Table of Contents

ARTICLES

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An Evolutionary Analysis of Orphan Genes in Drosophila
- Tomislav Domazet-Loso and
- Diethard Tautz
Genome Res. October 2003 13: 2213-2219; doi:10.1101/gr.1311003
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Extensive Exon Reshuffling Over Evolutionary Time Coupled to Trans-Splicing in Drosophila
- Mariano Labrador and
- Victor G. Corces
Genome Res. October 2003 13: 2220-2228; doi:10.1101/gr.1440703

LETTERS

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Gene Loss, Protein Sequence Divergence, Gene Dispensability, Expression Level, and Interactivity Are Correlated in Eukaryotic Evolution
- Dmitri M. Krylov,
- Yuri I. Wolf,
- Igor B. Rogozin,
- and Eugene V. Koonin
Genome Res. October 2003 13: 2229-2235; doi:10.1101/gr.1589103
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Mystery of Intron Gain
- Alexei Fedorov,
- Scott Roy,
- Larisa Fedorova,
- and Walter Gilbert
Genome Res. October 2003 13: 2236-2241; Published in Advance January 1, 2003, doi:10.1101/gr.1029803
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Two Distinct Modes of Microsatellite Mutation Processes: Evidence From the Complete Genomic Sequences of Nine Species
- Daniel Dieringer and
- Christian Schlötterer
Genome Res. October 2003 13: 2242-2251; doi:10.1101/gr.1416703
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Adaptive Evolution of MRG, a Neuron-Specific Gene Family Implicated in Nociception
- Sun Shim Choi and
- Bruce T. Lahn
Genome Res. October 2003 13: 2252-2259; doi:10.1101/gr.1431603
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The Signature of Selection Mediated by Expression on Human Genes
- Araxi O. Urrutia and
- Laurence D. Hurst
Genome Res. October 2003 13: 2260-2264; Published in Advance January 1, 2003, doi:10.1101/gr.641103
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The Secreted Protein Discovery Initiative (SPDI), a Large-Scale Effort to Identify Novel Human Secreted and Transmembrane Proteins: A Bioinformatics Assessment
- Hilary F. Clark,
- Austin L. Gurney,
- Evangeline Abaya,
- Kevin Baker,
- Daryl Baldwin,
- Jennifer Brush,
- Jian Chen,
- Bernard Chow,
- Clarissa Chui,
- Craig Crowley,
- Bridget Currell,
- Bethanne Deuel,
- Patrick Dowd,
- Dan Eaton,
- Jessica Foster,
- Christopher Grimaldi,
- Qimin Gu,
- Philip E. Hass,
- Sherry Heldens,
- Arthur Huang,
- Hok Seon Kim,
- Laura Klimowski,
- Yisheng Jin,
- Stephanie Johnson,
- James Lee,
- Lhney Lewis,
- Dongzhou Liao,
- Melanie Mark,
- Edward Robbie,
- Celina Sanchez,
- Jill Schoenfeld,
- Somasekar Seshagiri,
- Laura Simmons,
- Jennifer Singh,
- Victoria Smith,
- Jeremy Stinson,
- Alicia Vagts,
- Richard Vandlen,
- Colin Watanabe,
- David Wieand,
- Kathryn Woods,
- Ming-Hong Xie,
- Daniel Yansura,
- Sothy Yi,
- Guoying Yu,
- Jean Yuan,
- Min Zhang,
- Zemin Zhang,
- Audrey Goddard,
- William I. Wood,
- and Paul Godowski
Genome Res. October 2003 13: 2265-2270; Published in Advance January 1, 2003, doi:10.1101/gr.1293003
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Single Nucleotide Variation Analysis in 65 Candidate Genes for CNS Disorders in a Representative Sample of the European Population
- Yun Freudenberg-Hua,
- Jan Freudenberg,
- Nadine Kluck,
- Sven Cichon,
- Peter Propping,
- and Markus M. Nöthen
Genome Res. October 2003 13: 2271-2276; doi:10.1101/gr.1299703
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Ethnic India: A Genomic View, With Special Reference to Peopling and Structure
- Analabha Basu,
- Namita Mukherjee,
- Sangita Roy,
- Sanghamitra Sengupta,
- Sanat Banerjee,
- Madan Chakraborty,
- Badal Dey,
- Monami Roy,
- Bidyut Roy,
- Nitai P. Bhattacharyya,
- Susanta Roychoudhury,
- and Partha P. Majumder
Genome Res. October 2003 13: 2277-2290; doi:10.1101/gr.1413403
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Representational Oligonucleotide Microarray Analysis: A High-Resolution Method to Detect Genome Copy Number Variation
- Robert Lucito,
- John Healy,
- Joan Alexander,
- Andrew Reiner,
- Diane Esposito,
- Maoyen Chi,
- Linda Rodgers,
- Amy Brady,
- Jonathan Sebat,
- Jennifer Troge,
- Joseph A. West,
- Seth Rostan,
- Ken C.Q. Nguyen,
- Scott Powers,
- Kenneth Q. Ye,
- Adam Olshen,
- Ennapadam Venkatraman,
- Larry Norton,
- and Michael Wigler
Genome Res. October 2003 13: 2291-2305; Published in Advance January 1, 2003, doi:10.1101/gr.1349003

