Steven L Salzberg

Professor

1983 …2020

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Article
2020

Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing

Read, A. C., Moscou, M. J., Zimin, A. V., Pertea, G., Meyer, R. S., Purugganan, M. D., Leach, J. E., Triplett, L. R., Salzberg, S. L. & Bogdanove, A. J., Jan 1 2020, In : PLoS genetics. 16, 1, e1008571.

Research output: Contribution to journalArticle

Open Access

Microbial Diagnostics for Cancer: A Step Forward but Not Prime Time Yet

Sears, C. L. & Salzberg, S. L., May 11 2020, In : Cancer cell. 37, 5, p. 625-627 3 p.

Research output: Contribution to journalArticle

Pavian: Interactive analysis of metagenomics data for microbiome studies and pathogen identification

Breitwieser, F. P. & Salzberg, S. L., Feb 15 2020, In : Bioinformatics. 36, 4, p. 1303-1304 2 p.

Research output: Contribution to journalArticle

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

Steinegger, M. & Salzberg, S. L., May 12 2020, In : Genome biology. 21, 1, 115.

Research output: Contribution to journalArticle

Open Access
2019
Open Access

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., Dickinson, M. R., Vinther, J., Bull, I. D., Brooker, R. A., Martin, P., Donohoe, P., Knowles, T. D., Penkman, K. E. & Onstott, T., Jun 18 2019, In : eLife. 8

Research output: Contribution to journalArticle

Open Access

Genomic architecture of complex traits in loblolly pine

De La Torre, A. R., Puiu, D., Crepeau, M. W., Stevens, K., Salzberg, S. L., Langley, C. H. & Neale, D. B., Mar 2019, In : New Phytologist. 221, 4, p. 1789-1801 13 p.

Research output: Contribution to journalArticle

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

Kim, D., Paggi, J. M., Park, C., Bennett, C. & Salzberg, S. L., Aug 1 2019, In : Nature biotechnology. 37, 8, p. 907-915 9 p.

Research output: Contribution to journalArticle

Human contamination in bacterial genomes has created thousands of spurious proteins

Breitwieser, F. P., Pertea, M., Zimin, A. V. & Salzberg, S. L., Jun 1 2019, In : Genome research. 29, 6, p. 954-960 7 p.

Research output: Contribution to journalArticle

Open Access

The Terabase Search Engine: A large-scale relational database of short-read sequences

Wilton, R., Wheelan, S., Szalay, A. S. & Salzberg, S. L., Feb 15 2019, In : Bioinformatics. 35, 4, p. 665-670 6 p.

Research output: Contribution to journalArticle

Transcriptome assembly from long-read RNA-seq alignments with StringTie2

Kovaka, S., Zimin, A. V., Pertea, G. M., Razaghi, R., Salzberg, S. L. & Pertea, M., Dec 16 2019, In : Genome biology. 20, 1, 278.

Research output: Contribution to journalArticle

Open Access

Whole Genome Sequencing Identifies CRISPLD2 as a Lung Function Gene in Children With Asthma

National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine (TOPMed) Consortium, Dec 2019, In : CHEST. 156, 6, p. 1068-1079 12 p.

Research output: Contribution to journalArticle

2018

A review of methods and databases for metagenomic classification and assembly

Breitwieser, F. P., Lu, J. & Salzberg, S. L., Mar 27 2018, In : Briefings in bioinformatics. 20, 4, p. 1125-1139 15 p.

Research output: Contribution to journalArticle

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., Nov 28 2018, In : Genome Biology. 19, 1, 1590.

Research output: Contribution to journalArticle

Deep-coverage whole genome sequences and blood lipids among 16,324 individuals

NHLBI TOPMed Lipids Working Group, Dec 1 2018, In : Nature communications. 9, 1, 3391.

