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Stephen F. Altschul

National Institutes of Health

DOI: 10.1093/bioinformatics/btab374
Bioinformatics ·
2021
eCOMPASS: evaluative comparison of multiple protein alignments by statistical score.
Andrew F. Neuwald, Bryan Kolaczkowski, Stephen F. Altschul
Computer science
Computational biology
Data mining
DOI: 10.1038/s41598-019-55118-6
Scientific Reports ·
2020
Cited 8 times
Deep Analysis of Residue Constraints (DARC): identifying determinants of protein functional specificity.
Farzaneh Tondnevis, Elizabeth E. Dudenhausen, Andrew M. Miller, Robert McKenna, Stephen F. Altschul, Linda B. Bloom, Andrew F. Neuwald
Computational biology
Biology
Protein design
DOI: 10.1371/journal.pcbi.1006237
PLOS Computational Biology ·
2018
Cited 5 times
Statistical investigations of protein residue direct couplings.
Andrew F. Neuwald, Stephen F. Altschul
Residue (chemistry)
Chemistry
Computer science
DOI: 10.1101/334540
bioRxiv ·
2018
Statistical Investigations of Protein Residue Direct Couplings
Andrew F. Neuwald, Stephen F. Altschul
Chemistry
Residue (chemistry)
Biological system
DOI: 10.1186/s13015-018-0126-3
Algorithms for Molecular Biology ·
2018
Cited 9 times
Outlier detection in BLAST hits.
Nidhi Shah, Stephen F. Altschul, Mihai Pop
Data mining
Pattern recognition (psychology)
Machine learning
DOI: 10.7554/elife.29880
eLife ·
2018
Cited 11 times
Inferring joint sequence-structural determinants of protein functional specificity.
Andrew F. Neuwald, L. Aravind, Stephen F. Altschul
Sequence (biology)
Computer science
Joint (building)
DOI: 10.7554/elife.29880.030
eLife ·
2017
Author response: Inferring joint sequence-structural determinants of protein functional specificity
Andrew F. Neuwald, L. Aravind, Stephen F. Altschul
Computational biology
Joint (building)
Sequence (biology)
DOI: 10.1089/cmb.2017.0050
Journal of Computational Biology ·
2017
Cited 4 times
Initial Cluster Analysis.
Stephen F. Altschul, Andrew F. Neuwald
Cluster (spacecraft)
Computer science
Cluster analysis
DOI: 10.4230/lipics.wabi.2017.23
workshop on algorithms in bioinformatics ·
2017
Outlier Detection in BLAST Hits
Nidhi Shah, Stephen F. Altschul, Mihai Pop
Computer science
Anomaly detection
Outlier
DOI: 10.1371/journal.pcbi.1005294
PLOS Computational Biology ·
2016
Cited 5 times
Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations.
Andrew F. Neuwald, Stephen F. Altschul
Computer science
Inference
Biological system
DOI: 10.1371/journal.pcbi.1004936
PLOS Computational Biology ·
2016
Cited 16 times
Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties
Andrew F. Neuwald, Stephen F. Altschul
Computer science
Bayesian probability
Computational biology
DOI: 10.1093/bioinformatics/btu634
Bioinformatics ·
2015
Cited 8 times
Log-odds sequence logos
Yi-Kuo Yu, John A. Capra, Aleksandar Stojmirović, David Landsman, Stephen F. Altschul
Computer science
Logos Bible Software
Computational biology
DOI: 10.1007/978-3-642-27848-8_207-2
Encyclopedia of Algorithms ·
2015
Local Alignment (with Affine Gap Weights)
Stephen F. Altschul, Bruce W. Erickson, Henry Leung
Affine transformation
Computer science
Mathematics
DOI: 10.1038/nbt0614-592b
Nature Biotechnology ·
2014
Erratum: The anatomy of successful computational biology software
Stephen F. Altschul, Barry Demchak, Richard Durbin, Robert Gentleman, Martin Krzywinski, Heng Li, Anton Nekrutenko, James T. Robinson, Wayne Rasband, James Taylor, Cole Trapnell
Computer science
Software engineering
Software
DOI: 10.1038/nbt.2721
Nature Biotechnology ·
2013
Cited 26 times
The anatomy of successful computational biology software.
