Items where Community is "McCombie lab"
- CSHL Communities (258)
- CSHL labs (258)
- McCombie lab (258)
- CSHL labs (258)
Paper
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)
Aguzzoli Heberle, Bernardo, Brandon, J Anthony, Page, Madeline L, Nations, Kayla A, Dikobe, Ketsile I, White, Brendan J, Gordon, Lacey A, Fox, Grant A, Wadsworth, Mark E, Doyle, Patricia H, Williams, Brittney A, Fox, Edward J, Shantaraman, Anantharaman, Ryten, Mina, Goodwin, Sara, Ghiban, Elena, Wappel, Robert, Mavruk-Eskipehlivan, Senem, Miller, Justin B, Seyfried, Nicholas T, Nelson, Peter T, Fryer, John D, Ebbert, Mark TW (May 2024) Mapping medically relevant RNA isoform diversity in the aged human frontal cortex with deep long-read RNA-seq. Nature Biotechnology. ISSN 1087-0156 (Public Dataset)
Stern, Shani, Zhang, Lei, Wang, Meiyan, Wright, Rebecca, Rosh, Idan, Hussein, Yara, Stern, Tchelet, Choudhary, Ashwani, Tripathi, Utkarsh, Reed, Patrick, Sadis, Hagit, Nayak, Ritu, Shemen, Aviram, Agarwal, Karishma, Cordeiro, Diogo, Peles, David, Hang, Yuqing, Mendes, Ana PD, Baul, Tithi D, Roth, Julien G, Coorapati, Shashank, Boks, Marco P, McCombie, W Richard, Hulshoff Pol, Hilleke, Brennand, Kristen J, Réthelyi, János M, Kahn, René S, Marchetto, Maria C, Gage, Fred H (May 2024) Monozygotic twins discordant for schizophrenia differ in maturation and synaptic transmission. Molecular Psychiatry. ISSN 1359-4184 (Public Dataset)
Koren, Sergey, Bao, Zhigui, Guarracino, Andrea, Ou, Shujun, Goodwin, Sara, Jenike, Katharine M, Lucas, Julian, McNulty, Brandy, Park, Jimin, Rautianinen, Mikko, Rhie, Arang, Roelofs, Dick, Schneiders, Harrie, Vrijenhoek, Ilse, Nijbroek, Koen, Ware, Doreen, Schatz, Michael C, Garrison, Erik, Huang, Sanwen, McCombie, William Richard, Miga, Karen H, Wittenberg, Alexander HJ, Phillippy, Adam M (March 2024) Gapless assembly of complete human and plant chromosomes using only nanopore sequencing. bioRxiv. (Submitted)
Gustafson, Jonas A, Gibson, Sophia B, Damaraju, Nikhita, Zalusky, Miranda Pg, Hoekzema, Kendra, Twesigomwe, David, Yang, Lei, Snead, Anthony A, Richmond, Phillip A, De Coster, Wouter, Olson, Nathan D, Guarracino, Andrea, Li, Qiuhui, Miller, Angela L, Goffena, Joy, Anderson, Zachery, Storz, Sophie Hr, Ward, Sydney A, Sinha, Maisha, Gonzaga-Jauregui, Claudia, Clarke, Wayne E, Basile, Anna O, Corvelo, Andre, Reeves, Catherine E, Helland, Adrienne, Musunuri, Rajeeva Lochan, Revsine, Mahler, Patterson, Karynne E, Paschal, Cate, Zakarian, Christina, Goodwin, Sara, Jensen, Tanner D, Robb, Esther, 1000 Genomes ONT Sequencing Consortium, University of Washington Center for Rare Disease Research (UW-CR, Genomics Research to Elucidate the Genetics of Rare Diseases (GR, McCombie, W Richard, Sedlazeck, Fritz J, Zook, Justin M, Montgomery, Stephen B, Garrison, Erik, Kolmogorov, Mikhail, Schatz, Michael C, McLaughlin, Richard N, Dashnow, Harriet, Zody, Michael C, Loose, Matthew, Jain, Miten, Eichler, Evan E, Miller, Danny E (March 2024) Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation. medRxiv. (Public Dataset) (Submitted)
Critical Assessment of Genome Interpretation Consortium (February 2024) CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biology, 25 (1). p. 53. ISSN 1474-7596
Badger, Jonathan H, Giordano, Rosanna, Zimin, Aleksey, Wappel, Robert, Eskipehlivan, Senem M, Muller, Stephanie, Donthu, Ravikiran, Soto-Adames, Felipe, Vieira, Paulo, Zasada, Inga, Goodwin, Sara (February 2024) Direct sequencing of insect symbionts via nanopore adaptive sampling. Current Opinion in Insect Science, 61. p. 101135. ISSN 2214-5745
Heberle, Bernardo Aguzzoli, Brandon, J Anthony, Page, Madeline L, Nations, Kayla A, Dikobe, Ketsile I, White, Brendan J, Gordon, Lacey A, Fox, Grant A, Wadsworth, Mark E, Doyle, Patricia H, Williams, Brittney A, Fox, Edward J, Shantaraman, Anantharaman, Ryten, Mina, Goodwin, Sara, Ghiban, Elena, Wappel, Robert, Mavruk-Eskipehlivan, Senem, Miller, Justin B, Seyfried, Nicholas T, Nelson, Peter T, Fryer, John D, Ebbert, Mark TW (December 2023) Using deep long-read RNAseq in Alzheimer's disease brain to assess medical relevance of RNA isoform diversity. bioRxiv. (Submitted)
Hegelmeyer, Nuri K, Parkin, Lia A, Previti, Mary L, Andrade, Joshua, Utama, Raditya, Sejour, Richard J, Gardin, Justin, Muller, Stephanie, Ketchum, Steven, Yurovsky, Alisa, Futcher, Bruce, Goodwin, Sara, Ueberheide, Beatrix, Seeliger, Jessica C (October 2023) Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria. mBio. e0084123. ISSN 2150-7511
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)
Hegelmeyer, Nuri K, Previti, Mary L, Andrade, Joshua, Utama, Raditya, Sejour, Richard J, Gardin, Justin, Muller, Stephanie, Ketchum, Steven, Yurovsky, Alisa, Futcher, Bruce, Goodwin, Sara, Ueberheide, Beatrix, Seeliger, Jessica C (March 2023) Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria. bioRxiv. (Submitted)
Akagi, Keiko, Symer, David E, Mahmoud, Medhat, Jiang, Bo, Goodwin, Sara, Wangsa, Darawalee, Li, Zhengke, Xiao, Weihong, Dunn, Joe Dan, Ried, Thomas, Coombes, Kevin R, Sedlazeck, Fritz J, Gillison, Maura L (January 2023) Intratumoral heterogeneity and clonal evolution induced by HPV integration. Cancer Discovery. ISSN 2159-8274 (Public Dataset)
