Nature Biotechnology Contents: Volume 34 pp 445 - 572

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Produced with support from: KACST TABLE OF CONTENTS May 2016 Volume 34, Issue 5 Editorial News Bioentrepreneur Opinion and Comment Features News and Views Research Careers and Recruitment Advertisement nature.com webcasts Nature Publishing Group presents a custom webcast on: Overcoming the challenges of NGS-based RNA profiling using limited, precious samples Tuesday May 10, 2016 at 9AM PDT, 12PM EDT, 5PM BST, 6PM CEST  Register for the webcast and live Q&A session  Sponsored by: HTG Molecular Diagnostics Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement The Naturejobs Career Expo is coming back to Boston! May 18, 2016 This career fair offers young, talented researchers an excellent opportunity to meet a diverse selection of national and international employers from academic institutions and scientific industries, such as pharmaceutical organisations, digital technology companies, science publishing and more. Register for FREE today!   Advertisement BIOPHARMA DEALMAKERS Company Profiles and Partnering Opportunities   Advertisement Discovery and technology for human health  Now open for submissions Straddling the life sciences, the physical sciences and engineering, Nature Biomedical Engineering will publish — weekly and online-only — biological, medical and engineering advances that can directly inspire or lead to improvements in human health or healthcare.    Advertisement THE GENOMICS OF COMMON DISEASES 2016  Presented by Nature Genetics in association with the Wellcome Trust September 25-28, 2016 Renaissance Baltimore Harborplace Hotel | Baltimore, MD, USA REGISTER NOW!   Editorial Top In harm's way   p445 doi:10.1038/nbt.3581 A House panel's witch hunt against fetal tissue research demands a forceful response from the biomedical community. News Top Fetal tissue probe unsettles scientific community   pp447 - 448 Amy Maxmen doi:10.1038/nbt0516-447 NIH dengue vaccine leaps into phase 3 studies   p449 Jeffrey M. Perkel doi:10.1038/nbt0516-449 Wellness 'omics in clinics   p450 doi:10.1038/nbt0516-450a DNA-encoded drug libraries come of age   pp450 - 451 Asher Mullard doi:10.1038/nbt0516-450b Merck, Ionis prevail in Gilead HCV suit   p451 doi:10.1038/nbt0516-451 Amgen's PCSK9 patents upheld   p452 doi:10.1038/nbt0516-452a J&J incubators open in Belgium and Texas   p452 doi:10.1038/nbt0516-452b Citizen science lures gamers into Sweden's Human Protein Atlas   pp452 - 453 Mark Peplow doi:10.1038/nbt0516-452c Celltrion's infliximab copy shows path to biosimilars in US   pp454 - 455 Eva von Schaper doi:10.1038/nbt0516-454 Bento Lab   p455 doi:10.1038/nbt0516-455 Data Page 1Q16—the biotech bear growls   p456 Walter Yang doi:10.1038/nbt.3574 Drug pipeline: 1Q16   p457 Laura DeFrancesco doi:10.1038/nbt.3571 News Feature No longer going to waste   pp458 - 461 Ken Garber doi:10.1038/nbt.3557 Skeletal muscle atrophy offers a huge opportunity for an effective drug. After many failures, industry may be on the verge. Ken Garber reports. Advertisement Rapid, Reproducible Protein Separations  Shimadzu's Perfinity Workstation provides a seamlessly integrated solution for affinity enrichment and protein digestion. It offers serum to purified peptides in as little as 10 minutes, reduces a three day workflow to less than one hour, and offers high-quality, reproducible proteolysis data. Learn more.   