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Paper

Wroten, Mathew, Yoon, Seungtai, Andrews, Peter, Yamrom, Boris, Ronemus, Michael, Buja, Andreas, Krieger, Abba M, Levy, Dan, Ye, Kenny, Wigler, Michael, Iossifov, Ivan (June 2023) Sharing parental genomes by siblings concordant or discordant for autism. Cell Genomics, 3 (6). p. 100319. ISSN 2666-979X (Public Dataset)

Lammertse, E, Li, S, Kendall, J, Kim, C, Morris, P, Ranade, N, Levy, D, Wigler, M, Brouzes, E (January 2023) Magnetically Functionalized Hydrogels for High-Throughput Genomic Applications. Advanced Materials Technologies. ISSN 2365-709X

Wang, Zihua, Moffitt, Andrea B, Andrews, Peter, Wigler, Michael, Levy, Dan (September 2022) Accurate measurement of microsatellite length by disrupting its tandem repeat structure. Nucleic Acids Research. gkac723. ISSN 0305-1048

Li, Siran, Park, Sarah, Ye, Catherine, Danyko, Cassidy, Wroten, Matthew, Andrews, Peter, Wigler, Michael, Levy, Dan (July 2022) Targeted de novo phasing and long-range assembly by template mutagenesis. Nucleic Acids Research. ISSN 0305-1048

Yoon, Seungtai, Munoz, Adriana, Yamrom, Boris, Lee, Yoon-Ha, Andrews, Peter, Marks, Steven, Wang, Zihua, Reeves, Catherine, Winterkorn, Lara, Krieger, Abba M, Buja, Andreas, Pradhan, Kith, Ronemus, Michael, Baldwin, Kristin K, Levy, Dan, Wigler, Michael, Iossifov, Ivan (September 2021) Rates of contributory de novo mutation in high and low-risk autism families. Communications Biology, 4 (1). p. 1026. ISSN 2399-3642

Vasudevan, A., Baruah, P.S., Smith, J.C., Wang, Z., Sayles, N. M., Andrews, P., Kendall, J., Leu, J., Chunduri, N.K., Levy, D., Wigler, M., Storchova, Z., Sheltzer, J. M. (February 2020) Single-Chromosomal Gains Can Function as Metastasis Suppressors and Promoters in Colon Cancer. Developmental Cell, 52 (4). pp. 413-428. ISSN 1534-5807

Moffitt, A. B., Spector, M. S., Andrews, P., Kendall, J., Alexander, J., Stepansky, A., Ma, B., Kolitz, J., Chiorazzi, N., Allen, S.L., Krasnitz, A., Wigler, M., Levy, D., Wang, Z. (February 2020) Multiplex Accurate Sensitive Quantitation (MASQ) With Application to Minimal Residual Disease in Acute Myeloid Leukemia. Nucleic Acids Research, 48 (7). e40. ISSN 0305-1048 (Public Dataset)

Li, S., Kendall, J., Park, S., Wang, Z., Alexander, J., Moffitt, A., Ranade, N., Danyko, C., Gegenhuber, B., Fischer, S., Robinson, B. D., Lepor, H., Tollkuhn, J., Gillis, J., Brouzes, E., Krasnitz, A., Levy, D., Wigler, M. (November 2019) Copolymerization of single-cell nucleic acids into balls of acrylamide gel. Genome Res, 30 (1). pp. 49-61. ISSN 1088-9051 (Public Dataset)

Kumar, V., Rosenbaum, J., Wang, Z., Forcier, T., Ronemus, M., Wigler, M., Levy, D. (January 2018) Partial bisulfite conversion for unique template sequencing. Nucleic Acids Res, 46 (2). e10. ISSN 0305-1048

Alexander, J., Kendall, J., McIndoo, J., Rodgers, L., Aboukhalil, R., Levy, D., Stepansky, A., Sun, G., Chobadjiev, L., Riggs, M., Cox, H., Hakker, I., Nowak, D. G., Laze, J., Llukani, E., Srivastava, A., Gruschow, S., Yadav, S. S., Robinson, B. D., Atwal, G., Trotman, L. C., Lepor, H., Hicks, J. B., Wigler, M., Krasnitz, A. (January 2018) Utility of single cell genomics in diagnostic evaluation of prostate cancer. Cancer Res, 78 (2). pp. 348-358. ISSN 0008-5472

Ye, K., Iossifov, I., Levy, D., Yamrom, B., Buja, A., Krieger, A. M., Wigler, M. (July 2017) Measuring shared variants in cohorts of discordant siblings with applications to autism. Proc Natl Acad Sci U S A, 114 (27). pp. 7073-7076. ISSN 0027-8424

Krasnitz, Alexander, Kendall, Jude, Alexander, Joan, Levy, Dan, Wigler, Michael (July 2017) Early Detection of Cancer in Blood Using Single-Cell Analysis: A Proposal. Trends in Molecular Medicine, 23 (7). pp. 594-603. ISSN 1471-4914

Kumar, Vijay, Rosenbaum, Julie, Wang, Zihua, Forcier, Talitha, Ronemus, Michael, Wigler, Michael, Levy, Dan (June 2017) Mutational sequencing for accurate count and long-range assembly. bioRxiv.

