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Items: 1 to 50 of 61

1.

Statistical investigations of protein residue direct couplings.

Neuwald AF, Altschul SF.

PLoS Comput Biol. 2018 Dec 31;14(12):e1006237. doi: 10.1371/journal.pcbi.1006237. eCollection 2018 Dec.

2.

Outlier detection in BLAST hits.

Shah N, Altschul SF, Pop M.

Algorithms Mol Biol. 2018 Mar 22;13:7. doi: 10.1186/s13015-018-0126-3. eCollection 2018.

3.

Inferring joint sequence-structural determinants of protein functional specificity.

Neuwald AF, Aravind L, Altschul SF.

Elife. 2018 Jan 16;7. pii: e29880. doi: 10.7554/eLife.29880.

4.

Sequence Alignment.

Altschul SF, Pop M.

In: Rosen KH, Shier DR, Goddard W, editors. Handbook of Discrete and Combinatorial Mathematics. 2nd edition. Boca Raton (FL): CRC Press/Taylor & Francis; 2017 Nov. 20.1.

5.

Initial Cluster Analysis.

Altschul SF, Neuwald AF.

J Comput Biol. 2018 Feb;25(2):121-129. doi: 10.1089/cmb.2017.0050. Epub 2017 Aug 3.

6.

Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations.

Neuwald AF, Altschul SF.

PLoS Comput Biol. 2016 Dec 21;12(12):e1005294. doi: 10.1371/journal.pcbi.1005294. eCollection 2016 Dec.

7.

Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties.

Neuwald AF, Altschul SF.

PLoS Comput Biol. 2016 May 18;12(5):e1004936. doi: 10.1371/journal.pcbi.1004936. eCollection 2016 May.

8.

Log-odds sequence logos.

Yu YK, Capra JA, Stojmirović A, Landsman D, Altschul SF.

Bioinformatics. 2015 Feb 1;31(3):324-31. doi: 10.1093/bioinformatics/btu634. Epub 2014 Oct 6.

9.

Dirichlet mixtures, the Dirichlet process, and the structure of protein space.

Nguyen VA, Boyd-Graber J, Altschul SF.

J Comput Biol. 2013 Jan;20(1):1-18. doi: 10.1089/cmb.2012.0244.

10.

Domain enhanced lookup time accelerated BLAST.

Boratyn GM, Schäffer AA, Agarwala R, Altschul SF, Lipman DJ, Madden TL.

Biol Direct. 2012 Apr 17;7:12. doi: 10.1186/1745-6150-7-12.

11.

An assessment of substitution scores for protein profile-profile comparison.

Ye X, Wang G, Altschul SF.

Bioinformatics. 2011 Dec 15;27(24):3356-63. doi: 10.1093/bioinformatics/btr565. Epub 2011 Oct 13.

12.

The complexity of the dirichlet model for multiple alignment data.

Yu YK, Altschul SF.

J Comput Biol. 2011 Aug;18(8):925-39. doi: 10.1089/cmb.2011.0039. Epub 2011 Jun 24.

13.

On the inference of dirichlet mixture priors for protein sequence comparison.

Ye X, Yu YK, Altschul SF.

J Comput Biol. 2011 Aug;18(8):941-54. doi: 10.1089/cmb.2011.0040. Epub 2011 Jun 24.

14.

Compositional adjustment of Dirichlet mixture priors.

Ye X, Yu YK, Altschul SF.

J Comput Biol. 2010 Dec;17(12):1607-20. doi: 10.1089/cmb.2010.0117.

15.

The construction and use of log-odds substitution scores for multiple sequence alignment.

Altschul SF, Wootton JC, Zaslavsky E, Yu YK.

PLoS Comput Biol. 2010 Jul 15;6(7):e1000852. doi: 10.1371/journal.pcbi.1000852.

16.

PSI-BLAST pseudocounts and the minimum description length principle.

Altschul SF, Gertz EM, Agarwala R, Schäffer AA, Yu YK.

