QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments von Hartley, Stephen W, Mullikin, James C

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Systematic Evaluation of Sanger Validation of Next-Generation Sequencing Variants von Beck, Tyler F, Mullikin, James C, Biesecker, Leslie G

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Telomere-to-telomere assembly of a complete human X chromosome von Miga, Karen H., Koren, Sergey, Rhie, Arang, Vollger, Mitchell R., Gershman, Ariel, Bzikadze, Andrey, Brooks, Shelise, Howe, Edmund, Porubsky, David, Logsdon, Glennis A., Schneider, Valerie A., Potapova, Tamara, Wood, Jonathan, Chow, William, Armstrong, Joel, Fredrickson, Jeanne, Pak, Evgenia, Tigyi, Kristof, Kremitzki, Milinn, Markovic, Christopher, Maduro, Valerie, Dutra, Amalia, Bouffard, Gerard G., Chang, Alexander M., Hansen, Nancy F., Wilfert, Amy B., Thibaud-Nissen, Françoise, Schmitt, Anthony D., Belton, Jon-Matthew, Selvaraj, Siddarth, Dennis, Megan Y., Soto, Daniela C., Sahasrabudhe, Ruta, Kaya, Gulhan, Quick, Josh, Loman, Nicholas J., Holmes, Nadine, Loose, Matthew, Surti, Urvashi, Risques, Rosa ana, Graves Lindsay, Tina A., Fulton, Robert, Hall, Ira, Paten, Benedict, Howe, Kerstin, Timp, Winston, Young, Alice, Mullikin, James C., Pevzner, Pavel A., Gerton, Jennifer L., Sullivan, Beth A., Eichler, Evan E., Phillippy, Adam M.

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Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq von Hartley, Stephen W, Mullikin, James C

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Multidonor Analysis Reveals Structural Elements, Genetic Determinants, and Maturation Pathway for HIV-1 Neutralization by VRC01-Class Antibodies von Zhou, Tongqing, Zhu, Jiang, Wu, Xueling, Moquin, Stephanie, Zhang, Baoshan, Acharya, Priyamvada, Georgiev, Ivelin S., Altae-Tran, Han R., Chuang, Gwo-Yu, Joyce, M. Gordon, Do Kwon, Young, Longo, Nancy S., Louder, Mark K., Luongo, Timothy, McKee, Krisha, Schramm, Chaim A., Skinner, Jeff, Yang, Yongping, Yang, Zhongjia, Zhang, Zhenhai, Zheng, Anqi, Bonsignori, Mattia, Haynes, Barton F., Scheid, Johannes F., Nussenzweig, Michel C., Simek, Melissa, Burton, Dennis R., Koff, Wayne C., Mullikin, James C., Connors, Mark, Shapiro, Lawrence, Nabel, Gary J., Mascola, John R., Kwong, Peter D.

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Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains von Zhu, Jiang, Ofek, Gilad, Yang, Yongping, Zhang, Baoshan, Louder, Mark K., Lu, Gabriel, McKee, Krisha, Pancera, Marie, Skinner, Jeff, Zhang, Zhenhai, Parks, Robert, Eudailey, Joshua, Lloyd, Krissey E., Blinn, Julie, Alam, S. Munir, Haynes, Barton F., Simek, Melissa, Burton, Dennis R., Koff, Wayne C., Mullikin, James C., Mascola, John R., Shapiro, Lawrence, Kwong, Peter D.

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Vaccine-Induced Antibodies that Neutralize Group 1 and Group 2 Influenza A Viruses von Joyce, M. Gordon, Wheatley, Adam K., Thomas, Paul V., Chuang, Gwo-Yu, Soto, Cinque, Bailer, Robert T., Druz, Aliaksandr, Georgiev, Ivelin S., Gillespie, Rebecca A., Kanekiyo, Masaru, Kong, Wing-Pui, Leung, Kwanyee, Narpala, Sandeep N., Prabhakaran, Madhu S., Yang, Eun Sung, Zhang, Baoshan, Zhang, Yi, Asokan, Mangaiarkarasi, Boyington, Jeffrey C., Bylund, Tatsiana, Darko, Sam, Lees, Christopher R., Ransier, Amy, Shen, Chen-Hsiang, Wang, Lingshu, Whittle, James R., Wu, Xueling, Yassine, Hadi M., Santos, Celia, Matsuoka, Yumiko, Tsybovsky, Yaroslav, Baxa, Ulrich, Mullikin, James C., Subbarao, Kanta, Douek, Daniel C., Graham, Barney S., Koup, Richard A., Ledgerwood, Julie E., Roederer, Mario, Shapiro, Lawrence, Kwong, Peter D., Mascola, John R., McDermott, Adrian B.

