Requirements for a Deductive Query Language in a Genome-Mapping Database. - Nathan Goodman; Steve Rozen; Lincoln Stein (Workshop on Programming with Logic Databases (Book), ILPS, 1993)

Requirements for a Deductive Query Language in the MapBase Genome-Mapping Database. - Nathan Goodman; Steve Rozen; Lincoln Stein (Workshop on Programming with Logic Databases (Informal Proceedings), ILPS, 1993)

Constructing a Domain-Specific DBMS using a Persistent Object System. - Steve Rozen; Lincoln Stein; Nathan Goodman (POS, 1994)

Splicing UNIX into a Genome Mapping Laboratory. - Lincoln Stein; Andre Marquis; Robert Dredge; Mary Pat Reeve; Mark Daly; Steve Rozen; Nathan Goodman (USENIX Summer, 1994)

Building a Laboratory Information System Around a C++-Based Object-Oriented DBMS. - Nathan Goodman; Steve Rozen; Lincoln Stein (VLDB, 1994)

How to Set Up and Maintain a World Wide Web Site: The Guide for Information Providers. - Lincoln Stein (Addison-Wesley, 1995)

Building Human Genome Maps with Radiation Hybrids. - Donna K. Slonim; Leonid Kruglyak; Lincoln Stein; Eric S. Lander (J. Comput. Biol., 1997)

Exploring CGI with Perl. - Lincoln Stein (World Wide Web J., 1997)

The electronic medical record: promises and threats. - Lincoln D. Stein (World Wide Web J., 1997)

The LabFlow System for Workflow Management in Large Scale Biology Research Laboratories. - Nathan Goodman; Steve Rozen; Lincoln Stein (ISMB, 1998)

The LabBase system for data management in large scale biology research laboratories. - Nathan Goodman; Steve Rozen; Lincoln Stein; A. G. Smith (Bioinform., 1998)

Writing Apache modules with Perl and C - the Apache API and mod Perl. - Lincoln Stein; Doug MacEachern (O'Reilly, 1999)

SBOX: Put CGI Scripts in a Box. - Lincoln Stein (USENIX ATC, General Track, 1999)

AceDB: a genome database management system. - Lincoln D. Stein; Jean Thierry-Mieg (Comput. Sci. Eng., 1999)

The Distributed Annotation System. - Robin D. Dowell; Rodney M. Jokerst; Allen Day; Sean R. Eddy; Lincoln Stein (BMC Bioinform., 2001)

WormBase: network access to the genome and biology of Caenorhabditis elegans. - Lincoln Stein; Paul W. Sternberg; Richard Durbin; Jean Thierry-Mieg; John Spieth (Nucleic Acids Res., 2001)

Gramene: a resource for comparative grass genomics. - Doreen Ware; Pankaj Jaiswal; Junjian Ni; Xiaokang Pan; Kuan Y. Chang; Kenneth Clark; Leonid Teytelman; Steven Schmidt; Wei Zhao 005; Samuel Cartinhour; Susan McCouch; Lincoln Stein (Nucleic Acids Res., 2002)

WormBase: a cross-species database for comparative genomics. - 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; et al. (Nucleic Acids Res., 2003)

The SNP Consortium website: past, present and future. - Gudmundur A. Thorisson; Lincoln Stein (Nucleic Acids Res., 2003)

Identifying MicroRNAs in Plant Genomes. - Christopher Maher; Marja Timmermans; Lincoln Stein; Doreen Ware (CSB, 2004)

Applying Semantic Web Services to Bioinformatics: Experiences Gained, Lessons Learnt. - Phillip W. Lord; Sean Bechhofer; Mark D. Wilkinson; Gary S. Schiltz; Damian Gessler; Duncan Hull; Carole A. Goble; Lincoln Stein (ISWC, 2004)

WormBase: a multi-species resource for nematode biology and genomics. - 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; et al. (Nucleic Acids Res., 2004)

SynBrowse: a synteny browser for comparative sequence analysis. - Xiaokang Pan; Lincoln Stein; Volker Brendel (Bioinform., 2005)

WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. - 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; et al. (Nucleic Acids Res., 2005)

Reactome: a knowledgebase of biological pathways. - 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; et al. (Nucleic Acids Res., 2005)

Reactome - A Knowledgebase of Biological Pathways. - Esther Schmidt; Ewan Birney; David Croft 001; Bernard de Bono; Peter D'Eustachio; Marc Gillespie; Gopal Gopinath; Bijay Jassal; Suzanna Lewis; Lisa Matthews; Lincoln Stein; Imre Vastrik; et al. (OTM Workshops (1), 2006)

Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support. - Payan Canaran; Lincoln Stein; Doreen Ware (Bioinform., 2006)