Research output: Contribution to journalArticle

Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries

Zekavat, S. M., Ruotsalainen, S., Handsaker, R. E., Alver, M., Bloom, J., Poterba, T., Seed, C., Ernst, J., Chaffin, M., Engreitz, J., Peloso, G. M., Manichaikul, A., Yang, C., Ryan, K. A., Fu, M., Johnson, W. C., Tsai, M., Budoff, M., Ramachandran, V. S., Cupples, L. A. & 323 others, Rotter, J. I., Rich, S. S., Post, W., Mitchell, B. D., Correa, A., Metspalu, A., Wilson, J. G., Salomaa, V., Kellis, M., Daly, M. J., Neale, B. M., McCarroll, S., Surakka, I., Esko, T., Ganna, A., Ripatti, S., Kathiresan, S., Natarajan, P., Abe, N., Abecasis, G., Albert, C., Allred, N. P., Almasy, L., Alonso, A., Ament, S., Anderson, P., Anugu, P., Applebaum-Bowden, D., Arking, D., Arnett, D. K., Ashley-Koch, A., Aslibekyan, S., Assimes, T., Auer, P., Avramopoulos, D., Barnard, J., Barnes, K., Barr, R. G., 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. D. I., Cho, M., Choi, S. H., Chuang, L. M., Chung, M., Cornell, E., Crandall, C., Crapo, J., Curran, J., Curtis, J., Custer, B., Damcott, C., Darbar, D., Das, S., David, S., Davis, C., Daya, M., Andrade, M. D., Debaun, M., Deka, R., Demeo, D., Devine, S., Do, R., Duan, Q., Duggirala, R., Durda, P., Dutcher, S., Eaton, C., Ekunwe, L., Ellinor, P., Emery, L., Farber, C., Farnam, L., Fingerlin, T., Flickinger, M., Fornage, M., Franceschini, N., Fullerton, S. M., Fulton, L., Gabriel, S., Gan, W., Gao, Y., Gass, M., Gelb, B., Geng, X., Germer, S., Gignoux, C., Gladwin, M., Glahn, D., Gogarten, S., Gong, D. W., Goring, H., Gu, C. C., Guan, Y., Guo, X., Haessler, J., Hall, M., Harris, D., Hawley, N., He, J., Heavner, B., Heckbert, S., Hernandez, R., Herrington, D., Hersh, C., Hidalgo, B., Hixson, J., Hokanson, J., Hong, E., Hoth, K., Hsiung, C., Huston, H., Hwu, C. M., Irvin, M. R., Jackson, R., Jain, D., Jaquish, C., Jhun, M. A., Johnsen, J., Johnson, A., Johnston, R., Jones, K., Kang, H. M., Kaplan, R., Kardia, S., Kaufman, L., Kelly, S., Kenny, E., Kessler, M., Khan, A., Kinney, G., Konkle, B., Kooperberg, C., Kramer, H., Krauter, S., Lange, C., Lange, E., Lange, L., Laurie, C., Laurie, C., Leboff, M., Lee, S. S., Lee, W. J., Lefaive, J., Levine, D., Levy, D., Lewis, J., Li, Y., Lin, H., Lin, K. H., Liu, S., Liu, Y., Loos, R., Lubitz, S., Lunetta, K., Luo, J., Mahaney, M., Make, B., Manson, J. A., Margolin, L., Martin, L., Mathai, S., Mathias, R., McArdle, P., McDonald, M. L., McFarland, S., McGarvey, S., Mei, H., Meyers, D. A., Mikulla, J., Min, N., Minear, M., Minster, R. L., Montasser, M. E., Musani, S., Mwasongwe, S., Mychaleckyj, J. C., Nadkarni, G., Naik, R., Nekhai, S., Nickerson, D., North, K., O'connell, J., O'connor, T., Ochs-Balcom, H., Pankow, J., Papanicolaou, G., Parker, M., Parsa, A., Penchev, S., Peralta, J. M., Perez, M., Perry, J., Peters, U., Peyser, P., Phillips, L., Phillips, S., Pollin, T., Becker, J. P., Boorgula, M. P., Preuss, M., Prokopenko, D., Psaty, B., Qasba, P., Qiao, D., Qin, Z., Rafaels, N., Raffield, L., Rao, D. C., Rasmussen-Torvik, L., Ratan, A., Redline, S., Reed, R., Regan, E., Reiner, A., Rice, K., Roden, D., Roselli, C., Ruczinski, I., Russell, P., Ruuska, S., Sakornsakolpat, P., Salimi, S., Salzberg, S., Sandow, K., Sankaran, V., Scheller, C., Schmidt, E., Schwander, K., Schwartz, D., Sciurba, F., Seidman, C., Sheehan, V., Shetty, A., Shetty, A., Sheu, W. H. H., Shoemaker, M. B., Silver, B., Silverman, E., Smith, J., Smith, J., Smith, N., Smith, T., Smoller, S., Snively, B., Sofer, T., Sotoodehnia, N., Stilp, A., Streeten, E., Sung, Y. J., Sylvia, J., Szpiro, A., Sztalryd, C., Taliun, D., Tang, H., Taub, M., Taylor, K., Taylor, S., Telen, M., Thornton, T. A., Tinker, L., Tirschwell, D., Tiwari, H., Tracy, R., Vaidya, D., Vandehaar, P., Vrieze, S., Walker, T., Wallace, R., Walts, A., Wan, E., Wang, F. F., Watson, K., Weeks, D. E., Weir, B., Weiss, S., Weng, L. C., Willer, C., Williams, K., Williams, L. K., Wilson, C., Wong, Q., Xu, H., Yanek, L., Yang, I., Yang, R., Zaghloul, N., Zhang, Y., Zhao, S. X., Zhao, W., Zheng, X., Zhi, D., Zhou, X., Zody, M. & Zoellner, S., Dec 1 2018, In : Nature communications. 9, 1, 2606.

