Michael Schatz

Bloomberg Distinguished Professor

20042024

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  • 2024

    A common flanking variant is associated with enhanced stability of the FGF14-SCA27B repeat locus

    All of Us Research Program Long Read Working Group, Jul 2024, In: Nature genetics. 56, 7, p. 1366-1370 5 p.

    Research output: Contribution to journalArticlepeer-review

  • Convergent evolution of plant prickles by repeated gene co-option over deep time

    Satterlee, J. W., Alonso, D., Gramazio, P., Jenike, K. M., He, J., Arrones, A., Villanueva, G., Plazas, M., Ramakrishnan, S., Benoit, M., Gentile, I., Hendelman, A., Shohat, H., Fitzgerald, B., Robitaille, G. M., Green, Y., Swartwood, K., Passalacqua, M. J., Gagnon, E. & Hilgenhof, R. & 19 others, Huggins, T. D., Eizenga, G. C., Gur, A., Rutten, T., Stein, N., Yao, S., Poncet, A., Bellot, C., Frary, A., Knapp, S., Bendahmane, M., Särkinen, T., Gillis, J., Van Eck, J., Schatz, M. C., Eshed, Y., Prohens, J., Vilanova, S. & Lippman, Z. B., Aug 2 2024, In: Science (New York, N.Y.). 385, 6708, p. eado1663

    Research output: Contribution to journalArticlepeer-review

  • The complete sequence and comparative analysis of ape sex chromosomes

    Makova, K. D., Pickett, B. D., Harris, R. S., Hartley, G. A., Cechova, M., Pal, K., Nurk, S., Yoo, D. A., Li, Q., Hebbar, P., McGrath, B. C., Antonacci, F., Aubel, M., Biddanda, A., Borchers, M., Bornberg-Bauer, E., Bouffard, G. G., Brooks, S. Y., Carbone, L. & Carrel, L. & 64 others, Carroll, A., Chang, P. C., Chin, C. S., Cook, D. E., Craig, S. J. C., de Gennaro, L., Diekhans, M., Dutra, A., Garcia, G. H., Grady, P. G. S., Green, R. E., Haddad, D., Hallast, P., Harvey, W. T., Hickey, G., Hillis, D. A., Hoyt, S. J., Jeong, H., Kamali, K., Pond, S. L. K., LaPolice, T. M., Lee, C., Lewis, A. P., Loh, Y. H. E., Masterson, P., McGarvey, K. M., McCoy, R. C., Medvedev, P., Miga, K. H., Munson, K. M., Pak, E., Paten, B., Pinto, B. J., Potapova, T., Rhie, A., Rocha, J. L., Ryabov, F., Ryder, O. A., Sacco, S., Shafin, K., Shepelev, V. A., Slon, V., Solar, S. J., Storer, J. M., Sudmant, P. H., Sweetalana, Sweeten, A., Tassia, M. G., Thibaud-Nissen, F., Ventura, M., Wilson, M. A., Young, A. C., Zeng, H., Zhang, X., Szpiech, Z. A., Huber, C. D., Gerton, J. L., Yi, S. V., Schatz, M. C., Alexandrov, I. A., Koren, S., O’Neill, R. J., Eichler, E. E. & Phillippy, A. M., Jun 13 2024, In: Nature. 630, 8016, p. 401-411 11 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

