Salzberg, Steven

Bloomberg Distinguished Professor
Som Biomedical Engineering
http://salzberg-lab.org

Welch Medical Library Rm 107
(410) 614-6112
salzberg@jhu.edu

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About

Education
  • Ph.D. 1989, HARVARD UNIVERSITY
  • Master of Philosophy 1984, Yale University
  • Master of Science 1982, Yale University
  • Bachelor of Arts 1980, Yale University
Experience
  • 2014 - 2015:  Professor, SOM Medicine
  • 2011 - 2019:  Professor, SPH Biostatistics
  • 1995 - 1999:  Joint, SOM Health Sciences Informatics

Publications

Journal Articles
  • Zekavat SM, Ruotsalainen S, Handsaker RE, Alver M, Bloom J, Poterba T, Seed C, Ernst J, Chaffin M, Engreitz J, Peloso GM, Manichaikul A, Yang C, Ryan KA, Fu M, Johnson WC, Tsai M, Budoff M, Ramachandran VS, Cupples LA, Rotter JI, Rich SS, Post W, Mitchell BD, Correa A, Metspalu A, Wilson JG, Salomaa V, Kellis M, Daly MJ, Neale BM, McCarroll S, Surakka I, Esko T, Ganna A, Ripatti S, Kathiresan S, Natarajan P, Abe N, Abecasis G, Albert C, Allred NP, Almasy L, Alonso A, Ament S, Anderson P, Anugu P, Applebaum-Bowden D, Arking D, Arnett DK, Ashley-Koch A, Aslibekyan S, Assimes T, Auer P, Avramopoulos D, Barnard J, Barnes K, Barr RG, Barron-Casella E, Beaty T, Becker D, Becker L, Beer R, Begum F, Beitelshees A, Benjamin E, Bezerra M, Bielak L, Bis J, Blackwell T, Blangero J, Boerwinkle E, Borecki I, Bowler R, Brody J, Broeckel U, Broome J, Bunting K, Burchard E, Cardwell J, Carty C, Casaburi R, Casella J, Chang C, Chasman D, Chavan S, Chen B-J, Chen W-M, Chen Y-DI, Cho M, Choi ...Zoellner S (2018).  Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries.  Nature Communications.  9(1).
  • Natarajan P, Peloso GM, Zekavat SM, Montasser M, Ganna A, Chaffin M, Khera AV, Zhou W, Bloom JM, Engreitz JM, Ernst J, O’Connell JR, Ruotsalainen SE, Alver M, Manichaikul A, Johnson WC, Perry JA, Poterba T, Seed C, Surakka IL, Esko T, Ripatti S, Salomaa V, Correa A, Vasan RS, Kellis M, Neale BM, Lander ES, Abecasis G, Mitchell B, Rich SS, Wilson JG, Cupples LA, Rotter JI, Willer CJ, Kathiresan S, Abe N, Albert C, Allred NNP, Almasy L, Alonso A, Ament S, Anderson P, Anugu P, Applebaum-Bowden D, Arking D, Arnett DK, Ashley-Koch A, Aslibekyan S, Assimes T, Auer P, Avramopoulos D, Barnard J, Barnes K, Barr RG, Barron-Casella E, Beaty T, Becker D, Becker L, Beer R, Begum F, Beitelshees A, Benjamin E, Bezerra M, Bielak L, Bis J, Blackwell T, Blangero J, Boerwinkle E, Borecki I, Bowler R, Brody J, Broeckel U, Broome J, Bunting K, Burchard E, Cardwell J, Carty C, Casaburi R, Casella J, Chang C, Chasman D, Chavan S, Chen B-J, Chen W-M, Chen Y-DI, Cho M, Choi SH, Chuang L-M, Chung M...Zoellner S (2018).  Deep-coverage whole genome sequences and blood lipids among 16,324 individuals.  Nature Communications.  9(1).
  • Pertea M, Shumate A, Pertea G, Varabyou A, Breitwieser FP, Chang YC, Madugundu AK, Pandey A, Salzberg SL (2018).  CHESS: A new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise.  Genome Biology.  19(1).
  • Simner PJ, Miller HB, Breitwieser FP, Monsalve GP, Pardo CA, Salzberg SL, Sears CL, Thomas DL, Eberhart CG, Carrolla KC (2018).  Development and optimization of metagenomic next-generation sequencing methods for cerebrospinal fluid diagnostics.  Journal of Clinical Microbiology.  56(9).
  • 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 (2018).  Genomic variation among and within six Juglans species.  G3: Genes, Genomes, Genetics.  8(7).
  • Lu J, Salzberg SL (2018).  Removing contaminants from databases of draft genomes.  PLoS Computational Biology.  14(6).
  • Pallavajjala A, Kim D, Li T, Ghiaur G, Jones RJ, Burns KH, Salzberg SL, Ning Y (2018).  Genomic characterization of chromosome translocations in patients with T/myeloid mixed-phenotype acute leukemia.  Leukemia and Lymphoma.  59(5).
  • Li Z, Breitwieser FP, Lu J, Jun AS, Asnaghi L, Salzberg SL, Eberhart CG (2018).  Identifying corneal infections in formalin-fixed specimens using next generation sequencing.  Investigative Ophthalmology and Visual Science.  59(1).
  • Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A (2018).  MUMmer4: A fast and versatile genome alignment system.  PLoS Computational Biology.  14(1).
  • 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, Van Sonny L, Yuan L, Wang Z, Xia Z, Xiao L, Anderson OD, Ouyang S, Liang Y, Zimin AV, Pertea G, Qi P, Bennetzen JL, Dai X, Dawson MW, Müller HG, Kugler K, Rivarola-Duarte L, Spannagl M, Mayer KFX, Lu FH, Bevan MW, Leroy P, Li P, You FM, Sun Q, Liu Z, Lyons E, Wicker T, Salzberg SL, Devos KM, Dvoák J (2017).  Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.  Nature.  551(7681).
  • 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 (2017).  First draft genome sequence of the pathogenic fungus Lomentospora prolificans (formerly Scedosporium prolificans).  G3: Genes, Genomes, Genetics.  7(11).
  • Zimin AV, Puiu D, Hall R, Kingan S, Clavijo BJ, Salzberg SL (2017).  The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum.  GigaScience.  6(11).
  • 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, Cronn R, Yandell M, Holt C, Langley CH, Yorke JA, Salzberg SL, Wegrzyn JL (2017).  The Douglas-Fir genome sequence reveals specialization of the photosynthetic apparatus in Pinaceae.  G3: Genes, Genomes, Genetics.  7(9).
  • Kandathil AJ, Breitwieser FP, Sachithanandham J, Robinson M, Mehta SH, Timp W, Salzberg SL, Thomas DL, Balagopal A (2017).  Presence of human hepegivirus-1 in a cohort of people who inject drugs.  Annals of Internal Medicine.  167(1).
  • Zimin AV, Puiu D, Luo MC, Zhu T, Koren S, Marçais G, Yorke JA, Dvorák J, Salzberg SL (2017).  Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm.  Genome Research.  27(5).
  • Sun Z, Ke X, Salzberg SL, Kim D, Antonescu V, Cheng Y, Huang B, Song JH, Abraham JM, Ibrahim S, Tian H, Meltzer SJ (2017).  The novel fusion transcript NR5A2-KLHL29FT is generated by an insertion at the KLHL29 locus.  Cancer.  123(9).
  • Canzar S, Salzberg SL (2017).  Short Read Mapping: An Algorithmic Tour.  Proceedings of the IEEE.  105(3).
  • Lu J, Breitwieser FP, Thielen P, Salzberg SL (2017).  Bracken: Estimating species abundance in metagenomics data.  PeerJ.  2017(1).
  • Stevens KA, Wegrzyn JL, Zimin A, Puiu D, Crepeau M, Cardeno C, Paul R, Gonzalez-Ibeas D, Koriabine M, Holtz-Morris AE, Martínez-García PJ, Sezen UU, Marçais G, Jermstad K, McGuire PE, Loopstra CA, Davis JM, Eckert A, de Jong P, Yorke JA, Salzberg SL, Neale DB, Langley CH (2016).  Sequence of the sugar pine megagenome.  Genetics.  204(4).
  • Kim D, Song L, Breitwieser FP, Salzberg SL (2016).  Centrifuge: Rapid and sensitive classification of metagenomic sequences.  Genome Research.  26(12).
  • Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL (2016).  Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.  Nature Protocols.  11(9).
  • 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, Pratt K, Kuruganti S, Aradhya MK, Leslie CA, Dandekar AM, Salzberg SL, Wegrzyn JL, Langley CH, Neale DB (2016).  The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols.  The Plant journal : for cell and molecular biology.  87(5).
  • Sork VL, Fitz-Gibbon ST, Puiu D, Crepeau M, Gugger PF, Sherman R, Stevens K, Langley CH, Pellegrini M, Salzberg SL (2016).  First draft assembly and annotation of the genome of a California endemic oak Quercus lobata Née (Fagaceae).  G3: Genes, Genomes, Genetics.  6(11).
  • Pop M, Salzberg SL (2015).  Use and mis-use of supplementary material in science publications.  BMC Bioinformatics.  16(1).
