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Lincoln Stein
Lincoln D. Stein
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- affiliation: Ontario Institute for Cancer Research, Toronto, Canada
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2020 – today
- 2024
- [j75]Adam Wright
, Mark D. Wilkinson
, Christopher J. Mungall
, Scott Cain
, Stephen Richards
, Paul W. Sternberg
, Ellen Provin
, Jonathan L. Jacobs
, Scott Geib
, Daniela Raciti
, Karen Yook
, Lincoln Stein
, David C. Molik
:
FAIR Header Reference genome: a TRUSTworthy standard. Briefings Bioinform. 25(3) (2024) - [j74]Marija Orlic-Milacic
, Karen Rothfels
, Lisa Matthews
, Adam J. Wright
, Bijay Jassal
, Veronica Shamovsky
, Quang M. Trinh
, Marc Gillespie
, Cristoffer Sevilla
, Krishna Tiwari
, Eliot Ragueneau
, Chuqiao Gong
, Ralf Stephan
, Bruce May
, Robin Haw
, Joel Weiser, Deidre Beavers, Patrick Conley, Henning Hermjakob
, Lincoln D. Stein
, Peter D'Eustachio
, Guanming Wu
:
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes. Database J. Biol. Databases Curation 2024 (2024) - 2023
- [j73]Teresa De Jesus Martinez
, Elliot A. Hershberg
, Emma Guo, Garrett Stevens
, Colin M. Diesh
, Peter Xie, Caroline Bridge, Scott Cain, Robin Haw, Robert M. Buels, Lincoln D. Stein, Ian H. Holmes:
JBrowse Jupyter: a Python interface to JBrowse 2. Bioinform. 39(1) (2023) - [j72]Joshua Atienza
, Anjalee Benedict, Lincoln D. Stein, Kashif Pirzada, Cheryl White
, Shraddha Pai
:
Fourteen quick tips for crowdsourcing geographically linked data for public health advocacy. PLoS Comput. Biol. 19(9) (2023) - 2022
- [j71]Adam J. Wright, Marija Orlic-Milacic, Karen Rothfels, Joel Weiser, Quang M. Trinh, Bijay Jassal, Robin Haw, Lincoln D. Stein:
Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase. Database J. Biol. Databases Curation 2022(2022) (2022) - [j70]Marc Gillespie
, Bijay Jassal, Ralf Stephan
, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro
, Johannes Griss
, Cristoffer Sevilla
, Lisa Matthews, Chuqiao Gong
, Chuan Deng, Thawfeek M. Varusai
, Eliot Ragueneau
, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati
, Liam Beckman
, Xiang Shao, Antonio Fabregat
, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary D. Bader
, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob
, Peter D'Eustachio
:
The reactome pathway knowledgebase 2022. Nucleic Acids Res. 50(D1): 687-692 (2022) - 2021
- [j69]Elliot A. Hershberg
, Garrett Stevens
, Colin M. Diesh, Peter Xie, Teresa De Jesus Martinez, Robert M. Buels, Lincoln Stein, Ian H. Holmes:
JBrowseR: an R interface to the JBrowse 2 genome browser. Bioinform. 37(21): 3914-3915 (2021) - [j68]Marcela K. Tello-Ruiz
, Sushma Naithani
, Parul Gupta, Andrew Olson, Sharon Wei, Justin Preece, Yinping Jiao, Bo Wang, Kapeel Chougule, Priyanka Garg, Justin Elser, Sunita Kumari, Vivek Kumar, Bruno Contreras-Moreira
, Guy Naamati
, Nancy George, Justin Cook
, Dan M. Bolser, Peter D'Eustachio
, Lincoln D. Stein, Amit Gupta, Weijia Xu, Jennifer Regala
, Irene Papatheodorou
, Paul J. Kersey, Paul Flicek
, Crispin Taylor, Pankaj Jaiswal
, Doreen Ware:
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Res. 49(Database-Issue): D1452-D1463 (2021) - [j67]Seth Carbon, Eric Douglass, Benjamin M. Good, Deepak R. Unni
, Nomi L. Harris
, Christopher J. Mungall, Siddartha Basu, Rex L. Chisholm
, Robert J. Dodson, Eric Hartline, Petra Fey, Paul D. Thomas, Laurent-Philippe Albou
, Dustin Ebert, Michael J. Kesling, Huaiyu Mi, Anushya Muruganujan, Xiaosong Huang, Tremayne Mushayahama, Sandra A. LaBonte
, Deborah A. Siegele, Giulia Antonazzo
, Helen Attrill
, Nick H. Brown, Phani V. Garapati
, Steven J. Marygold
, Vitor Trovisco, Gilberto dos Santos, Kathleen Falls, Christopher J. Tabone
, Pinglei Zhou, Joshua L. Goodman
, Victor B. Strelets, Jim Thurmond
, Penelope Garmiri
, Rizwan Ishtiaq, Milagros Rodríguez-López, Marcio Luis Acencio
, Martin Kuiper, Astrid Lægreid, Colin Logie
, Ruth C. Lovering
, Barbara Kramarz
, Shirin C. C. Saverimuttu, Sandra M. Pinheiro, Heather Gunn, Renzhi Su, Katherine E. Thurlow
, Marcus C. Chibucos
, Michelle G. Giglio, Suvarna Nadendla, James B. Munro
, Rebecca C. Jackson, Margaret J. Duesbury, Noemi del-Toro, Birgit H. M. Meldal
