Steven Salzberg

Research output

Research output per year 1983 2000 2001 2002 2003 2004 2005 2007 2008 2009 2010 2011 2012 2013 2017 2018 2019 2020 2021 2022 2023 2024

• 282 Article
• 24 Comment/debate
• 16 Review article
• 15 Letter
• 30 More
  • 13 Conference contribution
  • 6 Chapter
  • 4 Editorial
  • 3 Paper
  • 3 Short survey
  • 1 Conference article

Research output per year

Research output per year

Search results

• 2024

  Detecting differential transcript usage in complex diseases with SPIT

  Erdogdu, B., Varabyou, A., Hicks, S., Salzberg, S. L. & Pertea, M., Mar 25 2024, In: Cell Reports Methods. 4, 3, 100736.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Heterogeneity 100%
  • RNA Sequencing 89%
  • Developmental 65%
  • Biodiversity 49%
  • Protein Deficiency 47%
• 2023

  Aberrant activation of TCL1A promotes stem cell expansion in clonal haematopoiesis

  NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Apr 27 2023, In: Nature. 616, 7958, p. 755-763 9 p.

  Research output: Contribution to journal › Article › peer-review

  • Hematopoiesis 100%
  • Hematopoietic Stem Cells 90%
  • Stem Cells 67%
  • Mutation 34%
  • Alleles 22%

• Author Correction: Clonal haematopoiesis and risk of chronic liver disease (Nature, (2023), 616, 7958, (747-754), 10.1038/s41586-023-05857-4)

  NHLBI TOPMed Hematology Working Group, Jul 20 2023, In: Nature. 619, 7970, p. E47

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • Hematopoiesis 100%
  • Liver Diseases 77%
  • Chronic Disease 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., Rincon, N., Puiu, D., Steinegger, M., Salzberg, S. L. & Pertea, M., Dec 2023, In: Genome biology. 24, 1, 249.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Catalogs 100%
  • protein structure 83%
  • phylogenetics 66%
  • gene 61%
  • Data Analysis 60%

• Clonal haematopoiesis and risk of chronic liver disease

  NHLBI TOPMed Hematology Working Group, Apr 27 2023, In: Nature. 616, 7958, p. 747-754 8 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Hematopoiesis 100%
  • Liver Diseases 77%
  • Chronic Disease 67%
  • Inflammation 36%
  • Odds Ratio 29%

• Epigenome-wide DNA methylation association study of circulating IgE levels identifies novel targets for asthma

  NHLBI Trans-Omics in Precision Medicine (TOPMed) Consortium, Sep 2023, In: EBioMedicine. 95, 104758.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Epigenome 100%
  • DNA Methylation 79%
  • Immunoglobulin E 74%
  • Asthma 62%
  • Quantitative Trait Loci 22%

• Investigating open reading frames in known and novel transcripts using ORFanage

  Varabyou, A., Erdogdu, B., Salzberg, S. L. & Pertea, M., Aug 2023, In: Nature Computational Science. 3, 8, p. 700-708 9 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • RNA 100%
  • Proteins 75%
  • Large dataset 44%
  • Medicine 41%
  • Genes 39%

• JASPER: A fast genome polishing tool that improves accuracy of genome assemblies

  Guo, A., Salzberg, S. L. & Zimin, A. V., Mar 2023, In: PLoS computational biology. 19, 3, e1011032.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Polishing 100%
  • Error Reduction 88%
  • jellyfish 82%
  • Scyphozoa 79%
  • genome assembly 76%

• Major data analysis errors invalidate cancer microbiome findings

  Gihawi, A., Ge, Y., Lu, J., Puiu, D., Xu, A., Cooper, C. S., Brewer, D. S., Pertea, M. & Salzberg, S. L., Sep 2023, In: mBio. 14, 5

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Microbiota 100%
  • Data Analysis 75%
  • Machine Learning 57%
  • Neoplasms 32%
  • Genome 17%

• Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies

  Li, X., Quick, C., Zhou, H., Gaynor, S. M., Liu, Y., Chen, H., Selvaraj, M. S., Sun, R., Dey, R., Arnett, D. K., Bielak, L. F., Bis, J. C., Blangero, J., Boerwinkle, E., Bowden, D. W., Brody, J. A., Cade, B. E., Correa, A., Cupples, L. A., Curran, J. E., & 404 othersde Vries, P. S., Duggirala, R., Freedman, B. I., Göring, H. H. H., Guo, X., Haessler, J., Kalyani, R. R., Kooperberg, C., Kral, B. G., Lange, L. A., Manichaikul, A., Martin, L. W., McGarvey, S. T., Mitchell, B. D., Montasser, M. E., Morrison, A. C., Naseri, T., O’Connell, J. R., Palmer, N. D., Peyser, P. A., Psaty, B. M., Raffield, L. M., Redline, S., Reiner, A. P., Reupena, M. S., Rice, K. M., Rich, S. S., Sitlani, C. M., Smith, J. A., Taylor, K. D., Vasan, R. S., Willer, C. J., Wilson, J. G., Yanek, L. R., Zhao, W., Rotter, J. I., Natarajan, P., Peloso, G. M., Li, Z., Lin, X., Abe, N., Abecasis, G., Aguet, F., Albert, C., Almasy, L., Alonso, A., Ament, S., Anderson, P., Anugu, P., Applebaum-Bowden, D., Ardlie, K., Dan Arking, A., Ashley-Koch, A., Aslibekyan, S., Assimes, T., Auer, P., Avramopoulos, D., Ayas, N., Balasubramanian, A., Barnard, J., Barnes, K., Barr, R. G., Barron-Casella, E., Barwick, L., Beaty, T., Beck, G., Becker, D., Becker, L., Beer, R., Beitelshees, A., Benjamin, E., Benos, T., Bezerra, M., Blackwell, T., Blue, N., Bowler, R., Broeckel, U., Broome, J., Brown, D., Bunting, K., Burchard, E., Bustamante, C., Buth, E., Cardwell, J., Carey, V., Carrier, J., Carson, A., Carty, C., Casaburi, R., Casas Romero, J. P., Casella, J., Castaldi, P., Chaffin, M., Chang, C., Chang, Y. C., Chasman, D., Chavan, S., Chen, B. J., Chen, W. M., Chen, Y. D. I., Cho, M., Choi, S. H., Chuang, L. M., Chung, M., Chung, R. H., Clish, C., Comhair, S., Conomos, M., Cornell, E., Crandall, C., Crapo, J., Curtis, J., Custer, B., Damcott, C., Darbar, D., David, S., Davis, C., Daya, M., de Andrade, M., de las Fuentes, L., DeBaun, M., Deka, R., DeMeo, D., Devine, S., Dinh, H., Doddapaneni, H., Duan, Q., Dugan-Perez, S., Durda, J. P., Dutcher, S. K., Eaton, C., Ekunwe, L., El Boueiz, A., Ellinor, P., Emery, L., Erzurum, S., Farber, C., Farek, J., Fingerlin, T., Flickinger, M., Fornage, M., Franceschini, N., Frazar, C., Fu, M., Fullerton, S. M., Fulton, L., Gabriel, S., Gan, W., Gao, S., Gao, Y., Gass, M., Geiger, H., Gelb, B., Geraci, M., Germer, S., Gerszten, R., Ghosh, A., Gibbs, R., Gignoux, C., Gladwin, M., Glahn, D., Gogarten, S., Gong, D. W., Graw, S., Gray, K. J., Grine, D., Gross, C., Gu, C. C., Guan, Y., Gupta, N., Hall, M., Han, Y., Hanly, P., Harris, D., Hawley, N. L., He, J., Ben Heavner, H., Heckbert, S., Hernandez, R., Herrington, D., Hersh, C., Hidalgo, B., Hixson, J., Hobbs, B., Hokanson, J., Hong, E., Hoth, K., Hsiung, C., Hu, J., Hung, Y. J., Huston, H., Hwu, C. M., Irvin, M. R., Jackson, R., Jain, D., Jaquish, C., Johnsen, J., Johnson, A., Johnson, C., Johnston, R., Jones, K., Kang, H. M., Kaplan, R., Kardia, S., Kelly, S., Kenny, E., Kessler, M., Khan, A., Khan, Z., Kim, W., Kimoff, J., Kinney, G., Konkle, B., Kramer, H., Lange, C., Lange, E., Laurie, C., Laurie, C., LeBoff, M., Lee, J., Lee, S., Lee, W. J., LeFaive, J., Levine, D., Levy, D., Lewis, J., Li, X., Li, Y., Lin, H., Lin, H., Liu, S., Liu, Y., Liu, Y., Loos, R. J. F., Lubitz, S., Lunetta, K., Luo, J., Magalang, U., Mahaney, M., Make, B., Manning, A., Manson, J. A., Marton, M., Mathai, S., Mathias, R., May, S., McArdle, P., McDonald, M. L., McFarland, S., McGoldrick, D., McHugh, C., McNeil, B., Mei, H., Meigs, J., Menon, V., Mestroni, L., Metcalf, G., Meyers, D. A., Mignot, E., Mikulla, J., Min, N., Minear, M., Minster, R. L., Moll, M., Momin, Z., Montgomery, C., Muzny, D., Mychaleckyj, J. C., Nadkarni, G., Naik, R., Nekhai, S., Nelson, S. C., Neltner, B., Nessner, C., Nickerson, D., Nkechinyere, O., North, K., O’Connor, T., Ochs-Balcom, H., Okwuonu, G., Pack, A., Paik, D. T., Pankow, J., Papanicolaou, G., Parker, C., Peralta, J. M., Perez, M., Perry, J., Peters, U., Phillips, L. S., Pleiness, J., Pollin, T., Post, W., Becker, J. P., Boorgula, M. P., Preuss, M., Qasba, P., Qiao, D., Qin, Z., Rafaels, N., Rajendran, M., Rao, D. C., Rasmussen-Torvik, L., Ratan, A., Reed, R., Reeves, C., Regan, E., Robillard, R., Robine, N., Dan Roden, R., Roselli, C., Ruczinski, I., Runnels, A., Russell, P., Ruuska, S., Ryan, K., Sabino, E. C., Saleheen, D., Salimi, S., Salvi, S., Salzberg, S., Sandow, K., Sankaran, V. G., Santibanez, J., Schwander, K., Schwartz, D., Sciurba, F., Seidman, C., Seidman, J., Sériès, F., Sheehan, V., Sherman, S. L., Shetty, A., Shetty, A., Sheu, W. H. H., Shoemaker, M. B., Silver, B., Silverman, E., Skomro, R., Smith, A. V., Smith, J., Smith, N., Smith, T., Smoller, S., Snively, B., Snyder, M., Sofer, T., Sotoodehnia, N., Stilp, A. M., Storm, G., Streeten, E., Su, J. L., Sung, Y. J., Sylvia, J., Szpiro, A., Taliun, D., Tang, H., Taub, M., Taylor, M., Taylor, S., Telen, M., Thornton, T. A., Threlkeld, M., Tinker, L., Tirschwell, D., Tishkoff, S., Tiwari, H., Tong, C., Tracy, R., Tsai, M., Vaidya, D., Van Den Berg, D., VandeHaar, P., Vrieze, S., Walker, T., Wallace, R., Walts, A., Wang, F. F., Wang, H., Wang, J., Watson, K., Watt, J., Weeks, D. E., Weinstock, J., Weir, B., Weiss, S. T., Weng, L. C., Wessel, J., Williams, K., Williams, L. K., Wilson, C., Winterkorn, L., Wong, Q., Wu, J., Xu, H., Yang, I., Yu, K., Zekavat, S. M., Zhang, Y., Zhao, S. X., Zhu, X., Ziv, E., Zody, M. & Zoellner, S., Jan 2023, In: Nature genetics. 55, 1, p. 154-164 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Whole Genome Sequencing 100%
  • Meta-Analysis 64%
  • Whole Exome Sequencing 34%
  • Precision Medicine 30%
  • Lipids 18%