Andrews, Peter A., Iossifov, Ivan, Kendall, Jude, Marks, Steven, Muthuswamy, Lakshmi, Wang, Zihua, Levy, Dan, Wigler, Michael (September 2016) MUMdex: MUM-based structural variation detection. bioRxiv. 078261.

Wang, Z., Andrews, P., Kendall, J., Ma, B., Hakker, I., Rodgers, L., Ronemus, M., Wigler, M., Levy, D. (June 2016) SMASH, a fragmentation and sequencing method for genomic copy number analysis. Genome Res, 26 (6). pp. 844-51. ISSN 1549-5469 (Electronic)1088-9051 (Linking) (Public Dataset)

Iossifov, I., Levy, D., Allen, J., Ye, K., Ronemus, M., Lee, Y. H., Yamrom, B., Wigler, M. (September 2015) Low load for disruptive mutations in autism genes and their biased transmission. Proc Natl Acad Sci U S A. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Mukhopadhyay, Swagatam, Wigler, Michael, Levy, Dan (March 2015) Simple genetic models for autism spectrum disorder. bioRxiv. 017301.

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. (November 2014) The contribution of de novo coding mutations to autism spectrum disorder. Nature, 515 (7526). pp. 216-221. ISSN 0028-0836

Levy, D., Wigler, M. (October 2014) Facilitated sequence counting and assembly by template mutagenesis. Proceedings of the National Academy of Sciences of the United States of America, 111 (43). E4632-E4637. ISSN 0027-8424

Warburton, D., Ronemus, M., Kline, J., Jobanputra, V., Williams, I., Anyane-Yeboa, K., Chung, W., Yu, L., Wong, N., Awad, D., Yu, C. Y., Leotta, A., Kendall, J., Yamrom, B., Lee, Y. H., Wigler, M., Levy, D. (January 2014) The contribution of de novo and rare inherited copy number changes to congenital heart disease in an unselected sample of children with conotruncal defects or hypoplastic left heart disease. Human Genetics, 133 (1). pp. 11-27. ISSN 1432-1203 (Electronic)0340-6717 (Linking)

Ronemus, M., Iossifov, I., Levy, D., Wigler, M. (2014) The role of de novo mutations in the genetics of autism spectrum disorders. Nature Reviews Genetics, 15 (2). pp. 133-141.

Regulski, M., Lu, Z., Kendall, J., Donoghue, M. T., Reinders, J., Llaca, V., Deschamps, S., Smith, A., Levy, D., McCombie, W. R., Tingey, S., Rafalski, A., Hicks, J., Ware, D., Martienssen, R. (June 2013) The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Research, 23 (10). pp. 1651-1662. ISSN 10889051 (ISSN)

Stadler, Z. K., Esposito, D., Shah, S., Vijai, J., Yamrom, B., Levy, D., Lee, Y. H., Kendall, J., Leotta, A., Ronemus, M., Hansen, N. , Sarrel, K., Rau-Murthy, R., Schrader, K., Kauff, N., Klein, R., Lipkin, S., Murali, R., Robson, M., Sheinfeld, J., Feldman, D., Bosl, G., Norton, L., Wigler, M., Offit, K. (August 2012) Rare De Novo Germline Copy-Number Variation in Testicular Cancer. The American Journal of Human Genetics, 91 (2). pp. 379-383. ISSN 0002-9297

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. (April 2012) De Novo Gene Disruptions in Children on the Autistic Spectrum. Neuron, 74 (2). pp. 285-299. ISSN 0896-6273

Lee, Y. H., Ronemus, M., Kendall, J., Lakshmi, B., Leotta, A., Levy, D., Esposito, D., Grubor, V., Ye, K., Wigler, M., Yamrom, B. (January 2012) Reducing system noise in copy number data using principal components of self-self hybridizations. Proceedings of the National Academy of Sciences of the United States of America, 109 (3). E103-E110. ISSN 0027-8424

Gilman, S. R, Iossifov, I., Levy, D., Ronemus, M., Wigler, M. H., Vitkup, D. (June 2011) Rare De Novo Variants Associated with Autism Implicate a Large Functional Network of Genes Involved in Formation and Function of Synapses. Neuron, 70 (5). pp. 898-907. ISSN 0896-6273

Levy, D., Ronemus, M., Yamrom, B., Lee, Y. H., Leotta, A., Kendall, J. T., Marks, S., Lakshmi, B., Pai, D., Ye, Kenny, Buja, Andreas, Krieger, Abba, Yoon, S., Troge, J. E., Rodgers,  L., Iossifov, I., Wigler, M. H. (June 2011) Rare De Novo and Transmitted Copy-Number Variation in Autistic Spectrum Disorders. Neuron, 70 (5). pp. 886-897. ISSN 0896-6273

