Using GBrowse 2.0 to visualize and share next-generation sequence data

by Stein, Lincoln D.
Published 2013

Modeling the evolution dynamics of exon-intron structure with a general random fragmentation process

by Wang, Liya, Stein, Lincoln D
Published 2013

RNASequel: accurate and repeat tolerant realignment of RNA-seq reads

by Wilson, Gavin W., Stein, Lincoln D.
Published 2015

The Reactome BioMart

by Haw, Robin A., Croft, David, Yung, Christina K., Ndegwa, Nelson, D'Eustachio, Peter, Hermjakob, Henning, Stein, Lincoln D.
Published 2011

Gallus GBrowse: a unified genomic database for the chicken

by Schmidt, Carl J., Romanov, Michael, Ryder, Oliver, Magrini, Vincent, Hickenbotham, Matthew, Glasscock, Jarret, McGrath, Sean, Mardis, Elaine, Stein, Lincoln D.
Published 2008

WormBook: the online review of Caenorhabditis elegans biology

by Girard, Lisa R., Fiedler, Tristan J., Harris, Todd W., Carvalho, Felicia, Antoshechkin, Igor, Han, Michael, Sternberg, Paul W., Stein, Lincoln D., Chalfie, Martin
Published 2007

Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE

by Trinh, Quang M, Jen, Fei-Yang Arthur, Zhou, Ziru, Chu, Kar Ming, Perry, Marc D, Kephart, Ellen T, Contrino, Sergio, Ruzanov, Peter, Stein, Lincoln D
Published 2013

Redefining Genomic Privacy: Trust and Empowerment

by Erlich, Yaniv, Williams, James B., Glazer, David, Yocum, Kenneth, Farahany, Nita, Olson, Maynard, Narayanan, Arvind, Stein, Lincoln D., Witkowski, Jan A., Kain, Robert C.
Published 2014

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

by Washington, Nicole L., Stinson, E. O., 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 2011

Exome sequencing identifies nonsegregating nonsense ATM and PALB2 variants in familial pancreatic cancer

by Grant, Robert C, Al-Sukhni, Wigdan, Borgida, Ayelet E, Holter, Spring, Kanji, Zaheer S, McPherson, Treasa, Whelan, Emily, Serra, Stefano, Trinh, Quang M, Peltekova, Vanya, Stein, Lincoln D, McPherson, John D, Gallinger, Steven
Published 2013

Downregulation of histone H2A and H2B pathways is associated with anthracycline sensitivity in breast cancer

by Braunstein, Marsela, Liao, Linda, Lyttle, Nicola, Lobo, Nazleen, Taylor, Karen J., Krzyzanowski, Paul M., Kalatskaya, Irina, Yao, Cindy Q., Stein, Lincoln D., Boutros, Paul C., Twelves, Christopher J., Marcellus, Richard, Bartlett, John M. S., Spears, Melanie
Published 2016

TDP-1, the Caenorhabditis elegans ortholog of TDP-43, limits the accumulation of double-stranded RNA

by Saldi, Tassa K, Ash, Peter EA, Wilson, Gavin, Gonzales, Patrick, Garrido-Lecca, Alfonso, Roberts, Christine M, Dostal, Vishantie, Gendron, Tania F, Stein, Lincoln D, Blumenthal, Thomas, Petrucelli, Leonard, Link, Christopher D
Published 2014

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, E. O., Washington, Nicole L., Perry, Marc D., Ruzanov, Peter, Zha, Zheng, Lewis, Suzanna E., Stein, Lincoln D., Micklem, Gos
Published 2012

Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics

by Chen, Nansheng, Mah, Allan, Blacque, Oliver E, Chu, Jeffrey, Phgora, Kiran, Bakhoum, Mathieu W, Hunt Newbury, C Rebecca, Khattra, Jaswinder, Chan, Susanna, Go, Anne, Efimenko, Evgeni, Johnsen, Robert, Phirke, Prasad, Swoboda, Peter, Marra, Marco, Moerman, Donald G, Leroux, Michel R, Baillie, David L, Stein, Lincoln D
Published 2006

WormBase 2007

by Rogers, Anthony, Antoshechkin, Igor, Bieri, Tamberlyn, Blasiar, Darin, Bastiani, Carol, Canaran, Payan, Chan, Juancarlos, Chen, Wen J., Davis, Paul, Fernandes, Jolene, Fiedler, Tristan J., Han, Michael, Harris, Todd W., Kishore, Ranjana, Lee, Raymond, McKay, Sheldon, Müller, Hans-Michael, Nakamura, Cecilia, Ozersky, Philip, Petcherski, Andrei, Schindelman, Gary, Schwarz, Erich M., Spooner, Will, Tuli, Mary Ann, Van Auken, Kimberly, Wang, Daniel, Wang, Xiaodong, Williams, Gary, Yook, Karen, Durbin, Richard, Stein, Lincoln D., Spieth, John, Sternberg, Paul W.
Published 2008

