| # | Title | Journal | Year | Citations |
|---|
| 1 | MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment | Briefings in Bioinformatics | 2004 | 10,598 |
| 2 | Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration | Briefings in Bioinformatics | 2013 | 7,249 |
| 3 | MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization | Briefings in Bioinformatics | 2019 | 4,864 |
| 4 | Recent developments in the MAFFT multiple sequence alignment program | Briefings in Bioinformatics | 2008 | 3,115 |
| 5 | MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences | Briefings in Bioinformatics | 2008 | 3,073 |
| 6 | Deep learning for healthcare: review, opportunities and challenges | Briefings in Bioinformatics | 2018 | 1,459 |
| 7 | A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis | Briefings in Bioinformatics | 2013 | 1,064 |
| 8 | Deep learning in bioinformatics | Briefings in Bioinformatics | 2017 | 865 |
| 9 | Using Tablet for visual exploration of second-generation sequencing data | Briefings in Bioinformatics | 2013 | 836 |
| 10 | PROSITE: A documented database using patterns and profiles as motif descriptors | Briefings in Bioinformatics | 2002 | 802 |
| 11 | A survey of sequence alignment algorithms for next-generation sequencing | Briefings in Bioinformatics | 2010 | 765 |
| 12 | The UCSC genome browser and associated tools | Briefings in Bioinformatics | 2013 | 736 |
| 13 | Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium | Briefings in Bioinformatics | 2011 | 723 |
| 14 | Gene co-expression analysis for functional classification and gene–disease predictions | Briefings in Bioinformatics | 2018 | 718 |
| 15 | Machine learning in bioinformatics | Briefings in Bioinformatics | 2006 | 674 |
| 16 | Analytic approaches to twin data using structural equation models | Briefings in Bioinformatics | 2002 | 648 |
| 17 | Partial least squares: a versatile tool for the analysis of high-dimensional genomic data | Briefings in Bioinformatics | 2006 | 611 |
| 18 | A survey of current work in biomedical text mining | Briefings in Bioinformatics | 2005 | 604 |
| 19 | The BioCyc collection of microbial genomes and metabolic pathways | Briefings in Bioinformatics | 2019 | 582 |
| 20 | Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology | Briefings in Bioinformatics | 2010 | 551 |
| 21 | Revealing protein–lncRNA interaction | Briefings in Bioinformatics | 2016 | 536 |
| 22 | MicroRNAs and complex diseases: from experimental results to computational models | Briefings in Bioinformatics | 2019 | 507 |
| 23 | Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences | Briefings in Bioinformatics | 2018 | 498 |
| 24 | Circular RNA identification based on multiple seed matching | Briefings in Bioinformatics | 2018 | 498 |
| 25 | Drug–target interaction prediction: databases, web servers and computational models | Briefings in Bioinformatics | 2016 | 496 |
| 26 | oncoPredict: an R package for predicting in vivo or cancer patient drug response and biomarkers from cell line screening data | Briefings in Bioinformatics | 2021 | 492 |
| 27 | A survey of tools for variant analysis of next-generation genome sequencing data | Briefings in Bioinformatics | 2014 | 480 |
| 28 | Long non-coding RNAs and complex diseases: from experimental results to computational models | Briefings in Bioinformatics | 2017 | 477 |
| 29 | A survey of current trends in computational drug repositioning | Briefings in Bioinformatics | 2016 | 459 |
| 30 | Exploiting drug-disease relationships for computational drug repositioning | Briefings in Bioinformatics | 2011 | 448 |
| 31 | Identifying miRNAs, targets and functions | Briefings in Bioinformatics | 2014 | 444 |
| 32 | Ultrafast clustering algorithms for metagenomic sequence analysis | Briefings in Bioinformatics | 2012 | 403 |
| 33 | PHAST and RPHAST: phylogenetic analysis with space/time models | Briefings in Bioinformatics | 2011 | 396 |
| 34 | Swiss-PDB Viewer (Deep View) | Briefings in Bioinformatics | 2001 | 392 |
| 35 | Genetic association studies: Design, analysis and interpretation | Briefings in Bioinformatics | 2002 | 392 |
| 36 | The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation | Briefings in Bioinformatics | 2008 | 390 |
| 37 | Graph-based methods for analysing networks in cell biology | Briefings in Bioinformatics | 2006 | 368 |
| 38 | A review of methods and databases for metagenomic classification and assembly | Briefings in Bioinformatics | 2019 | 368 |
| 39 | Comparison of software packages for detecting differential expression in RNA-seq studies | Briefings in Bioinformatics | 2015 | 361 |
| 40 | Trends in the development of miRNA bioinformatics tools | Briefings in Bioinformatics | 2019 | 361 |
| 41 | Flux balance analysis of biological systems: applications and challenges | Briefings in Bioinformatics | 2009 | 354 |
| 42 | Evaluation of variable selection methods for random forests and omics data sets | Briefings in Bioinformatics | 2019 | 342 |
| 43 | ProDom: Automated clustering of homologous domains | Briefings in Bioinformatics | 2002 | 341 |
| 44 | Swiss-Prot: Juggling between evolution and stability | Briefings in Bioinformatics | 2004 | 338 |
| 45 | Petri net modelling of biological networks | Briefings in Bioinformatics | 2007 | 336 |
| 46 | Toward more realistic drug-target interaction predictions | Briefings in Bioinformatics | 2015 | 331 |
| 47 | Vector NTI, a balanced all-in-one sequence analysis suite | Briefings in Bioinformatics | 2004 | 326 |
| 48 | Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle? | Briefings in Bioinformatics | 2013 | 324 |
| 49 | Similarity-based machine learning methods for predicting drug–target interactions: a brief review | Briefings in Bioinformatics | 2014 | 321 |
| 50 | LncTar: a tool for predicting the RNA targets of long noncoding RNAs | Briefings in Bioinformatics | 2015 | 318 |
