15 papers · ranked by Valyu relevance
Stuart M. Marshall, Alastair R. G. Murray, Leroy Cronin
One thing that discriminates living things from inanimate matter is their ability to generate similarly complex or non-random structures in a large abundance. From DNA sequences to folded protein structures, living cells, microbial communities and multicellular structures, the material configurations in biology can…
Tuan Nhon Dang, Paul Murray, Angus Graeme Forbes
Background Molecular activation pathways are inherently complex, and understanding relations across many biochemical reactions and reaction types is difficult. Visualizing and analyzing a pathway is a challenge due to the network size and the diversity of relations between proteins and molecules. Results In this paper…
Miguel A. García-Campos, Jesús Espinal-Enríquez, Enrique Hernández-Lemus
'Enrique Hernández-Lemus'] Pathway analysis is a set of widely used tools for research in life sciences intended to give meaning to high-throughput biological data. The methodology of these tools settles in the gathering and usage of knowledge that comprise biomolecular functioning, coupled with statistical testing and…
Yuzhen Ye, Thomas G. Doak, Christos A. Ouzounis
A common biological pathway reconstruction approach-as implemented by many automatic biological pathway services (such as the KAAS and RAST servers) and the functional annotation of metagenomic sequences-starts with the identification of protein functions or families (e.g., KO families for the KEGG database and the FIG…
Sarah M. Kim, Matthew I. Peña, Mark Moll, George N. Bennett + 1 more
'Lydia E. Kavraki'] Recent developments in metabolic engineering have led to the successful biosynthesis of valuable products, such as the precursor of the antimalarial compound, artemisinin, and opioid precursor, thebaine. Synthesizing these traditionally plant-derived compounds in genetically modified yeast cells…
Kevin Lim, Limsoon Wong
Background The metabolic network is an aggregation of enzyme catalyzed reactions that converts one compound to another. Paths in a metabolic network are a sequence of enzymes that describe how a chemical compound of interest can be produced in a biological system. As the number of such paths is quite large, many…
Allison Pon, Timothy Jewison, Yilu Su, Yongjie Liang + 4 more
'Adam Maciejewski' 'Michael Wilson' 'David S. Wishart'] PathWhiz ([http://smpdb.ca/pathwhiz]()) is a web server designed to create colourful, visually pleasing and biologically accurate pathway diagrams that are both machine-readable and interactive. As a web server, PathWhiz is accessible from almost any place and…
Liviu Popescu, Golan Yona
Background Accurate assignment of genes to pathways is essential in order to understand the functional role of genes and to map the existing pathways in a given genome. Existing algorithms predict pathways by extrapolating experimental data in one organism to other organisms for which this data is not available.…
Ganesh A Viswanathan, Jeremy Seto, Sonali Patil, German Nudelman + 2 more
Pathway analysis refers to the computational approaches used to investigate network behavior as a system. Pathway analysis can be broadly classified into two types: topological/structural network analysis and dynamical analysis. Topological analysis of a pathway identifies the global qualitative properties of the…
Daniel Domingo-Fernández, Charles Tapley Hoyt, Carlos Bobis-Álvarez, Josep Marín-Llaó + 1 more
Although pathways are widely used for the analysis and representation of biological systems, their lack of clear boundaries, their dispersion across numerous databases, and the lack of interoperability impedes the evaluation of the coverage, agreements, and discrepancies between them. Here, we present ComPath, an…
Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Geeta Joshi-Tope + 10 more
'Gopal Gopinath' 'David Croft' 'Bernard de Bono' 'Marc Gillespie' 'Bijay Jassal' 'Suzanna Lewis' 'Lisa Matthews' 'Guanming Wu' 'Ewan Birney' 'Lincoln Stein'] Reactome, an online curated resource for human pathway data, can be used to infer equivalent reactions in non-human species and as a tool to aid in the…
Cristina Mitrea, Zeinab Taghavi, Behzad Bokanizad, Samer Hanoudi + 4 more
'Rebecca Tagett' 'Michele Donato' 'Călin Voichiţa' 'Sorin Drăghici'] The goal of pathway analysis is to identify the pathways significantly impacted in a given phenotype. Many current methods are based on algorithms that consider pathways as simple gene lists, dramatically under-utilizing the knowledge that such…
Gianluca Mattei, Zhuohui Gan, Matteo Ramazzotti, Bernhard O. Palsson + 3 more
'Daniel C. Zielinski' 'Miha Moškon' 'Tadeja Režen'] Pathway analysis is ubiquitous in biological data analysis due to the ability to integrate small simultaneous changes in functionally related components. While pathways are often defined based on either manual curation or network topological properties, an attractive…
Xianwen Ren, Xiaobo Zhou, Ling-Yun Wu, Xiang-Sun Zhang
Background Biological systems process the genetic information and environmental signals through pathways. How to map the pathways systematically and efficiently from high-throughput genomic and proteomic data is a challenging open problem. Previous methods design different heuristics but do not describe explicitly the…
Melissa D Walker, Gabrielle E Giese, Amy D Holdorf, Sushila Bhattacharya + 15 more
'Sushila Bhattacharya' 'Cédric Diot' 'Aurian P García-González' 'Brent B Horowitz' 'Yong-Uk Lee' 'Thomas Leland' 'Xuhang Li' 'Zeynep Mirza' 'Huimin Na' 'Shivani Nanda' 'Olga Ponomarova' 'Hefei Zhang' 'Jingyan Zhang' 'L Safak Yilmaz' 'Albertha J M Walhout' 'P W Sternberg'] Title: Abstract In our group, we aim to…