• 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., Allen, J., Asri, M., Bzikadze, A. V., Chen, N. C., Chin, C. S., Diekhans, M., Flicek, P., Formenti, G., Fungtammasan, A., Garcia Giron, C., & 67 othersGarrison, E., Gershman, A., Gerton, J. L., Grady, P. G. S., Guarracino, A., Haggerty, L., Halabian, R., Hansen, N. F., Harris, R., Hartley, G. A., Harvey, W. T., Haukness, M., Heinz, J., Hourlier, T., Hubley, R. M., Hunt, S. E., Hwang, S., Jain, M., Kesharwani, R. K., Lewis, A. P., Li, H., Logsdon, G. A., Lucas, J. K., Makalowski, W., Markovic, C., Martin, F. J., Mc Cartney, A. M., McCoy, R. C., McDaniel, J., McNulty, B. M., Medvedev, P., Mikheenko, A., Munson, K. M., Murphy, T. D., Olsen, H. E., Olson, N. D., Paulin, L. F., Porubsky, D., Potapova, T., Ryabov, F., Salzberg, S. L., Sauria, M. E. G., Sedlazeck, F. J., Shafin, K., Shepelev, V. A., Shumate, A., Storer, J. M., Surapaneni, L., Taravella Oill, A. M., Thibaud-Nissen, F., Timp, W., Tomaszkiewicz, M., Vollger, M. R., Walenz, B. P., Watwood, A. C., Weissensteiner, M. H., Wenger, A. M., Wilson, M. A., Zarate, S., Zhu, Y., Zook, J. M., Eichler, E. E., O’Neill, R. J., Schatz, M. C., Miga, K. H., Makova, K. D. & Phillippy, A. M., Sep 14 2023, In: Nature. 621, 7978, p. 344-354 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Chromosomes, Human, Y 100%
  • Human Chromosomes 71%
  • Telomere 69%
  • Base Pairing 64%
  • Tandem Repeat Sequences 40%

• The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual

  Chao, K. H., Zimin, A. V., Pertea, M. & Salzberg, S. L., Mar 2023, In: G3: Genes, Genomes, Genetics. 13, 3, jkac321.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Genome 100%
  • Genes 59%
  • Proteins 27%
  • Human Genome 25%
  • DNA Sequence Analysis 24%

• The status of the human gene catalogue

  Amaral, P., Carbonell-Sala, S., De La Vega, F. M., Faial, T., Frankish, A., Gingeras, T., Guigo, R., Harrow, J. L., Hatzigeorgiou, A. G., Johnson, R., Murphy, T. D., Pertea, M., Pruitt, K. D., Pujar, S., Takahashi, H., Ulitsky, I., Varabyou, A., Wells, C. A., Yandell, M., Carninci, P., & 1 othersSalzberg, S. L., Oct 5 2023, In: Nature. 622, 7981, p. 41-47 7 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Catalogs 100%
  • Genes 32%
  • Untranslated RNA 30%
  • Human Genome 28%
  • Molecular Sequence Annotation 17%
• 2022