  • Chang TC, Pertea M, Lee S, Salzberg SL, Mendell JT (2015).  Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms.  Genome Research.  25(9).
  • Breitwieser FP, Pardo CA, Salzberg SL (2015).  Re-analysis of metagenomic sequences from acute flaccid myelitis patients reveals alternatives to enterovirus D68 infection.  F1000Research.  4.
  • 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, Kemp WP, Bosch J, Waterhouse RM, Zdobnov EM, Stolle E, Kraus FB, Helbing S, Moritz RFA, Glastad KM, Hunt BG, Goodisman MAD, Hauser F, Grimmelikhuijzen CJP, Pinheiro DG, Nunes FMF, Soares MPM, Tanaka ÉD, Simões ZLP, Hartfelder K, Evans JD, Barribeau SM, Johnson RM, Massey JH, Southey BR, Hasselmann M, Hamacher D, Biewer M, Kent CF, Zayed A, Blatti C, Sinha S, Johnston JS, Hanrahan SJ, Kocher SD, Wang J, Robinson GE, Zhang G (2015).  Genomic signatures of evolutionary transitions from solitary to group living.  Science.  348(6239).
  • Sadd BM, Barribeau SM, Bloch G, de Graaf DC, Dearden P, Elsik CG, Gadau J, Grimmelikhuijzen CJP, Hasselmann M, Lozier JD, Robertson HM, Smagghe G, Stolle E, Van Vaerenbergh M, Waterhouse RM, Bornberg-Bauer E, Klasberg S, Bennett AK, Câmara F, Guigó R, Hoff K, Mariotti M, Munoz-Torres M, Murphy T, Santesmasses D, Amdam GV, Beckers M, Beye M, Biewer M, Bitondi MMG, Blaxter ML, Bourke AFG, Brown MJF, Buechel SD, Cameron R, Cappelle K, Carolan JC, Christiaens O, Ciborowski KL, Clarke DF, Colgan TJ, Collins DH, Cridge AG, Dalmay T, Dreier S, du Plessis L, Duncan E, Erler S, Evans J, Falcon T, Flores K, Freitas FCP, Fuchikawa T, Gempe T, Hartfelder K, Hauser F, Helbing S, Humann FC, Irvine F, Jermiin LS, Johnson CE, Johnson RM, Jones AK, Kadowaki T, Kidner JH, Koch V, Köhler A, Kraus FB, Lattorff HMG, Leask M, Lockett GA, Mallon EB, Antonio DSM, Marxer M, Meeus I, Moritz RFA, Nair A, Näpflin K, Nissen I, Niu J, Nunes FMF, Oakeshott JG, Osborne A, Otte M, Pinheiro DG, Rossié N, Ru...Worley KC (2015).  The genomes of two key bumblebee species with primitive eusocial organization.  Genome Biology.  16(1).
  • 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, Deeks SG, Strowig T, Kumar P, Siliciano JD, Salzberg SL, Flavell RA, Shan L, Siliciano RF (2015).  Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations.  Nature.  517(7534).
  • Wilton R, Budavari T, Langmead B, Wheelan SJ, Salzberg SL, Szalay AS (2015).  Arioc: High-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space.  PeerJ.  2015(3).
  • Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL (2015).  StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.  Nature Biotechnology.  33(3).
  • Kim D, Langmead B, Salzberg SL (2015).  HISAT: A fast spliced aligner with low memory requirements.  Nature Methods.  12(4).
  • 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, Fuentes-Soriano S, Wu LS, Gilbert D, Marçais G, Roberts M, Holt C, Yandell M, Davis JM, Smith KE, Dean JFD, Lorenz WW, Whetten RW, Sederoff R, Wheeler N, McGuire PE, Main D, Loopstra CA, Mockaitis K, deJong PJ, Yorke JA, Salzberg SL, Langley CH (2014).  Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies.  Genome Biology.  15(3).
  • Wood DE, Salzberg SL (2014).  Kraken: Ultrafast metagenomic sequence classification using exact alignments.  Genome Biology.  15(3).
  • Salzberg SL, Pertea M, Fahrner JA, Sobreira N (2014).  DIAMUND: Direct comparison of genomes to detect mutations.  Human Mutation.  35(3).
  • Martinson VG, Mago T, Koch H, Salzberg SL, Moran NA (2014).  Genomic features of a bumble bee symbiont reflect its host environment.  Applied and Environmental Microbiology.  80(13).
  • 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 (2014).  Sequencing and assembly of the 22-Gb loblolly pine genome.  Genetics.  196(3).
  • Merchant S, Wood DE, Salzberg SL (2014).  Unexpected cross-species contamination in genome sequencing projects.  PeerJ.  2014(1).
  • 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, Puiu D, Salzberg SL, de Jong PJ, Mockaitis K, Main D, Langley CH, Neale DB (2014).  Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation.  Genetics.  196(3).
  • 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, Treangen T, Salzberg SL, Yorke JA, Norgren RB (2014).  A new rhesus macaque assembly and annotation for next-generation sequencing analyses.  Biology direct.  9(1).
  • Florea L, Song L, Salzberg SL (2013).  Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues.  F1000Research.  2.
  • Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA (2013).  The MaSuRCA genome assembler.  Bioinformatics.  29(21).
  • 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 (2013).  Insights into the Loblolly Pine Genome: Characterization of BAC and Fosmid Sequences.  PLoS ONE.  8(9).
  • Florea LD, Salzberg SL (2013).  Genome-guided transcriptome assembly in the age of next-generation sequencing.  IEEE/ACM Transactions on Computational Biology and Bioinformatics.  10(5).
  • 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, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu Sy, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S (2013).  The COMBREX Project: Design, Methodology, and Initial Results.  PLoS Biology.  11(8).
  • Magoc T, Pabinger S, Canzar S, Liu X, Su Q, Puiu D, Tallon LJ, Salzberg SL (2013).  GAGE-B: An evaluation of genome assemblers for bacterial organisms.  Bioinformatics.  29(14).
  • Neale DB, Langley CH, Salzberg SL, Wegrzyn JL (2013).  Open access to tree genomes: The path to a better forest.  Genome Biology.  14(6).
  • Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL (2013).  TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.  Genome Biology.  14(4).
  • Magoc T, Wood D, Salzberg SL (2013).  EDGE-pro: Eestimated Degree of Gene Expression in prokaryotic genomes.  Evolutionary Bioinformatics.  2013(9).
  • Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M (2013).  Hawkeye and AMOS: Visualizing and assessing the quality of genome assemblies.  Briefings in Bioinformatics.  14(2).
  • Wood DE, Lin H, Levy-Moonshine A, Swaminathan R, Chang YC, Anton BP, Osmani L, Steffen M, Kasif S, Salzberg SL (2012).  Thousands of missed genes found in bacterial genomes and their analysis with COMBREX.  Biology Direct.  7.
  • Zimin AV, Kelley DR, Roberts M, Marçais G, Salzberg SL, Yorke JA (2012).  Mis-assembled "segmental duplications" in two versions of the Bos taurus genome.  PLoS ONE.  7(8).
  • Salzberg S (2012).  A scientist and an advocate. An interview with Steven Salzberg by Kristie Nybo..  BioTechniques.  53(2).
  • Salzberg SL (2012).  The perils of gene patents.  Clinical Pharmacology and Therapeutics.  91(6).
  • Langmead B, Salzberg SL (2012).  Fast gapped-read alignment with Bowtie 2.  Nature Methods.  9(4).
  • Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012).  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.  Nature Protocols.  7(3).
  • Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marcxais G, Pop M, Yorke JA (2012).  GAGE: A critical evaluation of genome assemblies and assembly algorithms.  Genome Research.  22(3).
  • Treangen TJ, Salzberg SL (2012).  Repetitive DNA and next-generation sequencing: Computational challenges and solutions.  Nature Reviews Genetics.  13(1).
  • Kelley DR, Liu B, Delcher AL, Pop M, Salzberg SL (2012).  Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering.  Nucleic Acids Research.  40(1).
  • Dasmahapatra KK, Walters JR, Briscoe AD, Davey JW, Whibley A, Nadeau NJ, Zimin AV, Salazar C, Ferguson LC, Martin SH, Salazar C, Lewis JJ, Adler S, Ahn SJ, Baker DA, Baxter SW, Chamberlain NL, Ritika C, Counterman BA, Dalmay T, Gilbert LE, Gordon K, Heckel DG, Hines HM, Hoff KJ, Holland PWH, Jacquin-Joly E, Jiggins FM, Jones RT, Kapan DD, Kersey P, Lamas G, Lawson D, Mapleson D, Maroja LS, Martin A, Moxon S, Palmer WJ, Papa R, Papanicolaou A, Pauchet Yi, Ray DA, Rosser N, Salzberg SL, Supple MA, Surridge A, Tenger-Trolander A, Vogel H, Wilkinson PA, Wilson D, Yorke JA, Yuan F, Balmuth AL, Eland C, Gharbi K, Thomson M, Gibbs RA, Han Y, Jayaseelan JC, Kovar C, Mathew T, Muzny DM, Ongeri F, Pu LL, Qu J, Thornton RL, Worley KC, Wu YQ, Linares M, Blaxter ML, ffrench-Constant RH, Joron M, Kronforst MR, Mullen SP, Reed RD, Scherer SE, Richards S, Mallet J, Mc Millan WO, Jiggins CD (2012).  Butterfly genome reveals promiscuous exchange of mimicry adaptations among species.  Nature.  487(7405).