Nucleic Acids Res. 2009 Feb;37(3):815-24. doi: 10.1093/nar/gkn981. Epub 2008 Dec 16.

17.

The effectiveness of position- and composition-specific gap costs for protein similarity searches.

Stojmirović A, Gertz EM, Altschul SF, Yu YK.

Bioinformatics. 2008 Jul 1;24(13):i15-23. doi: 10.1093/bioinformatics/btn171.

18.

Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST.

Gertz EM, Yu YK, Agarwala R, Schäffer AA, Altschul SF.

BMC Biol. 2006 Dec 7;4:41.

19.

Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches.

Yu YK, Gertz EM, Agarwala R, Schäffer AA, Altschul SF.

Nucleic Acids Res. 2006;34(20):5966-73. Epub 2006 Oct 26.

20.

Protein database searches using compositionally adjusted substitution matrices.

Altschul SF, Wootton JC, Gertz EM, Agarwala R, Morgulis A, Schäffer AA, Yu YK.

FEBS J. 2005 Oct;272(20):5101-9. Review.

21.

A structure-based method for protein sequence alignment.

Kann MG, Thiessen PA, Panchenko AR, Schäffer AA, Altschul SF, Bryant SH.

Bioinformatics. 2005 Apr 15;21(8):1451-6. Epub 2004 Dec 21.

PMID:
15613392
22.

The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions.

Yu YK, Altschul SF.

Bioinformatics. 2005 Apr 1;21(7):902-11. Epub 2004 Oct 27.

PMID:
15509610
23.

The compositional adjustment of amino acid substitution matrices.

Yu YK, Wootton JC, Altschul SF.

Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15688-93. Epub 2003 Dec 8.

24.

Expression of a recombinant IRP-like Plasmodium falciparum protein that specifically binds putative plasmodial IREs.

Loyevsky M, Mompoint F, Yikilmaz E, Altschul SF, Madden T, Wootton JC, Kurantsin-Mills J, Kassim OO, Gordeuk VR, Rouault TA.

Mol Biochem Parasitol. 2003 Feb;126(2):231-8.

PMID:
12615322
25.

Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.

Strausberg RL, Feingold EA, Grouse LH, Derge JG, Klausner RD, Collins FS, Wagner L, Shenmen CM, Schuler GD, Altschul SF, Zeeberg B, Buetow KH, Schaefer CF, Bhat NK, Hopkins RF, Jordan H, Moore T, Max SI, Wang J, Hsieh F, Diatchenko L, Marusina K, Farmer AA, Rubin GM, Hong L, Stapleton M, Soares MB, Bonaldo MF, Casavant TL, Scheetz TE, Brownstein MJ, Usdin TB, Toshiyuki S, Carninci P, Prange C, Raha SS, Loquellano NA, Peters GJ, Abramson RD, Mullahy SJ, Bosak SA, McEwan PJ, McKernan KJ, Malek JA, Gunaratne PH, Richards S, Worley KC, Hale S, Garcia AM, Gay LJ, Hulyk SW, Villalon DK, Muzny DM, Sodergren EJ, Lu X, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madan A, Young AC, Shevchenko Y, Bouffard GG, Blakesley RW, Touchman JW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Krzywinski MI, Skalska U, Smailus DE, Schnerch A, Schein JE, Jones SJ, Marra MA; Mammalian Gene Collection Program Team.

Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

26.

Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.

Schäffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF.

Nucleic Acids Res. 2001 Jul 15;29(14):2994-3005. Review.

27.

The estimation of statistical parameters for local alignment score distributions.

Altschul SF, Bundschuh R, Olsen R, Hwa T.

Nucleic Acids Res. 2001 Jan 15;29(2):351-61.

28.

SAGEmap: a public gene expression resource.

Lash AE, Tolstoshev CM, Wagner L, Schuler GD, Strausberg RL, Riggins GJ, Altschul SF.

Genome Res. 2000 Jul;10(7):1051-60.

29.

IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices.

Schäffer AA, Wolf YI, Ponting CP, Koonin EV, Aravind L, Altschul SF.

