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Miller, J. R., Zhou, P., Mudge, J., Gurtowski, J., Lee, H., Ramaraj, T., Walenz, B. P., Liu, J., Stupar, R. M., Denny, R., Song, L., Singh, N., Maron, L. G., McCouch, S. R., McCombie, W. R., Schatz, M. C., Tiffin, P., Young, N. D., Silverstein, K. A. T. (2017) Hybrid assembly with long and short reads improves discovery of gene family expansions. BMC Genomics, 18 (1). p. 541. ISSN 1471-2164

Feigin, M. E., Garvin, T., Bailey, P., Waddell, N., Chang, D. K., Kelley, D. R., Shuai, S., Gallinger, S., McPherson, J. D., Grimmond, S. M., Khurana, E., Stein, L. D., Biankin, A. V., Schatz, M. C., Tuveson, D. A. (2017) Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma. Nat Genet, 49 (6). pp. 825-833. ISSN 1061-4036

Schatz, M. C. (2017) Nanopore sequencing meets epigenetics. Nat Methods, 14 (4). pp. 347-348. ISSN 1548-7091

Vurture, G. W., Sedlazeck, F. J., Nattestad, M., Underwood, C. J., Fang, H., Gurtowski, J., Schatz, M. C. (2017) GenomeScope: Fast reference-free genome profiling from short reads. Bioinformatics. ISSN 1367-4803

Heath, L. S., Bravo, H. C., Caccamo, M., Schatz, M. (2017) Bioinformatics of DNA. Proceedings of the Ieee, 105 (3). pp. 419-421. ISSN 0018-9219

Pal, D., Pertot, A., Shirole, N. H., Yao, Z., Anaparthy, N., Garvin, T., Cox, H., Chang, K., Rollins, F., Kendall, J., Edwards, L., Singh, V. A., Stone, G. C., Schatz, M. C., Hicks, J., Hannon, G., Sordella, R. (2017) TGF-beta reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24- cancer cells. Elife, 6. ISSN 2050-084X (Electronic)2050-084X (Linking)

Fang, H., Bergmann, E. A., Arora, K., Vacic, V., Zody, M. C., Iossifov, I., O'Rawe, J. A., Wu, Y., Jimenez Barron, L. T., Rosenbaum, J., Ronemus, M., Lee, Y. H., Wang, Z., Dikoglu, E., Jobanputra, V., Lyon, G. J., Wigler, M., Schatz, M. C., Narzisi, G. (2016) Indel variant analysis of short-read sequencing data with Scalpel. Nat Protoc, 11 (12). pp. 2529-2548. ISSN 1750-2799 (Electronic)1750-2799 (Linking)

Chin, C. S., Peluso, P., Sedlazeck, F. J., Nattestad, M., Concepcion, G. T., Clum, A., Dunn, C., O'Malley, R., Figueroa-Balderas, R., Morales-Cruz, A., Cramer, G. R., Delledonne, M., Luo, C., Ecker, J. R., Cantu, D., Rank, D. R., Schatz, M. C. (2016) Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods, 13 (12). pp. 1050-1054. ISSN 1548-7105 (Electronic)1548-7091 (Linking)

Lemmon, Z. H., Park, S. J., Jiang, K., Van Eck, J., Schatz, M. C., Lippman, Z. B. (2016) The evolution of inflorescence diversity in the nightshades and heterochrony during meristem maturation. Genome Res, 26 (12). pp. 1676-1686. ISSN 1549-5469 (Electronic)1088-9051 (Linking)

Nattestad, M., Schatz, M. C. (2016) Assemblytics: a web analytics tool for the detection of variants from an assembly. Bioinformatics, 32 (19). pp. 3021-3023. ISSN 1367-4811 (Electronic)1367-4803 (Linking)

Amin, M. R., Skiena, S., Schatz, M. C. (2016) NanoBLASTer: Fast alignment and characterization of Oxford Nanopore single molecule sequencing reads. 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS).

Vembar, S. S., Seetin, M., Lambert, C., Nattestad, M., Schatz, M. C., Baybayan, P., Scherf, A., Smith, M. L. (2016) Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing. DNA Res, 23 (4). pp. 339-351. ISSN 1756-1663 (Electronic)1340-2838 (Linking)

Bombarely, A., Moser, M., Amrad, A., Bao, M., Bapaume, L., Barry, C. S., Bliek, M., Boersma, M. R., Borghi, L., Bruggmann, R., Bucher, M., D'Agostino, N., Davies, K., Druege, U., Dudareva, N., Egea-Cortines, M., Delledonne, M., Fernandez-Pozo, N., Franken, P., Grandont, L., Heslop-Harrison, J. S., Hintzsche, J., Johns, M., Koes, R., Lv, X., Lyons, E., Malla, D., Martinoia, E., Mattson, N. S., Morel, P., Mueller, L. A., Muhlemann, J., Nouri, E., Passeri, V., Pezzotti, M., Qi, Q., Reinhardt, D., Rich, M., Richert-Poggeler, K. R., Robbins, T. P., Schatz, M. C., Schranz, M. E., Schuurink, R. C., Schwarzacher, T., Spelt, K., Tang, H., Urbanus, S. L., Vandenbussche, M., Vijverberg, K., Villarino, G. H., Warner, R. M., Weiss, J., Yue, Z., Zethof, J., Quattrocchio, F., Sims, T. L., Kuhlemeier, C. (2016) Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. Nat Plants, 2 (6). p. 16074. ISSN 2055-0278 (Electronic)2055-0278 (Linking)

