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Showing 1 to 12 of 35 entries
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A comparison of aggregate p-value methods and multivariate statistics for self-contained tests of metabolic pathway analysis.

PloS one

Mitchell MW.
PMID: 25927705
PLoS One. 2015 Apr 30;10(4):e0125081. doi: 10.1371/journal.pone.0125081. eCollection 2015.

For pathway analysis of genomic data, the most common methods involve combining p-values from individual statistical tests. However, there are several multivariate statistical methods that can be used to test whether a pathway has changed. Because of the large...

Computational identification of cellular networks and pathways.

Molecular bioSystems

Markowetz F, Troyanskaya OG.
PMID: 17579773
Mol Biosyst. 2007 Jul;3(7):478-82. doi: 10.1039/b617014p. Epub 2007 May 14.

In this article we highlight recent developments in computational functional genomics to identify networks of functionally related genes and proteins based on diverse sources of genomic data. Our specific focus is on statistical methods to identify genetic networks. We...

RMBNToolbox: random models for biochemical networks.

BMC systems biology

Aho T, Smolander OP, Niemi J, Yli-Harja O.
PMID: 17524136
BMC Syst Biol. 2007 May 24;1:22. doi: 10.1186/1752-0509-1-22.

BACKGROUND: There is an increasing interest to model biochemical and cell biological networks, as well as to the computational analysis of these models. The development of analysis methodologies and related software is rapid in the field. However, the number...

Human metabolic network reconstruction and its impact on drug discovery and development.

Drug discovery today

Ma H, Goryanin I.
PMID: 18468557
Drug Discov Today. 2008 May;13(9):402-8. doi: 10.1016/j.drudis.2008.02.002. Epub 2008 Mar 24.

This paper describes the process for the reconstruction of a high quality human metabolic network from the genome information, the existing problems in the reconstruction and why a time-consuming literature based consolidation process is needed. The reconstructed metabolic network...

KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database.

BMC bioinformatics

Moutselos K, Kanaris I, Chatziioannou A, Maglogiannis I, Kolisis FN.
PMID: 19814801
BMC Bioinformatics. 2009 Oct 08;10:324. doi: 10.1186/1471-2105-10-324.

BACKGROUND: The KEGG Pathway database is a valuable collection of metabolic pathway maps. Nevertheless, the production of simulation capable metabolic networks from KEGG Pathway data is a challenging complicated work, regardless the already developed tools for this scope. Originally...

Fragment recruitment on metabolic pathways: comparative metabolic profiling of metagenomes and metatranscriptomes.

Bioinformatics (Oxford, England)

Desai DK, Schunck H, Löser JW, Laroche J.
PMID: 23303511
Bioinformatics. 2013 Mar 15;29(6):790-1. doi: 10.1093/bioinformatics/bts721. Epub 2013 Jan 09.

MOTIVATION: The sheer scale of the metagenomic and metatranscriptomic datasets that are now available warrants the development of automated protocols for organizing, annotating and comparing the samples in terms of their metabolic profiles. We describe a user-friendly java program...

GLAMM: Genome-Linked Application for Metabolic Maps.

Nucleic acids research

Bates JT, Chivian D, Arkin AP.
PMID: 21624891
Nucleic Acids Res. 2011 Jul;39:W400-5. doi: 10.1093/nar/gkr433. Epub 2011 May 29.

The Genome-Linked Application for Metabolic Maps (GLAMM) is a unified web interface for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic networks and investigating the construction of novel, transgenic...

Cellular determinants of metabolite concentration ranges.

PLoS computational biology

Küken A, Eloundou-Mbebi JMO, Basler G, Nikoloski Z.
PMID: 30677015
PLoS Comput Biol. 2019 Jan 24;15(1):e1006687. doi: 10.1371/journal.pcbi.1006687. eCollection 2019 Jan.

Cellular functions are shaped by reaction networks whose dynamics are determined by the concentrations of underlying components. However, cellular mechanisms ensuring that a component's concentration resides in a given range remain elusive. We present network properties which suffice to...

Network Analysis of Genome-Wide Association Studies for Chronic Obstructive Pulmonary Disease in the Context of Biological Pathways.

American journal of respiratory and critical care medicine

Mount S, Cirillo E, Stewart K, Coort S, Evelo CT, Wesselius A, Zeegers MP, Schols AMWJ.
PMID: 31343902
Am J Respir Crit Care Med. 2019 Dec 01;200(11):1439-1441. doi: 10.1164/rccm.201904-0902LE.

No abstract available.

[An evolving and flourishing metabolic engineering].

Sheng wu gong cheng xue bao = Chinese journal of biotechnology

Liu Z, Wang Y.
PMID: 34085439
Sheng Wu Gong Cheng Xue Bao. 2021 May 25;37(5):1494-1509. doi: 10.13345/j.cjb.200729.

In 1990s, Bailey and Stephanopoulos put forward the concept of classic metabolic engineering, aiming to use DNA recombination technology to rewire metabolic network to achieve improved cell performance and increased target products. In the last 30 years since the...

iPath2.0: interactive pathway explorer.

Nucleic acids research

Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P.
PMID: 21546551
Nucleic Acids Res. 2011 Jul;39:W412-5. doi: 10.1093/nar/gkr313. Epub 2011 May 05.

iPath2.0 is a web-based tool (http://pathways.embl.de) for the visualization and analysis of cellular pathways. Its primary map summarizes the metabolism in biological systems as annotated to date. Nodes in the map correspond to various chemical compounds and edges represent...

A pathway-based view of human diseases and disease relationships.

PloS one

Li Y, Agarwal P.
PMID: 19194489
PLoS One. 2009;4(2):e4346. doi: 10.1371/journal.pone.0004346. Epub 2009 Feb 04.

It is increasingly evident that human diseases are not isolated from each other. Understanding how different diseases are related to each other based on the underlying biology could provide new insights into disease etiology, classification, and shared biological mechanisms....

Showing 1 to 12 of 35 entries