  • Lipman D, Flicek P, Salzberg S, Gerstein M, Knight R (2011).  Closure of the NCBI SRA and implications for the long-term future of genomics data storage..  Genome biology.  12(3).
  • Magoc T, Salzberg SL (2011).  FLASH: Fast length adjustment of short reads to improve genome assemblies.  Bioinformatics.  27(21).
  • 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, Schatz MC, Shumway M, Sommer DD, Trapnell C, Benahmed F, Dimitrov G, Madupu R, Radune D, Sullivan S, Jha G, Ishihara H, Lee SW, Pandey A, Sharma V, Sriariyanun M, Szurek B, Vera-Cruz CM, Dorman KS, Ronald PC, Verdier V, Dow JM, Sonti RV, Tsuge S, Brendel VP, Rabinowicz PD, Leach JE, White FF, Salzberg SL (2011).  Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp..  Journal of Bacteriology.  193(19).
  • Kim D, Salzberg SL (2011).  TopHat-Fusion: An algorithm for discovery of novel fusion transcripts.  Genome Biology.  12(8).
  • Pertea M, Pertea GM, Salzberg SL (2011).  Detection of lineage-specific evolutionary changes among primate species.  BMC Bioinformatics.  12.
  • Angiuoli SV, Dunning Hotopp JC, Salzberg SL, Tettelin H (2011).  Improving pan-genome annotation using whole genome multiple alignment.  BMC Bioinformatics.  12.
  • Florea L, Souvorov A, Kalbfleisch TS, Salzberg SL (2011).  Genome assembly has a major impact on gene content: A comparison of annotation in two bos Taurus assemblies.  PLoS ONE.  6(6).
  • Enk J, Devault A, Debruyne R, King CE, Treangen T, O'Rourke D, Salzberg SL, Fisher D, MacPhee R, Poinar H (2011).  Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths.  Genome Biology.  12(5).
  • 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, Keim PS, Fraser-Liggett CM, Ravel J (2011).  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(12).
  • Angiuoli SV, Salzberg SL (2011).  Mugsy: Fast multiple alignment of closely related whole genomes.  Bioinformatics.  27(3).
  • 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, Evans C, Harkins T, Kodira C, Desany B, Crasta OR, Jensen RV, Allan AC, Michael TP, Setubal JC, Celton JM, Rees DJG, Williams KP, Holt SH, Rojas JJR, Chatterjee M, Liu B, Silva H, Meisel L, Adato A, Filichkin SA, Troggio M, Viola R, Ashman TL, Wang H, Dharmawardhana P, Elser J, Raja R, Priest HD, Bryant DW, Fox SE, Givan SA, Wilhelm LJ, Naithani S, Christoffels A, Salama DY, Carter J, Girona EL, Zdepski A, Wang W, Kerstetter RA, Schwab W, Korban SS, Davik J, Monfort A, Denoyes-Rothan B, Arus P, Mittler R, Flinn B, Aharoni A, Bennetzen JL, Salzberg SL, Dickerman AW, Velasco R, Borodovsky M, Veilleux RE, Folta KM (2011).  The genome of woodland strawberry (Fragaria vesca).  Nature Genetics.  43(2).
  • 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 (2011).  COMBREX: A project to accelerate the functional annotation of prokaryotic genomes.  Nucleic Acids Research.  39(SUPPL. 1).
  • Salzberg SL (2010).  Recent advances in RNA sequence analysis.  F1000 Biology Reports.  2(1).
  • Kelley DR, Schatz MC, Salzberg SL (2010).  Quake: Quality-aware detection and correction of sequencing errors.  Genome Biology.  11(11).
  • Kelley DR, Salzberg SL (2010).  Clustering metagenomic sequences with interpolated Markov models.  BMC Bioinformatics.  11.
  • Miller TR, Delcher AL, Salzberg SL, Saunders E, Detter JC, Halden RU (2010).  Genome sequence of the dioxin-mineralizing bacterium Sphingomonas wittichii RW1.  Journal of Bacteriology.  192(22).
  • Deng X, Phillippy AM, Li Z, Salzberg SL, Zhang W (2010).  Probing the pan-genome of Listeria monocytogenes: New insights into intraspecific niche expansion and genomic diversification.  BMC Genomics.  11(1).
  • Schatz MC, Delcher AL, Salzberg SL (2010).  Assembly of large genomes using second-generation sequencing.  Genome Research.  20(9).
  • Pertea M, Salzberg SL (2010).  Between a chicken and a grape: Estimating the number of human genes.  Genome Biology.  11(5).
  • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, Van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010).  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.  Nature Biotechnology.  28(5).
  • Kelley DR, Salzberg SL (2010).  Detection and correction of false segmental duplications caused by genome mis-assembly.  Genome Biology.  11(3).
  • Suzuki JY, Tripathi S, Fermín GA, Jan FJ, Hou S, Saw JH, Ackerman CM, Yu Q, Schatz MC, Pitz KY, Yépes M, Fitch MMM, Manshardt RM, Slightom JL, Ferreira SA, Salzberg SL, Alam M, Ming R, Moore PH, Gonsalves D (2010).  Efforts to deregulate Rainbow papaya in Japan: Molecular characterization of transgene and vector inserts.  Acta Horticulturae.  851.
  • Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg LA, Bouffard P, Burt DW, Crasta O, Crooijmans RPMA, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Frederickson KM, Flicek P, Florea L, Folkerts O, Groenen MAM, Harkins TT, Herrero J, Hoffmann S, Megens HJ, Jiang A, de Jong P, Kaiser P, Kim H, Kim KW, Kim S, Langenberger D, Lee MK, Lee T, Mane S, Marcais G, Marz M, McElroy AP, Modise T, Nefedov M, Notredame C, Paton IR, Payne WS, Pertea G, Prickett D, Puiu D, Qioa D, Raineri E, Ruffier M, Salzberg SL, Schatz MC, Scheuring C, Schmidt CJ, Schroeder S, Searle SMJ, Smith EJ, Smith J, Sonstegard TS, Stadler PF, Tafer H, Tu Z, van Tassell CP, Vilella AJ, Williams KP, Yorke JA, Zhang L, Zhang HB, Zhang X, Zhang Y, Reed KM (2010).  Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): Genome assembly and analysis.  PLoS Biology.  8(9).
  • Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL (2009).  Searching for SNPs with cloud computing.  Genome Biology.  10(11).
  • Salzberg SL, Warnow T (2009).  Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface.  Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).  5724 LNBI.
  • Phillippy AM, Deng X, Zhang W, Salzberg SL (2009).  Efficient oligonucleotide probe selection for pan-genomic tiling arrays.  BMC Bioinformatics.  10.
  • Phillippy AM, Ayanbule K, Edwards NJ, Salzberg SL (2009).  Insignia: A DNA signature search web server for diagnostic assay development.  Nucleic Acids Research.  37(SUPPL. 2).
  • Brady A, Salzberg SL (2009).  Phymm and PhymmBL: Metagenomic phylogenetic classification with interpolated Markov models.  Nature Methods.  6(9).
  • Kingsford C, Nagarajan N, Salzberg SL (2009).  2009 swine-origin influenza A (H1N1) resembles previous influenza isolates.  PLoS ONE.  4(7).
  • 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, Coulson R, Day TA, Delcher A, Demarco R, Djikeng A, Eyre T, Gamble JA, Ghedin E, Gu Y, Hertz-Fowler C, Hirai H, Hirai Y, Houston R, Ivens A, Johnston DA, Lacerda D, MacEdo CD, McVeigh P, Ning Z, Oliveira G, Overington JP, Parkhill J, Pertea M, Pierce RJ, Protasio AV, Quail MA, Rajandream MA, Rogers J, Sajid M, Salzberg SL, Stanke M, Tivey AR, White O, Williams DL, Wortman J, Wu W, Zamanian M, Zerlotini A, Fraser-Liggett CM, Barrell BG, El-Sayed NM (2009).  The genome of the blood fluke Schistosoma mansoni.  Nature.  460(7253).
  • Trapnell C, Pachter L, Salzberg SL (2009).  TopHat: Discovering splice junctions with RNA-Seq.  Bioinformatics.  25(9).
  • Trapnell C, Salzberg SL (2009).  How to map billions of short reads onto genomes.  Nature Biotechnology.  27(5).
  • 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 (2009).  A whole-genome assembly of the domestic cow, Bos taurus.  Genome Biology.  10(4).
  • Langmead B, Trapnell C, Pop M, Salzberg SL (2009).  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.  Genome Biology.  10(3).
  • Salzberg SL, Puiu D, Sommer DD, Nene V, Lee NH (2009).  Genome sequence of the Wolbachia endosymbiont of Culex quinquefasciatus JHB.  Journal of Bacteriology.  191(5).
  • Pertea M, Ayanbule K, Smedinghoff M, Salzberg SL (2009).  OperonDB: A comprehensive database of predicted operons in microbial genomes.  Nucleic Acids Research.  37(SUPPL. 1).
