Nature Biotechnology Contents: Volume 33 pp 213 - 318

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Advertisement A*STAR Research - Highlighting the best of research at the Agency for Science, Technology and Research (A*STAR), Singapore's premier research organization  Recent Highlights Biotechnology: Using fungi to catch algae | Nanoparticles: Alcohol-free zone | Parasitology: Genes of carcinogenic liver fluke revealed Download the A*STAR Research app now! TABLE OF CONTENTS March 2015 Volume 33, Issue 3 Editorial News Correction Bioentrepreneur Opinion and Comment Features News and Views Computational Biology Research Careers and Recruitment Advertisement   NEW WHITE PAPER: The Advantage & Application of Genetically Humanized Mouse Models for Biomedical Research This white paper explores the technologies used to generate genetically humanized mice and explains their applications, including: Efficacy & Safety Testing of Therapeutic Compounds & Biologics Drug Metabolism & Disposition The Immune System Novel In Vivo Therapeutic Approaches Download Your Copy Today  Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement BIOPHARMA DEALMAKERS Company Profiles and Partnering Opportunities   Advertisement Epigenome Roadmap Nature Publishing Group presents an online portal - the Epigenome Roadmap - which collects key research papers from The NIH Roadmap Epigenomics Program, complemented by thematical 'threads' to help the readers mine the wealth of available information. Access the Epigenome Roadmap for FREE at:  nature.com/epigenomeroadmap Produced with exclusive support from  Illumina    Editorial Top Double-blind peer review   p213 doi:10.1038/nbt.3173 Nature Biotechnology, together with Nature and its sister journals, is now offering anonymity to authors during the peer-review process. News Top Roche spends $1 billion on Foundation Medicine's tumor profiling   pp215 - 216 Mark Ratner doi:10.1038/nbt0315-215 Obama 2016 budget calls for Precision Medicine   p216 doi:10.1038/nbt0315-216 $1-million price tag set for Glybera gene therapy   pp217 - 218 Chris Morrison doi:10.1038/nbt0315-217 House proposes 21st Century Cures   p218 doi:10.1038/nbt0315-218a FDA's Hamburg steps down   p218 doi:10.1038/nbt0315-218b Amgen's bispecific antibody puffs across finish line   pp219 - 221 Cormac Sheridan doi:10.1038/nbt0315-219 Smartphone HIV test   p221 doi:10.1038/nbt0315-221a Myriad settles BRCA disputes and moves on   p221 doi:10.1038/nbt0315-221b First US biosimilar edges towards market   pp222 - 223 Melanie Senior doi:10.1038/nbt0315-222 Scotts' GM grass grows free from regulation   p223 Emily Waltz doi:10.1038/nbt0315-223 Next-generation stem cell therapy poised to enter EU market   pp224 - 225 doi:10.1038/nbt0315-224 Around the world in a month   p225 doi:10.1038/nbt0315-225 AstraZeneca adopts CRISPR across drug discovery   p226 doi:10.1038/nbt0315-226a FDA strips breakthrough status   p226 doi:10.1038/nbt0315-226b Shire bags NPS, including newly approved biologic for hypoparathyroidism   p226 doi:10.1038/nbt0315-226c Weight loss 'electroceutical' device wins FDA okay   p226 Gunjan Sinha doi:10.1038/nbt0315-227a Correction Top Correction   p226 doi:10.1038/nbt0315-227b News Top News Feature Drugging the gut microbiome   pp228 - 231 Ken Garber doi:10.1038/nbt.3161 Using conventional drug discovery and novel synthetic biology approaches, some investigators and companies are mining our resident microbes and their metabolites for targets in small-molecule drug programs. Ken Garber reports. Advertisement Ready for a glimpse of tomorrow? Visit KAUST Discovery today KAUST Discovery highlights the cutting-edge research, technologies and innovations emerging from the King Abdullah University of Science and Technology. http://discovery.kaust.edu.sa Bioentrepreneur Top Building a business Keys to the kingdom   pp232 - 236 Sybil C K Wong, Laura S Sasportas, Katie Richardson, Brian R Gordon, Madura K P Jayatunga et al. doi:10.1038/nbt.3159 Opinion and Comment Top Correspondence How to set up collaborations between academia and industrial biotech companies   pp237 - 240 Jack T Pronk, Sang Yup Lee, Jeff Lievense, John Pierce, Bernhard Palsson et al. doi:10.1038/nbt.3171 Quality score compression improves genotyping accuracy   pp240 - 243 Y William Yu, Deniz Yorukoglu, Jian Peng and Bonnie Berger doi:10.1038/nbt.3170 Ballgown bridges the gap between transcriptome assembly and expression analysis   pp243 - 246 Alyssa C Frazee, Geo Pertea, Andrew E Jaffe, Ben Langmead, Steven L Salzberg et al. doi:10.1038/nbt.3172 Features Top Nature Biotechnology's academic spinouts of 2014   pp247 - 255 Aaron Bouchie and Laura DeFrancesco doi:10.1038/nbt.3163 Ventures focusing on drug testing or therapies against rare disease, cancer, gastrointestinal disease, fibrosis and pain are among those selected by the editors in 2014's crop of startups. Patents Law, history and lessons in the CRISPR patent conflict   pp256 - 257 Jacob S Sherkow doi:10.1038/nbt.3160 Predicting the outcome of the ongoing patent disputes surrounding genome-editing technology is equal parts patent analysis and history. Recent patent applications in antibody