Selected Publications

2011-2012

13.Fast gapped-read alignment with Bowtie 2. B. Langmead and S.L. Salzberg. Nature Methods 9 (2012), 357-359. (PDF reprint).
14.The perils of gene patents. S.L. Salzberg. Clinical Pharmacology & Therapeutics 91:6 (2012), 969-971.
15.Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. The Heliconius Genome Consortium. Nature 487 (2012), 94-98. (PDF reprint)
16.GAGE: A critical evaluation of genome assemblies and assembly algorithms. S.L. Salzberg, A.M. Phillippy, A.V. Zimin, D. Puiu, T. Magoc, S. Koren, T. Treangen, M.C. Schatz, A.L. Delcher, M. Roberts, G. Marcais, M. Pop, and J.A. Yorke. Genome Research 22:3 (2012), 557-567. (PDF reprint) (Supplementary material) (Suppl Figure 1) (Suppl Figure 2) (Suppl Table 1)
17.Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. C. Trapnell, A. Roberts, L. Goff, G. Pertea, D. Kim, D.R. Kelley, H. Pimental, S.L. Salzberg, J.L. Rinn, and L. Pachter. Nature Protocols 7:3 (2012), 562-578.
18.Repetitive DNA and next-generation sequencing: computational challenges and solutions. T.J. Treangen and S.L. Salzberg. Nature Reviews Genetics 13 (2012), 557-567.
19.Mis-assembled segmental duplications in two versions of the Bos taurus genome. A.V. Zimin, D.R. Kelley, M. Roberts, S.L. Salzberg, and J.A. Yorke. PLoS ONE 7(8): e42680 (2012).
20.Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering. D.R. Kelley, B. Liu, A.L. Delcher, M. Pop, and S.L. Salzberg. Nucleic Acids Research (2012) 40 (1): e9. doi:10.1093/nar/gkr1067.
21.TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. D. Kim and S.L. Salzberg. Genome Biology 2011, 12:R72.
22.FLASH: Fast length adjustment of short reads to improve genome assemblies. T. Magoc and S.L. Salzberg. Bioinformatics 27:21 (2011), 2957-63.
23.PhymmBL expanded: confidence scores, custom databases, parallelization and more. A. Brady and S. Salzberg. Nature Methods 8, 367 (2011).
24.Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp.. A.J. Bogdanove, R. Koebnik, H. Lu, ..., and S.L. Salzberg. J. Bacteriology 193:19 (2011), 5450-64.
25.Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths. J. Enk et al., Genome Biology 2011, 12:R51.
26.Detection of lineage-specific evolutionary changes among primate species. M. Pertea, G.M. Pertea, and S.L. Salzberg. BMC Bioinformatics 2011, 12:274.
27.Mugsy: Fast multiple alignment of closely related whole genomes. S. V. Angiuoli and S.L. Salzberg. Bioinformatics (2011), 27(3), 334-342.
28.Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. D. Rasko et al. Proc. National Acad. Sci. 108:12 (2011), 5027-32.
29.The genome of woodland strawberry (Fragaria vesca). V. Shulaev et al. Nature Genetics 43(2011), 109-116.

2009-2010

30.Do-it-yourself genetic testing. S.L. Salzberg and M. Pertea. Genome Biology 2010, 11:404.
31.Cloud computing and the DNA data race. M.C. Schatz, B. Langmead, and S.L. Salzberg. Nature Biotechnology 28, 691-693 (2010).
32.Quake: quality-aware detection and correction of sequencing errors. D.R. Kelley, M.C. Schatz, and S.L. Salzberg. Genome Biology 2010, 11:R116.
33.Between a chicken and a grape: estimating the number of human genes. M. Pertea and S.L. Salzberg. Genome Biology 2010, 11:206.
34.Assembly of large genomes using second-generation sequencing. M.C. Schatz, A.L. Delcher, and S.L. Salzberg. Genome Research 20 (2010), 1165-1173.
35.[The Cufflinks paper] Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. C. Trapnell, B.A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M.J. van Baren, S.L. Salzberg, B.J. Wold, and L. Pachter (2010). Nature Biotechnology 28, 511-515 (2010).