    Abueg, L. A. L., Afgan, E., Allart, O., Awan, A. H., Bacon, W. A., Baker, D., Bassetti, M., Batut, B., Bernt, M., Blankenberg, D., Bombarely, A., Bretaudeau, A., Bromhead, C. J., Burke, M. L., Capon, P. K., Čech, M., Chavero-Díez, M., Chilton, J. M., Collins, T. J. & Coppens, F. & 110 others, Coraor, N., Cuccuru, G., Cumbo, F., Davis, J., De Geest, P. F., de Koning, W., Demko, M., DeSanto, A., Begines, J. M. D., Doyle, M. A., Droesbeke, B., Erxleben-Eggenhofer, A., Föll, M. C., Formenti, G., Fouilloux, A., Gangazhe, R., Genthon, T., Goecks, J., Gonzalez Beltran, A. N., Goonasekera, N. A., Goué, N., Griffin, T. J., Grüning, B. A., Guerler, A., Gundersen, S., Gustafsson, O. J. R., Hall, C., Harrop, T. W., Hecht, H., Heidari, A., Heisner, T., Heyl, F., Hiltemann, S., Hotz, H. R., Hyde, C. J., Jagtap, P. D., Jakiela, J., Johnson, J. E., Joshi, J., Jossé, M., Jum’ah, K., Kalaš, M., Kamieniecka, K., Kayikcioglu, T., Konkol, M., Kostrykin, L., Kucher, N., Kumar, A., Kuntz, M., Lariviere, D., Lazarus, R., Le Bras, Y., Le Corguillé, G., Lee, J., Leo, S., Liborio, L., Libouban, R., López Tabernero, D., Lopez-Delisle, L., Los, L. S., Mahmoud, A., Makunin, I., Marin, P., Mehta, S., Mok, W., Moreno, P. A., Morier-Genoud, F., Mosher, S., Müller, T., Nasr, E., Nekrutenko, A., Nelson, T. M., Oba, A. J., Ostrovsky, A., Polunina, P. V., Poterlowicz, K., Price, E. J., Price, G. R., Rasche, H., Raubenolt, B., Royaux, C., Sargent, L., Savage, M. T., Savchenko, V., Savchenko, D., Schatz, M. C., Seguineau, P., Serrano-Solano, B., Soranzo, N., Srikakulam, S. K., Suderman, K., Syme, A. E., Tangaro, M. A., Tedds, J. A., Tekman, M., Thang, W. C., Thanki, A. S., Uhl, M., van den Beek, M., Varshney, D., Vessio, J., Videm, P., Von Kuster, G., Watson, G. R., Whitaker-Allen, N., Winter, U., Wolstencroft, M., Zambelli, F., Zierep, P. & Zoabi, R., Jul 5 2024, In: Nucleic acids research. 52, W1, p. W83-W94

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Utility of long-read sequencing for All of Us

    Mahmoud, M., Huang, Y., Garimella, K., Audano, P. A., Wan, W., Prasad, N., Handsaker, R. E., Hall, S., Pionzio, A., Schatz, M. C., Talkowski, M. E., Eichler, E. E., Levy, S. E. & Sedlazeck, F. J., Dec 2024, In: Nature communications. 15, 1, 837.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • 2023

    Characterization of large-scale genomic differences in the first complete human genome

    Yang, X., Wang, X., Zou, Y., Zhang, S., Xia, M., Fu, L., Vollger, M. R., Chen, N. C., Taylor, D. J., Harvey, W. T., Logsdon, G. A., Meng, D., Shi, J., McCoy, R. C., Schatz, M. C., Li, W., Eichler, E. E., Lu, Q. & Mao, Y., Dec 2023, In: Genome biology. 24, 1, 157.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Concerning the eXclusion in human genomics: the choice of sex chromosome representation in the human genome drastically affects the number of identified variants

    Pinto, B. J., Connor, B. O., Schatz, M. C., Zarate, S. & Wilson, M. A., Oct 2023, In: G3: Genes, Genomes, Genetics. 13, 10, jkad169.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome

    He, J., Alonge, M., Ramakrishnan, S., Benoit, M., Soyk, S., Reem, N. T., Hendelman, A., Van Eck, J., Schatz, M. C. & Lippman, Z. B., Jan 2023, In: Plant Cell. 35, 1, p. 351-368 18 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Fast and accurate genome-wide predictions and structural modeling of protein–protein interactions using Galaxy

    Guerler, A., Baker, D., van den Beek, M., Gruening, B., Bouvier, D., Coraor, N., Shank, S. D., Zehr, J. D., Schatz, M. C. & Nekrutenko, A., Dec 2023, In: BMC Bioinformatics. 24, 1, 263.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet

