Open Questions: Genetics and Genomics

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Introduction

DNA sequencing

Gene mapping

Functional genomics

Phylogenetics

Pharmacogenomics

Recommended references: Web sites

Recommended references: Magazine/journal articles

Recommended references: Books

Introduction

Recommended references: Web sites

Site indexes

Open Directory Project: Human Genome: Categorized and annotated links. A version of this list is at Google, with entries sorted in "page rank" order. May also be found at Netscape.
International Human Genome Sequencing Consortium Genome Hub: Directory of Web sites containing human genome information. Maintained by NHGRI.
The Human Genome: Guide to online information resources. Maintained by the National Center for Biotechnology Information (NCBI). Includes the NCBI Genome Guide: External Links, a directory of Web sites containing human genome information. The NCBI also has guides to the chimpanzee genome, dog genome, mouse genome, zebrafish genome, and rat genome.
Project Ensemble Human Genome Central: Directory of Web sites containing human genome information. Maintained by the European Bioinformatics Institute (EBI).
Human Genome Project Resources: Directory of Web sites containing human genome information. Part of The Genome Database.
The Institute for Genomic Research: Related Links: Good categorized list of links provided by TIGR.
GenomeWeb: Categorized links to genomics sites, maintained by the UK Human Genome Mapping Project Resource Centre.
Galaxy: Genome Projects: Categorized site directory. Entries usually include descriptive annotations.
Galaxy: Genomics: Categorized site directory. Entries usually include descriptive annotations.

Sites with general resources

Genome Biology: Free online scientific journal covering research in genomics and related medical biology.
Nature Genome Gateway: Excellent portal/gateway for genomics research. Provides general news on genomics research, library of original research papers, external links, and other services for professionals. Of particular interest is the human genome section.
Nature Web Focus: The Human Genome: Provides access to a huge collection of papers and information published by Nature on genomics research and the human genome.
National Human Genome Reserach Institute (NHGRI): Agency that heads the Human Genome Project for the U. S. National Institutes of Health. Site contains information on the Human Genome Project and an excellent glossary of genetic terms.
DOEgenomes.org: Umbrella site for the U. S. Department of Energy's genome-related projects. These include the Human Genome Project, Genomics: GTL, and the Microbial Genome Program.
Human Genome Project Information: Extensive collection of information on the Human Genome Project provided by U. S. Department of Energy. Noteworthy features include many publications, and some excellent genomics primers, including Genomics and Its Impact on Science and Society.
Human Genome Research: A top-level site maintained by the U. S. Department of Energy to document the DOE's involvement in the Human Genome Project.
Genomics: GTL: GTL is governmentese for Genomes to Life. The site is the Web site for the U. S. Department of Energy's research program which investigates genomes for a better understanding of interactions between life and the environment. A more complete description is here.
The Human Genome: Site maintained by The Wellcome Trust to provide information on the human genome and the impact of genome research on health, disease, and society. Resources include news stories, more news stories, feature articles, many informative background articles, and a glossary.
The Genome Database (GDB): An organization Established at Johns Hopkins University in 1990, GDB is the official central repository for genomic mapping data resulting from the Human Genome Initiative. Among other things, it contains information on each human chromosome.
GenomeNet: Site maintained by the Bioinformatics Center of Kyoto University (Japan). Contains a number of databases for researchers, such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) and some external links.
Genome News Network: A very informative online news magazine for a general audience about genomics, published approximately every two weeks with approximately 8 articles per issue. The site also includes various general information resources.
The Whitehead Institute Center for Genome Research: Associated with MIT. Site contains information about the Institute, a number of research-oriented databases, and recent press releases.
Stanford Human Genome Center: Contains information on genome sequencing and mapping.
The SNP Consortium Home Page: The Consortium is a nonprofit organization that makes SNP information publicly available. Contains tutorial information on single nucleotide polymorphisms here.
Mouse Genome Special: Collection of featured articles and information from Nature concerning completion of sequencing of the mouse genome, December 2002. Links to many of Nature's relevant articles and papers.
Rat Genome Special: Collection of featured articles and information from Nature concerning completion of sequencing of the rat genome, April 2004.
The ENCODE Project: ENCyclopedia Of DNA Elements: Home page of a major project of the National Human Genome Research Institute to catalog all functional elements in the human genome sequence.
UCSU Genome Bioinformatics: "This site contains the reference sequence for the human and C. elegans genomes and working drafts for the mouse, rat, C. briggsae, and SARS genomes. It also provides access to the Target 1 sequence and annotations for the NIH Intramural Sequencing Center (NISC) Comparative Sequencing Program." Although intended for professional researchers, the site illustrates how genomic information is analyzed.
The Institute for Genomic Research: TIGR provides a variety of resources in genomics, such as genome databases, educational programs, information on functional genomics, genomics software, and scientfic conferences. The site has a good list of external links.
The Center for the Advancement of Genomics: "The Center for the Advancement of Genomics (TCAG) is a not-for-profit policy center dedicated to advancing science through education and enlightenment of the general public, elected officials, and students." It publishes Genome News Network.
Human Genome Sequencing Center: A research institute involved in various sequencing projects, including rats, chimpanzees, and honey bees. The site includes information for the general public as well as more specialized information for researchers.
International HapMap Project: Web site of a collaborative project. "The goal of the International HapMap Project is to develop a haplotype map of the human genome, the HapMap, which will describe the common patterns of human DNA sequence variation. The HapMap is expected to be a key resource for researchers to use to find genes affecting health, disease, and responses to drugs and environmental factors."
Washington University Genome Sequencing Center: A genomics research facility that "focuses on the large scale generation and analysis of DNA sequence". Projects include genomes of chickens and chimpanzees.
The Dog Genome Project: Research project to map the genome of the domestic dog. Site includes a statement of principles and goals.
The UCR Institute for Integrative Genome Biology: A genomics research facility for the University of California at Riverside. The site includes bioinformatics resources, and a Biotech Impacts Center which serves "as an 'honest broker' forum to identify the relevant policy issues, act as a clearinghouse for credible information on those issues."
International Genomics Consortium: "A non-profit medical research organization established to expand upon the discoveries of the Human Genome Project and other systematic sequencing efforts by combining world-class genomic research, bioinformatics, and diagnostic technologies in the fight against cancer and other complex genetic diseases."
Epigenomics AG: German biotechnology company which focuses on "treatment of cancer and other complex diseases by developing novel diagnostic and pharmacodiagnostic products based on DNA methylation."