  • Ravel J, Jiang L, Stanley ST, Wilson MR, Decker RS, Read TD, Worsham P, Keim PS, Salzberg SL, Fraser-Liggett CM, Rasko DA (2009).  The complete genome sequence of Bacillus anthracis Ames "Ancestor".  Journal of Bacteriology.  91(1).
  • 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 (2008).  Acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in Xanthomonas.  PLoS ONE.  3(11).
  • Puiu D, Salzberg SL (2008).  Re-assembly of the genome of Francisella tularensis subsp. holarctica OSU18.  PLoS ONE.  3(10).
  • Carlton JM, Adams JH, Silva JC, Bidwell SL, Lorenzi H, Caler E, Crabtree J, Angiuoli SV, Merino EF, Amedeo P, Cheng Q, Coulson RMR, Crabb BS, Del Portillo HA, Essien K, Feldblyum TV, Fernandez-Becerra C, Gilson PR, Gueye AH, Guo X, Kang'A S, Kooij TWA, Korsinczky M, Meyer EVS, Nene V, Paulsen I, White O, Ralph SA, Ren Q, Sargeant TJ, Salzberg SL, Stoeckert CJ, Sullivan SA, Yamamoto MM, Hoffman SL, Wortman JR, Gardner MJ, Galinski MR, Barnwell JW, Fraser-Liggett CM (2008).  Comparative genomics of the neglected human malaria parasite Plasmodium vivax.  Nature.  455(7214).
  • Salzberg SL, Sommer DD, Puiu D, Lee VT (2008).  Gene-boosted assembly of a novel bacterial genome from very short reads.  PLoS Computational Biology.  4(9).
  • Kingsford C, Salzberg SL (2008).  What are decision trees?.  Nature Biotechnology.  26(9).
  • 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, Aparna G, Jha G, Pandey A, Patil PB, Ishihara H, Meyer DF, Szurek B, Verdier V, Koebnik R, Maxwell JM, Ryan RP, Hirata H, Tsuyumu S, Won Lee S, Ronald PC, Sonti RV, Van Sluys MA, Leach JE, White FF, Bogdanove AJ (2008).  Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A.  BMC Genomics.  9.
  • Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KLT, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, Chen C, Qian W, Shen J, Du P, Eustice M, Tong E, Tang H, Lyons E, Paull RE, Michael TP, Wall K, Rice DW, Albert H, Wang M-L, Zhu YJ, Schatz M, Nagarajan N, Acob RA, Guan P, Blas A, Wai CM, Ackerman CM, Ren Y, Liu C, Wang J, Wang J, Na J-K, Shakirov EV, Haas B, Thimmapuram J, Nelson D, Wang X, Bowers JE, Gschwend AR, Delcher AL, Singh R, Suzuki JY, Tripathi S, Neupane K, Wei H, Irikura B, Paidi M, Jiang N, Zhang W, Presting G, Windsor A, Navajas-Pérez R, Torres MJ, Feltus FA, Porter B, Li Y, Burroughs AM, Luo M-C, Liu L, Christopher DA, Mount SM, Moore PH, Sugimura T, Jiang J, Schuler MA, Friedman V, Mitchell-Olds T, Shippen DE, Depamphilis CW, Palmer JD, Freeling M, Paterson AH, Gonsalves D, Wang L, Alam M (2008).  The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).  Nature.  452(7190).
  • Pop M, Salzberg SL (2008).  Bioinformatics challenges of new sequencing technology.  Trends in Genetics.  24(3).
  • Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Robin CR, Wortman JR (2008).  Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.  Genome Biology.  9(1).
  • Pertea M, Salzberg SL (2007).  Using protein domains to improve the accuracy of Ab Initio gene finding.  Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).  4645 LNBI.
  • Schriml LM, Gussman A, Phillippy K, Angiuoli S, Hari K, Goates A, Jain R, Davidsen T, Ganapathy A, Ghedin E, Salzberg S, White O, Hall N (2007).  Gemina: A web-based epidemiology and genomic metadata system designed to identify infectious agents.  Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).  4506 LNCS.
  • Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo De Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiß S, Freyhult E, Fulton L, Fulton R, Garcia ACL, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL...MacCallum I (2007).  Evolution of genes and genomes on the Drosophila phylogeny.  Nature.  450(7167).
  • 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, Wortman JR, Feldblyum T, Tallon L, Schatz M, Shumway M, Koo H, Salzberg SL, Schobel S, Pertea M, Pop M, White O, Barton GJ, Carlow CKS, Crawford MJ, Daub J, Dimmic MW, Estes CF, Foster JM, Ganatra M, Gregory WF, Johnson NM, Jin M, Komuniecki R, Korf I, Kumar S, Laney S, Li BW, Li W, Lindblom TH, Lustigman S, Ma D, Maina CV, Martin DMA, McCarter JP, McReynolds L, Mitreva M, Nutman TB, Parkinson J, Peregrín-Alvarez JM, Poole C, Ren Q, Saunders L, Sluder AE, Smith K, Stanke M, Unnasch TR, Ware J, Wei AD, Weil G, Williams DJ, Zhang Y, Williams SA, Fraser-Liggett C, Slatko B, Blaxter ML, Scott AL (2007).  Draft genome of the filarial nematode parasite Brugia malayi.  Science.  317(5845).
  • Kingsford C, Delcher AL, Salzberg SL (2007).  A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genes.  Molecular Biology and Evolution.  24(9).
  • Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu Z, Loftus B, Xi Z, Megy K, Grabherr M, Ren Q, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, Bonaldo MF, Zhu J, Sinkins SP, Hogenkamp DG, Amedeo P, Arensburger P, Atkinson PW, Bidwell S, Biedler J, Birney E, Bruggner RV, Costas J, Coy MR, Crabtree J, Crawford M, DeBruyn B, DeCaprio D, Eiglmeier K, Eisenstadt E, El-Dorry H, Gelbart WM, Gomes SL, Hammond M, Hannick LI, Hogan JR, Holmes MH, Jaffe D, Johnston JS, Kennedy RC, Koo H, Kravitz S, Kriventseva EV, Kulp D, LaButti K, Lee E, Li S, Lovin DD, Mao C, Mauceli E, Menck CFM, Miller JR, Montgomery P, Mori A, Nascimento AL, Naveira HF, Nusbaum C, O'Leary S, Orvis J, Pertea M, Quesneville H, Reidenbach KR, Rogers Y-H, Roth CW, Schneider JR, Schatz M, Shumway M, Stanke M, Stinson EO, Tubio JMC, VanZee JP, Verjovski-Almeida S, Werner D, White O, Wyder S, Zeng Q, Zhao Q, Zhao Y, Hill CA, Raikhel AS, Soares MB, Knudson DL, Lee NH, Galagan J, Salzberg SL, Paulsen IT, Dimopoulos G, Co...Severson DW (2007).  Genome sequence of Aedes aegypti, a major arbovirus vector.  Science.  316(5832).
  • Pertea M, Mount SM, Salzberg SL (2007).  A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana.  BMC Bioinformatics.  8.
  • Phillippy AM, Mason JA, Ayanbule K, Sommer DD, Taviani E, Huq A, Colwell RR, Knight IT, Salzberg SL (2007).  Comprehensive DNA signature discovery and validation.  PLoS Computational Biology.  3(5).
  • Delcher AL, Bratke KA, Powers EC, Salzberg SL (2007).  Identifying bacterial genes and endosymbiont DNA with Glimmer.  Bioinformatics.  23(6).
  • Schatz MC, Phillippy AM, Shneiderman B, Salzberg SL (2007).  Hawkeye: An interactive visual analytics tool for genome assemblies.  Genome Biology.  8(3).
  • Sommer DD, Delcher AL, Salzberg SL, Pop M (2007).  Minimus: A fast, lightweight genome assembler.  BMC Bioinformatics.  8.
  • Kingsford CL, Ayanbule K, Salzberg SL (2007).  Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake.  Genome Biology.  8(2).
  • Salzberg SL (2007).  Genome re-annotation: A wiki solution?.  Genome Biology.  8(1).
  • Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman JR, Bidwell SL, Alsmark UCM, Besteiro S, Sicheritz-Ponten T, Noel CJ, Dacks JB, Foster PG, Simillion C, Van De Peer Y, Miranda-Saavedra D, Barton GJ, Westrop GD, Müller S, Dessi D, Fiori PL, Ren Q, Paulsen I, Zhang H, Bastida-Corcuera FD, Simoes-Barbosa A, Brown MT, Hayes RD, Mukherjee M, Okumura CY, Schneider R, Smith AJ, Vanacova S, Villalvazo M, Haas BJ, Pertea M, Feldblyum TV, Utterback TR, Shu CL, Osoegawa K, De Jong PJ, Hrdy I, Horvathova L, Zubacova Z, Dolezal P, Malik SB, Logsdon JM, Henze K, Gupta A, Wang CC, Dunne RL, Upcroft JA, Upcroft P, White O, Salzberg SL, Tang P, Chiu CH, Lee YS, Embley TM, Coombs GH, Mottram JC, Tachezy J, Fraser-Liggett CM, Johnson PJ (2007).  Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis.  Science.  315(5809).
