Literature DB >> 16118415

Data clustering in life sciences.

Ying Zhao1, George Karypis.   

Abstract

Clustering has a wide range of applications in life sciences and over the years has been used in many areas ranging from the analysis of clinical information, phylogeny, genomics, and proteomics. The primary goal of this article is to provide an overview of the various issues involved in clustering large biological datasets, describe the merits and underlying assumptions of some of the commonly used clustering approaches, and provide insights on how to cluster datasets arising in various areas within life sciences. We also provide a brief introduction to CLUTO, a general purpose toolkit for clustering various datasets, with an emphasis on its applications to problems and analysis requirements within life sciences.

Mesh:

Year:  2005        PMID: 16118415     DOI: 10.1385/MB:31:1:055

Source DB:  PubMed          Journal:  Mol Biotechnol        ISSN: 1073-6085            Impact factor:   2.695


  27 in total

1.  Validating clustering for gene expression data.

Authors:  K Y Yeung; D R Haynor; W L Ruzzo
Journal:  Bioinformatics       Date:  2001-04       Impact factor: 6.937

2.  One-stop shop for microarray data.

Authors:  A Brazma; A Robinson; G Cameron; M Ashburner
Journal:  Nature       Date:  2000-02-17       Impact factor: 49.962

3.  Clustering protein sequences--structure prediction by transitive homology.

Authors:  E Bolten; A Schliep; S Schneckener; D Schomburg; R Schrader
Journal:  Bioinformatics       Date:  2001-10       Impact factor: 6.937

4.  A stability based method for discovering structure in clustered data.

Authors:  Asa Ben-Hur; Andre Elisseeff; Isabelle Guyon
Journal:  Pac Symp Biocomput       Date:  2002

5.  Detecting folding motifs and similarities in protein structures.

Authors:  G J Kleywegt; T A Jones
Journal:  Methods Enzymol       Date:  1997       Impact factor: 1.600

6.  Multiplexed biochemical assays with biological chips.

Authors:  S P Fodor; R P Rava; X C Huang; A C Pease; C P Holmes; C L Adams
Journal:  Nature       Date:  1993-08-05       Impact factor: 49.962

7.  Rapid and sensitive protein similarity searches.

Authors:  D J Lipman; W R Pearson
Journal:  Science       Date:  1985-03-22       Impact factor: 47.728

8.  Improved tools for biological sequence comparison.

Authors:  W R Pearson; D J Lipman
Journal:  Proc Natl Acad Sci U S A       Date:  1988-04       Impact factor: 11.205

9.  Quantitative monitoring of gene expression patterns with a complementary DNA microarray.

Authors:  M Schena; D Shalon; R W Davis; P O Brown
Journal:  Science       Date:  1995-10-20       Impact factor: 47.728

10.  Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm.

Authors:  H M Grindley; P J Artymiuk; D W Rice; P Willett
Journal:  J Mol Biol       Date:  1993-02-05       Impact factor: 5.469

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  26 in total

1.  Document clustering of clinical narratives: a systematic study of clinical sublanguages.

Authors:  Olga Patterson; John F Hurdle
Journal:  AMIA Annu Symp Proc       Date:  2011-10-22

2.  Mapping L1 ligase ribozyme conformational switch.

Authors:  George M Giambaşu; Tai-Sung Lee; William G Scott; Darrin M York
Journal:  J Mol Biol       Date:  2012-07-03       Impact factor: 5.469

3.  Development of a HIPAA-compliant environment for translational research data and analytics.

Authors:  Wayne Bradford; John F Hurdle; Bernie LaSalle; Julio C Facelli
Journal:  J Am Med Inform Assoc       Date:  2013-08-02       Impact factor: 4.497

4.  Learning from data: recognizing glaucomatous defect patterns and detecting progression from visual field measurements.

Authors:  Siamak Yousefi; Michael H Goldbaum; Madhusudhanan Balasubramanian; Felipe A Medeiros; Linda M Zangwill; Jeffrey M Liebmann; Christopher A Girkin; Robert N Weinreb; Christopher Bowd
Journal:  IEEE Trans Biomed Eng       Date:  2014-04-01       Impact factor: 4.538

5.  Recognizing patterns of visual field loss using unsupervised machine learning.

Authors:  Siamak Yousefi; Michael H Goldbaum; Linda M Zangwill; Felipe A Medeiros; Christopher Bowd
Journal:  Proc SPIE Int Soc Opt Eng       Date:  2014-03-21

6.  Potentially amyloidogenic conformational intermediates populate the unfolding landscape of transthyretin: insights from molecular dynamics simulations.

Authors:  J Rui Rodrigues; Carlos J V Simões; Cândida G Silva; Rui M M Brito
Journal:  Protein Sci       Date:  2010-02       Impact factor: 6.725

7.  Conservation of small RNA pathways in platypus.

Authors:  Elizabeth P Murchison; Pouya Kheradpour; Ravi Sachidanandam; Carly Smith; Emily Hodges; Zhenyu Xuan; Manolis Kellis; Frank Grützner; Alexander Stark; Gregory J Hannon
Journal:  Genome Res       Date:  2008-05-07       Impact factor: 9.043

8.  The distribution of HLA haplotypes in the ethnic groups that make up the Brazilian Bone Marrow Volunteer Donor Registry (REDOME).

Authors:  Michael Halagan; Danielli Cristina Oliveira; Martin Maiers; Raquel A Fabreti-Oliveira; Maria Elisa Hue Moraes; Jeane Eliete Laguila Visentainer; Noemi Farah Pereira; Matilde Romero; Juliana Fernandes Cardoso; Luís Cristóvão Porto
Journal:  Immunogenetics       Date:  2018-04-26       Impact factor: 2.846

Review 9.  Gene module level analysis: identification to networks and dynamics.

Authors:  Xuewei Wang; Ertugrul Dalkic; Ming Wu; Christina Chan
Journal:  Curr Opin Biotechnol       Date:  2008-09-03       Impact factor: 9.740

10.  jClust: a clustering and visualization toolbox.

Authors:  Georgios A Pavlopoulos; Charalampos N Moschopoulos; Sean D Hooper; Reinhard Schneider; Sophia Kossida
Journal:  Bioinformatics       Date:  2009-05-19       Impact factor: 6.937

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