36.Recent advances in RNA sequence analysis. F1000 Biology Reports 2010, 2:64.
37.Mind the gaps. S.L. Salzberg, Nature Methods 7:2 (2010), 105-6.
38.[the turkey genome] Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. R.A. Dalloul et al.,PLoS Biology 8(9): e1000475 (2010).
39.Searching for SNPs with cloud computing. B. Langmead, M.C. Schatz, J. Lin, M. Pop, and S.L. Salzberg. Genome Biology 2009, 10:R134.
40.Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. A. Brady and S.L. Salzberg. Nature Methods, 6:673-676, 2009.
41.[The Bowtie paper] Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. B. Langmead, C. Trapnell, M. Pop, and S.L. Salzberg. Genome Biology 2009, 10:R25. doi:10.1186/gb-2009-10-3-r25.
42.TopHat: discovering splice junctions with RNA-Seq. C. Trapnell, L. Pachter, and S.L. Salzberg. Bioinformatics, 25:1105-11, 2009.
43.A whole-genome assembly of the domestic cow, Bos taurus. A.V. Zimin, A.L. Delcher, L. Florea, D.R. Kelley, M.C. Schatz, D. Puiu, F. Hanrahan, G. Pertea, C.P. Van Tassell, T.S. Sonstegard, G. Marcais, M. Roberts, P. Subramanian, J.A. Yorke, and S.L. Salzberg. Genome Biology 2009, 10:R42.
44.How to map billions of short reads onto genomes. C. Trapnell and S.L. Salzberg. Nature Biotechnology 27:5 (2009), 455-7.
45.OperonDB: a comprehensive database of predicted operons in microbial genomes. M. Pertea, K. Ayanbule, M. Smedinghoff, and S.L. Salzberg. Nucleic Acids Research 2009, 37:D479-482. doi:10.1093/nar/gkn784.

2013-2014

1.Kraken: ultrafast metagenomic sequence classification using exact alignments. D.E. Wood and S.L. Salzberg. Genome Biology 2014, 15:R46.
2.A new rhesus macaque assembly and annotation for next-generation sequencing analyses. A.V. Zimin et al., Biology Direct 9:20 (2014),
3.Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. D.B. Neale et al., Genome Biology 2014, 15:R59.
4.Sequencing and assembly of the 22-Gb loblolly pine genome. A. Zimin et al., Genetics (2014) 196:3, 875-890.
5.DIAMUND: Direct comparison of genomes to detect mutations. S.L. Salzberg, M. Pertea, J.A. Fahrner, and N. Sobreira. Human Mutation 35:3 (2014), 283-288.
6.V.G. Martinson, T. Magoc, H. Koch, S.L. Salzberg, and N.A. Moran. Genomic features of a bumble bee symbiont reflect its host environment. Applied Environmental Microbiology 80:13 (2014), 3793-3803.
7.GAGE-B: An evaluation of genome assemblers for bacterial organisms. T. Magoc, S. Pabinger, S. Canzar, X. Liu, Q. Su, D. Puiu, L.J. Tallon, and S.L. Salzberg. Bioinformatics 29:14 (2013), 1718-1725.
8.The MaSuRCA genome assembler. A.V. Zimin et al. Bioinformatics 29(21), 2669-2677.
9.TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. D. Kim, G. Pertea, C. Trapnell, H. Pimentel, R. Kelley, and S.L. Salzberg. Genome Biology 2013, 14: R36.
10.NIH funding: It does support innovators. S.L. Salzberg. Nature (2013) 493, 26.
11.Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. M.C. Schatz et al., Briefings in Bioinf. 14(2), 213-224.
12.Genome-guided transcriptome assembly in the age of next-generation sequencing. L.D. Florea and S.L. Salzberg. IEEE/ACM Trans. on Comp. Biology and Bioinf. 10:5 (2013), 1234-1240.
13.Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues. L. Florea, L. Song, and S.L. Salzberg. F1000Research 2013, 2:188.