Gladman, Nicholas, Goodwin, Sara, Chougule, Kapeel, Richard McCombie, William, Ware, Doreen (January 2023) Era of gapless plant genomes: innovations in sequencing and mapping technologies revolutionize genomics and breeding. Current Opinion in Biotechnology, 79. p. 102886. ISSN 0958-1669
Anderson, Erik W, Jin, Ying, Shih, Andrew, Arazi, Arnon, Goodwin, Sara, Roeser, Julien, Furie, Richard A, Aranow, Cynthia, Volpe, Bruce, Diamond, Betty, Mackay, Meggan (November 2022) Associations between circulating interferon and kynurenine/tryptophan pathway metabolites: support for a novel potential mechanism for cognitive dysfunction in SLE. Lupus Science & Medicine, 9 (1). e000808. ISSN 2053-8790
Baslan, Timour, Morris, John P, Zhao, Zhen, Reyes, Jose, Ho, Yu-Jui, Tsanov, Kaloyan M, Bermeo, Jonathan, Tian, Sha, Zhang, Sean, Askan, Gokce, Yavas, Aslihan, Lecomte, Nicolas, Erakky, Amanda, Varghese, Anna M, Zhang, Amy, Kendall, Jude, Ghiban, Elena, Chorbadjiev, Lubomir, Wu, Jie, Dimitrova, Nevenka, Chadalavada, Kalyani, Nanjangud, Gouri J, Bandlamudi, Chaitanya, Gong, Yixiao, Donoghue, Mark TA, Socci, Nicholas D, Krasnitz, Alex, Notta, Faiyaz, Leach, Steve D, Iacobuzio-Donahue, Christine A, Lowe, Scott W (August 2022) Ordered and deterministic cancer genome evolution after p53 loss. Nature. ISSN 0028-0836
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
Brennan, Christina M, Nadella, Sandeep, Zhao, Xiang, Dima, Richard J, Jordan-Martin, Nicole, Demestichas, Breanna R, Kleeman, Sam O, Ferrer, Miriam, von Gablenz, Eva Carlotta, Mourikis, Nicholas, Rubin, Michael E, Adnani, Harsha, Lee, Hassal, Ha, Taehoon, Prum, Soma, Schleicher, Cheryl B, Fox, Sharon S, Ryan, Michael G, Pili, Christina, Goldberg, Gary, Crawford, James M, Goodwin, Sara, Zhang, Xiaoyue, Preall, Jonathan B, Costa, Ana SH, Conigliaro, Joseph, Masci, Joseph R, Yang, Jie, Tuveson, David A, Tracey, Kevin J, Janowitz, Tobias (February 2022) Oral famotidine versus placebo in non-hospitalised patients with COVID-19: a randomised, double-blind, data-intense, phase 2 clinical trial. Gut. ISSN 0017-5749
Baslan, Timour, Kovaka, Sam, Sedlazeck, Fritz J, Zhang, Yanming, Wappel, Robert, Tian, Sha, Lowe, Scott W, Goodwin, Sara, Schatz, Michael C (September 2021) High resolution copy number inference in cancer using short-molecule nanopore sequencing. Nucleic Acids Research. ISSN 0305-1048
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
Jia, Xiaoming, Goes, Fernando S, Locke, Adam E, Palmer, Duncan, Wang, Weiqing, Cohen-Woods, Sarah, Genovese, Giulio, Jackson, Anne U, Jiang, Chen, Kvale, Mark, Mullins, Niamh, Nguyen, Hoang, Pirooznia, Mehdi, Rivera, Margarita, Ruderfer, Douglas M, Shen, Ling, Thai, Khanh, Zawistowski, Matthew, Zhuang, Yongwen, Abecasis, Gonçalo, Akil, Huda, Bergen, Sarah, Burmeister, Margit, Chapman, Sinéad, DelaBastide, Melissa, Juréus, Anders, Kang, Hyun Min, Kwok, Pui-Yan, Li, Jun Z, Levy, Shawn E, Monson, Eric T, Moran, Jennifer, Sobell, Janet, Watson, Stanley, Willour, Virginia, Zöllner, Sebastian, Adolfsson, Rolf, Blackwood, Douglas, Boehnke, Michael, Breen, Gerome, Corvin, Aiden, Craddock, Nick, DiFlorio, Arianna, Hultman, Christina M, Landen, Mikael, Lewis, Cathryn, McCarroll, Steven A, Richard McCombie, W, McGuffin, Peter, McIntosh, Andrew, McQuillin, Andrew, Morris, Derek, Myers, Richard M, O'Donovan, Michael, Ophoff, Roel, Boks, Marco, Kahn, Rene, Ouwehand, Willem, Owen, Michael, Pato, Carlos, Pato, Michele, Posthuma, Danielle, Potash, James B, Reif, Andreas, Sklar, Pamela, Smoller, Jordan, Sullivan, Patrick F, Vincent, John, Walters, James, Neale, Benjamin, Purcell, Shaun, Risch, Neil, Schaefer, Catherine, Stahl, Eli A, Zandi, Peter P, Scott, Laura J (September 2021) Correction: Investigating rare pathogenic/likely pathogenic exonic variation in bipolar disorder. Molecular Psychiatry, 26 (9). p. 5251. ISSN 1359-4184
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
Jia, Xiaoming, Goes, Fernando S, Locke, Adam E, Palmer, Duncan, Wang, Weiqing, Cohen-Woods, Sarah, Genovese, Giulio, Jackson, Anne U, Jiang, Chen, Kvale, Mark, Mullins, Niamh, Nguyen, Hoang, Pirooznia, Mehdi, Rivera, Margarita, Ruderfer, Douglas M, Shen, Ling, Thai, Khanh, Zawistowski, Matthew, Zhuang, Yongwen, Abecasis, Gonçalo, Akil, Huda, Bergen, Sarah, Burmeister, Margit, Chapman, Sinéad, DelaBastide, Melissa, Juréus, Anders, Kang, Hyun Min, Kwok, Pui-Yan, Li, Jun Z, Levy, Shawn E, Monson, Eric T, Moran, Jennifer, Sobell, Janet, Watson, Stanley, Willour, Virginia, Zöllner, Sebastian, Adolfsson, Rolf, Blackwood, Douglas, Boehnke, Michael, Breen, Gerome, Corvin, Aiden, Craddock, Nick, DiFlorio, Arianna, Hultman, Christina M, Landen, Mikael, Lewis, Cathryn, McCarroll, Steven A, Richard McCombie, W, McGuffin, Peter, McIntosh, Andrew, McQuillin, Andrew, Morris, Derek, Myers, Richard M, O'Donovan, Michael, Ophoff, Roel, Boks, Marco, Kahn, Rene, Ouwehand, Willem, Owen, Michael, Pato, Carlos, Pato, Michele, Posthuma, Danielle, Potash, James B, Reif, Andreas, Sklar, Pamela, Smoller, Jordan, Sullivan, Patrick F, Vincent, John, Walters, James, Neale, Benjamin, Purcell, Shaun, Risch, Neil, Schaefer, Catherine, Stahl, Eli A, Zandi, Peter P, Scott, Laura J (January 2021) Investigating rare pathogenic/likely pathogenic exonic variation in bipolar disorder. Molecular Psychiatry. ISSN 1359-4184
