Localizing triplet periodicity in DNA and cDNA sequences

by Stein Lincoln D, Wang Liya
Published 2010-11-01

nGASP – the nematode genome annotation assessment project

by Harris Todd W, Flicek Paul, McKay Sheldon J, Fiedler Tristan J, Coghlan Avril, Blasiar Darin, Stein Lincoln D
Published 2008-12-01

The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details.

by Washington, Nicole L, Stinson, EO, Perry, Marc D, Ruzanov, Peter, Contrino, Sergio, Smith, Richard, Zha, Zheng, Lyne, Rachel, Carr, Adrian, Lloyd, Paul, Kephart, Ellen, McKay, Sheldon J, Micklem, Gos, Stein, Lincoln D, Lewis, Suzanna E
Published 2018

modMine: flexible access to modENCODE data.

by Contrino, Sergio, Smith, Richard N, Butano, Daniela, Carr, Adrian, Hu, Fengyuan, Lyne, Rachel, Rutherford, Kim, Kalderimis, Alex, Sullivan, Julie, Carbon, Seth, Kephart, Ellen T, Lloyd, Paul, Stinson, EO, Washington, Nicole L, Perry, Marc D, Ruzanov, Peter, Zha, Zheng, Lewis, Suzanna E, Stein, Lincoln D, Micklem, Gos
Published 2018

A brain precursor atlas reveals the acquisition of developmental-like states in adult cerebral tumours.

by Hamed, Akram A, Kunz, Daniel, El-Hamamy, Ibrahim, Trinh, Quang M, Subedar, Omar D, Richards, Laura M, Foltz, Warren, Bullivant, Garrett, Ware, Matthaeus, Vladoiu, Maria C, Zhang, Jiao, Raj, Antony M, Pugh, Trevor J, Taylor, Michael D, Teichmann, Sarah, Stein, Lincoln D, Simons, Benjamin, Dirks, Peter B
Published 2022

A brain precursor atlas reveals the acquisition of developmental-like states in adult cerebral tumours.

by Hamed, Akram A, Kunz, Daniel J, El-Hamamy, Ibrahim, Trinh, Quang M, Subedar, Omar D, Richards, Laura M, Foltz, Warren, Bullivant, Garrett, Ware, Matthaeus, Vladoiu, Maria C, Zhang, Jiao, Raj, Antony M, Pugh, Trevor J, Taylor, Michael D, Teichmann, Sarah A, Stein, Lincoln D, Simons, Benjamin D, Dirks, Peter B
Published 2022

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns.

by Jiao, Wei, Atwal, Gurnit, Polak, Paz, Karlic, Rosa, Cuppen, Edwin, PCAWG Tumor Subtypes and Clinical Translation Working Group, Danyi, Alexandra, de Ridder, Jeroen, van Herpen, Carla, Lolkema, Martijn P, Steeghs, Neeltje, Getz, Gad, Morris, Quaid, Stein, Lincoln D, PCAWG Consortium
Published 2020

Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma

by Feigin, Michael E., Garvin, Tyler, Bailey, Peter, Waddell, Nicola, Chang, David K., Kelley, David R., Shuai, Shimin, Gallinger, Steven, McPherson, John D., Grimmond, Sean M., Khurana, Ekta, Stein, Lincoln D., Biankin, Andrew V., Schatz, Michael C., Tuveson, David A.
Published 2017

Distinct routes of lineage development reshape the human blood hierarchy across ontogeny.

by Notta, Faiyaz, Zandi, Sasan, Takayama, Naoya, Dobson, Stephanie, Gan, Olga I, Wilson, Gavin, Kaufmann, Kerstin B, McLeod, Jessica, Laurenti, Elisa, Dunant, Cyrille F, McPherson, John D, Stein, Lincoln D, Dror, Yigal, Dick, John E
Published 2015

