Genomics and Phylogenetic Studies

Most cited papers

1. Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research · 1997 · 75,091 citations
2. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choiceNucleic Acids Research · 1994 · 65,374 citations
3. STAR: ultrafast universal RNA-seq alignerBioinformatics · 2012 · 58,430 citations
4. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and UsabilityMolecular Biology and Evolution · 2013 · 50,278 citations
5. MUSCLE: multiple sequence alignment with high accuracy and high throughputNucleic Acids Research · 2004 · 47,425 citations
6. Cutadapt removes adapter sequences from high-throughput sequencing readsEMBnet journal · 2011 · 37,307 citations
7. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genomeBMC Bioinformatics · 2011 · 24,108 citations
8. Ultrafast and memory-efficient alignment of short DNA sequences to the human genomeGenome biology · 2009 · 23,395 citations
9. HTSeq—a Python framework to work with high-throughput sequencing dataBioinformatics · 2014 · 23,354 citations
10. Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial CommunitiesApplied and Environmental Microbiology · 2009 · 22,129 citations
11. Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial TaxonomyApplied and Environmental Microbiology · 2007 · 20,833 citations
12. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transformNucleic Acids Research · 2002 · 18,272 citations
13. Minimap2: pairwise alignment for nucleotide sequencesBioinformatics · 2018 · 17,805 citations
14. FastTree 2 – Approximately Maximum-Likelihood Trees for Large AlignmentsPLoS ONE · 2010 · 16,480 citations
15. The Pfam Protein Families DatabaseNucleic Acids Research · 2002 · 14,196 citations
16. Prodigal: prokaryotic gene recognition and translation initiation site identificationBMC Bioinformatics · 2010 · 13,803 citations
17. The Sequence of the Human GenomeScience · 2001 · 13,708 citations
18. Fast and accurate long-read alignment with Burrows–Wheeler transformBioinformatics · 2010 · 13,175 citations
19. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequencesBioinformatics · 2006 · 12,464 citations
20. Improved tools for biological sequence comparison.Proceedings of the National Academy of Sciences · 1988 · 11,371 citations
21. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic SequenceNucleic Acids Research · 1997 · 11,340 citations
22. Database resources of the National Center for Biotechnology Information: updateNucleic Acids Research · 2003 · 10,979 citations
23. InterProScan 5: genome-scale protein function classificationBioinformatics · 2014 · 10,406 citations
24. ColabFold: making protein folding accessible to allNature Methods · 2022 · 10,204 citations
25. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platformsThe ISME Journal · 2012 · 9,303 citations
26. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studiesNucleic Acids Research · 2012 · 9,292 citations
27. UniFrac: a New Phylogenetic Method for Comparing Microbial CommunitiesApplied and Environmental Microbiology · 2005 · 8,702 citations
28. UniProt: a worldwide hub of protein knowledgeNucleic Acids Research · 2018 · 8,547 citations
29. dbSNP: the NCBI database of genetic variationNucleic Acids Research · 2001 · 7,965 citations
30. Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing PlatformApplied and Environmental Microbiology · 2013 · 7,693 citations
31. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier pluginMicrobiome · 2018 · 6,287 citations
32. Phytozome: a comparative platform for green plant genomicsNucleic Acids Research · 2011 · 5,914 citations
33. The diversity and biogeography of soil bacterial communitiesProceedings of the National Academy of Sciences · 2006 · 5,849 citations
34. TOWARD AN ECOLOGICAL CLASSIFICATION OF SOIL BACTERIAEcology · 2007 · 5,185 citations
35. Kraken: ultrafast metagenomic sequence classification using exact alignmentsGenome biology · 2014 · 5,012 citations
36. The Ribosomal Database Project: improved alignments and new tools for rRNA analysisNucleic Acids Research · 2008 · 4,875 citations
37. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samplesEnvironmental Microbiology · 2015 · 4,331 citations
38. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomesGenome biology · 2020 · 4,174 citations
39. Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental ScaleApplied and Environmental Microbiology · 2009 · 4,145 citations
40. Decoupling function and taxonomy in the global ocean microbiomeScience · 2016 · 3,730 citations
41. A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and LeuconostocaceaeINTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · 2020 · 3,361 citations
42. MEME: discovering and analyzing DNA and protein sequence motifsNucleic Acids Research · 2006 · 2,805 citations
43. Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under SelectionMolecular Biology and Evolution · 2005 · 2,513 citations