Methods

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Annotating Large Genomes With Exact Word Matches
- John Healy,
- Elizabeth E. Thomas,
- Jacob T. Schwartz,
- and Michael Wigler
Genome Res. October 2003 13: 2306-2315; Published in Advance January 1, 2003, doi:10.1101/gr.1350803
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DNA Enrichment by Allele-Specific Hybridization (DEASH): A Novel Method for Haplotyping and for Detecting Low-Frequency Base Substitutional Variants and Recombinant DNA Molecules
- Alec J. Jeffreys and
- Celia A. May
Genome Res. October 2003 13: 2316-2324; doi:10.1101/gr.1214603
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Adenoviral Vectors Expressing siRNAs for Discovery and Validation of Gene Function
- Gert-Jan Arts,
- Ellen Langemeijer,
- Rudi Tissingh,
- Libin Ma,
- Heidi Pavliska,
- Kristina Dokic,
- Richele Dooijes,
- Emir Mešić,
- Remko Clasen,
- Frits Michiels,
- Jan van der Schueren,
- Mark Lambrecht,
- Sofie Herman,
- Reginald Brys,
- Kim Thys,
- Marcel Hoffmann,
- Peter Tomme,
- and Helmuth van Es
Genome Res. October 2003 13: 2325-2332; Published in Advance January 1, 2003, doi:10.1101/gr.1332603
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High-Throughput Selection of Effective RNAi Probes for Gene Silencing
- Rajeev Kumar,
- Douglas S. Conklin,
- and Vivek Mittal
Genome Res. October 2003 13: 2333-2340; doi:10.1101/gr.1575003
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RNAi Microarray Analysis in Cultured Mammalian Cells
- Spyro Mousses,
- Natasha J. Caplen,
- Robert Cornelison,
- Don Weaver,
- Mark Basik,
- Sampsa Hautaniemi,
- Abdel G. Elkahloun,
- Roberto A. Lotufo,
- Ashish Choudary,
- Edward R. Dougherty,
- Ed Suh,
- and Olli Kallioniemi
Genome Res. October 2003 13: 2341-2347; doi:10.1101/gr.1478703
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Microfabricated Fountain Pens for High-Density DNA Arrays
- Matthew O. Reese,
- R. Michae van Dam,
- Axel Scherer,
- and Stephen R. Quake
Genome Res. October 2003 13: 2348-2352; Published in Advance January 1, 2003, doi:10.1101/gr.623903
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Comprehensive Analysis of Orthologous Protein Domains Using the HOPS Database
- Christian E.V. Storm and
- Erik L.L. Sonnhammer
Genome Res. October 2003 13: 2353-2362; doi:10.1101/gr1305203

