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Cahn, Jonathan, Regulski, Michael, Lynn, Jason, Ernst, Evan, de Santis Alves, Cristiane, Ramakrishnan, Srividya, Chougule, Kapeel, Wei, Sharon, Lu, Zhenyuan, Xu, Xiaosa, Ramu, Umamaheswari, Drenkow, Jorg, Kramer, Melissa, Seetharam, Arun, Hufford, Matthew B, McCombie, W Richard, Ware, Doreen, Jackson, David, Schatz, Michael C, Gingeras, Thomas R, Martienssen, Robert A (December 2024) MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication. Nature Communications, 15 (1). p. 10854. ISSN 2041-1723 (Public Dataset)

Kramer, Melissa, Goodwin, Sara, Wappel, Robert, Borio, Matilde, Offit, Kenneth, Feldman, Darren R, Stadler, Zsofia K, McCombie, W Richard (July 2024) Exploring the genetic and epigenetic underpinnings of early-onset cancers: Variant prioritization for long read whole genome sequencing from family cancer pedigrees. bioRxiv. (Submitted)

Cahn, Jonathan, Regulski, Michael, Lynn, Jason, Ernst, Evan, Alves, Cristiane de Santis, Ramakrishnan, Srividya, Chougule, Kapeel, Wei, Sharon, Lu, Zhenyuan, Xu, Xiaosa, Drenkow, Jorg, Kramer, Melissa, Seetharam, Arun, Hufford, Matthew, McCombie, Richard, Ware, Doreen, Jackson, David, Schatz, Michael, Gingeras, Thomas, Martienssen, Robert (February 2024) MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication. bioRxiv. (Submitted)

Scheben, Armin, Mendivil Ramos, Olivia, Kramer, Melissa, Goodwin, Sara, Oppenheim, Sara, Becker, Daniel J, Schatz, Michael C, Simmons, Nancy B, Siepel, Adam, McCombie, W Richard (September 2023) Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats. Genome Biology and Evolution, 15 (9). ISSN 1759-6653 (Public Dataset)

Stevenson, Dennis Wm, Ramakrishnan, Srividya, Alves, Cristiane de Santis, Coelho, Laís Araujo, Kramer, Melissa, Goodwin, Sara, Ramos, Olivia Mendevil, Eshel, Gil, Sondervan, Veronica M, Frangos, Samantha, Zumajo-Cardona, Cecilia, Jenike, Katherine, Ou, Shujun, Wang, Xiaojin, Lee, Yin Peng, Loke, Stella, Rossetto, Maurizio, McPherson, Hannah, Nigris, Sebastiano, Moschin, Silvia, Little, Damon P, Katari, Manpreet S, Varala, Kranthi, Kolokotronis, Sergios-Orestis, Ambrose, Barbara, Croft, Larry J, Coruzzi, Gloria M, Schatz, Michael, McCombie, W Richard, Martienssen, Robert A (August 2023) The genome of the Wollemi pine, a critically endangered "living fossil" unchanged since the Cretaceous, reveals extensive ancient transposon activity. bioRxiv. (Public Dataset) (Submitted)

Noyes, Michelle D, Harvey, William T, Porubsky, David, Sulovari, Arvis, Li, Ruiyang, Rose, Nicholas R, Audano, Peter A, Munson, Katherine M, Lewis, Alexandra P, Hoekzema, Kendra, Mantere, Tuomo, Graves-Lindsay, Tina A, Sanders, Ashley D, Goodwin, Sara, Kramer, Melissa, Mokrab, Younes, Zody, Michael C, Hoischen, Alexander, Korbel, Jan O, McCombie, W Richard, Eichler, Evan E (March 2022) Familial long-read sequencing increases yield of de novo mutations. American Journal of Human Genetics. ISSN 0002-9297

Bhatia, Sonam, Kramer, Melissa, Russo, Suzanne, Naik, Payal, Arun, Gayatri, Brophy, Kyle, Andrews, Peter, Fan, Cheng, Perou, Charles M, Preall, Jonathan, Ha, Taehoon, Plenker, Dennis, Tuveson, David A, Rishi, Arvind, Wilkinson, John E, McCombie, W Richard, Kostroff, Karen, Spector, David L (February 2022) Patient-derived triple-negative breast cancer organoids provide robust model systems that recapitulate tumor-intrinsic characteristics. Cancer Research. ISSN 0008-5472