Vij, S., Kuhl, H., Kuznetsova, I. S., Komissarov, A., Yurchenko, A. A., Van Heusden, P., Singh, S., Thevasagayam, N. M., Prakki, S. R., Purushothaman, K., Saju, J. M., Jiang, J., Mbandi, S. K., Jonas, M., Hin Yan Tong, A., Mwangi, S., Lau, D., Ngoh, S. Y., Liew, W. C., Shen, X., Hon, L. S., Drake, J. P., Boitano, M., Hall, R., Chin, C. S., Lachumanan, R., Korlach, J., Trifonov, V., Kabilov, M., Tupikin, A., Green, D., Moxon, S., Garvin, T., Sedlazeck, F. J., Vurture, G. W., Gopalapillai, G., Kumar Katneni, V., Noble, T. H., Scaria, V., Sivasubbu, S., Jerry, D. R., O'Brien, S. J., Schatz, M. C., Dalmay, T., Turner, S. W., Lok, S., Christoffels, A., Orban, L. (2016) Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genet, 12 (4). e1005954. ISSN 1553-7404 (Electronic)1553-7390 (Linking)

Rosenfeld, J. A., Reeves, D., Brugler, M. R., Narechania, A., Simon, S., Durrett, R., Foox, J., Shianna, K., Schatz, M. C., Gandara, J., Afshinnekoo, E., Lam, E. T., Hastie, A. R., Chan, S., Cao, H., Saghbini, M., Kentsis, A., Planet, P. J., Kholodovych, V., Tessler, M., Baker, R., DeSalle, R., Sorkin, L. N., Kolokotronis, S. O., Siddall, M. E., Amato, G., Mason, C. E. (2016) Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius. Nat Commun, 7. p. 10164. ISSN 2041-1723 (Electronic)2041-1723 (Linking)

Ming, R., VanBuren, R., Wai, C. M., Tang, H., Schatz, M. C., Bowers, J. E., Lyons, E., Wang, M. L., Chen, J., Biggers, E., Zhang, J., Huang, L., Zhang, L., Miao, W., Zhang, J., Ye, Z., Miao, C., Lin, Z., Wang, H., Zhou, H., Yim, W. C., Priest, H. D., Zheng, C., Woodhouse, M., Edger, P. P., Guyot, R., Guo, H. B., Guo, H., Zheng, G., Singh, R., Sharma, A., Min, X., Zheng, Y., Lee, H., Gurtowski, J., Sedlazeck, F. J., Harkess, A., McKain, M. R., Liao, Z., Fang, J., Liu, J., Zhang, X., Zhang, Q., Hu, W., Qin, Y., Wang, K., Chen, L. Y., Shirley, N., Lin, Y. R., Liu, L. Y., Hernandez, A. G., Wright, C. L., Bulone, V., Tuskan, G. A., Heath, K., Zee, F., Moore, P. H., Sunkar, R., Leebens-Mack, J. H., Mockler, T., Bennetzen, J. L., Freeling, M., Sankoff, D., Paterson, A. H., Zhu, X., Yang, X., Smith, J. A., Cushman, J. C., Paull, R. E., Yu, Q. (2015) The pineapple genome and the evolution of CAM photosynthesis. Nat Genet, 47. pp. 1435-1442. ISSN 1546-1718 (Electronic)1061-4036 (Linking)

Zhou, X., Battistoni, G., El Demerdash, O., Gurtowski, J., Wunderer, J., Falciatori, I., Ladurner, P., Schatz, M. C., Hannon, G. J., Wasik, K. A. (2015) Dual functions of Macpiwi1 in transposon silencing and stem cell maintenance in the flatworm Macrostomum lignano. RNA, 21 (11). pp. 1885-1897. ISSN 1469-9001 (Electronic)1355-8382 (Linking)

Garvin, T., Aboukhalil, R., Kendall, J., Baslan, T., Atwal, G. S., Hicks, J., Wigler, M., Schatz, M. C. (2015) Interactive analysis and assessment of single-cell copy-number variations. Nat Methods, 12. pp. 1058-1060. ISSN 1548-7105 (Electronic)1548-7091 (Linking)

Goodwin, S., Gurtowski, J., Ethe-Sayers, S., Deshpande, P., Schatz, M. C., McCombie, W. R. (2015) Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Res, 25 (11). pp. 1750-1756. ISSN 1088-9051

Smolka, M., Rescheneder, P., Schatz, M. C., von Haeseler, A., Sedlazeck, F. J. (2015) Teaser: Individualized benchmarking and optimization of read mapping results for NGS data. Genome Biol, 16 (1). p. 235. ISSN 1474-760X (Electronic)1474-7596 (Linking)

Tscherner, M., Zwolanek, F., Jenull, S., Sedlazeck, F. J., Petryshyn, A., Frohner, I. E., Mavrianos, J., Chauhan, N., von Haeseler, A., Kuchler, K. (2015) The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways. PLoS Pathog, 11 (10). e1005218. ISSN 1553-7374 (Electronic)1553-7366 (Linking)

Schatz, M. C. (2015) Biological data sciences in genome research. Genome Res, 25 (10). pp. 1417-22. ISSN 1549-5469 (Electronic)1088-9051 (Linking)

Wences, A. H., Schatz, M. C. (2015) Metassembler: merging and optimizing de novo genome assemblies. Genome Biol, 16 (1). p. 207. ISSN 1474-760X (Electronic)1474-7596 (Linking)

Cheng, J., Sedlazek, F., Altmuller, J., Nolte, A. W. (2015) Ectodysplasin signalling genes and phenotypic evolution in sculpins (Cottus). Proc Biol Sci, 282 (1815). ISSN 1471-2954 (Electronic)0962-8452 (Linking)