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

by Jiao, Wei, Karlic, Rosa, Cuppen, Edwin, Danyi, Alexandra, de Ridder, Jeroen, van Herpen, Carla, Lolkema, Martijn P., Steeghs, Neeltje, Morris, Quaid, Al-Shahrour, Fatima, Atwal, Gurnit, Bailey, Peter J., Biankin, Andrew V., Boutros, Paul C., Campbell, Peter J., Chang, David K., Cooke, Susanna L., Deshpande, Vikram, Faltas, Bishoy M., Faquin, William C., Garraway, Levi, Getz, Gad, Grimmond, Sean M., Haider, Syed, Hoadley, Katherine A., Kaiser, Vera B., Karlić, Rosa, Kato, Mamoru, Kübler, Kirsten, Lazar, Alexander J., Li, Constance H., Louis, David N., Margolin, Adam, Martin, Sancha, Nahal-Bose, Hardeep K., Nielsen, G. Petur, Nik-Zainal, Serena, Omberg, Larsson, P’ng, Christine, Perry, Marc D., Polak, Paz, Rheinbay, Esther, Rubin, Mark A., Semple, Colin A., Sgroi, Dennis C., Shibata, Tatsuhiro, Siebert, Reiner, Smith, Jaclyn, Stein, Lincoln D., Stobbe, Miranda D., Sun, Ren X., Thai, Kevin, Wright, Derek W., Wu, Chin-Lee, Yuan, Ke, Zhang, Junjun
Published 2021

Inferring structural variant cancer cell fraction

by Cmero, Marek, Yuan, Ke, Ong, Cheng Soon, Schröder, Jan, Corcoran, Niall M., Papenfuss, Tony, Hovens, Christopher M., Markowetz, Florian, Macintyre, Geoff, Adams, David J., Anur, Pavana, Beroukhim, Rameen, Boutros, Paul C., Bowtell, David D. L., Campbell, Peter J., Cao, Shaolong, Christie, Elizabeth L., Cun, Yupeng, Dawson, Kevin J., Demeulemeester, Jonas, Dentro, Stefan C., Deshwar, Amit G., Donmez, Nilgun, Drews, Ruben M., Eils, Roland, Fan, Yu, Fittall, Matthew W., Garsed, Dale W., Gerstung, Moritz, Getz, Gad, Gonzalez, Santiago, Ha, Gavin, Haase, Kerstin, Imielinski, Marcin, Jerman, Lara, Ji, Yuan, Jolly, Clemency, Kleinheinz, Kortine, Lee, Juhee, Lee-Six, Henry, Leshchiner, Ignaty, Livitz, Dimitri, Malikic, Salem, Martincorena, Iñigo, Mitchell, Thomas J., Morris, Quaid D., Mustonen, Ville, Oesper, Layla, Peifer, Martin, Peto, Myron, Raphael, Benjamin J., Rosebrock, Daniel, Rubanova, Yulia, Sahinalp, S. Cenk, Salcedo, Adriana, Schlesner, Matthias, Schumacher, Steven E., Sengupta, Subhajit, Shi, Ruian, Shin, Seung Jun, Spellman, Paul T., Spiro, Oliver, Stein, Lincoln D., Tarabichi, Maxime, Van Loo, Peter, Vembu, Shankar, Vázquez-García, Ignacio, Wang, Wenyi, Wedge, David C., Wheeler, David A., Wintersinger, Jeffrey A., Yang, Tsun-Po, Yao, Xiaotong, Yu, Kaixian, Zhu, Hongtu
Published 2021