Wei, Yiliang, Huang, Yu-Han, Skopelitis, Damianos S, Iyer, Shruti V, Costa, Ana SH, Yang, Zhaolin, Kramer, Melissa, Adelman, Emmalee R, Klingbeil, Olaf, Demerdash, Osama E, Polyanskaya, Sofya A, Chang, Kenneth, Goodwin, Sara, Hodges, Emily, McCombie, W Richard, Figueroa, Maria E, Vakoc, Christopher R (September 2021) SLC5A3-dependent myo-inositol auxotrophy in acute myeloid leukemia. Cancer Discovery. candisc.1849.2020-candisc.1849.2020. ISSN 2159-8274

Bhatia, Sonam, Kramer, Melissa, Russo, Suzanne, Naik, Payal, Arun, Gayatri, Brophy, Kyle, Andrews, Peter A, Fan, Cheng, Perou, Charles M, Preall, Jonathan, Ha, Taehoon, Rishi, Arvind, Wilkinson, John Erby, McCombie, William Richard, Kostroff, Karen, Spector, David L (August 2021) Patient-derived triple negative breast cancer organoids provide robust model systems that recapitulate tumor intrinsic characteristics. BioRxiv.

Yang, Zhaolin, Wu, Xiaoli S, Wei, Yiliang, Polyanskaya, Sofya A, Iyer, Shruti V, Jung, Moonjung, Lach, Francis P, Adelman, Emmalee R, Klingbeil, Olaf, Milazzo, Joseph P, Kramer, Melissa, Demerdash, Osama E, Chang, Kenneth, Goodwin, Sara, Hodges, Emily, McCombie, W Richard, Figueroa, Maria E, Smogorzewska, Agata, Vakoc, Christopher R (April 2021) Transcriptional silencing of ALDH2 confers a dependency on Fanconi anemia proteins in acute myeloid leukemia. Cancer Discovery. ISSN 2159-8274

Malik, Sarah A, Zhu, Chencan, Li, Jinyu, LaComb, Joseph F, Denoya, Paula I, Kravets, Igor, Miller, Joshua D, Yang, Jie, Kramer, Melissa, McCombie, W Richard, Robertson, Charles E, Frank, Daniel N, Li, Ellen (April 2021) Impact of preoperative antibiotics and other variables on integrated microbiome-host transcriptomic data generated from colorectal cancer resections. World Journal of Gastroenterology, 27 (14). pp. 1465-1482. ISSN 1007-9327

Scheben, Armin, Ramos, Olivia Mendivil, Kramer, Melissa, Goodwin, Sara, Oppenheim, Sara, Becker, Daniel, Schatz, Michael, Simmons, Nancy, Siepel, Adam, McCombie, Richard (September 2020) Unraveling molecular mechanisms of immunity and cancer-resistance using the genomes of the Neotropical bats Artibeus jamaicensis and Pteronotus mesoamericanus. BioRxiv. (Unpublished)

Aganezov, S., Goodwin, S., Sherman, R. M., Sedlazeck, F. J., Arun, G., Bhatia, S., Lee, I., Kirsche, M., Wappel, R., Kramer, M., Kostroff, K., Spector, D. L., Timp, W., McCombie, W. R., Schatz, M. C. (September 2020) Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing. Genome Res, 30 (9). pp. 1258-1273. ISSN 1088-9051 (Print)1088-9051

Alonge, M., Wang, X., Benoit, M., Soyk, S., Pereira, L., Zhang, L., Suresh, H., Ramakrishnan, S., Maumus, F., Ciren, D., Levy, Y., Harel, T. H., Shalev-Schlosser, G., Amsellem, Z., Razifard, H., Caicedo, A. L., Tieman, D. M., Klee, H., Kirsche, M., Aganezov, S., Ranallo-Benavidez, T. R., Lemmon, Z. H., Kim, J., Robitaille, G., Kramer, M., Goodwin, S., McCombie, W. R., Hutton, S., Van Eck, J., Gillis, J., Eshed, Y., Sedlazeck, F. J., van der Knaap, E., Schatz, M. C., Lippman, Z. B. (July 2020) Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato. Cell, 182 (1). 145-161.e23. ISSN 0092-8674 (Print)0092-8674

