An overview of clustering applied to molecular biology

Methods in Molecular Biology
Rebecca Nugent, Marina Meila

Abstract

In molecular biology, we are often interested in determining the group structure in, e.g., a population of cells or microarray gene expression data. Clustering methods identify groups of similar observations, but the results can depend on the chosen method's assumptions and starting parameter values. In this chapter, we give a broad overview of both attribute- and similarity-based clustering, describing both the methods and their performance. The parametric and nonparametric approaches presented vary in whether or not they require knowing the number of clusters in advance as well as the shapes of the estimated clusters. Additionally, we include a biclustering algorithm that incorporates variable selection into the clustering procedure. We finish with a discussion of some common methods for comparing two clustering solutions (possibly from different methods). The user is advised to devote time and attention to determining the appropriate clustering approach (and any corresponding parameter values) for the specific application prior to analysis.

Citations

Jan 22, 2013·Expert Opinion on Medical Diagnostics·Jason E McDermottKarin D Rodland
Dec 18, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Tianwei Yu, Hesen Peng
Mar 7, 2014·Journal of Biomolecular Screening·Yann AbrahamChristian N Parker
Aug 22, 2017·SLAS Discovery·Kishore Kumar Jagadeesan, Simon Ekström
Dec 1, 2011·Statistical Analysis and Data Mining·Anna J BlackstockTianwei Yu
Oct 1, 2020·BMC Bioinformatics·Lili Blumenberg, Kelly V Ruggles
Jun 11, 2019·Frontiers in Computational Neuroscience·Hany AlashwalAhmed A Moustafa
Apr 8, 2020·Royal Society Open Science·Omar Shetta, Mahesan Niranjan
Jun 18, 2021·Computers in Biology and Medicine·Evangelos KaratzasGeorgios A Pavlopoulos

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Frontiers in Bioscience : a Journal and Virtual Library
David J MillerGeorge Kesidis
Algorithms for Molecular Biology : AMB
Burton Kuan Hui Chia, R Krishna Murthy Karuturi
Advances and Applications in Bioinformatics and Chemistry : AABC
Sawannee SutheeworapongKengo Kinoshita
© 2021 Meta ULC. All rights reserved