, Kalpana Paneerselvam, Livia Perfetto, Pablo Porras
, Sandra E. Orchard
, Anjali Shrivastava, Hsin-Yu Chang
, Robert D. Finn
, Alex L. Mitchell
, Neil D. Rawlings, Lorna J. Richardson
, Amaia Sangrador-Vegas
, Judith A. Blake, Karen R. Christie, Mary E. Dolan, Harold J. Drabkin, David P. Hill, Li Ni, Dmitry M. Sitnikov, Midori A. Harris, Stephen G. Oliver, Kim Rutherford
, Valerie Wood, Jaqueline Hayles, Jürg Bähler, Elizabeth R. Bolton, Jeffrey DePons, Melinda R. Dwinell, G. Thomas Hayman, Mary L. Kaldunski, Anne E. Kwitek
, Stanley J. F. Laulederkind, Cody Plasterer, Marek Tutaj, Mahima Vedi
, Shur-Jen Wang, Peter D'Eustachio, Lisa Matthews, James P. Balhoff, Suzi A. Aleksander, Michael J. Alexander, J. Michael Cherry
, Stacia R. Engel
, Felix Gondwe, Kalpana Karra, Stuart R. Miyasato, Robert S. Nash, Matt Simison, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Marc Feuermann
, Pascale Gaudet
, Anne Morgat, Erica Bakker, Tanya Z. Berardini
, Leonore Reiser
, Shabari Subramaniam
, Eva Huala
, Cecilia N. Arighi, Andrea H. Auchincloss, Kristian B. Axelsen
, Ghislaine Argoud-Puy, Alex Bateman
, Marie-Claude Blatter, Emmanuel Boutet, Emily Bowler
, Lionel Breuza, Alan J. Bridge
, Ramona Britto
, Hema Bye-A-Jee
, Cristina Casals-Casas, Elisabeth Coudert, Paul Denny
, Anne Estreicher, Maria Livia Famiglietti, George E. Georghiou
, Arnaud Gos, Nadine Gruaz-Gumowski, Emma Hatton-Ellis, Chantal Hulo, Alexandr Ignatchenko
, Florence Jungo, Kati Laiho, Philippe Le Mercier
, Damien Lieberherr, Antonia Lock
, Yvonne Lussi, Alistair MacDougall, Michele Magrane
, Maria Jesus Martin
, Patrick Masson
, Darren A. Natale
, Nevila Hyka-Nouspikel, Ivo Pedruzzi
, Lucille Pourcel, Sylvain Poux, Sangya Pundir, Catherine Rivoire
, Elena Speretta
, Shyamala Sundaram, Nidhi Tyagi, Kate Warner
, Rossana Zaru
, Cathy H. Wu
, Alexander D. Diehl, Juancarlos Chan, Christian A. Grove, Raymond Y. N. Lee, Hans-Michael Müller, Daniela Raciti
, Kimberly Van Auken, Paul W. Sternberg, Matthew Berriman, Michael Paulini, Kevin L. Howe
, Sibyl Gao, Adam Wright, Lincoln Stein, Douglas G. Howe, Sabrina Toro
, Monte Westerfield, Pankaj Jaiswal, Laurel Cooper
, Justin Elser:
The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res. 49(Database-Issue): D325-D334 (2021) - [j66]Denis Yuen
, Louise Cabansay, Andrew G. Duncan, Gary Luu, Gregory Hogue, Charles Overbeck, Natalie Perez, Walt Shands, David Steinberg, Chaz Reid, Nneka Olunwa, Richard Hansen, Elizabeth Sheets
, Ash O'farrell
, Kim Cullion, Brian D. O'Connor
, Benedict Paten, Lincoln Stein:
The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols. Nucleic Acids Res. 49(Webserver-Issue): 624-632 (2021) - 2020
- [j65]Sushma Naithani
, Parul Gupta, Justin Preece, Peter D'Eustachio
, Justin Elser, Priyanka Garg, Daemon A. Dikeman, Jason Kiff, Justin Cook
, Andrew Olson, Sharon Wei, Marcela K. Tello-Ruiz, Antonio Fabregat Mundo
, Alfonso Muñoz-Pomer Fuentes, Suhaib Mohammed
, Tiejun Cheng, Evan Bolton
, Irene Papatheodorou
, Lincoln Stein, Doreen Ware, Pankaj Jaiswal
:
Plant Reactome: a knowledgebase and resource for comparative pathway analysis. Nucleic Acids Res. 48(Database-Issue): D1093-D1103 (2020) - [j64]Bijay Jassal
, Lisa Matthews, Guilherme Viteri
, Chuqiao Gong
, Pascual Lorente, Antonio Fabregat
, Konstantinos Sidiropoulos, Justin Cook
, Marc Gillespie
, Robin Haw, Fred Loney, Bruce May, Marija Milacic
, Karen Rothfels, Cristoffer Sevilla
, Veronica Shamovsky, Solomon Shorser, Thawfeek M. Varusai
, Joel Weiser, Guanming Wu, Lincoln Stein, Henning Hermjakob
, Peter D'Eustachio
:
The reactome pathway knowledgebase. Nucleic Acids Res. 48(Database-Issue): D498-D503 (2020) - [j63]Todd W. Harris
, Valerio Arnaboldi, Scott Cain, Juancarlos Chan, Wen J. Chen, Jae-Hyoung Cho, Paul Davis
, Sibyl Gao, Christian A. Grove
, Ranjana Kishore, Raymond Y. N. Lee, Hans-Michael Müller, Cecilia Nakamura, Paulo A. S. Nuin, Michael Paulini
, Daniela Raciti
, Faye Rodgers
, Matthew Russell
, Gary Schindelman, Kimberly Van Auken, Qinghua Wang, Gary Williams, Adam Wright, Karen Yook, Kevin L. Howe
, Tim Schedl, Lincoln Stein, Paul W. Sternberg:
WormBase: a modern Model Organism Information Resource. Nucleic Acids Res. 48(Database-Issue): D762-D767 (2020) - [j62]Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M. Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann
, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin
, Pratiti Bandopadhayay, Johanna Bertl
, Keith A. Boroevich
, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti
, Nuno A. Fonseca
, Abel Gonzalez-Perez
, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, André Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee
, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin
, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jüri Reimand
, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Núria López-Bigas, Gary D. Bader, Jonathan Barenboim, Rameen Beroukhim, Søren Brunak, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, J. Lynn Fink
, Joan Frigola, Carlo Gambacorti Passerini, Dale W. Garsed, Gad Getz, Ivo Glynne Gut, David Haan, Arif Ozgun Harmanci, Mohamed Helmy, Ermin Hodzic, José M. G. Izarzugaza, Jong K. Kim, Jan O. Korbel, Erik Larsson, Shantao Li, Xiaotong Li, Shaoke Lou, Kathleen Marchal
, Iñigo Martincorena, Alexander Martínez-Fundichely, Patrick D. McGillivray, William Meyerson, Ferran Muiños, Marta Paczkowska, Kiejung Park, Jakob Skou Pedersen
, Tirso Pons
, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Carlota Rubio-Perez, Süleyman Cenk Sahinalp, Leonidas Salichos, Mark Shackleton, Raunak Shrestha, Alfonso Valencia, Miguel Vazquez, Lieven P. C. Verbeke, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak
, Joachim Weischenfeldt, Guanming Wu, Jun Yu, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, Kadir C. Akdemir, Eva G. Alvarez, Adrian Baez-Ortega, Paul C. Boutros, David D. L. Bowtell, Benedikt Brors, Kathleen H. Burns, Kin Chan, Isidro Cortés-Ciriano
, Ana Dueso-Barroso, Andrew J. Dunford, Paul A. Edwards, Xavier Estivill, Dariush Etemadmoghadam, Milana Frenkel-Morgenstern
, Dmitry A. Gordenin, Barbara Hutter, David T. W. Jones, Young Seok Ju, Marat D. Kazanov
, Leszek J. Klimczak, Youngil Koh, Eunjung Alice Lee, Jake June-Koo Lee, Andy G. Lynch
, Geoff MacIntyre, Florian Markowetz, Matthew Meyerson, Satoru Miyano, Fabio C. P. Navarro, Stephan Ossowski, Peter J. Park, John V. Pearson, Montserrat Puiggròs, Karsten Rippe, Steven A. Roberts, Bernardo Rodriguez-Martin, Ralph Scully, David Torrents, Izar Villasante, Nicola Waddell, Jeremiah A. Wala, Lixing Yang, Sung-Soo Yoon, Jorge Zamora:
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578(7793): 102-111 (2020) - [j61]Moritz Gerstung
, Clemency Jolly, Ignaty Leshchiner, Stefan C. Dentro
, Santiago Gonzalez, Thomas J. Mitchell
, Yulia Rubanova, Pavana Anur, Kaixian Yu, Maxime Tarabichi
, Amit G. Deshwar, Jeff Wintersinger, Kortine Kleinheinz, Ignacio Vázquez-García, Kerstin Haase, Lara Jerman, Subhajit Sengupta, Geoff MacIntyre, Salem Malikic
, Nilgun Donmez, Dimitri G. Livitz
, Marek Cmero, Jonas Demeulemeester
, Steven E. Schumacher, Yu Fan, Xiaotong Yao
, Juhee Lee, Matthias Schlesner, Paul C. Boutros, David D. L. Bowtell, Hongtu Zhu, Gad Getz, Marcin Imielinski, Rameen Beroukhim, Süleyman Cenk Sahinalp, Yuan Ji, Martin Peifer
, Florian Markowetz, Ville Mustonen
, Ke Yuan, Wenyi Wang
, Quaid D. Morris
, David J. Adams
, Peter J. Campbell, Shaolong Cao, Elizabeth L. Christie
, Yupeng Cun, Kevin J. Dawson, Ruben M. Drews, Roland Eils
, Matthew Fittall
, Dale W. Garsed
, Gavin Ha, Henry Lee-Six, Iñigo Martincorena, Layla Oesper, Myron Peto, Benjamin J. Raphael, Daniel T. Rosebrock
, Adriana Salcedo, Ruian Shi, Seung Jun Shin, Oliver Spiro, Lincoln D. Stein, Shankar Vembu, David A. Wheeler, Tsun-Po Yang, Paul T. Spellman, David C. Wedge
, Peter Van Loo:
The evolutionary history of 2,658 cancers. Nat. 578(7793): 122-128 (2020) - [j60]Eric Yao, Robert M. Buels
, Lincoln Stein, Taner Z. Sen
, Ian H. Holmes
:
JBrowse Connect: A server API to connect JBrowse instances and users. PLoS Comput. Biol. 16(8) (2020)
2010 – 2019
- 2019
- [j59]Guilherme Viteri
, Lisa Matthews, Thawfeek M. Varusai
, Marc Gillespie
, Marija Milacic
, Justin Cook
, Joel Weiser, Solomon Shorser, Konstantinos Sidiropoulos, Antonio Fabregat, Robin Haw, Guanming Wu, Lincoln Stein, Peter D'Eustachio
, Henning Hermjakob
:
Reactome and ORCID - fine-grained credit attribution for community curation. Database J. Biol. Databases Curation 2019: baz123 (2019) - [j58]Deena M. A. Gendoo