Research output: Contribution to journalArticle

Development and optimization of metagenomic next-generation sequencing methods for cerebrospinal fluid diagnostics

Simner, P. J., Miller, H. B., Breitwieser, F. P., Monsalve, G. P., Pardo, C. A., Salzberg, S. L., Sears, C. L., Thomas, D. L., Eberhart, C. G. & Carrolla, K. C., Sep 2018, In : Journal of clinical microbiology. 56, 9, e00472.

Research output: Contribution to journalArticle

Genomic variation among and within six Juglans species

Stevens, K. A., Woeste, K., Chakraborty, S., Crepeau, M. W., Leslie, C. A., Martínez-García, P. J., Puiu, D., Romero-Severson, J., Coggeshall, M., Dandekar, A. M., Kluepfel, D., Neale, D. B., Salzberg, S. L. & Langley, C. H., Jul 1 2018, In : G3: Genes, Genomes, Genetics. 8, 7, p. 2153-2165 13 p.

Research output: Contribution to journalArticle

Identifying corneal infections in formalin-fixed specimens using next generation sequencing

Li, Z., Breitwieser, F. P., Lu, J., Jun, A., Asnaghi, L., Salzberg, S. L. & Eberhart, C. G., Jan 1 2018, In : Investigative Ophthalmology and Visual Science. 59, 1, p. 280-288 9 p.

Research output: Contribution to journalArticle

KrakenUniq: confident and fast metagenomics classification using unique k-mer counts

Breitwieser, F. P., Baker, D. N. & Salzberg, S. L., Nov 16 2018, In : Genome Biology. 19, 1, 1 p.

Research output: Contribution to journalArticle

MUMmer4: A fast and versatile genome alignment system

Marçais, G., Delcher, A. L., Phillippy, A. M., Coston, R., Salzberg, S. L. & Zimin, A., Jan 1 2018, In : PLoS Computational Biology. 14, 1, e1005944.

Research output: Contribution to journalArticle

Removing contaminants from databases of draft genomes

Lu, J. & Salzberg, S. L., Jun 1 2018, In : PLoS Computational Biology. 14, 6, e1006277.

Research output: Contribution to journalArticle

2017

Bracken: Estimating species abundance in metagenomics data

Lu, J., Breitwieser, F. P., Thielen, P. & Salzberg, S. L., Jan 1 2017, In : PeerJ Computer Science. 2017, 1, e104.

Research output: Contribution to journalArticle

First draft genome sequence of the pathogenic fungus Lomentospora prolificans (formerly Scedosporium prolificans)

Luo, R., Zimin, A., Workman, R., Fan, Y., Pertea, G., Grossman, N., Wear, M. P., Jia, B., Miller, H., Casadevall, A., Timp, W., Zhang, S. X. & Salzberg, S. L., Nov 1 2017, In : G3: Genes, Genomes, Genetics. 7, 11, p. 3831-3836 6 p.

Research output: Contribution to journalArticle

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii

Luo, M. C., Gu, Y. Q., Puiu, D., Wang, H., Twardziok, S. O., Deal, K. R., Huo, N., Zhu, T., Wang, L., Wang, Y., McGuire, P. E., Liu, S., Long, H., Ramasamy, R. K., Rodriguez, J. C., Van Sonny, L., Yuan, L., Wang, Z., Xia, Z., Xiao, L. & 26 others, Anderson, O. D., Ouyang, S., Liang, Y., Zimin, A. V., Pertea, G., Qi, P., Bennetzen, J. L., Dai, X., Dawson, M. W., Müller, H. G., Kugler, K., Rivarola-Duarte, L., Spannagl, M., Mayer, K. F. X., Lu, F. H., Bevan, M. W., Leroy, P., Li, P., You, F. M., Sun, Q., Liu, Z., Lyons, E., Wicker, T., Salzberg, S. L., Devos, K. M. & Dvoák, J., Nov 23 2017, In : Nature. 551, 7681, p. 498-502 5 p.

