23 papers · ranked by Valyu relevance
Purvesh Khatri, Marina Sirota, Atul J. Butte, Christos A. Ouzounis
Pathway analysis has become the first choice for gaining insight into the underlying biology of differentially expressed genes and proteins, as it reduces complexity and has increased explanatory power. We discuss the evolution of knowledge base-driven pathway analysis over its first decade, distinctly divided into…
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…
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…
William G. Ryan V., Smita Sahay, John Vergis, Corey Weistuch + 3 more
'Jarek Meller' 'Robert E. McCullumsmith' 'Gerald Lushington'] In bioinformatics, pathway analyses are used to interpret biological data by mapping measured molecules with known pathways to discover their functional processes and relationships. Pathway analysis has become an essential tool for interpreting large-scale…
Gabriel J. Odom, Yuguang Ban, Lizhong Liu, Xiaodian Sun + 4 more
With the advance in high-throughput technology for molecular assays, multi-omics datasets have become increasingly available. However, most currently available pathway analysis software provide little or no functionalities for analyzing multiple types of -omics data simultaneously. In addition, most tools do not…
Marina Evangelou, Augusto Rendon, Willem H. Ouwehand, Lorenz Wernisch + 2 more
Pathways are groups of biologically related genes that act together in a specific biological process. Different pathways are responsible for different outcomes varying in complexity. An example of a biological pathway is the metabolic Gluconeogenesis pathway that is responsible for the generation of glucose. According…
Tibo Vande Moortele, Pieter Verschaffelt, Qingyao Huang, Nadezhda T. Doncheva + 6 more
Metaproteomics, the study of collective proteomes in environmental communities, plays a crucial role in understanding microbial functionalities affecting ecosystems and human health. Pathway analysis offers structured insights into the biochemical processes within these communities. However, no existing tool…
Bram Burger, Luis Francisco Hernández Sánchez, Ragnhild Reehorst Lereim, Harald Barsnes + 1 more
Biochemical pathways are commonly used as a reference to conduct functional analysis on biomedical omics datasets, where experimental results are mapped to knowledgebases comprising known molecular interactions collected from the literature. Due to their central role, the content of the functional knowledgebases…
Maria K. Jaakkola, Anu Kukkonen-Macchi, Tomi Suomi, Laura L. Elo
We introduce a new method for Pathway Analysis of Longitudinal data (PAL), which is suitable for complex study designs, such as longitudinal data. The main advantages of PAL are the use of pathway structures and the suitability of the approach for study settings beyond currently available tools. We demonstrate the…
Rosemary Braun, Sahil Shah
Rapid advances in high–throughput technologies have led to considerable interest in analyzing genome– scale data in the context of biological pathways, with the goal of identifying functional systems that are involved in a given phenotype. In the most common approaches, biological pathways are modeled as simple sets of…
Denise Slenter, M. Kutmon, Chris T. Evelo, Egon L. Willighagen
Metabolomics data analysis for phenotype identification commonly reveals only a small set of biochemical markers, often containing overlapping metabolites for individual phenotypes. Differentiation between distinctive sample groups requires understanding the underlying causes of metabolic changes. However, combining…
Yue Zhao
Motivation: Recent breakthroughs in cancer research have come via the up-and-coming field of pathway analysis. By applying statistical methods to prior known gene and protein regulatory information, pathway analysis provides a meaningful way to interpret genomic data. While many gene/protein regulatory relationships…
Layan Nahlawi
| 1 | Introduction | | 1 | | --- | --- | --- | --- | | 2 | Disease Association Studies | | 4 | | | 2.1 | Disease Association Studies Data | 4 | | | 2.2 | History of Disease Association Studies | 5 | | | 2.3 | Categorization of Disease Association Studies | 6 | | | 2.4 | Standard Statistical Approaches for Disease…
Gustavo S. Jeuken, Nicholas P. Tobin, Lukas Käll
Most activities in a cell are dependent on not individual, but rather sets of biomolecules. Such sets are often referred to as pathways. Pathways are useful to study as their activities are frequently more directly related to the behavior of the cell than their components. Traditional pathway analysis gives…
Kathleen M. Chen, Jie Tan, Gregory P. Way, Georgia Doing + 2 more
Investigators often interpret genome-wide data by analyzing the expression levels of genes within pathways. While this within-pathway analysis is routine, the products of any one pathway can affect the activity of other pathways. Past efforts to identify relationships between biological processes have evaluated overlap…
Jing Ma, Ali Shojaie, George Michailidis
Motivation: Pathway enrichment analysis has become a key tool for biomedical researchers to gain insight into the underlying biology of differentially expressed genes, proteins and metabolites. It reduces complexity and provides a system-level view of changes in cellular activity in response to treatments and/or in…
Thomas Kelder, Bruce R. Conklin, Chris T. Evelo, Alexander R. Pico + 1 more
'Jonathan A. Eisen'] This Essay discusses the role of pathways for exploratory data analysis in present-day biology.
Peter D. Karp, Suzanne Paley, Peter Midford, Markus Krummenacker + 6 more
'Richard Billington' 'Anamika Kothari' 'Wai Kit Ong' 'Pallavi Subhraveti' 'Ingrid M. Keseler' 'Ron Caspi'] Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and…
Vidhi Kulkarni, Igor Tsigelny, Valentina Kouznetsova
Feline mammary carcinoma (FMC) is a prevalent and fatal carcinoma that predominantly affects unsprayed female cats. FMC is the third most common carcinoma in cats but is still underrepresented in research. Current diagnosis methods include physical examinations, imaging tests, and fine-needle aspiration. The diagnosis…
Ryan Miller, Sebastian Muraru, Ana Belén Malpartida, Josh Low + 7 more
Within the next twenty years, the number of cancer patients is expected to rise by 70%. Current cancer treatments still face several limitations, such as severe side effects and a high incidence of disease recurrence. Drug combination therapies are a promising strategy to achieve higher therapeutic effects while…
Sarah Mubeen, Alpha Tom Kodamullil, Martin Hofmann‐Apitius, Daniel Domingo‐Fernándéz
'Daniel Domingo‐Fernándéz'] Pathway enrichment analysis has become a widely used knowledge-based approach for the interpretation of biomedical data. Its popularity has led to an explosion of both enrichment methods and pathway databases. While the elegance of pathway enrichment lies in its simplicity, multiple factors…
Authors not listed
The identification of kinetically feasible reaction pathways that connect a reactant to its product, including numerous intermediates and transition states, is crucial for predicting chemical reactions and elucidating reaction mechanisms. However, as molecular systems become increasingly complex or larger, the number…
Chonghuan Zhang, Alexei Lapkin
Computer assisted synthesis planning (CASP) accelerates the development of organic synthesis routes of pharmaceuticals and industrial chemicals. CASP tools are generally developed on the rules or data of synthetic chemistry which include some enzymatic reactions. However, synthetic biology offers a new degree of…