, Robert E. Denroche
, Amy Zhang, Nikolina Radulovich
, Gun Ho Jang, Mathieu Lemire, Sandra Fischer, Dianne Chadwick, Ilinca M. Lungu
, Emin Ibrahimov, Ping-Jiang Cao, Lincoln D. Stein, Julie M. Wilson, John M. S. Bartlett, Ming-Sound Tsao
, Neesha Dhani, David Hedley, Steven Gallinger, Benjamin Haibe-Kains
:
Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer. PLoS Comput. Biol. 15(1) (2019) - 2018
- [j57]Antonio Fabregat
, Konstantinos Sidiropoulos
, Guilherme Viteri, Pablo Marín-García
, Peipei Ping, Lincoln Stein, Peter D'Eustachio
, Henning Hermjakob
:
Reactome diagram viewer: data structures and strategies to boost performance. Bioinform. 34(7): 1208-1214 (2018) - [j56]Marcela K. Tello-Ruiz, Sushma Naithani
, Joshua C. Stein
, Parul Gupta, Michael Campbell, Andrew Olson, Sharon Wei, Justin Preece, Matthew J. Geniza
, Yinping Jiao, Young Koung Lee, Bo Wang
, Joseph Mulvaney, Kapeel Chougule, Justin Elser, Noor Al-Bader, Sunita Kumari, James Thomason, Vivek Kumar, Daniel M. Bolser
, Guy Naamati
, Electra Tapanari, Nuno A. Fonseca
, Laura Huerta
, Haider Iqbal
, Maria Keays
, Alfonso Muñoz-Pomer Fuentes, Y. Amy Tang
, Antonio Fabregat
, Peter D'Eustachio
, Joel Weiser, Lincoln D. Stein, Robert Petryszak
, Irene Papatheodorou
, Paul J. Kersey
, Patti Lockhart
, Crispin Taylor, Pankaj Jaiswal
, Doreen Ware:
Gramene 2018: unifying comparative genomics and pathway resources for plant research. Nucleic Acids Res. 46(Database-Issue): D1181-D1189 (2018) - [j55]Antonio Fabregat
, Steven Jupe
, Lisa Matthews, Konstantinos Sidiropoulos
, Marc Gillespie
, Phani V. Garapati
, Robin Haw
, Bijay Jassal
, Florian Korninger, Bruce May, Marija Milacic
, Corina Duenas, Karen Rothfels, Cristoffer Sevilla
, Veronica Shamovsky, Solomon Shorser, Thawfeek M. Varusai
, Guilherme Viteri, Joel Weiser, Guanming Wu, Lincoln Stein, Henning Hermjakob
, Peter D'Eustachio
:
The Reactome Pathway Knowledgebase. Nucleic Acids Res. 46(Database-Issue): D649-D655 (2018) - [j54]Raymond Y. N. Lee
, Kevin L. Howe
, Todd W. Harris
, Valerio Arnaboldi
, Scott Cain, Juancarlos Chan, Wen J. Chen, Paul Davis
, Sibyl Gao, Christian A. Grove, Ranjana Kishore, Hans-Michael Müller, Cecilia Nakamura, Paulo A. S. Nuin, Michael Paulini
, Daniela Raciti
, Faye Rodgers
, Matthew Russell, Gary Schindelman, Mary Ann Tuli, Kimberly Van Auken, Qinghua Wang, Gary Williams, Adam Wright, Karen Yook, Matthew Berriman, Paul J. Kersey
, Tim Schedl, Lincoln Stein, Paul W. Sternberg:
WormBase 2017: molting into a new stage. Nucleic Acids Res. 46(Database-Issue): D869-D874 (2018) - [j53]Antonio Fabregat
, Florian Korninger, Guilherme Viteri
, Konstantinos Sidiropoulos
, Pablo Marín-García
, Peipei Ping, Guanming Wu, Lincoln Stein, Peter D'Eustachio
, Henning Hermjakob
:
Reactome graph database: Efficient access to complex pathway data. PLoS Comput. Biol. 14(1) (2018) - 2017
- [j52]Konstantinos Sidiropoulos
, Guilherme Viteri, Cristoffer Sevilla
, Steven Jupe
, Marissa Webber, Marija Orlic-Milacic
, Bijay Jassal
, Bruce May, Veronica Shamovsky, Corina Duenas, Karen Rothfels, Lisa Matthews, Heeyeon Song, Lincoln Stein, Robin Haw
, Peter D'Eustachio
, Peipei Ping, Henning Hermjakob
, Antonio Fabregat
:
Reactome enhanced pathway visualization. Bioinform. 33(21): 3461-3467 (2017) - [j51]Antonio Fabregat
, Konstantinos Sidiropoulos
, Guilherme Viteri, Oscar Forner-Martinez, Pablo Marín-García
, Vicente Arnau
, Peter D'Eustachio, Lincoln Stein, Henning Hermjakob
:
Reactome pathway analysis: a high-performance in-memory approach. BMC Bioinform. 18(1): 142:1-142:9 (2017) - [j50]Sushma Naithani
, Justin Preece, Peter D'Eustachio
, Parul Gupta, Vindhya Amarasinghe, Palitha Dharmawardhana, Guanming Wu, Antonio Fabregat
, Justin Elser, Joel Weiser, Maria Keays
, Alfonso Muñoz-Pomer Fuentes
, Robert Petryszak
, Lincoln D. Stein, Doreen Ware, Pankaj Jaiswal
:
Plant Reactome: a resource for plant pathways and comparative analysis. Nucleic Acids Res. 45(Database-Issue): D1029-D1039 (2017) - [i4]Brian D. O'Connor
, Denis Yuen
, Vincent Chung, Andrew G. Duncan, Xiangkun Liu, Janice Patricia, Benedict Paten, Lincoln Stein, Vincent Ferretti:
The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows. F1000Research 6: 52- (2017) - 2016
