Debbie Marks
Harvard University
6 Papers
22 Citations
Debbie Marks is an academic researcher from Harvard University. The author has contributed to research in topics: BioPAX : Biological Pathways Exchange & Computer science. The author has an hindex of 4, co-authored 6 publications.
Chat about Author
Papers
The BioPAX community standard for pathway data sharing
Emek Demir,Emek Demir,Michael P. Cary,Suzanne M. Paley,Ken Fukuda,Christian Lemer,Imre Vastrik,Guanming Wu,Peter D'Eustachio,Carl F. Schaefer,Joanne S. Luciano,Frank Schacherer,Irma Martínez-Flores,Zhenjun Hu,Verónica Jiménez-Jacinto,Geeta Joshi-Tope,Kumaran Kandasamy,Alejandra López-Fuentes,Huaiyu Mi,Elgar Pichler,Igor Rodchenkov,Andrea Splendiani,Andrea Splendiani,Sasha Tkachev,Jeremy Zucker,Gopal R. Gopinath,Harsha Rajasimha,Harsha Rajasimha,Ranjani Ramakrishnan,Imran Shah,Mustafa H Syed,Nadia Anwar,Özgün Babur,Özgün Babur,Michael L. Blinov,Erik Brauner,Dan Corwin,Sylva L. Donaldson,Frank Gibbons,Robert N. Goldberg,Peter Hornbeck,Augustin Luna,Peter Murray-Rust,Eric K. Neumann,Oliver Reubenacker,Matthias Samwald,Matthias Samwald,Martijn P. van Iersel,Sarala M. Wimalaratne,Keith Allen,Burk Braun,Michelle Whirl-Carrillo,Kei-Hoi Cheung,Kam D. Dahlquist,Andrew Finney,Marc Gillespie,Elizabeth M. Glass,Li Gong,Robin Haw,Michael Honig,Olivier Hubaut,David W. Kane,Shiva Krupa,Martina Kutmon,Julie Leonard,Debbie Marks,David Merberg,Victoria Petri,Alexander R. Pico,Dean Ravenscroft,Liya Ren,Nigam H. Shah,Margot Sunshine,Rebecca Tang,Ryan Whaley,Stan Letovksy,Kenneth H. Buetow,Andrey Rzhetsky,Vincent Schächter,Bruno S. Sobral,Ugur Dogrusoz,Shannon K. McWeeney,Mirit I. 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 +94 more
TL;DR: Thousands of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases, and this large amount of pathway data in a computable form will support visualization, analysis and biological discovery.
BioPAX - Biological Pathways Exchange Language Level 2, Version 1.0 Documentation
Gary D. Bader,Eric Brauner,Michael P. Cary,Kam D. Dahlquist,Emek Demir,Peter D'Eustachio,Ken Fukuda,Frank Gibbons,Marc Gillespie,Robert N. Goldberg,Christopher W. V. Hogue,Michael Hucka,Geeta Joshi-Tope,David W. Kane,Peter D. Karp,Teri Klein,Christian Lemer,Joanne S. Luciano,Debbie Marks,Natalia Maltsev,Elizabeth Marland,E.J. Neumann,Suzanne M. Paley,Jonathan Rees,Aviv Regev,Alan Ruttenberg,Andrey Rzhetsky,Chris Sander,Imran Shah,Andrea Splendiani,Mustafa H Syed,Edgar Wingender,Guanming Wu,Jeremy Zucker +33 more
- 01 Jan 2005
TL;DR: The scope of BioPAX is expanded to include representation of molecular binding interactions, protein post-translational modifications, basic experimental descriptions, and hierarchical pathways, which will increase access to and uniformity of pathway data from varied sources, thus increasing the efficiency of computational pathway research.
Erratum: The BioPAX community standard for pathway data sharing (Nat. Biotechnol. (2010) 28 (935-942)
Emek Demir,Suzanne M. Paley,Ken Fukuda,Christian Lemer,Imre Vastrik,Guanming Wu,Peter D'Eustachio,Carl F. Schaefer,Joanne S. Luciano,Frank Schacherer,Irma Martínez-Flores,Zhenjun Hu,Verónica Jiménez-Jacinto,Geeta Joshi-Tope,Kumaran Kandasamy,Alejandra López-Fuentes,Huaiyu Mi,Elgar Pichler,Igor Rodchenkov,Andrea Splendiani,Sasha Tkachev,Jeremy Zucker,Gopal R. Gopinath,Harsha Rajasimha,Ranjani Ramakrishnan,Imran Shah,Mustafa H Syed,Nadia Anwar,Özgün Babur,Michael L. Blinov,Erik Brauner,Dan Corwin,Sylva L. Donaldson,Frank Gibbons,Robert N. Goldberg,Peter Hornbeck,Augustin Luna,Peter Murray-Rust,Eric K. Neumann,Oliver Reubenacker,Matthias Samwald,Martijn P. van Iersel,Sarala M. Wimalaratne,Keith Allen,Burk Braun,Michelle Whirl-Carrillo,Kei-Hoi Cheung,Kam D. Dahlquist,Andrew Finney,Marc Gillespie,Elizabeth M. Glass,Li Gong,Robin Haw,Michael Honig,Olivier Hubaut,David W. Kane,Shiva Krupa,Martina Kutmon,Julie Leonard,Debbie Marks,David Merberg,Victoria Petri,Alexander R. Pico,Dean Ravenscroft,Liya Ren,Nigam H. Shah,Margot Sunshine,Rebecca Tang,Ryan Whaley,Stan Letovksy,Kenneth H. Buetow,Andrey Rzhetsky,Vincent Schächter,Bruno S. Sobral,Ugur Dogrusoz,Shannon K. McWeeney,Mirit I. 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 +88 more
TL;DR: The author’s aim is to contribute towards the humanizing of science through the application of science and technology to the community of learners.
Viral gain-of-function experiments uncover residues under diversifying selection in nature
Rohan Maddamsetti,Daniel T Johnson,Stephanie J. Spielman,Katherine L. Petrie,Debbie Marks,Meyer +5 more
TL;DR: It is identified that two key residues in the host recognition protein of bacteriophage λ that are necessary to exploit a new receptor repeatedly evolved among homologs from environmental samples.
3D protein structure from genetic epistasis experiments
Nathan J Rollins,Kelly P Brock,Frank J. Poelwijk,Michael A Stiffler,Nicholas P. Gauthier,Chris Sander,Debbie Marks +6 more
TL;DR: Folded models generated from top-ranked epistatic pairs were accurate within 2.4 Å over 53 residues, indicating the possibility that 3D protein folds can be determined experimentally with good accuracy from functional assays of mutant libraries, at least for small proteins.