Bioinformatics. 1999 Dec;15(12):1000-11.

PMID:
10745990
30.

A public database for gene expression in human cancers.

Lal A, Lash AE, Altschul SF, Velculescu V, Zhang L, McLendon RE, Marra MA, Prange C, Morin PJ, Polyak K, Papadopoulos N, Vogelstein B, Kinzler KW, Strausberg RL, Riggins GJ.

Cancer Res. 1999 Nov 1;59(21):5403-7.

31.

Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases.

Altschul SF, Koonin EV.

Trends Biochem Sci. 1998 Nov;23(11):444-7. Review. No abstract available.

PMID:
9852764
32.

Characterization of gene expression in resting and activated mast cells.

Chen H, Centola M, Altschul SF, Metzger H.

J Exp Med. 1998 Nov 2;188(9):1657-68. Erratum in: J Exp Med 1998 Dec 21;188(12):2387.

33.

Protein sequence similarity searches using patterns as seeds.

Zhang Z, Schäffer AA, Miller W, Madden TL, Lipman DJ, Koonin EV, Altschul SF.

Nucleic Acids Res. 1998 Sep 1;26(17):3986-90.

34.

Generalized affine gap costs for protein sequence alignment.

Altschul SF.

Proteins. 1998 Jul 1;32(1):88-96.

PMID:
9672045
35.

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ.

Nucleic Acids Res. 1997 Sep 1;25(17):3389-402. Review.

36.

A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins.

Bork P, Hofmann K, Bucher P, Neuwald AF, Altschul SF, Koonin EV.

FASEB J. 1997 Jan;11(1):68-76.

PMID:
9034168
37.

BRCA1 protein products ... Functional motifs...

Koonin EV, Altschul SF, Bork P.

Nat Genet. 1996 Jul;13(3):266-8. No abstract available.

PMID:
8673121
38.

Local alignment statistics.

Altschul SF, Gish W.

Methods Enzymol. 1996;266:460-80. No abstract available.

PMID:
8743700
39.

Statistics of sequence-structure threading.

Bryant SH, Altschul SF.

Curr Opin Struct Biol. 1995 Apr;5(2):236-44. Review.

PMID:
7648327
40.

Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks.

Tatusov RL, Altschul SF, Koonin EV.

Proc Natl Acad Sci U S A. 1994 Dec 6;91(25):12091-5.

41.
42.

Issues in searching molecular sequence databases.

Altschul SF, Boguski MS, Gish W, Wootton JC.

Nat Genet. 1994 Feb;6(2):119-29. Review.

PMID:
8162065
43.

Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.

Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC.

Science. 1993 Oct 8;262(5131):208-14.

PMID:
8211139
44.

Applications and statistics for multiple high-scoring segments in molecular sequences.

Karlin S, Altschul SF.

Proc Natl Acad Sci U S A. 1993 Jun 15;90(12):5873-7.

45.

A protein alignment scoring system sensitive at all evolutionary distances.

Altschul SF.

J Mol Evol. 1993 Mar;36(3):290-300.

PMID:
8483166
46.

Amino acid substitution matrices from an information theoretic perspective.

Altschul SF.

J Mol Biol. 1991 Jun 5;219(3):555-65.

PMID:
2051488
47.

A workbench for multiple alignment construction and analysis.

Schuler GD, Altschul SF, Lipman DJ.

Proteins. 1991;9(3):180-90.

PMID:
2006136
48.

Statistical methods and insights for protein and DNA sequences.

Karlin S, Bucher P, Brendel V, Altschul SF.

Annu Rev Biophys Biophys Chem. 1991;20:175-203. Review. No abstract available.

PMID:
1867715
49.

Equal animals.

Altschul SF, Lipman DJ.

Nature. 1990 Dec 6;348(6301):493-4. No abstract available.

PMID:
2247160
50.

Basic local alignment search tool.

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ.

J Mol Biol. 1990 Oct 5;215(3):403-10.

PMID:
2231712

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