Literature DB >> 21587248

Social engineering for virtual 'big science' in systems biology.

Hiroaki Kitano1, Samik Ghosh, Yukiko Matsuoka.   

Abstract

Mesh:

Year:  2011        PMID: 21587248     DOI: 10.1038/nchembio.574

Source DB:  PubMed          Journal:  Nat Chem Biol        ISSN: 1552-4450            Impact factor:   15.040


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  13 in total

1.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Authors:  M Hucka; A Finney; H M Sauro; H Bolouri; J C Doyle; H Kitano; A P Arkin; B J Bornstein; D Bray; A Cornish-Bowden; A A Cuellar; S Dronov; E D Gilles; M Ginkel; V Gor; I I Goryanin; W J Hedley; T C Hodgman; J-H Hofmeyr; P J Hunter; N S Juty; J L Kasberger; A Kremling; U Kummer; N Le Novère; L M Loew; D Lucio; P Mendes; E Minch; E D Mjolsness; Y Nakayama; M R Nelson; P F Nielsen; T Sakurada; J C Schaff; B E Shapiro; T S Shimizu; H D Spence; J Stelling; K Takahashi; M Tomita; J Wagner; J Wang
Journal:  Bioinformatics       Date:  2003-03-01       Impact factor: 6.937

Review 2.  Virtual drug discovery and development for neglected diseases through public-private partnerships.

Authors:  Solomon Nwaka; Robert G Ridley
Journal:  Nat Rev Drug Discov       Date:  2003-11       Impact factor: 84.694

3.  No rest for the bio-wikis.

Authors:  Ewen Callaway
Journal:  Nature       Date:  2010-11-18       Impact factor: 49.962

4.  Opening up to precompetitive collaboration.

Authors:  Jill S Altshuler; Erin Balogh; Anna D Barker; Stephen L Eck; Stephen H Friend; Geoffrey S Ginsburg; Roy S Herbst; Sharyl J Nass; Christopher M Streeter; John A Wagner
Journal:  Sci Transl Med       Date:  2010-10-06       Impact factor: 17.956

5.  The global burden of tuberculosis--combating drug resistance in difficult times.

Authors:  Peter R Donald; Paul D van Helden
Journal:  N Engl J Med       Date:  2009-06-04       Impact factor: 91.245

6.  India takes an open source approach to drug discovery.

Authors:  Seema Singh
Journal:  Cell       Date:  2008-04-18       Impact factor: 41.582

7.  Payao: a community platform for SBML pathway model curation.

Authors:  Yukiko Matsuoka; Samik Ghosh; Norihiro Kikuchi; Hiroaki Kitano
Journal:  Bioinformatics       Date:  2010-04-05       Impact factor: 6.937

8.  The BioPAX community standard for pathway data sharing.

Authors:  Emek Demir; Michael P Cary; Suzanne Paley; Ken Fukuda; Christian Lemer; Imre Vastrik; Guanming Wu; Peter D'Eustachio; Carl Schaefer; Joanne Luciano; Frank Schacherer; Irma Martinez-Flores; Zhenjun Hu; Veronica Jimenez-Jacinto; Geeta Joshi-Tope; Kumaran Kandasamy; Alejandra C Lopez-Fuentes; Huaiyu Mi; Elgar Pichler; Igor Rodchenkov; Andrea Splendiani; Sasha Tkachev; Jeremy Zucker; Gopal Gopinath; Harsha Rajasimha; Ranjani Ramakrishnan; Imran Shah; Mustafa Syed; Nadia Anwar; Ozgün Babur; Michael Blinov; Erik Brauner; Dan Corwin; Sylva Donaldson; Frank Gibbons; Robert Goldberg; Peter Hornbeck; Augustin Luna; Peter Murray-Rust; Eric Neumann; Oliver Ruebenacker; Oliver Reubenacker; Matthias Samwald; Martijn van Iersel; Sarala Wimalaratne; Keith Allen; Burk Braun; Michelle Whirl-Carrillo; Kei-Hoi Cheung; Kam Dahlquist; Andrew Finney; Marc Gillespie; Elizabeth Glass; Li Gong; Robin Haw; Michael Honig; Olivier Hubaut; David Kane; Shiva Krupa; Martina Kutmon; Julie Leonard; Debbie Marks; David Merberg; Victoria Petri; Alex Pico; Dean Ravenscroft; Liya Ren; Nigam Shah; Margot Sunshine; Rebecca Tang; Ryan Whaley; Stan Letovksy; Kenneth H Buetow; Andrey Rzhetsky; Vincent Schachter; Bruno S Sobral; Ugur Dogrusoz; Shannon McWeeney; Mirit Aladjem; Ewan Birney; Julio Collado-Vides; Susumu Goto; Michael Hucka; Nicolas Le Novère; Natalia Maltsev; Akhilesh Pandey; Paul Thomas; Edgar Wingender; Peter D Karp; Chris Sander; Gary D Bader
Journal:  Nat Biotechnol       Date:  2010-09-09       Impact factor: 54.908

