| MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment | 2004/01/01 | English | 9,117 |
| Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration | 2012/04/19 | English | 5,402 |
| MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization | 2017/09/06 | English | 4,023 |
| Recent developments in the MAFFT multiple sequence alignment program | 2008/03/27 | English | 2,631 |
| MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences | 2008/03/27 | English | 2,626 |
| Deep learning for healthcare: review, opportunities and challenges | 2017/05/06 | English | 967 |
| A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis | 2012/09/17 | English | 741 |
| Using Tablet for visual exploration of second-generation sequencing data | 2012/03/24 | English | 665 |
| Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium | 2011/08/27 | English | 571 |
| PROSITE: A documented database using patterns and profiles as motif descriptors | 2002/01/01 | English | 545 |
| The UCSC genome browser and associated tools | 2012/08/20 | English | 501 |
| Analytic approaches to twin data using structural equation models | 2002/01/01 | English | 500 |
| Partial least squares: a versatile tool for the analysis of high-dimensional genomic data | 2006/05/26 | English | 484 |
| oncoPredict: an R package for predicting in vivo or cancer patient drug response and biomarkers from cell line screening data | 2021/07/15 | English | 459 |
| The BioCyc collection of microbial genomes and metabolic pathways | 2017/08/17 | English | 427 |
| Revealing protein–lncRNA interaction | 2015/06/02 | English | 424 |
| A survey of sequence alignment algorithms for next-generation sequencing | 2010/05/11 | English | 412 |
| MicroRNAs and complex diseases: from experimental results to computational models | 2017/10/17 | English | 405 |
| Machine learning in bioinformatics | 2006/03/01 | English | 401 |
| Drug–target interaction prediction: databases, web servers and computational models | 2015/08/17 | English | 383 |
| Identifying miRNAs, targets and functions | 2012/11/22 | English | 374 |
| Circular RNA identification based on multiple seed matching | 2017/02/28 | English | 364 |
| Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences | 2016/11/22 | English | 364 |
| Ultrafast clustering algorithms for metagenomic sequence analysis | 2012/07/06 | English | 349 |
| A survey of current trends in computational drug repositioning | 2015/03/31 | English | 330 |
| Swiss-PDB Viewer (Deep View) | 2001/01/01 | English | 329 |
| A survey of tools for variant analysis of next-generation genome sequencing data | 2013/01/21 | English | 320 |
| Trends in the development of miRNA bioinformatics tools | 2019/06/17 | English | 314 |
| Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology | 2009/12/02 | English | 310 |
| Genetic association studies: Design, analysis and interpretation | 2002/06/01 | English | 309 |