- [j49]Antonio Fabregat
, Konstantinos Sidiropoulos
, Phani V. Garapati, Marc Gillespie
, Kerstin Hausmann, Robin Haw
, Bijay Jassal
, Steven Jupe, Florian Korninger, Sheldon J. McKay, Lisa Matthews
, Bruce May, Marija Milacic
, Karen Rothfels, Veronica Shamovsky, Marissa Webber, Joel Weiser, Mark Williams, Guanming Wu, Lincoln Stein, Henning Hermjakob
, Peter D'Eustachio
:
The Reactome pathway Knowledgebase. Nucleic Acids Res. 44(Database-Issue): 481-487 (2016) - [j48]Kevin L. Howe
, Bruce J. Bolt
, Scott Cain, Juancarlos Chan, Wen J. Chen, Paul Davis
, James Done, Thomas A. Down, Sibyl Gao, Christian A. Grove, Todd W. Harris
, Ranjana Kishore, Raymond Y. N. Lee, Jane Lomax
, Yuling Li, Hans-Michael Müller, Cecilia Nakamura, Paulo A. S. Nuin, Michael Paulini, Daniela Raciti
, Gary Schindelman, Eleanor Stanley, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Adam Wright, Karen Yook, Matthew Berriman
, Paul J. Kersey
, Tim Schedl, Lincoln Stein, Paul W. Sternberg:
WormBase 2016: expanding to enable helminth genomic research. Nucleic Acids Res. 44(Database-Issue): 774-780 (2016) - [j47]Marcela K. Tello-Ruiz, Joshua C. Stein
, Sharon Wei, Justin Preece, Andrew Olson, Sushma Naithani
, Vindhya Amarasinghe, Palitha Dharmawardhana, Yinping Jiao, Joseph Mulvaney, Sunita Kumari, Kapeel Chougule, Justin Elser, Bo Wang
, James Thomason, Daniel M. Bolser, Arnaud Kerhornou, Brandon Walts, Nuno A. Fonseca
, Laura Huerta
, Maria Keays
, Y. Amy Tang
, Helen E. Parkinson
, Antonio Fabregat
, Sheldon J. McKay, Joel Weiser, Peter D'Eustachio
, Lincoln Stein, Robert Petryszak, Paul J. Kersey
, Pankaj Jaiswal, Doreen Ware:
Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Res. 44(Database-Issue): 1133-1140 (2016) - 2015
- [j46]Liya Wang, Doreen Ware, Carol Lushbough, Nirav C. Merchant
, Lincoln Stein:
A genome-wide association study platform built on iPlant cyber-infrastructure. Concurr. Comput. Pract. Exp. 27(2): 420-432 (2015) - [j45]Lincoln D. Stein, Bartha M. Knoppers, Peter Campbell, Gad Getz, Jan O. Korbel:
Data analysis: Create a cloud commons. Nat. 523(7559): 149-151 (2015) - 2014
- [j44]Wei Jiao, Shankar Vembu, Amit G. Deshwar, Lincoln Stein, Quaid Morris
:
Inferring clonal evolution of tumors from single nucleotide somatic mutations. BMC Bioinform. 15: 35 (2014) - [j43]David Croft, Antonio Fabregat Mundo
, Robin Haw, Marija Milacic
, Joel Weiser, Guanming Wu, Michael Caudy, Phani V. Garapati
, Marc Gillespie
, Maulik R. Kamdar
, Bijay Jassal
, Steven Jupe
, Lisa Matthews
, Bruce May, Stanislav Palatnik, Karen Rothfels, Veronica Shamovsky, Heeyeon Song, Mark Williams, Ewan Birney, Henning Hermjakob
, Lincoln Stein, Peter D'Eustachio
:
The Reactome pathway knowledgebase. Nucleic Acids Res. 42(Database-Issue): 472-477 (2014) - [j42]Todd W. Harris
, Joachim Baran, Tamberlyn Bieri, Abigail Cabunoc
, Juancarlos Chan, Wen J. Chen, Paul Davis, James Done, Christian A. Grove
, Kevin L. Howe
, Ranjana Kishore, Raymond Y. N. Lee, Yuling Li, Hans-Michael Müller, Cecilia Nakamura, Philip Ozersky, Michael Paulini, Daniela Raciti
, Gary Schindelman, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, J. D. Wong, Karen Yook, Tim Schedl, Jonathan Hodgkin, Matthew Berriman
, Paul J. Kersey
, John Spieth, Lincoln Stein, Paul W. Sternberg:
WormBase 2014: new views of curated biology. Nucleic Acids Res. 42(Database-Issue): 789-793 (2014) - [j41]Marcela K. Monaco, Joshua C. Stein
, Sushma Naithani
, Sharon Wei, Palitha Dharmawardhana, Sunita Kumari, Vindhya Amarasinghe, Ken Youens-Clark
, James Thomason, Justin Preece, Shiran Pasternak, Andrew Olson, Yinping Jiao, Zhenyuan Lu, Daniel M. Bolser
, Arnaud Kerhornou
, Daniel M. Staines
, Brandon Walts, Guanming Wu, Peter D'Eustachio
, Robin Haw, David Croft, Paul J. Kersey
, Lincoln Stein, Pankaj Jaiswal, Doreen Ware:
Gramene 2013: comparative plant genomics resources. Nucleic Acids Res. 42(Database-Issue): 1193-1199 (2014) - [i3]Amit G. Deshwar, Shankar Vembu, Christina K. Yung, Gun Ho Jang, Lincoln Stein, Quaid Morris:
Reconstructing subclonal composition and evolution from whole genome sequencing of tumors. CoRR abs/1406.7250 (2014) - [i2]Guanming Wu
, Eric T. Dawson
, Adrian Duong, Robin Haw
, Lincoln Stein:
ReactomeFIViz: the Reactome FI Cytoscape app for pathway and network-based data analysis. F1000Research 3: 146 (2014) - 2013
- [j40]Lincoln D. Stein:
Using GBrowse 2.0 to visualize and share next-generation sequence data. Briefings Bioinform. 14(2): 162-171 (2013) - 2012
- [j39]Karen Yook
, Todd W. Harris
, Tamberlyn Bieri, Abigail Cabunoc
, Juancarlos Chan, Wen J. Chen, Paul Davis
, Norie De La Cruz, Adrian Duong, Ruihua Fang, Uma Ganesan, Christian A. Grove
, Kevin L. Howe
, Snehalata Kadam, Ranjana Kishore, Raymond Y. N. Lee, Yuling Li, Hans-Michael Müller, Cecilia Nakamura, Bill Nash, Philip Ozersky, Michael Paulini
, Daniela Raciti
, Arun Rangarajan, Gary Schindelman, Xiaoqi Shi, Erich M. Schwarz
, Mary Ann Tuli
, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Jonathan Hodgkin, Matthew Berriman
, Richard Durbin
, Paul J. Kersey
, John Spieth, Lincoln Stein, Paul W. Sternberg
:
WormBase 2012: more genomes, more data, new website. Nucleic Acids Res. 40(Database-Issue): 735-741 (2012) - [j38]Sergio Contrino
, Richard N. Smith, Daniela Butano, Adrian Carr, Fengyuan Hu
, Rachel Lyne, Kim Rutherford
, Alex Kalderimis, Julie M. Sullivan
, Seth Carbon, Ellen T. Kephart, Paul Lloyd
, E. O. Stinson, Nicole L. Washington
, Marc D. Perry
, Peter Ruzanov, Zheng Zha, Suzanna E. Lewis
, Lincoln D. Stein, Gos Micklem
:
modMine: flexible access to modENCODE data. Nucleic Acids Res. 40(Database-Issue): 1082-1088 (2012) - [i1]Wei Jiao, Shankar Vembu, Amit G. Deshwar, Lincoln Stein, Quaid Morris:
Modeling the Clonal Evolution of Cancer from Next Generation Sequencing Data. CoRR abs/1210.3384 (2012) - 2011
- [j37]Robin Haw
, David Croft
, Christina K. Yung
, Nelson Ndegwa
, Peter D'Eustachio
, Henning Hermjakob
, Lincoln D. Stein:
The Reactome BioMart. Database J. Biol. Databases Curation 2011 (2011) - [j36]Nicole L. Washington
, E. O. Stinson, Marc D. Perry
, Peter Ruzanov, Sergio Contrino
, Richard N. Smith, Zheng Zha, Rachel Lyne, Adrian Carr, Paul Lloyd
, Ellen T. Kephart, Sheldon J. McKay
, Gos Micklem
, Lincoln D. Stein, Suzanna E. Lewis
:
The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details. Database J. Biol. Databases Curation 2011 (2011) - [j35]Xin Feng, Robert Grossman, Lincoln Stein:
PeakRanger: A cloud-enabled peak caller for ChIP-seq data. BMC Bioinform. 12: 139 (2011) - [j34]David Croft
, Gavin O'Kelly, Guanming Wu, Robin Haw
, Marc Gillespie
, Lisa Matthews
, Michael Caudy, Phani V. Garapati
, Gopal Gopinath, Bijay Jassal
, Steven Jupe
, Irina Kalatskaya
, Shahana Mahajan, Bruce May, Nelson Ndegwa
, Esther Schmidt, Veronica Shamovsky, Christina K. Yung
, Ewan Birney
, Henning Hermjakob
, Peter D'Eustachio
, Lincoln Stein:
Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res. 39(Database-Issue): 691-697 (2011) - 2010
- [j33]Bijay Jassal
, Steven Jupe
, Michael Caudy, Ewan Birney
, Lincoln Stein, Henning Hermjakob
, Peter D'Eustachio
:
The systematic annotation of the three main GPCR families in Reactome. Database J. Biol. Databases Curation 2010 (2010) - [j32]Liya Wang
, Lincoln D. Stein:
Localizing triplet periodicity in DNA and cDNA sequences. BMC Bioinform. 11: 550 (2010) - [j31]Todd W. Harris
, Igor Antoshechkin, Tamberlyn Bieri, Darin Blasiar, Juancarlos Chan, Wen J. Chen, Norie De La Cruz, Paul Davis
, Margaret J. Duesbury
, Ruihua Fang, Jolene Fernandes, Michael Han
, Ranjana Kishore, Raymond Y. N. Lee, Hans-Michael Müller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Arun Rangarajan, Anthony Rogers, Gary Schindelman, Erich M. Schwarz
, Mary Ann Tuli
, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Karen Yook
, Richard Durbin
, Lincoln D. Stein, John Spieth, Paul W. Sternberg
:
WormBase: a comprehensive resource for nematode research. Nucleic Acids Res. 38(Database-Issue): 463-467 (2010)
2000 – 2009
- 2009
- [j30]Junjian Ni, Anuradha Pujar, Ken Youens-Clark
, Immanuel Yap, Pankaj Jaiswal, Isaak Y. Tecle, Chih-Wei Tung
, Liya Ren, William Spooner, Xuehong Wei, Shuly Avraham, Doreen Ware, Lincoln Stein, Susan McCouch:
Gramene QTL database: development, content and applications. Database J. Biol. Databases Curation 2009 (2009) - [j29]Ken Youens-Clark
, Benjamin Faga, Immanuel Yap, Lincoln Stein, Doreen Ware:
CMap 1.01: a comparative mapping application for the Internet. Bioinform. 25(22): 3040-3042 (2009) - [j28]Lisa Matthews
, Gopal Gopinath, Marc Gillespie
, Michael Caudy, David Croft
, Bernard de Bono
, Phani V. Garapati
, Jill Hemish, Henning Hermjakob
, Bijay Jassal
, Alexander Kanapin
, Suzanna Lewis
, Shahana Mahajan, Bruce May, Esther Schmidt, Imre Vastrik
, Guanming Wu, Ewan Birney
, Lincoln Stein, Peter D'Eustachio
:
Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 37(Database-Issue): 619-622 (2009) - 2008
- [j27]Avril Coghlan
, Tristan J. Fiedler
, Sheldon J. McKay
, Paul Flicek
, Todd W. Harris
, Darin Blasiar, Lincoln D. Stein:
nGASP - the nematode genome annotation assessment project. BMC Bioinform. 9 (2008) - [j26]Shulamit Avraham, Chih-Wei Tung
, Katica Ilic, Pankaj Jaiswal, Elizabeth A. Kellogg
, Susan McCouch, Anuradha Pujar, Leonore Reiser
, Seung Yon Rhee, Martin M. Sachs, Mary L. Schaeffer, Lincoln Stein, Peter F. Stevens, Leszek Vincent, Felipe Zapata
, Doreen Ware:
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Res. 36(Database-Issue): 449-454 (2008) - [j25]Anthony Rogers, Igor Antoshechkin, Tamberlyn Bieri, Darin Blasiar, Carol Bastiani, Payan Canaran, Juancarlos Chan, Wen J. Chen, Paul Davis
, Jolene Fernandes, Tristan J. Fiedler
, Michael Han
, Todd W. Harris
, Ranjana Kishore, Raymond Y. N. Lee, Sheldon J. McKay
, Hans-Michael Müller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Gary Schindelman, Erich M. Schwarz
, William Spooner, Mary Ann Tuli
, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Karen Yook
, Richard Durbin
, Lincoln D. Stein, John Spieth, Paul W. Sternberg
:
WormBase 2007. Nucleic Acids Res. 36(Database-Issue): 612-617 (2008) - [j24]Carl J. Schmidt
, Michael Romanov
, Oliver Ryder, Vincent J. Magrini
, Matthew T. Hickenbotham, Jarret Glasscock, Sean McGrath
, Elaine R. Mardis, Lincoln D. Stein:
Gallus GBrowse: a unified genomic database for the chicken. Nucleic Acids Res. 36(Database-Issue): 719-723 (2008) - [j23]Chengzhi Liang, Pankaj Jaiswal, Claire Hebbard
, Shuly Avraham, Edward S. Buckler
, Terry M. Casstevens
, Bonnie L. Hurwitz, Susan McCouch, Junjian Ni, Anuradha Pujar, Dean Ravenscroft, Liya Ren, William Spooner, Isaak Y. Tecle, Jim Thomason, Chih-Wei Tung
, Xuehong Wei, Immanuel Yap, Ken Youens-Clark
, Doreen Ware, Lincoln Stein:
Gramene: a growing plant comparative genomics resource. Nucleic Acids Res. 36(Database-Issue): 947-953 (2008) - [j22]Payan Canaran, Edward S. Buckler
, Jeffrey Glaubitz, Lincoln Stein, Qi Sun, Wei Zhao, Doreen Ware:
Panzea: an update on new content and features. Nucleic Acids Res. 36(Database-Issue): 1041-1043 (2008) - 2007
- [j21]Bernard de Bono, Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Gopal Gopinath, David Croft, Marc Gillespie, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Guanming Wu, Ewan Birney, Lincoln Stein:
Reactome: An integrated expert model of human molecular processes and access toolkit. J. Integr. Bioinform. 4(3) (2007) - [j20]Lisa R. Girard, Tristan J. Fiedler, Todd W. Harris
, Felicia Carvalho, Igor Antoshechkin, Michael Han
, Paul W. Sternberg, Lincoln D. Stein, Martin Chalfie:
WormBook: the online review of Caenorhabditis elegans biology. Nucleic Acids Res. 35(Database-Issue): 472-475 (2007) - [j19]Tamberlyn Bieri, Darin Blasiar, Philip Ozersky, Igor Antoshechkin, Carol Bastiani, Payan Canaran, Juancarlos Chan, Nansheng Chen, Wen J. Chen, Paul Davis
, Tristan J. Fiedler
, Lisa R. Girard, Michael Han
, Todd W. Harris
, Ranjana Kishore, Raymond Y. N. Lee, Sheldon J. McKay
, Hans-Michael Müller, Cecilia Nakamura, Andrei Petcherski, Arun Rangarajan, Anthony Rogers, Gary Schindelman, Erich M. Schwarz
, William Spooner, Mary Ann Tuli
, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Richard Durbin
, Lincoln D. Stein, Paul W. Sternberg, John Spieth:
WormBase: new content and better access. Nucleic Acids Res. 35(Database-Issue): 506-510 (2007) - 2006
- [j18]Payan Canaran, Lincoln Stein, Doreen Ware:
Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support. Bioinform. 22(7): 885-886 (2006) - [j17]Erich M. Schwarz
, Igor Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin Blasiar, Payan Canaran, Juancarlos Chan, Nansheng Chen, Wen J. Chen, Paul Davis