Wasik, K., Gurtowski, J., Zhou, X., Ramos, O. M., Delas, M. J., Battistoni, G., El Demerdash, O., Falciatori, I., Vizoso, D. B., Smith, A. D., Ladurner, P., Scharer, L., McCombie, W. R., Hannon, G. J., Schatz, M. (2015) Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano. Proc Natl Acad Sci U S A, 112 (40). pp. 12462-12467. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Al-Jouie, A., Esfandiari, M., Ramakrishnan, S., Roshan, U. (2015) Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test. BMC Res Notes, 8. p. 436. ISSN 1756-0500 (Electronic)1756-0500 (Linking)

Stephens, Z. D., Lee, S. Y., Faghri, F., Campbell, R. H., Zhai, C., Efron, M. J., Iyer, R., Schatz, M. C., Sinha, S., Robinson, G. E. (2015) Big Data: Astronomical or Genomical? PLoS Biol, 13 (7). e1002195. ISSN 1545-7885 (Electronic)1544-9173 (Linking)

MacColl, Elisabeth, Therkelsen, Matthew D., Sherpa, Tshering, Ellerbrock, Hannah, Johnston, Lily A., Jariwala, Ravi, Chang, WeiShu, Gurtowski, James, Schatz, Michael C., Mozammal Hossain, M., Cassidy-Hanley, Donna M., Clark, Theodore G., Chang, Wei-Jen (2015) Molecular Genetic Diversity and Characterization of Conjugation Genes in the Fish Parasite Ichthyophthirius multifiliis. Molecular Phylogenetics and Evolution, 86. pp. 1-7. ISSN 1055-7903

Garvin, Tyler, Aboukhalil, Robert, Kendall, Jude, Baslan, Timour, Atwal, Gurinder S, Hicks, James, Wigler, Michael, Schatz, Michael (2015) Interactive analysis and quality assessment of single-cell copy-number variations. Nature Methods, 12. pp. 1058-1060. ISSN 15487091 (ISSN)

Narzisi, G., Schatz, M. C. (2015) The challenge of small-scale repeats for indel discovery. Front Bioeng Biotechnol, 3. p. 8. ISSN 2296-4185

Schatz, M. C., Maron, L. G., Stein, J. C., Hernandez Wences, A., Gurtowski, J., Biggers, E., Lee, H., Kramer, M., Antoniou, E., Ghiban, E., Wright, M. H., Chia, J. M., Ware, D., McCouch, S. R., McCombie, W. R. (2014) Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol, 15 (11). p. 506. ISSN 1465-6906

Iossifov, I., O'Roak, B. J., Sanders, S. J., Ronemus, M., Krumm, N., Levy, D., Stessman, H. A., Witherspoon, K. T., Vives, L., Patterson, K. E., Smith, J. D., Paeper, B., Nickerson, D. A., Dea, J., Dong, S., Gonzalez, L. E., Mandell, J. D., Mane, S. M., Murtha, M. T., Sullivan, C. A., Walker, M. F., Waqar, Z., Wei, L., Willsey, A. J., Yamrom, B., Lee, Y. H., Grabowska, E., Dalkic, E., Wang, Z., Marks, S., Andrews, P., Leotta, A., Kendall, J., Hakker, I., Rosenbaum, J., Ma, B., Rodgers, L., Troge, J., Narzisi, G., Yoon, S., Schatz, M. C., Ye, K., McCombie, W. R., Shendure, J., Eichler, E. E., State, M. W., Wigler, M. (2014) The contribution of de novo coding mutations to autism spectrum disorder. Nature, 515 (7526). pp. 216-221. ISSN 0028-0836

Marcus, S., Lee, H., Schatz, M. C. (2014) SplitMEM: A graphical algorithm for pan-genome analysis with suffix skips. Bioinformatics, 30 (24). pp. 3476-3483. ISSN 1367-4803

Narzisi, G., O'Rawe, Jason, Iossifov, I., Fang, Han, Lee, Y. H., Wang, Zihua, Wu, Yiyang, Lyon, Gholson J., Wigler, M. H., Schatz, M. C. (2014) Accurate de novo and transmitted indel detection in exome-capture data using microassembly. Nature Methods, 11 (10). pp. 1033-1036.

Blood, P. D., Marcus, S., Schatz, M. C. (2014) Large-scale sequencing and assembly of cereal genomes using blacklight. Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment. Article number 20.

Ganapathy, G., Howard, J. T., Ward, J. M., Li, J., Li, B., Li, Y., Xiong, Y., Zhang, Y., Zhou, S., Schwartz, D. C., Schatz, M., Aboukhalil, R., Fedrigo, O., Bukovnik, L., Wang, T., Wray, G., Rasolonjatovo, I., Winer, R., Knight, J. R., Koren, S., Warren, W. C., Zhang, G., Phillippy, A. M., Jarvis, E. D. (2014) High-coverage sequencing and annotated assemblies of the budgerigar genome. Gigascience, 3. p. 11. ISSN 2047-217x

Titmus, M. A., Gurtowski, J., Schatz, M. C. (2014) Answering the demands of digital genomics. Concurrency Computation Practice and Experience, 26 (4). pp. 917-928. ISSN 15320626

Fang, Han, Wu, Yiyang, Narzisi, G., O'Rawe, Jason, Jimenez Barron, Laura, Rosenbaum, J., Ronemus, M., Iossifov, I., Schatz, M. C., Lyon, Gholson J. (2014) Reducing INDEL calling errors in whole genome and exome sequencing data. Genome Med, 6 (10). p. 89.