  • Salzberg SL, Kingsford C, Cattoli G, Spiro DJ, Janies DA, Aly MM, Brown IH, Couacy-Hymann E, De Mia GM, Do HD, Guercio A, Joannis T, Ali ASM, Osmani A, Padalino I, Saad MD, Savic V, Sengamalay NA, Yingst S, Zaborsky J, Zorman-Rojs O, Ghedin E, Capua I (2007).  Genome analysis linking recent European and African influenza (H5N1) viruses.  Emerging Infectious Diseases.  13(5).
  • Allen JE, Majoros WH, Pertea M, Salzberg SL (2006).  JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions..  Genome biology.  7 Suppl 1.
  • 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, Majoros WH, Farzad M, Carlton JM, Smith RK, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, Del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E (2006).  Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.  PLoS Biology.  4(9).
  • Allen JE, Salzberg SL (2006).  A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons.  Algorithms for Molecular Biology.  1(1).
  • Quackenbush J, Salzberg SL (2006).  It is time to end the patenting of software.  Bioinformatics.  22(12).
  • 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, Sajadi H, Salzberg SL, Sultana R, Thiagarajan M, Tsai J, Veratti K, White J, Quackenbush J, Jacob HJ, Lee NH (2006).  Physiogenomic resources for rat models of heart, lung and blood disorders.  Nature Genetics.  38(2).
  • 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, Davies R, Dyer PS, Farman M, Fedorova N, Fedorova N, Feldblyum TV, Fischer R, Fosker N, Fraser A, García JL, García MJ, Goble A, Goldman GH, Gomi K, Griffith-Jones S, Gwilliam R, Haas B, Haas H, Harris D, Horiuchi H, Huang J, Humphray S, Jiménez J, Keller N, Khouri H, Kitamoto K, Kobayashi T, Konzack S, Kulkarni R, Kumagai T, Lafton A, Latgé J-P, Li W, Lord A, Lu C, Majoros WH, May GS, Miller BL, Mohamoud Y, Molina M, Monod M, Mouyna I, Mulligan S, Murphy L, O'Neil S, Paulsen I, Peñalva MA, Pertea M, Price C, Pritchard BL, Quail MA, Rabbinowitsch E, Rawlins N, Rajandream M-A, Reichard U, Renauld H, Robson GD, Rodriguez De Cordoba S, Rodríguez-Peña JM, Ronning CM, Rutter S, Salzberg SL, Sanchez M, Sánchez-Ferrero JC, Saunders D, Seeger K, Squares R, Squares S, Takeuchi M, Tekaia F, Turner G, Vazquez De Aldana CR, Weidman ...Denning DW (2005).  Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus.  Nature.  438(7071).
  • 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, Lipman DJ, Fraser CM, Taubenberger JK, Salzberg SL (2005).  Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution.  Nature.  437(7062).
  • Choisne N, Demange N, Orjeda G, Samain S, D'Hont A, Cattolico L, Pelletier E, Couloux A, Segurens B, Wincker P, Scarpelli C, Weissenbach J, Salanoubat M, Singh NK, Mohapatra T, Sharma TR, Gaikwad K, Singh A, Dalal V, Srivastava SK, Dixit A, Pal AK, Ghazi IA, Yadav M, Pandit A, Bhargava A, Sureshbabu K, Dixit R, Singh H, Swain SC, Pal S, Ragiba M, Singh PK, Singhal V, Mendiratta SD, Batra K, Raghuvanshi S, Mohanty A, Bharti AK, Gaur A, Gupta V, Kumar D, Vydianathan R, Vij S, Kapur A, Khurana P, Sharma S, Khurana P, Khurana JP, Tyagi AK, Yuan Q, Ouyang S, Liu J, Zhu W, Wang A, Lin H, Hamilton J, Haas B, Wortman J, Jones KM, Kim M, Overton L, Tsitrin T, Fadrosh D, Bera J, Weaver B, Jin S, Johri S, Reardon M, Vuong H, Tallon L, Van Aken S, Lewis M, Utterback T, Feldblyum T, Zismann V, Iobst S, Hsiao J, de Vazeille AR, Salzberg SL, White O, Fraser C, Buell CR, Yu Y, Rambo T, Currie J, Collura K, Kim HR, Stum D, Wang W, Kudrna D, Mueller C, Wing RA, Kramer M, Spiegel L, Nasciment...Messing J (2005).  The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications.  BMC Biology.  3.
  • Allen JE, Salzberg SL (2005).  JIGSAW: Integration of multiple sources of evidence for gene prediction.  Bioinformatics.  21(18).
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  • Majoros WH, Pertea M, Salzberg SL (2005).  Efficient implementation of a generalized pair hidden Markov model for comparative gene finding.  Bioinformatics.  21(9).
  • 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, Donlin MJ, D'Souza CA, Fox DS, Grinberg V, Fu J, Fukushima M, Haas BJ, Huang JC, Janbon G, Jones SJM, Koo HL, Krzywinski MI, Kwon-Chung JK, Lengeler KB, Maiti R, Marra MA, Marra RE, Mathewson CA, Mitchell TG, Pertea M, Riggs FR, Salzberg SL, Schein JE, Shvartsbeyn A, Shin H, Shumway M, Specht CA, Suh BB, Tenney A, Utterback TR, Wickes BL, Wortman JR, Wye NH, Kronstad JW, Lodge JK, Heitman J, Davis RW, Fraser CM, Hyman RW (2005).  The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans.  Science.  307(5713).
  • Majoros WH, Pertea M, Delcher AL, Salzberg SL (2005).  Efficient decoding algorithms for generalized hidden Markov model gene finders.  BMC Bioinformatics.  6.
  • Holmes EC, Ghedin E, Miller N, Taylor J, Bao Y, St. George K, Grenfell BT, Salzberg SL, Fraser CM, Lipman DJ, Taubenberger JK (2005).  Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses.  PLoS Biology.  3(9).
  • Salzberg SL, Dunning Hotopp JC, Delcher AL, Pop M, Smith DR, Eisen MB, Nelson WC (2005).  Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.  Genome Biology.  6(3).
  • Majoros WH, Salzberg SL (2004).  An empirical analysis of training protocols for probabilistic gene finders.  BMC Bioinformatics.  5.
  • Haas BJ, Delcher AL, Wortman JR, Salzberg SL (2004).  DAGchainer: A tool for mining segmental genome duplications and synteny.  Bioinformatics.  20(18).
  • Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, Eisen MB, Celniker SE (2004).  Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura..  Genome biology.  5(9).
  • Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL (2004).  Versatile and open software for comparing large genomes..  Genome biology.  5(2).
  • Majoros WH, Pertea M, Salzberg SL (2004).  TigrScan and GlimmerHMM: Two open source ab initio eukaryotic gene-finders.  Bioinformatics.  20(16).
  • 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, Paulsen IT, Fouts D, Ravel J, Tettelin H, Ren Q, Read T, DeBoy RT, Seshadri R, Salzberg SL, Jensen HB, Birkeland NK, Nelson WC, Dodson RJ, Grindhaug SH, Holt I, Eidhammer I, Jonasen I, Vanaken S, Utterback T, Feldblyum TV, Fraser CM, Lillehaug JR, Eisen JA (2004).  Genomic insights into methanotrophy: The complete genome sequence of Methylococcus capsulatus (Bath).  PLoS Biology.  2(10).
  • Salzberg SL, Church D, DiCuccio M, Yaschenko E, Ostell J (2004).  The genome assembly archive: A new public resource.  PLoS Biology.  2(9).
  • 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, Rabbinowitsch E, Rajandream MA, Salzberg S, Saunders D, Seeger K, Sharp S, Warren T, Denning DW, Barrell B, Hall N (2004).  Insight into the genome of Aspergillus fumigatus: Analysis of a 922 kb region encompassing the nitrate assimilation gene cluster.  Fungal Genetics and Biology.  41(4).
  • 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, Adams MD, White O, Hall N, Stuart K, Fraser CM, El-Sayed NMA (2004).  Gene synteny and evolution of genome architecture in trypanosomatids.  Molecular and Biochemical Parasitology.  134(2).
  • Gajer P, Schatz M, Salzberg SL (2004).  Automated correction of genome sequence errors.  Nucleic Acids Research.  32(2).
  • Allen JE, Pertea M, Salzberg SL (2004).  Computational gene prediction using multiple sources of evidence.  Genome Research.  14(1).
  • Pop M, Kosack DS, Salzberg SL (2004).  Hierarchical scaffolding with Bambus.  Genome Research.  14(1).
  • Pop M, Phillippy A, Delcher AL, Salzberg SL (2004).  Comparative genome assembly..  Briefings in bioinformatics.  5(3).
  • Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD, Salzberg SL, White O (2003).  Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.  Nucleic Acids Research.  31(19).
  • El-Sayed NMA, 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, Hannick L, Caler E, Blandin G, Bartholomeu D, Simpson AJ, Kaul S, Zhao H, Pai G, Van Aken S, Utterback T, Haas B, Koo HL, Umayam L, Suh B, Gerrard C, Leech V, Qi R, Zhou S, Schwartz D, Feldblyum T, Salzberg S, Tait A, Turner CMR, Ullu E, White O, Melville S, Adams MD, Fraser CM, Donelson JE (2003).  The sequence and analysis of Trypanosoma brucei chromosome II.  Nucleic Acids Research.  31(16).
