Bioinformatics in the Classroom

Resources

Books Matt Ridley: Genome - The Autobiography of a Species in 23 Chapters. HarperCollins Publishers, 2000. ISBN 0-06-019497-9. Bryan Sykes: Genome - The Seven Daughters of Eve. W.W. Norton and Company, 2001. ISBN 0-393-02018-5. A. Malcolm Campbell & Laurie J. Heyer - Discovering Genomics, Proteomics, & Bioinformatics. Benjamin Cummings, 2003. ISBN 0-8053-4722-4. David W. Mount: Bioinformatics - Sequence and Genome Analysis. Cold Spring Harbor Laboratory Press, 2001. ISBN 0-87969-608-7. Andreas D. Baxecvanis, B. F. Francis Ouelette - Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. John Wiley & Sons, 2001. ISBN 0-471-38391-0. Minoru Kanehisa: Post-genome Informatics. Oxford Universitgy Press, 2001. ISBN 0-19-850326-1. Charles R. Kantor, Cassandra l. Smith: Genomics - The Science and Technology Behind the Human Genome Project. John Wiley & Sons, Inc., 1999. ISBN 0-471-59908-5. Cynthia Gibas, Per Jambeck: Developing Bioinformatics Computer Skills. O'Reilly & Associates, Inc., 2001. ISBN 1-56592-664-1. James Tisdall - Beginning Perl for Bioinformatics. O'Reilly & Associates, Inc., 2001. ISBN 0-596-00080-4. Electronic Media The Human Genome Project. Multimedia Kit. National Human Genome Research Institute, 2000. NIH-Publication No. 00-4873. Web Sites Mitomap Volcanoes NCBI Tutorials GenBank Field Guide Publications About Database Resources NCBI GenBank RefSeq and LocusLink Various Genomes The Human Genome (HGP; Nature) Mining the Human Genome (HGP; Nature) Road Map to the Human Genome (HGP; Nature) Editorial About the Human Genome (HGP; Nature) The Human Genome (Celera; Science) Pharmacogenomics: A Clinician's Primer on Emerging Technologies for Improved Patient Care Web Resources to Access the Human Genome Draft (Colin, 2001) 35,000 Genes in Human Genome Another Estimate of Genes in Human Genome 120,000 Genes in Human Genome How to Estimate the Genes in The Human Genome ... Genome Sequence of D. melanogaster Genome Sequence of C. elegans Sequence Analysis Defining Genes in the Genomics Era Genome Annotation: From Sequence to Biology Sequence Analysis: Comparison of Functional Annotation Schemes for Genomes Sequence Analysis: Gapped Blast and PSI-Blast: a New Generation of Protein Database Search Programs Sequence Analysis: Genome Annotation Assessment in Drosophila melanogaster Sequence Analysis: Prediction of Complete Genome Gene Structures in Human Genomic DNA Sequence Analysis: Locating Protein Coding Regions in Human DNA Sequences Sequence Analysis: PIP_Maker: A Webserver for Aligning DNA Sequences Sequence Analysis: Prediction of Splice Sites in Plant Pre-mRNA From Sequence Properties Sequence Analysis: Accuracy of Gene Prediction Tools I (Reese et al., 2000) Sequence Analysis: Accuracy of Gene Prediction Tools II (Rogic et al., 2001) Fingerprint Analysis of Large Insert Clones A Genomic Perspective on Plant Transcription Factors Microarrays: Cluster Analysis and Displays of Genome-Wide Expression Patterns Sequence Analysis: 1,000 Putative New Human Signalling Proteins Revealed by EST Data Mining Finding Genes by Computer Identification of Regulatory Regions Which Confer Muscle_Specific Gene Expression Gene Prediction: Evaluation of Gene Prediction Programs I (Guico et al., 2000) Gene Prediction: Evaluation of Gene Prediction Programs II (Reese et al., 2000) Gene Prediction: Evaluation of Gene Prediction Programs III (Rogic et al., 2001) NCBI Electronic PCR 1 NCBI Electronic PCR 2 Alternative Splicing Frequent Alternative Splicing of Human Genes Listening to Silence and Understanding Nonsense: Exonic Mutations That Affect Splicing Gene Prediction Through GRAIL Gene-Finding Approaches for Eukaryotes Eukaryotic Promotor Recognition Human Mouse Genome Comparison to Locate Regulatory Sites Comparative DNA Analysis Across Diverse Genomes Gene Prediction GRAIL (Uberbacher, 1991) GenScan (Burge, 1997) Gene Expression Gene Expression Informatics - It's All In Your Mine SNPs SNP: SNP Detection (DASH) SNP: SNP Detection (PolyBayes) SNP: Guilt By Association SNP: A SNP Map Of the Human Genome SNP: A Polymorphism associated with Decreased Risk for