Salzberg, Steven L.

Fast gapped-read alignment with Bowtie 2

Langmead, B., & Salzberg, S. L. (2012) · Nature Methods

Genomics and Phylogenetic StudiesAlgorithms and Data Compression

Cited by 56,400

HISAT: a fast spliced aligner with low memory requirements

Kim, D., Langmead, B., & Salzberg, S. L. (2015) · Nature Methods

Genomics and Phylogenetic StudiesAlgorithms and Data Compression

Cited by 24,112

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology

Genomics and Phylogenetic StudiesAlgorithms and Data Compression

Cited by 21,849

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 15,556

FLASH: fast length adjustment of short reads to improve genome assemblies

Magoč, T., & Salzberg, S. L. (2011) · Bioinformatics

Genomics and Phylogenetic StudiesAlgorithms and Data Compression

Cited by 15,366

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

Kim, D., Paggi, J. M., Park, C., Bennett, C., & Salzberg, S. L. (2019) · Nature Biotechnology

Genomics and Phylogenetic StudiesAlgorithms and Data Compression

Cited by 15,022

The sequence of the human genome

Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science

Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalities

Cited by 13,909

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.

Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., & Salzberg, S. L. (2013) · Genome Biology

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 12,668

Versatile and open software for comparing large genomes

Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology

Genomics and Phylogenetic StudiesGenome Rearrangement Algorithms

Cited by 5,254

Kraken: ultrafast metagenomic sequence classification using exact alignments

Wood, D. E., & Salzberg, S. L. (2014) · Genome Biology

Genomics and Phylogenetic StudiesEnvironmental DNA in Biodiversity Studies

Cited by 4,521

Genome sequence of the human malaria parasite Plasmodium falciparum

Gardner, M. J., Hall, N., Fung, E., White, O., Berriman, M., Hyman, R. W., Carlton, J. M., Pain, A., Nelson, K. E., Bowman, S., et al. (2002) · Nature

Malaria Research and ControlBird parasitology and diseases

Cited by 4,407

The complete sequence of a human genome

Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L., Gershman, A., et al. (2022) · Science

Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalities

Cited by 3,136

MUMmer4: A fast and versatile genome alignment system

Marçais, G., Delcher, A. L., Phillippy, A. M., Coston, R., Salzberg, S. L., & Zimin, A. (2018) · PLOS Computational Biology

Genomics and Phylogenetic StudiesAlgorithms and Data Compression

Cited by 2,484

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

Taliun, D., Harris, D. N., Kessler, M. D., Carlson, J., Szpiech, Z. A., Torres, R., Taliun, S. A. G., Corvelo, A., Gogarten, S. M., Kang, H. M., et al. (2021) · Nature

Genetic Associations and EpidemiologyGenomics and Rare Diseases

Cited by 2,213

Centrifuge: rapid and sensitive classification of metagenomic sequences

Kim, D., Song, L., Breitwieser, F. P., & Salzberg, S. L. (2016) · Genome Research

Genomics and Phylogenetic StudiesAlgorithms and Data Compression

Cited by 1,438

Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

Nierman, W. C., Pain, A., Anderson, M. J., Wortman, J. R., Kim, H. S., Arroyo, J., Berriman, M., Abe, K., Archer, D. B., Bermejo, C., et al. (2005) · Nature

Fungal and yeast genetics researchAntifungal resistance and susceptibility

Cited by 1,391

Alignment of whole genomes

Delcher, A. L., Kasif, S., Fleischmann, R. D., Peterson, J., White, O., & Salzberg, S. L. (1999) · Nucleic Acids Research

Genomics and Phylogenetic StudiesAlgorithms and Data Compression

Cited by 893

C4.5: Programs for Machine Learning by J. Ross Quinlan. Morgan Kaufmann Publishers, Inc., 1993

Salzberg, S. L. (1994) · Machine Learning

Data Mining Algorithms and ApplicationsData Mining and Machine Learning Applications

Cited by 746

Inherited causes of clonal haematopoiesis in 97,691 whole genomes

Bick, A. G., Weinstock, J. S., Nandakumar, S. K., Fulco, C. P., Bao, E. L., Zekavat, S. M., Szeto, M. D., Liao, X., Leventhal, M. J., Nasser, J., et al. (2020) · Nature

Acute Myeloid Leukemia ResearchGenetic Associations and Epidemiology

Cited by 733

Comparative Genome and Proteome Analysis of Anopheles gambiae and Drosophila melanogaster

Zdobnov, E. M., von Mering, C., Letunic, I., Torrents, D., Suyama, M., Copley, R. R., Christophides, G. K., Thomasova, D., Holt, R. A., Subramanian, G. M., et al. (2002) · Science

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 553

The complete sequence of a human Y chromosome

Rhie, A., Nurk, S., Cechova, M., Hoyt, S. J., Taylor, D. J., Altemose, N., Hook, P. W., Koren, S., Rautiainen, M., Alexandrov, I. A., et al. (2023) · Nature

Genetic and Clinical Aspects of Sex Determination and Chromosomal AbnormalitiesGenomics and Phylogenetic Studies

Cited by 471

Mugsy: Fast multiple alignment of closely related whole genomes

Angiuoli, S. V., & Salzberg, S. L. (2011) · Bioinformatics

Genomics and Phylogenetic StudiesGenome Rearrangement Algorithms

Cited by 444

Next-generation sequencing: insights to advance clinical investigations of the microbiome

Wensel, C. R., Pluznick, J. L., Salzberg, S. L., & Sears, C. L. (2022) · Journal of Clinical Investigation

Gut microbiota and healthGenomics and Phylogenetic Studies

Cited by 437

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis

Dalloul, R. A., Long, J. A., Zimin, A. V., Aslam, L., Beal, K., Ann Blomberg, L., Bouffard, P., Burt, D. W., Crasta, O., Crooijmans, R. P. M. A., et al. (2010) · PLoS Biology

Genomics and Phylogenetic StudiesGenetic and phenotypic traits in livestock

Cited by 416