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Secondary Variants in Individuals Undergoing Exome Sequencing: Screening of 572 Individuals Identifies High-Penetrance Mutations in Cancer-Susceptibility Genes von Johnston, Jennifer J., Rubinstein, Wendy S., Facio, Flavia M., Ng, David, Singh, Larry N., Teer, Jamie K., Mullikin, James C., Biesecker, Leslie G.

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De novo identification of VRC01 class HIV-1–neutralizing antibodies by next-generation sequencing of B-cell transcripts von Zhu, Jiang, Wu, Xueling, Zhang, Baoshan, McKee, Krisha, O'Dell, Sijy, Soto, Cinque, Zhou, Tongqing, Casazza, Joseph P., Mullikin, James C., Kwong, Peter D., Mascola, John R., Shapiro, Lawrence

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Exome sequencing: the sweet spot before whole genomes von Teer, Jamie K., Mullikin, James C.

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Low Incidence of DNA Sequence Variation in Human Induced Pluripotent Stem Cells Generated by Nonintegrating Plasmid Expression von Cheng, Linzhao, Hansen, Nancy F., Zhao, Ling, Du, Yutao, Zou, Chunlin, Donovan, Frank X., Chou, Bin-Kuan, Zhou, Guangyu, Li, Shijie, Dowey, Sarah N., Ye, Zhaohui, Chandrasekharappa, Settara C., Yang, Huanming, Mullikin, James C., Liu, P. Paul

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Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies von Doria-Rose, Nicole A., Schramm, Chaim A., Gorman, Jason, Moore, Penny L., Bhiman, Jinal N., DeKosky, Brandon J., Ernandes, Michael J., Georgiev, Ivelin S., Kim, Helen J., Pancera, Marie, Staupe, Ryan P., Altae-Tran, Han R., Bailer, Robert T., Crooks, Ema T., Cupo, Albert, Druz, Aliaksandr, Garrett, Nigel J., Hoi, Kam H., Kong, Rui, Louder, Mark K., Longo, Nancy S., McKee, Krisha, Nonyane, Molati, O’Dell, Sijy, Roark, Ryan S., Rudicell, Rebecca S., Schmidt, Stephen D., Sheward, Daniel J., Soto, Cinque, Wibmer, Constantinos Kurt, Yang, Yongping, Zhang, Zhenhai, Mullikin, James C., Binley, James M., Sanders, Rogier W., Wilson, Ian A., Moore, John P., Ward, Andrew B., Georgiou, George, Williamson, Carolyn, Abdool Karim, Salim S., Morris, Lynn, Kwong, Peter D., Shapiro, Lawrence, Mascola, John R.

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Loss-of-function mutations in TNFAIP3 leading to A20 haploinsufficiency cause an early-onset autoinflammatory disease von Zhou, Qing, Wang, Hongying, Schwartz, Daniella M, Stoffels, Monique, Park, Yong Hwan, Zhang, Yuan, Yang, Dan, Demirkaya, Erkan, Takeuchi, Masaki, Tsai, Wanxia Li, Lyons, Jonathan J, Yu, Xiaomin, Ouyang, Claudia, Chen, Celeste, Chin, David T, Zaal, Kristien, Chandrasekharappa, Settara C, P Hanson, Eric, Yu, Zhen, Mullikin, James C, Hasni, Sarfaraz A, Wertz, Ingrid E, Ombrello, Amanda K, Stone, Deborah L, Hoffmann, Patrycja, Jones, Anne, Barham, Beverly K, Leavis, Helen L, van Royen-Kerkof, Annet, Sibley, Cailin, Batu, Ezgi D, Gül, Ahmet, Siegel, Richard M, Boehm, Manfred, Milner, Joshua D, Ozen, Seza, Gadina, Massimo, Chae, JaeJin, Laxer, Ronald M, Kastner, Daniel L, Aksentijevich, Ivona

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Draft Sequence of the Neandertal Genome von Green, Richard E, Krause, Johannes, Briggs, Adrian W, Maricic, Tomislav, Stenzel, Udo, Kircher, Martin, Patterson, Nick, Li, Heng, Zhai, Weiwei, Fritz, Markus Hsi-Yang, Hansen, Nancy F, Durand, Eric Y, Malaspinas, Anna-Sapfo, Jensen, Jeffrey D, Marques-Bonet, Tomas, Alkan, Can, Prüfer, Kay, Meyer, Matthias, Burbano, Hernán A, Good, Jeffrey M, Schultz, Rigo, Aximu-Petri, Ayinuer, Butthof, Anne, Höber, Barbara, Höffner, Barbara, Siegemund, Madlen, Weihmann, Antje, Nusbaum, Chad, Lander, Eric S, Russ, Carsten, Novod, Nathaniel, Affourtit, Jason, Egholm, Michael, Verna, Christine, Rudan, Pavao, Brajkovic, Dejana, Kucan, Željko, Gušic, Ivan, Doronichev, Vladimir B, Golovanova, Liubov V, Lalueza-Fox, Carles, de la Rasilla, Marco, Fortea, Javier, Rosas, Antonio, Schmitz, Ralf W, Johnson, Philip L.F, Eichler, Evan E, Falush, Daniel, Birney, Ewan, Mullikin, James C, Slatkin, Montgomery, Nielsen, Rasmus, Kelso, Janet, Lachmann, Michael, Reich, David, Pääbo, Svante

