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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, Jérémie 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, Yuzong 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, Roula Tsonaka, Jelle J. Goeman:
Simultaneous Enrichment Analysis of all Possible Gene-sets: Unifying Self-Contained and Competitive Methods. 1302-1312 - Juan Cui, Jiang Shu:
Circulating microRNA trafficking and regulation: computational principles and practice. 1313-1326 - Pingjian Ding, Wenjue Ouyang, Jiawei Luo, Chee-Keong Kwoh:
Heterogeneous information network and its application to human health and disease. 1327-1346 - Chaodong Zhang, Yingjiao Ju, Na Tang, Yun Li, Gang Zhang, Yuqin Song, Hailing Fang, Liang Yang, Jie Feng:
Systematic analysis of supervised machine learning as an effective approach to predicate β-lactam resistance phenotype in Streptococcus pneumoniae. 1347-1355 - Hang Wei, Bin Liu:
iCircDA-MF: identification of circRNA-disease associations based on matrix factorization. 1356-1367 - Dan Wang, Hai Xiang, Chao Ning, Hao Liu, Jian-Feng Liu, Xingbo Zhao:
Mitochondrial DNA enrichment reduced NUMT contamination in porcine NGS analyses. 1368-1377 - Jing Tang, Yunxia Wang, Jianbo Fu, Ying Zhou, Yongchao Luo, Ying Zhang, Bo Li, Qingxia Yang, Weiwei Xue, Yan Lou, Yunqing Qiu, Feng Zhu:
A critical assessment of the feature selection methods used for biomarker discovery in current metaproteomics studies. 1378-1390 - Meik Kunz, Beat Wolf, Maximilian Fuchs, Jan Christoph, Ke Xiao, Thomas Thum, David Atlan, Hans-Ulrich Prokosch, Thomas Dandekar:
A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs. 1391-1396 - Hebing Chen, Zhuo Zhang, Shuai Jiang, Ruijiang Li, Wanying Li, Chenghui Zhao, Hao Hong, Xin Huang, Hao Li, Xiaochen Bo:
New insights on human essential genes based on integrated analysis and the construction of the HEGIAP web-based platform. 1397-1410 - Meng Li, Jianmei Zhao, Xuecang Li, Yang Chen, Chenchen Feng, Fengcui Qian, Yuejuan Liu, Jian Zhang, Jianzhong He, Bo Ai, Ziyu Ning, Wei Liu, Xuefeng Bai, Xiaole Han, Zhiyong Wu, Xiue Xu, Zhidong Tang, Qi Pan, Liyan Xu, Chunquan Li, Qiuyu Wang, Enmin Li:
HiFreSP: A novel high-frequency sub-pathway mining approach to identify robust prognostic gene signatures. 1411-1424 - Xiangxiang Zeng, Yue Zhong, Wei Lin, Quan Zou:
Predicting disease-associated circular RNAs using deep forests combined with positive-unlabeled learning methods. 1425-1436 - Jiajun Hong, Yongchao Luo, Yang Zhang, Junbiao Ying, Weiwei Xue, Tian Xie, Lin Tao, Feng Zhu:
Protein functional annotation of simultaneously improved stability, accuracy and false discovery rate achieved by a sequence-based deep learning. 1437-1447 - Yuli Gao, Guohui Chuai, Weichuan Yu, Shen Qu, Qi Liu:
Data imbalance in CRISPR off-target prediction. 1448-1454 - Juncai Pu, Yue Yu, Yiyun Liu, Lu Tian, Siwen Gui, Xiaogang Zhong, Chu Fan, Shaohua Xu, Xuemian Song, Lanxiang Liu, Lining Yang, Peng Zheng, Jianjun Chen, Ke Cheng, Chanjuan Zhou, Haiyang Wang, Peng Xie:
MENDA: a comprehensive curated resource of metabolic characterization in depression. 1455-1464 - Aimin Li, Peilin Jia, Saurav Mallik, Rong Fei, Hiroki Yoshioka, Akiko Suzuki, Junichi Iwata, Zhongming Zhao:
Critical microRNAs and regulatory motifs in cleft palate identified by a conserved miRNA-TF-gene network approach in humans and mice. 1465-1478 - Jie Ping, Olufunmilola Oyebamiji, Hui Yu, Scott Ness, Jeremy Chien, Fei Ye, Huining Kang, David C. Samuels, Sergey Ivanov, Danqian Chen, Ying-Yong Zhao, Yan Guo:
MutEx: a multifaceted gateway for exploring integrative pan-cancer genomic data. 1479-1486 - José A. Ferreira, Susana Fuentes:
