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2021 Journal Article Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptomeTroskie, Robin-Lee, Jafrani, Yohaann, Mercer, Tim R., Ewing, Adam D., Faulkner, Geoffrey J. and Cheetham, Seth W. (2021). Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome. Genome Biology, 22 (1) 146, 1-15. doi: 10.1186/s13059-021-02369-0 |
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2021 Journal Article Microdeletion of 9q22.3: a patient with minimal deletion size associated with a severe phenotypeEwing, Adam D., Cheetham, Seth W., McGill, James J., Sharkey, Michael, Walker, Rick, West, Jennifer A., West, Malcolm J. and Summers, Kim M. (2021). Microdeletion of 9q22.3: a patient with minimal deletion size associated with a severe phenotype. American Journal of Medical Genetics Part A, 185 (7) ajmg.a.62224, 2070-2083. doi: 10.1002/ajmg.a.62224 |
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2020 Journal Article Nanopore sequencing enables comprehensive transposable element epigenomic profilingEwing, Adam D., Smits, Nathan, Sanchez-Luque, Francisco J., Faivre, Jamila, Brennan, Paul M., Richardson, Sandra R., Cheetham, Seth W. and Faulkner, Geoffrey J. (2020). Nanopore sequencing enables comprehensive transposable element epigenomic profiling. Molecular Cell, 80 (5), 915-928.e5. doi: 10.1016/j.molcel.2020.10.024 |
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2020 Journal Article Multiscale imaging of basal cell dynamics in the functionally mature mammary glandStevenson, Alexander J., Vanwalleghem, Gilles, Stewart, Teneale A., Condon, Nicholas D., Lloyd-Lewis, Bethan, Marino, Natascia, Putney, James W., Scott, Ethan K., Ewing, Adam D. and Davis, Felicity M. (2020). Multiscale imaging of basal cell dynamics in the functionally mature mammary gland. Proceedings of the National Academy of Sciences, 117 (43), 1-11. doi: 10.1073/pnas.2016905117 |
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2020 Journal Article Whole genome investigation of an atypical autism case identifies a novel ANOS1 mutation with subsequent diagnosis of Kallmann syndromeDawson, Paul A., Lee, Soohyun, Ewing, Adam D., Prins, Johannes B. and Heussler, Helen S. (2020). Whole genome investigation of an atypical autism case identifies a novel ANOS1 mutation with subsequent diagnosis of Kallmann syndrome. Molecular Genetics and Metabolism Reports, 23 100593, 100593. doi: 10.1016/j.ymgmr.2020.100593 |
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2020 Journal Article Modulation of placental gene expression in small-for-gestational-age infantsO’Callaghan, Jessica L., Clifton, Vicki L., Prentis, Peter, Ewing, Adam, Miller, Yvette D. and Pelzer, Elise S. (2020). Modulation of placental gene expression in small-for-gestational-age infants. Genes, 11 (1) 80, 80. doi: 10.3390/genes11010080 |
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2020 Journal Article A community effort to create standards for evaluating tumor subclonal reconstructionSalcedo, Adriana, Tarabichi, Maxime, Espiritu, Shadrielle Melijah G., Deshwar, Amit G., David, Matei, Wilson, Nathan M., Dentro, Stefan, Wintersinger, Jeff A., Liu, Lydia Y., Ko, Minjeong, Sivanandan, Srinivasan, Zhang, Hongjiu, Zhu, Kaiyi, Ou Yang, Tai-Hsien, Chilton, John M., Buchanan, Alex, Lalansingh, Christopher M., P’ng, Christine, Anghel, Catalina V., Umar, Imaad, Lo, Bryan, Zou, William, Jha, Alokkumar, Huang, Tanxiao, Yang, Tsun-Po, Peifer, Martin, Sahinalp, Cenk, Malikic, Salem, Vázquez-García, Ignacio ... Boutros, Paul C. (2020). A community effort to create standards for evaluating tumor subclonal reconstruction. Nature Biotechnology, 38 (1), 97-107. doi: 10.1038/s41587-019-0364-z |