  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., Hatos, A., Hegedus, T., Hekkelman, M. L., Joosten, R., Jumper, J., Laydon, A., Molodenskiy, D., Piovesan, D., Salladini, E., Salzberg, S. L., & 12 othersSommer, M. J., Steinegger, M., Suhajda, E., Svergun, D., Tenorio-Ku, L., Tosatto, S., Tunyasuvunakool, K., Waterhouse, A. M., Zídek, A., Schwede, T., Orengo, C. & Velankar, S., 2022, In: GigaScience. 11, giac118.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Proteins 100%
  • Metadata 32%
  • Research Personnel 30%
  • Theoretical Models 17%
  • Databases 13%

• A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies

  NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium & TOPMed Lipids Working Group, Dec 1 2022, In: Nature Methods.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Whole Genome Sequencing 100%
  • Precision Medicine 92%
  • Lipid 59%
  • Genes 34%
  • Genome 19%

• A reference-quality, fully annotated genome from a Puerto Rican individual

  Zimin, A. V., Shumate, A., Shinder, I., Heinz, J., Puiu, D., Pertea, M. & Salzberg, S. L., Feb 2022, In: Genetics. 220, 2, iyab227.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Genome 100%
  • Human Genome 61%
  • Genes 47%
  • Technology 38%
  • DNA 16%

• Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin

  Neale, D. B., Zimin, A. V., Zaman, S., Scott, A. D., Shrestha, B., Workman, R. E., Puiu, D., Allen, B. J., Moore, Z. J., Sekhwal, M. K., de la Torre, A. R., McGuire, P. E., Burns, E., Timp, W., Wegrzyn, J. L. & Salzberg, S. L., Jan 2022, In: G3: Genes, Genomes, Genetics. 12, 1, jkab380.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Sequoia 100%
  • Tracheophyta 54%
  • Genome 40%
  • Sequoiadendron 35%
  • Diploidy 32%

• Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data

  TOPMed Anthropometry Working Group & NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Mar 2022, In: Nature genetics. 54, 3, p. 263-273 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Multifactorial Inheritance 100%
  • Linkage Disequilibrium 92%
  • Single Nucleotide Polymorphism 67%
  • Body Mass Index 58%
  • Genome 54%

• Genome-wide association identifies candidate genes for drought tolerance in coast redwood and giant sequoia

  De La Torre, A. R., Sekhwal, M. K., Puiu, D., Salzberg, S. L., Scott, A. D., Allen, B., Neale, D. B., Chin, A. R. O. & Buckley, T. N., Jan 2022, In: Plant Journal. 109, 1, p. 7-22 16 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Sequoiadendron 100%
  • Sequoiadendron giganteum 71%
  • Sequoia 69%
  • Droughts 66%
  • Sequoia sempervirens 62%

• High-quality genome and methylomes illustrate features underlying evolutionary success of oaks

  Sork, V. L., Cokus, S. J., Fitz-Gibbon, S. T., Zimin, A. V., Puiu, D., Garcia, J. A., Gugger, P. F., Henriquez, C. L., Zhen, Y., Lohmueller, K. E., Pellegrini, M. & Salzberg, S. L., Dec 2022, In: Nature communications. 13, 1, 2047.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • genome 100%
  • Epigenome 95%
  • genes 89%
  • Quercus 86%
  • Poaceae 64%

• Metagenome analysis using the Kraken software suite

  Lu, J., Rincon, N., Wood, D. E., Breitwieser, F. P., Pockrandt, C., Langmead, B., Salzberg, S. L. & Steinegger, M., Dec 2022, In: Nature protocols. 17, 12, p. 2815-2839 25 p.

  Research output: Contribution to journal › Article › peer-review

  • Metagenome 100%
  • Metagenomics 86%
  • Software 52%
  • DNA Sequencing 43%
  • Pipeline 40%

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

  Wensel, C. R., Pluznick, J. L., Salzberg, S. L. & Sears, C. L., Apr 1 2022, In: Journal of Clinical Investigation. 132, 7, e154944.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Microbiota 100%
  • High-Throughput Nucleotide Sequencing 96%
  • Metagenomics 41%
  • Firearms 38%
  • 16S Ribosomal RNA 34%

• PhyloCSF++: A fast and user-friendly implementation of PhyloCSF with annotation tools

  Pockrandt, C., Steinegger, M. & Salzberg, S. L., Mar 1 2022, In: Bioinformatics. 38, 5, p. 1440-1442 3 p.