  • Majoros WH, Pertea M, Antonescu C, Salzberg SL (2003).  GlimmerM, Exonomy and Unveil: Three ab initio eukaryotic genefinders.  Nucleic Acids Research.  31(13).
  • Yu Y, Rambo T, Currie J, Saski C, Kim HR, Collura K, Thompson S, Simmons J, Yang T-J, Nah G, Patel AJ, Thurmond S, Henry D, Oates R, Palmer M, Pries G, Gibson J, Anderson H, Paradkar M, Crane L, Dale J, Carver MB, Wood T, Frisch D, Engler F, Soderlund C, Palmer LE, Tetylman L, Nascimento L, de la Bastide M, Spiegel L, Ware D, O'Shaughnessy A, Dike S, Dedhia N, Preston R, Huang E, Ferraro K, Kuit K, Miller B, Zutavern T, Katzenberger F, Muller S, Balija V, Martienssen RA, Stein L, Minx P, Johnson D, Cordum H, Mardis E, Cheng Z, Jiang J, Wilson R, McCombie WR, Wing RA, Yuan Q, Ouyang S, Liu J, Jones KM, Gansberger K, Moffat K, Hill J, Tsitrin T, Overton L, Bera J, Kim M, Jin S, Tallon L, Ciecko A, Pai G, van Aken S, Utterback T, Reidmuller S, Bormann J, Feldblyum T, Hsiao J, Zismann V, Blunt S, de Vazeilles A, Shaffer T, Koo H, Suh B, Yang Q, Haas B, Peterson J, Pertea M, Volfovsky N, Wortman J, White O, Salzberg SL, Fraser CM, Robin Buell C, Messing J, Song R, Fuks G, Llaca V,...Dean RA (2003).  In-depth view of structure, activity, and evolution of rice chromosome 10.  Science.  300(5625).
  • Volfovsky N, Haas BJ, Salzberg SL (2003).  Computational discovery of internal micro-exons.  Genome Research.  13(6 A).
  • Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, Holtzapple EK, Økstad OA, Helgason E, Rilstone J, Wu M, Kolonay JF, Beanan MJ, Dodson RJ, Brinkac LM, Gwinn M, DeBoy RT, Madpu R, Daugherty SC, Durkin AS, Haft DH, Nelson WC, Peterson JD, Pop M, Khouri HM, Radune D, Benton JL, Mahamoud Y, Jiang L, Hance IR, Weidman JF, Berry KJ, Plaut RD, Wolf AM, Watkins KL, Nierman WC, Hazen A, Cline R, Redmond C, Thwaite JE, White O, Salzberg SL, Thomason B, Friedlander AM, Koehler TM, Hanna PC, Kolstø AB, Fraser CM (2003).  The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria.  Nature.  423(6935).
  • Read TD, Myers GSA, Brunham RC, Nelson WC, Paulsen IT, Heidelberg J, Holtzapple E, Khouri H, Federova NB, Carty HA, Umayam LA, Haft DH, Peterson J, Beanan MJ, White O, Salzberg SL, Hsia RC, McClarty G, Rank RG, Bavoil PM, Fraser CM (2003).  Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): Examining the role of niche-specific genes in the evolution of the Chlamydiaceae.  Nucleic Acids Research.  31(8).
  • Ermolaeva MD, Wu M, Eisen JA, Salzberg SL (2003).  The age of the Arabidopsis thaliana genome duplication.  Plant Molecular Biology.  51(6).
  • Delcher AL, Salzberg SL, Phillippy AM (2003).  Using MUMmer to identify similar regions in large sequence sets..  Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.].  Chapter 10.
  • Mural RJ, Myers EW, Smith H, Gabor Miklos GL, Wides R, Halpern A, Li PW, Sutton G, Nadeau JH, Salzberg SL, Holt R, Evans CA, Lu F, Biddick K, Bonazzi V, Delcher A, Zheng XH, Yandell M, Rusch D, Majoros W, Hoover J, Wang J, Venter JC, Adams MD (2002).  A preliminary comparison of the mouse and human genomes.  International Congress Series.  1246(C).
  • Pertea M, Salzberg SL (2002).  Using GlimmerM to find genes in eukaryotic genomes..  Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.].  Chapter 4.
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  • Holt RA, Mani Subramanian G, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JMC, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, Lai Z, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, Cai S, Center A, Chatuverdi K, Christophides GK, Chrystal MA, Clamp M, Cravchik A, Curwen V, Dana A, Delcher A, Dew I, Evans CA, Flanigan M, Grundschober-Freimoser A, Friedli L, Gu Z, Guan P, Guigo R, Hillenmeyer ME, Hladun SL, Hogan JR, Hong YS, Hoover J, Jaillon O, Ke Z, Kodira C, Kokoza E, Koutsos A, Letunic I, Levitsky A, Liang Y, Lin J-J, Lobo NF, Lopez JR, Malek JA, McIntosh TC, Meister S, Miller J, Mobarry C, Mongin E, Murphy SD, O'Brochta DA, Pfannkoch C, Qi R, Regier MA, Remington K, Shao H, Sharakhova MV, Sitter CD, Shetty J, Smith TJ, Strong R, Sun J, Thomasova D, Ton LQ, Topalis P, Tu Z, Unger MF, Walenz B, Wang A, Wang J, Wa...Hoffman SL (2002).  The genome sequence of the malaria mosquito Anopheles gambiae.  Science.  298(5591).
  • 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, Shallom SJ, Van Aken SE, Riedmuller SB, Feldblyum TV, Cho JK, Quackenbush J, Sedegah M, Shoaibi A, Cummings LM, Florens L, Yates JR, Raine JD, Sinden RE, Harris MA, Cunningham DA, Preiser PR, Bergman LW, Vaidya AB, Van Lin LH, Janse CJ, Waters AP, Smith HO, White OR, Salzberg SL, Venter JC, Fraser CM, Hoffman SL, Gardner MJ, Carucci DJ (2002).  Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii.  Nature.  419(6906).
  • 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, Granger D, Fujii C, Hansen C, Pederson J, Feldblyum T, Peterson J, Suh B, Angiuoli S, Pertea M, Allen J, Selengut J, White O, Cummings LM, Smith HO, Adams MD, Venter JC, Carucci DJ, Hoffman SL, Fraser CM (2002).  Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14.  Nature.  419(6906).
  • Fleischmann RD, Alland D, Eisen JA, Carpenter L, White O, Peterson J, DeBoy R, Dodson R, Gwinn M, Haft D, Hickey E, Kolonay JF, Nelson WC, Umayam LA, Ermolaeva M, Salzberg SL, Delcher A, Utterback T, Weidman J, Khouri H, Gill J, Mikula A, Bishai W, Jacobs WR, Venter JC, Fraser CM (2002).  Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains.  Journal of Bacteriology.  184(19).
  • 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, Nelson WC, Ayodeji B, Kraul M, Shetty J, Malek J, Van Aken SE, Riedmuller S, Tettelin H, Gill SR, White O, Salzberg SL, Hoover DL, Lindler LE, Halling SM, Boyle SM, Fraser CM (2002).  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(20).
  • Haas BJ, Volfovsky N, Town CD, Troukhan M, Alexandrov N, Feldmann KA, Flavell RB, White O, Salzberg SL (2002).  Full-length messenger RNA sequences greatly improve genome annotation..  Genome biology.  3(6).
  • 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 (2002).  Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis.  Science.  296(5575).
  • Delcher AL, Phillippy A, Carlton J, Salzberg SL (2002).  Fast algorithms for large-scale genome alignment and comparison.  Nucleic Acids Research.  30(11).
  • Mural RJ, Adams MD, Myers EW, Smith HO, Gabor Miklos GL, Wides R, Halpern A, Li PW, Sutton GG, Nadeau J, Salzberg SL, Holt RA, Kodira CD, Lu F, Chen L, Deng Z, Evangelista CC, Gan W, Heiman TJ, Li J, Li Z, Merkulov GV, Milshina NV, Naik AK, Qi R, Chris Shue B, Wang A, Wang J, Wang X, Yan X, Ye J, Yooseph S, Zhao Q, Zheng L, Zhu SC, Biddick K, Bolanos R, Delcher AL, Dew IM, Fasulo D, Flanigan MJ, Huson DH, Kravitz SA, Miller JR, Mobarry CM, Reinert K, Remington KA, Zhang Q, Zheng XH, Nusskern DR, Lai Z, Lei Y, Zhong W, Yao A, Guan P, Ji RR, Gu Z, Wang ZY, Zhong F, Xiao C, Chiang CC, Yandell M, Wortman JR, Amanatides PG, Hladun SL, Pratts EC, Johnson JE, Dodson KL, Woodford KJ, Evans CA, Gropman B, Rusch DB, Venter E, Wang M, Smith TJ, Houck JT, Tompkins DE, Haynes C, Jacob D, Chin SH, Allen DR, Dahlke CE, Sanders R, Li K, Liu X, Levitsky AA, Majoros WH, Chen Q, Xia AC, Lopez JR, Donnelly MT, Newman MH, Glodek A, Kraft CL, Nodell M, Ali F, An HJ, Baldwin-Pitts D, Beeson KY, Cai S (2002).  A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome.  Science.  296(5573).