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2019 Journal Article CDCP1 enhances Wnt signaling in colorectal cancer promoting nuclear localization of β-catenin and E-cadherinHe, Yaowu, Davies, Claire M., Harrington, Brittney S., Hellmers, Linh, Sheng, Yonghua, Broomfield, Amy, McGann, Thomas, Bastick, Kate, Zhong, Laurie, Wu, Andy, Maresh, Grace, McChesney, Shannon, Yau Wong, Kuan, Adams, Mark N., Sullivan, Ryan C., Palmer, James S., Burke, Lez J., Ewing, Adam D., Zhang, Xin, Margolin, David, Li, Li, Lourie, Rohan, Matsika, Admire, Srinivasan, Bhuvana, McGuckin, Michael A., Lumley, John W. and Hooper, John D. (2019). CDCP1 enhances Wnt signaling in colorectal cancer promoting nuclear localization of β-catenin and E-cadherin. Oncogene, 39 (1), 219-233. doi: 10.1038/s41388-019-0983-3 |
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2019 Journal Article LINE-1 Evasion of epigenetic repression in humansSanchez-Luque, Francisco J., Kempen, Marie-Jeanne H.C., Gerdes, Patricia, Vargas-Landin, Dulce B., Richardson, Sandra R., Troskie, Robin-Lee, Jesuadian, J. Samuel, Cheetham, Seth W., Carreira, Patricia E., Salvador-Palomeque, Carmen, García-Cañadas, Marta, Muñoz-Lopez, Martin, Sanchez, Laura, Lundberg, Mischa, Macia, Angela, Heras, Sara R., Brennan, Paul M., Lister, Ryan, Garcia-Perez, Jose L., Ewing, Adam D. and Faulkner, Geoffrey J. (2019). LINE-1 Evasion of epigenetic repression in humans. Molecular Cell, 75 (3), 590-604.e12. doi: 10.1016/j.molcel.2019.05.024 |
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2019 Journal Article Dynamic methylation of an L1 transduction family during reprogramming and neurodifferentiationSalvador-Palomeque, Carmen, Sanchez-Luque, Francisco J., Fortuna, Patrick R. J., Ewing, Adam D., Wolvetang, Ernst J., Richardson, Sandra R. and Faulkner, Geoffrey J. (2019). Dynamic methylation of an L1 transduction family during reprogramming and neurodifferentiation. Molecular and Cellular Biology, 39 (7) e00499-18, 1-19. doi: 10.1128/mcb.00499-18 |
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2019 Journal Article Arginine to glutamine variant in olfactomedin like 3 (OLFML3) is a candidate for severe goniodysgenesis and glaucoma in the border collie dog breedPugh, Carys A., Farrell, Lindsay L., Carlisle, Ailsa J., Bush, Stephen J., Ewing, Adam, Trejo-Reveles, Violeta, Matika, Oswald, de Kloet, Arne, Walsh, Caitlin, Bishop, Stephen C., Prendergast, James G. D., Rainger, Joe, Schoenebeck, Jeffrey J. and Summers, Kim M. (2019). Arginine to glutamine variant in olfactomedin like 3 (OLFML3) is a candidate for severe goniodysgenesis and glaucoma in the border collie dog breed. G3: Genes, Genomes, Genetics, 9 (3), 943-954. doi: 10.1534/g3.118.200944 |
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2018 Journal Article Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detectionLee, Anna Y., Ewing, Adam D., Ellrott, Kyle, Hu, Yin, Houlahan, Kathleen E., Bare, J. Christopher, Espiritu, Shadrielle Melijah G., Huang, Vincent, Dang, Kristen, Chong, Zechen, Caloian, Cristian, Yamaguchi, Takafumi N., Kellen, Michael R., Chen, Ken, Norman, Thea C., Friend, Stephen H., Guinney, Justin, Stolovitzky, Gustavo, Haussler, David, Margolin, Adam A., Stuart, Joshua M. and Boutros, Paul C. (2018). Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection. Genome Biology, 19 (1) 188, 188. doi: 10.1186/s13059-018-1539-5 |
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2018 Journal Article Rare variants in Fanconi anemia genes are enriched in acute myeloid leukemiaMaung, Kyaw Ze Ya, Leo, Paul J., Bassal, Mahmoud, Casolari, Debora A., Gray, James X., Bray, Sarah C., Pederson, Stephen, Singhal, Deepak, Samaraweera, Saumya E., Nguyen, Tran, Cildir, Gökhan, Marshall, Mhairi, Ewing, Adam, Duncan, Emma L., Brown, Matthew A., Saal, Russell, Tergaonkar, Vinay, To, Luen Bik, Marlton, Paula, Gill, Devinder, Lewis, Ian, Deans, Andrew J., Brown, Anna L., D’Andrea, Richard J. and Gonda, Thomas J. (2018). Rare variants in Fanconi anemia genes are enriched in acute myeloid leukemia. Blood Cancer Journal, 8 (6) 50, 50. doi: 10.1038/s41408-018-0090-7 |