Research output: Contribution to journalArticle

Genomic characterization of chromosome translocations in patients with T/myeloid mixed-phenotype acute leukemia

Pallavajjalla, A., Kim, D., Li, T., Ghiaur, G., Jones, R. J., Burns, K., Salzberg, S. L. & Ning, Y., Sep 8 2017, (Accepted/In press) In : Leukemia and Lymphoma. p. 1-8 8 p.

Research output: Contribution to journalArticle

Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm

Zimin, A. V., Puiu, D., Luo, M. C., Zhu, T., Koren, S., Marçais, G., Yorke, J. A., Dvořák, J. & Salzberg, S. L., May 2017, In : Genome research. 27, 5, p. 787-792 6 p.

Research output: Contribution to journalArticle

Presence of human hepegivirus-1 in a cohort of people who inject drugs

Kandathil, A., Breitwieser, F. P., Sachithanandham, J., Robinson, M., Mehta, S. H., Timp, W., Salzberg, S. L., Thomas, D. L. & Balagopal, A., Jul 4 2017, In : Annals of Internal Medicine. 167, 1, p. 1-7 7 p.

Research output: Contribution to journalArticle

Short Read Mapping: An Algorithmic Tour

Canzar, S. & Salzberg, S. L., Mar 2017, In : Proceedings of the IEEE. 105, 3, p. 436-458 23 p., 7244195.

Research output: Contribution to journalArticle

The Douglas-Fir genome sequence reveals specialization of the photosynthetic apparatus in Pinaceae

Neale, D. B., McGuire, P. E., Wheeler, N. C., Stevens, K. A., Crepeau, M. W., Cardeno, C., Zimin, A. V., Puiu, D., Pertea, G. M., Sezen, U. U., Casola, C., Koralewski, T. E., Paul, R., Gonzalez-Ibeas, D., Zaman, S., Cronn, R., Yandell, M., Holt, C., Langley, C. H., Yorke, J. A. & 2 others, Salzberg, S. L. & Wegrzyn, J. L., Sep 1 2017, In : G3: Genes, Genomes, Genetics. 7, 9, p. 3157-3167 11 p.

Research output: Contribution to journalArticle

The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum

Zimin, A. V., Puiu, D., Hall, R., Kingan, S., Clavijo, B. J. & Salzberg, S. L., Nov 1 2017, In : GigaScience. 6, 11, gix097.

Research output: Contribution to journalArticle

The novel fusion transcript NR5A2-KLHL29FT is generated by an insertion at the KLHL29 locus

Sun, Z., Ke, X., Salzberg, S. L., Kim, D., Antonescu, V., Cheng, Y., Huang, B., Song, J. H., Abraham, J. M., Ibrahim, S., Tian, H. & Meltzer, S., 2017, (Accepted/In press) In : Cancer.

Research output: Contribution to journalArticle

2016

Centrifuge: Rapid and sensitive classification of metagenomic sequences

Kim, D., Song, L., Breitwieser, F. P. & Salzberg, S. L., Dec 2016, In : Genome research. 26, 12, p. 1721-1729 9 p.

Research output: Contribution to journalArticle

Databases: Reminder to deposit DNA sequences

Salzberg, S. L., May 11 2016, In : Nature. 533, p. 179 1 p.

Research output: Contribution to journalArticle

First draft assembly and annotation of the genome of a California endemic oak Quercus lobata Née (Fagaceae)

Sork, V. L., Fitz-Gibbon, S. T., Puiu, D., Crepeau, M., Gugger, P. F., Sherman, R., Stevens, K., Langley, C. H., Pellegrini, M. & Salzberg, S. L., 2016, In : G3: Genes, Genomes, Genetics. 6, 11, p. 3485-3495 11 p.

Research output: Contribution to journalArticle

Reminder to deposit DNA sequences

Blaxter, M., Danchin, A., Savakis, B., Fukami-Kobayashi, K., Kurokawa, K., Sugano, S., Roberts, R. J., Salzberg, S. L. & Wu, C. I., May 13 2016, In : Science. 352, 6287, p. 780 1 p.

