Standout Papers
- Algorithms on strings, trees, and sequences computer science and computational biology (1997)
Citation Impact
Citing Papers
Removing T-cell epitopes with computational protein design
2014 StandoutNobel
STAR: ultrafast universal RNA-seq aligner
2012 Standout
Limits of long-term selection against Neandertal introgression
2019 StandoutNobel
Transposition-Driven Genomic Heterogeneity in the Drosophila Brain
2013 StandoutScienceNobel
fastp: an ultra-fast all-in-one FASTQ preprocessor
2018 Standout
VSEARCH: a versatile open source tool for metagenomics
2016 Standout
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
2014 Standout
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
2013 Standout
Global Identification and Characterization of Both O-GlcNAcylation and Phosphorylation at the Murine Synapse
2012
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
2000 StandoutNature
An integrated map of genetic variation from 1,092 human genomes
2012 StandoutNature
The GEM mapper: fast, accurate and versatile alignment by filtration
2012
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
2014 Standout
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
2011 Standout
Collapse of Germline piRNAs in the Absence of Argonaute3 Reveals Somatic piRNAs in Flies
2009
Clustering algorithm for determining community structure in large networks
2006
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
2010 Standout
The genomic landscape of Neanderthal ancestry in present-day humans
2014 StandoutNatureNobel
Versatile and open software for comparing large genomes
2004 Standout
New CRISPR–Cas systems from uncultivated microbes
2016 StandoutNatureNobel
Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins
1998 StandoutNobel
Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes
2016
MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes
2006
MUSCLE: multiple sequence alignment with high accuracy and high throughput
2004 Standout
MicroRNAs: Target Recognition and Regulatory Functions
2009 Standout
Differential oestrogen receptor binding is associated with clinical outcome in breast cancer
2012 StandoutNature
The impact of microRNAs on protein output
2008 StandoutNature
Alignment of whole genomes
1999
Fast algorithms for large-scale genome alignment and comparison
2002
On the Complexity of Multiple Sequence Alignment
1994 Standout
LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA
2003
RNA-guided genetic silencing systems in bacteria and archaea
2012 StandoutNatureNobel
Diet rapidly and reproducibly alters the human gut microbiome
2013 StandoutNature
Improved Prediction of Signal Peptides: SignalP 3.0
2004 Standout
A Pattern-Based Method for the Identification of MicroRNA Binding Sites and Their Corresponding Heteroduplexes
2006 Standout
Tunicates and not cephalochordates are the closest living relatives of vertebrates
2006 StandoutNature
An obesity-associated gut microbiome with increased capacity for energy harvest
2006 StandoutNature
Adaptive seeds tame genomic sequence comparison
2011
An early modern human from Romania with a recent Neanderthal ancestor
2015 StandoutNatureNobel
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
1994 Standout
Fast gapped-read alignment with Bowtie 2
2012 Standout
Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting
2012 StandoutNatureNobel
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats
2007 Standout
Using quality scores and longer reads improves accuracy of Solexa read mapping
2008
Optimization algorithms for functional deimmunization of therapeutic proteins
2010
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
2002 Standout
SSAHA: A Fast Search Method for Large DNA Databases
2001
Survey of Clustering Algorithms
2005 Standout
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
1997 Standout
Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
2008
Complete Alternative Splicing Events Are Bubbles in Splicing Graphs
2009
The Efficient Computation of Position-Specific Match Scores with the Fast Fourier Transform
2002
The map-based sequence of the rice genome
2005 StandoutNature
Hidden Markov models of biological primary sequence information.
1994 StandoutNobel
Genome-wide nucleotide-level mammalian ancestor reconstruction
2008
CloudBurst: highly sensitive read mapping with MapReduce
2009
Efficient construction of an assembly string graph using the FM-index
2010
Comparative analysis of multiple protein-sequence alignment methods.
1994
Detecting Subtle Sequence Signals: a Gibbs Sampling Strategy for Multiple Alignment
1993 Science
Community detection in graphs
2009 Standout
Graph clustering
2007 Standout
Systematic discovery of natural CRISPR-Cas12a inhibitors
2018 StandoutScienceNobel
Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals
2016 StandoutScienceNobel
Comparative Performance of Bayesian and AIC-Based Measures of Phylogenetic Model Uncertainty
2006
Compressed Suffix Arrays and Suffix Trees with Applications to Text Indexing and String Matching
2005
Programmed DNA destruction by miniature CRISPR-Cas14 enzymes
2018 StandoutScienceNobel
Cutadapt removes adapter sequences from high-throughput sequencing reads
2011 Standout
CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly \ninterspaced palindromic repeats
2008
Stable matchings with couples
1996
Compressed Suffix Arrays and Suffix Trees with Applications to Text Indexing and String Matching Read More: http://epubs.siam.org/doi/abs/10.1137/S0097539702402354
2005
Compressed indexing and local alignment of DNA
2008
Fast and accurate short read alignment with Burrows–Wheeler transform
2009 Standout
Nuclear and mitochondrial DNA sequences from two Denisovan individuals
2015 StandoutNobel
High Throughput Short Read Alignment via Bi-directional BWT
2009
Comparison and validation of community structures in complex networks
2006
Parallelized phylogenetic post-analysis on multi-core architectures
2010
Clustering by fast search and find of density peaks
2014 StandoutScience
Anomaly detection
2009 Standout
A metric model of amino acid substitution
2004
The Long-Term Stability of the Human Gut Microbiota
2013 StandoutScience
A unified statistical framework for sequence comparison and structure comparison
1998 StandoutNobel
The Effects of the Change in the NRMP Matching Algorithm
1997 StandoutNobel
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
2013 Standout
Generalized affine gap costs for protein sequence alignment
1998
Trimmomatic: a flexible trimmer for Illumina sequence data
2014 Standout
Chemical Glycoproteomics
2016 StandoutNobel
Works of Dan Gusfield being referenced
Parametric optimization of sequence alignment
1994
Efficient methods for multiple sequence alignment with guaranteed error bounds
1993
Algorithms in Bioinformatics
2002
ReCombinatorics
2014
Efficient algorithms for inferring evolutionary trees
1991
OPTIMAL, EFFICIENT RECONSTRUCTION OF PHYLOGENETIC NETWORKS WITH CONSTRAINED RECOMBINATION
2004
Linear time algorithms for finding and representing all the tandem repeats in a string
2004
Partition-distance: A problem and class of perfect graphs arising in clustering
2002
Efficient methods for multiple sequence alignment with guaranteed error bounds
1993
The Stable Marriage Problem: Structure and Algorithms
1991
Algorithms on strings, trees, and sequences computer science and computational biology
1997 Standout
Algorithms on Strings, Trees and Sequences
1997
Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology
1999