Steven Salzberg - Publications

Computer Science Johns Hopkins University, Baltimore, MD 

219 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Varabyou A, Pockrandt C, Salzberg SL, Pertea M. Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie. Genetics. PMID 33983397 DOI: 10.1093/genetics/iyab074  1
2021 Ramos AP, Leonhard SE, Halstead SK, Cuba MA, Castañeda CC, Dioses JA, Tipismana MA, Abanto JT, Llanos A, Gourlay D, Grogl M, Ramos M, Rojas JD, Meza R, Puiu D, ... ... Salzberg SL, et al. Guillain-Barré Syndrome Outbreak in Peru 2019 Associated With Infection. Neurology(R) Neuroimmunology & Neuroinflammation. 8. PMID 33547152 DOI: 10.1212/NXI.0000000000000952  1
2021 De La Torre AR, Wilhite B, Puiu D, St Clair JB, Crepeau MW, Salzberg SL, Langley CH, Allen B, Neale DB. Dissecting the Polygenic Basis of Cold Adaptation Using Genome-Wide Association of Traits and Environmental Data in Douglas-fir. Genes. 12. PMID 33477542 DOI: 10.3390/genes12010110  1
2020 Varabyou A, Salzberg SL, Pertea M. Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments. Genome Research. PMID 33361112 DOI: 10.1101/gr.266213.120  1
2020 Shumate A, Salzberg SL. Liftoff: accurate mapping of gene annotations. Bioinformatics (Oxford, England). PMID 33320174 DOI: 10.1093/bioinformatics/btaa1016  1
2020 Lu J, Salzberg SL. SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes. Plos Computational Biology. 16: e1008439. PMID 33275607 DOI: 10.1371/journal.pcbi.1008439  1
2020 Puiu D, Zimin A, Shumate A, Ge Y, Qiu J, Bhaskaran M, Salzberg SL. The genome of the American groundhog, . F1000research. 9: 1137. PMID 33274050 DOI: 10.12688/F1000Research.25970.1  1
2020 Varabyou A, Pockrandt C, Salzberg SL, Pertea M. Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie. Biorxiv : the Preprint Server For Biology. PMID 32995774 DOI: 10.1101/2020.09.21.300913  1
2020 Scott AD, Zimin AV, Puiu D, Workman R, Britton M, Zaman S, Caballero M, Read AC, Bogdanove AJ, Burns E, Wegrzyn J, Timp W, Salzberg SL, Neale DB. A Reference Genome Sequence for Giant Sequoia. G3 (Bethesda, Md.). PMID 32948606 DOI: 10.1534/G3.120.401612  1
2020 Lu J, Salzberg SL. Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2. Microbiome. 8: 124. PMID 32859275 DOI: 10.1186/s40168-020-00900-2  1
2020 Gemmell NJ, Rutherford K, Prost S, Tollis M, Winter D, Macey JR, Adelson DL, Suh A, Bertozzi T, Grau JH, Organ C, Gardner PP, Muffato M, Patricio M, Billis K, ... ... Salzberg SL, et al. Publisher Correction: The tuatara genome reveals ancient features of amniote evolution. Nature. PMID 32811988 DOI: 10.1038/S41586-020-2661-6  1
2020 Alonge M, Shumate A, Puiu D, Zimin A, Salzberg SL. Chromosome-Scale Assembly of the Bread Wheat Genome Reveals Thousands of Additional Gene Copies. Genetics. PMID 32796007 DOI: 10.1534/Genetics.120.303501  1
2020 Gemmell NJ, Rutherford K, Prost S, Tollis M, Winter D, Macey JR, Adelson DL, Suh A, Bertozzi T, Grau JH, Organ C, Gardner PP, Muffato M, Patricio M, Billis K, ... ... Salzberg SL, et al. The tuatara genome reveals ancient features of amniote evolution. Nature. PMID 32760000 DOI: 10.1038/S41586-020-2561-9  1
2020 Weiss M, Sniezko RA, Puiu D, Crepeau MW, Stevens K, Salzberg SL, Langley CH, Neale DB, De La Torre AR. Genomic basis of white pine blister rust quantitative disease resistance and its relationship with qualitative resistance. The Plant Journal : For Cell and Molecular Biology. PMID 32654344 DOI: 10.1111/Tpj.14928  1
2020 Zimin AV, Salzberg SL. The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies. Plos Computational Biology. 16: e1007981. PMID 32589667 DOI: 10.1371/Journal.Pcbi.1007981  1
2020 Shumate A, Zimin AV, Sherman RM, Puiu D, Wagner JM, Olson ND, Pertea M, Salit ML, Zook JM, Salzberg SL. Assembly and annotation of an Ashkenazi human reference genome. Genome Biology. 21: 129. PMID 32487205 DOI: 10.1186/S13059-020-02047-7  1
2020 Marrano A, Britton M, Zaini PA, Zimin AV, Workman RE, Puiu D, Bianco L, Pierro EAD, Allen BJ, Chakraborty S, Troggio M, Leslie CA, Timp W, Dandekar A, Salzberg SL, et al. High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome. Gigascience. 9. PMID 32432329 DOI: 10.1093/Gigascience/Giaa050  1
2020 Steinegger M, Salzberg SL. Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank. Genome Biology. 21: 115. PMID 32398145 DOI: 10.1186/S13059-020-02023-1  1
2020 Read AC, Moscou MJ, Zimin AV, Pertea G, Meyer RS, Purugganan MD, Leach JE, Triplett LR, Salzberg SL, Bogdanove AJ. Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing. Plos Genetics. 16: e1008571. PMID 31986137 DOI: 10.1371/Journal.Pgen.1008571  1
2019 Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biology. 20: 278. PMID 31842956 DOI: 10.1186/S13059-019-1910-1  1
2019 Breitwieser FP, Salzberg SL. Pavian: Interactive analysis of metagenomics data for microbiome studies and pathogen identification. Bioinformatics (Oxford, England). PMID 31553437 DOI: 10.1093/bioinformatics/btz715  1
2019 Daya M, Rafaels N, Brunetti TM, Chavan S, Levin AM, Shetty A, Gignoux CR, Boorgula MP, Wojcik G, Campbell M, Vergara C, Torgerson DG, Ortega VE, Doumatey A, Johnston HR, ... ... Salzberg S, et al. Author Correction: Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations. Nature Communications. 10: 4082. PMID 31484942 DOI: 10.1038/S41467-019-12158-W  1
2019 Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature Biotechnology. 37: 907-915. PMID 31375807 DOI: 10.1038/S41587-019-0201-4  1
2019 Breitwieser FP, Pertea M, Zimin A, Salzberg SL. Human contamination in bacterial genomes has created thousands of spurious proteins. Genome Research. PMID 31064768 DOI: 10.1101/Gr.245373.118  1
2019 Daya M, Rafaels N, Brunetti TM, Chavan S, Levin AM, Shetty A, Gignoux CR, Boorgula MP, Wojcik G, Campbell M, Vergara C, Torgerson DG, Ortega VE, Doumatey A, Johnston HR, ... ... Salzberg S, et al. Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations. Nature Communications. 10: 880. PMID 30787307 DOI: 10.1038/S41467-019-08469-7  1