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
Chou, H. C., Bhalla, K., El Demerdash, O., Klingbeil, O., Hanington, Kaarina, Aganezov, S., Andrews, P., Alsudani, H., Chang, K., Vakoc, C. R., Schatz, M. C., McCombie, W. R., Stillman, B. (August 2020) The human Origin Recognition Complex is essential for pre-RC assembly, mitosis and maintenance of nuclear structure. BioRxiv. (Unpublished)
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
Wang, L., Lu, Z., Delabastide, M., Van Buren, P., Wang, X., Ghiban, C., Regulski, M., Drenkow, J., Xu, X., Ortiz-Ramirez, C., Marco, C.F., Goodwin, S., Dobin, A., Birnbaum, K. D., Jackson, D. P., Martienssen, R. A., McCombie, W. R., Micklos, D. A., Schatz, M. C., Ware, D. H., Gingeras, T. R. (March 2020) Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud. Frontiers in Plant Science, 11 (289). ISSN 1664-462X (Public Dataset)
Goodwin, S., McCombie, W. R. (December 2019) Sequencing Complex Genomes with PromethION Technology in a Core Setting. J Biomol Tech, 30 (Suppl). S36-s37. ISSN 1524-0215
Wang, Liya, Lu, Zhenyuan, delaBastide, Melissa, Van Buren, Peter, Wang, Xiaofei, Ghiban, Cornel, Regulski, Michael, Drenkow, Jorg, Xu, Xiaosa, Ortiz-Ramirez, Carlos, Fernandez-Marco, Cristina, Goodwin, Sara, Dobin, Alexander, Birnbaum, Kenneth, Jackson, David, Martienssen, Robert, McCombie, William, Micklos, David, Schatz, Michael, Ware, Doreen, Gingeras, Thomas (November 2019) Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud. BioRxiv. (Unpublished)
Li, Y., Brooks, M., Yeoh-Wang, J., McCoy, R. M., Rock, T. M., Pasquino, A., Moon, C. I., Patrick, R. M., Tanurdzic, M., Ruffel, S., Widhalm, J. R., McCombie, W. R., Coruzzi, G. M. (October 2019) SDG8-mediated histone methylation and RNA processing function in the response to nitrate signaling. Plant Physiol. ISSN 0032-0889
Iyer, S., Goodwin, S., McCombie, W. R. (July 2019) Adapting long read sequencing technologies for targeted and single cell applications. Cancer Research, 79 (13S). p. 5136. ISSN 0008-5472
Harold, D., Connolly, S., Riley, B. P., Kendler, K. S., McCarthy, S. E., McCombie, W. R., Richards, A., Owen, M. J., O'Donovan, M. C., Walters, J., Donohoe, G., Gill, M., Corvin, A., Morris, D. W. (February 2019) Population-based identity-by-descent mapping combined with exome sequencing to detect rare risk variants for schizophrenia. American Journal of Medical Genetics Part B-Neuropsychiatric Genetics, 180 (3). pp. 223-231. ISSN 0148-7299
McCombie, W. R., McPherson, J. D. (November 2018) Future Promises and Concerns of Ubiquitous Next-Generation Sequencing. Cold Spring Harb Perspect Med, 9 (9). ISSN 2157-1422
McCombie, W. R., McPherson, J. D., Mardis, E. R. (November 2018) Next-Generation Sequencing Technologies. Cold Spring Harb Perspect Med, 9 (11). ISSN 2157-1422
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
Wang, B., Regulski, M., Tseng, E., Olson, A., Goodwin, S., McCombie, W. R., Ware, D. (June 2018) A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing. Genome Res, 28 (6). pp. 921-932. ISSN 1088-9051
Varala, K., Marshall-Colon, A., Cirrone, J., Brooks, M. D., Pasquino, A. V., Leran, S., Mittal, S., Rock, T. M., Edwards, M. B., Kim, G. J., Ruffel, S., McCombie, W. R., Shasha, D., Coruzzi, G. M. (May 2018) Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants. Proc Natl Acad Sci U S A. ISSN 0027-8424
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
Grochowski, C. M., Gu, S., Yuan, B., Tcw, J., Brennand, K. J., Sebat, J., Malhotra, D., McCarthy, S., Rudolph, U., Lindstrand, A., Chong, Z., Levy, D. L., Lupski, J. R., Carvalho, C. M. B. (April 2018) Marker chromosome genomic structure and temporal origin implicate a chromoanasynthesis event in a family with pleiotropic psychiatric phenotypes. Hum Mutat, 39 (7). pp. 939-946. ISSN 1059-7794
McCartney, D. L., Walker, R. M., Morris, S. W., Anderson, S. M., Duff, B. J., Marioni, R. E., Millar, J. K., McCarthy, S. E., Ryan, N. M., Lawrie, S. M., Watson, A. R., Blackwood, D. H. R., Thomson, P. A., McIntosh, A. M., McCombie, W. R., Porteous, D. J., Evans, K. L. (March 2018) Altered DNA methylation associated with a translocation linked to major mental illness. NPJ Schizophr, 4 (1). p. 5. ISSN 2334-265X (Print)2334-265x
Martin, P. M., Stanley, R. E., Ross, A. P., Freitas, A. E., Moyer, C. E., Brumback, A. C., Iafrati, J., Stapornwongkul, K. S., Dominguez, S., Kivimae, S., Mulligan, K. A., Pirooznia, M., McCombie, W. R., Potash, J. B., Zandi, P. P., Purcell, S. M., Sanders, S. J., Zuo, Y., Sohal, V. S., Cheyette, B. N. (February 2018) DIXDC1 contributes to psychiatric susceptibility by regulating dendritic spine and glutamatergic synapse density via GSK3 and Wnt/beta-catenin signaling. Mol Psychiatry, 23 (2). pp. 467-475. ISSN 1476-5578 (Electronic)1359-4184 (Linking)
Monson, E., Pirooznia, M., Parla, J., Kramer, M., Goes, F., Breen, M., Gaynor, S., de Klerk, K., Jancic, D., Karchin, R., McCombie, W., Zandi, P., Potash, J., Willour, V. (October 2017) ASSESSMENT OF WHOLE-EXOME SEQUENCE DATA IN ATTEMPTED SUICIDE WITHIN A BIPOLAR COHORT. European Neuropsychopharmacology, 27. Meeting Abstract 20; S267-S268. ISSN 0924-977X