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Biallelic hypomorphic mutations in a linear deubiquitinase define otulipenia, an early-onset autoinflammatory disease von Zhou, Qing, Yu, Xiaomin, Demirkaya, Erkan, Deuitch, Natalie, Stone, Deborah, Tsai, Wanxia Li, Kuehn, Hye Sun, Wang, Hongying, Yang, Dan, Park, Yong Hwan, Ombrello, Amanda K., Blake, Mary, Romeo, Tina, Remmers, Elaine F., Chae, Jae Jin, Mullikin, James C., Güzel, Ferhat, Milner, Joshua D., Boehm, Manfred, Rosenzweig, Sergio D., Gadina, Massimo, Welch, Steven B., Özen, Seza, Topaloglu, Rezan, Abinun, Mario, Kastner, Daniel L., Aksentijevich, Ivona

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Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus von Liao, Hua-Xin, Lynch, Rebecca, Zhou, Tongqing, Gao, Feng, Alam, S. Munir, Boyd, Scott D., Fire, Andrew Z., Roskin, Krishna M., Schramm, Chaim A., Zhang, Zhenhai, Zhu, Jiang, Shapiro, Lawrence, Mullikin, James C., Gnanakaran, S., Hraber, Peter, Wiehe, Kevin, Kelsoe, Garnett, Yang, Guang, Xia, Shi-Mao, Montefiori, David C., Parks, Robert, Lloyd, Krissey E., Scearce, Richard M., Soderberg, Kelly A., Cohen, Myron, Kamanga, Gift, Louder, Mark K., Tran, Lillian M., Chen, Yue, Cai, Fangping, Chen, Sheri, Moquin, Stephanie, Du, Xiulian, Joyce, M. Gordon, Srivatsan, Sanjay, Zhang, Baoshan, Zheng, Anqi, Shaw, George M., Hahn, Beatrice H., Kepler, Thomas B., Korber, Bette T. M., Kwong, Peter D., Mascola, John R., Haynes, Barton F.

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Developmental Pathway of the MPER-Directed HIV-1-Neutralizing Antibody 10E8 von Soto, Cinque, Ofek, Gilad, Joyce, M Gordon, Zhang, Baoshan, McKee, Krisha, Longo, Nancy S, Yang, Yongping, Huang, Jinghe, Parks, Robert, Eudailey, Joshua, Lloyd, Krissey E, Alam, S Munir, Haynes, Barton F, Mullikin, James C, Connors, Mark, Mascola, John R, Shapiro, Lawrence, Kwong, Peter D

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Genomic features defining exonic variants that modulate splicing von Woolfe, Adam, Mullikin, James C, Elnitski, Laura

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Whole-exome sequencing identifies homozygous AFG3L2 mutations in a spastic ataxia-neuropathy syndrome linked to mitochondrial m-AAA proteases von Pierson, Tyler Mark, Adams, David, Bonn, Florian, Martinelli, Paola, Cherukuri, Praveen F, Teer, Jamie K, Hansen, Nancy F, Cruz, Pedro, Mullikin For The Nisc Comparative Sequencing Program, James C, Blakesley, Robert W, Golas, Gretchen, Kwan, Justin, Sandler, Anthony, Fuentes Fajardo, Karin, Markello, Thomas, Tifft, Cynthia, Blackstone, Craig, Rugarli, Elena I, Langer, Thomas, Gahl, William A, Toro, Camilo

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Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection von Wu, Xueling, Zhang, Zhenhai, Schramm, Chaim A, Joyce, M Gordon, Kwon, Young Do, Zhou, Tongqing, Sheng, Zizhang, Zhang, Baoshan, O'Dell, Sijy, McKee, Krisha, Georgiev, Ivelin S, Chuang, Gwo-Yu, Longo, Nancy S, Lynch, Rebecca M, Saunders, Kevin O, Soto, Cinque, Srivatsan, Sanjay, Yang, Yongping, Bailer, Robert T, Louder, Mark K, Mullikin, James C, Connors, Mark, Kwong, Peter D, Mascola, John R, Shapiro, Lawrence

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