2019 Sherman RM, Forman J, Antonescu V, Puiu D, Daya M, Rafaels N, Boorgula MP, Chavan S, Vergara C, Ortega VE, Levin AM, Eng C, Yazdanbakhsh M, Wilson JG, Marrugo J, ... ... Salzberg SL, et al. Author Correction: Assembly of a pan-genome from deep sequencing of 910 humans of African descent. Nature Genetics. PMID 30647471 DOI: 10.1038/S41588-018-0335-1  1
2019 Lu J, Salzberg S. Fast and accurate 16S microbial community analysis using Kraken 2 F1000research. 8. DOI: 10.7490/F1000Research.1117607.1  1
2018 Pertea M, Shumate A, Pertea G, Varabyou A, Breitwieser FP, Chang YC, Madugundu AK, Pandey A, Salzberg SL. CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise. Genome Biology. 19: 208. PMID 30486838 DOI: 10.1186/S13059-018-1590-2  1
2018 Sherman RM, Forman J, Antonescu V, Puiu D, Daya M, Rafaels N, Boorgula MP, Chavan S, Vergara C, Ortega VE, Levin AM, Eng C, Yazdanbakhsh M, Wilson JG, Marrugo J, ... ... Salzberg SL, et al. Assembly of a pan-genome from deep sequencing of 910 humans of African descent. Nature Genetics. PMID 30455414 DOI: 10.1038/S41588-018-0273-Y  1
2018 De La Torre AR, Puiu D, Crepeau MW, Stevens K, Salzberg SL, Langley CH, Neale DB. Genomic architecture of complex traits in loblolly pine. The New Phytologist. PMID 30318590 DOI: 10.1111/Nph.15535  1
2018 Wilton R, Wheelan SJ, Szalay AS, Salzberg SL. The Terabase Search Engine: a large-scale relational database of short-read sequences. Bioinformatics (Oxford, England). PMID 30052772 DOI: 10.1093/Bioinformatics/Bty657  1
2018 Simner PJ, Miller HB, Breitweiser FP, Pinilla Monsalve G, Pardo CA, Salzberg SL, Sears C, Thomas DL, Eberhart CG, Carroll KC. Development and Optimization of Metagenomic Next-Generation Sequencing Methods for Cerebral Spinal Fluid Diagnostics. Journal of Clinical Microbiology. PMID 29976594 DOI: 10.1128/Jcm.00472-18  1
2018 Lu J, Salzberg SL. Removing contaminants from databases of draft genomes. Plos Computational Biology. 14: e1006277. PMID 29939994 DOI: 10.1371/journal.pcbi.1006277  1
2018 Stevens KA, Woeste K, Chakraborty S, Crepeau MW, Leslie CA, Martínez-García PJ, Puiu D, Romero-Severson J, Coggeshall M, Dandekar AM, Kluepfel D, Neale DB, Salzberg SL, Langley CH. Genomic Variation Among and Within Six Species. G3 (Bethesda, Md.). PMID 29792315 DOI: 10.1534/G3.118.200030  1
2018 Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. MUMmer4: A fast and versatile genome alignment system. Plos Computational Biology. 14: e1005944. PMID 29373581 DOI: 10.1371/Journal.Pcbi.1005944  1
2018 Li Z, Breitwieser FP, Lu J, Jun AS, Asnaghi L, Salzberg SL, Eberhart CG. Identifying Corneal Infections in Formalin-Fixed Specimens Using Next Generation Sequencing. Investigative Ophthalmology & Visual Science. 59: 280-288. PMID 29340642 DOI: 10.1167/Iovs.17-21617  1
2017 Luo MC, Gu YQ, Puiu D, Wang H, Twardziok SO, Deal KR, Huo N, Zhu T, Wang L, Wang Y, McGuire PE, Liu S, Long H, Ramasamy RK, Rodriguez JC, ... ... Salzberg SL, et al. Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature. PMID 29143815 DOI: 10.1038/Nature24486  1
2017 Zimin AV, Puiu D, Hall R, Kingan S, Clavijo BJ, Salzberg SL. The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum. Gigascience. PMID 29069494 DOI: 10.1093/Gigascience/Gix097  1
2017 Breitwieser FP, Lu J, Salzberg SL. A review of methods and databases for metagenomic classification and assembly. Briefings in Bioinformatics. PMID 29028872 DOI: 10.1093/bib/bbx120  1
2017 Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL. Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing. Gigascience. 6: 1. PMID 29020755 DOI: 10.1093/Gigascience/Gix072  1
2017 Luo R, Zimin A, Workman R, Fan Y, Pertea G, Grossman N, Wear MP, Jia B, Miller H, Casadevall A, Timp W, Zhang SX, Salzberg SL. First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (formerly Scedosporium prolificans). G3 (Bethesda, Md.). PMID 28963165 DOI: 10.1534/G3.117.300107  1
2017 Pallavajjala A, Kim D, Li T, Ghiaur G, Jones RJ, Burns KH, Salzberg SL, Ning Y. Genomic characterization of chromosome translocations in patients with T/myeloid mixed-phenotype acute leukemia. Leukemia & Lymphoma. 1-8. PMID 28882084 DOI: 10.1080/10428194.2017.1372577  1
2017 Neale DB, McGuire PE, Wheeler NC, Stevens KA, Crepeau MW, Cardeno C, Zimin AV, Puiu D, Pertea GM, Sezen UU, Casola C, Koralewski TE, Paul R, Gonzalez-Ibeas D, Zaman S, ... ... Salzberg SL, et al. The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae. G3 (Bethesda, Md.). PMID 28751502 DOI: 10.1534/G3.117.300078  1
2017 Luo R, Schatz MC, Salzberg SL. 16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model. Gigascience. PMID 28637275 DOI: 10.1093/Gigascience/Gix045  1
2017 Kandathil AJ, Breitwieser FP, Sachithanandham J, Robinson M, Mehta SH, Timp W, Salzberg SL, Thomas DL, Balagopal A. Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs. Annals of Internal Medicine. PMID 28586923 DOI: 10.7326/M17-0085  1
2017 Canzar S, Salzberg SL. Short Read Mapping: An Algorithmic Tour. Proceedings of the Ieee. Institute of Electrical and Electronics Engineers. 105: 436-458. PMID 28502990 DOI: 10.1109/JPROC.2015.2455551  1
2017 Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL. An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing. Gigascience. 6: 1-4. PMID 28369353 DOI: 10.1093/Gigascience/Giw016  1
2017 Zimin AV, Puiu D, Luo MC, Zhu T, Koren S, Marcais G, Yorke JA, Dvorak J, Salzberg SL. Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the mega-reads algorithm. Genome Research. PMID 28130360 DOI: 10.1101/Gr.213405.116  1
2017 Sun Z, Ke X, Salzberg SL, Kim D, Antonescu V, Cheng Y, Huang B, Song JH, Abraham JM, Ibrahim S, Tian H, Meltzer SJ. The novel fusion transcript NR5A2-KLHL29FT is generated by an insertion at the KLHL29 locus. Cancer. PMID 28081303 DOI: 10.1002/Cncr.30510  1
2016 Kim D, Song L, Breitwieser FP, Salzberg SL. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Research. PMID 27852649 DOI: 10.1101/Gr.210641.116  1
2016 Stevens KA, Wegrzyn J, Zimin A, Puiu D, Crepeau M, Cardeno C, Paul R, Gonzalez-Ibeaz D, Koriabine M, Holtz-Morris A, Martinez-Garcia P, Sezen U, Marcais G, Jermstad K, McGuire P, ... ... Salzberg SL, et al. Sequence of the Sugar Pine Megagenome. Genetics. PMID 27794028 DOI: 10.1534/Genetics.116.193227  1