Lee, Yoon-ha, Ronemus, Michael, Kendall, Jude, Lakshmi, B, Leotta, Anthony, Levy, Dan, Esposito, Diane, Grubor, Vladimir, Ye, Kenny, Wigler, Michael, Yamrom, Boris (May 2011) Removing System Noise from Comparative Genomic Hybridization Data by Self-Self Analysis. (Submitted)

Kamalakaran, S., Varadan, V., Giercksky Russnes, H. E., Levy, D., Kendall, J. T., Janevski, A., Riggs, M., Banerjee, N., Synnestvedt, M., Schlichting, E., Kåresen, R., Shama Prasada, K., Rotti, H., Rao, R., Rao, L., Eric Tang, M. H., Satyamoorthy, K., Lucito, R., Wigler, M. H., Dimitrova, N., Naume, B., Borresen-Dale, A. L., Hicks, J. B. (February 2011) DNA methylation patterns in luminal breast cancers differ from non-luminal subtypes and can identify relapse risk independent of other clinical variables. Molecular Oncology, 5 (1). pp. 77-92.

Navin, N. E., Kendall, J. T., Troge, J. E., Andrews, P., Rodgers,  L., McIndoo, J., Cook, K., Stepansky,  A., Levy, D., Esposito, D., Muthuswamy, L., Krasnitz, A., McCombie, W. R., Hicks, J. B., Wigler, M. H. (2011) Tumour evolution inferred by single-cell sequencing. Nature, 472 (7341). pp. 90-94. ISSN 00280836 (ISSN)

Levy, Dan, Pachter, Lior (2011) The neighbor-net algorithm. Advances in Applied Mathematics, 47 (2). pp. 240-258. ISSN 0196-8858

Hicks, J. B., Navin, N. E., Kendall, J. T., Levy, D., Wigler, M. H. (May 2010) Tracing Tumor Lineage and Progression through Genomic Copy Number Profiling at the Single Cell Level. Annals of Oncology, 21 (S4). iv49. ISSN 0923-7534

Schnable, P. S., Ware, D., Fulton, R. S., Stein, J. C., Wei, F., Pasternak, S., Liang, C., Zhang, J., Fulton, L., Graves, T. A., Minx, P., Reily, A. D., Courtney, L., Kruchowski, S. S., Tomlinson, C., Strong, C., Delehaunty, K., Fronick, C., Courtney, B., Rock, S. M., Belter, E., Du, F., Kim, K., Abbott, R. M., Cotton, M., Levy, A., Marchetto, P., Ochoa, K., Jackson, S. M., Gillam, B., Chen, W., Yan, L., Higginbotham, J., Cardenas, M., Waligorski, J., Applebaum, E., Phelps, L., Falcone, J., Kanchi, K., Thane, T., Scimone, A., Thane, N., Henke, J., Wang, T., Ruppert, J., Shah, N., Rotter, K., Hodges, J., Ingenthron, E., Cordes, M., Kohlberg, S., Sgro, J., Delgado, B., Mead, K., Chinwalla, A., Leonard, S., Crouse, K., Collura, K., Kudrna, D., Currie, J., He, R., Angelova, A., Rajasekar, S., Mueller, T., Lomeli, R., Scara, G., Ko, A., Delaney, K., Wissotski, M., Lopez, G., Campos, D., Braidotti, M., Ashley, E., Golser, W., Kim, H., Lee, S., Lin, J., Dujmic, Z., Kim, W., Talag, J., Zuccolo, A., Fan, C., Sebastian, A., Kramer, M., Spiegel, L., Nascimento, L., Zutavern, T., Miller, B., Ambroise, C., Muller, S., Spooner, W., Narechania, A., Ren, L., Wei, S., Kumari, S., Faga, B., Levy, M. J., McMahan, L., Van Buren, P., Vaughn, M. W. (November 2009) The B73 maize genome: complexity, diversity, and dynamics. Science, 326 (5956). pp. 1112-5. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Conference or Workshop Item

Moffitt, Andrea B, Alexander, Joan, Stepansky, Asya, Boyle, Erin, Stauder, Danielle, Lopez, Carlos Alberto, Wu, Vernon, Hakim, Nausheen, Wang, Zihua, Kolitz, Jonathan E, Chiorazzi, Nicholas, Chitty, David W, Allen, Steven L, Levy, Dan, Wigler, Michael (November 2023) Personalized Residual Disease Detection in Acute Myeloid Leukemia with a Multiplexed Genomic Fingerprint Predicts Patient Outcomes. In: UNSPECIFIED.

Moffitt, Andrea B, Alexander, Joan, Stepansky, Asya, Famulare, Christopher, Lopez, Carlos A, Hakim, Nausheen, Wu, Vernon, Wang, Zihua, Kolitz, Jonathan E, Chiorazzi, Nicholas, Allen, Steven L, Levine, Ross L, Levy, Dan, Wigler, Michael (2022) Whole Genome Sequencing Comparison of Acute Myeloid Leukemia at Presentation and Remission Predicts Patient Outcome. In: Meeting Abstract.