Volume 21, Issue 3 | March 2011

Research
- - Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection
    Asger Hobolth
    Julien Y. Dutheil
    John Hawks
    Mikkel H. Schierup
    Thomas Mailund
    First Published January 26, 2011
  - Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication
    Julien Roux
    Marc Robinson-Rechavi
    First Published December 20, 2010
  - Interactome mapping suggests new mechanistic details underlying Alzheimer's disease
    Montserrat Soler-López
    Andreas Zanzoni
    Ricart Lluís
    Ulrich Stelzl
    Patrick Aloy
    First Published December 16, 2010
  - Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription
    Larry D. Mesner
    Veena Valsakumar
    Neerja Karnani
    Anindya Dutta
    Joyce L. Hamlin
    First Published December 20, 2010
  - Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation
    Joanna Y. Ip
    Dominic Schmidt
    Qun Pan
    Arun K. Ramani
    Andrew G. Fraser
    First Published December 16, 2010
  - Clcn4-2 genomic structure differs between the X locus in Mus spretus and the autosomal locus in Mus musculus: AT motif enrichment on the X
    Di Kim Nguyen
    Fan Yang
    Rajinder Kaul
    Can Alkan
    Anthony Antonellis
    First Published January 31, 2011
  - Nucleotide composition-linked divergence of vertebrate core promoter architecture
    Simon J. van Heeringen
    Waseem Akhtar
    Ulrike G. Jacobi
    Robert C. Akkers
    Yutaka Suzuki
    First Published January 10, 2011
  - Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch
    Angel Carlos Román
    Francisco J. González-Rico
    Eduardo Moltó
    Henar Hernando
    Ana Neto
    Cristina Vicente-Garcia Esteban Ballestar José L. Gómez-Skarmeta
    ...[+3 authors]...,
    Jana Vavrova-Anderson
    Robert J. White
    Lluís Montoliu
    Pedro M. Fernández-Salguero
    First Published February 3, 2011
  - Genome-scale RNAi on living-cell microarrays identifies novel regulators of Drosophila melanogaster TORC1–S6K pathway signaling
    Robert A. Lindquist
    Kathleen A. Ottina
    Douglas B. Wheeler
    Peggy P. Hsu
    Carson C. Thoreen
    David A. Guertin Siraj M. Ali Shomit Sengupta Yoav D. Shaul Michael R. Lamprecht Katherine L. Madden
    ...[+6 authors]...,
    Adam R. Papallo
    Thouis R. Jones
    David M. Sabatini
    Anne E. Carpenter
    First Published January 14, 2011
Methods
- - Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
    Roger Pique-Regi
    Jacob F. Degner
    Athma A. Pai
    Daniel J. Gaffney
    Yoav Gilad
    First Published November 24, 2010
  - High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells
    Alan P. Boyle
    Lingyun Song
    Bum-Kyu Lee
    Darin London
    Damian Keefe
    First Published November 24, 2010
  - A novel approach identifies new differentially methylated regions (DMRs) associated with imprinted genes
    Sanaa Choufani
    Jonathan S. Shapiro
    Martha Susiarjo
    Darci T. Butcher
    Daria Grafodatskaya
    Youliang Lou Jose C. Ferreira Dalila Pinto Stephen W. Scherer Lisa G. Shaffer Philippe Coullin Isabella Caniggia
    ...[+7 authors]...,
    Joseph Beyene
    Rima Slim
    Marisa S. Bartolomei
    Rosanna Weksberg
    First Published February 7, 2011
  - Selective ploidy ablation, a high-throughput plasmid transfer protocol, identifies new genes affecting topoisomerase I–induced DNA damage
    Robert J.D. Reid
    Sergio González-Barrera
    Ivana Sunjevaric
    David Alvaro
    Samantha Ciccone
    First Published December 20, 2010
Resources
- - Adaptive seeds tame genomic sequence comparison
    Szymon M. Kiełbasa
    Raymond Wan
    Kengo Sato
    Paul Horton
    Martin C. Frith
    First Published January 5, 2011
  - Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
    Brian J. Haas
    Dirk Gevers
    Ashlee M. Earl
    Mike Feldgarden
    Doyle V. Ward
    Georgia Giannoukos Dawn Ciulla Diana Tabbaa Sarah K. Highlander Erica Sodergren Barbara Methé
    ...[+6 authors]...,
    Todd Z. DeSantis
    Joseph F. Petrosino
    Rob Knight
    Bruce W. Birren
    First Published January 6, 2011

Table of Contents

Volume 21, Issue 3 | March 2011

Research

Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection

Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication

Interactome mapping suggests new mechanistic details underlying Alzheimer's disease

Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription

Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation

Clcn4-2 genomic structure differs between the X locus in Mus spretus and the autosomal locus in Mus musculus: AT motif enrichment on the X

Nucleotide composition-linked divergence of vertebrate core promoter architecture

Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch

Genome-scale RNAi on living-cell microarrays identifies novel regulators of Drosophila melanogaster TORC1–S6K pathway signaling

Methods

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

A novel approach identifies new differentially methylated regions (DMRs) associated with imprinted genes

Selective ploidy ablation, a high-throughput plasmid transfer protocol, identifies new genes affecting topoisomerase I–induced DNA damage

Resources

Adaptive seeds tame genomic sequence comparison

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

Table of Contents

Volume 21, Issue 3 | March 2011

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Research

Methods

Resources