2016 Sork VL, Fitz-Gibbon ST, Puiu D, Crepeau M, Gugger PF, Sherman R, Stevens K, Langley CH, Pellegrini M, Salzberg SL. First Draft Assembly and Annotation of the Genome of a California Endemic Oak Quercus lobata Née (Fagaceae). G3 (Bethesda, Md.). PMID 27621377 DOI: 10.1534/G3.116.030411  1
2016 Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nature Protocols. 11: 1650-1667. PMID 27560171 DOI: 10.1038/Nprot.2016.095  1
2016 Salzberg SL, Breitwieser FP, Kumar A, Hao H, Burger P, Rodriguez FJ, Lim M, Quiñones-Hinojosa A, Gallia GL, Tornheim JA, Melia MT, Sears CL, Pardo CA. Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system. Neurology® Neuroimmunology & Neuroinflammation. 3: e251. PMID 27340685 DOI: 10.1212/Nxi.0000000000000251  1
2016 Salzberg SL. Databases: Reminder to deposit DNA sequences Nature. 533: 179. PMID 27172038 DOI: 10.1038/533179a  1
2016 Blaxter M, Danchin A, Savakis B, Fukami-Kobayashi K, Kurokawa K, Sugano S, Roberts RJ, Salzberg SL, Wu CI. Reminder to deposit DNA sequences. Science (New York, N.Y.). 352: 780. PMID 27169596 DOI: 10.1126/Science.Aaf7672  1
2016 Martínez-García PJ, Crepeau MW, Puiu D, Gonzalez-Ibeas D, Whalen J, Stevens KA, Paul R, Butterfield TS, Britton MT, Reagan RL, Chakraborty S, Walawage SL, Vasquez-Gross HA, Cardeno C, Famula RA, ... ... Salzberg SL, et al. The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of nonstructural polyphenols. The Plant Journal : For Cell and Molecular Biology. PMID 27145194 DOI: 10.1111/Tpj.13207  1
2015 Pop M, Salzberg SL. Use and mis-use of supplementary material in science publications. Bmc Bioinformatics. 16: 237. PMID 26525146 DOI: 10.1186/S12859-015-0668-Z  1
2015 Breitwieser FP, Pardo CA, Salzberg SL. Re-analysis of metagenomic sequences from acute flaccid myelitis patients reveals alternatives to enterovirus D68 infection. F1000research. 4: 180. PMID 26309730 DOI: 10.12688/f1000research.6743.2  1
2015 Chang TC, Pertea M, Lee S, Salzberg SL, Mendell JT. Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms. Genome Research. 25: 1401-9. PMID 26290535 DOI: 10.1101/Gr.193607.115  1
2015 Kapheim KM, Pan H, Li C, Salzberg SL, Puiu D, Magoc T, Robertson HM, Hudson ME, Venkat A, Fischman BJ, Hernandez A, Yandell M, Ence D, Holt C, Yocum GD, et al. Social evolution. Genomic signatures of evolutionary transitions from solitary to group living. Science (New York, N.Y.). 348: 1139-43. PMID 25977371 DOI: 10.1126/Science.Aaa4788  1
2015 Wilton R, Budavari T, Langmead B, Wheelan SJ, Salzberg SL, Szalay AS. Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space. Peerj. 3: e808. PMID 25780763 DOI: 10.7717/Peerj.808  1
2015 Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods. 12: 357-60. PMID 25751142 DOI: 10.1038/Nmeth.3317  1
2015 Frazee AC, Pertea G, Jaffe AE, Langmead B, Salzberg SL, Leek JT. Ballgown bridges the gap between transcriptome assembly and expression analysis. Nature Biotechnology. 33: 243-6. PMID 25748911 DOI: 10.1038/Nbt.3172  1
2015 Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology. 33: 290-5. PMID 25690850 DOI: 10.1038/Nbt.3122  1
2015 Deng K, Pertea M, Rongvaux A, Wang L, Durand CM, Ghiaur G, Lai J, McHugh HL, Hao H, Zhang H, Margolick JB, Gurer C, Murphy AJ, Valenzuela DM, Yancopoulos GD, ... ... Salzberg SL, et al. Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations. Nature. 517: 381-5. PMID 25561180 DOI: 10.1038/Nature14053  1
2014 Merchant S, Wood DE, Salzberg SL. Unexpected cross-species contamination in genome sequencing projects. Peerj. 2: e675. PMID 25426337 DOI: 10.7717/peerj.675  1
2014 Zimin AV, Cornish AS, Maudhoo MD, Gibbs RM, Zhang X, Pandey S, Meehan DT, Wipfler K, Bosinger SE, Johnson ZP, Tharp GK, Marçais G, Roberts M, Ferguson B, Fox HS, ... ... Salzberg SL, et al. A new rhesus macaque assembly and annotation for next-generation sequencing analyses. Biology Direct. 9: 20. PMID 25319552 DOI: 10.1186/1745-6150-9-20  1
2014 Martinson VG, Magoc T, Koch H, Salzberg SL, Moran NA. Genomic features of a bumble bee symbiont reflect its host environment. Applied and Environmental Microbiology. 80: 3793-803. PMID 24747890 DOI: 10.1128/Aem.00322-14  1
2014 Wegrzyn JL, Liechty JD, Stevens KA, Wu LS, Loopstra CA, Vasquez-Gross HA, Dougherty WM, Lin BY, Zieve JJ, Martínez-García PJ, Holt C, Yandell M, Zimin AV, Yorke JA, Crepeau MW, ... ... Salzberg SL, et al. Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics. 196: 891-909. PMID 24653211 DOI: 10.1534/Genetics.113.159996  1
2014 Zimin A, Stevens KA, Crepeau MW, Holtz-Morris A, Koriabine M, Marçais G, Puiu D, Roberts M, Wegrzyn JL, de Jong PJ, Neale DB, Salzberg SL, Yorke JA, Langley CH. Sequencing and assembly of the 22-gb loblolly pine genome. Genetics. 196: 875-90. PMID 24653210 DOI: 10.1534/Genetics.113.159715  1
2014 Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW, Cardeno C, Koriabine M, Holtz-Morris AE, Liechty JD, Martínez-García PJ, Vasquez-Gross HA, Lin BY, Zieve JJ, Dougherty WM, ... ... Salzberg SL, et al. Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biology. 15: R59. PMID 24647006 DOI: 10.1186/Gb-2014-15-3-R59  1
2014 Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biology. 15: R46. PMID 24580807 DOI: 10.1186/gb-2014-15-3-r46  1
2014 Salzberg SL, Pertea M, Fahrner JA, Sobreira N. DIAMUND: direct comparison of genomes to detect mutations. Human Mutation. 35: 283-8. PMID 24375697 DOI: 10.1002/Humu.22503  1
2013 Florea L, Song L, Salzberg SL. Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues. F1000research. 2: 188. PMID 24555089 DOI: 10.12688/F1000Research.2-188.V2  1
2013 Florea LD, Salzberg SL. Genome-guided transcriptome assembly in the age of next-generation sequencing. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 10: 1234-40. PMID 24524156 DOI: 10.1109/Tcbb.2013.140  1
2013 Wegrzyn JL, Lin BY, Zieve JJ, Dougherty WM, Martínez-García PJ, Koriabine M, Holtz-Morris A, deJong P, Crepeau M, Langley CH, Puiu D, Salzberg SL, Neale DB, Stevens KA. Insights into the loblolly pine genome: characterization of BAC and fosmid sequences. Plos One. 8: e72439. PMID 24023741 DOI: 10.1371/Journal.Pone.0072439  1
