Articles for Bioinformatics

	*Bioinformatics* Articles
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Below are links to articles in portable document format (PDF). These papers will be useful for the each section of the course. Access to the articles stored on this site requires a password to protect copyrights. Clicking on the title should cause the pdf to begin downloading in a few seconds. Please be patient.

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Databases

Genomics

Gene Expression

Phylogenetics

Structure-Function Prediction

Networks and Data Mining

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Bioinformatics: bringing it all together.: M Chicurel (2002)
Nature 419: 751-757

Bioinformatics becomes respectable.: SM Brown (2003)
BioTechniques 34: 1124-1127

From sequence to biology: the impact on bioinformatics.: R Fuchs (2002)
Bioinformatics 18(4): 505-506

Information retrieval in biochemistry: Some exercises to develop a fundamental skill.: S Brown (2000)
Biochemistry and Molecular Biology Education 28: 194-199

What is bioinformatics?: a proposed definition and overview of the field.: NM Luscombe, D Greenbaum, M Gerstein (2001)
J. Methods of Information in Medicine 4: 346-358

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Databases

Basic local alignment search tool.: SF Altschul, W Gish, W Miller, EW Myers, DJ Lipman (1990)
Journal of Molecular Biology 215: 403-410

Sequence similarity searches on the world wide web.: SM Brown (1998)
BioTechniques 24(2): 248-250

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Genomics

Genome Sequencing, Assembly, Feature Detection

Introduction: putting it together.: A. Baxevanis, F. Collins (eds) (2002) The Genome User's Guide
Nature Genetics Supplement September issue, pp. 5-8

CAP3: A DNA Sequence Assembly Program.: X Huang and A Madan (1999)
Genome Research 9: 868-877

EMBOSS: the European Molecular Biology Open Software Suite.: P Rice, I Longden, A Bleasby (2000)
Trends Genet. 16(6): 276-277

Tracking evolution's footprints in the genome.: JB Weitzman (2003)
Journal of Biology 2: article 9

The Bioperl toolkit: Perl modules for the life sciences.: JE Stajich et al. (2002)
Genome Res. 12(10): 1611-1618

Creating a bioinformatics nation.: L Stein (2002)
Nature 417: 119-120

Genome Structure

Evolving Genomic Metaphors: A New Look at the Language of DNA.: JC Avise (2001)
Science 294: 86-87

Complicity of gene and pseudogene.: JT Lee (2003)
Nature 423: 26-28

The Genetic Code

The genome chose its alphabet with care.: D Bradley (2002)
Science 297: 1789-1791

The Invention of the Genetic Code.: B Hayes (1998)
American Scientist January-February issue

The Nobel Prize in Physiology or Medicine 1968.: Nobel e-Museum (2003)
The Official Web Site of The Nobel Foundation

Annotated Chromosome and Genome Maps

Tales of the Y-chromosome.: HF Willard (2003)
Nature 423: 810-813

A physical map of the mouse genome.: SG Gregory et al. (2002)
Nature 418: 743-750

Genome Comparison

Comparative genetics in the grasses.: MD Gale, KM Devos (1998)
Proc. Natl. Acad. Sci. USA 95: 1971-1974

Almost human ... Sequencing the chimpanzee has emerged as a top genomic priority.: D Cyranoski (2002)
Nature 418: 910-912

Construction and analysis of a human-chimpanzee comparative clone map.: A Fujiyama et al. (2002)
Science 295: 131-134

The dog genome: Survey sequencing and comparative analysis: EF Kirkness et al. (2003)
Science 301: 1898-1903

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Gene Expression

Functional Genomics

Mining the mouse genome: We have the draft sequence - but how do we unlock its secrets?: A Bradley (2002)
Nature 420: 512-514

Transcription Profiling

DNA Arrays Reveal Cancer in Its Many Forms: J Marx (2000)
Science 289 (5485): 1670-1672

An anatomy of normal and malignant gene expression: K Boon et al. (2002)
Proc. Natl. Acad. Sci. 99(17): 11287-11292

Classifying Breast Cancer Models: Bioinformatics sorts gene expression data for mouse mammary tumor models into oncogenic signatures: T Hollon (2002)
The Scientist 16 (17): 20-27

Altered gene expression could explain the genetic difference between human and chimp: Evolutionists Present Their 1.3% Solution: L Pray (2002)
The Scientist 16(16): 36-41

Intra- and Interspecific Variation in Primate Gene Expression Patterns: W Enard et al. (2002)
Science 296: 341-343

Genomic Analysis of Gene Expression in C. elegans: AA Hill (2000)
Science 290: 809-812

