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Nature Biotechnology | Advertisement | | Transfect with Confidence using X-tremeGENE Reagents from Roche
Efficiently transfect DNA or siRNA to power your cell-based applications
- Obtain high numbers of healthy, viable cells
- Achieve high transfection efficiency
- Generate high recombinant protein yields
Minimize cytotoxicity and off-target effects
- Assess true cell response rather than the effects of your transfection reagents
- Generate physiologically relevant data by minimizing reagent-induced changes
To learn more, please visit: X-tremeGENE.roche.com | | | | | |
TABLE OF CONTENTS | September 2014 Volume 32, Issue 9 | | | | | In This Issue Editorial News Bioentrepreneur Opinion and Comment Features News and Views Computational Biology Research Careers and Recruitment
| | | | | | Advertisement | | | | | Advertisement | | | | | | | | | Focus on RNA sequencing quality control (SEQC | | | Research in regenerative medicine is advancing toward the goal of repairing damaged tissue and organs. Nature Biotechnology and Nature Medicine present a collection of reviews, features and commentaries that explore our current mechanistic understanding of stem cells, and the emerging technologies that will bring regenerative medicine to the clinic. | | | | | | Top | | | | In This Issue | Top | | | | Focus on RNA sequencing quality control (SEQC) ppvii - vii doi:10.1038/nbt.3025
| | Editorial | Top | | | | Honing our reading skills p845 doi:10.1038/nbt.3021 Studies from the RNA Sequencing Quality Control (SEQC) initiative exemplify the kind of experimental groundwork needed to expand RNA-seq into a broader array of basic and translational applications.
| | News | Top | | | | First PD-1 inhibitor breezes across finish line pp847 - 848 Cormac Sheridan doi:10.1038/nbt0914-847
| | | | Organs-on-chips Harvard spinout p849 doi:10.1038/nbt0914-849b
| | | | Roche snaps up RNA-medicines firm Santaris p849 doi:10.1038/nbt0914-849c
| | | | Rabbit milk Ruconest for hereditary angioedema p849 doi:10.1038/nbt0914-849d
| | | | Biotech drugs too little, too late for Ebola outbreak pp849 - 850 Stephen Strauss doi:10.1038/nbt0914-849a
| | | | CAR-T cell therapy gets breakthrough status p851 doi:10.1038/nbt0914-851b
| | | | NCATs drug candidate attracts first buyer p851 doi:10.1038/nbt0914-851c
| | | | Sanofi to propel inhalable insulin Afrezza into market pp851 - 852 Jim Kling doi:10.1038/nbt0914-851a
| | | | First-in-class BTK inhibitor Imbruvica gets CLL approval p852 doi:10.1038/nbt0914-852a
| | | | Google Ventures launches London office p852 doi:10.1038/nbt0914-852b
| | | | Small biotech steers HDAC inhibitor to clinic pp853 - 854 Mark Ratner doi:10.1038/nbt0914-853
| | | | Around the world in a month p854 doi:10.1038/nbt0914-854
| | | | FDA pushes for control over laboratory-developed tests p855 Mark Ratner doi:10.1038/nbt0914-855a
| | | | Bioelectronics SPARC at NIH p855 doi:10.1038/nbt0914-855b
| | | | First biosimilars trickle into US pathway p855 doi:10.1038/nbt0914-855c
| | | | Novartis signs up for Google smart lens p856 Melanie Senior doi:10.1038/nbt0914-856
| | | | Vitamin A Super Banana in human trials p857 Emily Waltz doi:10.1038/nbt0914-857
| | | | RAC to finally relax gene therapy oversight p858 Asher Mullard doi:10.1038/nbt0914-858
| | | | News Feature | | | | Stepping into the sunshine pp859 - 862 Charles Schmidt doi:10.1038/nbt.3008 Is the imminent release of the database of industry's 'gifts' to doctors cause for concern or celebration? Charles Schmidt investigates.