2013 Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, ... ... Salzberg SL, et al. The COMBREX project: design, methodology, and initial results. Plos Biology. 11: e1001638. PMID 24013487 DOI: 10.1371/Journal.Pbio.1001638  1
2013 Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. The MaSuRCA genome assembler. Bioinformatics (Oxford, England). 29: 2669-77. PMID 23990416 DOI: 10.1093/Bioinformatics/Btt476  1
2013 Neale DB, Langley CH, Salzberg SL, Wegrzyn JL. Open access to tree genomes: the path to a better forest. Genome Biology. 14: 120. PMID 23796049 DOI: 10.1186/Gb-2013-14-6-120  1
2013 Magoc T, Pabinger S, Canzar S, Liu X, Su Q, Puiu D, Tallon LJ, Salzberg SL. GAGE-B: an evaluation of genome assemblers for bacterial organisms. Bioinformatics (Oxford, England). 29: 1718-25. PMID 23665771 DOI: 10.1093/Bioinformatics/Btt273  1
2013 Leek JT, Salzberg SL. Sequestration: Inadvertently killing biomedical research to score political points Genome Biology. 14. PMID 23651812 DOI: 10.1186/gb-2013-14-3-109  1
2013 Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology. 14: R36. PMID 23618408 DOI: 10.1186/Gb-2013-14-4-R36  1
2013 Magoc T, Wood D, Salzberg SL. EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes. Evolutionary Bioinformatics Online. 9: 127-36. PMID 23531787 DOI: 10.4137/Ebo.S11250  1
2013 Salzberg SL. NIH funding: It does support innovators Nature. 493: 26. PMID 23282352 DOI: 10.1038/493026b  1
2013 Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M. Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Briefings in Bioinformatics. 14: 213-24. PMID 22199379 DOI: 10.1093/Bib/Bbr074  1
2012 Wood DE, Lin H, Levy-Moonshine A, Swaminathan R, Chang YC, Anton BP, Osmani L, Steffen M, Kasif S, Salzberg SL. Thousands of missed genes found in bacterial genomes and their analysis with COMBREX. Biology Direct. 7: 37. PMID 23111013 DOI: 10.1186/1745-6150-7-37  1
2012 Zimin AV, Kelley DR, Roberts M, Marçais G, Salzberg SL, Yorke JA. Mis-assembled "segmental duplications" in two versions of the Bos taurus genome. Plos One. 7: e42680. PMID 22880081 DOI: 10.1371/Journal.Pone.0042680  1
2012 Salzberg S. A scientist and an advocate. An interview with Steven Salzberg by Kristie Nybo. Biotechniques. 53: 71. PMID 22873510 DOI: 10.2144/000113898  1
2012 Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2 Nature Methods. 9: 357-359. PMID 22388286 DOI: 10.1038/Nmeth.1923  1
2012 Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols. 7: 562-78. PMID 22383036 DOI: 10.1038/Nprot.2012.016  1
2012 Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA. GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Research. 22: 557-67. PMID 22147368 DOI: 10.1101/Gr.131383.111  1
2012 Treangen TJ, Salzberg SL. Repetitive DNA and next-generation sequencing: Computational challenges and solutions Nature Reviews Genetics. 13: 36-46. PMID 22124482 DOI: 10.1038/nrg3117  1
2012 Kelley DR, Liu B, Delcher AL, Pop M, Salzberg SL. Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering. Nucleic Acids Research. 40: e9. PMID 22102569 DOI: 10.1093/Nar/Gkr1067  1
2011 Magoč T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics (Oxford, England). 27: 2957-63. PMID 21903629 DOI: 10.1093/bioinformatics/btr507  1
2011 Kim D, Salzberg SL. TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biology. 12: R72. PMID 21835007 DOI: 10.1186/Gb-2011-12-8-R72  1
2011 Bogdanove AJ, Koebnik R, Lu H, Furutani A, Angiuoli SV, Patil PB, Van Sluys MA, Ryan RP, Meyer DF, Han SW, Aparna G, Rajaram M, Delcher AL, Phillippy AM, Puiu D, ... ... Salzberg SL, et al. Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp. Journal of Bacteriology. 193: 5450-64. PMID 21784931 DOI: 10.1128/Jb.05262-11  1
2011 Florea L, Souvorov A, Kalbfleisch TS, Salzberg SL. Genome assembly has a major impact on gene content: A comparison of annotation in two bos Taurus assemblies Plos One. 6. PMID 21731731 DOI: 10.1371/Journal.Pone.0021400  1
2011 Pertea M, Pertea GM, Salzberg SL. Detection of lineage-specific evolutionary changes among primate species Bmc Bioinformatics. 12. PMID 21726447 DOI: 10.1186/1471-2105-12-274  1
2011 Angiuoli SV, Dunning Hotopp JC, Salzberg SL, Tettelin H. Improving pan-genome annotation using whole genome multiple alignment. Bmc Bioinformatics. 12: 272. PMID 21718539 DOI: 10.1186/1471-2105-12-272  1
2011 Enk J, Devault A, Debruyne R, King CE, Treangen T, O'Rourke D, Salzberg SL, Fisher D, MacPhee R, Poinar H. Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths. Genome Biology. 12: R51. PMID 21627792 DOI: 10.1186/Gb-2011-12-5-R51  1
2011 Brady A, Salzberg S. PhymmBL expanded: Confidence scores, custom databases, parallelization and more Nature Methods. 8: 367. PMID 21527926 DOI: 10.1038/Nmeth0511-367  1
2011 Lipman D, Flicek P, Salzberg S, Gerstein M, Knight R. Closure of the NCBI SRA and implications for the long-term future of genomics data storage. Genome Biology. 12: 402. PMID 21418618 DOI: 10.1186/Gb-2011-12-3-402  1
2011 Rasko DA, Worsham PL, Abshire TG, Stanley ST, Bannan JD, Wilson MR, Langham RJ, Decker RS, Jiang L, Read TD, Phillippy AM, Salzberg SL, Pop M, Van Ert MN, Kenefic LJ, et al. Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proceedings of the National Academy of Sciences of the United States of America. 108: 5027-32. PMID 21383169 DOI: 10.1073/Pnas.1016657108  1
2011 Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P, Mockaitis K, Liston A, Mane SP, Burns P, Davis TM, Slovin JP, Bassil N, Hellens RP, ... ... Salzberg SL, et al. The genome of woodland strawberry (Fragaria vesca). Nature Genetics. 43: 109-16. PMID 21186353 DOI: 10.1038/Ng.740  1
2011 Angiuoli SV, Salzberg SL. Mugsy: Fast multiple alignment of closely related whole genomes Bioinformatics. 27: 334-342. PMID 21148543 DOI: 10.1093/bioinformatics/btq665  1
2011 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, ... ... Salzberg SL, et al. COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. Nucleic Acids Research. 39: D11-4. PMID 21097892 DOI: 10.1093/Nar/Gkq1168  1
2010 Kelley DR, Schatz MC, Salzberg SL. Quake: quality-aware detection and correction of sequencing errors. Genome Biology. 11: R116. PMID 21114842 DOI: 10.1186/gb-2010-11-11-r116  1