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

by modENCODE Consortium, Roy, Sushmita, Ernst, Jason, Kharchenko, Peter V., Kheradpour, Pouya, Negre, Nicolas, Eaton, Matthew L., Landolin, Jane M., Bristow, Christopher A., Ma, Lijia, Lin, Michael F., Washietl, Stefan, Arshinoff, Bradley I., Ay, Ferhat, Meyer, Patrick E., Robine, Nicolas, Washington, Nicole L., Stefano, Luisa Di, Berezikov, Eugene, Brown, Christopher D., Candeias, Rogerio, Carlson, Joseph W., Carr, Adrian, Jungreis, Irwin, Marbach, Daniel, Sealfon, Rachel, Tolstorukov, Michael Y., Will, Sebastian, Alekseyenko, Artyom A., Artieri, Carlo, Booth, Benjamin W., Brooks, Angela N., Dai, Qi, Davis, Carrie A., Duff, Michael O., Feng, Xin, Gorchakov, Andrey A., Gu, Tingting, Henikoff, Jorja G., Kapranov, Philipp, Li, Renhua, MacAlpine, Heather K., Malone, John, Minoda, Aki, Nordman, Jared, Okamura, Katsutomo, Perry, Marc, Powell, Sara K., Riddle, Nicole C., Sakai, Akiko, Samsonova, Anastasia, Sandler, Jeremy E., Schwartz, Yuri B., Sher, Noa, Spokony, Rebecca, Sturgill, David, Baren, Marijke van, Wan, Kenneth H., Yang, Li, Yu, Charles, Feingold, Elise, Good, Peter, Guyer, Mark, Lowdon, Rebecca, Ahmad, Kami, Andrews, Justen, Berger, Bonnie, Brenner, Steven E., Brent, Michael R., Cherbas, Lucy, Elgin, Sarah R., Gingeras, Thomas R., Grossman, Robert, Hoskins, Roger A., Kaufman, Thomas C., Kent, William, Kuroda, Mitzi I., Orr-Weaver, Terry, Perrimon, Norbert, Pirrotta, Vincenzo, Posakony, James W., Ren, Bing, Russell, Steven, Cherbas, Peter, Graveley, Brenton R., Lewis, Suzanna, Micklem, Gos, Oliver, Brian, Park, Peter J., Celniker, Susan E., Henikoff, Steven, Karpen, Gary H., Lai, Eric C., MacAlpine, David M., Stein, Lincoln D., White, Kevin P., Kellis, Manolis
Published 2019

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

by Rheinbay, Esther, Nielsen, Morten Muhlig, Abascal, Federico, Wala, Jeremiah A, Shapira, Ofer, Tiao, Grace, Hornshøj, Henrik, Hess, Julian M, Juul, Randi Istrup, Lin, Ziao, Feuerbach, Lars, Sabarinathan, Radhakrishnan, Madsen, Tobias, Kim, Jaegil, Mularoni, Loris, Shuai, Shimin, Lanzós, Andrés, Herrmann, Carl, Maruvka, Yosef E, Shen, Ciyue, Amin, Samirkumar B, Bandopadhayay, Pratiti, Bertl, Johanna, Boroevich, Keith A, Busanovich, John, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Craft, David, Dhingra, Priyanka, Diamanti, Klev, Fonseca, Nuno A, Gonzalez-Perez, Abel, Guo, Qianyun, Hamilton, Mark P, Haradhvala, Nicholas J, Hong, Chen, Isaev, Keren, Johnson, Todd A, Juul, Malene, Kahles, Andre, Kahraman, Abdullah, Kim, Youngwook, Komorowski, Jan, Kumar, Kiran, Kumar, Sushant, Lee, Donghoon, Lehmann, Kjong-Van, Li, Yilong, Liu, Eric Minwei, Lochovsky, Lucas, Park, Keunchil, Pich, Oriol, Roberts, Nicola D, Saksena, Gordon, Schumacher, Steven E, Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stewart, Chip, Tamborero, David, Tubio, Jose M C, Umer, Husen M, Uusküla-Reimand, Liis, Wadelius, Claes, Wadi, Lina, Yao, Xiaotong, Zhang, Cheng-Zhong, Zhang, Jing, Haber, James E, Hobolth, Asger, Imielinski, Marcin, Kellis, Manolis, Lawrence, Michael S, von Mering, Christian, Nakagawa, Hidewaki, Raphael, Benjamin J, Rubin, Mark A, Sander, Chris, Stein, Lincoln D, Stuart, Joshua M, Tsunoda, Tatsuhiko, Wheeler, David A, Johnson, Rory, Reimand, Jüri, Gerstein, Mark, Khurana, Ekta, Campbell, Peter J, López-Bigas, Núria, Weischenfeldt, Joachim, Beroukhim, Rameen, Martincorena, Iñigo, Pedersen, Jakob Skou, Getz, Gad
Published 2020