| Advertisement | Nobel Laureate to Give Keynote Address at The International Symposium for Tissue Phenomics™ Hear Dr. Gerd Binnig, Nobel Laureate, Founder, and Chief Technology Officer at Definiens, present on Tissue Phenomics™ and how tissue images can be turned into big data for robust correlation to clinical outcomes. Register today to join us October 17-18 in San Francisco. | | | | Bioentrepreneur | Top | | | | Building a business | | | | Building a curriculum for bioentrepreneurs pp863 - 865 Lynn Johnson Langer doi:10.1038/nbt.3012
| | | | SciCafé | | | | Startups on the menu: Alnylam p866 doi:10.1038/nbt.3009
| | Opinion and Comment | Top | | | | Correspondence | | | | OpenBiome remains open to serve the medical community p867 Mark Smith, Zain Kassam, Carolyn Edelstein, James Burgess and Eric Alm doi:10.1038/nbt.3006
| | | | Field trial of Xanthomonas wilt disease-resistant bananas in East Africa pp868 - 870 Leena Tripathi, Jaindra Nath Tripathi, Andrew Kiggundu, Sam Korie, Frank Shotkoski et al. doi:10.1038/nbt.3007
| | | | Commentary | | | | Scientific rigor and the art of motorcycle maintenance pp871 - 873 Marcus Munafo, Simon Noble, William J Browne, Dani Brunner, Katherine Button et al. doi:10.1038/nbt.3004 The reliability of scientific research is under scrutiny. A recently convened working group proposes cultural adjustments to incentivize better research practices.
| | | | The special case of gene therapy pricing pp874 - 876 Troyen A Brennan and James M Wilson doi:10.1038/nbt.3003 Gene therapy companies that pursue high, one-time payments for their products risk a backlash from payors. A better solution may lie in a pay-for-performance model.
| | Features | Top | | | | Patents | | | | Patents or patients: who loses? pp877 - 880 Joanna Brougher and Konstantin M Linnik doi:10.1038/nbt.3005 The unprecedented weakening of patent rights in the United States undermines necessary incentives for the discovery and development of innovative medicines.
| | | | Recent patent applications in differential gene expression p881 doi:10.1038/nbt.3023
| | News and Views | Top | | | | | | Computational Biology | Top | | | | Analysis | | | | Detecting and correcting systematic variation in large-scale RNA sequencing data pp888 - 895 Sheng Li, Pawel P Labaj, Paul Zumbo, Peter Sykacek, Wei Shi et al. doi:10.1038/nbt.3000 Li et al. identify the top-performing methods to improve cross-site differential gene expression analysis with RNA-seq.
See also: News and Views by Kratz & Carninci | News and Views by Van Keuren-Jensen et al.
| | | | Normalization of RNA-seq data using factor analysis of control genes or samples pp896 - 902 Davide Risso, John Ngai, Terence P Speed and Sandrine Dudoit doi:10.1038/nbt.2931 Remove unwanted variation (RUV) is a new statistical method for RNA-seq data normalization that uses control genes or samples to improve differential expression analysis.
See also: News and Views by Kratz & Carninci | News and Views by Van Keuren-Jensen et al.
| | Research | Top | | | | Articles | | | | A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium pp903 - 914 Zhenqiang Su, Pawel P Labaj, Sheng Li, Jean Thierry-Mieg, Danielle Thierry-Mieg et al. doi:10.1038/nbt.2957 The Sequencing Quality Control (SEQC) consortium shows that junction discovery and differential gene expression profiling with RNA-seq can be robust but transcript-level and absolute measurements remain challenging.
See also: News and Views by Kratz & Carninci | News and Views by Van Keuren-Jensen et al.
| | | | Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study pp915 - 925 Sheng Li, Scott W Tighe, Charles M Nicolet, Deborah Grove, Shawn Levy et al. doi:10.1038/nbt.2972 For intact RNA, gene expression profiles from rRNA-depletion and poly-A enrichment are similar. In addition, rRNA- depletion enables effective analysis of degraded RNA samples.