Aguirre-Chen, C., Stec, N., Ramos, O. M., Kim, N., Kramer, M., McCarthy, S., Gillis, J., McCombie, W. R., Hammell, C. M. (May 2020) A Caenorhabditis elegans Model for Integrating the Functions of Neuropsychiatric Risk Genes Identifies Components Required for Normal Dendritic Morphology. G3: Genes, Genomes, Genetics, 10 (5). pp. 1617-1628. ISSN 21601836

Nattestad, M., Goodwin, S., Ng, K., Baslan, T., Sedlazeck, F., Rescheneder, P., Garvin, T., Fang, H., Gurtowski, J., Hutton, E., Tseng, E., Chin, J., Beck, T., Sundaravadanam, Y., Kramer, M., Antoniou, E., McPherson, J., Hicks, J., McCombie, W. R., Schatz, M. C. (August 2018) Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. Genome Res, 28 (8). pp. 1126-1135. ISSN 1088-9051

Ryan, N. M., Lihm, J., Kramer, M., McCarthy, S., Morris, S. W., Arnau-Soler, A., Davies, G., Duff, B., Ghiban, E., Hayward, C., Deary, I. J., Blackwood, D. H. R., Lawrie, S. M., McIntosh, A. M., Evans, K. L., Porteous, D. J., McCombie, W. R., Thomson, P. A. (June 2018) DNA sequence-level analyses reveal potential phenotypic modifiers in a large family with psychiatric disorders. Mol Psychiatry, 23 (12). pp. 2254-2285. ISSN 1359-4184

Tamura, K., Yu, J., Hata, T., Suenaga, M., Shindo, K., Abe, T., MacGregor-Das, A., Borges, M., Wolfgang, C. L., Weiss, M. J., He, J., Canto, M. I., Petersen, G. M., Gallinger, S., Syngal, S., Brand, R. E., Rustgi, A., Olson, S. H., Stoffel, E., Cote, M. L., Zogopoulos, G., Potash, J. B., Goes, F. S., McCombie, R. W., Zandi, P. P., Pirooznia, M., Kramer, M., Parla, J., Eshleman, J. R., Roberts, N. J., Hruban, R. H., Klein, A. P., Goggins, M. (May 2018) Mutations in the pancreatic secretory enzymes CPA1 and CPB1 are associated with pancreatic cancer. Proc Natl Acad Sci U S A, 115 (18). pp. 4767-4772. ISSN 0027-8424

Teng, S., Thomson, P. A., McCarthy, S., Kramer, M., Muller, S., Lihm, J., Morris, S., Soares, D. C., Hennah, W., Harris, S., Camargo, L. M., Malkov, V., McIntosh, A. M., Millar, J. K., Blackwood, D. H., Evans, K. L., Deary, I. J., Porteous, D. J., McCombie, W. R. (May 2018) Rare disruptive variants in the DISC1 Interactome and Regulome: association with cognitive ability and schizophrenia. Mol Psychiatry, 23 (5). pp. 1270-1277. ISSN 1359-4184

Berstein, Y., McCarthy, S., Kramer, M., Zandi, P., Goes, F., Potash, J., McCombie, R. (October 2017) RARE VARIANT DETECTION IN COMPLEX DISORDERS USING THE BIRTHDAY MODEL. European Neuropsychopharmacology, 27 (Supple). S367-S368, Meeting Abstract 2. ISSN 0924-977X

Monson, E. T., Pirooznia, M., Parla, J., Kramer, M., Goes, F. S., Gaine, M. E., Gaynor, S. C., de Klerk, K., Jancic, D., Karchin, R., McCombie, W. R., Zandi, P. P., Potash, J. B., Willour, V. L. (July 2017) Assessment of Whole-Exome Sequence Data in Attempted Suicide within a Bipolar Disorder Cohort. Mol Neuropsychiatry, 3 (1). pp. 1-11. ISSN 2296-9209 (Print)2296-9179

