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ORCIDBriefings in Bioinformatics, Volume 21
Volume 21, Number 1, January 2020
- Quan Zou
, Gang Lin, Xingpeng Jiang, Xiangrong Liu, Xiangxiang Zeng:
Sequence clustering in bioinformatics: an empirical study. 1-10
- Xiaoli Qiang, Chen Zhou, Xiucai Ye, Pufeng Du, Ran Su, Leyi Wei:
CPPred-FL: a sequence-based predictor for large-scale identification of cell-penetrating peptides by feature representation learning. 11-23 - Mark N. Read, Kieran Alden, Jon Timmis, Paul S. Andrews:
Strategies for calibrating models of biology. 24-35 - Sangsoo Lim, Sangseon Lee, Inuk Jung, SungMin Rhee, Sun Kim:
Comprehensive and critical evaluation of individualized pathway activity measurement tools on pan-cancer data. 36-46 - Xing Chen, Na-Na Guan, Ya-Zhou Sun, Jian-Qiang Li, Jia Qu:
MicroRNA-small molecule association identification: from experimental results to computational models. 47-61 - Martin Siebenhaller, Sune S. Nielsen, Fintan McGee, Irina Balaur, Charles Auffray, Alexander Mazein:
Human-like layout algorithms for signalling hypergraphs: outlining requirements. 62-72 - Liu Qin, Yanhong Liu, Menglong Li, Xuemei Pu, Yanzhi Guo:
The landscape of miRNA-related ceRNA networks for marking different renal cell carcinoma subtypes. 73-84 - Hong Wang, Xiaoyan Lu, Fukun Chen, Yu Ding, Hewei Zheng, Lianzong Wang, Guosi Zhang, Jiaxin Yang, Yu Bai, Jing Li, Jingqi Wu, Meng Zhou, Liangde Xu:
Landscape of SNPs-mediated lncRNA structural variations and their implication in human complex diseases. 85-95 - Jamie J. Alnasir, Hugh P. Shanahan:
The application of Hadoop in structural bioinformatics. 96-105 - Leyi Wei, Jie Hu, Fuyi Li, Jiangning Song, Ran Su, Quan Zou:
Comparative analysis and prediction of quorum-sensing peptides using feature representation learning and machine learning algorithms. 106-119 - Tianlei Xu, Xiaoqi Zheng, Ben Li, Peng Jin, Zhaohui S. Qin, Hao Wu:
A comprehensive review of computational prediction of genome-wide features. 120-134 - Qinjie Chu, Panpan Bai, Xintian Zhu, Xingchen Zhang, Lingfeng Mao, Qian-Hao Zhu, Longjiang Fan, Chu-Yu Ye:
Characteristics of plant circular RNAs. 135-143 - Emile R. Chimusa, Joel Defo, Prisca K. Thami, Denis Awany, Delesa D. Mulisa, Imane Allali, Hassan Ghazal, Ahmed Moussa, Gaston K. Mazandu:
Dating admixture events is unsolved problem in multi-way admixed populations. 144-155 - Haitao Yang, Hongyan Cao, Tao He, Tong Wang, Yuehua Cui:
Multilevel heterogeneous omics data integration with kernel fusion. 156-170 - Chuan Dong, Yan-Ting Jin, Hong-Li Hua, Qing-Feng Wen, Sen Luo, Wen-Xin Zheng, Feng-Biao Guo:
Comprehensive review of the identification of essential genes using computational methods: focusing on feature implementation and assessment. 171-181 - Chang Su, Jie Tong, Yongjun Zhu, Peng Cui, Fei Wang:
Network embedding in biomedical data science. 182-197 - Fei Liu, Monika Heiner, David R. Gilbert:
Fuzzy Petri nets for modelling of uncertain biological systems. 198-210 - ZiaurRehman Tanoli, Zaid Alam, Aleksandr Ianevski, Krister Wennerberg, Markus Vähä-Koskela, Tero Aittokallio:
Interactive visual analysis of drug-target interaction networks using Drug Target Profiler, with applications to precision medicine and drug repurposing. 211-220 - Jifan Shi, Andrew E. Teschendorff, Weiyan Chen, Luonan Chen, Tiejun Li:
Quantifying Waddington's epigenetic landscape: a comparison of single-cell potency measures. 248-261 - Michiel Stock, Tapio Pahikkala, Antti Airola, Willem Waegeman, Bernard De Baets:
Algebraic shortcuts for leave-one-out cross-validation in supervised network inference. 262-271 - Adriana Pitea, Ivan Kondofersky, Steffen Sass, Fabian J. Theis, Nikola S. Müller, Kristian Unger:
Copy number aberrations from Affymetrix SNP 6.0 genotyping data - how accurate are commonly used prediction approaches? 272-281 - Chao Shen, Zhe Wang, Xiaojun Yao, Youyong Li, Tailong Lei, Ercheng Wang, Lei Xu, Feng Zhu, Dan Li, Tingjun Hou:
Comprehensive assessment of nine docking programs on type II kinase inhibitors: prediction accuracy of sampling power, scoring power and screening power. 282-297 - Bin Liu, Shuangyan Jiang, Quan Zou:
HITS-PR-HHblits: protein remote homology detection by combining PageRank and Hyperlink-Induced Topic Search. 298-308 - Zhenyu Yue, Le Zhao, Junfeng Xia:
dbCPM: a manually curated database for exploring the cancer passenger mutations. 309-317 - Feng-Xu Wu, Fan Wang, Jing-Fang Yang, Wen Jiang, Meng-Yao Wang, Chen-Yang Jia, Ge-Fei Hao, Guangfu Yang:
AIMMS suite: a web server dedicated for prediction of drug resistance on protein mutation. 318-328 - Dan Yao, Hainan Wu, Yuhua Chen, Wenguo Yang, Hua Gao, Chunfa Tong:
gmRAD: an integrated SNP calling pipeline for genetic mapping with RADseq across a hybrid population. 329-337 - Quanhu Sheng, David C. Samuels, Hui Yu, Scott Ness, Ying-Yong Zhao, Yan Guo:
Cancer-specific expression quantitative loci are affected by expression dysregulation. 338-347 - Sameer Salunkhe, Naren Chandran, Pratik Chandrani, Amit Dutt, Shilpee Dutt:
CytoPred: 7-gene pair metric for AML cytogenetic risk prediction. 348-354 - Eugenio Del Prete, Angelo M. Facchiano, Pietro Liò:
Bioinformatics methodologies for coeliac disease and its comorbidities. 355-367
Volume 21, Number 2, March 2020
- Saurav Mallik, Zhongming Zhao:
Graph- and rule-based learning algorithms: a comprehensive review of their applications for cancer type classification and prognosis using genomic data. 368-394 - Tony C. Y. Kuo, Masaomi Hatakeyama, Toshiaki Tameshige, Kentaro K. Shimizu, Jun Sese:
Homeolog expression quantification methods for allopolyploids. 395-407 - Ran Su, Jie Hu, Quan Zou, Balachandran Manavalan, Leyi Wei:
Empirical comparison and analysis of web-based cell-penetrating peptide prediction tools. 408-420 - Alex Alves Freitas:
Investigating the role of Simpson's paradox in the analysis of top-ranked features in high-dimensional bioinformatics datasets. 421-428 - Basant K. Tiwary:
Computational medicine: quantitative modeling of complex diseases. 429-440 - Xin Qi, Yuxin Lin, Jiajia Chen, Bairong Shen:
Decoding competing endogenous RNA networks for cancer biomarker discovery. 441-457 - Pablo Mier, Lisanna Paladin, Stella Tamana, Sophia Petrosian, Borbála Hajdu-Soltész, Annika Urbanek, Aleksandra Gruca, Dariusz Plewczynski, Marcin Grynberg, Pau Bernadó, Zoltán Gáspári, Christos A. Ouzounis, Vasilis J. Promponas, Andrey V. Kajava, John M. Hancock, Silvio C. E. Tosatto, Zsuzsanna Dosztányi, Miguel A. Andrade-Navarro:
Disentangling the complexity of low complexity proteins. 458-472 - Manuel Franco, Juana-María Vivo, Manuel Quesada-Martínez, Astrid Duque-Ramos, Jesualdo Tomás Fernández-Breis:
Evaluation of ontology structural metrics based on public repository data. 473-485 - Xiangrong Liu, Zengyan Hong, Juan Liu, Yuan Lin, Alfonso Rodríguez-Patón, Quan Zou, Xiangxiang Zeng:
Computational methods for identifying the critical nodes in biological networks. 486-497 - Xu Zhou, Enyu Dai, Qian Song, Xueyan Ma, Qianqian Meng, Yongshuai Jiang, Wei Jiang:
In silico drug repositioning based on drug-miRNA associations. 498-510 - Abukari Mohammed Yakubu, Yi-Ping Phoebe Chen:
Ensuring privacy and security of genomic data and functionalities. 511-526 - Giulia Simoni, Vo Hong Thanh, Corrado Priami, Luca Marchetti:
A comparison of deterministic and stochastic approaches for sensitivity analysis in computational systems biology. 527-540 - Cecile Chauvel, Alexei Novoloaca, Pierre Veyre, Frédéric Reynier, Jeremie Becker:
Evaluation of integrative clustering methods for the analysis of multi-omics data. 541-552 - John J. Dziak, Donna L. Coffman, Stephanie T. Lanza, Runze Li, Lars S. Jermiin:
Sensitivity and specificity of information criteria. 553-565 - Xingyi Li, Wenkai Li, Min Zeng, Ruiqing Zheng, Min Li:
Network-based methods for predicting essential genes or proteins: a survey. 566-583 - Martin Ayling, Matthew D. Clark, Richard M. Leggett:
New approaches for metagenome assembly with short reads. 584-594
- Man Cao, Guodong Chen, Jialin Yu, Shaoping Shi:
Computational prediction and analysis of species-specific fungi phosphorylation via feature optimization strategy. 595-608
- Hui-Fang Liu, Rong Liu:
Structure-based prediction of post-translational modification cross-talk within proteins using complementary residue- and residue pair-based features. 609-620
- Jing Tang, Jianbo Fu, Yunxia Wang, Bo Li, Yinghong Li, Qingxia Yang, Xuejiao Cui, Jiajun Hong, Xiaofeng Li, Yuzong Chen, Weiwei Xue, Feng Zhu:
ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies. 621-636 - Aritro Nath, Paul Geeleher, Rong Stephanie Huang:
Long non-coding RNA transcriptome of uncharacterized samples can be accurately imputed using protein-coding genes. 637-648 - Ying Hong Li, Xiao Xu Li, Jiajun Hong, Yunxia Wang, Jianbo Fu, Hong Yang, Chun Yan Yu, Feng Cheng Li, Jie Hu, Weiwei Xue, Yu Yang Jiang, Yu Zong Chen, Feng Zhu:
Clinical trials, progression-speed differentiating features and swiftness rule of the innovative targets of first-in-class drugs. 649-662 - Hyung-Yong Kim, Hee-Joo Choi, Jeong-Yeon Lee, Gu Kong:
Cancer Target Gene Screening: a web application for breast cancer target gene screening using multi-omics data analysis. 663-675 - Siyuan Chen, Chengzhi Ren, Jingjing Zhai, Jiantao Yu, Xuyang Zhao, Zelong Li, Ting Zhang, Wenlong Ma, Zhaoxue Han, Chuang Ma:
CAFU: a Galaxy framework for exploring unmapped RNA-Seq data. 676-686 - Ran Su, Xinyi Liu, Leyi Wei:
MinE-RFE: determine the optimal subset from RFE by minimizing the subset-accuracy-defined energy. 687-698
- Cong Pian, Guang-Le Zhang, Libin Gao, Xiaodan Fan, Fei Li:
miR+Pathway: the integration and visualization of miRNA and KEGG pathways. 699-708
- Yunxia An, Nan Wei, Xiangsong Cheng, Ying Li, Haiyang Liu, Jia Wang, Zhiwei Xu, Zhifu Sun, Xiaoju Zhang:
MCAM abnormal expression and clinical outcome associations are highly cancer dependent as revealed through pan-cancer analysis. 709-718
- Azza E. Ahmed, Ayah A Awadallah, Mawada Tagelsir, Maram A Suliman, Atheer Eltigani, Hassan Elsafi, Basil D. Hamdelnile, Mohamed A Mukhtar, Faisal M. Fadlelmola:
Delivering blended bioinformatics training in resource-limited settings: a case study on the University of Khartoum H3ABioNet node. 719-728 - Helena Cirenajwis, Martin Lauss, Maria Planck, Johan Vallon-Christersson, Johan Staaf:
Performance of gene expression-based single sample predictors for assessment of clinicopathological subgroups and molecular subtypes in cancers: a case comparison study in non-small cell lung cancer. 729-740 - Zhi Ruan, Yunsong Yu, Ye Feng:
The global dissemination of bacterial infections necessitates the study of reverse genomic epidemiology. 741-750
- Corrigendum to: Dating admixture events is unsolved problem in multi-way admixed populations. 751
- Corrigendum to: gm RAD: an integrated SNP calling pipeline for genetic mapping with RADseq across a hybrid population. 752
Volume 21, Number 3, May 2020
- Regina Brinster, Dominique Scherer, Justo Lorenzo Bermejo:
Optimal selection of genetic variants for adjustment of population stratification in European association studies. 753-761 - Yu Ding, Hong Wang, Hewei Zheng, Lianzong Wang, Guosi Zhang, Jiaxin Yang, Xiaoyan Lu, Yu Bai, Haotian Zhang, Jing Li, Wenyan Gao, Fukun Chen, Shui Hu, Jingqi Wu, Liangde Xu:
Evaluation of drug efficacy based on the spatial position comparison of drug-target interaction centers. 762-776 - Ziye Wang, Ying Wang, Jed A. Fuhrman, Fengzhu Sun, Shanfeng Zhu:
Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences. 777-790 - Neann Mathai, Ya Chen, Johannes Kirchmair:
Validation strategies for target prediction methods. 791-802 - Fabio Fabris, Daniel Palmer, João Pedro de Magalhães, Alex Alves Freitas:
Comparing enrichment analysis and machine learning for identifying gene properties that discriminate between gene classes. 803-814 - Zhongjie Liang, Gennady M. Verkhivker, Guang Hu:
Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications. 815-835 - Edwin Yu-Kiu Ho, Qin Cao, Mengting Gu, Ricky Wai-Lun Chan, Qiong Wu, Mark Gerstein, Kevin Y. Yip:
Shaping the nebulous enhancer in the era of high-throughput assays and genome editing. 836-850 - Charalampos Papachristou, Swati Biswas:
Comparison of haplotype-based tests for detecting gene-environment interactions with rare variants. 851-862 - Jianjian Wang, Yuze Cao, Xiaoyu Lu, Tianfeng Wang, Shuang Li, Xiaotong Kong, Chunrui Bo, Jie Li, Xiaolong Wang, Heping Ma, Lei Li, Huixue Zhang, Shangwei Ning, Lihua Wang:
MicroRNAs and nervous system diseases: network insights and computational challenges. 863-875 - Ansuman Chattopadhyay, Carrie L. Iwema, Barbara A Epstein, Adrian V. Lee, Arthur S. Levine:
Molecular Biology Information Service: an innovative medical library-based bioinformatics support service for biomedical researchers. 876-884 - Saman Zeeshan, Ruoyun Xiong, Bruce T. Liang, Zeeshan Ahmed:
100 Years of evolving gene-disease complexities and scientific debutants. 885-905 - Jimmy Omony, Thomas Nussbaumer, Ruben Gutzat:
DNA methylation analysis in plants: review of computational tools and future perspectives. 906-918 - Mengying Sun, Sendong Zhao, Coryandar Gilvary, Olivier Elemento, Jiayu Zhou, Fei Wang:
Graph convolutional networks for computational drug development and discovery. 919-935 - Charles Vesteghem, Rasmus Froberg Brøndum, Mads Sønderkær, Mia Sommer, Alexander Schmitz, Julie Støve Bødker, Karen Dybkær, Tarec Christoffer El-Galaly, Martin Bøgsted:
Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives. 936-945 - Zijie Shen, Yuan Lin, Quan Zou:
Transcription factors-DNA interactions in rice: identification and verification. 946-956 - Feng Li, Tan Wu, Yanjun Xu, Qun Dong, Jing Xiao, Yingqi Xu, Qian Li, Chunlong Zhang, Jianxia Gao, Liqiu Liu, Xiaoxu Hu, Jian Huang, Xia Li, Yunpeng Zhang:
A comprehensive overview of oncogenic pathways in human cancer. 957-969 - Na Cheng, Menglu Li, Le Zhao, Bo Zhang, Yuhua Yang, Chun-Hou Zheng, Junfeng Xia:
Comparison and integration of computational methods for deleterious synonymous mutation prediction. 970-981 - Hao Lv, Zi-Mei Zhang, Shi-Hao Li, Jiu-Xin Tan, Wei Chen, Hao Lin:
Evaluation of different computational methods on 5-methylcytosine sites identification. 982-995
- Ran Su, Xinyi Liu, Guobao Xiao, Leyi Wei:
Meta-GDBP: a high-level stacked regression model to improve anticancer drug response prediction. 996-1005 - Yadong Yang, Tao Zhang, Rudan Xiao, Xiaopeng Hao, Huiqiang Zhang, Hongzhu Qu, Bingbing Xie, Tao Wang, Xiangdong Fang:
Platform-independent approach for cancer detection from gene expression profiles of peripheral blood cells. 1006-1015 - Shiqiang Cheng, Bei Han, Miao Ding, Yan Wen, Mei Ma, Lu Zhang, Xin Qi, Bolun Cheng, Ping Li, Om Prakash Kafle, Xiao Liang, Li Liu, Yanan Du, Yan Zhao, Feng Zhang:
Identifying psychiatric disorder-associated gut microbiota using microbiota-related gene set enrichment analysis. 1016-1022 - Zhijie Han, Weiwei Xue, Lin Tao, Yan Lou, Yunqing Qiu, Feng Zhu:
Genome-wide identification and analysis of the eQTL lncRNAs in multiple sclerosis based on RNA-seq data. 1023-1037 - Sijia Zhang, Le Zhao, Chun-Hou Zheng, Junfeng Xia:
A feature-based approach to predict hot spots in protein-DNA binding interfaces. 1038-1046 - Zhen Chen, Pei Zhao, Fuyi Li, Tatiana T. Marquez-Lago, André Leier, Jerico Nico De Leon Revote, Yan Zhu, David R. Powell, Tatsuya Akutsu, Geoffrey I. Webb, Kuo-Chen Chou, Alexander Ian Smith, Roger J. Daly, Jian Li, Jiangning Song:
iLearn : an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data. 1047-1057 - Qingxia Yang, Bo Li, Jing Tang, Xuejiao Cui, Yunxia Wang, Xiaofeng Li, Jie Hu, Yuzong Chen, Weiwei Xue, Yan Lou, Yunqing Qiu, Feng Zhu:
Consistent gene signature of schizophrenia identified by a novel feature selection strategy from comprehensive sets of transcriptomic data. 1058-1068 - Fuyi Li, Cunshuo Fan, Tatiana T. Marquez-Lago, André Leier, Jerico Nico De Leon Revote, Cangzhi Jia, Yan Zhu, Alexander Ian Smith, Geoffrey I. Webb, Quanzhong Liu, Leyi Wei, Jian Li, Jiangning Song:
PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact. 1069-1079 - Ji Zhang, Meige Guan, Qianliang Wang, Jiajun Zhang, Tianshou Zhou, Xiaoqiang Sun:
Single-cell transcriptome-based multilayer network biomarker for predicting prognosis and therapeutic response of gliomas. 1080-1097