Gramene: a bird's eye view of cereal genomes. - Pankaj Jaiswal; Junjian Ni; Immanuel Yap; Doreen Ware; William Spooner; Ken Youens-Clark; Liya Ren; Chengzhi Liang; Wei Zhao 005; Kiran Ratnapu; Benjamin Faga; Payan Canaran; et al. (Nucleic Acids Res., 2006)

WormBase: better software, richer content. - Erich M. Schwarz; Igor Antoshechkin; Carol Bastiani; Tamberlyn Bieri; Darin Blasiar; Payan Canaran; Juancarlos Chan; Nansheng Chen; Wen J. Chen; Paul Davis 001; Tristan J. Fiedler; Lisa R. Girard; et al. (Nucleic Acids Res., 2006)

Panzea: a database and resource for molecular and functional diversity in the maize genome. - Wei Zhao 005; 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; et al. (Nucleic Acids Res., 2006)

Reactome: An integrated expert model of human molecular processes and access toolkit. - Bernard de Bono; Imre Vastrik; Peter D'Eustachio; Esther Schmidt; Gopal Gopinath; David Croft 001; Marc Gillespie; Bijay Jassal; Suzanna Lewis; Lisa Matthews; Guanming Wu; Ewan Birney; et al. (J. Integr. Bioinform., 2007)

WormBase: new content and better access. - Tamberlyn Bieri; Darin Blasiar; Philip Ozersky; Igor Antoshechkin; Carol Bastiani; Payan Canaran; Juancarlos Chan; Nansheng Chen; Wen J. Chen; Paul Davis 001; Tristan J. Fiedler; Lisa R. Girard; et al. (Nucleic Acids Res., 2007)

WormBook: the online review of Caenorhabditis elegans biology. - Lisa R. Girard; Tristan J. Fiedler; Todd W. Harris; Felicia Carvalho; Igor Antoshechkin; Michael Han 001; Paul W. Sternberg; Lincoln D. Stein; Martin Chalfie (Nucleic Acids Res., 2007)

nGASP - the nematode genome annotation assessment project. - Avril Coghlan; Tristan J. Fiedler; Sheldon J. McKay; Paul Flicek; Todd W. Harris; Darin Blasiar; Lincoln D. Stein (BMC Bioinform., 2008)

The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. - 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; et al. (Nucleic Acids Res., 2008)

Panzea: an update on new content and features. - Payan Canaran; Edward S. Buckler; Jeffrey Glaubitz; Lincoln Stein; Qi Sun; Wei Zhao 005; Doreen Ware (Nucleic Acids Res., 2008)

Gramene: a growing plant comparative genomics resource. - 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; et al. (Nucleic Acids Res., 2008)

WormBase 2007. - Anthony Rogers; Igor Antoshechkin; Tamberlyn Bieri; Darin Blasiar; Carol Bastiani; Payan Canaran; Juancarlos Chan; Wen J. Chen; Paul Davis 001; Jolene Fernandes; Tristan J. Fiedler; Michael Han 001; et al. (Nucleic Acids Res., 2008)

Gallus GBrowse: a unified genomic database for the chicken. - Carl J. Schmidt; Michael Romanov; Oliver Ryder; Vincent J. Magrini; Matthew T. Hickenbotham; Jarret Glasscock; Sean McGrath 003; Elaine R. Mardis; Lincoln D. Stein (Nucleic Acids Res., 2008)

Gramene QTL database: development, content and applications. - 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; et al. (Database J. Biol. Databases Curation, 2009)

CMap 1.01: a comparative mapping application for the Internet. - Ken Youens-Clark; Benjamin Faga; Immanuel Yap; Lincoln Stein; Doreen Ware (Bioinform., 2009)

Reactome knowledgebase of human biological pathways and processes. - Lisa Matthews; Gopal Gopinath; Marc Gillespie; Michael Caudy; David Croft 001; Bernard de Bono; Phani V. Garapati; Jill Hemish; Henning Hermjakob; Bijay Jassal; Alexander Kanapin; Suzanna Lewis; et al. (Nucleic Acids Res., 2009)

The systematic annotation of the three main GPCR families in Reactome. - Bijay Jassal; Steven Jupe; Michael Caudy; Ewan Birney; Lincoln Stein; Henning Hermjakob; Peter D'Eustachio (Database J. Biol. Databases Curation, 2010)

Localizing triplet periodicity in DNA and cDNA sequences. - Liya Wang; Lincoln D. Stein (BMC Bioinform., 2010)

WormBase: a comprehensive resource for nematode research. - Todd W. Harris; Igor Antoshechkin; Tamberlyn Bieri; Darin Blasiar; Juancarlos Chan; Wen J. Chen; Norie De La Cruz; Paul Davis 001; Margaret J. Duesbury; Ruihua Fang; Jolene Fernandes; Michael Han 001; et al. (Nucleic Acids Res., 2010)