    Devos, K. M., Qi, P., Bahri, B. A., Gimode, D. M., Jenike, K., Manthi, S. J., Lule, D., Lux, T., Martinez-Bello, L., Pendergast, T. H., Plott, C., Saha, D., Sidhu, G. S., Sreedasyam, A., Wang, X., Wang, H., Wright, H., Zhao, J., Deshpande, S. & de Villiers, S. & 12 others, Dida, M. M., Grimwood, J., Jenkins, J., Lovell, J., Mayer, K. F. X., Mneney, E. E., Ojulong, H. F., Schatz, M. C., Schmutz, J., Song, B., Tesfaye, K. & Odeny, D. A., Dec 2023, In: Nature communications. 14, 1, 3694.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Jasmine and Iris: population-scale structural variant comparison and analysis

    Kirsche, M., Prabhu, G., Sherman, R., Ni, B., Battle, A., Aganezov, S. & Schatz, M. C., Mar 2023, In: Nature Methods. 20, 3, p. 408-417 10 p.

    Research output: Contribution to journalArticlepeer-review

  • Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats

    Scheben, A., Mendivil Ramos, O., Kramer, M., Goodwin, S., Oppenheim, S., Becker, D. J., Schatz, M. C., Simmons, N. B., Siepel, A. & McCombie, W. R., Sep 1 2023, In: Genome biology and evolution. 15, 9, evad148.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Multicentre genetic diversity study of carbapenem-resistant Enterobacterales: predominance of untypeable pUVA-like blaKPC bearing plasmids

    Simner, P. J., Bergman, Y., Fan, Y., Jacobs, E. B., Ramakrishnan, S., Lu, J., Lewis, S., Hanlon, A., Tamma, P. D., Schatz, M. C., Timp, W. & Carroll, K. C., Jun 1 2023, In: JAC-Antimicrobial Resistance. 5, 3, dlad061.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • National Human Genome Research Institute Genomic Data Science Analysis, Visualization, and Informatics Lab-Space: Reaching out to Clinicians

    Hall, J. L., Honeycutt, S., Gonzalez, N., O'Donnell-Luria, A., Overby Taylor, C., Stevens, L., Philippakis, A. A. & Schatz, M. C., Jun 1 2023, In: Circulation: Cardiovascular Genetics. 16, 3, p. 275-276 2 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • 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 others, Garrison, 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 journalArticlepeer-review

    Open Access
  • The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

    Rozowsky, J., Gao, J., Borsari, B., Yang, Y. T., Galeev, T., Gürsoy, G., Epstein, C. B., Xiong, K., Xu, J., Li, T., Liu, J., Yu, K., Berthel, A., Chen, Z., Navarro, F., Sun, M. S., Wright, J., Chang, J., Cameron, C. J. F. & Shoresh, N. & 83 others, Gaskell, E., Drenkow, J., Adrian, J., Aganezov, S., Aguet, F., Balderrama-Gutierrez, G., Banskota, S., Corona, G. B., Chee, S., Chhetri, S. B., Cortez Martins, G. C., Danyko, C., Davis, C. A., Farid, D., Farrell, N. P., Gabdank, I., Gofin, Y., Gorkin, D. U., Gu, M., Hecht, V., Hitz, B. C., Issner, R., Jiang, Y., Kirsche, M., Kong, X., Lam, B. R., Li, S., Li, B., Li, X., Lin, K. Z., Luo, R., Mackiewicz, M., Meng, R., Moore, J. E., Mudge, J., Nelson, N., Nusbaum, C., Popov, I., Pratt, H. E., Qiu, Y., Ramakrishnan, S., Raymond, J., Salichos, L., Scavelli, A., Schreiber, J. M., Sedlazeck, F. J., See, L. H., Sherman, R. M., Shi, X., Shi, M., Sloan, C. A., Strattan, J. S., Tan, Z., Tanaka, F. Y., Vlasova, A., Wang, J., Werner, J., Williams, B., Xu, M., Yan, C., Yu, L., Zaleski, C., Zhang, J., Ardlie, K., Cherry, J. M., Mendenhall, E. M., Noble, W. S., Weng, Z., Levine, M. E., Dobin, A., Wold, B., Mortazavi, A., Ren, B., Gillis, J., Myers, R. M., Snyder, M. P., Choudhary, J., Milosavljevic, A., Schatz, M. C., Bernstein, B. E., Guigó, R., Gingeras, T. R. & Gerstein, M., Mar 30 2023, In: Cell. 186, 7, p. 1493-1511.e40