Analyses of non-coding somatic drivers in 2,658cancer whole genomes

by Group, PCAWG Drivers, Functional Interpretation Working, Group, PCAWG Structural Variation Working, Consortium, PCAWG, PCAWG Consortium, Rheinbay, Esther, Nielsen, Morten M., Abascal, Federico, Wala, Jeremiah A, Shapira, Ofer, Tiao, Grace, Hornshøj, Henrik, Hess, Julian M, Juul, Randi I., Lin, Ziao, Feuerbach, Lars, Sabarinathan, Radhakrishnan, Madsen, Tobias, Kim, Jaegil, Mularoni, Loris, Shuai, Shimin, Lanzós, Andrés, Herrmann, Carl, Maruvka, Yosef E., Shen, Ciyue, Amin, Samirkumar B., Bandopadhayay, Pratiti, Bertl, Johanna, Boroevich, Keith A., Busanovich, John, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Craft, David, Dhingra, Priyanka, Diamanti, Klev, Fonseca, Nuno A., Gonzalez-Perez, Abel, Guo, Qianyun, Hamilton, Mark P., Haradhvala, Nicholas J., Hong, Chen, Isaev, Keren, Johnson, Todd A., Juul, Malene, Kahles, Andre, Kahraman, Abdullah, Kim, Youngwook, Komorowski, Jan, Kumar, Kiran, Kumar, Sushant, Lee, Donghoon, Lehmann, Kjong-Van, Li, Yilong, Liu, Eric M., Lochovsky, Lucas, Park, Keunchil, Pich, Oriol, Roberts, Nicola D., Saksena, Gordon, Schumacher, Steven E, Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stewart, Chip, Tamborero, David, Tubio, Jose M.C., Umer, Husen M., Uusküla-Reimand, Liis, Wadelius, Claes, Wadi, Lina, Yao, Xiaotong, Zhang, Cheng-Zhong, Zhang, Jing, Haber, James E., Hobolth, Asger, Imielinski, Marcin, Kellis, Manolis, Lawrence, Michael S., von Mering, Christian, Nakagawa, Hidewaki, Raphael, Benjamin J., Rubin, Mark A., Sander, Chris, Stein, Lincoln D., Stuart, Joshua M., Tsunoda, Tatsuhiko, Wheeler, David A., Johnson, Rory, Reimand, Jüri, Gerstein, Mark, Khurana, Ekta, Campbell, Peter J., López-Bigas, Núria, Weischenfeldt, Joachim, Beroukhim, Rameen, Martincorena, Iñigo, Pedersen, Jakob S., Getz, Gad
Published 2020