Saw, J. H. W., Schatz, M., Brown, M. V., Kunkel, D. D., Foster, J. S., Shick, H., Christensen, S., Hou, S., Wan, X., Donachie, S. P. (2013) Cultivation and Complete Genome Sequencing of Gloeobacter kilaueensis sp. nov., from a Lava Cave in Kīlauea Caldera, Hawai'i. PLoS ONE, 8 (10). ISSN 19326203 (ISSN)

Schatz, M. C., Taylor, J., Schelhorn, S. E. (2013) The DNA60IFX contest. Genome Biol, 14 (6). p. 124. ISSN 1465-6914 (Electronic)1465-6906 (Linking)

Doolittle, W. F., Fraser, P., Gerstein, M. B., Graveley, B. R., Henikoff, S., Huttenhower, C., Oshlack, A., Ponting, C. P., Rinn, J. L., Schatz, M. C., Ule, J., Weigel, D., Weinstock, G. M. (2013) Sixty years of genome biology. Genome Biology, 14 (4). ISSN 1474-7596

Maron, L. G., Guimaraes, C. T., Kirst, M., Albert, P. S., Birchler, J. A., Bradbury, P. J., Buckler, E. S., Coluccio, A. E., Danilova, T. V., Kudrna, D., Magalhaes, J. V., Pineros, M. A., Schatz, M. C., Wing, R. A., Kochian, L. V. (2013) Aluminum tolerance in maize is associated with higher MATE1 gene copy number. Proceedings of the National Academy of Sciences of the United States of America, 110 (13). pp. 5241-5246. ISSN 0027-8424

Schatz, M. C., Phillippy, A. M., Sommer, D. D., Delcher, A. L., Puiu, D., Narzisi, G., Salzberg, S. L., Pop, M. (2013) Hawkeye and AMOS: Visualizing and assessing the quality of genome assemblies. Briefings in Bioinformatics, 14 (2). pp. 213-224. ISSN 14675463

Bradnam, K. R., Fass, J. N., Alexandrov, A., Baranay, P., Bechner, M., Birol, I., Boisvert, S., Chapman, J. A., Chapuis, G., Chikhi, R., Chitsaz, H., Chou, W. C., Corbeil, J., Del Fabbro, C., Docking, T. R., Durbin, R., Earl, D., Emrich, S., Fedotov, P., Fonseca, N. A., Ganapathy, G., Gibbs, R. A., Gnerre, S., Godzaridis, E., Goldstein, S., Haimel, M., Hall, G., Haussler, D., Hiatt, J. B., Ho, I. Y., Howard, J., Hunt, M., Jackman, S. D., Jaffe, D. B., Jarvis, E. D., Jiang, H., Kazakov, S., Kersey, P. J., Kitzman, J. O., Knight, J. R., Koren, S., Lam, T. W., Lavenier, D., Laviolette, F., Li, Y., Li, Z., Liu, B., Liu, Y., Luo, R., Maccallum, I., Macmanes, M. D., Maillet, N., Melnikov, S., Naquin, D., Ning, Z., Otto, T. D., Paten, B., Paulo, O. S., Phillippy, A. M., Pina-Martins, F., Place, M., Przybylski, D., Qin, X., Qu, C., Ribeiro, F. J., Richards, S., Rokhsar, D. S., Ruby, J. G., Scalabrin, S., Schatz, M. C., Schwartz, D. C., Sergushichev, A., Sharpe, T., Shaw, T. I., Shendure, J., Shi, Y., Simpson, J. T., Song, H., Tsarev, F., Vezzi, F., Vicedomini, R., Vieira, B. M., Wang, J., Worley, K. C., Yin, S., Yiu, S. M., Yuan, J., Zhang, G., Zhang, H., Zhou, S., Korf, I. F. (2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience, 2 (1). p. 10. ISSN 2047-217x

Ming, R., VanBuren, R., Liu, Y. L., Yang, M., Han, Y. P., Li, L. T., Zhang, Q., Kim, M. J., Schatz, M. C., Campbell, M., Li, J. P., Bowers, J. E., Tang, H. B., Lyons, E., Ferguson, A. A., Narzisi, G., Nelson, D. R., Blaby-Haas, C. E., Gschwend, A. R., Jiao, Y. N., Der, J. P., Zeng, F. C., Han, J., Min, X. J., Hudson, K. A., Singh, R., Grennan, A. K., Karpowicz, S. J., Watling, J. R., Ito, K., Robinson, S. A., Hudson, M. E., Yu, Q. Y., Mockler, T. C., Carroll, A., Zheng, Y., Sunkar, R., Jia, R. Z., Chen, N., Arro, J., Wai, C. M., Wafula, E., Spence, A., Han, Y. N., Xu, L. M., Zhang, J. S., Peery, R., Haus, M. J., Xiong, W. W., Walsh, J. A., Wu, J., Wang, M. L., Zhu, Y. J., Paull, R. E., Britt, A. B., Du, C. G., Downie, S. R., Schuler, M. A., Michael, T. P., Long, S. P., Ort, D. R., Schopf, J. W., Gang, D. R., Jiang, N., Yandell, M., dePamphilis, C. W., Merchant, S. S., Paterson, A. H., Buchanan, B. B., Li, S. H., Shen-Miller, J. (2013) Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology, 14 (5). ISSN 1465-6906

Roberts, R. J., Carneiro, M. O., Schatz, M. C. (2013) The advantages of SMRT sequencing. Genome Biology, 14 (7). p. 4. ISSN 1465-6906

Schatz, M. C. (2012) Computational thinking in the era of big data biology. Genome Biology, 13 (11). p. 177. ISSN 1465-6906

Gurtowski, J., Schatz, M. C., Langmead, B. (2012) Genotyping in the cloud with crossbow. Current Protocols in Bioinformatics. 15.3. ISSN 1934-340X (Electronic)1934-3396 (Linking)