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Mardis, E., McPherson, J., Martienssen, R., Wilson, R. K., McCombie, W. R. (May 2002) What is finished, and why does it matter. Genome Research, 12 (5). pp. 669-671. ISSN 1088-9051
Xuan, Z., McCombie, W. R., Zhang, M. Q. (2002) GFScan: A gene family search tool at genomic DNA level. Genome Research, 12 (7). pp. 1142-1149. ISSN 10889051 (ISSN)
Waterston, R. H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J. F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P., Antonarakis, S. E., Attwood, J., Baertsch, R., Bailey, J., Barlow, K., Beck, S., Berry, E., Birren, B., Bloom, T., Bork, P., Botcherby, M., Bray, N., Brent, M. R., Brown, D. G., Brown, S. D., Bult, C., Burton, J., Butler, J., Campbell, R. D., Carninci, P., Cawley, S., Chiaromonte, F., Chinwalla, A. T., Church, D. M., Clamp, M., Clee, C., Collins, F. S., Cook, L. L., Copley, R. R., Coulson, A., Couronne, O., Cuff, J., Curwen, V., Cutts, T., Daly, M., David, R., Davies, J., Delehaunty, K. D., Deri, J., Dermitzakis, E. T., Dewey, C., Dickens, N. J., Diekhans, M., Dodge, S., Dubchak, I., Dunn, D. M., Eddy, S. R., Elnitski, L., Emes, R. D., Eswara, P., Eyras, E., Felsenfeld, A., Fewell, G. A., Flicek, P., Foley, K., Frankel, W. N., Fulton, L. A., Fulton, R. S., Furey, T. S., Gage, D., Gibbs, R. A., Glusman, G., Gnerre, S., Goldman, N., Goodstadt, L., Grafham, D., Graves, T. A., Green, E. D., Gregory, S., Guigó, R., Guyer, M., Hardison, R. C., Haussler, D., Hayashizaki, Y., LaHillier, D. W., Hinrichs, A., Hlavina, W., Holzer, T., Hsu, F., Hua, A., Hubbard, T., Hunt, A., Jackson, I., Jaffe, D. B., Johnson, L. S., Jones, M., Jones, T. A., Joy, A., Kamal, M., Karlsson, E. K. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420 (6915). pp. 520-562. ISSN 00280836 (ISSN)
Palmer, L. E., McCombie, W. R. (2002) On the importance of being finished. Genome Biology, 3 (10). 2010.1-2010.4. ISSN 14656906 (ISSN)
Wood, V., Gwilliam, R., Rajandream, M. A., Lyne, M., Lyne, R., Stewart, A., Sgouros, J., Peat, N., Hayles, J., Baker, S., Basham, D., Bowman, S., Brooks, K., Brown, D., Brown, S., Chillingworth, T., Churcher, C., Collins, M., Connor, R., Cronin, A., Davis, P., Feltwell, T., Fraser, A., Gentles, S., Goble, A., Hamlin, N., Harris, D., Hidalgo, J., Hodgson, G., Holroyd, S., Hornsby, T., Howarth, S., Huckle, E. J., Hunt, S., Jagels, K., James, K., Jones, L., Jones, M., Leather, S., McDonald, S., McLean, J., Mooney, P., Moule, S., Mungall, K., Murphy, L., Niblett, D., Odell, C., Oliver, K., O'Neil, S., Pearson, D., Quail, M. A., Rabbinowitsch, E., Rutherford, K., Rutter, S., Saunders, D., Seeger, K., Sharp, S., Skelton, J., Simmonds, M., Squares, R., Squares, S., Stevens, K., Taylor, K., Taylor, R. G., Tivey, A., Walsh, S., Warren, T., Whitehead, S., Woodward, J., Volckaert, G., Aert, R., Robben, J., Grymonprez, B., Weltjens, I., Vanstreels, E., Rieger, M., Schäfer, M., Müller-Auer, S., Gabel, C., Fuchs, M., Fritzc, C., Holzer, E., Moestl, D., Hilbert, H., Borzym, K., Langer, I., Beck, A., Lehrach, H., Reinhardt, R., Pohl, T. M., Eger, P., Zimmermann, W., Wedler, H., Wambutt, R., Purnelle, B., Goffeau, A., Cadieu, E., Dréano, S., Gloux, S., Lelaure, V. (2002) The genome sequence of Schizosaccharomyces pombe. Nature, 415 (6874). pp. 871-880. ISSN 00280836 (ISSN)
Wines, M. E., Lee, L., Katari, M. S., Zhang, L., DeRossi, C., Shi, Y., Perkins, S., Feldman, M., McCombie, W. Richard, Holdener, B. C. (2001) Identification of mesoderm development (mesd) candidate genes by comparative mapping and genome sequence analysis. Genomics, 72 (1). pp. 88-98. ISSN 08887543 (ISSN)
Soengas, M. S., Capodieci, P., Polsky, D., Mora, J., Esteller, M., Opitz-Araya, X., McCombie, R., Herman, J. G., Gerald, W. L., Lazebnik, Y. A., Cordon-Cardo, C., Lowe, S. W. (2001) Inactivation of the apoptosis effector Apaf-1 in malignant melanoma. Nature, 409 (6817). pp. 207-211. ISSN 0028-0836
Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., Fitzhugh, W., Funke, R., Gage, D., Harris, K., Heaford, A., Howland, J., Kann, L., Lehoczky, J., Levine, R., McEwan, P., McKernan, K., Meldrim, J., Mesirov, J. P., Miranda, C., Morris, W., Naylor, J., Raymond, C., Rosetti, M., Santos, R., Sheridan, A., Sougnez, C., Stange-Thomann, N., Stojanovic, N., Subramanian, A., Wyman, D., Rogers, J., Sulston, J., Ainscough, R., Beck, S., Bentley, D., Burton, J., Clee, C., Carter, N., Coulson, A., Deadman, R., Deloukas, P., Dunham, A., Dunham, I., Durbin, R., French, L., Grafham, D., Gregory, S., Hubbard, T., Humphray, S., Hunt, A., Jones, M., Lloyd, C., McMurray, A., Matthews, L., Mercer, S., Milne, S., Mullikin, J. C., Mungall, A., Plumb, R., Ross, M., Shownkeen, R., Sims, S., Waterston, R. H., Wilson, R. K., Hillier, L. W., McPherson, J. D., Marra, M. A., Mardis, E. R., Fulton, L. A., Chinwalla, A. T., Pepin, K. H., Gish, W. R., Chissoe, S. L., Wendl, M. C., Delehaunty, K. D., Miner, T. L., Delehaunty, A., Kramer, J. B., Cook, L. L., Fulton, R. S., Johnson, D. L., Minx, P. J., Clifton, S. W., Hawkins, T., Branscomb, E., Predki, P., Richardson, P., Wenning, S., Slezak, T., Doggett, N., Cheng, J. F., Olsen, A., Lucas, S., Elkin, C., Uberbacher, E., Frazier, M. (2001) Initial sequencing and analysis of the human genome. Nature, 409 (6822). pp. 860-921. ISSN 00280836 (ISSN)
