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ORCIDBriefings in Bioinformatics, Volume 22
Volume 22, Number 1, January 2021
- Simona E. Rombo, Domenico Ursino:
Integrative bioinformatics and omics data source interoperability in the next-generation sequencing era - Editorial. 1-2 - Juan José Galano-Frutos
, Helena García-Cebollada, Javier Sancho:
Molecular dynamics simulations for genetic interpretation in protein coding regions: where we are, where to go and when. 3-19 - Mattia Forcato, Oriana Romano, Silvio Bicciato:
Computational methods for the integrative analysis of single-cell data. 20-29 - Anna Bernasconi, Arif Canakoglu, Marco Masseroli, Stefano Ceri:
The road towards data integration in human genomics: players, steps and interactions. 30-44 - Oscar Pastor, Ana Palacio León, José Fabián Reyes Román, Alberto García Simón, Juan Carlos Casamayor Ródenas:
Using conceptual modeling to improve genome data management. 45-54 - Alba Gutiérrez-Sacristán, Carlos De Niz, Cartik Kothari, Sek Won Kong, Kenneth D. Mandl, Paul Avillach:
GenoPheno: cataloging large-scale phenotypic and next-generation sequencing data within human datasets. 55-65 - Minsik Oh, Sungjoon Park, Sun Kim, Heejoon Chae:
Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulations. 66-76 - Susana Vinga:
Structured sparsity regularization for analyzing high-dimensional omics data. 77-87 - Matteo Comin, Barbara Di Camillo, Cinzia Pizzi, Fabio Vandin:
Comparison of microbiome samples: methods and computational challenges. 88-95 - Sergey Knyazev, Lauren Hughes, Pavel Skums, Alexander Zelikovsky:
Epidemiological data analysis of viral quasispecies in the next-generation sequencing era. 96-108 - Peter D. Karp, Peter E. Midford, Richard Billington, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Wai Kit Ong, Pallavi Subhraveti, Ron Caspi, Carol A. Fulcher, Ingrid M. Keseler, Suzanne M. Paley:
Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology. 109-126 - Yun Zhang, Jonavelle Cuerdo, Marc K. Halushka, Matthew N. McCall:
The effect of tissue composition on gene co-expression. 127-139 - Joël Simoneau, Simon Dumontier, Ryan Gosselin, Michelle S. Scott:
Current RNA-seq methodology reporting limits reproducibility. 140-145 - Mariana Neves, Jurica Seva:
An extensive review of tools for manual annotation of documents. 146-163 - Duc Anh Nguyen, Canh Hao Nguyen, Hiroshi Mamitsuka:
A survey on adverse drug reaction studies: data, tasks and machine learning methods. 164-177 - Richa Bharti, Dominik G. Grimm:
Current challenges and best-practice protocols for microbiome analysis. 178-193 - Qiang Shi, Weiya Chen, Siqi Huang, Yan Wang, Zhidong Xue:
Deep learning for mining protein data. 194-218 - Beatriz T. Magalhães, Anália Lourenço, Nuno F. Azevedo:
Computational resources and strategies to assess single-molecule dynamics of the translation process in S. cerevisiae. 219-231 - Jinyu Chen, Louxin Zhang:
A survey and systematic assessment of computational methods for drug response prediction. 232-246 - Maryam Bagherian, Elyas Sabeti, Kai Wang, Maureen A. Sartor, Zaneta Nikolovska-Coleska, Kayvan Najarian:
Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. 247-269 - Ammu Prasanna Kumar, Chandra S. Verma, Suryani Lukman:
Structural dynamics and allostery of Rab proteins: strategies for drug discovery and design. 270-287 - Marieke Vromman, Jo Vandesompele, Pieter-Jan Volders:
Closing the circle: current state and perspectives of circular RNA databases. 288-297 - Shaofeng Lin, Chenwei Wang, Jiaqi Zhou, Ying Shi, Chen Ruan, Yiran Tu, Lan Yao, Di Peng, Yu Xue:
EPSD: a well-annotated data resource of protein phosphorylation sites in eukaryotes. 298-307 - Aidan R. O'Brien, Gaetan Burgio, Denis C. Bauer:
Domain-specific introduction to machine learning terminology, pitfalls and opportunities in CRISPR-based gene editing. 308-314 - Lan Huang, Dan Shao, Yan Wang, Xueteng Cui, Yufei Li, Qian Chen, Juan Cui:
Human body-fluid proteome: quantitative profiling and computational prediction. 315-333 - Han Fu, Kellie J. Archer:
High-dimensional variable selection for ordinal outcomes with error control. 334-345 - Betül Güvenç Paltun, Hiroshi Mamitsuka, Samuel Kaski:
Improving drug response prediction by integrating multiple data sources: matrix factorization, kernel and network-based approaches. 346-359 - Delora Baptista, Pedro G. Ferreira, Miguel Rocha:
Deep learning for drug response prediction in cancer. 360-379 - Saidi Wang, Amlan Talukder, Mingyu Cha, Xiaoman Li, Haiyan Hu:
Computational annotation of miRNA transcription start sites. 380-392 - Md. Rezaul Karim, Oya Beyan, Achille Zappa, Ivan G. Costa, Dietrich Rebholz-Schuhmann, Michael Cochez, Stefan Decker:
Deep learning-based clustering approaches for bioinformatics. 393-415 - Meichen Dong, Aatish Thennavan, Eugene Urrutia, Yun Li, Charles M. Perou, Fei Zou, Yuchao Jiang:
SCDC: bulk gene expression deconvolution by multiple single-cell RNA sequencing references. 416-427 - Ran Su, Huichen Wu, Xinyi Liu, Leyi Wei:
Predicting drug-induced hepatotoxicity based on biological feature maps and diverse classification strategies. 428-437 - Fei Liu, Wujie Sun, Monika Heiner, David R. Gilbert:
Hybrid modelling of biological systems using fuzzy continuous Petri nets. 438-450 - Yanyi Chu, Aman Chandra Kaushik, Xiangeng Wang, Wei Wang, Yufang Zhang, Xiaoqi Shan, Dennis Russell Salahub, Yi Xiong, Dong-Qing Wei:
DTI-CDF: a cascade deep forest model towards the prediction of drug-target interactions based on hybrid features. 451-462 - Qi Liu, Changjun Ding, Xiaoqiang Lang, Ganggang Guo, Jiafei Chen, Xiaohua Su:
Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing. 463-473 - Jie Dong, Min-Feng Zhu, Yong-Huan Yun, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao:
BioMedR: an R/CRAN package for integrated data analysis pipeline in biomedical study. 474-484 - Xing Chen, Lian-Gang Sun, Yan Zhao:
NCMCMDA: miRNA-disease association prediction through neighborhood constraint matrix completion. 485-496 - Chao Shen, Ye Hu, Zhe Wang, Xujun Zhang, Haiyang Zhong, Gaoang Wang, Xiaojun Yao, Lei Xu, Dong-Sheng Cao, Tingjun Hou:
Can machine learning consistently improve the scoring power of classical scoring functions? Insights into the role of machine learning in scoring functions. 497-514 - Le Zhang, Zichun Dai, Jun Yu, Ming Xiao:
CpG-island-based annotation and analysis of human housekeeping genes. 515-525 - Zhao-Yue Zhang, Yu-He Yang, Hui Ding, Dong Wang, Wei Chen, Hao Lin:
Design powerful predictor for mRNA subcellular location prediction in Homo sapiens. 526-535 - Jiangpeng Wu, Yifan Yang, Long Cheng, Jing Wu, Lili Xi, Ying Ma, Pengyi Zhang, Xiaoying Xu, Dekui Zhang, Shuyan Li:
GCdiscrimination: identification of gastric cancer based on a milliliter of blood. 536-544 - Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity W. Law, Sean R. Davis, Vincent J. Carey, Martin Morgan, Ralf Zimmer, Levi Waldron:
Toward a gold standard for benchmarking gene set enrichment analysis. 545-556 - Mo Zhu, Kai Kang, Kang Ning:
Meta-Prism: Ultra-fast and highly accurate microbial community structure search utilizing dual indexing and parallel computation. 557-567 - Nansu Zong, Rachael Sze Nga Wong, Yue Yu, Andrew Wen, Ming Huang, Ning Li:
Drug-target prediction utilizing heterogeneous bio-linked network embeddings. 568-580 - Xueyan Liu, Yong Xu, Ran Wang, Sheng Liu, Jun Wang, Yonglun Luo, Kwong-Sak Leung, Lixin Cheng:
A network-based algorithm for the identification of moonlighting noncoding RNAs and its application in sepsis. 581-588 - Jie Wu, Li Zhang, Qian Song, Lei Yu, Shuyuan Wang, Bo Zhang, Weida Wang, Peng Xia, Xiaowen Chen, Yun Xiao, Chaohan Xu:
Systematical identification of cell-specificity of CTCF-gene binding based on epigenetic modifications. 589-600 - Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Piero Fariselli:
On the critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation. 601-603 - Juan José Galano-Frutos, Helena García-Cebollada, Javier Sancho:
Erratum to: Molecular dynamics simulations for genetic interpretation in protein coding regions: where we are, where to go and when. 604 - Jing-Fang Yang, Fan Wang, Yuzong Chen, Ge-Fei Hao, Guangfu Yang:
Erratum to: LARMD: integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor. 605 - Maryam Bagherian, Elyas Sabeti, Kai Wang, Maureen A. Sartor, Zaneta Nikolovska-Coleska, Kayvan Najarian:
Erratum to: Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. 606 - Minsik Oh, Sungjoon Park, Sun Kim, Heejoon Chae:
Erratum to: Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulations. 607 - David Hoksza, Piotr Gawron, Marek Ostaszewski, Jan Hasenauer, Reinhard Schneider:
Closing the gap between formats for storing layout information in systems biology. 608 - Saidi Wang, Amlan Talukder, Mingyu Cha, Xiaoman Li, Haiyan Hu:
Corrigendum to: Computational annotation of miRNA transcription start sites. 609 - Maria Victoria Schneider, Rafael C. Jiménez:
Corrigendum to: Bioinformatics: scalability, capabilities and training in the data-driven era. 610 - Ziye Wang, Ying Wang, Jed A. Fuhrman, Fengzhu Sun, Shanfeng Zhu:
Corrigendum to: Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences. 611
Volume 22, Number 2, March 2021
- Mario Cannataro, Andrew Harrison:
Bioinformatics helping to mitigate the impact of COVID-19 - Editorial. 613-615 - Matteo Chiara, Anna Maria D'Erchia, Carmela Gissi, Caterina Manzari, Antonio Parisi, Nicoletta Resta, Federico Zambelli, Ernesto Picardi, Giulio Pavesi, David Stephen Horner, Graziano Pesole:
Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. 616-630 - Tao Hu, Juan Li, Hong Zhou, Cixiu Li, Edward C. Holmes, Weifeng Shi:
Bioinformatics resources for SARS-CoV-2 discovery and surveillance. 631-641 - Franziska Hufsky, Kevin Lamkiewicz, Alexandre Almeida, Abdel Aouacheria, Cecilia N. Arighi, Alex Bateman, Jan Baumbach, Niko Beerenwinkel, Christian Brandt, Marco Cacciabue, Sara Chuguransky, Oliver Drechsel, Robert D. Finn, Adrian Fritz, Stephan Fuchs, Georges Hattab, Anne-Christin Hauschild, Dominik Heider, Marie Hoffmann, Martin Hölzer, Stefan Hoops, Lars Kaderali, Ioanna Kalvari, Max von Kleist, Renó Kmiecinski, Denise Kühnert, Gorka Lasso, Pieter Libin, Markus List, Hannah F. Löchel, Maria Jesus Martin, Roman Martin, Julian O. Matschinske, Alice C. McHardy, Pedro Mendes, Jaina Mistry, Vincent Navratil, Eric P. Nawrocki, Áine Niamh O'toole, Nancy Ontiveros-Palacios, Anton I. Petrov, Guillermo Rangel-Pineros, Nicole Redaschi, Susanne Reimering, Knut Reinert, Alejandro Reyes, Lorna J. Richardson, David L. Robertson, Sepideh Sadegh, Joshua B. Singer, Kristof Theys, Chris Upton, Marius Welzel, Lowri Williams, Manja Marz:
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. 642-663 - Anna Bernasconi, Arif Canakoglu, Marco Masseroli, Pietro Pinoli, Stefano Ceri:
A review on viral data sources and search systems for perspective mitigation of COVID-19. 664-675 - Giuseppe Agapito, Chiara Pastrello, Igor Jurisica:
Comprehensive pathway enrichment analysis workflows: COVID-19 case study. 676-689 - Daniele Mercatelli, Andrew N. Holding, Federico M. Giorgi:
Web tools to fight pandemics: the COVID-19 experience. 690-700 - Francesca P. Caruso, Giovanni Scala, Luigi Cerulo, Michele Ceccarelli:
A review of COVID-19 biomarkers and drug targets: resources and tools. 701-713 - Md. Asif Ahsan, Yongjing Liu, Cong Feng, Yincong Zhou, Guangyuan Ma, Youhuang Bai, Ming Chen:
Bioinformatics resources facilitate understanding and harnessing clinical research of SARS-CoV-2. 714-725 - Serena Dotolo, Anna Marabotti, Angelo M. Facchiano, Roberto Tagliaferri:
A review on drug repurposing applicable to COVID-19. 726-741 - Vaishali P. Waman, Neeladri Sen, Mihaly Varadi, Antoine Daina, Shoshana J. Wodak, Vincent Zoete, Sameer Velankar, Christine A. Orengo:
The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies. 742-768 - Ali F. Alsulami, Sherine E. Thomas, Arian R. Jamasb, Christopher A. Beaudoin, Ismail Moghul, Bridget Bannerman, Liviu Copoiu, Sundeep Chaitanya Vedithi, Pedro Torres, Tom L. Blundell:
SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets. 769-780 - Lucy Lu Wang, Kyle Lo:
Text mining approaches for dealing with the rapidly expanding literature on COVID-19. 781-799 - Xu Zuo, Yong Chen, Lucila Ohno-Machado, Hua Xu:
How do we share data in COVID-19 research? A systematic review of COVID-19 datasets in PubMed Central Articles. 800-811 - Arianna Dagliati, Alberto Malovini, Valentina Tibollo, Riccardo Bellazzi:
Health informatics and EHR to support clinical research in the COVID-19 pandemic: an overview. 812-822 - Valeria Seidita, Francesco Lanza, Arianna Pipitone, Antonio Chella:
Robots as intelligent assistants to face COVID-19 pandemic. 823-831 - Xiaodi Yang, Xianyi Lian, Chen Fu, Stefan Wuchty, Shiping Yang, Ziding Zhang:
HVIDB: a comprehensive database for human-virus protein-protein interactions. 832-844 - Yibo Dong, Chang Li, Kami Kim, Liwang Cui, Xiaoming Liu:
Genome annotation of disease-causing microorganisms. 845-854 - Jayanta Kumar Das, Giuseppe Tradigo, Pierangelo Veltri, Pietro H. Guzzi, Swarup Roy:
Data science in unveiling COVID-19 pathogenesis and diagnosis: evolutionary origin to drug repurposing. 855-872 - Krishan Gupta, Sanjay Kumar Mohanty, Aayushi Mittal, Siddhant Kalra, Suvendu Kumar, Tripti Mishra, Jatin Ahuja, Debarka Sengupta, Gaurav Ahuja:
The Cellular basis of loss of smell in 2019-nCoV-infected individuals. 873-881 - Zhiwei Feng, Maozi Chen, Tianjian Liang, Mingzhe Shen, Hui Chen, Xiang-Qun Xie:
Virus-CKB: an integrated bioinformatics platform and analysis resource for COVID-19 research. 882-895 - Tong Shao, Wenfang Wang, Meiyu Duan, Jiahui Pan, Zhuoyuan Xin, Baoyue Liu, Fengfeng Zhou, Guoqing Wang:
Application of Bayesian phylogenetic inference modelling for evolutionary genetic analysis and dynamic changes in 2019-nCoV. 896-904 - Wenzhong Yang, Guangxu Jin:
Origin-independent analysis links SARS-CoV-2 local genomes with COVID-19 incidence and mortality. 905-913 - Ashmita Dey, Sagnik Sen, Ujjwal Maulik:
Unveiling COVID-19-associated organ-specific cell types and cell-specific pathway cascade. 914-923 - Shifu Chen, Chang-Shou He, Yingqiang Li, Zhicheng Li, Charles E. Melançon:
A computational toolset for rapid identification of SARS-CoV-2, other viruses and microorganisms from sequencing data. 924-935 - Anjali Dhall, Sumeet Patiyal, Neelam Sharma, Salman Sadullah Usmani, Gajendra P. S. Raghava:
Computer-aided prediction and design of IL-6 inducing peptides: IL-6 plays a crucial role in COVID-19. 936-945 - Zhiwei Feng, Maozi Chen, Ying Xue, Tianjian Liang, Hui Chen, Yuehan Zhou, Thomas D. Nolin, Randall B. Smith, Xiang-Qun Xie:
MCCS: a novel recognition pattern-based method for fast track discovery of anti-SARS-CoV-2 drugs. 946-962 - Senbiao Fang, Ruoqian Zheng, Chuqi Lei, Jianxin Wang, Ruiqing Zheng, Min Li:
Key residues influencing binding affinities of 2019-nCoV with ACE2 in different species. 963-975 - Zhiting Wei, Yuli Gao, Fangliangzi Meng, Xin Chen, Yukang Gong, Chenyu Zhu, Bin Ju, Chao Zhang, Zhongmin Liu, Qi Liu:
iDMer: an integrative and mechanism-driven response system for identifying compound interventions for sudden virus outbreak. 976-987 - Jinyu Cheng, Ji Zhang, Zhongdao Wu, Xiaoqiang Sun:
Inferring microenvironmental regulation of gene expression from single-cell RNA sequencing data using scMLnet with an application to COVID-19. 988-1005 - Yashpal Singh Malik, Mohd Ikram Ansari, Jobin Jose Kattoor, Rahul Kaushik, Shubhankar Sircar, Anbazhagan Subbaiyan, Ruchi Tiwari, Kuldeep Dhama, Souvik Ghosh, Shailly Tomar, Kam Y. J. Zhang:
Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2. 1006-1022 - Burak Berber, Osman Doluca:
A comprehensive drug repurposing study for COVID19 treatment: novel putative dihydroorotate dehydrogenase inhibitors show association to serotonin-dopamine receptors. 1023-1037 - Antonio J. Pérez-Pulido, Gualberto Asencio-Cortés, Ana M. Brokate-Llanos, Gloria Brea-Calvo, Rosario Rodríguez-Griñolo, Andrés Garzón, Manuel J. Muñoz:
Serial co-expression analysis of host factors from SARS-CoV viruses highly converges with former high-throughput screenings and proposes key regulators. 1038-1052 - Yanqing Yang, Zhengdan Zhu, Xiaoyu Wang, Xinben Zhang, Kaijie Mu, Yulong Shi, Cheng Peng, Zhijian Xu, Weiliang Zhu:
Ligand-based approach for predicting drug targets and for virtual screening against COVID-19. 1053-1064 - Sanket Desai, Sonal Rashmi, Aishwarya Rane, Bhasker Dharavath, Aniket Sawant, Amit Dutt:
An integrated approach to determine the abundance, mutation rate and phylogeny of the SARS-CoV-2 genome. 1065-1075 - Akanksha Rajput, Archit Kumar, Kirti Megha, Anamika Thakur, Manoj Kumar:
DrugRepV: a compendium of repurposed drugs and chemicals targeting epidemic and pandemic viruses. 1076-1084 - Yuxuan Pang, Zhuo Wang, Jhih-Hua Jhong, Tzong-Yi Lee:
Identifying anti-coronavirus peptides by incorporating different negative datasets and imbalanced learning strategies. 1085-1095 - Qingren Meng, Yanan Chu, Changjun Shao, Jing Chen, Jian Wang, Zhancheng Gao, Jun Yu, Yu Kang:
Roles of host small RNAs in the evolution and host tropism of coronaviruses. 1096-1105 - Indrajit Saha, Nimisha Ghosh, Ayan Pradhan, Nikhil Sharma, Debasree Maity, Kaushik Mitra:
Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. 1106-1121 - Fang-Fang Yan, Feng Gao:
Comparison of the binding characteristics of SARS-CoV and SARS-CoV-2 RBDs to ACE2 at different temperatures by MD simulations. 1122-1136 - Song Zhang, Kuerbannisha Amahong, Xiuna Sun, Xichen Lian, Jin Liu, Huaicheng Sun, Yan Lou, Feng Zhu, Yunqing Qiu:
The miRNA: a small but powerful RNA for COVID-19. 1137-1149 - Danyang Ji, Mario Juhas, Chi Man Tsang, Chun Kit Kwok, Yongshu Li, Yang Zhang:
Discovery of G-quadruplex-forming sequences in SARS-CoV-2. 1150-1160 - Rong Li, Ka Wu, Yu Li, Xiao Liang, Keng Po Lai, Jian Chen:
Integrative pharmacological mechanism of vitamin C combined with glycyrrhizic acid against COVID-19: findings of bioinformatics analyses. 1161-1174 - Zulkar Nain, Humayan Kabir Rana, Pietro Liò, Sheikh Mohammed Shariful Islam, Matthew A. Summers, Mohammad Ali Moni:
Pathogenetic profiling of COVID-19 and SARS-like viruses. 1175-1196 - Safaa M. Naeem, Mai S. Mabrouk, Samir Y. Marzouk, Mohamed A. Eldosoky:
A diagnostic genomic signal processing (GSP)-based system for automatic feature analysis and detection of COVID-19. 1197-1205 - Abdul Arif Khan, Zakir Khan:
Comparative host-pathogen protein-protein interaction analysis of recent coronavirus outbreaks and important host targets identification. 1206-1214 - Tao Xu, Jingu Wang, Bingjie Hu, Guosi Zhang, Wu Zhou, Meiqin Zheng, Bo Shen, Baochang Sun, Yanjun Zhang, Yin Chen, Jian Yu, Min Liang, Jingye Pan, Chengshui Chen, Haixiao Chen, Minghua Jiang, Liangde Xu, Jia Qu, Jiang-Fan Chen:
Identification of the RNase-binding site of SARS-CoV-2 RNA for anchor primer-PCR detection of viral loading in 306 COVID-19 patients. 1215-1224 - Yanqiang Han, Zhilong Wang, Jiahao Ren, Zhiyun Wei, Jin-Jin Li:
Potential inhibitors for the novel coronavirus (SARS-CoV-2). 1225-1231 - Ying Jing, Lixia Diao, Leng Han:
Adverse events associated with potential drugs for COVID-19: a case study from real-world data. 1232-1238 - Shaolei Teng, Adebiyi Sobitan, Raina Rhoades, Dongxiao Liu, Qiyi Tang:
Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. 1239-1253 - Tasnimul Alam Taz, Kawsar Ahmed, Bikash Kumar Paul, Md. Kawsar, Nargis Aktar, S. M. Hasan Mahmud, Mohammad Ali Moni:
Network-based identification genetic effect of SARS-CoV-2 infections to Idiopathic pulmonary fibrosis (IPF) patients. 1254-1266