The Reactome BioMart. - Robin Haw; David Croft 001; Christina K. Yung; Nelson Ndegwa; Peter D'Eustachio; Henning Hermjakob; Lincoln D. Stein (Database J. Biol. Databases Curation, 2011)

The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details. - 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; et al. (Database J. Biol. Databases Curation, 2011)

PeakRanger: A cloud-enabled peak caller for ChIP-seq data. - Xin Feng; Robert Grossman; Lincoln Stein (BMC Bioinform., 2011)

Reactome: a database of reactions, pathways and biological processes. - David Croft 001; Gavin O'Kelly; Guanming Wu; Robin Haw; Marc Gillespie; Lisa Matthews; Michael Caudy; Phani V. Garapati; Gopal Gopinath; Bijay Jassal; Steven Jupe; Irina Kalatskaya; et al. (Nucleic Acids Res., 2011)

Modeling the Clonal Evolution of Cancer from Next Generation Sequencing Data - Wei Jiao; Shankar Vembu; Amit G. Deshwar; Lincoln Stein; Quaid Morris (CoRR, 2012)

modMine: flexible access to modENCODE data. - 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; et al. (Nucleic Acids Res., 2012)

WormBase 2012: more genomes, more data, new website. - Karen Yook; Todd W. Harris; Tamberlyn Bieri; Abigail Cabunoc; Juancarlos Chan; Wen J. Chen; Paul Davis 001; Norie De La Cruz; Adrian Duong; Ruihua Fang; Uma Ganesan; Christian A. Grove; et al. (Nucleic Acids Res., 2012)

Using GBrowse 2.0 to visualize and share next-generation sequence data. - Lincoln D. Stein (Briefings Bioinform., 2013)

Inferring clonal evolution of tumors from single nucleotide somatic mutations. - Wei Jiao; Shankar Vembu; Amit G. Deshwar; Lincoln Stein; Quaid Morris (BMC Bioinform., 2014)

Reconstructing subclonal composition and evolution from whole genome sequencing of tumors. - Amit G. Deshwar; Shankar Vembu; Christina K. Yung; Gun Ho Jang; Lincoln Stein; Quaid Morris (CoRR, 2014)

ReactomeFIViz: the Reactome FI Cytoscape app for pathway and network-based data analysis. - Guanming Wu; Eric T. Dawson; Adrian Duong; Robin Haw; Lincoln Stein (F1000Research, 2014)

The Reactome pathway knowledgebase. - David Croft 001; 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; et al. (Nucleic Acids Res., 2014)

WormBase 2014: new views of curated biology. - Todd W. Harris; Joachim Baran; Tamberlyn Bieri; Abigail Cabunoc; Juancarlos Chan; Wen J. Chen; Paul Davis 001; James Done; Christian A. Grove; Kevin L. Howe; Ranjana Kishore; Raymond Y. N. Lee; et al. (Nucleic Acids Res., 2014)

Gramene 2013: comparative plant genomics resources. - 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; et al. (Nucleic Acids Res., 2014)

A genome-wide association study platform built on iPlant cyber-infrastructure. - Liya Wang; Doreen Ware; Carol Lushbough; Nirav C. Merchant; Lincoln Stein (Concurr. Comput. Pract. Exp., 2015)

Data analysis: Create a cloud commons. - Lincoln D. Stein; Bartha M. Knoppers; Peter Campbell; Gad Getz; Jan O. Korbel (Nat., 2015)

The Reactome pathway Knowledgebase. - 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; et al. (Nucleic Acids Res., 2016)

WormBase 2016: expanding to enable helminth genomic research. - Kevin L. Howe; Bruce J. Bolt; Scott Cain; Juancarlos Chan; Wen J. Chen; Paul Davis 001; James Done; Thomas A. Down; Sibyl Gao; Christian A. Grove; Todd W. Harris; Ranjana Kishore; et al. (Nucleic Acids Res., 2016)

Gramene 2016: comparative plant genomics and pathway resources. - 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; et al. (Nucleic Acids Res., 2016)

Reactome enhanced pathway visualization. - 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; et al. (Bioinform., 2017)

Reactome pathway analysis: a high-performance in-memory approach. - Antonio Fabregat; Konstantinos Sidiropoulos; Guilherme Viteri; Oscar Forner-Martinez; Pablo Marín-García; Vicente Arnau; Peter D'Eustachio; Lincoln Stein; Henning Hermjakob (BMC Bioinform., 2017)

The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows. - Brian D. O'Connor; Denis Yuen; Vincent Chung; Andrew G. Duncan; Xiangkun Liu; Janice Patricia; Benedict Paten; Lincoln Stein; Vincent Ferretti (F1000Research, 2017)