14.EDGE-pro: Estimated Degree of Gene Expression in prokaryotic genomes. T. Magoc, D. Wood, and S.L. Salzberg. Evolutionary Bioinf. (2013), 9:127.

2007-2008

46.Re-assembly of the genome of Francisella tularensis subsp. holarctica OSU18. D. Puiu and S.L. Salzberg, PLoS ONE 3:10 (2008): e3427.
47.The complete genome sequence of Bacillus anthracis Ames “Ancestor.” J. Ravel et al., J. Bacteriology 191:1 (2009), 445-446.
48.Comparative genomics of the neglected human malaria parasite Plasmodium vivax. J.M. Carlton et al., Nature 455 (2008), 757-763.
49.Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. Steven L. Salzberg et al., BMC Genomics 9:204 (2008).
50.Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads. S.L. Salzberg, D.D. Sommer, D. Puiu, and V.T. Lee. PLoS Computational Biology 4:9 (2008): e1000186.
51.Bioinformatics challenges of new sequencing technology. Mihai Pop and Steven L. Salzberg, Trends in Genetics 24:3 (2008), 142-149.
52.The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). R. Ming et al., Nature 452 (2008), 991-6.
53.Automated eukaryotic gene structure annotation using EVidenceModeler. B.J. Haas, S.L. Salzberg, et al. Genome Biology 2008, 9:R7.
54.Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. C.L. Kingsford, K. Ayanbule, and S.L. Salzberg. Genome Biology 2007, 8(2):R22.
55.Genome analysis linking recent European and African influenza (H5N1) viruses. Steven L. Salzberg, Carl Kingsford, Giovanni Cattoli, David J. Spiro, Daniel A. Janies, Mona Mehrez Aly, Ian H. Brown, Emmanuel Couacy-Hymann, Gian Mario De Mia, Do Huu Dung, Annalisa Guercio, Tony Joannis, Ali Safar Maken Ali, Azizullah Osmani, Iolanda Padalino, Magdi D. Saad, Vladimir Savić, Naomi A. Sengamalay, Samuel Yingst, Jennifer Zaborsky, Olga Zorman-Rojs, Elodie Ghedin, and Ilaria Capua. Emerging Infectious Diseases 13:5 (2007).
56.A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genes. C. Kingsford, A.L. Delcher, and S.L. Salzberg. Molec. Biol. and Evol 24:9 (2007), 2091-98.
57.Identifying bacterial genes and endosymbiont DNA with Glimmer. A.L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Bioinformatics 2007 Mar 15;23(6):673-9. This is the Glimmer 3 paper.
58.Draft Genome of the Filarial Nematode Parasite Brugia malayi. E. Ghedin et al., Science 317:5845 (2007), 1756-60.
59.Comprehensive DNA signature discovery and validation. A.M. Phillippy, J.A. Mason, K. Ayanbule, D.D. Sommer, E. Taviani, A. Huq, R.R. Colwell, I.T. Knight, and S.L. Salzberg. PLoS Computational Biology 3:5 (2007), e98.
60.Hawkeye: an interactive visual analytics tool for genome assemblies. M. Schatz, A.M. Phillippy, B. Shneiderman, and S.L. Salzberg. Genome Biology 2007 Mar 9;8(3):R34.
61.Minimus: a fast, lightweight genome assembler. D.D. Sommer, A.L. Delcher, S.L. Salzberg, and M. Pop. BMC Bioinformatics 2007 Feb 26;8:64.
62.Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis. J.M. Carlton, et al., Science 315 (2007), 207-212.

(Older machine learning papers here)

2006 and earlier
A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons. J.E. Allen and S.L. Salzberg. Algorithms for Molecular Biology 1:14 (2006).
It is time to end the patenting of software. J. Quackenbush and S.L. Salzberg. Bioinformatics 22:12 (2006), 1416-7.
JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions. J.E. Allen, W.H. Majoros, M. Pertea, and S.L. Salzberg. Genome Biology 2006, 7(Suppl):S9.