Goes, F. S., Pirooznia, M., Parla, J. S., Kramer, M., Ghiban, E., Mavruk, S., Chen, Y. C., Monson, E. T., Willour, V. L., Karchin, R., Flickinger, M., Locke, A. E., Levy, S. E., Scott, L. J., Boehnke, M., Stahl, E., Moran, J. L., Hultman, C. M., Landen, M., Purcell, S. M., Sklar, P., Zandi, P. P., McCombie, W. R., Potash, J. B. (July 2016) Exome Sequencing of Familial Bipolar Disorder. JAMA Psychiatry, 73 (6). pp. 590-597. ISSN 2168-6238 (Electronic)2168-622X (Linking)

Roberts, N. J., Norris, A. L., Petersen, G. M., Bondy, M. L., Brand, R., Gallinger, S., Kurtz, R. C., Olson, S. H., Rustgi, A. K., Schwartz, A. G., Stoffel, E. M., Syngal, S., Zogopoulos, G., Ali, S. Z., Axilbund, J., Chaffee, K. G., Chen, Y. C., Cote, M. L., Childs, E. J., Douville, C., Goes, F. S., Herman, J. M., Iacobuzio-Donahue, C., Kramer, M., Makohon-Moore, A., McCombie, R. W., McMahon, K. W., Niknafs, N., Parla, J., Pirooznia, M., Potash, J. B., Rhim, A. D., Smith, A. L., Wang, Y., Wolfgang, C. L., Wood, L. D., Zandi, P. P., Goggins, M., Karchin, R., Eshleman, J. R., Papadopoulos, N., Kinzler, K. W., Vogelstein, B., Hruban, R. H., Klein, A. P. (February 2016) Whole genome sequencing defines the genetic heterogeneity of familial pancreatic cancer. Cancer Discov, 6 (2). pp. 166-175. ISSN 2159-8290 (Electronic)2159-8274 (Linking)

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. (December 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

Pirooznia, M., Kramer, M., Parla, J., Goes, F. S., Potash, J. B., McCombie, W. R., Zandi, P. P. (July 2014) Validation and assessment of variant calling pipelines for next-generation sequencing. Human Genomics, 8. ISSN 1473-95421479-7364 eISSN

Thomson, P. A., Parla, J. S., McRae, A. F., Kramer, M., Ramakrishnan, K., Yao, J., Soares, D. C., McCarthy, S., Morris, S. W., Cardone, L., Cass, S., Ghiban, E., Hennah, W., Evans, K. L., Rebolini, D., Millar, J. K., Harris, S. E., Starr, J. M., MacIntyre, D. J., McIntosh, A. M., Watson, J. D., Deary, I. J., Visscher, P. M., Blackwood, D. H., McCombie, W. R., Porteous, D. J. (June 2014) 708 Common and 2010 rare DISC1 locus variants identified in 1542 subjects: Analysis for association with psychiatric disorder and cognitive traits. Molecular Psychiatry, 19 (6). pp. 668-675. ISSN 14765578

McCarthy, S. E., Gillis, J., Kramer, M., Lihm, J., Yoon, S., Berstein, Y., Mistry, M., Pavlidis, P., Solomon, R., Ghiban, E., Antoniou, E., Kelleher, E., O'Brien, C., Donohoe, G., Gill, M., Morris, D. W., McCombie, W. R., Corvin, A. (June 2014) De novo mutations in schizophrenia implicate chromatin remodeling and support a genetic overlap with autism and intellectual disability. Molecular Psychiatry, 19 (6). pp. 652-658. ISSN 14765578

Yao, J., Zhang, K. X., Kramer, M., Pellegrini, M., McCombie, W. R. (January 2014) FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies. Bioinformatics. ISSN 1367-4803

