| 1 | -- | 2 | Simona E. Rombo, Domenico Ursino. Integrative bioinformatics and omics data source interoperability in the next-generation sequencing era - Editorial |
| 3 | -- | 19 | 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 |
| 20 | -- | 29 | Mattia Forcato, Oriana Romano, Silvio Bicciato. Computational methods for the integrative analysis of single-cell data |
| 30 | -- | 44 | Anna Bernasconi 0002, Arif Canakoglu, Marco Masseroli, Stefano Ceri. The road towards data integration in human genomics: players, steps and interactions |
| 45 | -- | 54 | Oscar Pastor 0001, Ana Palacio León, José Fabián Reyes Román, Alberto García Simón, Juan Carlos Casamayor Ródenas. Using conceptual modeling to improve genome data management |
| 55 | -- | 65 | 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 |
| 66 | -- | 76 | Minsik Oh, Sungjoon Park, Sun Kim, Heejoon Chae. Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulations |
| 77 | -- | 87 | Susana Vinga. Structured sparsity regularization for analyzing high-dimensional omics data |
| 88 | -- | 95 | Matteo Comin, Barbara Di Camillo, Cinzia Pizzi, Fabio Vandin. Comparison of microbiome samples: methods and computational challenges |
| 96 | -- | 108 | Sergey Knyazev, Lauren Hughes, Pavel Skums, Alexander Zelikovsky. Epidemiological data analysis of viral quasispecies in the next-generation sequencing era |
| 109 | -- | 126 | 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 |
| 127 | -- | 139 | Yun Zhang, Jonavelle Cuerdo, Marc K. Halushka, Matthew N. McCall. The effect of tissue composition on gene co-expression |
| 140 | -- | 145 | Joël Simoneau, Simon Dumontier, Ryan Gosselin, Michelle S. Scott. Current RNA-seq methodology reporting limits reproducibility |
| 146 | -- | 163 | Mariana Neves 0002, Jurica Seva. An extensive review of tools for manual annotation of documents |
| 164 | -- | 177 | Anh Nguyen Duc, Canh Hao Nguyen, Hiroshi Mamitsuka. A survey on adverse drug reaction studies: data, tasks and machine learning methods |
| 178 | -- | 193 | Richa Bharti, Dominik G. Grimm. Current challenges and best-practice protocols for microbiome analysis |
| 194 | -- | 218 | Qiang Shi, Weiya Chen, Siqi Huang, Yan Wang, Zhidong Xue. Deep learning for mining protein data |
| 219 | -- | 231 | Beatriz T. Magalhães, Anália Lourenço, Nuno F. Azevedo. Computational resources and strategies to assess single-molecule dynamics of the translation process in S. cerevisiae |
| 232 | -- | 246 | Jinyu Chen, Louxin Zhang. A survey and systematic assessment of computational methods for drug response prediction |
| 247 | -- | 269 | 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 |
| 270 | -- | 287 | Ammu Prasanna Kumar, Chandra S. Verma 0001, Suryani Lukman. Structural dynamics and allostery of Rab proteins: strategies for drug discovery and design |
| 288 | -- | 297 | Marieke Vromman, Jo Vandesompele, Pieter-Jan Volders. Closing the circle: current state and perspectives of circular RNA databases |
| 298 | -- | 307 | Shaofeng Lin, Chenwei Wang, Jiaqi Zhou 0003, Ying Shi, Chen Ruan, Yiran Tu, Lan Yao, Di Peng, Yu Xue 0001. EPSD: a well-annotated data resource of protein phosphorylation sites in eukaryotes |
| 308 | -- | 314 | Aidan R. O'Brien, Gaetan Burgio, Denis C. Bauer. Domain-specific introduction to machine learning terminology, pitfalls and opportunities in CRISPR-based gene editing |
| 315 | -- | 333 | Lan Huang 0002, Dan Shao, Yan Wang 0028, Xueteng Cui, Yufei Li, Qian Chen, Juan Cui. Human body-fluid proteome: quantitative profiling and computational prediction |
| 334 | -- | 345 | Han Fu, Kellie J. Archer. High-dimensional variable selection for ordinal outcomes with error control |