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • 2022

    A complete reference genome improves analysis of human genetic variation

    Aganezov, S., Yan, S. M., Soto, D. C., Kirsche, M., Zarate, S., Avdeyev, P., Taylor, D. J., Shafin, K., Shumate, A., Xiao, C., Wagner, J., McDaniel, J., Olson, N. D., Sauria, M. E. G., Vollger, M. R., Rhie, A., Meredith, M., Martin, S., Lee, J. & Koren, S. & 13 others, Rosenfeld, J. A., Paten, B., Layer, R., Chin, C. S., Sedlazeck, F. J., Hansen, N. F., Miller, D. E., Phillippy, A. M., Miga, K. H., McCoy, R. C., Dennis, M. Y., Zook, J. M. & Schatz, M. C., Apr 1 2022, In: Science. 376, 6588, eabl3533.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing

    Alonge, M., Lebeigle, L., Kirsche, M., Jenike, K., Ou, S., Aganezov, S., Wang, X., Lippman, Z. B., Schatz, M. C. & Soyk, S., Dec 2022, In: Genome biology. 23, 1, 258.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Benchmarking challenging small variants with linked and long reads

    Wagner, J., Olson, N. D., Harris, L., Khan, Z., Farek, J., Mahmoud, M., Stankovic, A., Kovacevic, V., Yoo, B., Miller, N., Rosenfeld, J. A., Ni, B., Zarate, S., Kirsche, M., Aganezov, S., Schatz, M. C., Narzisi, G., Byrska-Bishop, M., Clarke, W. & Evani, U. S. & 21 others, Markello, C., Shafin, K., Zhou, X., Sidow, A., Bansal, V., Ebert, P., Marschall, T., Lansdorp, P., Hanlon, V., Mattsson, C. A., Barrio, A. M., Fiddes, I. T., Xiao, C., Fungtammasan, A., Chin, C. S., Wenger, A. M., Rowell, W. J., Sedlazeck, F. J., Carroll, A., Salit, M. & Zook, J. M., May 11 2022, In: Cell Genomics. 2, 5, 100128.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Complete genomic and epigenetic maps of human centromeres

    Altemose, N., Logsdon, G. A., Bzikadze, A. V., Sidhwani, P., Langley, S. A., Caldas, G. V., Hoyt, S. J., Uralsky, L., Ryabov, F. D., Shew, C. J., Sauria, M. E. G., Borchers, M., Gershman, A., Mikheenko, A., Shepelev, V. A., Dvorkina, T., Kunyavskaya, O., Vollger, M. R., Rhie, A. & McCartney, A. M. & 39 others, Asri, M., Lorig-Roach, R., Shafin, K., Lucas, J. K., Aganezov, S., Olson, D., de Lima, L. G., Potapova, T., Hartley, G. A., Haukness, M., Kerpedjiev, P., Gusev, F., Tigyi, K., Brooks, S., Young, A., Nurk, S., Koren, S., Salama, S. R., Paten, B., Rogaev, E. I., Streets, A., Karpen, G. H., Dernburg, A. F., Sullivan, B. A., Straight, A. F., Wheeler, T. J., Gerton, J. L., Eichler, E. E., Phillippy, A. M., Timp, W., Dennis, M. Y., O'Neill, R. J., Zook, J. M., Schatz, M. C., Pevzner, P. A., Diekhans, M., Langley, C. H., Alexandrov, I. A. & Miga, K. H., Apr 1 2022, In: Science. 376, 6588, eabl4178.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome

    Fields, P. D., Waneka, G., Naish, M., Schatz, M. C., Henderson, I. R. & Sloan, D. B., May 1 2022, In: Genome biology and evolution. 14, 5, evac059.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Diversifying the genomic data science research community