See also: News and Views by Kratz & Carninci | News and Views by Van Keuren-Jensen et al.
| | | | The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance pp926 - 932 Charles Wang, Binsheng Gong, Pierre R Bushel, Jean Thierry-Mieg, Danielle Thierry-Mieg et al. doi:10.1038/nbt.3001 A comparison of RNA-seq and microarray data from samples treated with diverse drugs highlights a dependency of cross-platform concordance on treatment effect.
See also: News and Views by Kratz & Carninci | News and Views by Van Keuren-Jensen et al.
| | | | Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification pp933 - 940 Jeffrey J Quinn, Ibrahim A Ilik, Kun Qu, Plamen Georgiev, Ci Chu et al. doi:10.1038/nbt.2943 Domain-specific chromatin isolation by RNA purification (dChIRP) identifies interacting partners of functional regions of long noncoding RNAs.
| | | | Letters | | | | Generation of mouse models of myeloid malignancy with combinatorial genetic lesions using CRISPR-Cas9 genome editing pp941 - 946 Dirk Heckl, Monika S Kowalczyk, David Yudovich, Roger Belizaire, Rishi V Puram et al. doi:10.1038/nbt.2951 The genetic complexity of human leukemia is modeled using the CRISPR-Cas9 system in mice.
| | | | Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew pp947 - 951 Yanpeng Wang, Xi Cheng, Qiwei Shan, Yi Zhang, Jinxing Liu et al. doi:10.1038/nbt.2969 TALEN-induced mutation of all homologous copies of a gene that represses resistance to an important wheat pathogen confers a trait that has eluded plant breeders for decades.
See also: News and Views by Gil-Humanes & Voytas
| | | | Errata | | | | Erratum: HIV immunity goes direct p952 doi:10.1038/nbt0914-952a
| | | | Erratum: University biotech patenting 2013 p952 Brady Huggett and Kathryn Paisner doi:10.1038/nbt0914-952b
| | | | Erratum: In Their Words p952 doi:10.1038/nbt0914-952c
| | | | Corrigendum | | | | Corrigendum: Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype p952 Hao Yin, Wen Xue, Sidi Chen, Roman L Bogorad, Eric Benedetti et al. doi:10.1038/nbt0914-952d
| | Careers and Recruitment | Top | | | | Mobility, retention and productivity of genomics scientists in the United States pp953 - 958 Kenneth Guang-Lih Huang and Gokhan Ertug doi:10.1038/nbt.3016 The United States appears to have an increasingly weakening ability to attract and retain genomics scientists.
| | | | People | | | | People p960 doi:10.1038/nbt.3024
| | Top | | Advertisement | Wellcome Trust and Nature Genetics present: The Genomics of Common Diseases 2014 September 17-20, 2014 Bolger Center, Potomac, MD, USA Click here for more information to register for this conference today! | | | | | | | | | | | | Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. For event advertising opportunities across the Nature Publishing Group portfolio please contact natureevents@nature.com | | | | | |
| | | | | | You have been sent this Table of Contents Alert because you have opted in to receive it. You can change or discontinue your e-mail alerts at any time, by modifying your preferences on your nature.com account at: www.nature.com/myaccount (You will need to log in to be recognised as a nature.com registrant) For further technical assistance, please contact our registration department For print subscription enquiries, please contact our subscription department For other enquiries, please contact our customer feedback department Nature Publishing Group | 75 Varick Street, 9th Floor | New York | NY 10013-1917 | USA Nature Publishing Group's worldwide offices: London - Paris - Munich - New Delhi - Tokyo - Melbourne San Diego - San Francisco - Washington - New York - Boston Macmillan Publishers Limited is a company incorporated in England and Wales under company number 785998 and whose registered office is located at Brunel Road, Houndmills, Basingstoke, Hampshire RG21 6XS. © 2014 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. |