Microarray Data Analysis

MedMiner: An Internet Text-Mining Tool for Biomedical Information, with Application to Gene Expression Profiling: L Tanabe et al. (1999)
BioTechniques 27(6): 1210-1217

Retriever and CompareTable, Two Informatics Tools for Data Analysis of High-Density Oligonucleotide Arrays: AR Brasier (2002)
BioTechniques 32: 100-109

A Concise Guide to cDNA Microarray Analysis: P Hegde et al. (2000)
BioTechniques 29: 548-562

Polymorphism Studies

SNP Mappers Confront Reality and Find It Daunting: L Roberts (2000)
Science 287(5460): 1898-1899

SNPs as Windows on Evolution: Recent studies reveal that the human species is young and genetically uniform: R Lewis (2002)
The Scientist 16(1): 16-21

Haplotype Variation and Linkage Disequilibrium in 313 Human Genes: JC Stephens et al. (2001)
Science 293: 489-493

Detecting recent positive selection in the human genome from haplotype structure: PC Sabeti et al. (2002)
Nature 419: 833-837

Disease Gene Mapping

Speech Gene Tied to Modern Humans: M Balter (2002)
Science 297: 1105

Molecular evolution of FOXP2, a gene involved in speech and language: W Enard et al. (2002)
Nature 418: 869-872

Functional genetic analysis of mouse chromosome 11: BT Kile et al. (2003)
Nature 425: 81-86

In Silico Mapping of Complex Disease-Related Traits in Mice: A Grupe et al. (2001)
Science 292: 1915-1918

Ethical Issues

The ethics of patenting DNA: a discussion paper: Nuffield Council on Bioethics (2002)
Nature Supplement, Nuffield Council on Bioethics, 2002

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Phylogenetics

Gene and Genome Duplication

Duplication, duplication.: A Meyer (2003)
Nature 421: 31-32

Positive selection of a gene family during the emergence of humans and African apes.: ME Johnson et al. (2001)
Nature 413: 514-519

It's all relative.: EA Kellogg (2003)
Nature 422: 383-384

The evolutionary fate and consequences of duplicate genes.: M Lynch, JS Conery (2000)
Science 290: 1151-1154

Genome duplications: the stuff of evolution?: E. Pennisi (2001)
Science 294: 2458-2460

Gene duplication and evolution.: M Lynch (2002)
Science 297: 945-947

Horizontal (Lateral) Gene Transfer

Sequences reveal borrowed genes.: E. Pennisi (2001)
Science 294: 1634-1635

Passages found through labyrinth of bacterial evolution.: E. Pennisi (2003)
Science 301: 745-746

Model Organisms

The mouse that roared.: MS Bogulski (2002)
Nature 420: 525-516

Return of a little squirt.: H Gee (2002)
Nature 420: 755-756

Zebrafish -- the canonical vertebrate: MC Fishman (2001)
Science 294: 1290-1291

Vertebrate genomes compared.: SB Hedges, S Kumar (2002)
Science 297: 1283-1285

Tunicate genome shows a little backbone.: E. Pennisi (2002)
Science 298: 2111-2112

Factors Affecting Rate of Molecular Evolution

Rate of evolution and gene dispensability.: C Pal, B Papp, LD Hurst (2003)
Nature 421: 496-497

Opportunity versus innovation.: PH Harvey, A Purvis (2003)
Nature 425: 676-677

Testing the neutral theory of molecular evolution with genomic data from Drosophila.: JC Fay, GJ Wyckoff, C-I Wu (2002)
Nature 415: 1024-1026

Chromosomal speciation in primates.: LH Rieseberg, K Livingstone (2003)
Science 300: 267-268

Molecular phylogenies link rates of evolution and speciation.: AJ Webster, RJH Payne, M Pagel (2003)
Science 301: 478

Solving Problems with Phylogenetics

Placentals' family tree drawn and quartered.: E. Pennisi (2001)
Science 294: 2266-2268

Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events.: JE Bowers et al. (2003)
Nature 422: 433-438

Single-gene speciation by left-right reversal.: R Ueshima, T Asami (2003)
Nature 425: 679

Hybrid origin of SIV in chimpanzees.: E Bailes et al. (2003)
Science 300: 1713

Phylogenic Analysis Tools

GHOST: a gene homology online search tool.: http://www.hgmp.mrc.ac.uk/
VA Curwen, GW Williams, JBL Bard
Trends in Genetics 16(7): 321-323

Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology.: JP Huelsenbeck et al. (2001)
Science 294: 2310-2314

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Structure-Function Prediction