    The Genomic Data Science Community Network, Jul 2022, In: Genome research. 32, 8, p. 1231-1241 11 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Epigenetic patterns in a complete human genome

    Gershman, A., Sauria, M. E. G., Guitart, X., Vollger, M. R., Hook, P. W., Hoyt, S. J., Jain, M., Shumate, A., Razaghi, R., Koren, S., Altemose, N., Caldas, G. V., Logsdon, G. A., Rhie, A., Eichler, E. E., Schatz, M. C., O'Neill, R. J., Phillippy, A. M., Miga, K. H. & Timp, W., Apr 1 2022, In: Science. 376, 6588, eabj5089.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

    Hoyt, S. J., Storer, J. M., Hartley, G. A., Grady, P. G. S., Gershman, A., de Lima, L. G., Limouse, C., Halabian, R., Wojenski, L., Rodriguez, M., Altemose, N., Rhie, A., Core, L. J., Gerton, J. L., Makalowski, W., Olson, D., Rosen, J., Smit, A. F. A., Straight, A. F. & Vollger, M. R. & 7 others, Wheeler, T. J., Schatz, M. C., Eichler, E. E., Phillippy, A. M., Timp, W., Miga, K. H. & O'Neill, R. J., Apr 1 2022, In: Science. 376, 6588, eabk3112.

    Research output: Contribution to journalArticlepeer-review

  • Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes

    CRyPTIC consortium, Dec 2022, In: Genome biology. 23, 1, 147.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Same-Cell Co-Occurrence of RAS Hotspot and BRAF V600E Mutations in Treatment-Naive Colorectal Cancer

    Gularte-Mérida, R., Smith, S., Bowman, A. S., da Cruz Paula, A., Chatila, W., Bielski, C. M., Vyas, M., Borsu, L., Zehir, A., Martelotto, L. G., Shia, J., Yaeger, R., Fang, F., Gardner, R., Luo, R., Schatz, M. C., Shen, R., Weigelt, B., Sánchez-Vega, F. & Reis-Filho, J. S. & 1 others, Hechtman, J. F., 2022, In: JCO Precision Oncology. 6, e2100365.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • 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 journalArticlepeer-review

    Open Access
  • Sketching and sampling approaches for fast and accurate long read classification

    Das, A. & Schatz, M. C., Dec 2022, In: BMC Bioinformatics. 23, 1, 452.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • 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 others, Chen, 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 journalArticlepeer-review

    Open Access
  • The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

    Afgan, E., Nekrutenko, A., Grüning, B. A., Blankenberg, D., Goecks, J., Schatz, M. C., Ostrovsky, A. E., Mahmoud, A., Lonie, A. J., Syme, A., Fouilloux, A., Bretaudeau, A., Kumar, A., Eschenlauer, A. C., Desanto, A. D., Guerler, A., Serrano-Solano, B., Batut, B., Grüning, B. A. & Langhorst, B. W. & 84 others, Carr, B., Raubenolt, B. A., Hyde, C. J., Bromhead, C. J., Barnett, C. B., Royaux, C., Gallardo, C., Blankenberg, D., Fornika, D. J., Baker, D., Bouvier, D., Clements, D., De Lima Morais, D. A., Tabernero, D. L., Lariviere, D., Nasr, E., Afgan, E., Zambelli, F., Heyl, F., Psomopoulos, F., Coppens, F., Price, G. R., Cuccuru, G., Corguillé, G. L., Von Kuster, G., Akbulut, G. G., Rasche, H., Hans-Rudolf, H., Eguinoa, I., Makunin, I., Ranawaka, I. J., Taylor, J. P., Joshi, J., Hillman-Jackson, J., Chilton, J. M., Kamali, K., Suderman, K., Poterlowicz, K., Yvan, L. B., Lopez-Delisle, L., Sargent, L., Bassetti, M. E., Tangaro, M. A., Van Den Beek, M., Cech, M., Bernt, M., Fahrner, M., Tekman, M., Föll, M. C., Schatz, M. C., Crusoe, M. R., Roncoroni, M., Kucher, N., Coraor, N., Stoler, N., Rhodes, N., Soranzo, N., Pinter, N., Goonasekera, N. A., Moreno, P. A., Videm, P., Melanie, P., Mandreoli, P., Jagtap, P. D., Gu, Q., Weber, R. J. M., Lazarus, R., Vorderman, R. H. P., Hiltemann, S., Golitsynskiy, S., Garg, S., Bray, S. A., Gladman, S. L., Leo, S., Mehta, S. P., Griffin, T. J., Jalili, V., Yves, V., Wen, V., Nagampalli, V. K., Bacon, W. A., De Koning, W., Maier, W. & Briggs, P. J., Jul 5 2022, In: Nucleic acids research. 50, W1, p. W345-W351