Some comments on certain statistical aspects of the study of the microbiome. 1487-1494
Volume 21, Number 5, September 2020
- Antonio Mora:
Gene set analysis methods for the functional interpretation of non-mRNA data - Genomic range and ncRNA data. 1495-1508 - Akila Katuwawala, Christopher J. Oldfield, Lukasz A. Kurgan:
Accuracy of protein-level disorder predictions. 1509-1522 - Stefania Salvatore, Knut Dagestad Rand, Ivar Grytten, Egil Ferkingstad, Diana Domanska, Lars Holden, Marius Gheorghe, Anthony Mathelier, Ingrid Kristine Glad, Geir Kjetil Sandve:
Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis. 1523-1530 - Zhourun Wu, Qing Liao, Bin Liu:
A comprehensive review and evaluation of computational methods for identifying protein complexes from protein-protein interaction networks. 1531-1548 - Richard A. Norman, Francesco Ambrosetti, Alexandre M. J. J. Bonvin, Lucy J. Colwell, Sebastian Kelm, Sandeep Kumar, Konrad Krawczyk:
Computational approaches to therapeutic antibody design: established methods and emerging trends. 1549-1567 - Hui Yang, Wuritu Yang, Fu-Ying Dao, Hao Lv, Hui Ding, Wei Chen, Hao Lin:
A comparison and assessment of computational method for identifying recombination hotspots in Saccharomyces cerevisiae. 1568-1580 - Xinlei Zhao, Shuang Wu, Nan Fang, Xiao Sun, Jue Fan:
Evaluation of single-cell classifiers for single-cell RNA sequencing data sets. 1581-1595 - Robert Rentzsch, Carlus Deneke, Andreas Nitsche, Bernhard Y. Renard:
Predicting bacterial virulence factors - evaluation of machine learning and negative data strategies. 1596-1608 - Tianlin Zhang, Jiaxu Leng, Ying Liu:
Deep learning for drug-drug interaction extraction from the literature: a review. 1609-1627 - Yinan Shen, Yijie Ding, Jijun Tang, Quan Zou, Fei Guo:
Critical evaluation of web-based prediction tools for human protein subcellular localization. 1628-1640 - Weifeng Guo, Shaowu Zhang, Tao Zeng, Tatsuya Akutsu, Luonan Chen:
Network control principles for identifying personalized driver genes in cancer. 1641-1662 - Francis E. Agamah, Gaston K. Mazandu, Radia Hassan, Christian D. Bope, Nicholas E. Thomford, Anita Ghansah, Emile R. Chimusa:
Computational/in silico methods in drug target and lead prediction. 1663-1675 - Zhen Chen, Pei Zhao, Fuyi Li, Yanan Wang, Alexander Ian Smith, Geoffrey I. Webb, Tatsuya Akutsu, Abdelkader Baggag, Halima Bensmail, Jiangning Song:
Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences. 1676-1696 - Jon C. Ison, Hervé Ménager, Bryan Brancotte, Erik Jaaniso, Ahto Salumets, Tomás Racek, Anna-Lena Lamprecht, Magnus Palmblad, Matús Kalas, Piotr Chmura, John M. Hancock, Veit Schwämmle, Hans-Ioan Ienasescu:
Community curation of bioinformatics software and data resources. 1697-1705 - Yanfang Zhang, Xiujia Yang, Yanxia Zhang, Yan Zhang, Minhui Wang, Jin Xia Ou, Yan Zhu, Huikun Zeng, Jiaqi Wu, Chunhong Lan, Hong-Wei Zhou, Wei Yang, Zhenhai Zhang:
Tools for fundamental analysis functions of TCR repertoires: a systematic comparison. 1706-1716 - Xu Chi, Maureen A. Sartor, Sanghoon Lee, Meenakshi Anurag, Snehal Patil, Pelle Hall, Matthew Wexler, Xiao-Song Wang:
Universal concept signature analysis: genome-wide quantification of new biological and pathological functions of genes and pathways. 1717-1732 - Bin Liu, Chen-Chen Li, Ke Yan:
DeepSVM-fold: protein fold recognition by combining support vector machines and pairwise sequence similarity scores generated by deep learning networks. 1733-1741 - Siqi Bao, Hengqiang Zhao, Jian Yuan, Dandan Fan, Zicheng Zhang, Jianzhong Su, Meng Zhou:
Computational identification of mutator-derived lncRNA signatures of genome instability for improving the clinical outcome of cancers: a case study in breast cancer. 1742-1755 - Bo Sun, Liang Chen:
Quantile regression for challenging cases of eQTL mapping. 1756-1765 - Marco Cacciabue, Anabella Currá, Elisa Carrillo, Guido König, María Inés Gismondi:
A beginner's guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing. 1766-1775 - Bin Tang, Bin Li, Liang-Di Gao, Na He, Xiao-Rong Liu, Yue-Sheng Long, Yang Zeng, Yong-Hong Yi, Tao Su, Wei-Ping Liao:
Optimization of in silico tools for predicting genetic variants: individualizing for genes with molecular sub-regional stratification. 1776-1786 - Chenyang Hong, Kevin Y. Yip:
Flexible k-mers with variable-length indels for identifying binding sequences of protein dimers. 1787-1797 - Kai Yu, Qingfeng Zhang, Zekun Liu, Yimeng Du, Xinjiao Gao, Qi Zhao, Han Cheng, Xiaoxing Li, Zexian Liu:
Deep learning based prediction of reversible HAT/HDAC-specific lysine acetylation. 1798-1805 - Wei-Yang Bai, Xiao-Wei Zhu, Pei-Kuan Cong, Xue-Jun Zhang, J. Brent Richards, Hou-Feng Zheng:
Genotype imputation and reference panel: a systematic evaluation on haplotype size and diversity. 1806-1817 - Qi Zhao, Yu Sun, Zekun Liu, Hongwan Zhang, Xingyang Li, Kaiyu Zhu, Zexian Liu, Jian Ren, Zhixiang Zuo:
CrossICC: iterative consensus clustering of cross-platform gene expression data without adjusting batch effect. 1818-1824 - Jiajun Hong, Yongchao Luo, Minjie Mou, Jianbo Fu, Yang Zhang, Weiwei Xue, Tian Xie, Lin Tao, Yan Lou, Feng Zhu:
Convolutional neural network-based annotation of bacterial type IV secretion system effectors with enhanced accuracy and reduced false discovery. 1825-1836 - Ephifania Geza, Nicola J. Mulder, Emile R. Chimusa, Gaston K. Mazandu:
FRANC: a unified framework for multi-way local ancestry deconvolution with high density SNP data. 1837-1845 - Bing Rao, Chen Zhou, Guoying Zhang, Ran Su, Leyi Wei:
ACPred-Fuse: fusing multi-view information improves the prediction of anticancer peptides. 1846-1855 - Jian Zhang, Zhiqiang Ma, Lukasz A. Kurgan:
Corrigendum to: Comprehensive review and empirical analysis of hallmarks of DNA-, RNA- and protein-binding residues in protein chains. 1856
Volume 21, Number 6, December 2020
- Xiaoxia Ma, Yijun Meng, Pu Wang, Zhonghai Tang, Huizhong Wang, Tian Xie:
Bioinformatics-assisted, integrated omics studies on medicinal plants. 1857-1874 - Ehsan Ullah, Mona Yosafshahi, Soha Hassoun:
Towards scaling elementary flux mode computation. 1875-1885 - Hongcheng Yao, Qian Liang, Xinyi Qian, Junwen Wang, Pak Chung Sham, Mulin Jun Li:
Methods and resources to access mutation-dependent effects on cancer drug treatment. 1886-1903 - Riccardo De Bin, Anne-Laure Boulesteix, Axel Benner, Natalia Becker, Willi Sauerbrei:
Combining clinical and molecular data in regression prediction models: insights from a simulation study. 1904-1919 - Anita Sathyanarayanan, Rohit Gupta, Erik W. Thompson, Dale R. Nyholt, Denis C. Bauer, Shivashankar H. Nagaraj:
A comparative study of multi-omics integration tools for cancer driver gene identification and tumour subtyping. 1920-1936 - Jussi Paananen, Vittorio Fortino:
An omics perspective on drug target discovery platforms. 1937-1953 - Yiwen Wang, Kim-Anh Lê Cao:
Managing batch effects in microbiome data. 1954-1970 - Matteo Chiara, Federico Zambelli, Ernesto Picardi, David Stephen Horner, Graziano Pesole:
Critical assessment of bioinformatics methods for the characterization of pathological repeat expansions with single-molecule sequencing data. 1971-1986 - Sebastiano Di Bella, Alessandro La Ferlita, Giovanni Carapezza, Salvatore Alaimo, Antonella Isacchi, Alfredo Ferro, Alfredo Pulvirenti, Roberta Bosotti:
A benchmarking of pipelines for detecting ncRNAs from RNA-Seq data. 1987-1998 - Fabian Kern, Christina Backes, Pascal Hirsch, Tobias Fehlmann, Martin Hart, Eckart Meese, Andreas Keller:
What's the target: understanding two decades of in silico microRNA-target prediction. 1999-2010 - Morgane Pierre-Jean, Jean-Francois Deleuze, Edith Le Floch, Florence Mauger:
Clustering and variable selection evaluation of 13 unsupervised methods for multi-omics data integration. 2011-2030 - Bohdan B. Khomtchouk, Diem-Trang T. Tran, Kasra A. Vand, Matthew Might, Or Gozani, Themistocles L. Assimes:
Cardioinformatics: the nexus of bioinformatics and precision cardiology. 2031-2051 - Arfa Mehmood, Asta Laiho, Mikko S. Venäläinen, Aidan J. McGlinchey, Ning Wang, Laura L. Elo:
Systematic evaluation of differential splicing tools for RNA-seq studies. 2052-2065 - Yu-Chiao Chiu, Hung-I Harry Chen, Aparna Gorthi, Milad Mostavi, Siyuan Zheng, Yufei Huang, Yidong Chen:
Deep learning of pharmacogenomics resources: moving towards precision oncology. 2066-2083 - Jun Sun, Qianqian Shi, Xi Chen, Rong Liu:
Decoding the similarities and specific differences between latent and active tuberculosis infections based on consistently differential expression networks. 2084-2098 - Xuan Lin, Zhe Quan, Zhi-Jie Wang, Huang Huang, Xiangxiang Zeng:
A novel molecular representation with BiGRU neural networks for learning atom. 2099-2111 - Süleyman Selim Çinaroglu, Emel Timuçin:
Comprehensive evaluation of the MM-GBSA method on bromodomain-inhibitor sets. 2112-2125 - Xiao Ding, Xuye Yuan, Longfei Mao, Aiping Wu, Taijiao Jiang:
FluReassort: a database for the study of genomic reassortments among influenza viruses. 2126-2132 - Chen-Chen Li, Bin Liu:
MotifCNN-fold: protein fold recognition based on fold-specific features extracted by motif-based convolutional neural networks. 2133-2141 - Qingxia Yang, Jiajun Hong, Yi Li, Weiwei Xue, Song Li, Hui Yang, Feng Zhu:
A novel bioinformatics approach to identify the consistently well-performing normalization strategy for current metabolomic studies. 2142-2152 - Yanjun Xu, Tan Wu, Feng Li, Qun Dong, Jingwen Wang, Desi Shang, Yingqi Xu, Chunlong Zhang, Yiying Dou, Congxue Hu, Haixiu Yang, Xuan Zheng, Yunpeng Zhang, Lihua Wang, Xia Li:
Identification and comprehensive characterization of lncRNAs with copy number variations and their driving transcriptional perturbed subpathways reveal functional significance for cancer. 2153-2166 - Qun Dong, Feng Li, Yanjun Xu, Jing Xiao, Yingqi Xu, Desi Shang, Chunlong Zhang, Haixiu Yang, Zihan Tian, Kai Mi, Xia Li, Yunpeng Zhang:
RNAactDrug: a comprehensive database of RNAs associated with drug sensitivity from multi-omics data. 2167-2174 - Yao Lv, Sheng-Yan Lin, Fei-Fei Hu, Zheng Ye, Qiong Zhang, Yan Wang, An-Yuan Guo:
Landscape of cancer diagnostic biomarkers from specifically expressed genes. 2175-2184 - Bin Liu, Yulin Zhu, Ke Yan:
Fold-LTR-TCP: protein fold recognition based on triadic closure principle. 2185-2193 - Kequan Lin, Lu Li, Yifei Dai, Huili Wang, Shuaishuai Teng, Xilinqiqige Bao, Zhi John Lu, Dong Wang:
A comprehensive evaluation of connectivity methods for L1000 data. 2194-2205 - Jing-Fang Yang, Fan Wang, Yuzong Chen, Ge-Fei Hao, Guangfu Yang:
LARMD: integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor. 2206-2218 - Ming-Siang Huang, Po-Ting Lai, Pei-Yen Lin, Yu-Ting You, Richard Tzong-Han Tsai, Wen-Lian Hsu:
Biomedical named entity recognition and linking datasets: survey and our recent development. 2219-2238
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