- Chia-Ru Chung, Ting-Rung Kuo, Li-Ching Wu, Tzong-Yi Lee, Jorng-Tzong Horng:
Characterization and identification of antimicrobial peptides with different functional activities. 1098-1114
- Meik Kunz, Julian Jeromin, Maximilian Fuchs, Jan Christoph, Giulia Veronesi, Michael Flentje, Sarah Nietzer, Gudrun Dandekar, Thomas Dandekar:
In silico signaling modeling to understand cancer pathways and treatment responses. 1115-1117
- Corrigendum to: Comprehensive and critical evaluation of individualized pathway activity measurement tools on pan-cancer data. 1118
Volume 21, Number 4, July 2020
- Shutao Mei, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Kailin Giam, Nathan P. Croft, Tatsuya Akutsu, Alexander Ian Smith, Jian Li, Jamie Rossjohn, Anthony W. Purcell, Jiangning Song:
A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction. 1119-1135 - Vincent Briane, Myriam Vimond, Charles Kervrann:
An overview of diffusion models for intracellular dynamics analysis. 1136-1150 - Asmita Gupta, Manju Bansal:
RNA-mediated translation regulation in viral genomes: computational advances in the recognition of sequences and structures. 1151-1163 - Leandro Lima, Camille Marchet, Ségolène Caboche, Corinne Da Silva, Benjamin Istace, Jean-Marc Aury, Hélène Touzet, Rayan Chikhi:
Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data. 1164-1181 - Andrew C. Liu, Krishna Patel, Ramya Dhatri Vunikili, Kipp W. Johnson, Fahad Abdu, Shivani Kamath Belman, Benjamin S. Glicksberg, Pratyush Tandale, Roberto Fontanez, Oommen K. Mathew, Andrew Kasarskis, Priyabrata Mukherjee, Lakshminarayanan Subramanian, Joel T. Dudley, Khader Shameer:
Sepsis in the era of data-driven medicine: personalizing risks, diagnoses, treatments and prognoses. 1182-1195 - Ren Qi, Anjun Ma, Qin Ma, Quan Zou:
Clustering and classification methods for single-cell RNA-sequencing data. 1196-1208 - Raphael Petegrosso, Zhuliu Li, Rui Kuang:
Machine learning and statistical methods for clustering single-cell RNA-sequencing data. 1209-1223 - Dimitri Guala, Christoph Ogris, Nikola Müller, Erik L. L. Sonnhammer:
Genome-wide functional association networks: background, data & state-of-the-art resources. 1224-1237 - Fu Chen, Le Yuan, Shaozhen Ding, Yu Tian, Qian-Nan Hu:
Data-driven rational biosynthesis design: from molecules to cell factories. 1238-1248 - David Hoksza, Piotr Gawron, Marek Ostaszewski, Jan Hasenauer, Reinhard Schneider:
Closing the gap between formats for storing layout information in systems biology. 1249-1260 - Moliang Chen, Guoli Ji, Hongjuan Fu, Qianmin Lin, Congting Ye, Wenbin Ye, Yaru Su, Xiaohui Wu:
A survey on identification and quantification of alternative polyadenylation sites from RNA-seq data. 1261-1276 - Sean D. McCabe, Dan-Yu Lin, Michael I. Love:
Consistency and overfitting of multi-omics methods on experimental data. 1277-1284 - Jianwen Fang:
A critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation. 1285-1292 - Hewei Zheng, Xueying Zhao, Hong Wang, Yu Ding, Xiaoyan Lu, Guosi Zhang, Jiaxin Yang, Lianzong Wang, Haotian Zhang, Yu Bai, Jing Li, Jingqi Wu, Yongshuai Jiang, Liangde Xu:
Location deviations of DNA functional elements affected SNP mapping in the published databases and references. 1293-1301 - Mitra Ebrahimpoor, Pietro Spitali, Kristina M. Hettne