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Metabolic pathways variability and sequence/networks comparisons [PDF]

BMC Bioinformatics, 2006
Background In this work a simple method for the computation of relative similarities between homologous metabolic network modules is presented. The method is similar to classical sequence alignment and allows for the generation of phenotypic trees ...
Palumbo Maria, Dhar Pawan K, Tun Kyaw, Giuliani Alessandro   +3 more
doaj   +3 more sources

Analysis on relationship between extreme pathways and correlated reaction sets [PDF]

BMC Bioinformatics, 2009
Background Constraint-based modeling of reconstructed genome-scale metabolic networks has been successfully applied on several microorganisms. In constraint-based modeling, in order to characterize all allowable phenotypes, network-based pathways, such ...
Wang Weirong, Cao Ming, Chen Yi-Ping, Xi Yanping, Wang Fei   +4 more
doaj   +4 more sources

Advances in network-based metabolic pathway analysis and gene expression data integration [PDF]

Briefings in Bioinformatics, 2014
With the emergence of metabolic networks, novel mathematical pathway concepts were introduced in the past decade, aiming to go beyond canonical maps. However, the use of network-based pathways to interpret 'omics' data has been limited owing to the fact that their computation has, until very recently, been infeasible in large (genome-scale) metabolic ...
Alberto Rezola, Jon Pey, Luis Tobalina, Ángel Rubio, J. E. Beasley, Francisco J. Planes   +5 more
openalex   +3 more sources

Reconstruction of phyletic trees by global alignment of multiple metabolic networks [PDF]

BMC Bioinformatics, 2013
Background In the last decade, a considerable amount of research has been devoted to investigating the phylogenetic properties of organisms from a systems-level perspective. Most studies have focused on the classification of organisms based on structural
Ma Cheng-Yu, Lin Shu-Hsi, Lee Chi-Ching, Tang Chuan Yi, Berger Bonnie, Liao Chung-Shou   +5 more
doaj   +2 more sources

Beyond the Biosynthetic Gene Cluster Paradigm: Genome-Wide Coexpression Networks Connect Clustered and Unclustered Transcription Factors to Secondary Metabolic Pathways

Microbiology Spectrum, 2021
Fungal secondary metabolites are widely used as therapeutics and are vital components of drug discovery programs. A major challenge hindering discovery of novel secondary metabolites is that the underlying pathways involved in their biosynthesis are ...
Min Jin Kwon, Charlotte Steiniger, Timothy C. Cairns, Jennifer H. Wisecaver, Abigail L. Lind, Carsten Pohl, Carmen Regner, Antonis Rokas, Vera Meyer   +8 more
doaj   +2 more sources

Modular decomposition of metabolic reaction networks based on flux analysis and pathway projection [PDF]

Bioinformatics, 2007
AbstractMotivation: The rational decomposition of biochemical networks into sub-structures has emerged as a useful approach to study the design of these complex systems. A biochemical network is characterized by an inhomogeneous connectivity distribution, which gives rise to several organizational features, including modularity.
Jeongah Yoon, Yaguang Si, Ryan P. Nolan, Kyongbum Lee   +3 more
openalex   +4 more sources

Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool [PDF]

Cancer & Metabolism, 2016
Colorectal cancers (CRC) are associated with perturbations in cellular amino acids, nucleotides, pentose-phosphate pathway carbohydrates, and glycolytic, gluconeogenic, and tricarboxylic acid intermediates. A non-targeted global metabolome approach was utilized for exploring human CRC, adjacent mucosa, and stool.
Dustin G. Brown, Sangeeta Rao, Tiffany L. Weir, Joanne O’Malia, Marlon Bazan, Regina J. Brown, Elizabeth P. Ryan   +6 more
openalex   +3 more sources

Serum and urine metabolomic biomarkers for predicting prognosis in patients with immunoglobulin A nephropathy [PDF]

Kidney Research and Clinical Practice, 2023
Background Immunoglobulin A nephropathy (IgAN) is the most prevalent form of glomerulonephritis worldwide. Prediction of disease progression in IgAN can help to provide individualized treatment based on accurate risk stratification.
You Hyun Jeon, Sujin Lee, Da Woon Kim, Suhkmann Kim, Sun Sik Bae, Miyeun Han, Eun Young Seong, Sang Heon Song   +7 more
doaj   +1 more source

Metabolomic approaches applied to the study of cervical cancer: a systematic review

Brazilian Journal of Oncology, 2022
Background: Cervical cancer (CC) is the fourth leading cause of cancer among women in the world. Metabolomics can provide a deeper understanding of the underlying metabolic alterations associated with its pathophysiology ...
Natalia Damasceno Almeida, Marcos Almeida Matos, Milena Bastos Brito, Amancio Jose de Souza   +3 more
doaj   +1 more source

Integrated RNA-sequencing and network analysis approach to identify the Hub genes and vital pathways associated with gastric cancer [PDF]

Journal of Pharmacy & Pharmacognosy Research, 2023
Context: Gastric cancer is one of the most prevalent types of cancer in developing countries and ranks fourth in terms of death causes. Helicobacter pylori infection is a significant contributor to the emergence of gastric cancer. Lack of early diagnosis
Karthick Vasudevan, Raghavendra B, Mithun A, Dhanushkumar T, Fazil Ahmad, Manoj Goyal, Monika Bansal, Tasneem Mohammed, Riyaz Ahmed Khan, Gayathri Pandurangam, George Priya Doss, Balu Kamaraj, Gurudeeban Selvaraj   +12 more
doaj   +1 more source