Table of Contents

Forum

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Mouse SNPs for evolutionary biology: Beware of ascertainment biases
- Pierre Boursot and
- Khalid Belkhir
Genome Res. October 2006 16: 1191-1192; doi:10.1101/gr.5541806
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Regions of high differentiation—Worth a check
- Bettina Harr
Genome Res. October 2006 16: 1193-1194; doi:10.1101/gr.5787706

PERSPECTIVE

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Ultrasensitive RNA profiling: Counting single molecules on microarrays
- Kalim U. Mir
Genome Res. October 2006 16: 1195-1197; Published in Advance September 8, 2006, doi:10.1101/gr.5825506

LETTERS

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Mapping of the juxtacentromeric heterochromatin-euchromatin frontier of human chromosome 21
- Christoph Grunau,
- Jérome Buard,
- Marie-Elisabeth Brun,
- and Albertina De Sario
Genome Res. October 2006 16: 1198-1207; Published in Advance September 8, 2006, doi:10.1101/gr.5440306
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Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire
- Ali Mortazavi,
- Evonne Chen Leeper Thompson,
- Sarah T. Garcia,
- Richard M. Myers,
- and Barbara Wold
Genome Res. October 2006 16: 1208-1221; Published in Advance September 8, 2006, doi:10.1101/gr.4997306
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Common fragile sites are conserved features of human and mouse chromosomes and relate to large active genes
- Anne Helmrich,
- Karen Stout-Weider,
- Klaus Hermann,
- Evelin Schrock,
- and Thomas Heiden
Genome Res. October 2006 16: 1222-1230; Published in Advance September 5, 2006, doi:10.1101/gr.5335506
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Genomic organization of the Drosophila telomere retrotransposable elements
- Janet A. George,
- P. Gregory DeBaryshe,
- Karen L. Traverse,
- Susan E. Celniker,
- and Mary-Lou Pardue
Genome Res. October 2006 16: 1231-1240; Published in Advance September 8, 2006, doi:10.1101/gr.5348806
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Uneven chromosome contraction and expansion in the maize genome
- Rémy Bruggmann,
- Arvind K. Bharti,
- Heidrun Gundlach,
- Jinsheng Lai,
- Sarah Young,
- Ana C. Pontaroli,
- Fusheng Wei,
- Georg Haberer,
- Galina Fuks,
- Chunguang Du,
- Christina Raymond,
- Matt C. Estep,
- Renyi Liu,
- Jeffrey L. Bennetzen,
- Agnes P. Chan,
- Pablo D. Rabinowicz,
- John Quackenbush,
- W. Brad Barbazuk,
- Rod A. Wing,
- Bruce Birren,
- Chad Nusbaum,
- Steve Rounsley,
- Klaus F.X. Mayer,
- and Joachim Messing
Genome Res. October 2006 16: 1241-1251; Published in Advance August 10, 2006, doi:10.1101/gr.5338906
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Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium
- Jennifer S. Hawkins,
- HyeRan Kim,
- John D. Nason,
- Rod A. Wing,
- and Jonathan F. Wendel
Genome Res. October 2006 16: 1252-1261; Published in Advance September 5, 2006, doi:10.1101/gr.5282906
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Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice
- Benoit Piegu,
- Romain Guyot,
- Nathalie Picault,
- Anne Roulin,
- Abhijit Saniyal,
- Hyeran Kim,
- Kristi Collura,
- Darshan S. Brar,
- Scott Jackson,
- Rod A. Wing,
- and Olivier Panaud
Genome Res. October 2006 16: 1262-1269; Published in Advance September 8, 2006, doi:10.1101/gr.5290206
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Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution
- Scott William Roy and
- David Penny
Genome Res. October 2006 16: 1270-1275; Published in Advance September 8, 2006, doi:10.1101/gr.5410606
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MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant
- Cheng Lu,
- Karthik Kulkarni,
- Frédéric F. Souret,
- Ramesh MuthuValliappan,
- Shivakundan Singh Tej,
- R. Scott Poethig,
- Ian R. Henderson,
- Steven E. Jacobsen,
- Wenzhong Wang,
- Pamela J. Green,
- and Blake C. Meyers
Genome Res. October 2006 16: 1276-1288; Published in Advance September 5, 2006, doi:10.1101/gr.5530106
OPEN ACCESS ARTICLE

Methods

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Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis
- Eugene Berezikov,
- Geert van Tetering,
- Mark Verheul,
- Jose van de Belt,
- Linda van Laake,
- Joost Vos,
- Robert Verloop,
- Marc van de Wetering,
- Victor Guryev,
- Shuji Takada,
- Anton Jan van Zonneveld,
- Hiroyuki Mano,
- Ronald Plasterk,
- and Edwin Cuppen
Genome Res. October 2006 16: 1289-1298; Published in Advance September 5, 2006, doi:10.1101/gr.5159906
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Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements
- Josée Dostie,
- Todd A. Richmond,
- Ramy A. Arnaout,
- Rebecca R. Selzer,
- William L. Lee,
- Tracey A. Honan,
- Eric D. Rubio,
- Anton Krumm,
- Justin Lamb,
- Chad Nusbaum,
- Roland D. Green,
- and Job Dekker
Genome Res. October 2006 16: 1299-1309; Published in Advance September 5, 2006, doi:10.1101/gr.5571506
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Identifying gene regulatory elements by genomic microarray mapping of DNaseI hypersensitive sites
- George A. Follows,
- Pawan Dhami,
- Berthold Göttgens,
- Alexander W. Bruce,
- Peter J. Campbell,
- Shane C. Dillon,
- Aileen M. Smith,
- Christoph Koch,
- Ian J. Donaldson,
- Mike A. Scott,
- Ian Dunham,
- Mary E. Janes,
- David Vetrie,
- and Anthony R. Green
Genome Res. October 2006 16: 1310-1319; Published in Advance September 8, 2006, doi:10.1101/gr.5373606
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Inference of population genetic parameters in metagenomics: A clean look at messy data
- Philip L.F. Johnson and
- Montgomery Slatkin
Genome Res. October 2006 16: 1320-1327; Published in Advance September 5, 2006, doi:10.1101/gr.5431206

Forum

Mouse SNPs for evolutionary biology: Beware of ascertainment biases

Regions of high differentiation—Worth a check

PERSPECTIVE

Ultrasensitive RNA profiling: Counting single molecules on microarrays

LETTERS

Mapping of the juxtacentromeric heterochromatin-euchromatin frontier of human chromosome 21

Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire

Common fragile sites are conserved features of human and mouse chromosomes and relate to large active genes

Genomic organization of the Drosophila telomere retrotransposable elements

Uneven chromosome contraction and expansion in the maize genome

Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium

Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice

Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution

MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant

Methods

Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis

Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements

Identifying gene regulatory elements by genomic microarray mapping of DNaseI hypersensitive sites

Inference of population genetic parameters in metagenomics: A clean look at messy data

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