Lee, H., Schatz, M. C. (2012) Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score. Bioinformatics, 28 (16). pp. 2097-2105. ISSN 1367-4803

Koren, S., Schatz, M. C., Walenz, B. P., Martin, J., Howard, J. T., Ganapathy, G., Wang, Z., Rasko, D. A., McCombie, W. R., Jarvis, E. D., Phillippy, A. M. (2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology, 30 (7). pp. 693-700. ISSN 1087-0156

Schatz, M. C., Witkowski, J., McCombie, W. R. (2012) Current challenges in de novo plant genome sequencing and assembly. Genome Biology, 13 (4). p. 243. ISSN 1474-7596

Iossifov, I., Ronemus, M., Levy, D., Wang, Z. H., Hakker, I., Rosenbaum, J., Yamrom, B., Lee, Y. H., Narzisi, G., Leotta, A., Kendall, J., Grabowska, E., Ma, B. C., Marks, S., Rodgers, L., Stepansky, A., Troge, J., Andrews, P., Bekritsky, M., Pradhan, K., Ghiban, E., Kramer, M., Parla, J., Demeter, R., Fulton, L. L., Fulton, R. S., Magrini, V. J., Ye, K., Darnell, J. C., Darnell, R. B., Mardis, E. R., Wilson, R. K., Schatz, M. C., McCombie, W. R., Wigler, M. (2012) De Novo Gene Disruptions in Children on the Autistic Spectrum. Neuron, 74 (2). pp. 285-299. ISSN 0896-6273

Salzberg, S. L., Phillippy, A. M., Zimin, A., Puiu, D., Magoc, T., Koren, S., Treangen, T. J., Schatz, M. C., Delcher, A. L., Roberts, M., Marcais, G., Pop, M., Yorke, J. A. (2012) GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Res, 22 (3). pp. 557-67. ISSN 1549-5469 (Electronic)1088-9051 (Linking)

Park, S. J., Jiang, K., Schatz, M. C., Lippman, Z. B. (2012) Rate of meristem maturation determines inflorescence architecture in tomato. Proceedings of the National Academy of Sciences of the United States of America, 109 (2). pp. 639-44. ISSN 0027-8424

Earl, D., Bradnam, K., St. John, J., Darling, A., Lin, D., Fass, J., Yu, H. O. K., Buffalo, V., Zerbino, D. R., Diekhans, M., Nguyen, N., Ariyaratne, P. N., Sung, W. K., Ning, Z., Haimel, M., Simpson, J. T., Fonseca, N. A., Birol, I., Docking, T. R., Ho, I. Y., Rokhsar, D. S., Chikhi, R., Lavenier, D., Chapuis, G., Naquin, D., Maillet, N., Schatz, M. C., Kelley, D. R., Phillippy, A. M., Koren, S., Yang, S. P., Wu, W., Chou, W. C., Srivastava, A., Shaw, T. I., Ruby, J. G., Skewes-Cox, P., Betegon, M., Dimon, M. T., Solovyev, V., Seledtsov, I., Kosarev, P., Vorobyev, D., Ramirez-Gonzalez, R., Leggett, R., MacLean, D., Xia, F., Luo, R., Li, Z., Xie, Y., Liu, B., Gnerre, S., MacCallum, I., Przybylski, D., Ribeiro, F. J., Sharpe, T., Hall, G., Kersey, P. J., Durbin, R., Jackman, S. D., Chapman, J. A., Huang, X., DeRisi, J. L., Caccamo, M., Li, Y., Jaffe, D. B., Green, R. E., Haussler, D., Korf, I., Paten, B. (2011) Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Research, 21 (12). pp. 2224-2241. ISSN 10889051 (ISSN)

Donia, M. S., Fricke, W. F., Partensky, F., Cox, J., Elshahawi, S. I., White, J. R., Phillippy, A. M., Schatz, M. C., Piel, J., Haygood, M. G., Ravel, J., Schmidt, E. W. (2011) Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis. Proceedings of the National Academy of Sciences of the United States of America, 108 (51). E1423-E1432. ISSN 00278424 (ISSN)

Bogdanove, A. J., Koebnik, R., Lu, H., Furutani, A., Angiuoli, S. V., Patil, P. B., Van Sluys, M. A., Ryan, R. P., Meyer, D. F., Han, S. W., Aparna, G., Rajaram, M., Delcher, A. L., Phillippy, A. M., Puiu, D., Schatz, M. C., Shumway, M., Sommer, D. D., Trapnell, C., Benahmed, F., Dimitrov, G., Madupu, R., Radune, D., Sullivan, S., Jha, G., Ishihara, H., Lee, S. W., Pandey, A., Sharma, V., Sriariyanun, M., Szurek, B., Vera-Cruz, C. M., Dorman, K. S., Ronald, P. C., Verdier, V., Dow, J. M., Sonti, R. V., Tsuge, S., Brendel, V. P., Rabinowicz, P. D., Leach, J. E., White, F. F., Salzberg, S. L. (2011) Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp. Journal of Bacteriology, 193 (19). pp. 5450-5464. ISSN 00219193 (ISSN)

Kelley, D. R., Schatz, M. C., Salzberg, S. L. (2010) Quake: Quality-aware detection and correction of sequencing errors. Genome Biology, 11 (11). ISSN 1474-7596

Schatz, M. C., Langmead, B., Salzberg, S. L. (2010) Cloud computing and the DNA data race. Nature Biotechnology, 28 (7). pp. 691-693.