Review 9.  A comprehensive map of the mTOR signaling network.

Authors:  Etienne Caron; Samik Ghosh; Yukiko Matsuoka; Dariel Ashton-Beaucage; Marc Therrien; Sébastien Lemieux; Claude Perreault; Philippe P Roux; Hiroaki Kitano
Journal:  Mol Syst Biol       Date:  2010-12-21       Impact factor: 11.429

10.  A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.

Authors:  Markus J Herrgård; Neil Swainston; Paul Dobson; Warwick B Dunn; K Yalçin Arga; Mikko Arvas; Nils Blüthgen; Simon Borger; Roeland Costenoble; Matthias Heinemann; Michael Hucka; Nicolas Le Novère; Peter Li; Wolfram Liebermeister; Monica L Mo; Ana Paula Oliveira; Dina Petranovic; Stephen Pettifer; Evangelos Simeonidis; Kieran Smallbone; Irena Spasić; Dieter Weichart; Roger Brent; David S Broomhead; Hans V Westerhoff; Betül Kirdar; Merja Penttilä; Edda Klipp; Bernhard Ø Palsson; Uwe Sauer; Stephen G Oliver; Pedro Mendes; Jens Nielsen; Douglas B Kell
Journal:  Nat Biotechnol       Date:  2008-10       Impact factor: 54.908

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  14 in total

Review 1.  Software for systems biology: from tools to integrated platforms.

Authors:  Samik Ghosh; Yukiko Matsuoka; Yoshiyuki Asai; Kun-Yi Hsin; Hiroaki Kitano
Journal:  Nat Rev Genet       Date:  2011-11-03       Impact factor: 53.242

2.  Integrative knowledge management to enhance pharmaceutical R&D.

Authors:  Maria Marti-Solano; Ewan Birney; Antoine Bril; Oscar Della Pasqua; Hiroaki Kitano; Barend Mons; Ioannis Xenarios; Ferran Sanz
Journal:  Nat Rev Drug Discov       Date:  2014-04       Impact factor: 84.694

3.  Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.

Authors:  Laurent Heirendt; Sylvain Arreckx; Thomas Pfau; Sebastián N Mendoza; Anne Richelle; Almut Heinken; Hulda S Haraldsdóttir; Jacek Wachowiak; Sarah M Keating; Vanja Vlasov; Stefania Magnusdóttir; Chiam Yu Ng; German Preciat; Alise Žagare; Siu H J Chan; Maike K Aurich; Catherine M Clancy; Jennifer Modamio; John T Sauls; Alberto Noronha; Aarash Bordbar; Benjamin Cousins; Diana C El Assal; Luis V Valcarcel; Iñigo Apaolaza; Susan Ghaderi; Masoud Ahookhosh; Marouen Ben Guebila; Andrejs Kostromins; Nicolas Sompairac; Hoai M Le; Ding Ma; Yuekai Sun; Lin Wang; James T Yurkovich; Miguel A P Oliveira; Phan T Vuong; Lemmer P El Assal; Inna Kuperstein; Andrei Zinovyev; H Scott Hinton; William A Bryant; Francisco J Aragón Artacho; Francisco J Planes; Egils Stalidzans; Alejandro Maass; Santosh Vempala; Michael Hucka; Michael A Saunders; Costas D Maranas; Nathan E Lewis; Thomas Sauter; Bernhard Ø Palsson; Ines Thiele; Ronan M T Fleming
Journal:  Nat Protoc       Date:  2019-03       Impact factor: 13.491

4.  Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network.