  • Pertea M, Salzberg SL (2002).  Computational gene finding in plants.  Plant Molecular Biology.  48(1-2).
  • Suzek BE, Ermolaeva MD, Schreiber M, Salzberg SL (2002).  A probabilistic method for identifying start codons in bacterial genomes.  Bioinformatics.  17(12).
  • Pertea M, Salzberg SL (2002).  A method to improve the performance of translation start site detection and its application for gene finding.  Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).  2452.
  • Pop M, Salzberg SL, Shumway M (2002).  Genome sequence assembly: Algorithms and issues.  Computer.  35(7).
  • 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, Craig A, Kyes S, Chan MS, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DMA, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, McFadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Davis RW, Fraser CM, Barrell B (2002).  Genome sequence of the human malaria parasite Plasmodium falciparum.  Nature.  419(6906).
  • Salzberg SL (2001).  Algorithms for whole genome analysis.  Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems and Technolgoy, CBGIST 2001.
  • Kennedy SP, Ng WV, Salzberg SL, Hood L, DasSarma S (2001).  Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence.  Genome Research.  11(10).
  • Volfovsky N, Haas BJ, Salzberg SL (2001).  A clustering method for repeat analysis in DNA sequences..  Genome biology.  2(8).
  • Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, Peterson S, Heidelberg J, DeBoy RT, Haft DH, Dodson RJ, Durkin AS, Gwinn M, Kolonay JF, Nelson WC, Peterson JD, Umayam LA, White O, Salzberg SL, Lewis MR, Radune D, Holtzapple E, Khouri H, Wolf AM, Utterback TR, Hansen CL, McDonald LA, Feldblyum TV, Angiuoli S, Dickinson T, Hickey EK, Holt IE, Loftus BJ, Yang F, Smith HO, Venter JC, Dougherty BA, Morrison DA, Hollingshead SK, Fraser CM (2001).  Complete genome sequence of a virulent isolate of Streptococcus pneumoniae.  Science.  293(5529).
  • Salzberg SL, White O, Peterson J, Eisen JA (2001).  Microbial genes in the human genome: Lateral transfer or gene loss?.  Science.  292(5523).
  • Yuan Q, Quackenbush J, Sultana R, Pertea M, Salzberg SL, Buell CR (2001).  Rice bioinformatics. Analysis of rice sequence data and leveraging the data to other plant species.  Plant Physiology.  125(3).
  • Nierman WC, Feldblyum TV, Laub MT, Paulsen IT, Nelson KE, Eisen J, Heidelberg JF, Alley MRK, Ohta N, Maddock JR, Potocka I, Nelson WC, Newton A, Stephens C, Phadke ND, Ely B, DeBoy RT, Dodson RJ, Durkin AS, Gwinn ML, Haft DH, Kolonay JF, Smit J, Craven MB, Khouri H, Shetty J, Berry K, Utterback T, Tran K, Wolf A, Vamathevan J, Ermolaeva M, White O, Salzberg SL, Venter JC, Shapiro L, Fraser CM (2001).  Complete genome sequence of Caulobacter crescentus.  Proceedings of the National Academy of Sciences of the United States of America.  98(7).
  • Ermolaeva MD, White O, Salzberg SL (2001).  Prediction of operons in microbial genomes.  Nucleic Acids Research.  29(5).
  • Pertea M, Lin X, Salzberg SL (2001).  GeneSplicer: A new computational method for splice site prediction.  Nucleic Acids Research.  29(5).
  • Craig Venter J, 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, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Yuan Wang Z, Wang A, ...Yan C (2001).  The sequence of the human genome.  Science.  291(5507).
  • Bevan M, Mayer K, White O, Eisen JA, Preuss D, Bureau T, Salzberg SL, Mewes HW (2001).  Sequence and analysis of the Arabidopsis genome.  Current Opinion in Plant Biology.  4(2).
  • Theologis A, Ecker JR, Palm CJ, Federspiel NA, Kaul S, White O, Alonso J, Altafi H, Araujo R, Bowman CL, Brooks SY, Buehler E, Chan A, Chao Q, Chen H, Cheuk RF, Chin CW, Chung MK, Conn L, Conway AB, Conway AR, Creasy TH, Dewar K, Dunn P, Etgu P, Feldblyum TV, Feng JD, Fong B, Fujii CY, Gill JE, Goldsmith AD, Haas B, Hansen NF, Hughes B, Huizar L, Hunter JL, Jenkins J, Johnson-Hopson C, Khan S, Khaykin E, Kim CJ, Koo HL, Kremenetskaia I, Kurtz DB, Kwan A, Lam B, Langin-Hooper S, Lee A, Lee JM, Lenz CA, Li JH, Li YP, Lin X, Liu SX, Liu ZA, Luros JS, Maiti R, Marziali A, Militscher J, Miranda M, Nguyen M, Nierman WC, Osborne BI, Pai G, Peterson J, Pham PK, Rizzo M, Rooney T, Rowley D, Sakano H, Salzberg SL, Schwartz JR, Shinn P, Southwick AM, Sun H, Tallon LJ, Tambunga G, Toriumi MJ, Town CD, Utterback T, Van Aken S, Vaysberg M, Vysotskaia VS, Walker M, Wu D, Yu G, Fraser CM, Venter JC, Davis RW (2000).  Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.  Nature.  408(6814).
  • Salanoubat M, Lemcke K, Rieger M, Ansorge W, Unseld M, Fartmann B, Valle G, Blöcker H, Perez-Alonso M, Obermaier B, Delseny M, Boutry M, Grivell LA, Mache R, Puigdomènech P, De Simone V, Choisne N, Artiguenave F, Robert C, Brottier P, Wincker P, Cattolico L, Weissenbach J, Saurin W, Quétier F, Schäfer M, Müller-Auer S, Gabel C, Fuchs M, Benes V, Wurmbach E, Drzonek H, Erfle H, Jordan N, Bangert S, Wiedelmann R, Kranz H, Voss H, Holland R, Brandt P, Nyakatura G, Vezzi A, D'Angelo M, Pallavicini A, Toppo S, Simionati B, Conrad A, Hornischer K, Kauer G, Löhnert T-H, Nordsiek G, Reichelt J, Scharfe M, Schön O, Bargues M, Terol J, Climent J, Navarro P, Collado C, Perez-Perez A, Ottenwälder B, Duchemin D, Cooke R, Laudie M, Berger-Llauro C, Purnelle B, Masuy D, de Haan M, Maarse AC, Alcaraz J-P, Cottet A, Casacuberta E, Monfort A, Argiriou A, Flores M, Liguori R, Vitale D, Mannhaupt G, Haase D, Schoof H, Rudd S, Zaccaria P, Mewes HW, Mayer KFX, Kaul S, Town CD, Koo HL, Tallon LJ, ...Tabata S (2000).  Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.  Nature.  408(6814).
  • Kaul S, Koo HL, Jenkins J, Rizzo M, Rooney T, Tallon LJ, Feldblyum T, Nierman W, Benito M-I, Lin X, Town CD, Venter JC, Fraser CM, Tabata S, Nakamura Y, Kaneko T, Sato S, Asamizu E, Kato T, Kotani H, Sasamoto S, Ecker JR, Theologis A, Federspiel NA, Palm CJ, Osborne BI, Shinn P, Dewar K, Kim CJ, Buehler E, Dunn P, Chao Q, Chen H, Theologis A, Osborne BI, Vysotskaia VS, Lenz CA, Kim CJ, Hansen NF, Liu SX, Buehler E, Alta H, Sakano H, Dunn P, Lam B, Pham PK, Chao Q, Nguyen M, Yu G, Chen H, Southwick A, Lee JM, Miranda M, Toriumi MJ, Davis RW, Federspiel NA, Palm CJ, Conway AB, Conn L, Hansen NF, Hootan A, Lam B, Wambutt R, Murphy G, Düsterhöft A, Stiekema W, Pohl T, Entian K-D, Terryn N, Volckaert G, Salanoubat M, Choisne N, Artiguenave F, Weissenbach J, Quetier F, Rieger M, Ansorge W, Unseld M, Fartmann B, Valle G, Wilson RK, Sekhon M, Pepin K, Murray J, Johnson D, Hillier L, de la Bastide M, Huang E, Spiegel L, Gnoj L, Habermann K, Dedhia N, Parnell L, Preston R, Marra M...Somerville C (2000).  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.  Nature.  408(6814).
  • Eisen JA, Heidelberg JF, White O, Salzberg SL (2000).  Evidence for symmetric chromosomal inversions around the replication origin in bacteria..  Genome biology.  1(6).
  • Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, Quackenbush J (2000).  An optimized protocol for analysis of EST sequences.  Nucleic Acids Research.  28(18).
  • Fraser CM, Eisen JA, Salzberg SL (2000).  Microbial genome sequencing.  Nature.  406(6797).
  • Ermolaeva MD, Khalak HG, White O, Smith HO, Salzberg SL (2000).  Prediction of transcription terminators in bacterial genomes.  Journal of Molecular Biology.  301(1).