engineering   p258 doi:10.1038/nbt.3174 News and Views Top An integrated microprobe for the brain   pp259 - 260 Carolina Gutierrez Herrera and Antoine R Adamantidis doi:10.1038/nbt.3169 A multimodal fiber can both record and manipulate neural activity in mice. See also: Research by Canales et al. Singling out blood development   pp260 - 261 Eva M Fast and Len I Zon doi:10.1038/nbt.3168 Analysis of gene expression in thousands of single cells generates a model of the blood regulatory network. See also: Research by Moignard et al. Engineering insect-free cereals   pp262 - 263 Saskia A Hogenhout and Cyril Zipfel doi:10.1038/nbt.3162 A cluster of three rice lectin receptor kinases confers resistance to planthopper insects. See also: Research by Liu et al. Research Highlights   p263 doi:10.1038/nbt.3164 Biotechnology JOBS of the week Research Associate - Bioinformatician University of Cambridge Postdoctoral Research Fellow The University of Hong Kong Postdoctoral Position - Molecular Signaling and Cell Death Unit VIB Inflammation Research Center Group Leader University of Helsinki More Science jobs from Biotechnology EVENT 3rd Conference on Cereal Biotechnology and Breeding November 2, 2015 Berlin, Germany More science events from Computational Biology Top Commentary A systems approach to traditional oriental medicine   pp264 - 268 Hyun Uk Kim, Jae Yong Ryu, Jong Ok Lee and Sang Yup Lee doi:10.1038/nbt.3167 Analyzing structural similarities between compounds derived from traditional oriental medicine and human metabolites is a systems-based approach that can help identify mechanisms of action and suggest approaches to reduce toxicity. Research Top Articles Decoding the regulatory network of early blood development from single-cell gene expression measurements   pp269 - 276 Victoria Moignard, Steven Woodhouse, Laleh Haghverdi, Andrew J Lilly, Yosuke Tanaka et al. doi:10.1038/nbt.3154 An early stage in mouse blood development is reconstructed from gene expression data on thousands of single cells. See also: News and Views by Fast & Zon Multifunctional fibers for simultaneous optical, electrical and chemical interrogation of neural circuits in vivo    pp277 - 284 Andres Canales, Xiaoting Jia, Ulrich P Froriep, Ryan A Koppes, Christina M Tringides et al. doi:10.1038/nbt.3093 Highly flexible fibers enable simultaneous electrical neural recording, optical stimulation and drug delivery in freely moving mice. See also: News and Views by Herrera & Adamantidis Letters Integrated genome and transcriptome sequencing of the same cell   pp285 - 289 Siddharth S Dey, Lennart Kester, Bastiaan Spanjaard, Magda Bienko and Alexander van Oudenaarden doi:10.1038/nbt.3129 Method for combined genome and transcriptome sequencing from the same single cell shows that copy number variations influence cell-to-cell variability in gene expression levels. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads   pp290 - 295 Mihaela Pertea, Geo M Pertea, Corina M Antonescu, Tsung-Cheng Chang, Joshua T Mendell et al. doi:10.1038/nbt.3122 Using a network flow algorithm from optimization theory enables improved assembly of transcriptomes from RNA-seq reads. MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island   pp296 - 300 Philip M Ashton, Satheesh Nair, Tim Dallman, Salvatore Rubino, Wolfgang Rabsch et al. doi:10.1038/nbt.3103 Results from the Oxford nanopore minION sequencer [ldquo]early-release[rdquo] program enable identification of the insertion site of an antibiotic resistance island in Salmonella Typhi. A gene cluster encoding lectin receptor kinases confers broad-spectrum and durable insect resistance in rice   pp301 - 305 Yuqiang Liu, Han Wu, Hong Chen, Yanling Liu, Jun He et al. doi:10.1038/nbt.3069 Liu et al. provide new resources for improving rice by cloning a gene cluster that enhances resistance to two species of planthoppers, which cause billions of dollars of crop loss. See also: News and Views by Hogenhout & Zipfel Resources A comprehensive transcriptional portrait of human cancer cell lines   pp306 - 312 Christiaan Klijn, Steffen Durinck, Eric W Stawiski, Peter M Haverty, Zhaoshi Jiang et al. doi:10.1038/nbt.3080 A comprehensive analysis of RNA sequencing and single-nucleotide polymorphism (SNP) array data provides new insights into the biology of 675 human cancer cell lines Careers and Recruitment Top Total target cash compensation shows a healthy increase at private life-science companies   pp313 - 316 Bruce Rychlik doi:10.1038/nbt.3166 Nonfounder total target cash compensation increased by 4.2% at private life-science companies in 2014. People People   p318 doi:10.1038/nbt.3175 Advertisement Animation: Targeting cancer cell metabolism This animation, created by Nature Reviews Drug Discovery, with distribution supported by Forma Therapeutics, explores the key aspects of the altered metabolism in cancer cells and explains how these can be exploited for the development of new anticancer strategies.  Access the animation free online  Produced with support from: Forma Therapeutics, Inc.      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 More Nature Events

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