Research output: Contribution to journalArticle

Sequence of the sugar pine megagenome

Stevens, K. A., Wegrzyn, J. L., Zimin, A., Puiu, D., Crepeau, M., Cardeno, C., Paul, R., Gonzalez-Ibeas, D., Koriabine, M., Holtz-Morris, A. E., Martínez-García, P. J., Sezen, U. U., Marçais, G., Jermstad, K., McGuire, P. E., Loopstra, C. A., Davis, J. M., Eckert, A., de Jong, P., Yorke, J. A. & 3 others, Salzberg, S. L., Neale, D. B. & Langley, C. H., Dec 1 2016, In : Genetics. 204, 4, p. 1613-1626 14 p.

Research output: Contribution to journalArticle

The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols

Martínez-García, P. J., Crepeau, M. W., Puiu, D., Gonzalez-Ibeas, D., Whalen, J., Stevens, K. A., Paul, R., Butterfield, T. S., Britton, M. T., Reagan, R. L., Chakraborty, S., Walawage, S. L., Vasquez-Gross, H. A., Cardeno, C., Famula, R. A., Pratt, K., Kuruganti, S., Aradhya, M. K., Leslie, C. A., Dandekar, A. M. & 4 others, Salzberg, S. L., Wegrzyn, J. L., Langley, C. H. & Neale, D. B., Sep 1 2016, In : Plant Journal. 87, 5, p. 507-532 26 p.

Research output: Contribution to journalArticle

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

Pertea, M., Kim, D., Pertea, G. M., Leek, J. T. & Salzberg, S. L., Sep 1 2016, In : Nature Protocols. 11, 9, p. 1650-1667 18 p.

Research output: Contribution to journalArticle

2015

Arioc: High-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

Wilton, R., Budavari, T., Langmead, B., Wheelan, S. J., Salzberg, S. L. & Szalay, A. S., Jan 1 2015, In : PeerJ. 2015, 3, e808.

Research output: Contribution to journalArticle

Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations

Deng, K., Pertea, M., Rongvaux, A., Wang, L., Durand, C. M., Ghiaur, G., Lai, J., McHugh, H. L., Hao, H., Zhang, H., Margolick, J. B., Gurer, C., Murphy, A. J., Valenzuela, D. M., Yancopoulos, G. D., Deeks, S. G., Strowig, T., Kumar, P., Siliciano, J. D., Salzberg, S. L. & 3 others, Flavell, R. A., Shan, L. & Siliciano, R. F., Jan 15 2015, In : Nature. 517, 7534, p. 381-385 5 p.

Research output: Contribution to journalArticle

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., Sep 1 2015, In : Genome research. 25, 9, p. 1401-1409 9 p.

Research output: Contribution to journalArticle

Genomic signatures of evolutionary transitions from solitary to group living

Kapheim, K. M., Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E. & 32 others, Kraus, F. B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. G., Nunes, F. M. F., Soares, M. P. M., Tanaka, É. D., Simões, Z. L. P., Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., Johnston, J. S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E. & Zhang, G., Jun 5 2015, In : Science. 348, 6239

Research output: Contribution to journalArticle

HISAT: A fast spliced aligner with low memory requirements

Kim, D., Langmead, B. & Salzberg, S. L., Mar 31 2015, In : Nature Methods. 12, 4, p. 357-360 4 p.

Research output: Contribution to journalArticle

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

Pertea, M., Pertea, G. M., Antonescu, C. M., Chang, T. C., Mendell, J. T. & Salzberg, S. L., Feb 2015, In : Nature biotechnology. 33, 3, p. 290-295 6 p.