Type II Diabetes SNP: SNPs in Coding Regions of Human Genes SNP: Variation is the Spice of Life SNP: DNA Sequence Diversity in the Human Lipoprotein Lipase Gene SNP: A General Approach to SNP Discovery SNP: Sequence Variation in the Human Angiotensin Converting Enzyme SNP: Patterns of Single_Nucleotide_Polymorphisms in Candidate Genes for Blood-Pressure Homeostasis SNP: A Map of Human Genome Sequence Variation Containing 1.42 million Single Nucleotide Polymorphisms SNP: SNPs and Asthma; Albuterol Efficacy Specific Genes Genes: Tumor Supressor Functions of BRCA 1 and BRCA 2 Genes: Molecular Targets for Breast Cancer Therapy and Prevention Genes: Breast Cancer Genetics: What We Know And What We Need Genes: BRCA2 Involved in Breast Cancer and in Prenatal Viability Genes: A Putative Role for Mitochondrial Genes in Cancer Genes: Ataxia Telangiectasia Locus Genes: Ataxia Telangiectasia Mutated is Essential During Adult Neurogenesis Genes: The DNA Damage Response Genes: Expression of NPAT Promotes S-Phase Entry Genes: Research on Juvenile Diabetes Genes: The Structural Basis of Phenylketonuria Microarrays Gene Expression Patterns in Human Liver Cancers (Chen et. al.; Mol. Biol. Cell 2002) Brown Lab publications Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes - Paper (Gasch et. al.; Mol. Biol. Cell 2000) Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes - Web Supplement Large-scale identification of secreted and membrane-associated gene products using DNA microarrays - Paper (Diehn et. al.; Nat. Genet. 2000) Large-scale identification of secreted and membrane-associated gene products using DNA microarrays - Web Supplement Proteomics A Question of Size: The Eukaryotic Proteome and the Problems in Defining It Transposable Elements Mobile Elements and the Human Genome (How Alu Jumps) Active Alu Element "A-Tails": Size Does Matter (Roy-Engel et al.; Genome Research 12, 2002) Potentially Positive Effects: The ACE Gene and Muscle Performance (Willimas et al.; Nature 403, 2000) Potentially Positive Effects: A role for Alu elements in cohesin binding? (Hakimi et al.; Nature 418, 2002) Potentially Positive Effects: The birth of an alternatively spliced exon (Lev-Maor et al.; Science 300, 2003) Potentially Positive Effects: Not Junk After All (Makalowski; Science 300, 2003) Population Genetics Alu Repeats and Human Genomic Diversity (Batzer & Deininger; NRG 03, 2002) Alu Elements and Disease African origin of human specific Alu insertions (Amplification of PV92; Batzer et al.; PNAS 91, 1994) Recent Alu Insertion Into A Prehistoric Alu In Chromosome 16 (Comas et al., Mol. Biol. Evol., 2001) Population Genetics: Y Chromosome Sequence Variation and the History of Human Populations Population Genetics: The Past Within Us Mitochondrial DNA From Lake Mungo Man Emergence of West Eurasian mtDNA: D-Loops and RFLPs (Macaulay et. al.; Am. J. Hum. Genet., 1999) Tracing European Founder Lineages in the Near Eastern mtDNA Pool (Richards et. al.; Am. J. Hum. Genet., 2000) The Molecular Genetics of European Ancestry (Sykes; Phil. Trans. Roy. Soc. Lond., 1999) Alu insertion polymorphisms in NW Africa and the Iberian Peninsula: evidence for a strong genetic boundary through the Gibraltar Straits Genetic Evidence on the Origins of Indian Caste Populations Patterns of Human Diversity Inferred From Biallelic Polymorphisms Alu Insertions; Romualdi et. al.; Genome Research, 2002) NYT about Alu Elements Curious The "Seti" Project of Cancer Research Genetic Counseling: Clinical and Ethical Challenges Presentations Course Lectures Course Objectives Concepts Introduction to Bioinformatics Introduction to Bioinformatics II Single Nucleotide Polymorphisms (SNPs) Similarity vs. Homology Guest Presentations Other Presentations DNA Homology and Similarity Human Genetic Variation; SNPs Microarrays Mapping and Sequencing Large Genomes The Arabidopsis Genome Rice Genome Sequencing The Human Genome (and some other eukaryotes) DNA Sequencing Reactions DNA Sequencing Reactions 2 Genome Sequencing Generating Sequence The Dynamic Human Genome ENSEMBL: Annotation of the Human Genome Gene Prediction and Genome Annotation A UNIX Primer