
 
Yanju Zhang; Sha Yu; Ruopeng Xie ; Jiahui Li; André Leier ...
 
 
neoepiscope improves neoepitope prediction with multivariant phasing 
 
Mary A Wood; Austin Nguyen; Adam J Struck ; Kyle Ellrott; Abhinav Nellore ...
 
 
Improved representation of sequence bloom trees 
 
Robert S Harris; Paul Medvedev
 
 
Accurate estimation of microbial sequence diversity with Distanced 
 
Timothy J Hackmann
 
 
ChaperISM: improved chaperone binding prediction using position-independent scoring matrices 
 
M B B Gutierres; C B C Bonorino; M M Rigo
 
 
 
PHYLOGENETICS
 
 
 
Accurate and efficient cell lineage tree inference from noisy single cell data: the maximum likelihood perfect phylogeny approach  
 
Yufeng Wu
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Integrating ab initio and template-based algorithms for protein'protein complex structure prediction 
 
Sweta Vangaveti; Thom Vreven; Yang Zhang ; Zhiping Weng
 
 
Learning from the ligand: using ligand-based features to improve binding affinity prediction 
 
Fergus Boyles; Charlotte M Deane; Garrett M Morris
 
 
Automatic local resolution-based sharpening of cryo-EM maps border= 
 
Erney Ramírez-Aportela ; Jose Luis Vilas; Alisa Glukhova; Roberto Melero; Pablo Conesa ...
 
 
 
GENE EXPRESSION
 
 
 
ECHO: an application for detection and analysis of oscillators identifies metabolic regulation on genome-wide circadian output  
 
Hannah De los Santos; Emily J Collins; Catherine Mann ; April W Sagan; Meaghan S Jankowski ...
 
 
Using multiple measurements of tissue to estimate subject- and cell-type-specific gene expression border= 
 
Jiebiao Wang ; Bernie Devlin; Kathryn Roeder
 
 
scHinter: imputing dropout events for single-cell RNA-seq data with limited sample size 
 
Pengchao Ye; Wenbin Ye; Congting Ye ; Shuchao Li; Lishan Ye ...
 
 
NExUS: Bayesian simultaneous network estimation across unequal sample sizes 
 
Priyam Das; Christine B Peterson; Kim-Anh Do ; Rehan Akbani; Veerabhadran Baladandayuthapani
 
 
Alternating EM algorithm for a bilinear model in isoform quantification from RNA-seq data border= 
 
Wenjiang Deng ; Tian Mou; Krishna R Kalari; Nifang Niu; Liewei Wang ...
 
 
DeepCOP: deep learning-based approach to predict gene regulating effects of small molecules 
 
Godwin Woo; Michael Fernandez; Michael Hsing ; Nathan A Lack; Ayse Derya Cavga ...
 
 
Tissue-specific deconvolution of immune cell composition by integrating bulk and single-cell transcriptomes 
 
Ziyi Chen; Chengyang Ji; Qin Shen ; Wei Liu; F Xiao-Feng Qin ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data 
 
J Víctor Moreno-Mayar; Thorfinn Sand Korneliussen; Jyoti Dalal ; Gabriel Renaud; Anders Albrechtsen ...
 
 
A latent unknown clustering integrating multi-omics data (LUCID) with phenotypic traits 
 
Cheng Peng; Jun Wang; Isaac Asante ; Stan Louie; Ran Jin ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
Graph convolution for predicting associations between miRNA and drug resistance 
 
Yu-an Huang; Pengwei Hu; Keith C C Chan ; Zhu-Hong You
 
 
Machine learning empowers phosphoproteome prediction in cancers 
 
Hongyang Li; Yuanfang Guan
 
 
Gene relevance based on multiple evidences in complex networks border= 
 
Noemi Di Nanni ; Matteo Gnocchi; Marco Moscatelli; Luciano Milanesi; Ettore Mosca
 
 
MEXCOwalk: mutual exclusion and coverage based random walk to identify cancer modules 
 
Rafsan Ahmed; Ilyes Baali; Cesim Erten ; Evis Hoxha; Hilal Kazan
 
 
A Gaussian process-based definition reveals new and bona fide genetic interactions compared to a multiplicative model in the Gram-negative Escherichia coli 
 
Ashwani Kumar; Ali Hosseinnia; Alla Gagarinova ; Sadhna Phanse; Sunyoung Kim ...
 
 
 
DATA AND TEXT MINING
 
 
 
Genome-phenome explorer (GePhEx): a tool for the visualization and interpretation of phenotypic relationships supported by genetic evidence  
 
Xavier Farré; Nino Spataro; Frederic Haziza; Jordi Rambla; Arcadi Navarro
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
PIRD: Pan Immune Repertoire Database 
 
Wei Zhang; Longlong Wang; Ke Liu ; Xiaofeng Wei; Kai Yang ...
 