Research output: Contribution to journalArticle

The genomes of two key bumblebee species with primitive eusocial organization

Sadd, B. M., Barribeau, S. M., Bloch, G., de Graaf, D. C., Dearden, P., Elsik, C. G., Gadau, J., Grimmelikhuijzen, C. J. P., Hasselmann, M., Lozier, J. D., Robertson, H. M., Smagghe, G., Stolle, E., Van Vaerenbergh, M., Waterhouse, R. M., Bornberg-Bauer, E., Klasberg, S., Bennett, A. K., Câmara, F., Guigó, R. & 124 others, Hoff, K., Mariotti, M., Munoz-Torres, M., Murphy, T., Santesmasses, D., Amdam, G. V., Beckers, M., Beye, M., Biewer, M., Bitondi, M. M. G., Blaxter, M. L., Bourke, A. F. G., Brown, M. J. F., Buechel, S. D., Cameron, R., Cappelle, K., Carolan, J. C., Christiaens, O., Ciborowski, K. L., Clarke, D. F., Colgan, T. J., Collins, D. H., Cridge, A. G., Dalmay, T., Dreier, S., du Plessis, L., Duncan, E., Erler, S., Evans, J., Falcon, T., Flores, K., Freitas, F. C. P., Fuchikawa, T., Gempe, T., Hartfelder, K., Hauser, F., Helbing, S., Humann, F. C., Irvine, F., Jermiin, L. S., Johnson, C. E., Johnson, R. M., Jones, A. K., Kadowaki, T., Kidner, J. H., Koch, V., Köhler, A., Kraus, F. B., Lattorff, H. M. G., Leask, M., Lockett, G. A., Mallon, E. B., Antonio, D. S. M., Marxer, M., Meeus, I., Moritz, R. F. A., Nair, A., Näpflin, K., Nissen, I., Niu, J., Nunes, F. M. F., Oakeshott, J. G., Osborne, A., Otte, M., Pinheiro, D. G., Rossié, N., Rueppell, O., Santos, C. G., Schmid-Hempel, R., Schmitt, B. D., Schulte, C., Simões, Z. L. P., Soares, M. P. M., Swevers, L., Winnebeck, E. C., Wolschin, F., Yu, N., Zdobnov, E. M., Aqrawi, P. K., Blankenburg, K. P., Coyle, M., Francisco, L., Hernandez, A. G., Holder, M., Hudson, M. E., Jackson, L. R., Jayaseelan, J., Joshi, V., Kovar, C., Lee, S. L., Mata, R., Mathew, T., Newsham, I. F., Ngo, R., Okwuonu, G., Pham, C., Pu, L. L., Saada, N., Santibanez, J., Simmons, D. N., Thornton, R., Venkat, A., Walden, K. K. O., Wu, Y. Q., Debyser, G., Devreese, B., Asher, C., Blommaert, J., Chipman, A. D., Chittka, L., Fouks, B., Liu, J., O'Neill, M. P., Sumner, S., Puiu, D., Qu, J., Salzberg, S. L., Scherer, S. E., Muzny, D. M., Richards, S., Robinson, G. E., Gibbs, R. A., Schmid-Hempel, P. & Worley, K. C., Apr 24 2015, In : Genome biology. 16, 1, 76.

Research output: Contribution to journalArticle

2014

A new rhesus macaque assembly and annotation for next-generation sequencing analyses

Zimin, A. V., Cornish, A. S., Maudhoo, M. D., Gibbs, R. M., Zhang, X., Pandey, S., Meehan, D. T., Wipfler, K., Bosinger, S. E., Johnson, Z. P., Tharp, G. K., Marçais, G., Roberts, M., Ferguson, B., Fox, H. S., Treangen, T., Salzberg, S. L., Yorke, J. A. & Norgren, R. B., Jan 1 2014, In : Biology direct. 9, 1, 1 p.

Research output: Contribution to journalArticle

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

Neale, D. B., Wegrzyn, J. L., Stevens, K. A., Zimin, A. V., Puiu, D., Crepeau, M. W., Cardeno, C., Koriabine, M., Holtz-Morris, A. E., Liechty, J. D., Martínez-García, P. J., Vasquez-Gross, H. A., Lin, B. Y., Zieve, J. J., Dougherty, W. M., Fuentes-Soriano, S., Wu, L. S., Gilbert, D., Marçais, G., Roberts, M. & 17 others, Holt, C., Yandell, M., Davis, J. M., Smith, K. E., Dean, J. F. D., Lorenz, W. W., Whetten, R. W., Sederoff, R., Wheeler, N., McGuire, P. E., Main, D., Loopstra, C. A., Mockaitis, K., deJong, P. J., Yorke, J. A., Salzberg, S. L. & Langley, C. H., Mar 4 2014, In : Genome biology. 15, 3, R59.

Research output: Contribution to journalArticle

DIAMUND: Direct comparison of genomes to detect mutations

Salzberg, S. L., Pertea, M., Fahrner, J. A. & Sobreira, N., Feb 20 2014, In : Human mutation. 35, 3, p. 283-288 6 p.

Research output: Contribution to journalArticle