Luo, M. C., Gu, Y. Q., You, F. M., Deal, K. R., Ma, Y., Hu, Y., Huo, N., Wang, Y., Wang, J., Chen, S., Jorgensen, C. M., Zhang, Y., McGuire, P. E., Pasternak, S., Stein, J. C., Ware, D., Kramer, M., McCombie, W. R., Kianian, S. F., Martis, M. M., Mayer, K. F. X., Sehgal, S. K., Li, W., Gill, B. S., Bevan, M. W., Šimková, H., Doležel, J., Weining, S., Lazo, G. R., Anderson, O. D., Dvorak, J. (May 2013) A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proceedings of the National Academy of Sciences of the United States of America, 110 (19). pp. 7940-7945. ISSN 00278424

Chen, Y. C., Carter, H., Parla, J., Kramer, M., Goes, F. S., Pirooznia, M., Zandi, P. P., McCombie, W. R., Potash, J. B., Karchin, R. (January 2013) A Hybrid Likelihood Model for Sequence-Based Disease Association Studies. PLoS Genetics, 9 (1). ISSN 15537390 (ISSN)

Brenchley, R., Spannagl, M., Pfeifer, M., Barker, G. L. A., D'Amore, R., Allen, A. M., McKenzie, N., Kramer, M., Kerhornou, A., Bolser, D., Kay, S., Waite, D., Trick, M., Bancroft, I., Gu, Y., Huo, N., Luo, M. C., Sehgal, S., Gill, B., Kianian, S., Anderson, O., Kersey, P., Dvorak, J., McCombie, W. R., Hall, A., Mayer, K. F. X., Edwards, K. J., Bevan, M. W., Hall, N. (November 2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature, 491 (7426). pp. 705-710. ISSN 00280836

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

Tyekucheva, S., Yolken, R. H., McCombie, W. R., Parla, J., Kramer, M., Wheelan, S. J., Sabunciyan, S. (October 2011) Establishing the baseline level of repetitive element expression in the human cortex. BMC Genomics, 12. article number 495. ISSN 1471-2164

Parla, J. S., Iossifov, I., Grabill, I., Spector, M. S., Kramer, M., McCombie, W. R. (September 2011) A comparative analysis of exome capture. Genome Biology, 12 (9). R97. ISSN 1474-7596

Argout, X., Salse, J., Aury, J. M., Guiltinan, M. J., Droc, G., Gouzy, J., Allegre, M., Chaparro, C., Legavre, T., Maximova, S. N., Abrouk, M., Murat, F., Fouet, O., Poulain, J., Ruiz, M., Roguet, Y., Rodier-Goud, M., Barbosa-Neto, J. F., Sabot, F., Kudrna, D., Ammiraju, J. S. S., Schuster, S. C., Carlson, J. E., Sallet, E., Schiex, T., Dievart, A., Kramer, M. R., Gelley, L., Shi, Z., Bérard, A., Viot, C., Boccara, M., Risterucci, A. M., Guignon, V., Sabau, X., Axtell, M. J., Ma, Z., Zhang, Y, Brown, S., Bourge, M., Golser, W., Song, X., Clement, D., Rivallan, R., Tahi, M., Akaza, J. M., Pitollat, B., Gramacho, K., D'Hont, A., Brunel, D., Infante, D., Kebe, I., Costet, P., Wing, R., McCombie, W. R., Guiderdoni, E., Quetier, F., Panaud, O., Wincker, P., Bocs, S., Lanaud, C. (2011) The genome of Theobroma cacao. Nature Genetics, 43 (2). pp. 101-108. ISSN 10614036

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)

Wei, F., Stein, J. C., Liang, C., Zhang, J., Fulton, R. S., Baucom, R. S., De Paoli, E., Zhou, S., Yang, L., Han, Y., Pasternak, S., Narechania, A., Zhang, L., Yeh, C. T., Ying, K., Nagel, D. H., Collura, K., Kudrna, D., Currie, J., Lin, J., Kim, H., Angelova, A., Scara, G., Wissotski, M., Golser, W., Courtney, L., Kruchowski, S., Graves, T. A., Rock, S. M., Adams, S., Fulton, L. A., Fronick, C., Courtney, W., Kramer, M., Spiegel, L., Nascimento, L., Kalyanaraman, A., Chaparro, C., Deragon, J. M., Miguel, P. S., Jiang, N., Wessler, S. R., Green, P. J., Yu, Y., Schwartz, D. C., Meyers, B. C., Bennetzen, J. L., Martienssen, R. A., McCombie, W. R., Aluru, S., Clifton, S. W., Schnable, P. S., Ware, D., Wilson, R. K., Wing, R. A. (November 2009) Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS genetics, 5 (11). e1000728. ISSN 1553-7404 (Electronic)1553-7390 (Linking)