Martienssen, R., McCombie, W. R. (2001) The first plant genome. Cell, 105 (5). pp. 571-574. ISSN 00928674 (ISSN)
Fransz, P. F., Armstrong, S., de Jong, J. H., Parnell, L. D., van Drunen, G., Dean, C., Zabel, P., Bisseling, T., Jones, G. H. (February 2000) Integrated cytogenetic map of chromosome arm 4S of A-thaliana: Structural organization of heterochromatic knob and centromere region. Cell, 100 (3). pp. 367-376. ISSN 0092-8674
Kaul, S., Koo, H. L., Jenkins, J., Rizzo, M., Rooney, T., Tallon, L. J., Feldblyum, T., Nierman, W., Benito, M. I., Lin, X., Town, C. D., Venter, J. C., Fraser, C. M., Tabata, S., Nakamura, Y., Kaneko, T., Sato, S., Asamizu, E., Kato, T., Kotani, H., Sasamoto, S., Ecker, J. R., Theologis, A., Federspiel, N. A., Palm, C. J., Osborne, B. I., Shinn, P., Dewar, K., Kim, C. J., Buehler, E., Dunn, P., Chao, Q., Chen, H., Vysotskaia, V. S., Lenz, C. A., Hansen, N. F., Liu, S. X., Alta, H., Sakano, H., Lam, B., Pham, P. K., Nguyen, M., Yu, G., Southwick, A., Lee, J. M., Miranda, M., Toriumi, M. J., Davis, R. W., Conway, A. B., Conn, L., Hootan, A., Wambutt, R., Murphy, G., Düsterhöft, A., Stiekema, W., Pohl, T., Entian, K. D., Terryn, N., Volckaert, G., Salanoubat, M., Choisne, N., Artiguenave, F., Weissenbach, J., Quetier, F., Rieger, M., Ansorge, W., Unseld, M., Fartmann, B., Valle, G., Wilson, R. K., Sekhon, M., Pepin, K., Murray, J., Johnson, D., Hillier, L., de la Bastide, M., Huang, E., Spiegel, L., Gnoj, L., Habermann, K., Dedhia, N., Parnell, L., Preston, R., Marra, M., McCombie, W. R., Chen, E., Martienssen, R., Mayer, K., Lemcke, K., Haas, B., Haase, D., Rudd, S., Schoof, H., Frishman, D., Morgenstern, B., Zaccaria, P., Mewes, H. W., White, O., Creasy, T. H., Bielke, C. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408 (6814). pp. 796-815. ISSN 00280836 (ISSN)
Tabata, S., Kaneko, T., Nakamura, Y., Kotani, H., Kato, T., Asamizu, E., Miyajima, N., Sasamoto, S., Kimura, T., Hosouchi, T., Kawashima, K., Kohara, M., Matsumoto, M., Matsuno, A., Muraki, A., Nakayama, S., Nakazaki, N., Naruo, K., Okumura, S., Shinpo, S., Takeuchi, C., Wada, T., Watanabe, A., Yamada, M., Yasuda, M., Sato, S., de la Bastide, M., Huang, E., Spiegel, L., Gnoj, L., O'Shaughnessy, A., Preston, R., Habermann, K., Murray, J., Johnson, D., Rohlfing, T., Nelson, J., Stoneking, T., Pepin, K., Spieth, J., Sekhon, M., Armstrong, J., Becker, M., Belter, E., Cordum, H., Cordes, M., Courtney, L., Courtney, W., Dante, M., Du, H., Edwards, J., Fryman, J., Haakensen, B., Lamar, E., Latreille, P., Leonard, S., Meyer, R., Mulvaney, E., Ozersky, P., Riley, A., Strowmatt, C., Wagner-McPherson, C., Wollam, A., Yoakum, M., Bell, M., Dedhia, N., Parnell, L., Shah, R., Rodriguez, M., See, L. H., Vil, D., Baker, J., Kirchoff, K., Toth, K., King, L., Bahret, A., Miller, B., Marra, M., Martienssen, R., McCombie, W. R., Wilson, R. K., Murphy, G., Bancroft, I., Volckaert, G., Wambutt, R., Düsterhöft, A., Stiekema, W., Pohl, T., Entian, K. D., Terryn, N., Hartley, N., Bent, E., Johnson, S., Langham, S. A., McCullagh, B., Robben, J., Grymonprez, B., Zimmermann, W., Ramsperger, U., Wedler, H. (2000) Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. Nature, 408 (6814). pp. 823-826. ISSN 00280836 (ISSN)
McCombie, W. R., De la Bastide, M., Habermann, K., Parnell, L., Dedhia, N., Gnoj, L., Schutz, K., Huang, E., Spiegel, L., Yordan, C., Sehkon, M., Murray, J., Sheet, P., Cordes, M., Threideh, J., Stoneking, T., Kalicki, J., Graves, T., Harmon, G., Edwards, J., Latreille, P., Courtney, L., Cloud, J., Abbott, A., Scott, K., Johnson, D., Minx, P., Bentley, D., Fulton, B., Miller, N., Greco, T., Kemp, K., Kramer, J., Fulton, L., Mardis, E., Dante, M., Pepin, K., Hillier, L., Nelson, J., Spieth, J., Simorowski, J., May, B., Ma, P., Preston, R., Vil, D., Lei, H. S., Shekher, M., Matero, A., Shah, R., Swaby, I., O'Shaughnessy, A., Rodriguez, M., Hoffman, J., Till, S., Granat, S., Shohdy, N., Hasegawa, A., Hameed, A., Lodhi, M., Johnson, A., Chen, E., Marra, M., Wilson, R. K., Martienssen, R. (2000) The complete sequence of a heterochromatic island from a higher eukaryote. Cell, 100 (3). pp. 377-386. ISSN 00928674 (ISSN)
Mayer, K., Schuller, C., Wambutt, R., Murphy, G., Volckaert, G., Pohl, T., Dusterhoft, A., Stiekema, W., Entian, K. D., Terryn, N., Harris, B., Ansorge, W., Brandt, P., Grivell, L., Rieger, M., Weichselgartner, M., de Simone, V., Obermaier, B., Mache, R., Muller, M., Kreis, M., Delseny, M., Puigdomenech, P., Watson, M., Schmidtheini, T., Reichert, B., Portatelle, D., Perez-Alonso, M., Boutry, M., Bancroft, I., Vos, P., Hoheisel, J., Zimmermann, W., Wedler, H., Ridley, P., Langham, S. A., McCullagh, B., Bilham, L., Robben, J., Van der Schueren, J., Grymonprez, B., Chuang, Y. J., Vandenbussche, F., Braeken, M., Weltjens, I., Voet, M., Bastiaens, I., Aert, R., Defoor, E., Weitzenegger, T., Bothe, G., Ramsperger, U., Hilbert, H., Braun, M., Holzer, E., Brandt, A., Peters, S., van Staveren, M., Dirske, W., Mooijman, P., Klein Lankhorst, R., Rose, M., Hauf, J., Kotter, P., Berneiser, S., Hempel, S., Feldpausch, M., Lamberth, S., Van den Daele, H., De Keyser, A., Buysshaert, C., Gielen, J., Villarroel, R., De Clercq, R., Van