Nature Biotechnology Contents: Volume 30 pp 1 - 116

Advertisement TALEN® Sure KO™: knock-out any gene within the 1st coding exon Our recently launched and very affordable TALEN® Sure KO™ service enables sure gene knock-out by introducing a frame shift within the first coding exon of any gene. TALENs® are next generation genome customization tools to knock-out genes or introduce modifications in any gene, at any position, in any genome. TABLE OF CONTENTS January 2012 Volume 30, Issue 1 In This Issue Editorial News News Feature Bioentrepreneur Correspondence Features News and Views Research Highlights Computational Biology Research Errata Corrigenda Careers and Recruitment Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement UC Berkeley Extension Intensive Seminars Develop the conceptual framework and vocabulary to succeed as a biotech business professional. Enroll now to understand the complex processes that drive the industry: Life Sciences Business and Marketing: Their Integral Role for Success, April 19-20 in Belmont, Calif. The Drug Development Process, April 23-27 in San Francisco   Advertisement BIOPHARMA DEALMAKERS Company Profiles and Partnering Opportunities   Advertisement Nature.com presents Antibodypedia Finding the right antibody for the right application just got easier! Visit www.antibodypedia.com to find antibodies that have proved themselves effective for particular applications or to submit antibody validation data from your own experiments.   Advertisement Trade Secrets A Nature Network blog by Bioentrepreneur Brought to you by Nature Biotechnology Access the insights, advice and commentary from scientists and entrepreneurs building biotech sectors around the world. Click here to join the global dialogue on life science entrepreneurship and don't forget to follow us on Twitter!   In This Issue Top In this issue ppvii - viii doi:10.1038/nbt.2104 Full Text | PDF Editorial Top What happened to personalized medicine? p1 doi:10.1038/nbt.2096 Personalized medicine falls a long way short of the predictive and preventative healthcare paradigm it once promised. Full Text | PDF News Top Incyte comes of age with JAK inhibitor approval pp3 - 5 Nuala Moran doi:10.1038/nbt0112-3 Full Text | PDF Eylea approval transforms Regeneron p4 Mark Ratner doi:10.1038/nbt0112-4 Full Text | PDF Avastin loses breast cancer indication p6 Karen Carey doi:10.1038/nbt0112-6a Full Text | PDF Pivotal FDA/Exelixis dispute p6 Mark Ratner doi:10.1038/nbt0112-6b Full Text | PDF Safety profiles come to fore as more drugs approach MS market pp6 - 8 Cormac Sheridan doi:10.1038/nbt0112-6c Full Text | PDF Spinal device cancer risk p8 Emily Waltz doi:10.1038/nbt0112-8a Full Text | PDF $352 million into microRNA p8 Sabine Louet doi:10.1038/nbt0112-8b Full Text | PDF Obama urges translation speed p9 Jeffrey L Fox doi:10.1038/nbt0112-9b Full Text | PDF Russian fund steps up investments in innovative biotechs pp9 - 11 Alla Katsnelson doi:10.1038/nbt0112-9a Full Text | PDF Monsanto to face biopiracy charges in India p11 Lucas Laursen doi:10.1038/nbt0112-11 Full Text | PDF Embryonic stem cell pioneer Geron exits field, cuts losses pp12 - 13 Simon Frantz doi:10.1038/nbt0112-12 Full Text | PDF Around the world in a month p13 doi:10.1038/nbt0112-13 Full Text | PDF Newsmaker Foundation Medicine p14 Michael Eisenstein doi:10.1038/nbt0112-14 The Cambridge, Massachusetts-based company plans to introduce next-generation gene sequencing into oncology practice and pathologists' laboratories. Full Text | PDF Data Page Drug pipeline: Q411 p15 H Craig Mak doi:10.1038/nbt.2090 Full Text | PDF Opinions The NIH's role in accelerating translational sciences pp16 - 19 John C Reed, E Lucile White, Jeffrey Aube, Craig Lindsley, Min Li, Larry Sklar and Stuart Schreiber doi:10.1038/nbt.2087 The NIH's proposed initiatives in translational science deserve solid financial backing from legislators and vocal support from the biomedical community. Full Text | PDF Building stem-cell genomics in California and beyond pp20 - 25 Natalie D DeWitt, Michael P Yaffe and Alan Trounson doi:10.1038/nbt.2086 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. Full