Title	Publication Date	Language	Citations
InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams	2015/05/22	English	1,295
Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis	2010/11/30	English	1,291
Interactive metagenomic visualization in a Web browser	2011/09/30	English	1,239
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects	2011/12/01	English	1,231
jvenn: an interactive Venn diagram viewer	2014/08/29	English	1,217
RNAstructure: software for RNA secondary structure prediction and analysis	2010/03/15	English	1,212
UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context	2006/08/07	English	1,124
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees	2018/05/01	English	1,092
Removing Noise From Pyrosequenced Amplicons	2011/01/28	English	1,091
TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses	2010/01/05	English	1,083
STEM: a tool for the analysis of short time series gene expression data	2006/04/05	English	1,072
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments	2010/02/18	English	1,039
SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data	2010/09/27	English	1,010
Bias in error estimation when using cross-validation for model selection	2006/02/23	English	936
Detecting outliers when fitting data with nonlinear regression – a new method based on robust nonlinear regression and the false discovery rate	2006/03/09	English	922
Dendroscope: An interactive viewer for large phylogenetic trees	2007/11/22	English	919
LOSITAN: A workbench to detect molecular adaptation based on a F st -outlier method	2008/07/28	English	890
ElliPro: a new structure-based tool for the prediction of antibody epitopes	2008/12/01	English	878
The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs	2002/01/17	English	876
GAGE: generally applicable gene set enrichment for pathway analysis	2009/05/27	English	868
Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads	2014/06/12	English	843
A flexible R package for nonnegative matrix factorization	2010/07/02	English	832
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons	2008/01/14	English	818
Fpocket: An open source platform for ligand pocket detection	2009/06/02	English	805
Proteinortho: Detection of (Co-)orthologs in large-scale analysis	2011/04/28	English	794
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory	2012/09/19	English	781
TreeDyn: towards dynamic graphics and annotations for analyses of trees	2006/10/10	English	773
Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry	2007/03/27	English	765
Highly sensitive feature detection for high resolution LC/MS	2008/11/28	English	761
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources	2006/02/09	English	745