Structural Genomics

Finding function through structural genomics.: L Shapiro and T Harris (2000)
Current Opinion in Biotechnology 11: 31-35

Protein structure prediction in the postgenomic era.: DT Jones (2000)
Current Opinion in Structural Biology 10: 371-379

Expectations from structural genomics.: SE Brenner and M Levitt (2000)
Protein Science 9: 197-200

X-ray vision in structural genomics.: G Smutzer (2001)
The Scientist 15(12): 28-29

Structure determination of biological macromolecules in solution using nuclear magnetic resonance spectroscopy.: G Wider (2000)
BioTechniques 29: 1278-1294

Tapping DNA for structures produces a trickle.: RF Service (2002)
Science 298: 948-950

Classification, Motifs & Domains

The structure of the protein universe and genome evolution.: EV Koonin et al. (2002)
Nature 420: 218-223

A 'periodic table' for protein structures.: WR Taylor (2002)
Nature 416: 657-660

Protein Folding

Do proteins predate DNA?: SJ Freeland et al. (1999)
Science 286(5440): 690-692

A surprising simplicity to protein folding.: D Baker (2000)
Nature 405: 39-42

Polymer principles and protein folding.: KA Dill (2000)
Protein Science 8: 1166-1180

Three key residues form a critical contact network in a protein folding transition state.: M Vendruscolo et al. (2001)
Nature 409: 641-645

Structure Prediction & Modeling

From fold to function.: J Moult and E Melamud (2000)
Current Opinion in Structural Biology 10: 384-389

Protein structure prediction and structural genomics.: D Baker and A Sali (2001)
Science 294: 93-96

Alignment algorithm for homology modeling and threading.: NN Alexandrov and R Luethy (1998)
Protein Science 7: 254-258

A normalized root-mean-square distance for comparing protein three-dimensional structures.: O Carugo and S Pongor (2001)
Protein Science 10: 1470-1473

In search of more accurate alignments in the twilight zone.: L Jaroszewski, W Li and A Godzik (2002)
Protein Science 11: 1702-1713

Visualization, Analysis & Databases

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.: S Altschul, T Madden, A Schaffer, J Zhang, Z Zhang, W Miller and D Lipman (1997)
Nucleic Acids Research 25(17): 3389-3402

The quest to deduce protein function from sequence: The role of pattern databases.: TK Attwood (1999)
Int. J Biochem. Cell Biol. 32: 139-155

Molecular modeling on the web.: S Ranganathan (2001)
BioTechniques 30(1): 50-52

An Introduction to Molecular Visualization: Seeing in Stereo with RasMol.: RM Horton (1997)
BioTechniques 22(4): 874-876

Scripting Wizards for Chime and RasMol: RM Horton (1999)
BioTechniques 26(5): 874-876

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Networks and Data Mining

Pharmacogenomics

Drug discovery: a historical perspective.: J Drews (2000)
Science 287: 1960-1964

Data Mining

Gene expression data mining: new tools help researchers cope with information overload.: G Dutton (2002)
The Scientist 16(20): 50

MedMiner: an internet text-mining tool for biomedical information, with application to gene expression profiling.: L Tanabe et al. (1999)
BioTechniques 27: 1210-1217

Cluster analysis and display of genome-wide expression patterns.: MB Eisen et al. (1998)
Proc. Natl. Acad. Sci. USA 95: 14863-14868

Microarrays--guilt by association.: J Quackenbush (2003)
Science 302: 240-241

A gene-coexpression network for global discovery of conserved genetic modules.: JM Stuart et al. (2003)
Science 302: 249-255

Protein Interaction Networks

Protein complexes take the bait.: A Kumar and M Snyder (2002)
Nature 415: 123-124

Probing protein interactions.: L DeFrancesco (2002)
The Scientist 16(8): 28

A bayesian networks approach for predicting protein-protein interactions from genomic data.: R Jansen et al. (2003)
Science 302: 449-453

DIP, the database of interacting proteins: a research tool for studying cellular networks of protein interactions.: I Xenarios et al. (2002)
Nucleic Acids Research 30(1): 303-305

Evolutionary Rate in the Protein Interaction Network.: HB Fraser et al. (2002)
Science 296: 750-752

Metabolism meets death.: J Downward (2003)
Nature 424: 896-897

Integrated Systems

The digital code of DNA.: L Hood and D Galas
Nature 421: 444-448

From sequence to biology: the impact on bioinformatics: R Fuchs (2002)
Bioinformatics 18(4): 505-506

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Updated on 12/09/2003 by bchapman@classroomtools.com.