De Novo Gene Disruptions in Children on the Autistic Spectrum von Iossifov, Ivan, Ronemus, Michael, Levy, Dan, Wang, Zihua, Hakker, Inessa, Rosenbaum, Julie, Yamrom, Boris, Lee, Yoon-ha, Narzisi, Giuseppe, Leotta, Anthony, Kendall, Jude, Grabowska, Ewa, Ma, Beicong, Marks, Steven, Rodgers, Linda, Stepansky, Asya, Troge, Jennifer, Andrews, Peter, Bekritsky, Mitchell, Pradhan, Kith, Ghiban, Elena, Kramer, Melissa, Parla, Jennifer, Demeter, Ryan, Fulton, Lucinda L., Fulton, Robert S., Magrini, Vincent J., Ye, Kenny, Darnell, Jennifer C., Darnell, Robert B., Mardis, Elaine R., Wilson, Richard K., Schatz, Michael C., McCombie, W. Richard, Wigler, Michael

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Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly von Schneider, Valerie A, Graves-Lindsay, Tina, Howe, Kerstin, Bouk, Nathan, Chen, Hsiu-Chuan, Kitts, Paul A, Murphy, Terence D, Pruitt, Kim D, Thibaud-Nissen, Françoise, Albracht, Derek, Fulton, Robert S, Kremitzki, Milinn, Magrini, Vincent, Markovic, Chris, McGrath, Sean, Steinberg, Karyn Meltz, Auger, Kate, Chow, William, Collins, Joanna, Harden, Glenn, Hubbard, Timothy, Pelan, Sarah, Simpson, Jared T, Threadgold, Glen, Torrance, James, Wood, Jonathan M, Clarke, Laura, Koren, Sergey, Boitano, Matthew, Peluso, Paul, Li, Heng, Chin, Chen-Shan, Phillippy, Adam M, Durbin, Richard, Wilson, Richard K, Flicek, Paul, Eichler, Evan E, Church, Deanna M

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Functional Heterogeneity of Genetically Defined Subclones in Acute Myeloid Leukemia von Klco, Jeffery M., Spencer, David H., Miller, Christopher A., Griffith, Malachi, Lamprecht, Tamara L., O’Laughlin, Michelle, Fronick, Catrina, Magrini, Vincent, Demeter, Ryan T., Fulton, Robert S., Eades, William C., Link, Daniel C., Graubert, Timothy A., Walter, Matthew J., Mardis, Elaine R., Dipersio, John F., Wilson, Richard K., Ley, Timothy J.

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High-Dimensional Analysis Delineates Myeloid and Lymphoid Compartment Remodeling during Successful Immune-Checkpoint Cancer Therapy von Gubin, Matthew M., Esaulova, Ekaterina, Ward, Jeffrey P., Malkova, Olga N., Runci, Daniele, Wong, Pamela, Noguchi, Takuro, Arthur, Cora D., Meng, Wei, Alspach, Elise, Medrano, Ruan F.V., Fronick, Catrina, Fehlings, Michael, Newell, Evan W., Fulton, Robert S., Sheehan, Kathleen C.F., Oh, Stephen T., Schreiber, Robert D., Artyomov, Maxim N.

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Sequencing the mouse Y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes von Soh, Y Q Shirleen, Alföldi, Jessica, Pyntikova, Tatyana, Brown, Laura G, Graves, Tina, Minx, Patrick J, Fulton, Robert S, Kremitzki, Colin, Koutseva, Natalia, Mueller, Jacob L, Rozen, Steve, Hughes, Jennifer F, Owens, Elaine, Womack, James E, Murphy, William J, Cao, Qing, de Jong, Pieter, Warren, Wesley C, Wilson, Richard K, Skaletsky, Helen, Page, David C

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A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing von Petti, Allegra A., Williams, Stephen R., Miller, Christopher A., Fiddes, Ian T., Srivatsan, Sridhar N., Chen, David Y., Fronick, Catrina C., Fulton, Robert S., Church, Deanna M., Ley, Timothy J.

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Mutant U2AF1 Expression Alters Hematopoiesis and Pre-mRNA Splicing In Vivo von Shirai, Cara Lunn, Ley, James N., White, Brian S., Kim, Sanghyun, Tibbitts, Justin, Shao, Jin, Ndonwi, Matthew, Wadugu, Brian, Duncavage, Eric J., Okeyo-Owuor, Theresa, Liu, Tuoen, Griffith, Malachi, McGrath, Sean, Magrini, Vincent, Fulton, Robert S., Fronick, Catrina, O’Laughlin, Michelle, Graubert, Timothy A., Walter, Matthew J.

