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Microbial gene identification using interpolated Markov models.
Salzberg SL, Delcher AL, Kasif S, White O. Salzberg SL, et al. Among authors: kasif s. Nucleic Acids Res. 1998 Jan 15;26(2):544-8. doi: 10.1093/nar/26.2.544. Nucleic Acids Res. 1998. PMID: 9421513 Free PMC article.
Optimized multiplex PCR: efficiently closing a whole-genome shotgun sequencing project.
Tettelin H, Radune D, Kasif S, Khouri H, Salzberg SL. Tettelin H, et al. Among authors: kasif s. Genomics. 1999 Dec 15;62(3):500-7. doi: 10.1006/geno.1999.6048. Genomics. 1999. PMID: 10644449
A computational framework for optimal masking in the synthesis of oligonucleotide microarrays.
Kasif S, Weng Z, Derti A, Beigel R, DeLisi C. Kasif S, et al. Nucleic Acids Res. 2002 Oct 15;30(20):e106. doi: 10.1093/nar/gnf105. Nucleic Acids Res. 2002. PMID: 12384608 Free PMC article.
A comparative genomic method for computational identification of prokaryotic translation initiation sites.
Walker M, Pavlovic V, Kasif S. Walker M, et al. Among authors: kasif s. Nucleic Acids Res. 2002 Jul 15;30(14):3181-91. doi: 10.1093/nar/gkf423. Nucleic Acids Res. 2002. PMID: 12136100 Free PMC article.
Identification of genes with fast-evolving regions in microbial genomes.
Zheng Y, Roberts RJ, Kasif S. Zheng Y, et al. Among authors: kasif s. Nucleic Acids Res. 2004 Dec 2;32(21):6347-57. doi: 10.1093/nar/gkh935. Print 2004. Nucleic Acids Res. 2004. PMID: 15576679 Free PMC article.
Alignment of whole genomes.
Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, Salzberg SL. Delcher AL, et al. Among authors: kasif s. Nucleic Acids Res. 1999 Jun 1;27(11):2369-76. doi: 10.1093/nar/27.11.2369. Nucleic Acids Res. 1999. PMID: 10325427 Free PMC article.
In each case it found an alignment of the input sequences, using between 30 s and 2 min of computation time. From the system output, information on single nucleotide changes, translocations and homologous genes can easily be extracted. ...
In each case it found an alignment of the input sequences, using between 30 s and 2 min of computation time. From the system output, …
Improved microbial gene identification with GLIMMER.
Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Delcher AL, et al. Among authors: kasif s. Nucleic Acids Res. 1999 Dec 1;27(23):4636-41. doi: 10.1093/nar/27.23.4636. Nucleic Acids Res. 1999. PMID: 10556321 Free PMC article.
COMBREX: a project to accelerate the functional annotation of prokaryotic genomes.
Roberts RJ, Chang YC, Hu Z, Rachlin JN, Anton BP, Pokrzywa RM, Choi HP, Faller LL, Guleria J, Housman G, Klitgord N, Mazumdar V, McGettrick MG, Osmani L, Swaminathan R, Tao KR, Letovsky S, Vitkup D, Segrè D, Salzberg SL, Delisi C, Steffen M, Kasif S. Roberts RJ, et al. Among authors: kasif s. Nucleic Acids Res. 2011 Jan;39(Database issue):D11-4. doi: 10.1093/nar/gkq1168. Epub 2010 Nov 21. Nucleic Acids Res. 2011. PMID: 21097892 Free PMC article.
Thousands of missed genes found in bacterial genomes and their analysis with COMBREX.
Wood DE, Lin H, Levy-Moonshine A, Swaminathan R, Chang YC, Anton BP, Osmani L, Steffen M, Kasif S, Salzberg SL. Wood DE, et al. Among authors: kasif s. Biol Direct. 2012 Oct 30;7:37. doi: 10.1186/1745-6150-7-37. Biol Direct. 2012. PMID: 23111013 Free PMC article.
The newly identified genes are available on COMBREX's website. REVIEWERS: This article was reviewed by Daniel Haft, Arcady Mushegian, and M. ...
The newly identified genes are available on COMBREX's website. REVIEWERS: This article was reviewed by Daniel Haft, Arcady Mushegian, …
Identification of rare germline copy number variations over-represented in five human cancer types.
Park RW, Kim TM, Kasif S, Park PJ. Park RW, et al. Among authors: kasif s. Mol Cancer. 2015 Feb 3;14:25. doi: 10.1186/s12943-015-0292-6. Mol Cancer. 2015. PMID: 25644941 Free PMC article.
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