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote. J.A. Eisen, et al. PLoS Biology 4:9 (2006): e286.
Physiogenomic resources for rat models of heart, lung and blood disorders. R.L. Malek et al. Nature Genetics 38 (2006), 234-239.
Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. (Reprint) (Abstract) E. Ghedin, N.A. Sengamalay, M. Shumway, J. Zaborsky, T. Feldblyum, V. Subbu, D.J. Spiro, J. Sitz, H. Koo, P. Bolotov, D. Dernovoy, T. Tatusova, Y. Bao, K. St George, J. Taylor, D.J. Lipman, C.M. Fraser, J.K. Taubenberger, and S.L. Salzberg. Nature (2005), 1162-1166.
Whole-Genome Analysis of Human Influenza A Virus Reveals Multiple Persistent Lineages and Reassortment among Recent H3N2 Viruses. E.C. Holmes, E. Ghedin, N. Miller, J. Taylor, Y. Bao, K. St. George, B.T. Grenfell, S.L. Salzberg, C.M. Fraser, D.J. Lipman, and J.K. Taubenberger. PLoS Biology 3:9 (2005), e300. [Local PDF copy]
Efficient implementation of a generalized pair hidden Markov model for comparative gene finding. W.H. Majoros, M. Pertea, and S.L. Salzberg. Bioinformatics 21:9 (2005), 1782-88.
Efficient decoding algorithms for generalized hidden Markov model gene finders. W.H. Majoros, M. Pertea, A.L. Delcher, and S.L. Salzberg. BMC Bioinformatics6 (2005), 16.
Comparative Genomics of Trypanosomatid Parasitic Protozoa. N.M. El-Sayed et al. Science 309 (2005), 404-409.
The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. B.J. Loftus et al. Science 309 (Feb 25 2005), 1321-4.
Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. (local PDF copy) S.L. Salzberg, J.C. Dunning Hotopp, A.L. Delcher, M. Pop, D.R. Smith, M.B. Eisen, and W.C. Nelson. Genome Biology 2005, 6:R23.
The genome assembly archive: a new public resource. S.L. Salzberg, D. Church, M. DiCuccio, E. Yaschenko, and J. Ostell. PLoS Biology 9:2 (2004), 1273-1275.
Comparative genome assembly. M. Pop, A. Phillippy, A.L. Delcher, S.L. Salzberg, Briefings in Bioinformatics 5:3 (2004), 237-248.
Automated correction of genome sequence errors. P. Gajer, M. Schatz, and S.L. Salzberg. Nucleic Acids Research 32:2 (2004), 562-569. This describes the AutoEditor system, with open source code available here.
TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. W.H. Majoros, M. Pertea, and S.L. Salzberg. Bioinformatics 20:16 (2004), 2878-79.
Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). N. Ward, et al., PLoS Biology 10:2 (2004), e303.
An empirical analysis of training protocols for probabilistic gene finders. W.H. Majoros and S.L. Salzberg. BMC Bioinformatics 5 (2004), 206.
Versatile and open software for comparing large genomes. S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu, and S.L. Salzberg. Genome Biology 5:R12 (2004), http://genomebiology.com/2004/5/2/R12. The is the MUMmer3 paper, with open source code available here.
DAGChainer: A tool for mining segmental genome duplications and synteny. B.J. Haas, A.L. Delcher, J.R. Wortman, and S.L. Salzberg. Bioinformatics 20:18 (2004), 3643-6.
Hierarchical scaffolding with Bambus. M. Pop, D. Kosack, and S.L. Salzberg. Genome Research 14(2004), 149-159. This describes our open source system for the scaffolding phase of genome assembly.
Computational gene prediction using multiple sources of evidence. J.E. Allen, M. Pertea, and S.L. Salzberg. Genome Research 14(2004), 142-148. This describes our open source system for producing a gene prediction based on multiple gene finders, alignment programs, and other evidence.
Yeast rises again. S.L. Salzberg, Nature 423 (2003), 233-234.
Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. T.D. Read, S.L. Salzberg, M. Pop, M. Shumway, L. Umayam, L. Jiang, E. Holtzapple, J. Busch, K.L. Smith, J.M. Schupp, D. Solomon, P. Keim, and C.M. Fraser. Science 296 (2002), 2028-2033.
Genome sequence of the human malaria parasite Plasmodium falciparum. M.J. Gardner et al., Nature 419 (2002), 498-511.
The genome sequence of the malaria mosquito Anopheles gambiae. R.A. Holt et al., Science 298 (2002), 129-149.
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. E.M. Zdobnov et al., Science 298 (2002), 149-159.
Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. J.M. Carlton et al., Nature 419 (2002), 512-519.
A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. R.J. Mural et al. (176 authors). Science 296 (2002), 1661-1671.
Fast algorithms for large-scale genome alignment and comparison (Abstract) (Full text PDF) A.L. Delcher. A. Phillippy, J. Carlton, and S.L. Salzberg. Nucleic Acids Research 30:11 (2002), 2478-2483. (This is the MUMmer 2 paper.)
Full-length messenger RNA sequences greatly improve genome annotation. B.J. Haas, N. Volfovsky, C.D. Town, M. Troukhan, N. Alexandrov, K.A. Feldmann, R.B. Flavell, O. White, and S.L. Salzberg. Genome Biology 3:6 (2002), research0029.1-12.
Microbial Genes in the Human Genome: Lateral Transfer or Gene Loss? (Abstract) (Local PDF copy) S.L. Salzberg, O. White, J. Peterson, and J.A. Eisen, Science 292 (2001), 1903-1906.   See also the Enhanced Perspective in Science. ANNOTATED! See the annotated version of this paper, designed to help students and teachers of science, developed by the SCOPE project and the Editors of Science.
The Sequence of the Human Genome. (free at the Science website) J. Craig Venter et al. (274 authors), Science 291 (2001), 1304-1351. Get the figures showing genome-scale duplications in PDF format here: [Page 1] [Page 2]
GeneSplicer: a new computational method for splice site prediction M. Pertea, X. Lin, and S.L. Salzberg. Nucleic Acids Research 29:5 (2001) 1185-1190.
A probabilistic method for identifying start codons in bacterial genomes. B.E. Suzek, M.D. Ermolaeva, M. Schreiber, and S.L. Salzberg. Bioinformatics 17:12, 1123-1130.
Prediction of operons in microbial genomes. M.D. Ermolaeva, O. White and S.L. Salzberg. Nucleic Acids Research 29:5 (2001), 1216-1221.
A clustering method for repeat analysis in DNA sequences. N. Volfovsky, B.J. Haas, and S.L. Salzberg. Genome Biology 2:8 (2001), research0027:1-11. This describes the RepeatFinder software.
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. The Arabidopsis Genome Initiative (143 authors), Nature 408 (2000), 796-815. (Also contains links to our papers on chromosomes 1, 2, and 3 of Arabidopsis.
Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Jonathan A. Eisen, John F. Heidelberg, Owen White, and Steven L. Salzberg. Genome Biology 1:6 (2000), 1-9.
Microbial genome sequencing. Claire M. Fraser, Jonathan A. Eisen, and Steven L. Salzberg. Nature 406 (2000), 799-803.
Finding genes in Plasmodium falciparum chromosome 3. M. Pertea, S.L. Salzberg, and M.J. Gardner. Nature 404 (2000), 34.
DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. John F. Heidelberg et al., Nature 406 (2000), 477-483.
Genome sequences of Chlamydia trachomatis MoPn and C. pneumoniae AR39. Timothy D. Read et al., Nucleic Acids Research 28:6 (2000), 1397-1406.
Gene Index analysis of the human genome estimates approximately 120,000* genes. F. Liang, I.E. Holt, G. Pertea, S. Karamycheva, S.L. Salzberg, and J. Quackenbush. Nature Genetics 25:2 (2000), 239-240. *Estimate corrected to 56,000 genes; Nature Genetics 26:4 (2000), 501.