 
MeLAD: an integrated resource for metalloenzyme-ligand associations 
 
Gen Li; Yu Su; Yu-Hang Yan ; Jia-Yi Peng; Qing-Qing Dai ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Semi-blind sparse affine spectral unmixing of autofluorescence-contaminated micrographs 
 
Blair J Rossetti; Steven A Wilbert; Jessica L Mark Welch ; Gary G Borisy; James G Nagy
 
 
 
APPLICATIONS NOTE
 
 
 
 
GENOME ANALYSIS
 
 
 
PyRanges: efficient comparison of genomic intervals in Python 
 
Endre Bakken Stovner; Pål Sætrom
 
 
MultiGuideScan: a multi-processing tool for designing CRISPR guide RNA libraries 
 
Tao Li; Shaokai Wang; Feng Luo ; Fang-Xiang Wu; Jianxin Wang
 
 
MsPAC: a tool for haplotype-phased structural variant detection 
 
Oscar L Rodriguez; Anna Ritz; Andrew J Sharp ; Ali Bashir
 
 
CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies border= 
 
Hrant Hovhannisyan ; Ahmed Hafez; Carlos Llorens; Toni Gabaldón
 
 
G3viz: an R package to interactively visualize genetic mutation data using a lollipop-diagram 
 
Xin Guo; Bo Zhang; Wenqi Zeng ; Shuting Zhao; Dongliang Ge
 
 
RICOPILI: Rapid Imputation for COnsortias PIpeLIne border=  
 
Max Lam; Swapnil Awasthi; Hunna J Watson ; Jackie Goldstein; Georgia Panagiotaropoulou ...
 
 
Tersect: a set theoretical utility for exploring sequence variant data 
 
Tomasz J Kurowski; Fady Mohareb
 
 
miComplete: weighted quality evaluation of assembled microbial genomes border= 
 
Eric Hugoson ; Wai Tin Lam; Lionel Guy
 
 
 
SEQUENCE ANALYSIS
 
 
 
HiLight-PTM: an online application to aid matching peptide pairs with isotopically labelled PTMs border= 
 
Harry J Whitwell ; Peter DiMaggio, Jr
 
 
CROSSalive: a web server for predicting the in vivo structure of RNA molecules border= 
 
Riccardo Delli Ponti; Alexandros Armaos ; Andrea Vandelli; Gian Gaetano Tartaglia
 
 
DDAP: docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases 
 
Tingyang Li; Ashootosh Tripathi; Fengan Yu ; David H Sherman; Arvind Rao
 
 
 
PHYLOGENETICS
 
 
 
StrainHub: a phylogenetic tool to construct pathogen transmission networks 
 
Adriano de Bernardi Schneider; Colby T Ford; Reilly Hostager ; John Williams; Michael Cioce ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Protein Homeostasis Database: protein quality control in E.coli  border= 
 
Reshmi Ramakrishnan; Bert Houben ; ukasz Kreft; Alexander Botzki; Joost Schymkowitz ...
 
 
LightDock goes information-driven border=  
 
Jorge Roel-Touris; Alexandre M J J Bonvin; Brian Jiménez-García
 
 
Knot_pull'python package for biopolymer smoothing and knot detection border= 
 
Aleksandra I Jarmolinska ; Anna Gambin; Joanna I Sulkowska
 
 
MEPSAnd: minimum energy path surface analysis over n-dimensional surfaces 
 
Iñigo Marcos-Alcalde; Eduardo López-Viñas; Paulino Gómez-Puertas
 
 
CRDS: Consensus Reverse Docking System for target fishing 
 
Aeri Lee; Dongsup Kim
 
 
pCRM1exportome: database of predicted CRM1-dependent Nuclear Export Signal (NES) motifs in cancer-related genes 
 
Yoonji Lee; Jordan M Baumhardt; Jimin Pei ; Yuh Min Chook; Nick V Grishin
 
 
 
GENE EXPRESSION
 
 
 
BBKNN: fast batch alignment of single cell transcriptomes border= 
 
Krzysztof Pola"ski; Matthew D Young; Zhichao Miao; Kerstin B Meyer; Sarah A Teichmann ...
 
 
baerhunter: an R package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data 
 
A Ozuna; D Liberto; R M Joyce ; K B Arnvig; I Nobeli
 
 
NACHO: an R package for quality control of NanoString nCounter data border= 
 
Mickaël Canouil ; Gerard A Bouland; Amélie Bonnefond; Philippe Froguel; Leen M 't Hart ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes border= 
 
Vinicius da Silva ; Marcel Ramos; Martien Groenen; Richard Crooijmans; Anna Johansson ...
 
 
U-PASS: unified power analysis and forensics for qualitative traits in genetic association studies 
 
Zheng Gao; Jonathan Terhorst; Cristopher V Van Hout ; Stilian Stoev
 
 
 
SYSTEMS BIOLOGY
 
 
 
EasyModel: user-friendly tool for building and analysis of simple mathematical models in systems biology 
 
Jordi Bartolome; Rui Alves; Francesc Solsona ; Ivan Teixido
 
 
 
DATA AND TEXT MINING
 
 
 
AntiHIV-Pred: web-resource for in silico prediction of anti-HIV/AIDS activity 
 
Leonid Stolbov; Dmitry Druzhilovskiy; Anastasia Rudik ; Dmitry Filimonov; Vladimir Poroikov ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
KRAB ZNF explorer'the online tool for the exploration of the transcriptomic profiles of KRAB-ZNF factors in The Cancer Genome Atlas  
 
Rafał Cylwa; Kornel Kiełczewski; Marta Machnik ; Urszula Oleksiewicz; Przemysław Biecek
 
 
COMBAT-TB-NeoDB: fostering tuberculosis research through integrative analysis using graph database technologies border= 
 
Thoba Lose ; Peter van Heusden; Alan Christoffels
 
 
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