2010 Kelley DR, Salzberg SL. Clustering metagenomic sequences with interpolated Markov models. Bmc Bioinformatics. 11: 544. PMID 21044341 DOI: 10.1186/1471-2105-11-544  1
2010 Salzberg SL, Pertea M. Do-it-yourself genetic testing Genome Biology. 11. PMID 20932271 DOI: 10.1186/Gb-2010-11-10-404  1
2010 Deng X, Phillippy AM, Li Z, Salzberg SL, Zhang W. Probing the pan-genome of Listeria monocytogenes: New insights into intraspecific niche expansion and genomic diversification Bmc Genomics. 11. PMID 20846431 DOI: 10.1186/1471-2164-11-500  1
2010 Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, ... ... Salzberg SL, et al. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. Plos Biology. 8. PMID 20838655 DOI: 10.1371/Journal.Pbio.1000475  1
2010 Miller TR, Delcher AL, Salzberg SL, Saunders E, Detter JC, Halden RU. Genome sequence of the dioxin-mineralizing bacterium Sphingomonas wittichii RW1. Journal of Bacteriology. 192: 6101-2. PMID 20833805 DOI: 10.1128/Jb.01030-10  1
2010 Schatz MC, Langmead B, Salzberg SL. Cloud computing and the DNA data race Nature Biotechnology. 28: 691-693. PMID 20622843 DOI: 10.1038/Nbt0710-691  1
2010 Schatz MC, Delcher AL, Salzberg SL. Assembly of large genomes using second-generation sequencing Genome Research. 20: 1165-1173. PMID 20508146 DOI: 10.1101/gr.101360.109  1
2010 Pertea M, Salzberg SL. Between a chicken and a grape: estimating the number of human genes. Genome Biology. 11: 206. PMID 20441615 DOI: 10.1186/Gb-2010-11-5-206  1
2010 Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology. 28: 511-5. PMID 20436464 DOI: 10.1038/Nbt.1621  1
2010 Kelley DR, Salzberg SL. Detection and correction of false segmental duplications caused by genome mis-assembly. Genome Biology. 11: R28. PMID 20219098 DOI: 10.1186/gb-2010-11-3-r28  1
2010 Salzberg SL. Mind the gaps Nature Methods. 7: 105-106. PMID 20111034 DOI: 10.1038/nmeth0210-105  1
2010 Kelley D, Schatz M, Salzberg S. Quality-aware error correction of sequencing reads F1000research. 1. DOI: 10.7490/F1000Research.274.1  1
2009 Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL. Searching for SNPs with cloud computing. Genome Biology. 10: R134. PMID 19930550 DOI: 10.1186/Gb-2009-10-11-R134  1
2009 Phillippy AM, Deng X, Zhang W, Salzberg SL. Efficient oligonucleotide probe selection for pan-genomic tiling arrays Bmc Bioinformatics. 10: 293. PMID 19758451 DOI: 10.1186/1471-2105-10-293  1
2009 Brady A, Salzberg SL. Phymm and PhymmBL: Metagenomic phylogenetic classification with interpolated Markov models Nature Methods. 6: 673-676. PMID 19648916 DOI: 10.1038/Nmeth.1358  1
2009 Kingsford C, Nagarajan N, Salzberg SL. 2009 Swine-origin influenza A (H1N1) resembles previous influenza isolates. Plos One. 4: e6402. PMID 19636415 DOI: 10.1371/journal.pone.0006402  1
2009 Eisen M, Salzberg S. Open access: the sooner the better. Science (New York, N.Y.). 325: 266; author reply 26. PMID 19608896 DOI: 10.1126/Science.325_266C  1
2009 Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP, Cerqueira GC, Mashiyama ST, Al-Lazikani B, Andrade LF, Ashton PD, Aslett MA, Bartholomeu DC, Blandin G, Caffrey CR, Coghlan A, ... ... Salzberg SL, et al. The genome of the blood fluke Schistosoma mansoni. Nature. 460: 352-8. PMID 19606141 DOI: 10.1038/Nature08160  1
2009 Trapnell C, Salzberg SL. How to map billions of short reads onto genomes Nature Biotechnology. 27: 455-457. PMID 19430453 DOI: 10.1038/Nbt0509-455  1
2009 Phillippy AM, Ayanbule K, Edwards NJ, Salzberg SL. Insignia: a DNA signature search web server for diagnostic assay development. Nucleic Acids Research. 37: W229-34. PMID 19417071 DOI: 10.1093/Nar/Gkp286  1
2009 Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS, Marçais G, Roberts M, Subramanian P, Yorke JA, Salzberg SL. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biology. 10: R42. PMID 19393038 DOI: 10.1186/Gb-2009-10-4-R42  1
2009 Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (Oxford, England). 25: 1105-11. PMID 19289445 DOI: 10.1093/Bioinformatics/Btp120  1
2009 Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology. 10: R25. PMID 19261174 DOI: 10.1186/Gb-2009-10-3-R25  1
2009 Salzberg SL, Puiu D, Sommer DD, Nene V, Lee NH. Genome sequence of the Wolbachia endosymbiont of Culex quinquefasciatus JHB. Journal of Bacteriology. 191: 1725. PMID 19114486 DOI: 10.1128/Jb.01731-08  1
2009 Ravel J, Jiang L, Stanley ST, Wilson MR, Decker RS, Read TD, Worsham P, Keim PS, Salzberg SL, Fraser-Liggett CM, Rasko DA. The complete genome sequence of Bacillus anthracis Ames "Ancestor". Journal of Bacteriology. 191: 445-6. PMID 18952800 DOI: 10.1128/Jb.01347-08  1
2009 Pertea M, Ayanbule K, Smedinghoff M, Salzberg SL. OperonDB: A comprehensive database of predicted operons in microbial genomes Nucleic Acids Research. 37. PMID 18948284 DOI: 10.1093/Nar/Gkn784  1
2008 Lu H, Patil P, Van Sluys MA, White FF, Ryan RP, Dow JM, Rabinowicz P, Salzberg SL, Leach JE, Sonti R, Brendel V, Bogdanove AJ. Acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in xanthomonas. Plos One. 3: e3828. PMID 19043590 DOI: 10.1371/Journal.Pone.0003828  1
2008 Puiu D, Salzberg SL. Re-assembly of the genome of Francisella tularensis subsp. holarctica OSU18 Plos One. 3. PMID 18927608 DOI: 10.1371/journal.pone.0003427  1
2008 Carlton JM, Adams JH, Silva JC, Bidwell SL, Lorenzi H, Caler E, Crabtree J, Angiuoli SV, Merino EF, Amedeo P, Cheng Q, Coulson RM, Crabb BS, Del Portillo HA, Essien K, ... ... Salzberg SL, et al. Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature. 455: 757-63. PMID 18843361 DOI: 10.1038/Nature07327  1
2008 Salzberg SL, Sommer DD, Puiu D, Lee VT. Gene-boosted assembly of a novel bacterial genome from very short reads Plos Computational Biology. 4. PMID 18818729 DOI: 10.1371/journal.pcbi.1000186  1
2008 Kingsford C, Salzberg SL. What are decision trees? Nature Biotechnology. 26: 1011-1012. PMID 18779814 DOI: 10.1038/nbt0908-1011  1
2008 Salzberg S. The contents of the syringe Nature. 454: 160-161. PMID 18615063 DOI: 10.1038/454160A  1