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • 2021

    An anchored chromosome-scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids

    Hulse-Kemp, A. M., Bostan, H., Chen, S., Ashrafi, H., Stoffel, K., Sanseverino, W., Li, L., Cheng, S., Schatz, M. C., Garvin, T., du Toit, L. J., Tseng, E., Chin, J., Iorizzo, M. & Van Deynze, A., Jul 2021, In: Plant Genome. 14, 2, e20101.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • A plasmid locus associated with Klebsiella clinical infections encodes a microbiomedependent gut fitness factor

    Vornhagen, J., Bassis, C. M., Ramakrishnan, S., Hein, R., Mason, S., Bergman, Y., Sunshine, N., Fan, Y., Holmes, C. L., Timp, W., Schatz, M. C., Young, V. B., Simner, P. J. & Bachman, M. A., Apr 30 2021, In: PLoS pathogens. 17, 4, e1009537.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Cell wall protein variation, break-induced replication, and subtelomere dynamics in Candida glabrata

    Xu, Z., Green, B., Benoit, N., Sobel, J. D., Schatz, M. C., Wheelan, S. & Cormack, B. P., Jul 2021, In: Molecular Microbiology. 116, 1, p. 260-276 17 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Democratizing long-read genome assembly

    Kirsche, M. & Schatz, M. C., Oct 20 2021, In: Cell Systems. 12, 10, p. 945-947 3 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore-Washington metropolitan area

    Thielen, P. M., Wohl, S., Mehoke, T., Ramakrishnan, S., Kirsche, M., Falade-Nwulia, O., Trovão, N. S., Ernlund, A., Howser, C., Sadowski, N., Morris, C. P., Hopkins, M., Schwartz, M., Fan, Y., Gniazdowski, V., Lessler, J., Sauer, L., Schatz, M. C., Evans, J. D. & Ray, S. C. & 2 others, Timp, W. & Mostafa, H. H., Mar 22 2021, In: JCI Insight. 6, 6, e144350.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • High resolution copy number inference in cancer using short-molecule nanopore sequencing

    Baslan, T., Kovaka, S., Sedlazeck, F. J., Zhang, Y., Wappel, R., Tian, S., Lowe, S. W., Goodwin, S. & Schatz, M. C., Dec 2 2021, In: Nucleic acids research. 49, 21, gkab812.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • IGenomics: Comprehensive DNA sequence analysis on your Smartphone

    Palatnick, A., Zhou, B., Ghedin, E. & Schatz, M. C., Dec 1 2021, In: GigaScience. 9, 12, giaa138.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Local adaptation and archaic introgression shape global diversity at human structural variant loci

    Yan, S. M., Sherman, R. M., Taylor, D. J., Nair, D. R., Bortvin, A. N., Schatz, M. C. & McCoy, R. C., Sep 2021, In: eLife. 10, e67615.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Natural Genetic Diversity in Tomato Flavor Genes

    Pereira, L., Sapkota, M., Alonge, M., Zheng, Y., Zhang, Y., Razifard, H., Taitano, N. K., Schatz, M. C., Fernie, A. R., Wang, Y., Fei, Z., Caicedo, A. L., Tieman, D. M. & van der Knaap, E., Jun 4 2021, In: Frontiers in Plant Science. 12, 642828.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Optimized sample selection for cost-efficient long-read population sequencing