Montagu, M., Rogers, J., Cronin, A., Quail, M., Bray-Allen, S., Clark, L., Doggett, J., Hall, S., Kay, M., Lennard, N., McLay, K., Mayes, R., Pettett, A., Rajandream, M. A., Lyne, M., Benes, V., Rechmann, S., Borkova, D., Blocker, H., Scharfe, M., Grimm, M., Lohnert, T. H., Dose, S., de Haan, M., Maarse, A., Schafer, M., Müller-Auer, S., Gabel, C., Fuchs, M., Fartmann, B., Granderath, K., Dauner, D., Herzl, A., Neumann, S., Argiriou, A., Vitale, D., Liguori, R., Piravandi, E., Massenet, O., Quigley, F., Clabauld, G., Mundlein, A., Felber, R., Schnabl, S., Hiller, R., Schmidt, W., Lecharny, A., Aubourg, S., Chefdor, F., Berger, C., Montfort, A., Casacuberta, E., Gibbons, T., Weber, N., Vandenbol, M., Bargues, M., Terol, J., Perez-Perez, A., Purnelle, B., Bent, E., Johnson, S., Tacon, D., Jesse, T., Heijnen, L., Schwarz, S., Scholler, P., Heber, S., Francs, P., Bielke, C., Frishman, D., Haase, D., Lemcke, K., Mewes, H. W., Stocker, S., Zaccaria, P., Bevan, M., Wilson, R. K., de la Bastide, M., Habermann, K., Parnell, L., Dedhia, N., Gnoj, L., Schutz, K., Huang, E., Spiegel, L., Sehkon, M., Murray, J., Sheet, P., Cordes, M., Abu-Threideh, J., Stoneking, T., Kalicki, J., Graves, T., Harmon, G., Edwards, J., Latreille, P., Courtney, L., Cloud, J., Abbott, A., Scott, K., Johnson, D., Minx, P., Bentley, D., Fulton, B., Miller, N., Greco, T., Kemp, K., Kramer, J., Fulton, L., Mardis, E., Pepin, K., Hillier, L., Nelson, J., Spieth, J., Ryan, E., Andrews, S., Geisel, C., Layman, D., Du, H., Ali, J., Berghoff, A., Jones, K., Drone, K., Cotton, M., Joshu, C., Antonoiu, B., Zidanic, M., Strong, C., Sun, H., Lamar, B., Yordan, C., Ma, P., Zhong, J., Preston, R., Vil, D., Shekher, M., Matero, A., Shah, R., Swaby, I.K., O'Shaughnessy, A., Rodriguez, M., Hoffmann, J., Till, S., Granat, S., Shohdy, N., Hasegawa, A., Hameed, A., Lodhi, M., Johnson, A., Chen, E., Marra, M., Martienssen, R., McCombie, W. R. (December 1999) Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature, 402 (6763). pp. 769-77. ISSN 0028-0836 (Print)0028-0836 (Linking)
Yang, M., Hu, Y., Lodhi, M., McCombie, W. R., Ma, H. (1999) The Arabidopsis SKP1-LIKE1 gene is essential for male meiosis and may control homologue separation. Proceedings of the National Academy of Sciences of the United States of America, 96 (20). pp. 11416-11421. ISSN 00278424 (ISSN)
Bevan, M., Bancroft, I., Mewes, H. W., Martienssen, R., McCombie, R. (1999) Clearing a path through the jungle: Progress in Arabidopsis genomics. Bioessays, 21 (2). pp. 110-120. ISSN 02659247 (ISSN)
Rabinowicz, P. D., Schutz, K., Dedhia, N., Yordan, C., Parnell, L. D., Stein, L., McCombie, W. R., Martienssen, R. A. (1999) Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nature Genetics, 23 (3). pp. 305-308. ISSN 10614036 (ISSN)
Copenhaver, G. P., Nickel, K., Kuromori, T., Benito, M. I., Kaul, S., Lin, X., Bevan, M., Murphy, G., Harris, B., Parnell, L. D., McCombie, W. R., Martienssen, R. A., Marra, M., Preuss, D. (1999) Genetic definition and sequence analysis of Arabidopsis centromeres. Science, 286 (5449). pp. 2468-2474. ISSN 00368075 (ISSN)
Marra, M., Kucaba, T., Sekhon, M., Hillier, L., Martienssen, R., Chinwalla, A., Crockett, J., Fedele, J., Grover, H., Gund, C., McCombie, W. R., McDonald, K., McPherson, J., Mudd, N., Parnell, L., Schein, J., Seim, R., Shelby, P., Waterston, R., Wilson, R. (1999) A map for sequence analysis of the Arabidopsis thaliana genome. Nature Genetics, 22 (3). pp. 265-270. ISSN 10614036 (ISSN)
Lucito, R., Nakimura, M., West, J. A., Han, Y., Chin, K., Jensen, K. R., McCombie, R. W., Gray, J. W., Wigler, M. H. (April 1998) Genetic analysis using genomic representations. Proceedings of the National Academy of Sciences of the United States of America, 95 (8). pp. 4487-92. ISSN 0027-8424
Hamaguchi, M., O'Connor, E. A., Chen, T., Parnell, L., McCombie, R. W., Wigler, M. H. (March 1998) Rapid isolation of cDNA by hybridization. Proceedings of the National Academy of Sciences of the United States of America, 95 (7). pp. 3764-9. ISSN 0027-8424
Dedhia, N. N., McCombie, W. R. (1998) Kaleidaseq: A Web-based tool to monitor data flow in a high throughput sequencing facility. Genome Research, 8 (3). pp. 313-318. ISSN 10889051 (ISSN)
Bevan, M., Ecker, J., Theologis, S., Federspiel, N., Davis, R., McCombie, D., Martienssen, R., Chen, E., Waterston, B., Wilson, R., Rounsley, S., Venter, C., Tabata, S., Salanoubat, M., Quetier, F., Cherry, J. M., Meinke, D. (April 1997) Objective: The complete sequence of a plant genome. Plant cell, 9 (4). pp. 476-478. ISSN 1040-4651
Li, J., Yen, C., Liaw, D., Podsypanina, K., Bose, S., Wang, S. I., Puc, J., Miliaresis, C., Rodgers, L., McCombie, R., Bigner, S. H., Giovanella, B. C., Ittmann, M., Tycko, B., Hibshoosh, H., Wigler, M. H., Parsons, R. (March 1997) PTEN, a putative protein tyrosine phosphatase gene mutated in human brain, breast, and prostate cancer. Science, 275 (5308). pp. 1943-7. ISSN 0036-8075 (Print)
Olde, B., McCombie, W. R. (1997) Molecular cloning and functional expression of a serotonin receptor from Caenorhabditis elegans. Journal of Molecular Neuroscience, 8 (1). pp. 53-62. ISSN 08958696 (ISSN)
Lodhi, M. A., McCombie, W. R. (January 1996) High-quality automated DNA sequencing primed with hexamer strings. Genome Research, 6 (1). pp. 10-18. ISSN 1054-9803