2008 Salzberg SL, Sommer DD, Schatz MC, Phillippy AM, Rabinowicz PD, Tsuge S, Furutani A, Ochiai H, Delcher AL, Kelley D, Madupu R, Puiu D, Radune D, Shumway M, Trapnell C, et al. Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. Bmc Genomics. 9: 204. PMID 18452608 DOI: 10.1186/1471-2164-9-204  1
2008 Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KL, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, et al. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature. 452: 991-6. PMID 18432245 DOI: 10.1038/Nature06856  1
2008 Pop M, Salzberg SL. Bioinformatics challenges of new sequencing technology. Trends in Genetics : Tig. 24: 142-9. PMID 18262676 DOI: 10.1016/J.Tig.2007.12.006  1
2008 Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biology. 9: R7. PMID 18190707 DOI: 10.1186/Gb-2008-9-1-R7  1
2007 Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J, Allen JE, Delcher AL, Guiliano DB, Miranda-Saavedra D, Angiuoli SV, Creasy T, Amedeo P, Haas B, El-Sayed NM, ... ... Salzberg SL, et al. Draft genome of the filarial nematode parasite Brugia malayi. Science (New York, N.Y.). 317: 1756-60. PMID 17885136 DOI: 10.1126/Science.1145406  1
2007 Kingsford C, Delcher AL, Salzberg SL. A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genes Molecular Biology and Evolution. 24: 2091-2098. PMID 17642473 DOI: 10.1093/molbev/msm145  1
2007 Salzberg SL, Kingsford C, Cattoli G, Spiro DJ, Janies DA, Aly MM, Brown IH, Couacy-Hymann E, De Mia GM, Dung do H, Guercio A, Joannis T, Maken Ali AS, Osmani A, Padalino I, et al. Genome analysis linking recent European and African influenza (H5N1) viruses. Emerging Infectious Diseases. 13: 713-8. PMID 17553249 DOI: 10.3201/eid1305.070013  1
2007 Pertea M, Mount SM, Salzberg SL. A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana. Bmc Bioinformatics. 8: 159. PMID 17517127 DOI: 10.1186/1471-2105-8-159  1
2007 Phillippy AM, Mason JA, Ayanbule K, Sommer DD, Taviani E, Huq A, Colwell RR, Knight IT, Salzberg SL. Comprehensive DNA signature discovery and validation. Plos Computational Biology. 3: e98. PMID 17511514 DOI: 10.1371/Journal.Pcbi.0030098  1
2007 Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K, Grabherr M, Ren Q, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, ... ... Salzberg SL, et al. Genome sequence of Aedes aegypti, a major arbovirus vector. Science (New York, N.Y.). 316: 1718-23. PMID 17510324 DOI: 10.1126/Science.1138878  1
2007 Schatz MC, Phillippy AM, Shneiderman B, Salzberg SL. Hawkeye: an interactive visual analytics tool for genome assemblies. Genome Biology. 8: R34. PMID 17349036 DOI: 10.1186/Gb-2007-8-3-R34  1
2007 Sommer DD, Delcher AL, Salzberg SL, Pop M. Minimus: a fast, lightweight genome assembler. Bmc Bioinformatics. 8: 64. PMID 17324286 DOI: 10.1186/1471-2105-8-64  1
2007 Kingsford CL, Ayanbule K, Salzberg SL. Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biology. 8: R22. PMID 17313685 DOI: 10.1186/gb-2007-8-2-r22  1
2007 Salzberg SL. Genome re-annotation: A wiki solution? Genome Biology. 8. PMID 17274839 DOI: 10.1186/gb-2007-8-1-102  1
2007 Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer Bioinformatics. 23: 673-679. PMID 17237039 DOI: 10.1093/bioinformatics/btm009  1
2007 Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman JR, Bidwell SL, Alsmark UC, Besteiro S, Sicheritz-Ponten T, Noel CJ, Dacks JB, Foster PG, Simillion C, ... ... Salzberg SL, et al. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science (New York, N.Y.). 315: 207-12. PMID 17218520 DOI: 10.1126/Science.1132894  1
2006 Allen JE, Salzberg SL. A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons. Algorithms For Molecular Biology : Amb. 1: 14. PMID 16934144 DOI: 10.1186/1748-7188-1-14  0.96
2006 Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, et al. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. Plos Biology. 4: e286. PMID 16933976 DOI: 10.1371/Journal.Pbio.0040286  1
2006 Allen JE, Majoros WH, Pertea M, Salzberg SL. JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions Genome Biology. 7. PMID 16925843 DOI: 10.1186/Gb-2006-7-S1-S9  1
2006 Quackenbush J, Salzberg SL. It is time to end the patenting of software Bioinformatics. 22: 1416-1417. PMID 16766564 DOI: 10.1093/Bioinformatics/Btl167  1
2006 Salzberg S, Ghedin E, Spiro D. Shared data are key to beating threat from flu [1] Nature. 440: 605. PMID 16572147 DOI: 10.1038/440605a  1
2006 Malek RL, Wang HY, Kwitek AE, Greene AS, Bhagabati N, Borchardt G, Cahill L, Currier T, Frank B, Fu X, Hasinoff M, Howe E, Letwin N, Luu TV, Saeed A, ... ... Salzberg SL, et al. Physiogenomic resources for rat models of heart, lung and blood disorders. Nature Genetics. 38: 234-9. PMID 16415889 DOI: 10.1038/Ng1693  1
2006 Allen JE, Salzberg SL. A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons Algorithms For Molecular Biology. 1. DOI: 10.1186/1748-7188-1-14  1
2005 Nierman WC, Pain A, Anderson MJ, Wortman JR, Kim HS, Arroyo J, Berriman M, Abe K, Archer DB, Bermejo C, Bennett J, Bowyer P, Chen D, Collins M, Coulsen R, ... ... Salzberg SL, et al. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature. 438: 1151-6. PMID 16372009 DOI: 10.1038/Nature04332  1
2005 Salzberg SL, Yorke JA. Beware of mis-assembled genomes. Bioinformatics (Oxford, England). 21: 4320-1. PMID 16332717 DOI: 10.1093/bioinformatics/bti769  1
2005 Ghedin E, Sengamalay NA, Shumway M, Zaborsky J, Feldblyum T, Subbu V, Spiro DJ, Sitz J, Koo H, Bolotov P, Dernovoy D, Tatusova T, Bao Y, St George K, Taylor J, ... ... Salzberg SL, et al. Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature. 437: 1162-6. PMID 16208317 DOI: 10.1038/Nature04239  1
2005 Buell CR, Yuan Q, Ouyang S, Liu J, Zhu W, Wang A, Maiti R, Haas B, Wortman J, Pertea M, Jones KM, Kim M, Overton L, Tsitrin T, Fadrosh D, ... ... Salzberg SL, et al. Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Research. 15: 1284-91. PMID 16109971 DOI: 10.1101/Gr.3869505  1
2005 Allen JE, Salzberg SL. JIGSAW: Integration of multiple sources of evidence for gene prediction Bioinformatics. 21: 3596-3603. PMID 16076884 DOI: 10.1093/bioinformatics/bti609  1