WormBase: better software, richer content

by Schwarz, Erich M., Antoshechkin, Igor, Bastiani, Carol, Bieri, Tamberlyn, Blasiar, Darin, Canaran, Payan, Chan, Juancarlos, Chen, Nansheng, Chen, Wen J., Davis, Paul, Fiedler, Tristan J., Girard, Lisa, Harris, Todd W., Kenny, Eimear E., Kishore, Ranjana, Lawson, Dan, Lee, Raymond, Müller, Hans-Michael, Nakamura, Cecilia, Ozersky, Phil, Petcherski, Andrei, Rogers, Anthony, Spooner, Will, Tuli, Mary Ann, Van Auken, Kimberly, Wang, Daniel, Durbin, Richard, Spieth, John, Stein, Lincoln D., Sternberg, Paul W.
Published 2006

WormBase: new content and better access

by Bieri, Tamberlyn, Blasiar, Darin, Ozersky, Philip, Antoshechkin, Igor, Bastiani, Carol, Canaran, Payan, Chan, Juancarlos, Chen, Nansheng, Chen, Wen J., Davis, Paul, Fiedler, Tristan J., Girard, Lisa, Han, Michael, Harris, Todd W., Kishore, Ranjana, Lee, Raymond, McKay, Sheldon, Müller, Hans-Michael, Nakamura, Cecilia, Petcherski, Andrei, Rangarajan, Arun, Rogers, Anthony, Schindelman, Gary, Schwarz, Erich M., Spooner, Will, Tuli, Mary Ann, Auken, Kimberly Van, Wang, Daniel, Wang, Xiaodong, Williams, Gary, Durbin, Richard, Stein, Lincoln D., Sternberg, Paul W., Spieth, John
Published 2007

WormBase: a comprehensive data resource for Caenorhabditis biology and genomics

by Chen, Nansheng, Harris, Todd W., Antoshechkin, Igor, Bastiani, Carol, Bieri, Tamberlyn, Blasiar, Darin, Bradnam, Keith, Canaran, Payan, Chan, Juancarlos, Chen, Chao-Kung, Chen, Wen J., Cunningham, Fiona, Davis, Paul, Kenny, Eimear, Kishore, Ranjana, Lawson, Daniel, Lee, Raymond, Muller, Hans-Michael, Nakamura, Cecilia, Pai, Shraddha, Ozersky, Philip, Petcherski, Andrei, Rogers, Anthony, Sabo, Aniko, Schwarz, Erich M., Van Auken, Kimberly, Wang, Qinghua, Durbin, Richard, Spieth, John, Sternberg, Paul W., Stein, Lincoln D.
Published 2005

Identification of pre-leukemic hematopoietic stem cells in acute leukemia

by Shlush, Liran I., Zandi, Sasan, Mitchell, Amanda, Chen, Weihsu Claire, Brandwein, Joseph M., Gupta, Vikas, Kennedy, James A., Schimmer, Aaron D., Schuh, Andre C., Yee, Karen W., McLeod, Jessica L., Doedens, Monica, Medeiros, Jessie J.F., Marke, Rene, Kim, Hyeoung Joon, Lee, Kwon, McPherson, John D., Hudson, Thomas J., Brown, Andrew M.K., Trinh, Quang M., Stein, Lincoln D., Minden, Mark D., Wang, Jean C.Y., Dick, John E.
Published 2014

The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics

by Stein, Lincoln D, Bao, Zhirong, Blasiar, Darin, Blumenthal, Thomas, Brent, Michael R, Chen, Nansheng, Chinwalla, Asif, Clarke, Laura, Clee, Chris, Coghlan, Avril, Coulson, Alan, D'Eustachio, Peter, Fitch, David H. A, Fulton, Lucinda A, Fulton, Robert E, Griffiths-Jones, Sam, Harris, Todd W, Hillier, LaDeana W, Kamath, Ravi, Kuwabara, Patricia E, Mardis, Elaine R, Marra, Marco A, Miner, Tracie L, Minx, Patrick, Mullikin, James C, Plumb, Robert W, Rogers, Jane, Schein, Jacqueline E, Sohrmann, Marc, Spieth, John, Stajich, Jason E, Wei, Chaochun, Willey, David, Wilson, Richard K, Durbin, Richard, Waterston, Robert H
Published 2003