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Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators von Bellott, Daniel W., Hughes, Jennifer F., Skaletsky, Helen, Brown, Laura G., Pyntikova, Tatyana, Cho, Ting-Jan, Koutseva, Natalia, Zaghlul, Sara, Graves, Tina, Rock, Susie, Kremitzki, Colin, Fulton, Robert S., Dugan, Shannon, Ding, Yan, Morton, Donna, Khan, Ziad, Lewis, Lora, Buhay, Christian, Wang, Qiaoyan, Watt, Jennifer, Holder, Michael, Lee, Sandy, Nazareth, Lynne, Alföldi, Jessica, Rozen, Steve, Muzny, Donna M., Warren, Wesley C., Gibbs, Richard A., Wilson, Richard K., Page, David C.

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Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma von Krysiak, Kilannin, Gomez, Felicia, White, Brian S., Matlock, Matthew, Miller, Christopher A., Trani, Lee, Fronick, Catrina C., Fulton, Robert S., Kreisel, Friederike, Cashen, Amanda F., Carson, Kenneth R., Berrien-Elliott, Melissa M., Bartlett, Nancy L., Griffith, Malachi, Griffith, Obi L., Fehniger, Todd A.

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CpG Island Hypermethylation Mediated by DNMT3A Is a Consequence of AML Progression von Spencer, David H., Russler-Germain, David A., Ketkar, Shamika, Helton, Nichole M., Lamprecht, Tamara L., Fulton, Robert S., Fronick, Catrina C., O’Laughlin, Michelle, Heath, Sharon E., Shinawi, Marwan, Westervelt, Peter, Payton, Jacqueline E., Wartman, Lukas D., Welch, John S., Wilson, Richard K., Walter, Matthew J., Link, Daniel C., DiPersio, John F., Ley, Timothy J.

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Cellular stressors contribute to the expansion of hematopoietic clones of varying leukemic potential von Wong, Terrence N., Miller, Christopher A., Jotte, Matthew R. M., Bagegni, Nusayba, Baty, Jack D., Schmidt, Amy P., Cashen, Amanda F., Duncavage, Eric J., Helton, Nichole M., Fiala, Mark, Fulton, Robert S., Heath, Sharon E., Janke, Megan, Luber, Kierstin, Westervelt, Peter, Vij, Ravi, DiPersio, John F., Welch, John S., Graubert, Timothy A., Walter, Matthew J., Ley, Timothy J., Link, Daniel C.

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INTEGRATE: gene fusion discovery using whole genome and transcriptome data von Zhang, Jin, White, Nicole M, Schmidt, Heather K, Fulton, Robert S, Tomlinson, Chad, Warren, Wesley C, Wilson, Richard K, Maher, Christopher A

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Recurrent WNT pathway alterations are frequent in relapsed small cell lung cancer von Wagner, Alex H., Devarakonda, Siddhartha, Skidmore, Zachary L., Krysiak, Kilannin, Ramu, Avinash, Trani, Lee, Kunisaki, Jason, Masood, Ashiq, Waqar, Saiama N., Spies, Nicholas C., Morgensztern, Daniel, Waligorski, Jason, Ponce, Jennifer, Fulton, Robert S., Maggi, Leonard B., Weber, Jason D., Watson, Mark A., O’Conor, Christopher J., Ritter, Jon H., Olsen, Rachelle R., Cheng, Haixia, Mukhopadhyay, Anandaroop, Can, Ismail, Cessna, Melissa H., Oliver, Trudy G., Mardis, Elaine R., Wilson, Richard K., Griffith, Malachi, Griffith, Obi L., Govindan, Ramaswamy

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Co-evolution of tumor and immune cells during progression of multiple myeloma von Liu, Ruiyang, Gao, Qingsong, Foltz, Steven M., Fowles, Jared S., Yao, Lijun, Wang, Julia Tianjiao, Cao, Song, Sun, Hua, Wendl, Michael C., Sethuraman, Sunantha, Weerasinghe, Amila, Rettig, Michael P., Storrs, Erik P., Yoon, Christopher J., Wyczalkowski, Matthew A., McMichael, Joshua F., Kohnen, Daniel R., King, Justin, Goldsmith, Scott R., O’Neal, Julie, Fulton, Robert S., Fronick, Catrina C., Ley, Timothy J., Jayasinghe, Reyka G., Fiala, Mark A., Oh, Stephen T., DiPersio, John F., Vij, Ravi, Ding, Li

