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Volume 30 Issue 1, January 2012

Structural models of chromosomes in nuclei on background image of raw experimental data. Kalhor et al. describe advances in mapping chromosome contacts and representing the resulting data as a population of structural models (p 90). Credit: Ian M. Slaymaker, Reza Kalhor and Harianto Tjong (three-dimensional rendering), and Marina Corral.

Volume 30 Issue 1

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Editorial

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News

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Data Page

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Opinion

  • The NIH's proposed initiatives in translational science deserve solid financial backing from legislators and vocal support from the biomedical community.

    • John C Reed
    • E Lucile White
    • Stuart Schreiber
    Opinion

  • By devoting funding to whole-genome studies, such as epigenetic and copy-number variation in stem cells, research on new genomic technology, and standards for methodologies and data collection/sharing, CIRM can spur both basic and translational research.

    • Natalie D DeWitt
    • Michael P Yaffe
    • Alan Trounson
    Opinion
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News Feature

  • In spite of its modest performance in clinical trials, Benlysta may offer effective relief against lupus. But physicians are still working to identify the right patients. Michael Eisenstein reports.

    • Michael Eisenstein
    News Feature
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Bioentrepreneur

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Correspondence

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Feature

  • As R&D costs spiral for drug developers, disruptive approaches to clinical trial design and management are gaining traction. Get ready for electronic data capture, precompetitive data sharing, virtual trials and a variety of bold new paradigms.

    • Malorye Allison
    Feature
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Patents

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News & Views

  • A new computational approach gives us the best chance at understanding how genomes are arranged in three-dimensional space and what that may mean for their function.

    • Tom Misteli
    News & Views

  • A differentiation protocol guided by developmental principles produces more-authentic dopaminergic neurons for transplantation in patients.

    • Olle Lindvall
    News & Views

  • An additional layer of RNA regulation in which RNAs encoded by genes and pseudogenes compete for microRNAs could offer new opportunities for oligonucleotide therapeutics.

    • Anastasia Khvorova
    • Alexey Wolfson
    News & Views
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Research Highlights

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Analysis

  • Data filters separate true genetic variants in sequencing data from sequencing errors, but their effectiveness is difficult to assess. Reumers et al. use the genome sequences of monozygotic twins to evaluate the performance of filters individually and in combination, leading to a 290-fold reduction in error rate in calling single-nucleotide variants.

    • Joke Reumers
    • Peter De Rijk
    • Jurgen Del-Favero
    Analysis
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Perspective

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Analysis

  • Over 90% of human whole-genome sequencing has been performed using instruments from two companies, Illumina and Complete Genomics. Lam et al. sequence the same DNA samples with both instruments and compare their performance for calling insertions, deletions and single-nucleotide variants.

    • Hugo Y K Lam
    • Michael J Clark
    • Michael Snyder
    Analysis
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Article

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Letter

  • Rare transcripts remain enigmatic in part because they are difficult to detect robustly on a large scale. Mercer et al. show that targeted RNA sequencing after array capture can reach saturating depth at the targeted loci and reveal unprecedented levels of rare noncoding transcripts and previously unrecognized spliced variants from important loci such as p53 and HOX.

    • Tim R Mercer
    • Daniel J Gerhardt
    • John L Rinn
    Letter
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Resource

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Erratum

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Corrigendum

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Careers and Recruitment

  • To provide formal education and training required for PhDs to perform their complex, multidisciplinary job functions, traditional PhD curricula should be restructured to include mandatory professional development course work.

    • Nathan L Vanderford
    Careers and Recruitment

  • Careers and Recruitment
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