Church, Deanna M., Goodstadt, Leo, Hillier, LaDeana W., Zody, Michael C., Goldstein, Steve, She, Xinwe, Bult, Carol J., Agarwala, Richa, Cherry, Joshua L., DiCuccio, Michael, Hlavina, Wratko, Kapustin, Yuri, Meric, Peter, Maglott, Donna, Birtle, Zoë, Marques, Ana C., Graves, Tina, Zhou, Shiguo, Teague, Brian, Potamousis, Konstantinos, Churas, Christopher, Place, Michael, Herschleb, Jill, Runnheim, Ron, Forrest, Daniel, Amos-Landgraf, James, Schwartz, David C., Cheng, Ze, Lindblad-Toh, Kerstin, Eichler, Evan E., Ponting, Chris P., The Mouse Genome Sequencing, Consortium (May 2009) Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse. PLoS Biol, 7 (5). e1000112.

Tanaka, T., Antonio, B. A., Kikuchi, S., Matsumoto, T., Nagamura, Y., Numa, H., Sakai, H., Wu, J., Itoh, T., Sasaki, T., Aono, R., Fujii, Y., Habara, T., Harada, E., Kanno, M., Kawahara, Y., Kawashima, H., Kubooka, H., Matsuya, A., Nakaoka, H., Saichi, N., Sanbonmatsu, R., Sato, Y., Shinso, Y., Suzuki, M., Takeda, J. I., Tanino, M., Todokoro, F., Yamaguchi, K., Yamamoto, N., Yamasaki, C., Imanishi, T., Okido, T., Tada, M., Ikeo, K., Tateno, Y., Gojobori, T., Lin, Y. C., Wei, F. J., Hsing, Y. I., Zhao, Q., Han, B., Kramer, M. R., McCombie, R. W., Lonsdale, D., O'Donovan, C. C., Whitfield, E. J., Apweiler, R., Koyanagi, K. O., Khurana, J. P., Raghuvanshi, S., Singh, N. K., Tyagi, A. K., Haberer, G., Fujisawa, M., Hosokawa, S., Ito, Y., Ikawa, H., Shibata, M., Yamamoto, M., Bruskiewich, R. M., Hoen, D. R., Bureau, T. E., Namiki, N., Ohyanagi, H., Sakai, Y., Nobushima, S., Sakata, K., Barrero, R. A., Sato, Y., Souvorov, A., Smith-White, B., Tatusova, T., An, S., An, G., Oota, S., Fuks, G., Messing, J., Christie, K. R., Lieberherr, D., Kim, H., Zuccolo, A., Wing, R. A., Nobuta, K., Green, P. J., Lu, C., Meyers, B. C., Chaparro, C., Piegu, B., Panaud, O., Echeverria, M. (January 2008) The rice annotation project database (RAP-DB): 2008 update. Nucleic Acids Research, 36 (Databa). D1028-D1033. ISSN 0305-1048

Hodges, E., Xuan, Z. Y., Balija, V., Kramer, M. R., Molla, M. N., Smith, S. W., Middle, C. M., Rodesch, M. J., Albert, T. J., Hannon, G. J., McCombie, W. R. (November 2007) Genome-wide in situ exon capture for selective resequencing. Nature Genetics, 39 (12). pp. 1522-7. ISSN 1061-4036