| |
Transfect with Confidence using X-tremeGENE Reagents from Roche Efficiently transfect DNA or siRNA to power your cell-based applications Obtain high numbers of healthy, viable cellsAchieve high transfection efficiencyGenerate high recombinant protein yields Minimize cytotoxicity and off-target effects Assess true cell response rather than the effects of your transfection reagentsGenerate physiologically relevant data by minimizing reagent-induced changes To learn more, please visit: X-tremeGENE.roche.com | | |
|
|
TABLE OF CONTENTS |
September 2014 Volume 32, Issue 9 |
| | |
| In This Issue Editorial News Bioentrepreneur Opinion and Comment Features News and Views Computational Biology Research Careers and Recruitment
| |
|
|
|
|
Advertisement |
|
|
|
|
Advertisement |
|
|
|
|
|
|
|
| Focus on RNA sequencing quality control (SEQC | | | Research in regenerative medicine is advancing toward the goal of repairing damaged tissue and organs. Nature Biotechnology and Nature Medicine present a collection of reviews, features and commentaries that explore our current mechanistic understanding of stem cells, and the emerging technologies that will bring regenerative medicine to the clinic. | |
|
|
|
| Top |
|
|
|
In This Issue | Top |
|
|
|
Focus on RNA sequencing quality control (SEQC) ppvii - vii doi:10.1038/nbt.3025
|
|
Editorial | Top |
|
|
|
Honing our reading skills p845 doi:10.1038/nbt.3021 Studies from the RNA Sequencing Quality Control (SEQC) initiative exemplify the kind of experimental groundwork needed to expand RNA-seq into a broader array of basic and translational applications.
|
|
News | Top |
|
|
|
First PD-1 inhibitor breezes across finish line pp847 - 848 Cormac Sheridan doi:10.1038/nbt0914-847
|
|
|
|
Organs-on-chips Harvard spinout p849 doi:10.1038/nbt0914-849b
|
|
|
|
Roche snaps up RNA-medicines firm Santaris p849 doi:10.1038/nbt0914-849c
|
|
|
|
Rabbit milk Ruconest for hereditary angioedema p849 doi:10.1038/nbt0914-849d
|
|
|
|
Biotech drugs too little, too late for Ebola outbreak pp849 - 850 Stephen Strauss doi:10.1038/nbt0914-849a
|
|
|
|
CAR-T cell therapy gets breakthrough status p851 doi:10.1038/nbt0914-851b
|
|
|
|
NCATs drug candidate attracts first buyer p851 doi:10.1038/nbt0914-851c
|
|
|
|
Sanofi to propel inhalable insulin Afrezza into market pp851 - 852 Jim Kling doi:10.1038/nbt0914-851a
|
|
|
|
First-in-class BTK inhibitor Imbruvica gets CLL approval p852 doi:10.1038/nbt0914-852a
|
|
|
|
Google Ventures launches London office p852 doi:10.1038/nbt0914-852b
|
|
|
|
Small biotech steers HDAC inhibitor to clinic pp853 - 854 Mark Ratner doi:10.1038/nbt0914-853
|
|
|
|
Around the world in a month p854 doi:10.1038/nbt0914-854
|
|
|
|
FDA pushes for control over laboratory-developed tests p855 Mark Ratner doi:10.1038/nbt0914-855a
|
|
|
|
Bioelectronics SPARC at NIH p855 doi:10.1038/nbt0914-855b
|
|
|
|
First biosimilars trickle into US pathway p855 doi:10.1038/nbt0914-855c
|
|
|
|
Novartis signs up for Google smart lens p856 Melanie Senior doi:10.1038/nbt0914-856
|
|
|
|
Vitamin A Super Banana in human trials p857 Emily Waltz doi:10.1038/nbt0914-857
|
|
|
|
RAC to finally relax gene therapy oversight p858 Asher Mullard doi:10.1038/nbt0914-858
|
|
|
|
News Feature |
|
|
|
Stepping into the sunshine pp859 - 862 Charles Schmidt doi:10.1038/nbt.3008 Is the imminent release of the database of industry's 'gifts' to doctors cause for concern or celebration? Charles Schmidt investigates.