Surveys, overviews, tutorials

NCBI Science Primer: General overview information on a number of topics related to genomics, including bioinformatics, genome mapping, protein structure, single nucleotide polymorphism, expressed sequence tags, microarrays, molecular genetics, pharmacogenomics, and phylogenetics.
Genomics and Its Impact on Science and Society The Human Genome Project and Beyond: A large and very informative "primer", in 10 chapters, on all aspects of the Human Genome Project.
A Vision for the Future of Genomics Research: April 2003 report on the future of the field of genomics, produced by the National Human Genome Research Institute. (PDF reader requried.)
Human Genome Project Frequently Asked Questions: Fair size list of questions and answers provided by the U. S. Human Genome Project.
The Science Behind the Human Genome Project: Good overview of "basic genetics, genome draft sequence, and post-genome science", provided by the U. S. Human Genome Project.
How do we Sequence DNA?: Nice, single-page overview of the process.
Background on Comparative Genomic Analysis: Short article about comparing genomes across species, at the NHGRI site.
Sequence - Evolution - Function: Computational Approaches in Comparative Genomics: Complete online textbook, by Eugene V. Koonin and Michael Y. Galperin. Index. Part of the NCBI Bookshelf.
Genomes: Complete online textbook, by T. A. Brown. Index. Part of the NCBI Bookshelf.
Gene Science: Matter of Mice, Men: December 2002 article from Wired News. Discusses sequencing of mouse, rat, and sea squirt genomes.
The Human Genome Race: April 2000 Scientific American In Focus article about the Human Genome Project.
GeneMap '99: Map of genes in the human genome as of 1999, provided by the U. S. National Center for Biotechnology Information.
Reading the Book of Life: February 2001 Scientific American In Depth article, by Julia Karow, subtitled "We have only about twice as many genes as a worm or flyfar fewer than anyone guessed. So now what?"
Pharmacogenomics: Single page of overview information with a number of external links, provided by the U. S. Human Genome Project.

Recommended references: Magazine/journal articles

Seeking genetic fate
Patrick Barry
Science News, July 4, 2009: Personal genomics companies offer forecasts of disease risk, but the science behind the packaging is still evolving.
What Makes Us Human?
Katherine S. Pollard
Scientific American, May 2009: Comparisons of the genomes of humans and chimpanzees are revealing those rare stretches of DNA that are ours alone.
Shared Differences
Tina Hesman Saey
Science News, April 25, 2009: The architecture of our genomes is anything but basic.
No gene is an island
Patrick Barry
Science News, December 6, 2008: Even as biologists catalog the discrete parts of life forms, an emerging picture reveals that life�s functions arise from interconnectedness.
Nabbing suspicious SNPs
Regina Nuzzo
Science News, June 21, 2008: Scientists search the whole genome for clues to common diseases.
Genome 2.0
Patrick Barry
Science News, September 8, 2007: Mountains of new data are challenging old views.
The Alternative Genome
Gil Ast
Scientific Amerian, April 2005
A Practical Guide to the HapMap
Aileen Constans
The Scientist, February 1, 2006: Here are five tips to getting the most out of your next gene-association study.
Bad Genes, Good Drugs
Jeff Wheelwright
Discover, April 2002, pp. 52-59: There are subtle differences between the genomes of every human, often merely differences in isolated nucleotides among the 3 billion in the whole genome. Such differences, if they occur commonly, are known as single nucleotide polymorphisms (SNPs). SNPs often occur in groups known as haplotypes. Knowledge of variant but frequently occurring haplotypes may lead to an understanding of diseases they can cause -- and possible cures.
The Meaning of Life
Tina Hesman Saey
Science News, April 29, 2000: Computers are unscrambling genomes to reveal the secrets in DNA codes.

Recommended references: Books

Jeffre L. Witherly; Galen P. Perry; Garry L. Leja -- An A to Z of DNA Science: What Scientists Mean When They Talk about Genes and Genomes
Cold Springs Harbor Laboratory Press, 2001: Excellent glossary of about a hundred terms used frequently in molecular biology and genomics. It does not pretend to explain the topics in any depth, but can serve to jog the memory of a beginner in the subjects of genes and genommics. The range of topics is very broad -- from "nucleotide" to "intellectual property rights". Yet the really important ones seem to be mostly here.

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