Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq

por Selvaraj, Siddarth, Schmitt, Anthony D., Dixon, Jesse R., Ren, Bing
Publicado 2015

InPhaDel: integrative shotgun and proximity-ligation sequencing to phase deletions with single nucleotide polymorphisms

por Patel, Anand, Edge, Peter, Selvaraj, Siddarth, Bansal, Vikas, Bafna, Vineet
Publicado 2016

Bayesian Inference of Spatial Organizations of Chromosomes

por Hu, Ming, Deng, Ke, Qin, Zhaohui, Dixon, Jesse, Selvaraj, Siddarth, Fang, Jennifer, Ren, Bing, Liu, Jun S.
Publicado 2013

Integrating Hi-C links with assembly graphs for chromosome-scale assembly

por Ghurye, Jay, Rhie, Arang, Walenz, Brian P., Schmitt, Anthony, Selvaraj, Siddarth, Pop, Mihai, Phillippy, Adam M., Koren, Sergey
Publicado 2019

Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions

por Dixon, Jesse R., Selvaraj, Siddarth, Yue, Feng, Kim, Audrey, Li, Yan, Shen, Yin, Hu, Ming, Liu, Jun S., Ren, Bing
Publicado 2012

CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells

por Li, Yan, Rivera, Chloe M., Ishii, Haruhiko, Jin, Fulai, Selvaraj, Siddarth, Lee, Ah Young, Dixon, Jesse R., Ren, Bing
Publicado 2014

A high-resolution map of three-dimensional chromatin interactome in human cells

por Jin, Fulai, Li, Yan, Dixon, Jesse R., Selvaraj, Siddarth, Ye, Zhen, Lee, Ah Young, Yen, Chia-An, Schmitt, Anthony D., Espinoza, Celso, Ren, Bing
Publicado 2013

Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression

por Greenwald, William W., Li, He, Benaglio, Paola, Jakubosky, David, Matsui, Hiroko, Schmitt, Anthony, Selvaraj, Siddarth, D’Antonio, Matteo, D’Antonio-Chronowska, Agnieszka, Smith, Erin N., Frazer, Kelly A.
Publicado 2019

Integrative analysis of haplotype-resolved epigenomes across human tissues

por Leung, Danny, Jung, Inkyung, Rajagopal, Nisha, Schmitt, Anthony, Selvaraj, Siddarth, Lee, Ah Young, Yen, Chia-An, Lin, Shin, Lin, Yiing, Qiu, Yunjiang, Xie, Wei, Yue, Feng, Hariharan, Manoj, Ray, Pradipta, Kuan, Samantha, Edsall, Lee, Yang, Hongbo, Chi, Neil C., Zhang, Michael Q., Ecker, Joseph R., Ren, Bing
Publicado 2015

Human Body Epigenome Maps Reveal Noncanonical DNA Methylation Variation

por Schultz, Matthew D., He, Yupeng, Whitaker, John W., Hariharan, Manoj, Mukamel, Eran A., Leung, Danny, Rajagopal, Nisha, Nery, Joseph R., Urich, Mark A., Chen, Huaming, Lin, Shin, Lin, Yiing, Jung, Inkyung, Schmitt, Anthony D., Selvaraj, Siddarth, Ren, Bing, Sejnowski, Terrence J., Wang, Wei, Ecker, Joseph R.
Publicado 2015