|
Advertisement |
Nobel Laureate to Give Keynote Address at The International Symposium for Tissue Phenomics™ Hear Dr. Gerd Binnig, Nobel Laureate, Founder, and Chief Technology Officer at Definiens, present on Tissue Phenomics™ and how tissue images can be turned into big data for robust correlation to clinical outcomes. Register today to join us October 17-18 in San Francisco. | | |
|
Bioentrepreneur | Top |
|
|
|
Building a business |
|
|
|
Building a curriculum for bioentrepreneurs pp863 - 865 Lynn Johnson Langer doi:10.1038/nbt.3012
|
|
|
|
SciCafé |
|
|
|
Startups on the menu: Alnylam p866 doi:10.1038/nbt.3009
|
|
Opinion and Comment | Top |
|
|
|
Correspondence |
|
|
|
OpenBiome remains open to serve the medical community p867 Mark Smith, Zain Kassam, Carolyn Edelstein, James Burgess and Eric Alm doi:10.1038/nbt.3006
|
|
|
|
Field trial of Xanthomonas wilt disease-resistant bananas in East Africa pp868 - 870 Leena Tripathi, Jaindra Nath Tripathi, Andrew Kiggundu, Sam Korie, Frank Shotkoski et al. doi:10.1038/nbt.3007
|
|
|
|
Commentary |
|
|
|
Scientific rigor and the art of motorcycle maintenance pp871 - 873 Marcus Munafo, Simon Noble, William J Browne, Dani Brunner, Katherine Button et al. doi:10.1038/nbt.3004 The reliability of scientific research is under scrutiny. A recently convened working group proposes cultural adjustments to incentivize better research practices.
|
|
|
|
The special case of gene therapy pricing pp874 - 876 Troyen A Brennan and James M Wilson doi:10.1038/nbt.3003 Gene therapy companies that pursue high, one-time payments for their products risk a backlash from payors. A better solution may lie in a pay-for-performance model.
|
|
Features | Top |
|
|
|
Patents |
|
|
|
Patents or patients: who loses? pp877 - 880 Joanna Brougher and Konstantin M Linnik doi:10.1038/nbt.3005 The unprecedented weakening of patent rights in the United States undermines necessary incentives for the discovery and development of innovative medicines.
|
|
|
|
Recent patent applications in differential gene expression p881 doi:10.1038/nbt.3023
|
|
News and Views | Top |
|
|
|
|
|
Computational Biology | Top |
|
|
|
Analysis |
|
|
|
Detecting and correcting systematic variation in large-scale RNA sequencing data pp888 - 895 Sheng Li, Pawel P Labaj, Paul Zumbo, Peter Sykacek, Wei Shi et al. doi:10.1038/nbt.3000 Li et al. identify the top-performing methods to improve cross-site differential gene expression analysis with RNA-seq.
See also: News and Views by Kratz & Carninci | News and Views by Van Keuren-Jensen et al.
|
|
|
|
Normalization of RNA-seq data using factor analysis of control genes or samples pp896 - 902 Davide Risso, John Ngai, Terence P Speed and Sandrine Dudoit doi:10.1038/nbt.2931 Remove unwanted variation (RUV) is a new statistical method for RNA-seq data normalization that uses control genes or samples to improve differential expression analysis.