  Research output: Contribution to journal › Article › peer-review

  • Multiple Sequence Alignment 100%
  • Annotation 87%
  • Sequence Alignment 76%
  • Genome 69%
  • Coding 62%

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

  Human Pangenome Reference Consortium, Nov 17 2022, In: Nature. 611, 7936, p. 519-531 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Diploidy 100%
  • Human Genome 95%
  • Genome 62%
  • Telomere 50%
  • Haplotypes 43%

• 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., Dec 2022, In: eLife. 11, e82556.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Forensic Anthropology 100%
  • Protein Structure 75%
  • Transcriptome 71%
  • RNA Sequencing 42%
  • Genome 35%

• 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., Aganezov, S., Hoyt, S. J., Diekhans, M., Logsdon, G. A., Alonge, M., Antonarakis, S. E., Borchers, M., Bouffard, G. G., Brooks, S. Y., Caldas, G. V., & 80 othersChen, N. C., Cheng, H., Chin, C. S., Chow, W., de Lima, L. G., Dishuck, P. C., Durbin, R., Dvorkina, T., Fiddes, I. T., Formenti, G., Fulton, R. S., Fungtammasan, A., Garrison, E., Grady, P. G. S., Graves-Lindsay, T. A., Hall, I. M., Hansen, N. F., Hartley, G. A., Haukness, M., Howe, K., Hunkapiller, M. W., Jain, C., Jain, M., Jarvis, E. D., Kerpedjiev, P., Kirsche, M., Kolmogorov, M., Korlach, J., Kremitzki, M., Li, H., Maduro, V. V., Marschall, T., McCartney, A. M., McDaniel, J., Miller, D. E., Mullikin, J. C., Myers, E. W., Olson, N. D., Paten, B., Peluso, P., Pevzner, P. A., Porubsky, D., Potapova, T., Rogaev, E. I., Rosenfeld, J. A., Salzberg, S. L., Schneider, V. A., Sedlazeck, F. J., Shafin, K., Shew, C. J., Shumate, A., Sims, Y., Smit, A. F. A., Soto, D. C., Sovi, I., Storer, J. M., Streets, A., Sullivan, B. A., Thibaud-Nissen, F., Torrance, J., Wagner, J., Walenz, B. P., Wenger, A., Wood, J. M. D., Xiao, C., Yan, S. M., Young, A. C., Zarate, S., Surti, U., McCoy, R. C., Dennis, M. Y., Alexandrov, I. A., Gerton, J. L., O'Neill, R. J., Timp, W., Zook, J. M., Schatz, M. C., Eichler, E. E., Miga, K. H. & Phillippy, A. M., Apr 1 2022, In: Science. 376, 6588, p. 44-53 10 p.

  Research output: Contribution to journal › Article › peer-review

  • Human Genome 100%
  • Telomere 69%
  • Base Pairing 65%
  • Genome 64%
  • Genomic Segmental Duplications 48%

• The Human "Contaminome" and Understanding Infectious Disease

  Simner, P. J. & Salzberg, S. L., Sep 8 2022, In: New England Journal of Medicine. 387, 10, p. 943-946 4 p.

  Research output: Contribution to journal › Article › peer-review

• The SAMBA tool uses long reads to improve the contiguity of genome assemblies

  Zimin, A. V. & Salzberg, S. L., Feb 2022, In: PLoS computational biology. 18, 2, e1009860.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Contiguity 100%
  • tool use 89%
  • genome assembly 85%
  • Genome 75%
  • Genomics 71%

• Whole Genome Association Study of the Plasma Metabolome Identifies Metabolites Linked to Cardiometabolic Disease in Black Individuals