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2018 Journal Article Human-specific NOTCH2NL genes affect notch signaling and cortical neurogenesisFiddes, Ian T., Lodewijk, Gerrald A., Mooring, Meghan, Bosworth, Colleen M., Ewing, Adam D., Mantalas, Gary L., Novak, Adam M., van den Bout, Anouk, Bishara, Alex, Rosenkrantz, Jimi L., Lorig-Roach, Ryan, Field, Andrew R., Haeussler, Maximilian, Russo, Lotte, Bhaduri, Aparna, Nowakowski, Tomasz J., Pollen, Alex A., Dougherty, Max L., Nuttle, Xander, Addor, Marie-Claude, Zwolinski, Simon, Katzman, Sol, Kriegstein, Arnold, Eichler, Evan E., Salama, Sofie R., Jacobs, Frank M.J. and Haussler, David (2018). Human-specific NOTCH2NL genes affect notch signaling and cortical neurogenesis. Cell, 173 (6), 1356-1369. doi: 10.1016/j.cell.2018.03.051 |
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2018 Journal Article L1 retrotransposition is a common feature of mammalian hepatocarcinogenesisSchauer, Stephanie N., Carreira, Patricia E., Shukla, Ruchi, Gerhardt, Daniel J., Gerdes, Patricia, Sanchez-Luque, Francisco J., Nicoli, Paola, Kindlova, Michaela, Ghisletti, Serena, Santos, Alexandre Dos, Rapoud, Delphine, Samuel, Didier, Faivre, Jamila, Ewing, Adam D., Richardson, Sandra R. and Faulkner, Geoffrey J. (2018). L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis. Genome Research, 28 (5), 639-653. doi: 10.1101/gr.226993.117 |
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2018 Journal Article Germline contamination and leakage in whole genome somatic single nucleotide variant detectionSendorek, Dorota H., Caloian, Cristian, Ellrott, Kyle, Bare, J Christopher, Yamaguchi, Takafumi N., Ewing, Adam D., Houlahan, Kathleen E., Norman, Thea C., Margolin, Adam A., Stuart, Joshua M. and Boutros, Paul C. (2018). Germline contamination and leakage in whole genome somatic single nucleotide variant detection. BMC Bioinformatics, 19 (1) 28, 1-9. doi: 10.1186/s12859-018-2046-0 |
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2018 Journal Article L1 retrotransposon heterogeneity in ovarian tumor cell evolutionNguyen, Thu H. M., Carreira, Patricia E., Sanchez-Luque, Francisco J., Schauer, Stephanie N., Fagg, Allister C., Richardson, Sandra R., Davies, Claire M., Jesuadian, J. Samuel, Kempen, Marie-Jeanne H. C., Troskie, Robin-Lee, James, Cini, Beaven, Elizabeth A., Wallis, Tristan P., Coward, Jermaine I. G., Chetty, Naven P., Crandon, Alexander J., Venter, Deon J., Armes, Jane E., Perrin, Lewis C., Hooper, John D., Ewing, Adam D., Upton, Kyle R. and Faulkner, Geoffrey J. (2018). L1 retrotransposon heterogeneity in ovarian tumor cell evolution. Cell Reports, 23 (13), 3730-3740. doi: 10.1016/j.celrep.2018.05.090 |
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2017 Other Outputs Combining accurate tumour genome simulation with crowd-sourcing to benchmark somatic structural variant detectionLee, Anna Y., Ewing, Adam D., Ellrott, Kyle, Hu, Yin, Houlahan, Kathleen E., Bare, J.Christopher, Espiritu, Shadrielle Melijah G., Huang, Vincent, Dang, Kristen, Chong, Zechen, Caloian, Cristian, Yamaguchi, Takafumi N., Participants, ICGC-TCGA DREAM Somatic Mutation Calling Challenge, Kellen, Michael R., Chen, Ken, Norman, Thea C., Friend, Stephen H., Guinney, Justin, Stolovitzky, Gustavo, Haussler, David, Margolin, Adam A., Stuart, Joshua M. and Boutros, Paul C. (2017). Combining accurate tumour genome simulation with crowd-sourcing to benchmark somatic structural variant detection. doi: 10.1101/224733 |
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2017 Other Outputs Germline Contamination and Leakage in Whole Genome Somatic Single Nucleotide Variant DetectionSendorek, Dorota H., Caloian, Cristian, Ellrott, Kyle, Bare, J. Christopher, Yamaguchi, Takafumi N., Ewing, Adam D., Houlahan, Kathleen E., Norman, Thea C., Margolin, Adam A., Stuart, Joshua M. and Boutros, Paul C. (2017). Germline Contamination and Leakage in Whole Genome Somatic Single Nucleotide Variant Detection. doi: 10.1101/204370 |
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2017 Journal Article On the role of H3.3 in retroviral silencingWolf, Gernot, Rebollo, Rita, Karimi, Mohammad M., Ewing, Adam D., Kamada, Rui, Wu, Warren, Wu, Brenda, Bachu, Mahesh, Ozato, Keiko, Faulkner, Geoffrey J., Mager, Dixie L., Lorincz, Matthew C. and Macfarlan, Todd S. (2017). On the role of H3.3 in retroviral silencing. Nature, 548 (7665), E1-E6. doi: 10.1038/nature23277 |
