Stephen F Altschul
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Explore the profile of Stephen F Altschul including associated specialties, affiliations and a list of published articles.
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26
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2106
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Recent Articles
1.
Neuwald A, Kolaczkowski B, Altschul S
Bioinformatics
. 2021 May;
37(20):3456-3463.
PMID: 33983436
Motivation: Detecting subtle biologically relevant patterns in protein sequences often requires the construction of a large and accurate multiple sequence alignment (MSA). Methods for constructing MSAs are usually evaluated using...
2.
Tondnevis F, Dudenhausen E, Miller A, McKenna R, Altschul S, Bloom L, et al.
Sci Rep
. 2020 Feb;
10(1):1691.
PMID: 32015389
Protein functional constraints are manifest as superfamily and functional-subgroup conserved residues, and as pairwise correlations. Deep Analysis of Residue Constraints (DARC) aids the visualization of these constraints, characterizes how they...
3.
Neuwald A, Altschul S
PLoS Comput Biol
. 2019 Jan;
14(12):e1006237.
PMID: 30596639
Protein Direct Coupling Analysis (DCA), which predicts residue-residue contacts based on covarying positions within a multiple sequence alignment, has been remarkably effective. This suggests that there is more to learn...
4.
Shah N, Altschul S, Pop M
Algorithms Mol Biol
. 2018 Mar;
13:7.
PMID: 29588650
Background: An important task in a metagenomic analysis is the assignment of taxonomic labels to sequences in a sample. Most widely used methods for taxonomy assignment compare a sequence in...
5.
Neuwald A, Aravind L, Altschul S
Elife
. 2018 Jan;
7.
PMID: 29336305
Residues responsible for allostery, cooperativity, and other subtle but functionally important interactions remain difficult to detect. To aid such detection, we employ statistical inference based on the assumption that residues...
6.
Altschul S, Neuwald A
J Comput Biol
. 2017 Aug;
25(2):121-129.
PMID: 28771374
We study a simple abstract problem motivated by a variety of applications in protein sequence analysis. Consider a string of 0s and 1s of length L, and containing D 1s....
7.
Neuwald A, Altschul S
PLoS Comput Biol
. 2016 Dec;
12(12):e1005294.
PMID: 28002465
Over evolutionary time, members of a superfamily of homologous proteins sharing a common structural core diverge into subgroups filling various functional niches. At the sequence level, such divergence appears as...
8.
Neuwald A, Altschul S
PLoS Comput Biol
. 2016 May;
12(5):e1004936.
PMID: 27192614
We describe a Bayesian Markov chain Monte Carlo (MCMC) sampler for protein multiple sequence alignment (MSA) that, as implemented in the program GISMO and applied to large numbers of diverse...
9.
Yu Y, Capra J, Stojmirovic A, Landsman D, Altschul S
Bioinformatics
. 2014 Oct;
31(3):324-31.
PMID: 25294922
Motivation: DNA and protein patterns are usefully represented by sequence logos. However, the methods for logo generation in common use lack a proper statistical basis, and are non-optimal for recognizing...
10.
Nguyen V, Boyd-Graber J, Altschul S
J Comput Biol
. 2013 Jan;
20(1):1-18.
PMID: 23294268
The Dirichlet process is used to model probability distributions that are mixtures of an unknown number of components. Amino acid frequencies at homologous positions within related proteins have been fruitfully...