Nature Biotechnology Contents: Volume 33 pp 213 - 318

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 appnow! 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 VivoTherapeutic Approaches Download Your Copy Today

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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
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
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
Correction   p226 doi:10.1038/nbt0315-227b
NEWS
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.
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BIOENTREPRENEUR
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
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
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
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
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
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 circuitsin 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
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
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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.
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