RESOURCE

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Development of Human Protein Reference Database as an Initial Platform for Approaching Systems Biology in Humans
- Suraj Peri,
- J. Daniel Navarro,
- Ramars Amanchy,
- Troels Z. Kristiansen,
- Chandra Kiran Jonnalagadda,
- Vineeth Surendranath,
- Vidya Niranjan,
- Babylakshmi Muthusamy,
- T.K.B. Gandhi,
- Mads Gronborg,
- Nieves Ibarrola,
- Nandan Deshpande,
- K. Shanker,
- H.N. Shivashankar,
- B.P. Rashmi,
- M.A. Ramya,
- Zhixing Zhao,
- K.N. Chandrika,
- N. Padma,
- H.C. Harsha,
- A.J. Yatish,
- M.P. Kavitha,
- Minal Menezes,
- Dipanwita Roy Choudhury,
- Shubha Suresh,
- Neelanjana Ghosh,
- R. Saravana,
- Sreenath Chandran,
- Subhalakshmi Krishna,
- Mary Joy,
- Sanjeev K. Anand,
- V. Madavan,
- Ansamma Joseph,
- Guang W. Wong,
- William P. Schiemann,
- Stefan N. Constantinescu,
- Lily Huang,
- Roya Khosravi-Far,
- Hanno Steen,
- Muneesh Tewari,
- Saghi Ghaffari,
- Gerard C. Blobe,
- Chi V. Dang,
- Joe G.N. Garcia,
- Jonathan Pevsner,
- Ole N. Jensen,
- Peter Roepstorff,
- Krishna S. Deshpande,
- Arul M. Chinnaiyan,
- Ada Hamosh,
- Aravinda Chakravarti,
- and Akhilesh Pandey
Genome Res. October 2003 13: 2363-2371; doi:10.1101/gr.1680803

ARTICLES

An Evolutionary Analysis of Orphan Genes in Drosophila

Extensive Exon Reshuffling Over Evolutionary Time Coupled to Trans-Splicing in Drosophila

LETTERS

Gene Loss, Protein Sequence Divergence, Gene Dispensability, Expression Level, and Interactivity Are Correlated in Eukaryotic Evolution

Mystery of Intron Gain

Two Distinct Modes of Microsatellite Mutation Processes: Evidence From the Complete Genomic Sequences of Nine Species

Adaptive Evolution of MRG, a Neuron-Specific Gene Family Implicated in Nociception

The Signature of Selection Mediated by Expression on Human Genes

The Secreted Protein Discovery Initiative (SPDI), a Large-Scale Effort to Identify Novel Human Secreted and Transmembrane Proteins: A Bioinformatics Assessment

Single Nucleotide Variation Analysis in 65 Candidate Genes for CNS Disorders in a Representative Sample of the European Population

Ethnic India: A Genomic View, With Special Reference to Peopling and Structure

Representational Oligonucleotide Microarray Analysis: A High-Resolution Method to Detect Genome Copy Number Variation

Methods

Annotating Large Genomes With Exact Word Matches

DNA Enrichment by Allele-Specific Hybridization (DEASH): A Novel Method for Haplotyping and for Detecting Low-Frequency Base Substitutional Variants and Recombinant DNA Molecules

Adenoviral Vectors Expressing siRNAs for Discovery and Validation of Gene Function

High-Throughput Selection of Effective RNAi Probes for Gene Silencing

RNAi Microarray Analysis in Cultured Mammalian Cells

Microfabricated Fountain Pens for High-Density DNA Arrays

Comprehensive Analysis of Orthologous Protein Domains Using the HOPS Database

RESOURCE

Development of Human Protein Reference Database as an Initial Platform for Approaching Systems Biology in Humans

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