Choisne, N., Demange, N., Orjeda, G., Samain, S., D'Hont, A., Cattolico, L., Pelletier, E., Couloux, A., Segurens, B., Wincker, P., Scarpelli, C., Weissenbach, J., Salanoubat, M., Quetier, F., Singh, N. K., Mohapatra, T., Sharma, T. R., Gaikwad, K., Singh, A., Dalal, V., Srivastava, S. K., Dixit, A., Pal, A. K., Ghazi, I. A., Yadav, M., Pandit, A., Bhargava, A., Sureshbabu, K., Dixit, R., Singh, H., Swain, S. C., Pal, S., Ragiba, M., Singh, P. K., Singhal, V., Mendiratta, S. D., Batra, K., Raghuvanshi, S., Mohanty, A., Bharti, A. K., Gaur, A., Gupta, V., Kumar, D., Vydianathan, R., Vij, S., Kapur, A., Khurana, P., Sharma, S., Khurana, J. P., Tyagi, A. K., Yuan, Q. P., Ouyang, S., Liu, J., Zhu, W., Wang, A. H., Lin, H. N., Hamilton, J., Haas, B., Wortman, J., Jones, K. M., Kim, M., Overton, L., Tsitrin, T., Fadrosh, D., Bera, J., Weaver, B., Jin, S. H., Johri, S., Reardon, M., Vuong, H., Tallon, L., Van Aken, S., Lewis, M., Utterback, T., Feldblyum, T., Zismann, V., Iobst, S., Hsiao, J., de Vazeille, A. R., Salzberg, S. L., White, O., Fraser, C., Buell, C. R., Yu, Y., Rambo, T., Currie, J., Collura, K., Kim, H. R., Stum, D., Wang, W. M., Kudrna, D., Mueller, C., Wing, R. A., Kramer, M., Spiegel, L., Nascimento, L., Preston, R., Zutavern, T., Palmer, L., O'Shaughnessy, A., McCombie, W. R. (September 2005) The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. BMC Biology, 3. ISSN 1741-7007

Book Section

Parla, J., Kramer, M. R., McCombie, W. R. (2011) High-Throughput Sequencing. In: Microbial Forensics (Second Edition). Academic Press, San Diego, pp. 461-478.

Parla, J, Kramer, M, McCombie, WR (January 2010) High-Throughput Sequencing. In: Microbial Forensics, Second Edition. UNSPECIFIED, pp. 461-478. ISBN 9780123820068

Conference or Workshop Item

Iyer, Shruti V, Kramer, Melissa, Goodwin, Sara, McCombie, W Richard (2022) Cas9 based targeted nanopore sequencing helps identify structural variants in breast cancer genes. In: Annual Meeting of the American-Association-for-Cancer-Research (AACR), APR 08-13, 2022, New Orleans, LA.

Iyer, Shruti V, Kramer, Melissa, Goodwin, Sara, McCombie, W Richard (July 2021) Understanding genetic variation in cancer using nanopore targeted sequencing. In: AACR Annual Meeting 2021.

Iyer, Shruti V, Goodwin, Sara, Kramer, Melissa, McCombie, W Richard (August 2020) Understanding genetic variation in cancer using targeted nanopore long read sequencing. In: AACR Annual Meeting.

Ryan, Niamh, Lihm, Jayon, Kramer, Melissa, McCarthy, Shane, Evans, Kathryn, Ghiban, Elena, Millar, J Kirsty, Scotland, Generation, McIntosh, Andrew, Blackwood, Douglas, Lawrie, Stephen, Porteous, David, McCombie, W Richard, Thomson, Pippa (2019) BEYOND THE TRANSLOCATION: WHOLE GENOME SEQUENCING ANALYSIS OF THE SCOTTISH T(1;11) FAMILY. In: 25th World Congress of Psychiatric Genetics (WCPG).

Nattestad, Maria, Ng, Karen, Goodwin, Sara, Baslan, Timour, Sedlazeck, Fritz, Gurtowski, James, Hutton, Elizabeth, Sundaravadanam, Yogi, Garvin, Tyler, Alford, Marley, Tseng, Elizabeth, Rescheneder, Philipp, Chin, Jason, Beck, Timothy, Kramer, Melissa, McPherson, John, Hicks, James, Schatz, Michael C, McCombie, William R (2016) Comprehensive genome and transcriptome structural analysis of a breast cancer cell line using single molecule sequencing. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research, 2016 Apr 16-20, New Orleans, LA.