Kingsford, C., Schatz, M. C., Pop, M. (2010) Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics, 11. ISSN 14712105 (ISSN)

Schatz, M. C., Delcher, A. L., Salzberg, S. L. (2010) Assembly of large genomes using second-generation sequencing. Genome Research, 20 (9). pp. 1165-1173. ISSN 10889051 (ISSN)

Suzuki, J. Y., Tripathi, S., Fermín, G. A., Jan, F. J., Hou, S., Saw, J. H., Ackerman, C. M., Yu, Q., Schatz, M. C., Pitz, K. Y., Yépes, M., Fitch, M. M. M., Manshardt, R. M., Slightom, J. L., Ferreira, S. A., Salzberg, S. L., Alam, M., Ming, R., Moore, P. H., Gonsalves, D. (2010) Efforts to deregulate Rainbow papaya in Japan: Molecular characterization of transgene and vector inserts. Acta Horticulturae, 851. pp. 235-240. ISSN 05677572 (ISSN); 9789066050655 (ISBN)

Cornman, S. R., Schatz, M. C., Johnston, S. J., Chen, Y., Pettis, J., Hunt, G., Bourgeois, L., Elsik, C., Anderson, D., Grozinger, C. M., Evans, J. D. (2010) Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera. BMC Genomics, 11 (1). ISSN 14712164 (ISSN)

Schatz, M. C., Phillippy, A. M., Gajer, P., DeSantis, T. Z., Andersen, G. L., Ravel, J. (2010) Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray. Applied and Environmental Microbiology, 76 (16). pp. 5636-5638. ISSN 00992240 (ISSN)

Dalloul, R. A., Long, J. A., Zimin, A. V., Aslam, L., Beal, K., Blomberg, L. A., Bouffard, P., Burt, D. W., Crasta, O., Crooijmans, R. P. M. A., Cooper, K., Coulombe, R. A., De, S., Delany, M. E., Dodgson, J. B., Dong, J. J., Evans, C., Frederickson, K. M., Flicek, P., Florea, L., Folkerts, O., Groenen, M. A. M., Harkins, T. T., Herrero, J., Hoffmann, S., Megens, H. J., Jiang, A., de Jong, P., Kaiser, P., Kim, H., Kim, K. W., Kim, S., Langenberger, D., Lee, M. K., Lee, T., Mane, S., Marcais, G., Marz, M., McElroy, A. P., Modise, T., Nefedov, M., Notredame, C., Paton, I. R., Payne, W. S., Pertea, G., Prickett, D., Puiu, D., Qioa, D., Raineri, E., Ruffier, M., Salzberg, S. L., Schatz, M. C., Scheuring, C., Schmidt, C. J., Schroeder, S., Searle, S. M. J., Smith, E. J., Smith, J., Sonstegard, T. S., Stadler, P. F., Tafer, H., Tu, Z., van Tassell, C. P., Vilella, A. J., Williams, K. P., Yorke, J. A., Zhang, L., Zhang, H. B., Zhang, X., Zhang, Y., Reed, K. M. (2010) Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): Genome assembly and analysis. PLoS Biology, 8 (9). ISSN 1544-9173

Schatz, M. C. (2010) The missing graphical user interface for genomics. Genome Biology, 11 (8). p. 128. ISSN 14656914 (ISSN)

Cornman, R. S., Chen, Y. P., Schatz, M. C., Street, C., Zhao, Y., Desany, B., Egholm, M., Hutchison, S., Pettis, J. S., Lipkin, W. I., Evans, J. D. (2009) Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees. PLoS Pathogens, 5 (6). ISSN 15537366 (ISSN)

Trapnell, C., Schatz, M. C. (2009) Optimizing data intensive GPGPU computations for DNA sequence alignment. Parallel Computing, 35 (8-9). pp. 429-440. ISSN 01678191 (ISSN)

Navlakha, S., Schatz, M. C., Kingsford, C. (2009) Revealing biological modules via graph summarization. Journal of Computational Biology, 16 (2). pp. 253-264. ISSN 10665277 (ISSN)

Langmead, B., Schatz, M. C., Lin, J., Pop, M., Salzberg, S. L. (2009) Searching for SNPs with cloud computing. Genome Biology, 10 (11). ISSN 14747596 (ISSN)

Zimin, A. V., Delcher, A. L., Florea, L., Kelley, D. R., Schatz, M. C., Puiu, D., Hanrahan, F., Pertea, G., Van Tassell, C. P., Sonstegard, T. S., Marçais, G., Roberts, M., Subramanian, P., Yorke, J. A., Salzberg, S. L. (2009) A whole-genome assembly of the domestic cow, Bos taurus. Genome Biology, 10 (4). ISSN 14747596 (ISSN)

Suzuki, Jon Y., Tripathi, Savarni, Fermín, Gustavo A., Jan, Fuh-Jyh, Hou, Shaobin, Saw, Jimmy H., Ackerman, Christine M., Yu, Qingyi, Schatz, Michael C., Pitz, Karen Y., Yépes, Marcela, Fitch, Maureen M. M., Manshardt, Richard M., Slightom, Jerry L., Ferreira, Stephen A., Salzberg, Steven L., Alam, Maqsudul, Ming, Ray, Moore, Paul H., Gonsalves, Dennis (2008) Characterization of Insertion Sites in Rainbow Papaya, the First Commercialized Transgenic Fruit Crop. Tropical Plant Biology, 1 (3-4). pp. 293-309. ISSN 1935-9756

Phillippy, A. M., Schatz, M. C., Pop, M. (2008) Genome assembly forensics: Finding the elusive mis-assembly. Genome Biology, 9 (3). ISSN 14747596 (ISSN)

