An integrated semiconductor device enabling non-optical genome sequencing von Rothberg, Jonathan M., Hinz, Wolfgang, Rearick, Todd M., Schultz, Jonathan, Mileski, William, Davey, Mel, Leamon, John H., Johnson, Kim, Milgrew, Mark J., Edwards, Matthew, Hoon, Jeremy, Simons, Jan F., Marran, David, Myers, Jason W., Davidson, John F., Branting, Annika, Nobile, John R., Puc, Bernard P., Light, David, Clark, Travis A., Huber, Martin, Branciforte, Jeffrey T., Stoner, Isaac B., Cawley, Simon E., Lyons, Michael, Fu, Yutao, Homer, Nils, Sedova, Marina, Miao, Xin, Reed, Brian, Sabina, Jeffrey, Feierstein, Erika, Schorn, Michelle, Alanjary, Mohammad, Dimalanta, Eileen, Dressman, Devin, Kasinskas, Rachel, Sokolsky, Tanya, Fidanza, Jacqueline A., Namsaraev, Eugeni, McKernan, Kevin J., Williams, Alan, Roth, G. Thomas, Bustillo, James

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Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs von Korn, Joshua M, Altshuler, David, Kuruvilla, Finny G, McCarroll, Steven A, Wysoker, Alec, Nemesh, James, Cawley, Simon, Hubbell, Earl, Veitch, Jim, Collins, Patrick J, Darvishi, Katayoon, Lee, Charles, Nizzari, Marcia M, Gabriel, Stacey B, Purcell, Shaun, Daly, Mark J

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Integrated detection and population-genetic analysis of SNPs and copy number variation von McCarroll, Steven A, Altshuler, David, Kuruvilla, Finny G, Korn, Joshua M, Cawley, Simon, Nemesh, James, Wysoker, Alec, Shapero, Michael H, de Bakker, Paul I W, Maller, Julian B, Kirby, Andrew, Elliott, Amanda L, Parkin, Melissa, Hubbell, Earl, Webster, Teresa, Mei, Rui, Veitch, James, Collins, Patrick J, Handsaker, Robert, Lincoln, Steve, Nizzari, Marcia, Blume, John, Jones, Keith W, Rava, Rich, Daly, Mark J, Gabriel, Stacey B

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Large-Scale Transcriptional Activity in Chromosomes 21 and 22 von Kapranov, Philipp, Cawley, Simon E., Drenkow, Jorg, Bekiranov, Stefan, Strausberg, Robert L., Stephen P. A. Fodor, Gingeras, Thomas R.

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Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs von Cawley, Simon, Bekiranov, Stefan, Ng, Huck H, Kapranov, Philipp, Sekinger, Edward A, Kampa, Dione, Piccolboni, Antonio, Sementchenko, Victor, Cheng, Jill, Williams, Alan J, Wheeler, Raymond, Wong, Brant, Drenkow, Jorg, Yamanaka, Mark, Patel, Sandeep, Brubaker, Shane, Tammana, Hari, Helt, Gregg, Struhl, Kevin, Gingeras, Thomas R

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Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22 von Kampa, Dione, Cheng, Jill, Kapranov, Philipp, Yamanaka, Mark, Brubaker, Shane, Cawley, Simon, Drenkow, Jorg, Piccolboni, Antonio, Bekiranov, Stefan, Helt, Gregg, Tammana, Hari, Gingeras, Thomas R

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Next generation genome-wide association tool: Design and coverage of a high-throughput European-optimized SNP array von Hoffmann, Thomas J., Kvale, Mark N., Hesselson, Stephanie E., Zhan, Yiping, Aquino, Christine, Cao, Yang, Cawley, Simon, Chung, Elaine, Connell, Sheryl, Eshragh, Jasmin, Ewing, Marcia, Gollub, Jeremy, Henderson, Mary, Hubbell, Earl, Iribarren, Carlos, Kaufman, Jay, Lao, Richard Z., Lu, Yontao, Ludwig, Dana, Mathauda, Gurpreet K., McGuire, William, Mei, Gangwu, Miles, Sunita, Purdy, Matthew M., Quesenberry, Charles, Ranatunga, Dilrini, Rowell, Sarah, Sadler, Marianne, Shapero, Michael H., Shen, Ling, Shenoy, Tanushree R., Smethurst, David, Van den Eeden, Stephen K., Walter, Larry, Wan, Eunice, Wearley, Reid, Webster, Teresa, Wen, Christopher C., Weng, Li, Whitmer, Rachel A., Williams, Alan, Wong, Simon C., Zau, Chia, Finn, Andrea, Schaefer, Catherine, Kwok, Pui-Yan, Risch, Neil

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HMM sampling and applications to gene finding and alternative splicing von Cawley, Simon L., Pachter, Lior