Bioentrepreneur Top Building a business Protecting products versus platforms   pp462 - 465 Jacob S Sherkow doi:10.1038/nbt.3553 Opinion and Comment Top Correspondence Developing context-specific next-generation sequencing policy   pp466 - 470 Margaret Ann Curnutte, Karen L Frumovitz, Juli M Bollinger, Robert M Cook-Deegan, Amy L McGuire et al. doi:10.1038/nbt.3545 Creating human germ cells for unmet reproductive needs   pp470 - 473 Tetsuya Ishii and Renee A Reijo Pera doi:10.1038/nbt.3559 Cibus' herbicide-resistant canola in European limbo   pp473 - 474 Matthias Fladung doi:10.1038/nbt.3558 Ending event-based regulation of GMO crops   pp474 - 477 Steven H Strauss and Joanna K Sax doi:10.1038/nbt.3541 Regulate genome-edited products, not genome editing itself   pp477 - 479 Dana Carroll, Alison L Van Eenennaam, Jeremy F Taylor, Jon Seger and Daniel F Voytas doi:10.1038/nbt.3566 Production of hornless dairy cattle from genome-edited cell lines   pp479 - 481 Daniel F Carlson, Cheryl A Lancto, Bin Zang, Eui-Soo Kim, Mark Walton et al. doi:10.1038/nbt.3560 On 'three decades of nanopore sequencing'   pp481 - 482 John J Kasianowicz and Sergey M Bezrukov doi:10.1038/nbt.3570 Author response to John Kasianowicz and Sergey Bezrukov   p482 David Deamer, Mark Akeson and Daniel Branton doi:10.1038/nbt.3561 Open-source guideseq software for analysis of GUIDE-seq data   p483 Shengdar Q Tsai, Ved V Topkar, J Keith Joung and Martin J Aryee doi:10.1038/nbt.3534 Features Top Nature Biotechnology's academic spinouts of 2015   pp484 - 492 Aaron Bouchie and Laura DeFrancesco doi:10.1038/nbt.3564 Immuno-oncology was hotly pursued by investors in 2015, along with drug delivery platforms. In the agbiotech world, a systems biology company set up shop. A risk-based approach to the regulation of genetically engineered organisms   pp493 - 503 Gregory Conko, Drew L Kershen, Henry Miller and Wayne A Parrott doi:10.1038/nbt.3568 Current regulatory regimes for genetically engineered crops fail to use a scientifically defensible approach or tailor the degree of regulatory review to the level of actual hazard or risk. We describe a rational way forward. Patents Intellectual property policies in early-phase research in public-private partnerships   pp504 - 510 Hilde Stevens, Geertrui Van Overwalle, Bart Van Looy and Isabelle Huys doi:10.1038/nbt.3562 Knowledge-sharing strategies differ depending on the nature of the research objectives of public-private partnerships, but information about such strategies is often vague. Recent patents in CRISPR technology   p511 doi:10.1038/nbt.3579 Advertisement Free naturejobs webcast From bench to business: Top tips from experts and entrepreneurs on how to take your research all the way from idea to product. You'll also learn how to find the right funding and how to create the perfect pitch to get your research off the ground. Wednesday May 25th, 2016 at 8AM PST, 11AM EST, 4PM BST & 5PM CEST Register for the webcast and the live Q&A session Produced with support from: Novo Nordisk     News and Views Top Superheroes of disease resistance   pp512 - 513 Daniel MacArthur doi:10.1038/nbt.3555 Individuals who remain healthy despite carrying a disease-causing mutation are identified in an analysis of over a half million people. See also: Research by Chen et al. A microbial factory for diverse chemicals   pp513 - 515 Chiam Yu Ng, Anupam Chowdhury and Costas D Maranas doi:10.1038/nbt.3565 An array of functionalized small molecules is efficiently synthesized in bacteria. See also: Research by Cheong et al. Inducing tolerance one antigen at a time   pp515 - 517 Rafael M Rezende and Howard L Weiner doi:10.1038/nbt.3573 Autoimmune diseases are reversed in mice using nanoparticles that display disease-associated antigens bound to MHC class II molecules. Research Highlights   p517 doi:10.1038/nbt.3575 Biotechnology JOBS of the week Post-doctoral Fellow Texas A&M University Health Science Center Postdoctoral fellow Universitatsklinikum Erlangen Postdoctoral Research Assistant University of Dundee Senior Lecturer in Dementia and Neurodegeneration King's College London More Science jobs from Biotechnology EVENT 2016 6th International Conference on Biotechnology and Environmental Management(ICBEM 2016) September 24, 2016 Toronto, Canada More science events from Research Top Perspective Three decades of nanopore sequencing   pp518 - 524 