Subject: Briefings in Bioinformatics Table of Contents for July 2019
 

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Oxford Academic

*** {Briefings in Bioinformatics} ***
Volume 20, Issue 4, 19 July 2019

Read this issue (https://academic.oup.com/bib/issue/20/4)

------------------------------
What research is making an impact in bioinformatics?
Explore our collection of highly cited articles from Briefings in Bioinformatics. These articles are freely available until the end of 2019. Read the collection
------------------------------

============================= Paper 
============================Microbial genome analysis: the COG approach
Michael Y Galperin, David M Kristensen, Kira S Makarova, Yuri I Wolf, Eugene V Koonin
(https://academic.oup.com/bib/article/20/4/1063/4158183)

MicroScope---an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data
Claudine Médigue, Alexandra Calteau, Stéphane Cruveiller, Mathieu Gachet, Guillaume Gautreau
(https://academic.oup.com/bib/article/20/4/1071/4157326)

The BioCyc collection of microbial genomes and metabolic pathways
Peter D Karp, Richard Billington, Ron Caspi, Carol A Fulcher, Mario Latendresse
(https://academic.oup.com/bib/article/20/4/1085/4084231)

PATRIC as a unique resource for studying antimicrobial resistance
Dionysios A Antonopoulos, Rida Assaf, Ramy Karam Aziz, Thomas Brettin, Christopher Bun
(https://academic.oup.com/bib/article/20/4/1094/4056412)

Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters
Kai Blin, Hyun Uk Kim, Marnix H Medema, Tilmann Weber
(https://academic.oup.com/bib/article/20/4/1103/4590131)

Recent development of Ori-Finder system and DoriC database for microbial replication origins
Hao Luo, Chun-Lan Quan, Chong Peng, Feng Gao
(https://academic.oup.com/bib/article/20/4/1114/4796864)

A review of methods and databases for metagenomic classification and assembly
Florian P Breitwieser, Jennifer Lu, Steven L Salzberg
(https://academic.oup.com/bib/article/20/4/1125/4210288)

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes
Nathan D Olson, Todd J Treangen, Christopher M Hill, Victoria Cepeda-Espinoza, Jay Ghurye
(https://academic.oup.com/bib/article/20/4/1140/4075034)

MG-RAST version 4---lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis
Folker Meyer, Saurabh Bagchi, Somali Chaterji, Wolfgang Gerlach, Ananth Grama
(https://academic.oup.com/bib/article/20/4/1151/4237462)

MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization
Kazutaka Katoh, John Rozewicki, Kazunori D Yamada
(https://academic.oup.com/bib/article/20/4/1160/4106928)

Towards dynamic genome-scale models
David Gilbert, Monika Heiner, Yasoda Jayaweera, Christian Rohr
(https://academic.oup.com/bib/article/20/4/1167/4524047)

Computational tools for plant small RNA detection and categorization
Lionel Morgado, Frank Johannes
(https://academic.oup.com/bib/article/20/4/1181/4558649)

Systematic review of computational methods for identifying miRNA-mediated RNA-RNA crosstalk
Yongsheng Li, Xiyun Jin, Zishan Wang, Lili Li, Hong Chen
(https://academic.oup.com/bib/article/20/4/1193/4565515)

Evaluation and comparison of methods for recapitulation of 3D spatial chromatin structures
Jincheol Park, Shili Lin
(https://academic.oup.com/bib/article/20/4/1205/4582342)

A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects
Gerhard Mayer, Christian Quast, Janine Felden, Matthias Lange, Manuel Prinz
(https://academic.oup.com/bib/article/20/4/1215/4582343)

A survey and evaluations of histogram-based statistics in alignment-free sequence comparison
Brian B Luczak, Benjamin T James, Hani Z Girgis
(https://academic.oup.com/bib/article/20/4/1222/4696316)

Conceptual and computational framework for logical modelling of biological networks deregulated in diseases
Arnau Montagud, Pauline Traynard, Loredana Martignetti, Eric Bonnet, Emmanuel Barillot
(https://academic.oup.com/bib/article/20/4/1238/4716963)

Comprehensive review and empirical analysis of hallmarks of DNA-, RNA- and protein-binding residues in protein chains
Jian Zhang, Zhiqiang Ma, Lukasz Kurgan
(https://academic.oup.com/bib/article/20/4/1250/4748786)

Multi-omics integration---a comparison of unsupervised clustering methodologies
Giulia Tini, Luca Marchetti, Corrado Priami, Marie-Pier Scott-Boyer
(https://academic.oup.com/bib/article/20/4/1269/4758623)

BioSeq-Analysis: a platform for DNA, RNA and protein sequence analysis based on machine learning approaches
Bin Liu
(https://academic.oup.com/bib/article/20/4/1280/4763667)

Link synthetic lethality to drug sensitivity of cancer cells
Ruiping Wang, Yue Han, Zhangxiang Zhao, Fan Yang, Tingting Chen
(https://academic.oup.com/bib/article/20/4/1295/4781362)

Drug knowledge bases and their applications in biomedical informatics research
Yongjun Zhu, Olivier Elemento, Jyotishman Pathak, Fei Wang
(https://academic.oup.com/bib/article/20/4/1308/4785946)

SEGreg: a database for human specifically expressed genes and their regulations in cancer and normal tissue
Qin Tang, Qiong Zhang, Yao Lv, Ya-Ru Miao, An-Yuan Guo
(https://academic.oup.com/bib/article/20/4/1322/4786617)

Characteristics and evolution of the ecosystem of software tools supporting research in molecular biology
Florencio Pazos, Monica Chagoyen
(https://academic.oup.com/bib/article/20/4/1329/4812639)