, Tristan J. Fiedler, Lisa R. Girard, Todd W. Harris, Eimear Kenny, Ranjana Kishore, Daniel Lawson
, Raymond Y. N. Lee, Hans-Michael Müller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Anthony Rogers, William Spooner, Mary Ann Tuli
, Kimberly Van Auken, Daniel Wang, Richard Durbin
, John Spieth, Lincoln D. Stein, Paul W. Sternberg:
WormBase: better software, richer content. Nucleic Acids Res. 34(Database-Issue): 475-478 (2006) - [j16]Pankaj Jaiswal, Junjian Ni, Immanuel Yap, Doreen Ware, William Spooner, Ken Youens-Clark, Liya Ren, Chengzhi Liang, Wei Zhao, Kiran Ratnapu, Benjamin Faga, Payan Canaran, Molly Fogleman, Claire Hebbard
, Shuly Avraham, Steven Schmidt, Terry M. Casstevens, Edward S. Buckler
, Lincoln Stein, Susan McCouch:
Gramene: a bird's eye view of cereal genomes. Nucleic Acids Res. 34(Database-Issue): 717-723 (2006) - [j15]Wei Zhao, Payan Canaran, Rebecca Jurkuta, Theresa Fulton, Jeffrey Glaubitz, Edward S. Buckler
, John Doebley, Brandon S. Gaut, Major Goodman, Jim Holland, Stephen Kresovich, Michael D. McMullen, Lincoln Stein, Doreen Ware:
Panzea: a database and resource for molecular and functional diversity in the maize genome. Nucleic Acids Res. 34(Database-Issue): 752-757 (2006) - [c11]Esther Schmidt, Ewan Birney, David Croft, Bernard de Bono, Peter D'Eustachio, Marc Gillespie
, Gopal Gopinath, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Lincoln Stein, Imre Vastrik, Guanming Wu:
Reactome - A Knowledgebase of Biological Pathways. OTM Workshops (1) 2006: 710-719 - 2005
- [j14]Xiaokang Pan, Lincoln Stein, Volker Brendel:
SynBrowse: a synteny browser for comparative sequence analysis. Bioinform. 21(17): 3461-3468 (2005) - [j13]Nansheng Chen, Todd W. Harris
, Igor Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin Blasiar, Keith Bradnam
, Payan Canaran, Juancarlos Chan, Chao-Kung Chen, Wen J. Chen, Fiona Cunningham
, Paul Davis
, Eimear Kenny, Ranjana Kishore, Daniel Lawson
, Raymond Y. N. Lee, Hans-Michael Müller, Cecilia Nakamura, Shraddha Pai, Philip Ozersky, Andrei Petcherski, Anthony Rogers, Aniko Sabo, Erich M. Schwarz
, Kimberly Van Auken, Qinghua Wang, Richard Durbin
, John Spieth, Paul W. Sternberg, Lincoln D. Stein:
WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucleic Acids Res. 33(Database-Issue): 383-389 (2005) - [j12]G. Joshi-Tope, Marc Gillespie, Imre Vastrik
, Peter D'Eustachio
, Esther Schmidt, Bernard de Bono
, Bijay Jassal
, Gopal R. Gopinath, G. R. Wu, Lisa Matthews
, Suzanna Lewis
, Ewan Birney
, Lincoln Stein:
Reactome: a knowledgebase of biological pathways. Nucleic Acids Res. 33(Database-Issue): 428-432 (2005) - 2004
- [j11]Todd W. Harris, Nansheng Chen, Fiona Cunningham
, Marcela K. Tello-Ruiz, Igor Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin Blasiar, Keith Bradnam
, Juancarlos Chan, Chao-Kung Chen, Wen J. Chen, Paul Davis
, Eimear Kenny, Ranjana Kishore, Daniel Lawson
, Raymond Y. N. Lee, Hans-Michael Müller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Anthony Rogers, Aniko Sabo, Erich M. Schwarz
, Kimberly Van Auken, Qinghua Wang, Richard Durbin
, John Spieth, Paul W. Sternberg, Lincoln D. Stein:
WormBase: a multi-species resource for nematode biology and genomics. Nucleic Acids Res. 32(Database-Issue): 411-417 (2004) - [c10]Christopher Maher, Marja Timmermans, Lincoln Stein, Doreen Ware:
Identifying MicroRNAs in Plant Genomes. CSB 2004: 718-723 - [c9]Phillip W. Lord, Sean Bechhofer
, Mark D. Wilkinson
, Gary S. Schiltz, Damian Gessler, Duncan Hull, Carole A. Goble, Lincoln Stein:
Applying Semantic Web Services to Bioinformatics: Experiences Gained, Lessons Learnt. ISWC 2004: 350-364 - 2003
- [j10]Gudmundur A. Thorisson
, Lincoln Stein:
The SNP Consortium website: past, present and future. Nucleic Acids Res. 31(1): 124-127 (2003) - [j9]Todd W. Harris
, Raymond Y. N. Lee, Erich M. Schwarz, Keith Bradnam
, Daniel Lawson
, Wen J. Chen, Darin Blasiar, Eimear Kenny, Fiona Cunningham
, Ranjana Kishore, Juancarlos Chan, Hans-Michael Müller, Andrei Petcherski, Gudmundur A. Thorisson
, Allen Day, Tamberlyn Bieri, Anthony Rogers, Chao-Kung Chen, John Spieth, Paul W. Sternberg, Richard Durbin
, Lincoln D. Stein:
WormBase: a cross-species database for comparative genomics. Nucleic Acids Res. 31(1): 133-137 (2003) - 2002
- [j8]