David Deamer, Mark Akeson and Daniel Branton doi:10.1038/nbt.3423 A long-held goal in sequencing has been to use a voltage-biased nanoscale pore in a membrane to measure the passage of a linear, single-stranded (ss) DNA or RNA molecule through that pore. With the development of enzyme-based methods that ratchet polynucleotides through the nanopore, nucleobase-by-nucleobase, measurements of changes in the current through the pore can now be decoded into a DNA sequence using an algorithm. In this Historical Perspective, we describe the key steps in nanopore strand-sequencing, from its earliest conceptualization more than 25 years ago to its recent commercialization and application. Brief Communications Near-optimal probabilistic RNA-seq quantification   pp525 - 527 Nicolas L Bray, Harold Pimentel, Pall Melsted and Lior Pachter doi:10.1038/nbt.3519 A pseudoalignment-based method enables faster quantification and measurement of uncertainty in RNA-seq experiments. Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow   pp528 - 530 Hanhui Ma, Li-Chun Tu, Ardalan Naseri, Maximiliaan Huisman, Shaojie Zhang et al. doi:10.1038/nbt.3526 Multiple chromosomal sites are readily labeled using Cas9 and guide RNAs that bind fluorescent proteins, enabling visualization of chromatin dynamics. Articles Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases   pp531 - 538 Rong Chen, Lisong Shi, Jorg Hakenberg, Brian Naughton, Pamela Sklar et al. doi:10.1038/nbt.3514 Human disease genetics is extended to the identification of individuals who remain healthy despite carrying highly penetrant disease-causing mutations. See also: News and Views by MacArthur Characterizing genomic alterations in cancer by complementary functional associations   pp539 - 546 Jong Wook Kim, Olga B Botvinnik, Omar Abudayyeh, Chet Birger, Joseph Rosenbluh et al. doi:10.1038/nbt.3527 Complementary genomic features associated with pathway activation, gene dependency and drug sensitivity are uncovered using REVEALER. Integrated digital error suppression for improved detection of circulating tumor DNA   pp547 - 555 Aaron M Newman, Alexander F Lovejoy, Daniel M Klass, David M Kurtz, Jacob J Chabon et al. doi:10.1038/nbt.3520 Circulating tumor DNA is detected with high sensitivity and specificity using molecular barcoding and in silico error correction. Letter Energy- and carbon-efficient synthesis of functionalized small molecules in bacteria using non-decarboxylative Claisen condensation reactions   pp556 - 561 Seokjung Cheong, James M Clomburg and Ramon Gonzalez doi:10.1038/nbt.3505 A wide array of functionalized small molecules can be synthesized in Escherichia coli by engineering orthogonal, modular pathways that are energy and carbon efficient. See also: News and Views by Ng et al. Resources Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity OPEN   pp562 - 570 Jessen V Bredeson, Jessica B Lyons, Simon E Prochnik, G Albert Wu, Cindy M Ha et al. doi:10.1038/nbt.3535 The global genetic diversity of cassava and related Manihot species is revealed by sequencing of 53 cultivated and wild accessions and genotyping of 268 African cassavas, providing a vital resource for breeding. Careers and Recruitment Top First-quarter biotech job picture   p571 Michael Francisco doi:10.1038/nbt.3572 People People   p572 doi:10.1038/nbt.3578 Advertisement Open for Submissions  npj Precision Oncology is a new open access, online-only, peer-reviewed journal committed to publishing cutting-edge scientific research in all aspects of precision oncology from basic science to translational applications, to clinical medicine. The journal is part of the Nature Partner Journals series and published in partnership with The Hormel Institute, University of Minnesota. Explore the benefits of submitting your manuscript >>   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. 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