Volume 23, Issue 12 | December 2013

Perspective
- - Functional transcriptomics in the post-ENCODE era
    Jonathan M. Mudge
    Adam Frankish
    Jennifer Harrow
    First Published October 30, 2013
Research
- - The influence of genomic context on mutation patterns in the human genome inferred from rare variants
    Valerie M. Schaibley
    Matthew Zawistowski
    Daniel Wegmann
    Margaret G. Ehm
    Matthew R. Nelson
    Pamela L. St. Jean
    ...[+1 authors]...,
    Gonçalo R. Abecasis
    John Novembre
    Sebastian Zöllner
    Jun Z. Li
    First Published August 29, 2013
  - Derived variants at six genes explain nearly half of size reduction in dog breeds
    Maud Rimbault
    Holly C. Beale
    Jeffrey J. Schoenebeck
    Barbara C. Hoopes
    Jeremy J. Allen
    First Published September 11, 2013
  - Identifying multiple causative genes at a single GWAS locus
    Michael J. Flister
    Shirng-Wern Tsaih
    Caitlin C. O'Meara
    Bradley Endres
    Matthew J. Hoffman
    Aron M. Geurts
    ...[+1 authors]...,
    Melinda R. Dwinell
    Jozef Lazar
    Howard J. Jacob
    Carol Moreno
    First Published September 4, 2013
  - The shared genomic architecture of human nucleolar organizer regions
    Ioanna Floutsakou
    Saumya Agrawal
    Thong T. Nguyen
    Cathal Seoighe
    Austen R.D. Ganley
    First Published August 29, 2013
  - Disclosing the crosstalk among DNA methylation, transcription factors, and histone marks in human pluripotent cells through discovery of DNA methylation motifs
    Phuc-Loi Luu
    Hans R. Schöler
    Marcos J. Araúzo-Bravo
    First Published October 22, 2013
  - DNA methylation profiling in human B cells reveals immune regulatory elements and epigenetic plasticity at Alu elements during B-cell activation
    Anne Y. Lai
    Deepak Mav
    Ruchir Shah
    Sara A. Grimm
    Dhiral Phadke
    Katerina Hatzi Ari Melnick
    ...[+2 authors]...,
    Cissy Geigerman
    Steve E. Sobol
    David L. Jaye
    Paul A. Wade
    First Published September 6, 2013
  - Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division
    Alexej Abyzov
    Rebecca Iskow
    Omer Gokcumen
    David W. Radke
    Suganthi Balasubramanian
    First Published September 11, 2013
  - H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction
    Gillian C.A. Taylor
    Ragnhild Eskeland
    Betül Hekimoglu-Balkan
    Madapura M. Pradeepa
    Wendy A. Bickmore
    First Published August 29, 2013
  - Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments
    Vlad C. Seitan
    Andre J. Faure
    Ye Zhan
    Rachel Patton McCord
    Bryan R. Lajoie
    Elizabeth Ing-Simmons Boris Lenhard Luca Giorgetti Edith Heard
    ...[+4 authors]...,
    Amanda G. Fisher
    Paul Flicek
    Job Dekker
    Matthias Merkenschlager
    First Published September 3, 2013
  - 3′ UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts
    Noah Spies
    Christopher B. Burge
    David P. Bartel
    First Published September 26, 2013
  - Distinct global shifts in genomic binding profiles of limb malformation-associated HOXD13 mutations
    Daniel M. Ibrahim
    Peter Hansen
    Christian Rödelsperger
    Asita C. Stiege
    Sandra C. Doelken
    Denise Horn Marten Jäger Catrin Janetzki Peter Krawitz Gundula Leschik Florian Wagner Till Scheuer Mareen Schmidt-von Kegler Petra Seemann
    ...[+9 authors]...,
    Bernd Timmermann
    Peter N. Robinson
    Stefan Mundlos
    Jochen Hecht
    First Published August 30, 2013
  - The altered landscape of the human skin microbiome in patients with primary immunodeficiencies
    Julia Oh
    Alexandra F. Freeman
    Morgan Park
    Robert Sokolic
    Fabio Candotti
    First Published October 29, 2013
Methods
- - Single-cell mutational profiling and clonal phylogeny in cancer
    Nicola E. Potter
    Luca Ermini
    Elli Papaemmanuil
    Giovanni Cazzaniga
    Gowri Vijayaraghavan
    Ian Titley
    ...[+1 authors]...,
    Anthony Ford
    Peter Campbell
    Lyndal Kearney
    Mel Greaves
    First Published September 20, 2013
  - Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing
    Hongshan Guo
    Ping Zhu
    Xinglong Wu
    Xianlong Li
    Lu Wen
    First Published October 31, 2013
Resources
- - Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps
    Ali Mortazavi
    Shirley Pepke
    Camden Jansen
    Georgi K. Marinov
    Jason Ernst
    First Published October 29, 2013
  - Quantitative interaction screen of telomeric repeat-containing RNA reveals novel TERRA regulators
    Marion Scheibe
    Nausica Arnoult
    Dennis Kappei
    Frank Buchholz
    Anabelle Decottignies
    First Published August 6, 2013
Author Index
- - Author Index, Volume 23, 2013
    First Published December 2, 2013
Reviewer Index
- - Reviewer Index, Volume 23, 2013
    First Published December 2, 2013

Table of Contents

Volume 23, Issue 12 | December 2013

Perspective

Functional transcriptomics in the post-ENCODE era

Research

The influence of genomic context on mutation patterns in the human genome inferred from rare variants

Derived variants at six genes explain nearly half of size reduction in dog breeds

Identifying multiple causative genes at a single GWAS locus

The shared genomic architecture of human nucleolar organizer regions

Disclosing the crosstalk among DNA methylation, transcription factors, and histone marks in human pluripotent cells through discovery of DNA methylation motifs

DNA methylation profiling in human B cells reveals immune regulatory elements and epigenetic plasticity at Alu elements during B-cell activation

Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division

H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction

Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments

3′ UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts

Distinct global shifts in genomic binding profiles of limb malformation-associated HOXD13 mutations

The altered landscape of the human skin microbiome in patients with primary immunodeficiencies

Methods

Single-cell mutational profiling and clonal phylogeny in cancer

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

Resources

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps

Quantitative interaction screen of telomeric repeat-containing RNA reveals novel TERRA regulators

Author Index

Author Index, Volume 23, 2013

Reviewer Index

Reviewer Index, Volume 23, 2013

Table of Contents

Volume 23, Issue 12 | December 2013

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Perspective

Research

Methods

Resources

Author Index

Reviewer Index