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- Text/Documents:
- GoMiner: a resource for biological interpretation of genomic and proteomic data (2003) (online version)
Zeeberg et al., NIH, Bethesda, MD
We have developed GoMiner, a program package that organizes lists of 'interesting' genes (for example, under- and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology. GoMiner provides quantitative and statistical output files and two useful visualizations. The first is a tree-like structure analogous to that in the AmiGO browser and the second is a compact, dynamically interactive 'directed acyclic graph'. Genes displayed in GoMiner are linked to major public bioinformatics resources.
- Automated genome sequence analysis and annotation (1999) (PDF, 950KB, 22pgs)
Andrade et al., European Bioinformatics Institute
Large-scale genome projects generate a rapidly increasing number of sequences, most of them biochemically uncharacterized. Research in bioinformatics contributes to the development of methods for the computational characterization of these sequences. However, the installation and application of these methods require experience and are time consuming. We present here an automatic system (GeneQuiz) for preliminary functional annotation of protein sequences that has been applied to the analysis of sets of sequences from complete genomes, both to refine overall performance and to make new discoveries comparable to those made by human experts.
- Genome sequences and great expectations (2000) (Online version)
Iliopoulos et al., European Bioinformatics Institute
To assess how automatic function assignment will contribute to genome annotation in the next five years, we have performed an analysis of 31 available genome sequences. An emerging pattern is that function can be predicted for almost two-thirds of the 73,500 genes that were analyzed. Despite progress in computational biology, there will always be a great need for large-scale experimental determination of protein function.
- DNA Microarray Data Analysis, second edition (2006) (Full Text avaliable at website)
From CSC - the Finnish IT center for science
This guidebook is written in collaboration between several Finnish researchers from different universities and research institutions. The first edition of the DNA microarray data analysis guidebook was written by M. Minna Laine, Tomi Pasanen, Janna Saarela, Ilana Saarikko, Teemu Toivanen, Martti Tolvanen, Jarno Tuimala, Mauno Vihinen, and Garry Wong. For the second edition, Iiris Hovatta, Katja Kimppa, Antti Lehmussola, Juha Saharinen, and Pekka Tiikkainen joined the writer team. The purpose of this book is to serve as course and teaching material to introduce basic concepts of microarray data analysis. We hope that especially researchers starting their data analysis can benefit from the book.
Example chapters:
Part II, Section 10: Data normalization
Part II, Section 11: Finding differentially expressed genes
- What is a DNA chip? (2002) (PDF, 1,024KB, 11pgs)
written for students by Russ Hodge and Christian Schwager, European Molecular Biology Laboratory (EMBL)
This presentation introduces DNA chips (w/photos of real chips after an experiment), followed by DNA chip analysis software, explaining the meaning of spots seen on the chips. The article then explains DNA chip score charts and correlation graphs through an example in which a healthy and an infected mosquito are compared.
- PUMA2—grid-based high-throughput analysis of genomes and metabolic pathways (2006) (Online version)
Maltsev et al., Argonne National Laboratory
The PUMA2 system (available at http://compbio.mcs.anl.gov/puma2) is an interactive, integrated bioinformatics environment for high-throughput genetic sequence analysis and metabolic reconstructions from sequence data. PUMA2 provides a framework for comparative and evolutionary analysis of genomic data and metabolic networks in the context of taxonomic and phenotypic information. Grid infrastructure is used to perform computationally intensive tasks.
- Article: "The Sequence of the Human Genome" (2001) (Online version)
J. Craig Venter et al. (Science, 16 February 2001)
A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies--a whole-genome assembly and a regional chromosome assembly--were used, each combining sequence data from Celera and the publicly funded genome effort...
- Software Downloads:
- Slide Presentations:
- Video Lectures:
- Genomic Study of Human Biology & Disease
September 29, 2005
- Chemical Genomics: New Tools for Medicine
December 6, 2002
- Breaking the Code: Sequencing the Arabidopsis Genome
December 8, 2000
- Probing Genes and Genomes
December 5, 2002
- By The Book with Author Helen Fisher
October 26, 2001
- The Human Genome Project: A Story of Scientific Discovery and Societal Values
January 31, 2002
- HHMI's Understanding Biomedical Research Series
Varies: series of lectures
- From Promoter to Expression - A Probabilistic Framework for Inferring Regulatory Mechanisms
January 31, 2005
- Genomics and the Future of Medicine - Francis Collins, M.D., Ph.D.
September 29, 2005
- A Platform for Computational Comparative Genomics on the Web
October 7, 2005
- Using Evolution to Explore the Human Genome
December 9, 2005
- Next Generation Scientists: Minority Outreach in Genome Sciences
October 2004
- Computational Discovery of Genetic Regulatory Networks
January 30, 2001
- Learning About the Genome: Discriminative and Generative Modeling of Heterogenous Data
March 1, 2001
- Genome: Transcriptional Regulatory Modules
November 7, 2002
- Reading Genes and Genomes
December 5, 2002
- DNA Time Series Expression Data
April 8, 2003
- Statistical Modeling: Genome Data
February 3, 2004
- Genomic Health Care
May 4, 2004
- Sample Scripts:
- Sample Data:
- General Web Resources:
- Mouse Genome Informatics (MGI) - provided by The Jackson Laboratory
- RCSB PDB Structural Genomics Information Portal - dedicated to the initiative of quickly determining a large number of protein structures using X-ray crystallographic and NMR technologies
- Applied Biosystems: online store - products for a variety of applications
- Genomics and Its Impact on Science and Society- The Human Genome Project and Beyond, provided by the U.S. Department of Energy Human Genome Program. This website covers a wide range of subjects, such as medicine and sociology, all focusing on the genome project.
- PUMA2 - High throughput comparative and evolutionary analysis of genomes and metabolic networks with Grid computational backend. Provided by the Bioinformatics group at Argonne National Laboratory.
- The SEED - An Annotation/Analysis Tool for genomes. Provided by F.I.G.(The Fellowship for Interpretation of Genomes, a nonprofit organization devoted to providing support for those analyzing genomes).
- Genomics Resources List - Compiled by Drs. A. Malcolm Campbell and Laurie Heyer from Davidson College at North Carolina.
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