  Tahir, U. A., Katz, D. H., Avila-Pachecho, J., Bick, A. G., Pampana, A., Robbins, J. M., Yu, Z., Chen, Z. Z., Benson, M. D., Cruz, D. E., Ngo, D., Deng, S., Shi, X., Zheng, S., Eisman, A. S., Farrell, L., Hall, M. E., Correa, A., Tracy, R. P., Durda, P., & 410 othersTaylor, K. D., Liu, Y., Johnson, W. C., Guo, X., Yao, J., Chen, Y. D. I., Manichaikul, A. W., Ruberg, F. L., Blaner, W. S., Jain, D., Bouchard, C., Sarzynski, M. A., Rich, S. S., Rotter, J. I., Wang, T. J., Wilson, J. G., Clish, C. B., Natarajan, P., Gerszten, R. E., Abe, N., Abecasis, G., Aguet, F., Albert, C., Almasy, L., Alonso, A., Ament, S., Anderson, P., Anugu, P., Applebaum-Bowden, D., Ardlie, K., Arking, D., Arnett, D. K., Ashley-Koch, A., Aslibekyan, S., Assimes, T., Auer, P., Avramopoulos, D., Ayas, N., Balasubramanian, A., Barnard, J., Barnes, K., Barr, R. G., Barron-Casella, E., Barwick, L., Beaty, T., Beck, G., Becker, D., Becker, L., Beer, R., Beitelshees, A., Benjamin, E., Benos, T., Bezerra, M., Bielak, L., Bis, J., Blackwell, T., Blangero, J., Blue, N., Boerwinkle, E., Bowden, D. W., Bowler, R., Brody, J., Broeckel, U., Broome, J., Brown, D., Bunting, K., Burchard, E., Bustamante, C., Buth, E., Cade, B., Cardwell, J., Carey, V., Carrier, J., Carson, A., Carty, C., Casaburi, R., Romero, J. P. C., Casella, J., Castaldi, P., Chaffin, M., Chang, C., Chang, Y. C., Chasman, D., Chavan, S., Chen, B. J., Chen, W. M., Cho, M., Choi, S. H., Chuang, L. M., Chung, M., Chung, R. H., Comhair, S., Conomos, M., Cornell, E., Crandall, C., Crapo, J., Cupples, L. A., Curran, J., Curtis, J., Custer, B., Damcott, C., Darbar, D., David, S., Davis, C., Daya, M., de Andrade, M., Fuentes, L. D. L., de Vries, P., DeBaun, M., Deka, R., DeMeo, D., Devine, S., Dinh, H., Doddapaneni, H., Duan, Q., Dugan-Perez, S., Duggirala, R., Dutcher, S. K., Eaton, C., Ekunwe, L., El Boueiz, A., Ellinor, P., Emery, L., Erzurum, S., Farber, C., Farek, J., Fingerlin, T., Flickinger, M., Fornage, M., Franceschini, N., Frazar, C., Fu, M., Fullerton, S. M., Fulton, L., Gabriel, S., Gan, W., Gao, S., Gao, Y., Gass, M., Geiger, H., Gelb, B., Geraci, M., Germer, S., Ghosh, A., Gibbs, R., Gignoux, C., Gladwin, M., Glahn, D., Gogarten, S., Gong, D. W., Goring, H., Graw, S., Gray, K. J., Grine, D., Gross, C., Gu, C. C., Guan, Y., Gupta, N., Haessler, J., Han, Y., Hanly, P., Harris, D., Hawley, N. L., He, J., Heavner, B., Heckbert, S., Hernandez, R., Herrington, D., Hersh, C., Hidalgo, B., Hixson, J., Hobbs, B., Hokanson, J., Hong, E., Hoth, K., Hsiung, C., Hu, J., Hung, Y. J., Huston, H., Hwu, C. M., Irvin, M. R., Jackson, R., Jaquish, C., Johnsen, J., Johnson, A., Johnston, R., Jones, K., Kang, H. M., Kaplan, R., Kardia, S., Kelly, S., Kenny, E., Kessler, M., Khan, A., Khan, Z., Kim, W., Kimoff, J., Kinney, G., Konkle, B., Kooperberg, C., Kramer, H., Lange, C., Lange, E., Lange, L., Laurie, C., Laurie, C., LeBoff, M., Lee, J., Lee, S., Lee, W. J., LeFaive, J., Levine, D., Levy, D., Lewis, J., Li, X., Li, Y., Lin, H., Lin, H., Lin, X., Liu, S., Liu, Y., Loos, R. J. F., Lubitz, S., Lunetta, K., Luo, J., Magalang, U., Mahaney, M., Make, B., Manning, A., Manson, J. A., Martin, L., Marton, M., Mathai, S., Mathias, R., May, S., McArdle, P., McDonald, M. L., McFarland, S., McGarvey, S., McGoldrick, D., McHugh, C., McNeil, B., Mei, H., Meigs, J., Menon, V., Mestroni, L., Metcalf, G., Meyers, D. A., Mignot, E., Mikulla, J., Min, N., Minear, M., Minster, R. L., Mitchell, B. D., Moll, M., Momin, Z., Montasser, M. E., Montgomery, C., Muzny, D., Mychaleckyj, J. C., Nadkarni, G., Naik, R., Naseri, T., Nekhai, S., Nelson, S. C., Neltner, B., Nessner, C., Nickerson, D., Nkechinyere, O., North, K., O’Connell, J., O’Connor, T., Ochs-Balcom, H., Okwuonu, G., Pack, A., Paik, D. T., Palmer, N., Pankow, J., Papanicolaou, G., Parker, C., Peloso, G., Peralta, J. M., Perez, M., Perry, J., Peters, U., Peyser, P., Phillips, L. S., Pleiness, J., Pollin, T., Post, W., Becker, J. P., Boorgula, M. P., Preuss, M., Psaty, B., Qasba, P., Qiao, D., Qin, Z., Rafaels, N., Raffield, L., Rajendran, M., Ramachandran, V. S., Rao, D. C., Rasmussen-Torvik, L., Ratan, A., Redline, S., Reed, R., Reeves, C., Regan, E., Reiner, A., Reupena, M. S., Rice, K., Robillard, R., Robine, N., Dan Roden, R., Roselli, C., Ruczinski, I., Runnels, A., Russell, P., Ruuska, S., Sabino, E. C., Saleheen, D., Salimi, S., Salvi, S., Salzberg, S., Sandow, K., Sankaran, V. G., Santibanez, J., Schwander, K., Schwartz, D., Sciurba, F., Seidman, C., Seidman, J., Sériès, F., Sheehan, V., Sherman, S. L., Shetty, A., Shetty, A., Sheu, W. H. H., Shoemaker, M. B., Silver, B., Silverman, E., Skomro, R., Smith, A. V., Smith, J., Smith, J., Smith, N., Smith, T., Smoller, S., Snively, B., Snyder, M., Sofer, T., Sotoodehnia, N., Stilp, A. M., Storm, G., Streeten, E., Su, J. L., Sung, Y. J., Sylvia, J., Szpiro, A., Taliun, D., Tang, H., Taub, M., Taylor, M., Taylor, S., Telen, M., Thornton, T. A., Threlkeld, M., Tinker, L., Tirschwell, D., Tishkoff, S., Tiwari, H., Tong, C., Tsai, M., Vaidya, D., Van Den Berg, D., VandeHaar, P., Vrieze, S., Walker, T., Wallace, R., Walts, A., Wang, F. F., Wang, H., Wang, J., Watson, K., Watt, J., Weeks, D. E., Weinstock, J., Weir, B., Weiss, S. T., Weng, L. C., Wessel, J., Willer, C., Williams, K., Williams, L. K., Wilson, C., Winterkorn, L., Wong, Q., Wu, J., Xu, H., Yanek, L., Yang, I., Yu, K., Zekavat, S. M., Zhang, Y., Zhao, S. X., Zhao, W., Zhu, X., Ziv, E., Zody, M. & Zoellner, S., Dec 2022, In: Nature communications. 13, 1, 4923.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • metabolites 100%
  • genome 98%
  • Metabolome 85%
  • Genome-Wide Association Study 79%
  • Black 66%