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BreakDancer: an algorithm for high-resolution mapping of genomic structural variation von Chen, Ken, Wallis, John W, McLellan, Michael D, Larson, David E, Kalicki, Joelle M, Pohl, Craig S, McGrath, Sean D, Wendl, Michael C, Zhang, Qunyuan, Locke, Devin P, Shi, Xiaoqi, Fulton, Robert S, Ley, Timothy J, Wilson, Richard K, Ding, Li, Mardis, Elaine R

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The prognostic effects of somatic mutations in ER-positive breast cancer von Griffith, Obi L., Spies, Nicholas C., Anurag, Meenakshi, Griffith, Malachi, Luo, Jingqin, Tu, Dongsheng, Yeo, Belinda, Kunisaki, Jason, Miller, Christopher A, Krysiak, Kilannin, Hundal, Jasreet, Ainscough, Benjamin J, Skidmore, Zachary L., Campbell, Katie, Kumar, Runjun, Fronick, Catrina, Cook, Lisa, Snider, Jacqueline E., Davies, Sherri, Kavuri, Shyam M., Chang, Eric C., Magrini, Vincent, Larson, David E., Fulton, Robert S, Liu, Shuzhen, Leung, Samuel, Voduc, David, Bose, Ron, Dowsett, Mitch, Wilson, Richard K., Nielsen, Torsten O., Mardis, Elaine R, Ellis, Matthew J.

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Somatic mutations and clonal hematopoiesis in congenital neutropenia von Xia, Jun, Miller, Christopher A., Baty, Jack, Ramesh, Amrita, Jotte, Matthew R.M., Fulton, Robert S., Vogel, Tiphanie P., Cooper, Megan A., Walkovich, Kelly J., Makaryan, Vahagn, Bolyard, Audrey A., Dinauer, Mary C., Wilson, David B., Vlachos, Adrianna, Myers, Kasiani C., Rothbaum, Robert J., Bertuch, Alison A., Dale, David C., Shimamura, Akiko, Boxer, Laurence A., Link, Daniel C.

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Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes von Graubert, Timothy A, Shen, Dong, Ding, Li, Okeyo-Owuor, Theresa, Lunn, Cara L, Shao, Jin, Krysiak, Kilannin, Harris, Christopher C, Koboldt, Daniel C, Larson, David E, McLellan, Michael D, Dooling, David J, Abbott, Rachel M, Fulton, Robert S, Schmidt, Heather, Kalicki-Veizer, Joelle, O'Laughlin, Michelle, Grillot, Marcus, Baty, Jack, Heath, Sharon, Frater, John L, Nasim, Talat, Link, Daniel C, Tomasson, Michael H, Westervelt, Peter, DiPersio, John F, Mardis, Elaine R, Ley, Timothy J, Wilson, Richard K, Walter, Matthew J

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Evolution of symbiotic bacteria in the distal human intestine von Xu, Jian, Mahowald, Michael A, Ley, Ruth E, Lozupone, Catherine A, Hamady, Micah, Martens, Eric C, Henrissat, Bernard, Coutinho, Pedro M, Minx, Patrick, Latreille, Philippe, Cordum, Holland, Van Brunt, Andrew, Kim, Kyung, Fulton, Robert S, Fulton, Lucinda A, Clifton, Sandra W, Wilson, Richard K, Knight, Robin D, Gordon, Jeffrey I

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The draft genome of the parasitic nematode Trichinella spiralis von Mitreva, Makedonka, Wilson, Richard K, Jasmer, Douglas P, Zarlenga, Dante S, Wang, Zhengyuan, Abubucker, Sahar, Martin, John, Taylor, Christina M, Yin, Yong, Fulton, Lucinda, Minx, Pat, Yang, Shiaw-Pyng, Warren, Wesley C, Fulton, Robert S, Bhonagiri, Veena, Zhang, Xu, Hallsworth-Pepin, Kym, Clifton, Sandra W, McCarter, James P, Appleton, Judith, Mardis, Elaine R

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