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

by Rheinbay, Esther, Nielsen, Morten Muhlig, Abascal, Federico, Wala, Jeremiah A, Shapira, Ofer, Tiao, Grace, Hornshøj, Henrik, Hess, Julian M, Juul, Randi Istrup, Lin, Ziao, Feuerbach, Lars, Sabarinathan, Radhakrishnan, Madsen, Tobias, Kim, Jaegil, Mularoni, Loris, Shuai, Shimin, Lanzós, Andrés, Herrmann, Carl, Maruvka, Yosef E, Shen, Ciyue, Amin, Samirkumar B, Bandopadhayay, Pratiti, Bertl, Johanna, Boroevich, Keith A, Busanovich, John, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Craft, David, Dhingra, Priyanka, Diamanti, Klev, Fonseca, Nuno A, Gonzalez-Perez, Abel, Guo, Qianyun, Hamilton, Mark P, Haradhvala, Nicholas J, Hong, Chen, Isaev, Keren, Johnson, Todd A, Juul, Malene, Kahles, Andre, Kahraman, Abdullah, Kim, Youngwook, Komorowski, Jan, Kumar, Kiran, Kumar, Sushant, Lee, Donghoon, Lehmann, Kjong-Van, Li, Yilong, Liu, Eric Minwei, Lochovsky, Lucas, Park, Keunchil, Pich, Oriol, Roberts, Nicola D, Saksena, Gordon, Schumacher, Steven E, Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stewart, Chip, Tamborero, David, Tubio, Jose MC, Umer, Husen M, Uusküla-Reimand, Liis, Wadelius, Claes, Wadi, Lina, Yao, Xiaotong, Zhang, Cheng-Zhong, Zhang, Jing, Haber, James E, Hobolth, Asger, Imielinski, Marcin, Kellis, Manolis, Lawrence, Michael S, von Mering, Christian, Nakagawa, Hidewaki, Raphael, Benjamin J, Rubin, Mark A, Sander, Chris, Stein, Lincoln D, Stuart, Joshua M, Tsunoda, Tatsuhiko, Wheeler, David A, Johnson, Rory, Reimand, Jüri, Gerstein, Mark, Khurana, Ekta, Campbell, Peter J, López-Bigas, Núria, PCAWG Drivers and Functional Interpretation Working Group, PCAWG Structural Variation Working Group, Weischenfeldt, Joachim, Beroukhim, Rameen, Martincorena, Iñigo, Pedersen, Jakob Skou, Getz, Gad, PCAWG Consortium
Published 2021

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

by Rheinbay, Esther, Nielsen, Morten Muhlig, Abascal, Federico, Wala, Jeremiah A., Shapira, Ofer, Tiao, Grace, Hornshøj, Henrik, Hess, Julian M., Juul, Randi Istrup, Lin, Ziao, Feuerbach, Lars, Sabarinathan, Radhakrishnan, Madsen, Tobias, Kim, Jaegil, Mularoni, Loris, Shuai, Shimin, Lanzós, Andrés, Herrmann, Carl, Maruvka, Yosef E., Shen, Ciyue, Amin, Samirkumar B., Bandopadhayay, Pratiti, Bertl, Johanna, Boroevich, Keith A., Busanovich, John, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Craft, David, Dhingra, Priyanka, Diamanti, Klev, Fonseca, Nuno A., Gonzalez-Perez, Abel, Guo, Qianyun, Hamilton, Mark P., Haradhvala, Nicholas J., Hong, Chen, Isaev, Keren, Johnson, Todd A., Juul, Malene, Kahles, Andre, Kahraman, Abdullah, Kim, Youngwook, Komorowski, Jan, Kumar, Kiran, Kumar, Sushant, Lee, Donghoon, Lehmann, Kjong-Van, Li, Yilong, Liu, Eric Minwei, Lochovsky, Lucas, Park, Keunchil, Pich, Oriol, Roberts, Nicola D., Saksena, Gordon, Schumacher, Steven E., Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stewart, Chip, Tamborero, David, Tubio, Jose M. C., Umer, Husen M., Uusküla-Reimand, Liis, Wadelius, Claes, Wadi, Lina, Yao, Xiaotong, Zhang, Cheng-Zhong, Zhang, Jing, Haber, James E., Hobolth, Asger, Imielinski, Marcin, Kellis, Manolis, Lawrence, Michael S., von Mering, Christian, Nakagawa, Hidewaki, Raphael, Benjamin J., Rubin, Mark A., Sander, Chris, Stein, Lincoln D., Stuart, Joshua M., Tsunoda, Tatsuhiko, Wheeler, David A., Johnson, Rory, Reimand, Jüri, Gerstein, Mark, Khurana, Ekta, Campbell, Peter J., López-Bigas, Núria, Weischenfeldt, Joachim, Beroukhim, Rameen, Martincorena, Iñigo, Pedersen, Jakob Skou, Getz, Gad
Published 2022