• Whole genome sequence analysis of blood lipid levels in >66,000 individuals

  NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Dec 2022, In: Nature communications. 13, 1, 5995.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • genome 100%
  • lipids 75%
  • blood 73%
  • Sequence Analysis 71%
  • Lipid 52%
• 2021

  A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response

  NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Oct 2021, In: Nature genetics. 53, 10, p. 1504-1516 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • HIV 100%
  • HLA-B Antigens 61%
  • Population 56%
  • Hispanic Americans 46%
  • Genome-Wide Association Study 25%

• Author Correction: Inherited causes of clonal haematopoiesis in 97,691 whole genomes (Nature, (2020), 586, 7831, (763-768), 10.1038/s41586-020-2819-2)

  NHLBI Trans-Omics for Precision Medicine Consortium, Mar 25 2021, In: Nature. 591, 7851, p. E27

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • Hematopoiesis 100%
  • Genome 62%
  • Medical Oncology 54%
  • Computational Biology 43%
  • Neoplasms 14%

• Author Correction: A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response (Nature Genetics, (2021), 53, 10, (1504-1516), 10.1038/s41588-021-00935-7)

  NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Dec 2021, In: Nature genetics. 53, 12, p. 1722 1 p.

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • Seoul 100%
  • HIV 53%
  • Republic of Korea 46%
  • Population 30%
  • Bioengineering 25%

• Balrog: A universal protein model for prokaryotic gene prediction

  Sommer, M. J. & Salzberg, S. L., Feb 26 2021, In: PLoS computational biology. 17, 2, e1008727.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Annotation 100%
  • Genome 79%
  • Protein 75%
  • Genomics 75%
  • Gene 70%

• Chromosome Xq23 is associated with lower atherogenic lipid concentrations and favorable cardiometabolic indices

  NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium & FinnGen, Dec 1 2021, In: Nature communications. 12, 1, 2182.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • chromosomes 100%
  • lipids 80%
  • Chromosomes 64%
  • blood 62%
  • Lipid 56%

• Dissecting the polygenic basis of cold adaptation using genome-wide association of traits and environmental data in douglas-fir

  De La Torre, A. R., Wilhite, B., Puiu, D., St. Clair, J. B., Crepeau, M. W., Salzberg, S. L., Langley, C. H., Allen, B. & Neale, D. B., Jan 2021, In: Genes. 12, 1, p. 1-28 28 p., 110.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Pseudotsuga 100%
  • Cold Temperature 47%
  • Genome 36%
  • Secondary Metabolism 13%
  • Climate Change 12%
  1 Scopus citations

• Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments

  Varabyou, A., Salzberg, S. L. & Pertea, M., 2021, In: Genome research. 31, 2, p. 301-308 8 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • RNA Sequence Analysis 100%
  • Noise 81%
  • Gene Expression 53%
  • Genes 26%
  • Animals 11%

• Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epithelium

  NHLBI SubPopulations and InteRmediate Outcome Measures In COPD Study (SPIROMICS), Dec 2021, In: Genome Medicine. 13, 1, 66.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • SARS Virus 100%
  • Epithelium 51%
  • Viruses 33%
  • Gene Expression 30%
  • Genes 27%

• Genome sequencing unveils a regulatory landscape of platelet reactivity

  NHLBI Trans-Omics for Precision (TOPMed) Consortium, Dec 1 2021, In: Nature communications. 12, 1, 3626.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • sequencing 100%
  • genome 95%
  • loci 82%
  • platelets 79%
  • reactivity 73%

• Guillain-Barré Syndrome Outbreak in Peru 2019 Associated with Campylobacter jejuni Infection