See also: News and Views by Kratz & Carninci | News and Views by Van Keuren-Jensen et al.
|
|
Research | Top |
|
|
|
Articles |
|
|
|
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium pp903 - 914 Zhenqiang Su, Pawel P Labaj, Sheng Li, Jean Thierry-Mieg, Danielle Thierry-Mieg et al. doi:10.1038/nbt.2957 The Sequencing Quality Control (SEQC) consortium shows that junction discovery and differential gene expression profiling with RNA-seq can be robust but transcript-level and absolute measurements remain challenging.
See also: News and Views by Kratz & Carninci | News and Views by Van Keuren-Jensen et al.
|
|
|
|
Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study pp915 - 925 Sheng Li, Scott W Tighe, Charles M Nicolet, Deborah Grove, Shawn Levy et al. doi:10.1038/nbt.2972 For intact RNA, gene expression profiles from rRNA-depletion and poly-A enrichment are similar. In addition, rRNA- depletion enables effective analysis of degraded RNA samples.
See also: News and Views by Kratz & Carninci | News and Views by Van Keuren-Jensen et al.
|
|
|
|
The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance pp926 - 932 Charles Wang, Binsheng Gong, Pierre R Bushel, Jean Thierry-Mieg, Danielle Thierry-Mieg et al. doi:10.1038/nbt.3001 A comparison of RNA-seq and microarray data from samples treated with diverse drugs highlights a dependency of cross-platform concordance on treatment effect.
See also: News and Views by Kratz & Carninci | News and Views by Van Keuren-Jensen et al.
|
|
|
|
Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification pp933 - 940 Jeffrey J Quinn, Ibrahim A Ilik, Kun Qu, Plamen Georgiev, Ci Chu et al. doi:10.1038/nbt.2943 Domain-specific chromatin isolation by RNA purification (dChIRP) identifies interacting partners of functional regions of long noncoding RNAs.
|
|
|
|
Letters |
|
|
|
Generation of mouse models of myeloid malignancy with combinatorial genetic lesions using CRISPR-Cas9 genome editing pp941 - 946 Dirk Heckl, Monika S Kowalczyk, David Yudovich, Roger Belizaire, Rishi V Puram et al. doi:10.1038/nbt.2951 The genetic complexity of human leukemia is modeled using the CRISPR-Cas9 system in mice.
|
|
|
|
Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew pp947 - 951 Yanpeng Wang, Xi Cheng, Qiwei Shan, Yi Zhang, Jinxing Liu et al. doi:10.1038/nbt.2969 TALEN-induced mutation of all homologous copies of a gene that represses resistance to an important wheat pathogen confers a trait that has eluded plant breeders for decades.
See also: News and Views by Gil-Humanes & Voytas
|
|
|
|
Errata |
|
|
|
Erratum: HIV immunity goes direct p952 doi:10.1038/nbt0914-952a
|
|
|
|
Erratum: University biotech patenting 2013 p952 Brady Huggett and Kathryn Paisner doi:10.1038/nbt0914-952b
|
|
|
|
Erratum: In Their Words p952 doi:10.1038/nbt0914-952c
|
|
|
|
Corrigendum |
|
|
|
Corrigendum: Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype p952 Hao Yin, Wen Xue, Sidi Chen, Roman L Bogorad, Eric Benedetti et al. doi:10.1038/nbt0914-952d
|
|
Careers and Recruitment | Top |
|
|
|
Mobility, retention and productivity of genomics scientists in the United States pp953 - 958 Kenneth Guang-Lih Huang and Gokhan Ertug doi:10.1038/nbt.3016 The United States appears to have an increasingly weakening ability to attract and retain genomics scientists.
|
|
|
|
People |
|
|
|
People p960 doi:10.1038/nbt.3024
|
|
Top |
|
Advertisement |
Wellcome Trust and Nature Genetics present: The Genomics of Common Diseases 2014 September 17-20, 2014 Bolger Center, Potomac, MD, USA Click here for more information to register for this conference today! | | | |
|
|
| | | | | | Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. For event advertising opportunities across the Nature Publishing Group portfolio please contact natureevents@nature.com | | | | | |
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