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Applications of generalized pair hidden Markov models to alignment and gene finding problems von Pachter, Lior, Alexandersson, Marina, Cawley, Simon

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Multiple testing methods for ChIP-Chip high density oligonucleotide array data von Keleş, Sündüz, van der Laan, Mark J, Dudoit, Sandrine, Cawley, Simon E

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Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology von Deveson, Ira W., Gong, Binsheng, Lai, Kevin, LoCoco, Jennifer S., Richmond, Todd A., Schageman, Jeoffrey, Zhang, Zhihong, Novoradovskaya, Natalia, Willey, James C., Jones, Wendell, Kusko, Rebecca, Chen, Guangchun, Madala, Bindu Swapna, Blackburn, James, Stevanovski, Igor, Bhandari, Ambica, Close, Devin, Conroy, Jeffrey, Hubank, Michael, Marella, Narasimha, Mieczkowski, Piotr A., Qiu, Fujun, Sebra, Robert, Stetson, Daniel, Sun, Lihyun, Szankasi, Philippe, Tan, Haowen, Tang, Lin-ya, Arib, Hanane, Best, Hunter, Burgher, Blake, Bushel, Pierre R., Casey, Fergal, Cawley, Simon, Chang, Chia-Jung, Choi, Jonathan, Dinis, Jorge, Duncan, Daniel, Eterovic, Agda Karina, Feng, Liang, Ghosal, Abhisek, Giorda, Kristina, Glenn, Sean, Happe, Scott, Haseley, Nathan, Horvath, Kyle, Hung, Li-Yuan, Jarosz, Mirna, Kushwaha, Garima, Li, Dan, Li, Quan-Zhen, Li, Zhiguang, Liu, Liang-Chun, Liu, Zhichao, Ma, Charles, Mason, Christopher E., Megherbi, Dalila B., Morrison, Tom, Pabón-Peña, Carlos, Pirooznia, Mehdi, Proszek, Paula Z., Raymond, Amelia, Rindler, Paul, Ringler, Rebecca, Scherer, Andreas, Shaknovich, Rita, Shi, Tieliu, Smith, Melissa, Song, Ping, Strahl, Maya, Thodima, Venkat J., Tom, Nikola, Verma, Suman, Wang, Jiashi, Wu, Leihong, Xiao, Wenzhong, Xu, Chang, Yang, Mary, Zhang, Guangliang, Zhang, Sa, Zhang, Yilin, Shi, Leming, Tong, Weida, Johann, Donald J., Mercer, Timothy R., Xu, Joshua

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Abstract 3492: A targeted semi-conductor based next-generation sequencing (NGS) test to characterize microsatellite instability in FFPE tumor samples von Kraltcheva, Anelia, El-Difrawy, Sameh, Kamat, Asha, Au-Young, Janice, Cawley, Simon, Sadis, Seth

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Progress in Ion Torrent semiconductor chip based sequencing von Merriman, Barry, R&D Team, Ion Torrent, Rothberg, Jonathan M.

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Abstract 2267: A novel method for classification of microsatellite instability (MSI) using the Oncomine Tumor Mutation Load assay von Pankov, Aleksandr, El-Difrawy, Sameh, Tom, Warren, Conroy, Jeffrey, Glenn, Sean, Pabla, Sarabjot, Morrison, Carl, Hyland, Fiona, Cawley, Simon

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SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model von Alexandersson, Marina, Cawley, Simon, Pachter, Lior

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Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays von Mei, Rui, Matsuzaki, Hajime, Dong, Shoulian, Loi, Halina, Di, Xiaojun, Liu, Guoying, Hubbell, Earl, Law, Jane, Berntsen, Tam, Chadha, Monica, Hui, Henry, Yang, Geoffrey, Kennedy, Giulia C, Webster, Teresa A, Cawley, Simon, Walsh, P Sean, Jones, Keith W, Fodor, Stephen P A

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Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarrays von Di, Xiaojun, Matsuzaki, Hajime, Webster, Teresa A., Hubbell, Earl, Liu, Guoying, Dong, Shoulian, Bartell, Dan, Huang, Jing, Chiles, Richard, Yang, Geoffrey, Shen, Mei-mei, Kulp, David, Kennedy, Giulia C., Mei, Rui, Jones, Keith W., Cawley, Simon

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Differential Dropout among SNP Genotypes and Impacts on Association Tests von Hao, Ke, Cawley, Simon

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ANOSVA: a statistical method for detecting splice variation from expression data von Cline, Melissa S., Blume, John, Cawley, Simon, Clark, Tyson A., Hu, Jing-Shan, Lu, Gang, Salomonis, Nathan, Wang, Hui, Williams, Alan

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METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR NUCLEIC ACID SEQUENCING von CAWLEY, Simon, DAVEY, Melville, WILLIAMS, Alan

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