Salzberg, Steven L.

DAGchainer: a tool for mining segmental genome duplications and synteny

Haas, B. J., Delcher, A. L., Wortman, J. R., & Salzberg, S. L. (2004) · Bioinformatics

Genome Rearrangement AlgorithmsGenomics and Phylogenetic Studies

Cited by 381

CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise

Pertea, M., Shumate, A., Pertea, G., Varabyou, A., Breitwieser, F. P., Chang, Y.-C., Madugundu, A. K., Pandey, A., & Salzberg, S. L. (2018) · Genome Biology

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 335

Microbial Genes in the Human Genome: Lateral Transfer or Gene Loss?

Salzberg, S. L., White, O., Peterson, J., & Eisen, J. A. (2001) · Science

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 326

Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank

Steinegger, M., & Salzberg, S. L. (2020) · Genome Biology

Genomics and Phylogenetic StudiesFractal and DNA sequence analysis

Cited by 246

Semi-automated assembly of high-quality diploid human reference genomes

Jarvis, E. D., Formenti, G., Rhie, A., Guarracino, A., Yang, C., Wood, J., Tracey, A., Thibaud-Nissen, F., Vollger, M. R., Porubsky, D., et al. (2022) · Nature

Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalities

Cited by 209

Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms

Chang, T.-C., Pertea, M., Lee, S., Salzberg, S. L., & Mendell, J. T. (2015) · Genome Research

MicroRNA in disease regulationRNA Research and Splicing

Cited by 103

Whole Genome Sequence Analysis of the Plasma Proteome in Black Adults Provides Novel Insights Into Cardiovascular Disease

Katz, D. H., Tahir, U. A., Bick, A. G., Pampana, A., Ngo, D., Benson, M. D., Yu, Z., Robbins, J. M., Chen, Z.-Z., Cruz, D. E., et al. (2022) · Circulation

Genetic Associations and EpidemiologyGenetic Mapping and Diversity in Plants and Animals

Cited by 92

Computational discovery of internal micro-exons

Volfovsky, N., Haas, B. J., & Salzberg, S. L. (2003) · Genome Research

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 87

Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities

Saitta, E. T., Liang, R., Lau, M. C., Brown, C. M., Longrich, N. R., Kaye, T. G., Novak, B. J., Salzberg, S. L., Norell, M. A., Abbott, G. D., et al. (2019) · eLife

Paleontology and Evolutionary BiologyPaleontology and Stratigraphy of Fossils

Cited by 67

CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure

Varabyou, A., Sommer, M. J., Erdogdu, B., Shinder, I., Minkin, I., Chao, K.-H., Park, S., Heinz, J., Pockrandt, C., Shumate, A., et al. (2023) · Genome Biology

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 54

CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure

Varabyou, A., Sommer, M. J., Erdogdu, B., Shinder, I., Minkin, I., Chao, K.-H., Park, S., Heinz, J., Pockrandt, C., Shumate, A., et al. (2022) · Genome biology

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 54

Structure-guided isoform identification for the human transcriptome

Sommer, M. J., Cha, S., Varabyou, A., Rincon, N., Park, S., Minkin, I., Pertea, M., Steinegger, M., & Salzberg, S. L. (2022) · eLife

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 40

Highly accurate isoform identification for the human transcriptome

Sommer, M. J., Cha, S., Varabyou, A., Rincon, N., Park, S., Minkin, I., Pertea, M., Steinegger, M., & Salzberg, S. L. (2022) · eLife

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 40

Whole-genome association analyses of sleep-disordered breathing phenotypes in the NHLBI TOPMed program

Cade, B. E., Lee, J., Sofer, T., Wang, H., Zhang, M., Chen, H., Gharib, S. A., Gottlieb, D. J., Guo, X., Lane, J. M., et al. (2021) · Genome Medicine

Obstructive Sleep Apnea ResearchGenetic Associations and Epidemiology

Cited by 33

3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

Varadi, M., Nair, S., Sillitoe, I., Tauriello, G., Anyango, S., Bienert, S., Borges, C., Deshpande, M., Green, T., Hassabis, D., et al. (2022) · GigaScience

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 32

PSAURON: a tool for assessing protein annotation across a broad range of species

Sommer, M. J., Zimin, A. V., & Salzberg, S. L. (2025) · NAR Genomics and Bioinformatics

Genomics and Phylogenetic StudiesFractal and DNA sequence analysis

Cited by 29

PSAURON: a tool for assessing protein annotation across a broad range of species

Sommer, M. J., Zimin, A. V., & Salzberg, S. L. (2024) · NAR Genomics and Bioinformatics

Genomics and Phylogenetic StudiesFractal and DNA sequence analysis

Cited by 29

Upstream open reading frames may contain hundreds of novel human exons

Ji, H. J., & Salzberg, S. L. (2024) · PLoS Computational Biology

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 6

Upstream open reading frames may contain hundreds of novel human exons

Ji, H. J., & Salzberg, S. L. (2024) · PLOS Computational Biology

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 6

3D-Beacons: Decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

Varadi, M., Nair, S., Sillitoe, I., Tauriello, G., Anyango, S., Bienert, S., Borges, C., Deshpande, M., Green, T., Hassabis, D., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 2