  • Read TD, Brunham RC, Shen C, Gill SR, Heidelberg JF, White O, Hickey EK, Peterson J, Utterback T, Berry K, Bass S, Linher K, Weidman J, Khouri H, Craven B, Bowman C, Dodson R, Gwinn M, Nelson W, DeBoy R, Kolonay J, McClarty G, Salzberg SL, Eisen J, Fraser CM (2000).  Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39.  Nucleic Acids Research.  28(6).
  • Tettelin H, Saunders NJ, Heidelberg J, Jeffries AC, Nelson KE, Eisen JA, Ketchum KA, Hood DW, Peden JF, Dodson RJ, Nelson WC, Gwinn ML, DeBoy R, Peterson JD, Hickey EK, Haft DH, Salzberg SL, White O, Fleischmann RD, Dougherty BA, Mason T, Ciecko A, Parksey DS, Blair E, Cittone H, Clark EB, Cotton MD, Utterback TR, Khouri H, Qin H, Vamathevan J, Gill J, Scarlato V, Masignani V, Pizza M, Grandi G, Sun L, Smith HO, Fraser CM, Moxon ER, Rappuoli R, Craig Venter J (2000).  Complete genome sequence of Neisseria meningitidis serogroup B strain MC58.  Science.  287(5459).
  • Pertea M, Salzberg SL, Gardner MJ, Lawson D, Bowman S, Barren B (2000).  Finding genes in Plasmodium falciparum.  Nature.  404(6773).
  • Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, Quackenbush J (2000).  Gene index analysis of the human genome estimates approximately 120,000 genes.  Nature Genetics.  25(2).
  • Lin X, Kaul S, Rounsley S, Shea TP, Benito MI, Town CD, Fujii CY, Mason T, Bowman CL, Barnstead M, Feldblyum TV, Buell CR, Ketchum KA, Lee J, Ronning CM, Koo HL, Moffat KS, Cronin LA, Shen M, Pal G, Van Aken S, Umayam L, Tallon LJ, Gill JE, Adams MD, Carrera AJ, Creasy TH, Goodman HM, Somerville CR, Copenhaver GP, Preuss D, Nierman WC, White O, Elsen JA, Salzberg SL, Fraser CM, Venter JC (1999).  Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.  Nature.  402(6763).
  • Tettelin H, Radune D, Kasif S, Khouri H, Salzberg SL (1999).  Optimized multiplex PCR: Efficiently closing a whole-genome shotgun sequencing project.  Genomics.  62(3).
  • Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999).  Improved microbial gene identification with GLIMMER.  Nucleic Acids Research.  27(23).
  • 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, Shen M, Vamathevan JJ, Lam P, McDonald L, Utterback T, Zalewski C, Makarova KS, Aravind L, Daly MJ, Minton KW, Fleischmann RD, Ketchum KA, Nelson KE, Salzberg S, Smith HO, Venter JC, Fraser CM (1999).  Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1.  Science.  286(5444).
  • Salzberg SL, Pertea M, Delcher AL, Gardner MJ, Tettelin H (1999).  Interpolated Markov models for eukaryotic gene finding.  Genomics.  59(1).
  • Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, Salzberg SL (1999).  Alignment of whole genomes.  Nucleic Acids Research.  27(11).
  • Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, Malek JA, Linher KD, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA, Richardson D, Heidelberg J, Sutton GG, Fleischmann RD, Eisen JA, White O, Salzberg SL, Smith HO, Venter JC, Fraser CM (1999).  Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima.  Nature.  399(6734).
  • Smith HO, Gwinn ML, Salzberg SL (1999).  DNA uptake signal sequences in naturally transformable bacteria.  Research in Microbiology.  150(9-10).
  • Salzberg SL (1999).  Gene Discovery in DNA Sequences.  IEEE Intelligent Systems and Their Applications.  14(6).
  • Fasman KH, Salzberg SL (1998).  Chapter 3 An introduction to biological sequence analysis.  New Comprehensive Biochemistry.  32(C).
  • Salzberg SL (1998).  Chapter 10 Decision trees and Markov chains for gene finding.  New Comprehensive Biochemistry.  32(C).
  • Salzberg S, Searls D, Kasif S (1998).  Preface.  New Comprehensive Biochemistry.  32(C).
  • Salzberg S (1998).  Chapter 2 A tutorial introduction to computation for biologists.  New Comprehensive Biochemistry.  32(C).
  • 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, Schwartz DC, Pertea M, Salzberg S, Zhou L, Sutton GG, Clayton R, White O, Smith HO, Fraser CM, Adams MD, Venter JC, Hoffman SL (1998).  Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum.  Science.  282(5391).
  • Salzberg SL, Salzberg AJ, Kerlavage AR, Tomb JF (1998).  Skewed oligomers and origins of replication.  Gene.  217(1-2).
  • Kasif S, Salzberg S, Waltz D, Rachlin J, Aha DW (1998).  A probabilistic framework for memory-based reasoning.  Artificial Intelligence.  104(1-2).
  • 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, Khalak H, Richardson D, Howell JK, Chidambaram M, Utterback T, McDonald L, Artiach P, Bowman C, Cotton MD, Fujii C, Garland S, Hatch B, Horst K, Roberts K, Sandusky M, Weidman J, Smith HO, Venter JC (1998).  Complete genome sequence of Treponema pallidum, the syphilis spirochete.  Science.  281(5375).
  • Salzberg SL, Deicher AL, Kasif S, White O (1998).  Microbial gene identification using interpolated Markov models.  Nucleic Acids Research.  26(2).
  • Salzberg S, Delcher AL, Fasman KH, Henderson J (1998).  A decision tree system for finding genes in DNA.  Journal of Computational Biology.  5(4).
  • 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, Peterson J, Kerlavage AR, Quackenbush J, Salzberg S, Hanson M, Van Vugt R, Palmer N, Adams MD, Gocayne J, Weidman J, Utterback T, Watthey L, McDonald L, Artiach P, Bowman C, Garland S, Fujii C, Cotton MD, Horst K, Roberts K, Hatch B, Smith HO, Venter JC (1997).  Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi.  Nature.  390(6660).
  • Sheppard JW, Salzberg SL (1997).  A Teaching Strategy for Memory-Based Control.  Artificial Intelligence Review.  11(1-5).
  • Arkin EM, Belleville P, Mitchell JSB, Mount D, Romanik K, Salzberg S, Souvaine D (1997).  Testing simple polygons.  Computational Geometry: Theory and Applications.  8(2).
  • Salzberg SL (1997).  On comparing classifiers: Pitfalls to avoid and a recommended approach.  Data Mining and Knowledge Discovery.  1(3).
  • Salzberg S, Chen X, Henderson J, Fasman K (1996).  Finding genes in DNA using decision trees and dynamic programming..  Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology.  4.
  • Heath D, Kasif S, Salzberg S (1996).  Chapter 18 Committees of decision trees.  Advances in Psychology.  113(C).
  • Heath D, Kasif S, Kosaraju R, Salzberg S, Sullivan G (1996).  Learning nested concept classes with limited storage.  Journal of Experimental and Theoretical Artificial Intelligence.  8(2).
  • Salzberg S, Heath D, Kasif S, Delcher AL (1995).  Best-Case Results for Nearest-Neighbor Learning.  IEEE Transactions on Pattern Analysis and Machine Intelligence.  17(6).
  • Salzberg S (1995).  Locating Protein Coding Regions in Human DNA Using a Decision Tree Algorithm.  Journal of Computational Biology.  2(3).
  • Romanik K, Salzberg S (1995).  Testing orthogonal shapes.  Computational Geometry: Theory and Applications.  5(1).
  • Murthy S, Kasif S, Salzberg S, Beigel R (1993).  OC1: randomized induction of oblique decision trees.  Proceedings of the National Conference on Artificial Intelligence.
  • Cost S, Salzberg S (1993).  A Weighted Nearest Neighbor Algorithm for Learning with Symbolic Features.  Machine Learning.  10(1).
  • Salzberg S, Cost S (1992).  Predicting protein secondary structure with a nearest-neighbor algorithm.  Journal of Molecular Biology.  227(2).
  • Salzberg S (1991).  Distance metrics for instance-based learning.  Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).  542 LNAI Part F2.
  • Salzberg S (1991).  A Nearest Hyperrectangle Learning Method.  Machine Learning.  6(3).
  • Salzberg S, Watkins M (1990).  Managing information for concurrent engineering: Challenges and barriers.  Research in Engineering Design.  2(1).
  • Salzberg S (1989).  Nested hyper-rectangles for exemplar-based learning.  Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).  397 LNAI.
  • Salzberg S, Atkinson DJ (1984).  LEARNING BY BUILDING CAUSAL EXPLANATIONS..
  • Salzberg S (1983).  GENERATING HYPOTHESES TO EXPLAIN PREDICTION FAILURES..
Book Chapters
  • Haas BJ, Salzberg SL (2008).  Finding Repeats in Genome Sequences.  Bioinformatics-From Genomes to Therapies.  1.
  • Slezak TR, Salzberg SL (2005).  Bioinformatics Methods for Microbial Detection and Forensic Diagnostic Design.  Microbial Forensics.
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