Telomere-to-telomere assembly of a complete human X chromosome

por 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.
Publicado 2020

Semi-automated assembly of high-quality diploid human reference genomes

por Jarvis, Erich D., Formenti, Giulio, Rhie, Arang, Guarracino, Andrea, Yang, Chentao, Wood, Jonathan, Tracey, Alan, Thibaud-Nissen, Francoise, Vollger, Mitchell R., Porubsky, David, Cheng, Haoyu, Asri, Mobin, Logsdon, Glennis A., Carnevali, Paolo, Chaisson, Mark J. P., Chin, Chen-Shan, Cody, Sarah, Collins, Joanna, Ebert, Peter, Escalona, Merly, Fedrigo, Olivier, Fulton, Robert S., Fulton, Lucinda L., Garg, Shilpa, Gerton, Jennifer L., Ghurye, Jay, Granat, Anastasiya, Green, Richard E., Harvey, William, Hasenfeld, Patrick, Hastie, Alex, Haukness, Marina, Jaeger, Erich B., Jain, Miten, Kirsche, Melanie, Kolmogorov, Mikhail, Korbel, Jan O., Koren, Sergey, Korlach, Jonas, Lee, Joyce, Li, Daofeng, Lindsay, Tina, Lucas, Julian, Luo, Feng, Marschall, Tobias, Mitchell, Matthew W., McDaniel, Jennifer, Nie, Fan, Olsen, Hugh E., Olson, Nathan D., Pesout, Trevor, Potapova, Tamara, Puiu, Daniela, Regier, Allison, Ruan, Jue, Salzberg, Steven L., Sanders, Ashley D., Schatz, Michael C., Schmitt, Anthony, Schneider, Valerie A., Selvaraj, Siddarth, Shafin, Kishwar, Shumate, Alaina, Stitziel, Nathan O., Stober, Catherine, Torrance, James, Wagner, Justin, Wang, Jianxin, Wenger, Aaron, Xiao, Chuanle, Zimin, Aleksey V., Zhang, Guojie, Wang, Ting, Li, Heng, Garrison, Erik, Haussler, David, Hall, Ira, Zook, Justin M., Eichler, Evan E., Phillippy, Adam M., Paten, Benedict, Howe, Kerstin, Miga, Karen H.
Publicado 2022

Towards complete and error-free genome assemblies of all vertebrate species

por Rhie, Arang, McCarthy, Shane A., Fedrigo, Olivier, Damas, Joana, Formenti, Giulio, Koren, Sergey, Uliano-Silva, Marcela, Chow, William, Fungtammasan, Arkarachai, Kim, Juwan, Lee, Chul, Ko, Byung June, Chaisson, Mark, Gedman, Gregory L., Cantin, Lindsey J., Thibaud-Nissen, Francoise, Haggerty, Leanne, Bista, Iliana, Smith, Michelle, Haase, Bettina, Mountcastle, Jacquelyn, Winkler, Sylke, Paez, Sadye, Howard, Jason, Vernes, Sonja C., Lama, Tanya M., Grutzner, Frank, Warren, Wesley C., Balakrishnan, Christopher N., Burt, Dave, George, Julia M., Biegler, Matthew T., Iorns, David, Digby, Andrew, Eason, Daryl, Robertson, Bruce, Edwards, Taylor, Wilkinson, Mark, Turner, George, Meyer, Axel, Kautt, Andreas F., Franchini, Paolo, Detrich, H. William, Svardal, Hannes, Wagner, Maximilian, Naylor, Gavin J. P., Pippel, Martin, Malinsky, Milan, Mooney, Mark, Simbirsky, Maria, Hannigan, Brett T., Pesout, Trevor, Houck, Marlys, Misuraca, Ann, Kingan, Sarah B., Hall, Richard, Kronenberg, Zev, Sović, Ivan, Dunn, Christopher, Ning, Zemin, Hastie, Alex, Lee, Joyce, Selvaraj, Siddarth, Green, Richard E., Putnam, Nicholas H., Gut, Ivo, Ghurye, Jay, Garrison, Erik, Sims, Ying, Collins, Joanna, Pelan, Sarah, Torrance, James, Tracey, Alan, Wood, Jonathan, Dagnew, Robel E., Guan, Dengfeng, London, Sarah E., Clayton, David F., Mello, Claudio V., Friedrich, Samantha R., Lovell, Peter V., Osipova, Ekaterina, Al-Ajli, Farooq O., Secomandi, Simona, Kim, Heebal, Theofanopoulou, Constantina, Hiller, Michael, Zhou, Yang, Harris, Robert S., Makova, Kateryna D., Medvedev, Paul, Hoffman, Jinna, Masterson, Patrick, Clark, Karen, Martin, Fergal, Howe, Kevin, Flicek, Paul, Walenz, Brian P., Kwak, Woori, Clawson, Hiram, Diekhans, Mark, Nassar, Luis, Paten, Benedict, Kraus, Robert H. S., Crawford, Andrew J., Gilbert, M. Thomas P., Zhang, Guojie, Venkatesh, Byrappa, Murphy, Robert W., Koepfli, Klaus-Peter, Shapiro, Beth, Johnson, Warren E., Di Palma, Federica, Marques-Bonet, Tomas, Teeling, Emma C., Warnow, Tandy, Graves, Jennifer Marshall, Ryder, Oliver A., Haussler, David, O’Brien, Stephen J., Korlach, Jonas, Lewin, Harris A., Howe, Kerstin, Myers, Eugene W., Durbin, Richard, Phillippy, Adam M., Jarvis, Erich D.
Publicado 2021