Stephen F. Altschul, Barry Demchak, Richard Durbin, Robert Gentleman, Martin Krzywinski, Heng Li, Anton Nekrutenko, James T. Robinson, Wayne Rasband, James Taylor, Cole Trapnell
Software engineering
DOI: 10.1089/cmb.2012.0244
Journal of Computational Biology ·
2013
Cited 26 times
Dirichlet Mixtures, the Dirichlet Process, and the Structure of Protein Space
Viet-An Nguyen, Jordan Boyd-Graber, Stephen F. Altschul
Dirichlet distribution
Multinomial distribution
Generalized Dirichlet distribution
DOI: 10.1186/1745-6150-7-12
Biology Direct ·
2012
Cited 565 times
Domain enhanced lookup time accelerated BLAST.
Grzegorz M. Boratyn, Alejandro A. Schäffer, Richa Agarwala, Stephen F. Altschul, David J. Lipman, Thomas L. Madden
Computer science
Sequence database
Context (archaeology)
DOI: 10.1093/bioinformatics/btr565
Bioinformatics ·
2011
Cited 10 times
An assessment of substitution scores for protein profile–profile comparison
Xugang Ye, Guoli Wang, Stephen F. Altschul
Computer science
Statistics
Substitution (logic)
DOI: 10.1089/cmb.2011.0039
Journal of Computational Biology ·
2011
Cited 4 times
The Complexity of the Dirichlet Model for Multiple Alignment Data
Yi-Kuo Yu, Stephen F. Altschul
Computer science
Mathematics
Artificial intelligence
DOI: 10.1089/cmb.2011.0040
Journal of Computational Biology ·
2011
Cited 5 times
On the Inference of Dirichlet Mixture Priors for Protein Sequence Comparison
Xugang Ye, Yi-Kuo Yu, Stephen F. Altschul
Prior probability
Inference
Computer science
DOI: 10.1089/cmb.2010.0117
Journal of Computational Biology ·
2010
Cited 9 times
Compositional adjustment of Dirichlet mixture priors.
Xugang Ye, Yi-Kuo Yu, Stephen F. Altschul
Prior probability
Dirichlet distribution
Artificial intelligence
DOI: 10.1371/journal.pcbi.1000852
PLOS Computational Biology ·
2010
Cited 52 times
The construction and use of log-odds substitution scores for multiple sequence alignment.
Stephen F. Altschul, John C. Wootton, Elena Zaslavsky, Yi-Kuo Yu
Substitution (logic)
Computer science
Sequence (biology)
DOI: 10.1093/nar/gkn981
Nucleic Acids Research ·
2009
Cited 99 times
PSI-BLAST pseudocounts and the minimum description length principle
Stephen F. Altschul, E. Michael Gertz, Richa Agarwala, Alejandro A. Schäffer, Yi-Kuo Yu
DOI: 10.1093/bioinformatics/btn171
Bioinformatics ·
2008
Cited 8 times
The effectiveness of position-and composition-specific gap costs for protein similarity searches
Aleksandar Stojmirović, E. Michael Gertz, Stephen F. Altschul, Yi-Kuo Yu
Computer science
Similarity (geometry)
Computational biology
DOI: 10.1186/1741-7007-4-41
BMC Biology ·
2006
Cited 306 times
Composition-based statistics and translated nucleotide searches: Improving the TBLASTN module of BLAST
E. Michael Gertz, Yi-Kuo Yu, Richa Agarwala, Alejandro A. Schäffer, Stephen F. Altschul
Computational biology
Genetics