    Ranallo-Benavidez, T. R., Lemmon, Z., Soyk, S., Aganezov, S., Salerno, W. J., McCoy, R. C., Lippman, Z. B., Schatz, M. C. & Sedlazeck, F. J., 2021, In: Genome research. 31, 5, p. 910-918 9 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Pan-genomic matching statistics for targeted nanopore sequencing

    Ahmed, O., Rossi, M., Kovaka, S., Schatz, M. C., Gagie, T., Boucher, C. & Langmead, B., Jun 25 2021, In: iScience. 24, 6, 102696.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Parliament2: Accurate structural variant calling at scale

    Zarate, S., Carroll, A., Mahmoud, M., Krasheninina, O., Jun, G., Salerno, W. J., Schatz, M. C., Boerwinkle, E., Gibbs, R. A. & Sedlazeck, F. J., Dec 1 2021, In: GigaScience. 9, 12, giaa145.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Ribbon: intuitive visualization for complex genomic variation

    Nattestad, M., Aboukhalil, R., Chin, C. S. & Schatz, M. C., Feb 1 2021, In: Bioinformatics. 37, 3, p. 413-415 3 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Sapling: Accelerating suffix array queries with learned data models

    Kirsche, M., Das, A. & Schatz, M. C., Mar 15 2021, In: Bioinformatics. 37, 6, p. 744-749 6 p.

    Research output: Contribution to journalArticlepeer-review

  • Snpc-1.3 is a sex-specific transcription factor that drives male pirna expression in c. elegans

    Choi, C. P., Tay, R. J., Starostik, M. R., Feng, S., Moresco, J. J., Montgomery, B. E., Xu, E., Hammonds, M. A., Schatz, M. C., Montgomery, T. A., Yates, J. R., Jacobsen, S. E. & Kim, J. K., Feb 2021, In: eLife. 10, p. 1-35 35 p., e60681.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED

    Kovaka, S., Fan, Y., Ni, B., Timp, W. & Schatz, M. C., Apr 2021, In: Nature biotechnology. 39, 4, p. 431-441 11 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • The genetic and epigenetic landscape of the Arabidopsis centromeres

    Naish, M., Alonge, M., Wlodzimierz, P., Tock, A. J., Abramson, B. W., Schmücker, A., Mandáková, T., Jamge, B., Lambing, C., Kuo, P., Yelina, N., Hartwick, N., Colt, K., Smith, L. M., Ton, J., Kakutani, T., Martienssen, R. A., Schneeberger, K., Lysak, M. A. & Berger, F. & 4 others, Bousios, A., Michael, T. P., Schatz, M. C. & Henderson, I. R., Nov 12 2021, In: Science. 374, 6569, eabi7489.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • The genomic basis of evolutionary differentiation among honey bees

    Fouks, B., Brand, P., Nguyen, H. N., Herman, J., Camara, F., Ence, D., Hagen, D. E., Hoff, K. J., Nachweide, S., Romoth, L., Walden, K. K. O., Guigo, R., Stanke, M., Narzisi, G., Yandell, M., Robertson, H. M., Koeniger, N., Chantawannakul, P., Schatz, M. C. & Worley, K. C. & 3 others, Robinson, G. E., Elsik, C. G. & Rueppell, O., Jul 2021, In: Genome research. 31, 7, p. 1203-1215 13 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • The human origin recognition complex is essential for pre-rc assembly, mitosis, and maintenance of nuclear structure

    Chou, H. C., Bhalla, K., Demerdesh, O. E. L., Klingbeil, O., Hanington, K., Aganezov, S., Andrews, P., Alsudani, H., Chang, K., Vakoc, C. R., Schatz, M. C., McCombie, W. R. & Stillman, B., Feb 2021, In: eLife. 10, p. 1-39 39 p., e61797.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Using Galaxy to Perform Large-Scale Interactive Data Analyses—An Update

    the Galaxy Team, Feb 2021, In: Current Protocols. 1, 2, e31.

    Research output: Contribution to journalArticlepeer-review

    Open Access