Plant Reactome: a resource for plant pathways and comparative analysis. - 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; et al. (Nucleic Acids Res., 2017)

Reactome diagram viewer: data structures and strategies to boost performance. - Antonio Fabregat; Konstantinos Sidiropoulos; Guilherme Viteri; Pablo Marín-García; Peipei Ping; Lincoln Stein; Peter D'Eustachio; Henning Hermjakob (Bioinform., 2018)

The Reactome Pathway Knowledgebase. - 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; et al. (Nucleic Acids Res., 2018)

WormBase 2017: molting into a new stage. - Raymond Y. N. Lee; Kevin L. Howe; Todd W. Harris; Valerio Arnaboldi; Scott Cain; Juancarlos Chan; Wen J. Chen; Paul Davis 001; Sibyl Gao; Christian A. Grove; Ranjana Kishore; Hans-Michael Müller; et al. (Nucleic Acids Res., 2018)

Gramene 2018: unifying comparative genomics and pathway resources for plant research. - 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 117; et al. (Nucleic Acids Res., 2018)

Reactome graph database: Efficient access to complex pathway data. - Antonio Fabregat; Florian Korninger; Guilherme Viteri; Konstantinos Sidiropoulos; Pablo Marín-García; Peipei Ping; Guanming Wu; Lincoln Stein; Peter D'Eustachio; Henning Hermjakob (PLoS Comput. Biol., 2018)

Reactome and ORCID - fine-grained credit attribution for community curation. - 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; et al. (Database J. Biol. Databases Curation, 2019)

Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer. - 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; et al. (PLoS Comput. Biol., 2019)

WormBase: a modern Model Organism Information Resource. - Todd W. Harris; Valerio Arnaboldi; Scott Cain; Juancarlos Chan; Wen J. Chen; Jae-Hyoung Cho; Paul Davis 001; Sibyl Gao; Christian A. Grove; Ranjana Kishore; Raymond Y. N. Lee; Hans-Michael Müller; et al. (Nucleic Acids Res., 2020)

The reactome pathway knowledgebase. - Bijay Jassal; Lisa Matthews; Guilherme Viteri; Chuqiao Gong; Pascual Lorente; Antonio Fabregat; Konstantinos Sidiropoulos; Justin Cook; Marc Gillespie; Robin Haw; Fred Loney 001; Bruce May; et al. (Nucleic Acids Res., 2020)

Plant Reactome: a knowledgebase and resource for comparative pathway analysis. - 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; et al. (Nucleic Acids Res., 2020)

The evolutionary history of 2,658 cancers. - 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; et al. (Nat., 2020)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - 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; et al. (Nat., 2020)

JBrowse Connect: A server API to connect JBrowse instances and users. - Eric Yao; Robert M. Buels; Lincoln Stein; Taner Z. Sen; Ian H. Holmes (PLoS Comput. Biol., 2020)

JBrowseR: an R interface to the JBrowse 2 genome browser. - Elliot A. Hershberg; Garrett Stevens; Colin M. Diesh; Peter Xie; Teresa De Jesus Martinez; Robert M. Buels; Lincoln Stein; Ian H. Holmes (Bioinform., 2021)

The Gene Ontology resource: enriching a GOld mine. - 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; et al. (Nucleic Acids Res., 2021)

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. - Marcela K. Tello-Ruiz; Sushma Naithani; Parul Gupta; Andrew Olson; Sharon Wei; Justin Preece; Yinping Jiao; Bo Wang 117; Kapeel Chougule; Priyanka Garg; Justin Elser; Sunita Kumari; et al. (Nucleic Acids Res., 2021)

The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols. - 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; et al. (Nucleic Acids Res., 2021)

Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase. - Adam J. Wright; Marija Orlic-Milacic; Karen Rothfels; Joel Weiser; Quang M. Trinh; Bijay Jassal; Robin Haw; Lincoln D. Stein (Database J. Biol. Databases Curation, 2022)

The reactome pathway knowledgebase 2022. - 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; et al. (Nucleic Acids Res., 2022)

Fourteen quick tips for crowdsourcing geographically linked data for public health advocacy. - Joshua Atienza; Anjalee Benedict; Lincoln D. Stein; Kashif Pirzada; Cheryl White; Shraddha Pai (PLoS Comput. Biol., 2023)

JBrowse Jupyter: a Python interface to JBrowse 2. - 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 (Bioinform., 2023)

FAIR Header Reference genome: a TRUSTworthy standard. - 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; et al. (Briefings Bioinform., 2024)

Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes. - 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; et al. (Database J. Biol. Databases Curation, 2024)

Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes. - 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; et al. (Zenodo, 2024)