Johnson, A. F., Lodhi, M. A., McCombie, W. R. (1996) Fluorescence-based sequencing of double-stranded DNA by hexamer string priming. Analytical Biochemistry, 241 (2). pp. 228-237. ISSN 00032697 (ISSN)
Springer, P. S., McCombie, W. R., Sundaresan, V., Martienssen, R. A. (May 1995) Gene trap tagging of PROLIFERA, an essential MCM2-3-5-like gene in Arabidopsis. Science, 268 (5212). pp. 877-880. ISSN 0036-8075
McCombie, W. R., Kieleczawa, J. (1994) Automated DNA sequencing using 4-color fluorescent detection of reactions primed with hexamer strings. Biotechniques, 17 (3). pp. 574-579. ISSN 07366205 (ISSN)
Brown, P., Cervenáková, L., Goldfarb, L. G., McCombie, W. R., Rubenstein, R., Will, R. G., Pocchiari, M., Martinez-Lage, J. F., Scalici, C., Masullo, C., Graupera, G., Ligan, J., Gajdusek, D. C. (1994) Iatrogenic Creutzfeldt-Jakob disease: An example of the interplay between ancient genes and modern medicine. Neurology, 44 (2). pp. 291-293. ISSN 00283878 (ISSN)
Scorer, C. A., Clare, J. J., McCombie, W. R., Romanos, M. A., Sreekrishna, K. (1994) Rapid selection using G418 of high copy number transformants of Pichia pastoris for high-level foreign gene expression. Nature Biotechnology, 12 (2). pp. 181-184. ISSN 10870156 (ISSN)
Mizukami, T., Chang, W. I., Garkavtsev, I., Kaplan, N., Lombardi, D., Matsumoto, T., Niwa, O., Kounosu, A., Yanagida, M., Marr, T. G., Beach, D. (April 1993) A 13-Kb Resolution Cosmid Map of the 14-Mb Fission Yeast Genome by Nonrandom Sequence-Tagged Site Mapping. Cell, 73 (1). pp. 121-132. ISSN 0092-8674
Goldfarb, L. G., Brown, P., Rubenstein, R., McCombie, W. R., Cervenakova, L., Graupera, G., Ligan, J., Sulima, M., Gibbs, C. J., Gajdusek, D. C. (August 1992) Genetic-characteristics of infectious forms of the transmissible spongiform encephalopathies. Annals of neurology, 32 (2). p. 233. ISSN 0364-5134
Brown, P., Goldfarb, L. G., McCombie, W. R., Nieto, A., Squillacote, D., Sheremata, W., Little, B. W., Godec, M. S., Gibbs Jr, C. J., Gajdusek, D. C. (1992) Atypical Creutzfeldt-Jakob disease in an American family with an insert mutation in the PRNP amyloid precursor gene. Neurology, 42 (2). pp. 422-427. ISSN 00283878 (ISSN)
Martin-Gallardo, A., McCombie, W. R., Gocayne, J. D., FitzGerald, M. G., Wallace, S., Lee, B. M. B., Lamerdin, J., Trapp, S., Kelley, J. M., Liu, L. I., Dubnick, M., Johnston-Dow, L. A., Kerlavage, A. R., De Jong, P., Carrano, A., Fields, C., Venter, J. C. (1992) Automated DNA sequencing and analysis of 106 kilobases from human chromosome 19q13.3. Nature Genetics, 1 (1). pp. 34-39. ISSN 10614036 (ISSN)
McCombie, W. R., Adams, M. D., Kelley, J. M., FitzGerald, M. G., Utterback, T. R., Khan, M., Dubnick, M., Kerlavage, A. R., Venter, J. C., Fields, C. (1992) Caenorhabditis elegans expressed sequence tags identify gene families and potential disease gene homologues. Nature Genetics, 1 (2). pp. 124-131. ISSN 10614036 (ISSN)
Goldfarb, L. G., Brown, P., Haltia, M., Cathala, F., McCombie, W. R., Kovanen, J., Červeňáková, L., Goldin, L., Nieto, A., Godec, M. S., Asher, D. M., Gajdusek, D. C. (1992) Creutzfeldt-Jakob disease cosegregates with the codon 178Asn PRNP mutation in families of European origin. Annals of neurology, 31 (3). pp. 274-281. ISSN 03645134 (ISSN)
McCombie, W. R., Martin-Gallardo, A., Gocayne, J. D., FitzGerald, M., Dubnick, M., Kelley, J. M., Castilla, L., Liu, L. I., Wallace, S., Trapp, S., Tagle, D., Whaley, W. L., Cheng, S., Gusella, J., Frischauf, A. M., Poustka, A., Lehrach, H., Collins, F. S., Kerlavage, A. R., Fields, C., Venter, J. C. (1992) Expressed genes, Alu repeats and polymorphisms in cosmids sequenced from chromosome 4p16.3. Nature Genetics, 1 (5). pp. 348-353. ISSN 10614036 (ISSN)
Venter, J. C., Adams, M. D., Martin-Gallardo, A., McCombie, W. R., Fields, C. (1992) Genome sequence analysis: Scientific objectives and practical strategies. Trends in Biotechnology, 10 (1-2). pp. 8-11. ISSN 01679430 (ISSN)
McCombie, W. R., Heiner, C., Kelley, J. M., Fitzgerald, M. G., Gocayne, J. D. (1992) Rapid and reliable fluorescent cycle sequencing of double-stranded templates. DNA sequence : the journal of DNA sequencing and mapping, 2 (5). pp. 289-296. ISSN 10425179 (ISSN)
Martin-Gallardo, A., Marchuk, D. A., Gocayne, J., Kerlavage, A. R., McCombie, W. R., Venter, J. C., Collins, F. S., Wallace, M. R. (1992) Sequencing and analysis of genomic fragments from the NF1 locus. DNA sequence : The journal of DNA sequencing and mapping, 3 (4). pp. 237-243. ISSN 10425179 (ISSN)
Goldfarb, L. G., Brown, P., Vrbovska, A., Baron, H., McCombie, W. R., Cathala, F., Gibbs Jr, C. J., Gajdusek, D. C. (1992) An insert mutation in the chromosome 20 amyloid precursor gene in a Gerstmann-Straussler-Scheinker family. Journal of the Neurological Sciences, 111 (2). pp. 189-194. ISSN 0022510X (ISSN)
Goldfarb, L. G., Brown, P., Nuez, A. N., McCombie, W. R., Goldgaber, D., Asher, D. M., Gaidusek, D. C. (October 1991) FAMILIAL CREUTZFELDT-JAKOB DISEASE IS ASSOCIATED WITH 3 SEPARATE MUTATIONS. American Journal of Human Genetics, 49 (4). p. 188. ISSN 0002-9297
Richard McCombie, W, Kirkness, E, Fleming, JT, Kerlavage, AR, Iovannisci, DM, Martin-Gallardo, A (January 1991) The use of exonuclease III deletions in automated DNA sequencing. Methods, 3 (1). pp. 33-40. ISSN 1046-2023