| 346 | -- | 359 | Betül Güvenç Paltun, Hiroshi Mamitsuka, Samuel Kaski. Improving drug response prediction by integrating multiple data sources: matrix factorization, kernel and network-based approaches |
| 360 | -- | 379 | Delora Baptista, Pedro G. Ferreira, Miguel Rocha. Deep learning for drug response prediction in cancer |
| 380 | -- | 392 | Saidi Wang, Amlan Talukder, Mingyu Cha, Xiaoman Li, Haiyan Hu. Computational annotation of miRNA transcription start sites |
| 393 | -- | 415 | Md. Rezaul Karim 0001, Oya Beyan, Achille Zappa, Ivan G. Costa, Dietrich Rebholz-Schuhmann, Michael Cochez, Stefan Decker. Deep learning-based clustering approaches for bioinformatics |
| 416 | -- | 427 | 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 |
| 428 | -- | 437 | Ran Su, Huichen Wu, Xinyi Liu, Leyi Wei. Predicting drug-induced hepatotoxicity based on biological feature maps and diverse classification strategies |
| 438 | -- | 450 | Fei Liu 0006, Wujie Sun, Monika Heiner, David R. Gilbert. Hybrid modelling of biological systems using fuzzy continuous Petri nets |
| 451 | -- | 462 | 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 |
| 463 | -- | 473 | 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 |
| 474 | -- | 484 | 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 |
| 485 | -- | 496 | Xing Chen, Lian-Gang Sun, Yan Zhao. NCMCMDA: miRNA-disease association prediction through neighborhood constraint matrix completion |
| 497 | -- | 514 | Chao Shen, Ye Hu, Zhe Wang, Xujun Zhang, Haiyang Zhong, Gaoang Wang, Xiaojun Yao, Lei Xu 0035, 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 |
| 515 | -- | 525 | Le Zhang 0004, Zichun Dai, Jun Yu, Ming Xiao. CpG-island-based annotation and analysis of human housekeeping genes |
| 526 | -- | 535 | 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 |
| 536 | -- | 544 | 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 |
| 545 | -- | 556 | Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity Law, Sean Davis, Vincent J. Carey, Martin Morgan, Ralf Zimmer, Levi Waldron. Toward a gold standard for benchmarking gene set enrichment analysis |
| 557 | -- | 567 | Mo Zhu, Kai Kang, Kang Ning 0001. Meta-Prism: Ultra-fast and highly accurate microbial community structure search utilizing dual indexing and parallel computation |
| 568 | -- | 580 | Nansu Zong, Rachael Sze Nga Wong, Yue Yu, Andrew Wen, Ming Huang, Ning Li. Drug-target prediction utilizing heterogeneous bio-linked network embeddings |
| 581 | -- | 588 | 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 |
| 589 | -- | 600 | 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 |
| 601 | -- | 603 | 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 |
| 604 | -- | 0 | 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 |
| 605 | -- | 0 | Jing-Fang Yang, Fan Wang, Yu Zong 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 |
| 606 | -- | 0 | 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 |
| 607 | -- | 0 | 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 |
| 608 | -- | 0 | David Hoksza, Piotr Gawron, Marek Ostaszewski, Jan Hasenauer, Reinhard Schneider 0002. Closing the gap between formats for storing layout information in systems biology |
| 609 | -- | 0 | Saidi Wang, Amlan Talukder, Mingyu Cha, Xiaoman Li, Haiyan Hu. Corrigendum to: Computational annotation of miRNA transcription start sites |
| 610 | -- | 0 | Maria Victoria Schneider, Rafael C. Jimenez. Corrigendum to: Bioinformatics: scalability, capabilities and training in the data-driven era |
| 611 | -- | 0 | 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 |