Authors:  Benjamin D Heavner; Kieran Smallbone; Brandon Barker; Pedro Mendes; Larry P Walker
Journal:  BMC Syst Biol       Date:  2012-06-04

5.  Feedback-based, system-level properties of vertebrate-microbial interactions.

Authors:  Ariel L Rivas; Mark D Jankowski; Renata Piccinini; Gabriel Leitner; Daniel Schwarz; Kevin L Anderson; Jeanne M Fair; Almira L Hoogesteijn; Wilfried Wolter; Marcelo Chaffer; Shlomo Blum; Tom Were; Stephen N Konah; Prakash Kempaiah; John M Ong'echa; Ulrike S Diesterbeck; Rachel Pilla; Claus-Peter Czerny; James B Hittner; James M Hyman; Douglas J Perkins
Journal:  PLoS One       Date:  2013-02-20       Impact factor: 3.240

6.  Crowd sourcing a new paradigm for interactome driven drug target identification in Mycobacterium tuberculosis.

Authors:  Rohit Vashisht; Anupam Kumar Mondal; Akanksha Jain; Anup Shah; Priti Vishnoi; Priyanka Priyadarshini; Kausik Bhattacharyya; Harsha Rohira; Ashwini G Bhat; Anurag Passi; Keya Mukherjee; Kumari Sonal Choudhary; Vikas Kumar; Anshula Arora; Prabhakaran Munusamy; Ahalyaa Subramanian; Aparna Venkatachalam; S Gayathri; Sweety Raj; Vijaya Chitra; Kaveri Verma; Salman Zaheer; J Balaganesh; Malarvizhi Gurusamy; Mohammed Razeeth; Ilamathi Raja; Madhumohan Thandapani; Vishal Mevada; Raviraj Soni; Shruti Rana; Girish Muthagadhalli Ramanna; Swetha Raghavan; Sunil N Subramanya; Trupti Kholia; Rajesh Patel; Varsha Bhavnani; Lakavath Chiranjeevi; Soumi Sengupta; Pankaj Kumar Singh; Naresh Atray; Swati Gandhi; Tiruvayipati Suma Avasthi; Shefin Nisthar; Meenakshi Anurag; Pratibha Sharma; Yasha Hasija; Debasis Dash; Arun Sharma; Vinod Scaria; Zakir Thomas; Nagasuma Chandra; Samir K Brahmachari; Anshu Bhardwaj
Journal:  PLoS One       Date:  2012-07-11       Impact factor: 3.240

7.  Systems toxicology: from basic research to risk assessment.

Authors:  Shana J Sturla; Alan R Boobis; Rex E FitzGerald; Julia Hoeng; Robert J Kavlock; Kristin Schirmer; Maurice Whelan; Martin F Wilks; Manuel C Peitsch
Journal:  Chem Res Toxicol       Date:  2014-01-21       Impact factor: 3.739

Review 8.  Integrating pathways of Parkinson's disease in a molecular interaction map.

Authors:  Kazuhiro A Fujita; Marek Ostaszewski; Yukiko Matsuoka; Samik Ghosh; Enrico Glaab; Christophe Trefois; Isaac Crespo; Thanneer M Perumal; Wiktor Jurkowski; Paul M A Antony; Nico Diederich; Manuel Buttini; Akihiko Kodama; Venkata P Satagopam; Serge Eifes; Antonio Del Sol; Reinhard Schneider; Hiroaki Kitano; Rudi Balling
Journal:  Mol Neurobiol       Date:  2013-07-07       Impact factor: 5.590

9.  Participatory medicine: a driving force for revolutionizing healthcare.

Authors:  Leroy Hood; Charles Auffray
Journal:  Genome Med       Date:  2013-12-23       Impact factor: 11.117

10.  NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps.

Authors:  Inna Kuperstein; David P A Cohen; Stuart Pook; Eric Viara; Laurence Calzone; Emmanuel Barillot; Andrei Zinovyev
Journal:  BMC Syst Biol       Date:  2013-10-07
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