Literature DB >> 18854235

Taming data.

Alan Aderem1, Ilya Shmulevich.   

Abstract

A challenge in systems-level investigations of the immune response is the principled integration of disparate data sets for constructing predictive models. InnateDB (Lynn et al., 2008; http://www.innatedb.ca), a publicly available, manually curated database of experimentally verified molecular interactions and pathways involved in innate immunity, is a powerful new resource that facilitates such integrative systems-level analyses.

Entities:  

Mesh：

Year:  2008        PMID： 18854235      PMCID： PMC3074406          DOI： 10.1016/j.chom.2008.09.011

Source DB:  PubMed          Journal:  Cell Host Microbe        ISSN： 1931-3128            Impact factor:   21.023


  9 in total

1.  Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Authors:  Paul Shannon; Andrew Markiel; Owen Ozier; Nitin S Baliga; Jonathan T Wang; Daniel Ramage; Nada Amin; Benno Schwikowski; Trey Ideker
Journal:  Genome Res       Date:  2003-11       Impact factor: 9.043

2.  Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation.

Authors:  Aaron Barsky; Jennifer L Gardy; Robert E W Hancock; Tamara Munzner
Journal:  Bioinformatics       Date:  2007-02-19       Impact factor: 6.937

3.  A predictive model for transcriptional control of physiology in a free living cell.

Authors:  Richard Bonneau; Marc T Facciotti; David J Reiss; Amy K Schmid; Min Pan; Amardeep Kaur; Vesteinn Thorsson; Paul Shannon; Michael H Johnson; J Christopher Bare; William Longabaugh; Madhavi Vuthoori; Kenia Whitehead; Aviv Madar; Lena Suzuki; Tetsuya Mori; Dong-Eun Chang; Jocelyne Diruggiero; Carl H Johnson; Leroy Hood; Nitin S Baliga
Journal:  Cell       Date:  2007-12-28       Impact factor: 41.582

4.  Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4.

Authors:  Mark Gilchrist; Vesteinn Thorsson; Bin Li; Alistair G Rust; Martin Korb; Jared C Roach; Kathleen Kennedy; Tsonwin Hai; Hamid Bolouri; Alan Aderem
Journal:  Nature       Date:  2006-05-11       Impact factor: 49.962

5.  Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics.

Authors:  Stephen A Ramsey; Sandy L Klemm; Daniel E Zak; Kathleen A Kennedy; Vesteinn Thorsson; Bin Li; Mark Gilchrist; Elizabeth S Gold; Carrie D Johnson; Vladimir Litvak; Garnet Navarro; Jared C Roach; Carrie M Rosenberger; Alistair G Rust; Natalya Yudkovsky; Alan Aderem; Ilya Shmulevich
Journal:  PLoS Comput Biol       Date:  2008-03-21       Impact factor: 4.475

6.  The Innate Immune Database (IIDB).

Authors:  Martin Korb; Aistair G Rust; Vesteinn Thorsson; Christophe Battail; Bin Li; Daehee Hwang; Kathleen A Kennedy; Jared C Roach; Carrie M Rosenberger; Mark Gilchrist; Daniel Zak; Carrie Johnson; Bruz Marzolf; Alan Aderem; Ilya Shmulevich; Hamid Bolouri
Journal:  BMC Immunol       Date:  2008-03-05       Impact factor: 3.615

7.  Systems biology driven software design for the research enterprise.

Authors:  John Boyle; Christopher Cavnor; Sarah Killcoyne; Ilya Shmulevich
Journal:  BMC Bioinformatics       Date:  2008-06-25       Impact factor: 3.169

8.  InnateDB: facilitating systems-level analyses of the mammalian innate immune response.

Authors:  David J Lynn; Geoffrey L Winsor; Calvin Chan; Nicolas Richard; Matthew R Laird; Aaron Barsky; Jennifer L Gardy; Fiona M Roche; Timothy H W Chan; Naisha Shah; Raymond Lo; Misbah Naseer; Jaimmie Que; Melissa Yau; Michael Acab; Dan Tulpan; Matthew D Whiteside; Avinash Chikatamarla; Bernadette Mah; Tamara Munzner; Karsten Hokamp; Robert E W Hancock; Fiona S L Brinkman
Journal:  Mol Syst Biol       Date:  2008-09-02       Impact factor: 11.429

9.  Probabilistic inference of transcription factor binding from multiple data sources.

Authors:  Harri Lähdesmäki; Alistair G Rust; Ilya Shmulevich
Journal:  PLoS One       Date:  2008-03-26       Impact factor: 3.240
  9 in total

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