Nieto, A., Goldfarb, L. G., Brown, P., McCombie, W. R., Trapp, S., Asher, D. M., Gajdusek, D. C. (1991) Codon 178 mutation in ethnically diverse Creutzfeldt-Jakob disease families [29]. Lancet, 337 (8741). pp. 622-623. ISSN 01406736 (ISSN)
Adams, M. D., Kelley, J. M., Gocayne, J. D., Dubnick, M., Polymeropoulos, M. H., Xiao, H., Merril, C. R., Wu, A., Olde, B., Moreno, R. F., Kerlavage, A. R., McCombie, W. R., Venter, J. C. (1991) Complementary DNA sequencing: Expressed sequence tags and human genome project. Science, 252 (5013). pp. 1651-1656. ISSN 00368075 (ISSN)
Goldfarb, L. G., Haltia, M., Brown, P., Nieto, A., Kovanen, J., McCombie, W. R., Trapp, S., Carleton Gajdusek, D. (1991) New mutation in scrapie amyloid precursor gene (at codon 178) in finnish Creutzfield-Jakob kindred. Lancet, 337 (8738). p. 425. ISSN 01406736 (ISSN)
Goldfarb, L. G., Brown, P., McCombie, W. R., Goldgaber, D., Swergold, G. D., Wills, P. R., Cervenakova, L., Baron, H., Gibbs Jr, C. J., Gajdusek, D. C. (1991) Transmissible familial Creutzfeldt-Jakob disease associated with five, seven, and eight extra octapeptide coding repeats in the PRNP gene. Proceedings of the National Academy of Sciences of the United States of America, 88 (23). pp. 10926-10930. ISSN 00278424 (ISSN)
Muzzin, P., Revelli, J. P., Kuhne, F., Gocayne, J. D., McCombie, W. R., Venter, J. C., Giacobino, J. P., Fraser, C. M. (1991) An adipose tissue-specific β-adrenergic receptor. Molecular cloning and down-regulation in obesity. Journal of Biological Chemistry, 266 (35). pp. 24053-24058. ISSN 00219258 (ISSN)
Arakawa, S., Gocayne, J. D., McCombie, W. R., Urquhart, D. A., Hall, L. M., Fraser, C. M., Venter, J. C. (1990) Cloning, localization, and permanent expression of a Drosophila octopamine receptor. Neuron, 4 (3). pp. 343-354. ISSN 08966273 (ISSN)
Venter, J. C., McCombie, W. R., McConnell, J. B. (1990) Genome sequencing conference I: Summary. Genomics, 8 (1). pp. 186-188. ISSN 08887543 (ISSN)
Onai, T., FitzGerald, M. G., Arakawa, S., Gocayne, J. D., Urquhart, D. A., Hall, L. M., Fraser, C. M., McCombie, W. R., Venter, J. C. (1989) Cloning, sequence analysis and chromosome localization of a Drosophila muscarinic acetylcholine receptor. FEBS Letters, 255 (2). pp. 219-225. ISSN 00145793 (ISSN)
Fraser, C. M., Arakawa, S., McCombie, W. R., Venter, J. C. (1989) Cloning, sequence analysis, and permanent expression of a human α2-adrenergic receptor in Chinese hamster ovary cells. Evidence for independent pathways of receptor coupling to adenylate cyclase attenuation and activation. Journal of Biological Chemistry, 264 (20). pp. 11754-11761. ISSN 00219258 (ISSN)
Zylstra, G. J., McCombie, W. R., Gibson, D. T., Finette, B. A. (June 1988) Toluene Degradation by Pseudomonas putida Fl:Genetic Organization of the tod Operon. Applied and Environmental Microbiology, 54 (6). pp. 1498-1503. ISSN 0099-2240
Sreekrishna, K., Potenz, R. H. B., Cruze, J. A., McCombie, W. R., Parker, K. A., Nelles, L., Mazzaferro, P. K., Holden, K. A., Harrison, R. G., Wood, P. J., Phelps, D. A., Hubbard, C. E., Fuke, M. (1988) High level expression of heterologous proteins in methylotrophic yeast Pichia pastoris. Journal of Basic Microbiology, 28 (4). pp. 265-278. ISSN 0233111X (ISSN)
Whited, G. M., McCombie, W. R., Kwart, L. D., Gibson, D. T. (June 1986) Identification of cis-diols as intermediates in the oxidation of aromatic acids by a strain of Pseudomonas putida that contains a TOL plasmid. Journal of Bacteriology, 166 (3). pp. 1028-1039. ISSN 0021-9193
McCombie, W. R., Hansen, J. B., Zylstra, G. J., Maurer, B., Olsen, R. H. (1983) Pseudomonas Streptomycin Resistance Transposon Associated with R-Plasmid Mobilization. Journal of Bacteriology, 155 (1). pp. 40-48. ISSN 0021-9193
Olsen, R. H., Debusscher, G., McCombie, W. R. (1982) Development of broad-host-range vectors and gene banks: self-cloning of the Pseudomonas aeruginosa PAO chromosome. Journal of Bacteriology, 150 (1). pp. 60-69. ISSN 0021-9193
Book Section
McCombie, W. R., Mardis, E. (2012) DNA Sequencing. In: Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, pp. 736-892. ISBN 9781936113422
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
McCombie, W. R. (1994) Large-scale automated sequencing human chromosomal regions. In: Automated DNA Sequencing and Analysis. Academic Press, pp. 159-166. ISBN 9780127170107
McCombie, W. R. (1994) The use of automated DNA sequencing in the analysis of cDNAs of model organisms. In: Automated DNA Sequencing and Analysis. Academic Press, pp. 77-80. ISBN 9780127170107
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).
Rosenfeld, Jeffrey, Goodwin, Sara, Ganesan, Shridar (2017) The use of long-read sequencing to determine the structure of the Her2 amplicon in breast cancer. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017, 2017 Apr 1-5, Washington, DC..
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.
Book
Pollock, L., McCombie, W. R., Witkowski, J., eds. (2018) Faces of the Genome. Cold Spring Harbor Laboratory Press. ISBN 9781621822936
Video
McCombie, W. R. (November 2012) Talk from Dick McCombie at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)