An optimized protocol for analysis of EST sequences. F. Liang, I.E. Holt, G. Pertea, S. Karamycheva, S.L. Salzberg, and J. Quackenbush. Nucleic Acids Research28:18 (2000), 3657-3665.
Prediction of transcription terminators in bacterial genomes (get abstract). M.D. Ermolaeva, H. Khalak, O. White, H.O. Smith, and S.L. Salzberg. J. Molecular Biology 301 (2000), 27-33.
Sequence and Analysis of Chromosome 2 of Arabidopsis thaliana (get abstract). Xiaoying Lin et al., Nature 402 (1999), 761-768.
Complete genome sequence of Neisseria meningitidis serogroup B strain MC58 (get abstract). Herve Tettelin et al.  Science287 (2000), 1809-1815.
Improved microbial gene identification with GLIMMER A.L. Delcher, D. Harmon, S. Kasif, O. White, and S.L. Salzberg. Nucleic Acids Research, 27:23 (1999), 4636-4641.
Interpolated Markov models for eukaryotic gene finding. S.L. Salzberg, M. Pertea, A.L. Delcher, M.J. Gardner, and H. Tettelin. Genomics, 59 (1999), 24-31. This describes the GlimmerM gene finder, available below.
Alignment of Whole Genomes. A.L. Delcher, S. Kasif, R.D. Fleischmann, J. Peterson, O. White, and S.L. Salzberg. Nucleic Acids Research, 27:11 (1999), 2369-2376. Note that Figure 6 is supposed to be in color, and was mistakenly printed as black and white. Click here for the color figure (PDF). This describes the MUMmer system, available below.
Optimized Multiplex PCR: Efficiently Closing a Whole-Genome Shotgun Sequencing Project (PDF). H. Tettelin, D. Radune, S. Kasif, H. Khouri, and S.L. Salzberg. Genomics 62(1999), 500-507.
Genome Sequence of the Radioresistant Bacterium Deinococcus radiodurans R1 (get abstract).   Owen White et al. , Science 286 (1999), 1571-1577.
DNA uptake signal sequences in naturally transformable bacteria. H.O. Smith, M.L. Gwinn, and S.L. Salzberg. Research in Microbiology, 150 (1999), 603-616.
Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima (get abstract). K.E. Nelson et al., Nature 399 (1999), 323-329.
Book: Computational Methods in Molecular Biology (1998; in paperback since 1999) edited by S.L. Salzberg, D.B. Searls, and S. Kasif. See the table of contents here.
Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum (get abstract). Malcolm J. Gardner et al., Science 282 (1998), 1126-1132.
Microbial gene identification using interpolated Markov models S.L. Salzberg, A.L. Delcher, S. Kasif, and O. White. Nucleic Acids Research, 26:2 (1998), 544-548.This is the original Glimmer paper.
A Decision Tree System for Finding Genes in DNA (preprint only). S.L. Salzberg, A.L. Delcher, K. Fasman, and J. Henderson. Journal of Computational Biology5:4 (1998), 667-680.
Skewed Oligomers and Origins of Replication. S.L. Salzberg, A.J. Salzberg, A.R. Kerlavage, and J.-F. Tomb. Gene 217:1-2 (1998), 57-67.
Complete Genomic Sequence of Treponema pallidum, the Syphilis Spirochete C.M. Fraser et al., Science 281 (1998), 375-388.
Finding Genes in Human DNA with a Hidden Markov Model. J. Henderson, S.L. Salzberg, and K. Fasman. This describes the VEIL system for finding genes.Journal of Computational Biology 4:2 (1997), 127-141.
A Method for Identifying Splice Sites and Translational Start Sites in Eukaryotic mRNA. S.L. Salzberg. Computer Applications in the Biosciences (CABIOS) 13:4 (1997), 365-376.
Genomic Sequence of a Lyme Disease Spirochaete, Borrelia burgdorferi. C.M. Fraser et al., Nature 390 (1997), 580-586.
Locating Protein Coding Regions in Human DNA using a Decision Tree Algorithm. S.L. Salzberg. Journal of Computational Biology, 2:3 (1995), 473-485.