2005 Holmes EC, Ghedin E, Miller N, Taylor J, Bao Y, St George K, Grenfell BT, Salzberg SL, Fraser CM, Lipman DJ, Taubenberger JK. Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. Plos Biology. 3: e300. PMID 16026181 DOI: 10.1371/Journal.Pbio.0030300  1
2005 Berriman M, Ghedin E, Hertz-Fowler C, Blandin G, Renauld H, Bartholomeu DC, Lennard NJ, Caler E, Hamlin NE, Haas B, Böhme U, Hannick L, Aslett MA, Shallom J, Marcello L, ... ... Salzberg SL, et al. The genome of the African trypanosome Trypanosoma brucei. Science (New York, N.Y.). 309: 416-22. PMID 16020726 DOI: 10.1126/Science.1112642  1
2005 El-Sayed NM, Myler PJ, Bartholomeu DC, Nilsson D, Aggarwal G, Tran AN, Ghedin E, Worthey EA, Delcher AL, Blandin G, Westenberger SJ, Caler E, Cerqueira GC, Branche C, Haas B, ... ... Salzberg SL, et al. The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science (New York, N.Y.). 309: 409-15. PMID 16020725 DOI: 10.1126/Science.1112631  1
2005 El-Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J, Aggarwal G, Caler E, Renauld H, Worthey EA, Hertz-Fowler C, Ghedin E, Peacock C, Bartholomeu DC, Haas BJ, Tran AN, ... ... Salzberg SL, et al. Comparative genomics of trypanosomatid parasitic protozoa. Science (New York, N.Y.). 309: 404-9. PMID 16020724 DOI: 10.1126/Science.1112181  1
2005 Salzberg SL, Dunning Hotopp JC, Delcher AL, Pop M, Smith DR, Eisen MB, Nelson WC. Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biology. 6: 402. PMID 15998463 DOI: 10.1186/Gb-2005-6-7-402  1
2005 Gardner MJ, Bishop R, Shah T, de Villiers EP, Carlton JM, Hall N, Ren Q, Paulsen IT, Pain A, Berriman M, Wilson RJ, Sato S, Ralph SA, Mann DJ, Xiong Z, ... ... Salzberg SL, et al. Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science (New York, N.Y.). 309: 134-7. PMID 15994558 DOI: 10.1126/Science.1110439  1
2005 Salzberg SL, Dunning Hotopp JC, Delcher AL, Pop M, Smith DR, Eisen MB, Nelson WC. Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biology. 6: R23. PMID 15774024 DOI: 10.1186/Gb-2005-6-3-R23  1
2005 Majoros WH, Pertea M, Delcher AL, Salzberg SL. Efficient decoding algorithms for generalized hidden Markov model gene finders. Bmc Bioinformatics. 6: 16. PMID 15667658 DOI: 10.1186/1471-2105-6-16  1
2005 Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D, Vamathevan J, Miranda M, Anderson IJ, Fraser JA, Allen JE, Bosdet IE, Brent MR, Chiu R, Doering TL, ... ... Salzberg SL, et al. The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science (New York, N.Y.). 307: 1321-4. PMID 15653466 DOI: 10.1126/Science.1103773  1
2004 Majoros WH, Salzberg SL. An empirical analysis of training protocols for probabilistic gene finders. Bmc Bioinformatics. 5: 206. PMID 15613242 DOI: 10.1186/1471-2105-5-206  0.48
2004 Ward N, Larsen Ø, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D, Kang KH, Lewis M, Nelson KE, Methé B, Wu M, Heidelberg JF, ... ... Salzberg SL, et al. Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). Plos Biology. 2: e303. PMID 15383840 DOI: 10.1371/Journal.Pbio.0020303  1
2004 Pop M, Phillippy A, Delcher AL, Salzberg SL. Comparative genome assembly. Briefings in Bioinformatics. 5: 237-48. PMID 15383210 DOI: 10.1093/Bib/5.3.237  1
2004 Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, Eisen MB, Celniker SE. Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biology. 5: R61. PMID 15345045 DOI: 10.1186/Gb-2004-5-9-R61  1
2004 Haas BJ, Delcher AL, Wortman JR, Salzberg SL. DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics (Oxford, England). 20: 3643-6. PMID 15247098 DOI: 10.1093/bioinformatics/bth397  1
2004 Majoros WH, Pertea M, Salzberg SL. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics (Oxford, England). 20: 2878-9. PMID 15145805 DOI: 10.1093/Bioinformatics/Bth315  0.68
2004 Ghedin E, Bringaud F, Peterson J, Myler P, Berriman M, Ivens A, Andersson B, Bontempi E, Eisen J, Angiuoli S, Wanless D, Von Arx A, Murphy L, Lennard N, Salzberg S, et al. Gene synteny and evolution of genome architecture in trypanosomatids. Molecular and Biochemical Parasitology. 134: 183-91. PMID 15003838 DOI: 10.1016/J.Molbiopara.2003.11.012  1
2004 Pain A, Woodward J, Quail MA, Anderson MJ, Clark R, Collins M, Fosker N, Fraser A, Harris D, Larke N, Murphy L, Humphray S, O'Neil S, Pertea M, Price C, ... ... Salzberg S, et al. Insight into the genome of Aspergillus fumigatus: analysis of a 922 kb region encompassing the nitrate assimilation gene cluster. Fungal Genetics and Biology : Fg & B. 41: 443-53. PMID 14998527 DOI: 10.1016/J.Fgb.2003.12.003  1
2004 Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. Versatile and open software for comparing large genomes. Genome Biology. 5: R12. PMID 14759262 DOI: 10.1186/Gb-2004-5-2-R12  1
2004 Gajer P, Schatz M, Salzberg SL. Automated correction of genome sequence errors. Nucleic Acids Research. 32: 562-9. PMID 14744981 DOI: 10.1093/Nar/Gkh216  1
2004 Pop M, Kosack DS, Salzberg SL. Hierarchical scaffolding with Bambus. Genome Research. 14: 149-59. PMID 14707177 DOI: 10.1101/Gr.1536204  1
2004 Allen JE, Pertea M, Salzberg SL. Computational gene prediction using multiple sources of evidence. Genome Research. 14: 142-8. PMID 14707176 DOI: 10.1101/Gr.1562804  1
2003 Delcher AL, Salzberg SL, Phillippy AM. Using MUMmer to identify similar regions in large sequence sets. Current Protocols in Bioinformatics. Unit 10.3. PMID 18428693 DOI: 10.1002/0471250953.bi1003s00  1
2003 Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD, Salzberg SL, White O. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Research. 31: 5654-66. PMID 14500829 DOI: 10.1093/Nar/Gkg770  1
2003 El-Sayed NM, Ghedin E, Song J, MacLeod A, Bringaud F, Larkin C, Wanless D, Peterson J, Hou L, Taylor S, Tweedie A, Biteau N, Khalak HG, Lin X, Mason T, ... ... Salzberg S, et al. The sequence and analysis of Trypanosoma brucei chromosome II. Nucleic Acids Research. 31: 4856-63. PMID 12907728 DOI: 10.1093/Nar/Gkg673  1
2003 Majoros WH, Pertea M, Antonescu C, Salzberg SL. GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders. Nucleic Acids Research. 31: 3601-4. PMID 12824375 DOI: 10.1093/Nar/Gkg527  1
2003 Volfovsky N, Haas BJ, Salzberg SL. Computational discovery of internal micro-exons. Genome Research. 13: 1216-21. PMID 12799353 DOI: 10.1101/Gr.677503  1
