Table of Contents

Methods

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Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome
- Ayelet T. Lamm,
- Michael R. Stadler,
- Huibin Zhang,
- Jonathan I. Gent,
- and Andrew Z. Fire
Genome Res. February 2011 21: 265-275; Published in Advance December 22, 2010, doi:10.1101/gr.108845.110
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Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data
- Zhi John Lu,
- Kevin Y. Yip,
- Guilin Wang,
- Chong Shou,
- LaDeana W. Hillier,
- Ekta Khurana,
- Ashish Agarwal,
- Raymond Auerbach,
- Joel Rozowsky,
- Chao Cheng,
- Masaomi Kato,
- David M. Miller,
- Frank Slack,
- Michael Snyder,
- Robert H. Waterston,
- Valerie Reinke,
- and Mark B. Gerstein
Genome Res. February 2011 21: 276-285; Published in Advance December 22, 2010, doi:10.1101/gr.110189.110
OPEN ACCESS ARTICLE
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Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans
- Wei-Jen Chung,
- Phaedra Agius,
- Jakub O. Westholm,
- Michael Chen,
- Katsutomo Okamura,
- Nicolas Robine,
- Christina S. Leslie,
- and Eric C. Lai
Genome Res. February 2011 21: 286-300; Published in Advance December 22, 2010, doi:10.1101/gr.113050.110
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Resources

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The transcriptional diversity of 25 Drosophila cell lines
- Lucy Cherbas,
- Aarron Willingham,
- Dayu Zhang,
- Li Yang,
- Yi Zou,
- Brian D. Eads,
- Joseph W. Carlson,
- Jane M. Landolin,
- Philipp Kapranov,
- Jacqueline Dumais,
- Anastasia Samsonova,
- Jeong-Hyeon Choi,
- Johnny Roberts,
- Carrie A. Davis,
- Haixu Tang,
- Marijke J. van Baren,
- Srinka Ghosh,
- Alexander Dobin,
- Kim Bell,
- Wei Lin,
- Laura Langton,
- Michael O. Duff,
- Aaron E. Tenney,
- Chris Zaleski,
- Michael R. Brent,
- Roger A. Hoskins,
- Thomas C. Kaufman,
- Justen Andrews,
- Brenton R. Graveley,
- Norbert Perrimon,
- Susan E. Celniker,
- Thomas R. Gingeras,
- and Peter Cherbas
Genome Res. February 2011 21: 301-314; Published in Advance December 22, 2010, doi:10.1101/gr.112961.110
OPEN ACCESS ARTICLE
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The Drosophila melanogaster transcriptome by paired-end RNA sequencing
- Bryce Daines,
- Hui Wang,
- Liguo Wang,
- Yumei Li,
- Yi Han,
- David Emmert,
- William Gelbart,
- Xia Wang,
- Wei Li,
- Richard Gibbs,
- and Rui Chen
Genome Res. February 2011 21: 315-324; Published in Advance December 22, 2010, doi:10.1101/gr.107854.110
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A spatial and temporal map of C. elegans gene expression
- W. Clay Spencer,
- Georg Zeller,
- Joseph D. Watson,
- Stefan R. Henz,
- Kathie L. Watkins,
- Rebecca D. McWhirter,
- Sarah Petersen,
- Vipin T. Sreedharan,
- Christian Widmer,
- Jeanyoung Jo,
- Valerie Reinke,
- Lisa Petrella,
- Susan Strome,
- Stephen E. Von Stetina,
- Menachem Katz,
- Shai Shaham,
- Gunnar Rätsch,
- and David M. Miller III
Genome Res. February 2011 21: 325-341; Published in Advance December 22, 2010, doi:10.1101/gr.114595.110
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Genome-wide analysis of alternative splicing in Caenorhabditis elegans
- Arun K. Ramani,
- John A. Calarco,
- Qun Pan,
- Sepand Mavandadi,
- Ying Wang,
- Andrew C. Nelson,
- Leo J. Lee,
- Quaid Morris,
- Benjamin J. Blencowe,
- Mei Zhen,
- and Andrew G. Fraser
Genome Res. February 2011 21: 342-348; Published in Advance December 22, 2010, doi:10.1101/gr.114645.110
OPEN ACCESS ARTICLE

Research

Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin

Chromatin signatures of the Drosophila replication program

Developmental control of the DNA replication and transcription programs

Genome-wide analysis of promoter architecture in Drosophila melanogaster

Conservation of an RNA regulatory map between Drosophila and mammals

Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence

Polycomb preferentially targets stalled promoters of coding and noncoding transcripts

Broad chromosomal domains of histone modification patterns in C. elegans

High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans

Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans

A global analysis of C. elegans trans-splicing

Methods

Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome

Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data

Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans

Resources

The transcriptional diversity of 25 Drosophila cell lines

The Drosophila melanogaster transcriptome by paired-end RNA sequencing

A spatial and temporal map of C. elegans gene expression

Genome-wide analysis of alternative splicing in Caenorhabditis elegans

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