Salzberg, S. L., Sommer, D. D., Schatz, M. C., Phillippy, A. M., Rabinowicz, P. D., Tsuge, S., Furutani, A., Ochiai, H., Delcher, A. L., Kelley, D., Madupu, R., Puiu, D., Radune, D., Shumway, M., Trapnell, C., Aparna, G., Jha, G., Pandey, A., Patil, P. B., Ishihara, H., Meyer, D. F., Szurek, B., Verdier, V., Koebnik, R., Maxwell, J. M., Ryan, R. P., Hirata, H., Tsuyumu, S., Won Lee, S., Ronald, P. C., Sonti, R. V., Van Sluys, M. A., Leach, J. E., White, F. F., Bogdanove, A. J. (2008) Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. BMC Genomics, 9. ISSN 1471-2164

Ghedin, E., Wang, S., Spiro, D., Caler, E., Zhao, Q., Crabtree, J., Allen, J. E., Delcher, A. L., Guiliano, D. B., Miranda-Saavedra, D., Angiuoli, S. V., Creasy, T., Amedeo, P., Haas, B., El-Sayed, N. M., Wortman, J. R., Feldblyum, T., Tallon, L., Schatz, M., Shumway, M., Koo, H., Salzberg, S. L., Schobel, S., Pertea, M., Pop, M., White, O., Barton, G. J., Carlow, C. K. S., Crawford, M. J., Daub, J., Dimmic, M. W., Estes, C. F., Foster, J. M., Ganatra, M., Gregory, W. F., Johnson, N. M., Jin, M., Komuniecki, R., Korf, I., Kumar, S., Laney, S., Li, B. W., Li, W., Lindblom, T. H., Lustigman, S., Ma, D., Maina, C. V., Martin, D. M. A., McCarter, J. P., McReynolds, L., Mitreva, M., Nutman, T. B., Parkinson, J., Peregrín-Alvarez, J. M., Poole, C., Ren, Q., Saunders, L., Sluder, A. E., Smith, K., Stanke, M., Unnasch, T. R., Ware, J., Wei, A. D., Weil, G., Williams, D. J., Zhang, Y., Williams, S. A., Fraser-Liggett, C., Slatko, B., Blaxter, M. L., Scott, A. L. (2007) Draft genome of the filarial nematode parasite Brugia malayi. Science, 317 (5845). pp. 1756-1760. ISSN 00368075 (ISSN)

Carlton, J. M., Hirt, R. P., Silva, J. C., Delcher, A. L., Schatz, M., Zhao, Q., Wortman, J. R., Bidwell, S. L., Alsmark, U. C. M., Besteiro, S., Sicheritz-Ponten, T., Noel, C. J., Dacks, J. B., Foster, P. G., Simillion, C., Van De Peer, Y., Miranda-Saavedra, D., Barton, G. J., Westrop, G. D., Müller, S., Dessi, D., Fiori, P. L., Ren, Q., Paulsen, I., Zhang, H., Bastida-Corcuera, F. D., Simoes-Barbosa, A., Brown, M. T., Hayes, R. D., Mukherjee, M., Okumura, C. Y., Schneider, R., Smith, A. J., Vanacova, S., Villalvazo, M., Haas, B. J., Pertea, M., Feldblyum, T. V., Utterback, T. R., Shu, C. L., Osoegawa, K., De Jong, P. J., Hrdy, I., Horvathova, L., Zubacova, Z., Dolezal, P., Malik, S. B., Logsdon Jr, J. M., Henze, K., Gupta, A., Wang, C. C., Dunne, R. L., Upcroft, J. A., Upcroft, P., White, O., Salzberg, S. L., Tang, P., Chiu, C. H., Lee, Y. S., Embley, T. M., Coombs, G. H., Mottram, J. C., Tachezy, J., Fraser-Liggett, C. M., Johnson, P. J. (2007) Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science, 315 (5809). pp. 207-212. ISSN 00368075 (ISSN)

Clark, A. G., Eisen, M. B., Smith, D. R., Bergman, C. M., Oliver, B., Markow, T. A., Kaufman, T. C., Kellis, M., Gelbart, W., Iyer, V. N., Pollard, D. A., Sackton, T. B., Larracuente, A. M., Singh, N. D., Abad, J. P., Abt, D. N., Adryan, B., Aguade, M., Akashi, H., Anderson, W. W., Aquadro, C. F., Ardell, D. H., Arguello, R., Artieri, C. G., Barbash, D. A., Barker, D., Barsanti, P., Batterham, P., Batzoglou, S., Begun, D., Bhutkar, A., Blanco, E., Bosak, S. A., Bradley, R. K., Brand, A. D., Brent, M. R., Brooks, A. N., Brown, R. H., Butlin, R. K., Caggese, C., Calvi, B. R., Bernardo De Carvalho, A., Caspi, A., Castrezana, S., Celniker, S. E., Chang, J. L., Chapple, C., Chatterji, S., Chinwalla, A., Civetta, A., Clifton, S. W., Comeron, J. M., Costello, J. C., Coyne, J. A., Daub, J., David, R. G., Delcher, A. L., Delehaunty, K., Do, C. B., Ebling, H., Edwards, K., Eickbush, T., Evans, J. D., Filipski, A., Findeiß, S., Freyhult, E., Fulton, L., Fulton, R., Garcia, A. C. L., Gardiner, A., Garfield, D. A., Garvin, B. E., Gibson, G., Gilbert, D., Gnerre, S., Godfrey, J., Good, R., Gotea, V., Gravely, B., Greenberg, A. J., Griffiths-Jones, S., Gross, S., Guigo, R., Gustafson, E. A., Haerty, W., Hahn, M. W., Halligan, D. L., Halpern, A. L., Halter, G. M., Han, M. V., Heger, A., Hillier, L., Hinrichs, A. S., Holmes, I., Hoskins, R. A., Hubisz, M. J., Hultmark, D., Huntley, M. A., Jaffe, D. B., Jagadeeshan, S. (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature, 450 (7167). pp. 203-218. ISSN 00280836 (ISSN)