2003 Ermolaeva MD, Wu M, Eisen JA, Salzberg SL. The age of the Arabidopsis thaliana genome duplication. Plant Molecular Biology. 51: 859-66. PMID 12777046 DOI: 10.1023/A:1023001130337  0.4
2003 Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, Holtzapple EK, Okstad OA, Helgason E, Rilstone J, Wu M, ... ... Salzberg SL, et al. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature. 423: 81-6. PMID 12721629 DOI: 10.1038/Nature01586  1
2003 Salzberg S, Birney E, Eddy S, White O. Unrestricted free access works and must continue. Nature. 422: 801. PMID 12712164 DOI: 10.1038/422801A  1
2002 Pertea M, Salzberg SL. Using GlimmerM to find genes in eukaryotic genomes. Current Protocols in Bioinformatics. Unit 4.4. PMID 18792941 DOI: 10.1002/0471250953.Bi0404S00  1
2002 Fraser CM, Eisen JA, Nelson KE, Paulsen IT, Salzberg SL. The value of complete microbial genome sequencing (you get what you pay for). Journal of Bacteriology. 184: 6403-5; discusion 64. PMID 12426324 DOI: 10.1128/Jb.184.23.6403-6405.2002  1
2002 Gardner MJ, Shallom SJ, Carlton JM, Salzberg SL, Nene V, Shoaibi A, Ciecko A, Lynn J, Rizzo M, Weaver B, Jarrahi B, Brenner M, Parvizi B, Tallon L, Moazzez A, et al. Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14. Nature. 419: 531-4. PMID 12368868 DOI: 10.1038/nature01094  1
2002 Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermolaeva MD, Allen JE, Selengut JD, Koo HL, Peterson JD, Pop M, Kosack DS, Shumway MF, Bidwell SL, ... ... Salzberg SL, et al. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature. 419: 512-9. PMID 12368865 DOI: 10.1038/Nature01099  1
2002 Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature. 419: 498-511. PMID 12368864 DOI: 10.1038/Nature01097  1
2002 Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, Mueller HM, Dimopoulos G, Law JH, Wells MA, Birney E, ... ... Salzberg SL, et al. Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (New York, N.Y.). 298: 149-59. PMID 12364792 DOI: 10.1126/Science.1077061  1
2002 Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, et al. The genome sequence of the malaria mosquito Anopheles gambiae. Science (New York, N.Y.). 298: 129-49. PMID 12364791 DOI: 10.1126/Science.1076181  1
2002 Paulsen IT, Seshadri R, Nelson KE, Eisen JA, Heidelberg JF, Read TD, Dodson RJ, Umayam L, Brinkac LM, Beanan MJ, Daugherty SC, Deboy RT, Durkin AS, Kolonay JF, Madupu R, ... ... Salzberg SL, et al. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proceedings of the National Academy of Sciences of the United States of America. 99: 13148-53. PMID 12271122 DOI: 10.1073/Pnas.192319099  1
2002 Haas BJ, Volfovsky N, Town CD, Troukhan M, Alexandrov N, Feldmann KA, Flavell RB, White O, Salzberg SL. Full-length messenger RNA sequences greatly improve genome annotation. Genome Biology. 3: RESEARCH0029. PMID 12093376 DOI: 10.1186/Gb-2002-3-6-Research0029  0.6
2002 Mural RJ, Adams MD, Myers EW, Smith HO, Miklos GL, Wides R, Halpern A, Li PW, Sutton GG, Nadeau J, Salzberg SL, Holt RA, Kodira CD, Lu F, Chen L, et al. A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (New York, N.Y.). 296: 1661-71. PMID 12040188 DOI: 10.1126/Science.1069193  1
2002 Delcher AL, Phillippy A, Carlton J, Salzberg SL. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Research. 30: 2478-83. PMID 12034836 DOI: 10.1093/Nar/30.11.2478  1
2002 Read TD, Salzberg SL, Pop M, Shumway M, Umayam L, Jiang L, Holtzapple E, Busch JD, Smith KL, Schupp JM, Solomon D, Keim P, Fraser CM. Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science (New York, N.Y.). 296: 2028-33. PMID 12004073 DOI: 10.1126/Science.1071837  1
2002 Pertea M, Salzberg SL. Computational gene finding in plants. Plant Molecular Biology. 48: 39-48. PMID 11860211 DOI: 10.1023/A:1013770123580  1
2002 Suzek BE, Ermolaeva MD, Schreiber M, Salzberg SL. A probabilistic method for identifying start codons in bacterial genomes Bioinformatics. 17: 1123-1130. PMID 11751220 DOI: 10.1093/bioinformatics/17.12.1123  1
2002 Pop M, Salzberg SL, Shumway M. Genome sequence assembly: Algorithms and issues Computer. 35: 47-54+9. DOI: 10.1109/Mc.2002.1016901  1
2001 Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, ... ... Salzberg S, et al. The sequence of the human genome. Science (New York, N.Y.). 291: 1304-51. PMID 11181995 DOI: 10.1126/Science.1058040  1
1999 White O, Eisen JA, Heidelberg JF, Hickey EK, Peterson JD, Dodson RJ, Haft DH, Gwinn ML, Nelson WC, Richardson DL, Moffat KS, Qin H, Jiang L, Pamphile W, Crosby M, ... ... Salzberg S, et al. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science (New York, N.Y.). 286: 1571-7. PMID 10567266 DOI: 10.1126/Science.286.5444.1571  1
1998 Salzberg S, Delcher AL, Fasman KH, Henderson J. A decision tree system for finding genes in DNA. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 5: 667-80. PMID 10072083 DOI: 10.1089/Cmb.1998.5.667  1
1998 Gardner MJ, Tettelin H, Carucci DJ, Cummings LM, Aravind L, Koonin EV, Shallom S, Mason T, Yu K, Fujii C, Pederson J, Shen K, Jing J, Aston C, Lai Z, ... ... Salzberg S, et al. Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science (New York, N.Y.). 282: 1126-32. PMID 9804551 DOI: 10.1126/Science.282.5391.1126  1
1998 Fraser CM, Norris SJ, Weinstock GM, White O, Sutton GG, Dodson R, Gwinn M, Hickey EK, Clayton R, Ketchum KA, Sodergren E, Hardham JM, McLeod MP, Salzberg S, Peterson J, et al. Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science (New York, N.Y.). 281: 375-88. PMID 9665876 DOI: 10.1126/Science.281.5375.375  1
1998 Kasif S, Salzberg S, Waltz D, Rachlin J, Aha DW. A probabilistic framework for memory-based reasoning Artificial Intelligence. 104: 287-311. DOI: 10.1016/S0004-3702(98)00046-0  1
1997 Fraser CM, Casjens S, Huang WM, Sutton GG, Clayton R, Lathigra R, White O, Ketchum KA, Dodson R, Hickey EK, Gwinn M, Dougherty B, Tomb JF, Fleischmann RD, Richardson D, ... ... Salzberg S, et al. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature. 390: 580-6. PMID 9403685 DOI: 10.1038/37551  1
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