Computational prediction of drug--target interactions using chemogenomic approaches: an empirical survey
Ali Ezzat, Min Wu, Xiao-Li Li, Chee-Keong Kwoh
(https://academic.oup.com/bib/article/20/4/1337/4824712)

Upstream analysis of alternative splicing: a review of computational approaches to predict context-dependent splicing factors
Fernando Carazo, Juan P Romero, Angel Rubio
(https://academic.oup.com/bib/article/20/4/1358/4829658)

Modeling biological problems in computer science: a case study in genome assembly
Paul Medvedev
(https://academic.oup.com/bib/article/20/4/1376/4830907)

How to design a single-cell RNA-sequencing experiment: pitfalls, challenges and perspectives
Alessandra Dal Molin, Barbara Di Camillo
(https://academic.oup.com/bib/article/20/4/1384/4831233)

Phylogenetic profiling, an untapped resource for the prediction of secreted proteins and its complementation with sequence-based classifiers in bacterial type III, IV and VI secretion systems
Andrés Zalguizuri, Gustavo Caetano-Anollés, Viviana Claudia Lepek
(https://academic.oup.com/bib/article/20/4/1395/4831237)

Inferring and analyzing module-specific lncRNA--mRNA causal regulatory networks in human cancer
Junpeng Zhang, Thuc Duy Le, Lin Liu, Jiuyong Li
(https://academic.oup.com/bib/article/20/4/1403/4833470)

Microarray is an efficient tool for circRNA profiling
Shasha Li, Shuaishuai Teng, Junquan Xu, Guannan Su, Yu Zhang
(https://academic.oup.com/bib/article/20/4/1420/4837254)

Artificial intelligence in drug combination therapy
Igor F Tsigelny
(https://academic.oup.com/bib/article/20/4/1434/4846893)

It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data
Juan Xie, Anjun Ma, Anne Fennell, Qin Ma, Jing Zhao
(https://academic.oup.com/bib/article/20/4/1449/4911545)

Open-source chemogenomic data-driven algorithms for predicting drug--target interactions
Ming Hao, Stephen H Bryant, Yanli Wang
(https://academic.oup.com/bib/article/20/4/1465/4840612)

============================= Review Article 
============================Where to search top-K biomedical ontologies?
Daniela Oliveira, Anila Sahar Butt, Armin Haller, Dietrich Rebholz-Schuhmann, Ratnesh Sahay
(https://academic.oup.com/bib/article/20/4/1477/4944514)

Comprehensive analysis of Helicobacter pylori infection-associated diseases based on miRNA-mRNA interaction network
Jue Yang, Hui Song, Kun Cao, Jialei Song, Jianjiang Zhou
(https://academic.oup.com/bib/article/20/4/1492/4944515)

Distinct telomere length and molecular signatures in seminoma and non-seminoma of testicular germ cell tumor
Hua Sun, Pora Kim, Peilin Jia, Ae Kyung Park, Han Liang
(https://academic.oup.com/bib/article/20/4/1502/4944720)

Interactive and coordinated visualization approaches for biological data analysis
António Cruz, Joel P Arrais, Penousal Machado
(https://academic.oup.com/bib/article/20/4/1513/4953976)

A survey and evaluation of Web-based tools/databases for variant analysis of TCGA data
Zhuo Zhang, Hao Li, Shuai Jiang, Ruijiang Li, Wanying Li
(https://academic.oup.com/bib/article/20/4/1524/4956394)

Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions
Damla Senol Cali, Jeremie S Kim, Saugata Ghose, Can Alkan, Onur Mutlu
(https://academic.oup.com/bib/article/20/4/1542/4958758)

============================= Software Review 
============================PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes
David Arndt, Ana Marcu, Yongjie Liang, David S Wishart
(https://academic.oup.com/bib/article/20/4/1560/4222653)

DOOR: a prokaryotic operon database for genome analyses and functional inference
Huansheng Cao, Qin Ma, Xin Chen, Ying Xu
(https://academic.oup.com/bib/article/20/4/1568/4055922)

Visualizing and comparing circular genomes using the CGView family of tools
Paul Stothard, Jason R Grant, Gary Van Domselaar
(https://academic.oup.com/bib/article/20/4/1576/4037458)

Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data
Shun H Yip, Pak Chung Sham, Junwen Wang
(https://academic.oup.com/bib/article/20/4/1583/4898116)

============================= Case Study 
============================Structural and functional analyses of microbial metabolic networks reveal novel insights into genome-scale metabolic fluxes
Gaoyang Li, Huansheng Cao, Ying Xu
(https://academic.oup.com/bib/article/20/4/1590/4955282)

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                                    <td style="border-collapse: collapse; font-family: " 'source="" sans="" pro'",="" helvetica,="" arial,="" sans-serif;="" font-size:="" 17px;="" line-height:="" 19px;="" color:="" #2a2a2a;="" font-weight:="" bold;"="" align="left"> What research is making an impact in bioinformatics? </td>
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                                    <a href="http://click.skem1.com/click/bbu3-1f11ty-l1eo1m-66q6ox38/">Read the collection</a> </td>
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                                            <td data-issue-plaintext-issue="" data-issue-plaintext-issuetitle="" data-issue-plaintext-dates="07 October 2019 - 08 October 2019" data-issue-plaintext-link="https://academic.oup.com/bib/issue/20/4"><table style="border-collapse: collapse;mso-table-lspace: 0px;mso-table-rspace: 0px" cellspacing="0" cellpadding="0" align="left" border="0" width="290">
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