  Ramos, A. P., Leonhard, S. E., Halstead, S. K., Cuba, M. A., Castañeda, C. C., Dioses, J. A., Tipismana, M. A., Abanto, J. T., Llanos, A., Gourlay, D., Grogl, M., Ramos, M., Rojas, J. D., Meza, R., Puiu, D., Sherman, R. M., Salzberg, S. L., Simner, P. J., Willison, H. J., Jacobs, B. C., & 3 othersCornblath, D. R., Umeres, H. F. & Pardo, C. A., Mar 5 2021, In: Neurology: Neuroimmunology and NeuroInflammation. 8, 2, e952.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Campylobacter Infections 100%
  • Campylobacter jejuni 91%
  • Peru 89%
  • Disease Outbreaks 62%
  • Arbovirus Infections 23%
  1 Scopus citations

• Identification of microbial agents in tissue specimens of ocular and periocular sarcoidosis using a metagenomics approach

  Shifera, A. S., Pockrandt, C., Rincon, N., Ge, Y., Lu, J., Varabyou, A., Jedlicka, A. E., Sun, K., Scott, A. L., Eberhart, C., Thorne, J. E. & Salzberg, S. L., 2021, In: F1000Research. 10, 820.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Ocular 100%
  • Metagenomics 96%
  • Sarcoidosis 84%
  • Eye 48%
  • Mupapillomavirus 37%

• Liftoff: Accurate mapping of gene annotations

  Shumate, A. & Salzberg, S. L., Jun 15 2021, In: Bioinformatics. 37, 12, p. 1639-1643 5 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Annotation 100%
  • Molecular Sequence Annotation 95%
  • DNA Sequencing 89%
  • Genome 79%
  • Genomics 75%

• Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie

  Varabyou, A., Pockrandt, C., Salzberg, S. L. & Pertea, M., Jul 2021, In: Genetics. 218, 3, iyab074.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • SARS Virus 100%
  • Genetic Recombination 65%
  • Genome 46%
  • Public Policy 18%
  • Health Policy 17%

• Rapidly fatal infection with Bacillus cereus/thuringiensis: genome assembly of the responsible pathogen and consideration of possibly contributing toxins

  Butcher, M., Puiu, D., Romagnoli, M., Carroll, K. C., Salzberg, S. L. & Nauen, D. W., Dec 2021, In: Diagnostic Microbiology and Infectious Disease. 101, 4, 115534.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Bacillus thuringiensis 100%
  • Antitoxins 94%
  • Bacillus cereus 89%
  • Immunocompromised Host 72%
  • Resuscitation 65%

• Releasing the Kraken

  Salzberg, S. L. & Wood, D. E., 2021, In: Frontiers in Bioinformatics. 1, 808003.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Microbial Genome 100%
  • Point of inflection 84%
  • Genome 72%
  • Heart 70%
  • Microbiota 65%

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

  NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Feb 11 2021, In: Nature. 590, 7845, p. 290-299 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • National Heart, Lung, and Blood Institute (U.S.) 100%
  • Precision Medicine 79%
  • Genome 49%
  • Genotype 21%
  • Catalogs 18%
  19 Scopus citations

• Variant-specific inflation factors for assessing population stratification at the phenotypic variance level

  NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Dec 1 2021, In: Nature communications. 12, 1, 3506.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Whole Genome Sequencing 100%
  • stratification 98%
  • Economic Inflation 96%
  • Hemoglobin 79%
  • sequencing 58%

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

  TOPMed Sleep Working Group & NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Dec 2021, In: Genome Medicine. 13, 1, 136.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • National Heart, Lung, and Blood Institute (U.S.) 100%
  • Sleep Apnea Syndromes 79%
  • Precision Medicine 79%
  • Genome-Wide Association Study 76%
  • Oxyhemoglobins 48%
• 2020

  A reference genome sequence for giant sequoia

  Scott, A. D., Zimin, A. V., Puiu, D., Workman, R., Britton, M., Zaman, S., Caballero, M., Read, A. C., Bogdanove, A. J., Burns, E., Wegrzyn, J., Timp, W., Salzberg, S. L. & Neale, D. B., Nov 2020, In: G3: Genes, Genomes, Genetics. 10, 11, p. 3907-3919 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Sequoiadendron 100%
  • Genome 28%
  • Cupressaceae 19%
  • Nanopore Sequencing 17%
  • Chromosomes 16%
  3 Scopus citations

• Assembly and annotation of an Ashkenazi human reference genome

  Shumate, A., Shumate, A., Zimin, A. V., Zimin, A. V., Sherman, R. M., Sherman, R. M., Puiu, D., Puiu, D., Wagner, J. M., Olson, N. D., Pertea, M., Salit, M. L., Zook, J. M. & Salzberg, S. L., Jun 2 2020, In: Genome biology. 21, 1, 129.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Human Genome 100%
  • genome 89%
  • Genome 64%
  • gene 46%
  • Genes 27%
  5 Scopus citations