Nene, V., Wortman, J. R., Lawson, D., Haas, B., Kodira, C., Tu, Z., Loftus, B., Xi, Z., Megy, K., Grabherr, M., Ren, Q., Zdobnov, E. M., Lobo, N. F., Campbell, K. S., Brown, S. E., Bonaldo, M. F., Zhu, J., Sinkins, S. P., Hogenkamp, D. G., Amedeo, P., Arensburger, P., Atkinson, P. W., Bidwell, S., Biedler, J., Birney, E., Bruggner, R. V., Costas, J., Coy, M. R., Crabtree, J., Crawford, M., DeBruyn, B., DeCaprio, D., Eiglmeier, K., Eisenstadt, E., El-Dorry, H., Gelbart, W. M., Gomes, S. L., Hammond, M., Hannick, L. I., Hogan, J. R., Holmes, M. H., Jaffe, D., Johnston, J. S., Kennedy, R. C., Koo, H., Kravitz, S., Kriventseva, E. V., Kulp, D., LaButti, K., Lee, E., Li, S., Lovin, D. D., Mao, C., Mauceli, E., Menck, C. F. M., Miller, J. R., Montgomery, P., Mori, A., Nascimento, A. L., Naveira, H. F., Nusbaum, C., O'Leary, S., Orvis, J., Pertea, M., Quesneville, H., Reidenbach, K. R., Rogers, Y. H., Roth, C. W., Schneider, J. R., Schatz, M., Shumway, M., Stanke, M., Stinson, E. O., Tubio, J. M. C., VanZee, J. P., Verjovski-Almeida, S., Werner, D., White, O., Wyder, S., Zeng, Q., Zhao, Q., Zhao, Y., Hill, C. A., Raikhel, A. S., Soares, M. B., Knudson, D. L., Lee, N. H., Galagan, J., Salzberg, S. L., Paulsen, I. T., Dimopoulos, G., Collins, F. H., Birren, B., Fraser-Liggett, C. M., Severson, D. W. (2007) Genome sequence of Aedes aegypti, a major arbovirus vector. Science, 316 (5832). pp. 1718-1723. ISSN 00368075 (ISSN)

Schatz, M. C., Phillippy, A. M., Shneiderman, B., Salzberg, S. L. (2007) Hawkeye: An interactive visual analytics tool for genome assemblies. Genome Biology, 8 (3). ISSN 14747596 (ISSN)

Schatz, M. C., Trapnell, C., Delcher, A. L., Varshney, A. (2007) High-throughput sequence alignment using Graphics Processing Units. Bmc Bioinformatics, 8. ISSN 14712105 (ISSN)

Desjardins, C. A., Gundersen-Rindal, D. E., Hostetler, J. B., Tallon, L. J., Fuester, R. W., Schatz, M. C., Pedroni, M. J., Fadrosh, D. W., Haas, B. J., Toms, B. S., Chen, D., Nene, V. (2007) Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirus. BMC Microbiology, 7. ISSN 14712180 (ISSN)

Fouts, D. E., Mongodin, E. F., Mandrell, R. E., Miller, W. G., Rasko, D. A., Ravel, J., Brinkac, L. M., Deboy, R. T., Parker, C. T., Daugherty, S. C., Dodson, R. J., Scott Durkin, A., Madupu, R., Sullivan, S. A., Shetty, J. U., Ayodeji, M. A., Shvartsbeyn, A., Schatz, M. C., Badger, J. H., Fraser, C. M., Nelson, K. E. (2005) Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. PLoS Biology, 3 (1). ISSN 15449173 (ISSN)

Gajer, P., Schatz, M., Salzberg, S. L. (2004) Automated correction of genome sequence errors. Nucleic Acids Research, 32 (2). pp. 562-569. ISSN 03051048 (ISSN)

Book Section

Narzisi, G., Mishra, B., Schatz, M. C. (2014) On algorithmic complexity of biomolecular sequence assembly problem. In: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Springer, pp. 183-195. ISBN 16113349 - ISSN978-331907952-3

Conference or Workshop Item

Fang, Han, Lyon, Gholson J. (2014) Reducing INDEL calling errors in whole-genome and exome sequencing. In: 64th Annual Meeting of the American Society of Human Genetics (ASHG), October 2014, San Diego, California. (Unpublished)

Lin, Jimmy, Schatz, Michael C. (2010) Design Patterns for Efficient Graph Algorithms in MapReduce. In: Eighth Workshop on Mining and Learning with Graphs, July 24th-25th 2010, Washington D.C..

Book

Menon, R. K., Bhat, G. P., Schatz, M. C. (2011) Rapid parallel genome indexing with MapReduce. 2nd International Workshop on MapReduce and Its Applications, MapReduce'11, Co-located with 20th International ACM Symposium on High-Performance Parallel and Distributed Computing, HPDC 2011 . ACM, pp. 51-58. ISBN 9781450307000 (ISBN)

Lin, J., Schatz, M. C. (2010) Design patterns for efficient graph algorithms in MapReduce. 8th Workshop on Mining and Learning with Graphs, MLG'10 . MLG, pp. 78-85. ISBN 9781450302142 (ISBN)

Video

Schatz, M. C. (2012) Talk from Mike Schatz at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

This list was generated on Wed Jul 26 16:35:18 2017 EDT.
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