Text | PDF News Feature Top Approval on a knife edge pp26 - 29 Michael Eisenstein doi:10.1038/nbt.2084 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. Full Text | PDF Bioentrepreneur Top Bringing business risk into sharp focus pp30 - 32 Bill Gruber and Emily Walsh doi:10.1038/nbt.2081 Full Text | PDF Correspondence Top Big data in small places pp33 - 34 Daniel MacLean and Sophien Kamoun doi:10.1038/nbt.2079 Full Text | PDF Exploiting host molecules to augment mycoinsecticide virulence pp35 - 37 Yanhua Fan, Dov Borovsky, Chloe Hawkings, Almudena Ortiz-Urquiza and Nemat O Keyhani doi:10.1038/nbt.2080 Full Text | PDF European discussion forum on transgenic tree biosafety pp37 - 38 Matthias Fladung, Illimar Altosaar, Detlef Bartsch, Marie Baucher, Fabio Boscaleri, Fernando Gallardo, Hely Haggman, Hans Hoenicka, Kaare Nielsen, Donatella Paffetti, Armand Seguin, Guenther Stotzky and Cristina Vettori doi:10.1038/nbt.2078 Full Text | PDF Factors influencing agbiotech adoption and development in sub-Saharan Africa pp38 - 40 Obidimma C Ezezika, Abdallah S Daar, Kathryn Barber, Justin Mabeya, Fiona Thomas, Jennifer Deadman, Debbie Wang and Peter A Singer doi:10.1038/nbt.2088 Full Text | PDF Features Top Reinventing clinical trials pp41 - 49 Malorye Allison doi:10.1038/nbt.2083 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. Full Text | PDF Patents Maintaining patents protecting biologics or small-molecule drugs pp50 - 53 Ganesan Marimuthu, Sangita Kumari, Muthukrishnakumar Kandasamy, Srivatsan Raghunathan and Gayatri Saberwal doi:10.1038/nbt.2082 A look at the maintenance rates of US patents protecting FDA-approved biologics and small molecules. Full Text | PDF Recent patent applications related to gene and DNA synthesis p54 doi:10.1038/nbt.2098 Full Text | PDF News and Views Top Parallel genome universes pp55 - 56 Tom Misteli doi:10.1038/nbt.2085 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. Full Text | PDF See also: Research by Kalhor et al. Dopaminergic neurons for Parkinson's therapy pp56 - 58 Olle Lindvall doi:10.1038/nbt.2077 A differentiation protocol guided by developmental principles produces more-authentic dopaminergic neurons for transplantation in patients. Full Text | PDF New competition in RNA regulation pp58 - 59 Anastasia Khvorova and Alexey Wolfson doi:10.1038/nbt.2092 An additional layer of RNA regulation in which RNAs encoded by genes and pseudogenes compete for microRNAs could offer new opportunities for oligonucleotide therapeutics. Full Text | PDF Research Highlights Top Pituitary in a dish | The strategizing of crowds | Detection of beta cell death | Clinical gene therapies progress | Natural products from symbionts Computational Biology Top Analysis Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing pp61 - 68 Joke Reumers, Peter De Rijk, Hui Zhao, Anthony Liekens, Dominiek Smeets, John Cleary, Peter Van Loo, Maarten Van Den Bossche, Kirsten Catthoor, Bernard Sabbe, Evelyn Despierre, Ignace Vergote, Brian Hilbush, Diether Lambrechts and Jurgen Del-Favero doi:10.1038/nbt.2053 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. Abstract | Full Text | PDF Research Top Perspective The discovery and development of belimumab: the anti-BLyS-lupus connection pp69 - 77 William Stohl and David M Hilbert doi:10.1038/nbt.2076 Abstract | Full Text | PDF Analysis Performance comparison of whole-genome sequencing platforms pp78 - 82 Hugo Y K Lam, Michael J Clark, Rui Chen, Rong Chen, Georges Natsoulis, Maeve O'Huallachain, Frederick E Dewey, Lukas Habegger, Euan A Ashley, Mark B Gerstein, Atul J Butte, Hanlee P Ji and Michael Snyder doi:10.1038/nbt.2065 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. Abstract | Full Text | PDF Articles Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers pp83 - 89 Rajeev K Varshney, Wenbin Chen, Yupeng Li, Arvind K Bharti, Rachit K Saxena, Jessica A Schlueter, Mark T A Donoghue, Sarwar Azam, Guangyi Fan, Adam M Whaley, Andrew D Farmer, Jaime Sheridan, Aiko Iwata, Reetu Tuteja, R Varma Penmetsa, Wei Wu, Hari D Upadhyaya, Shiaw-Pyng Yang, Trushar Shah, K B Saxena, Todd Michael, W Richard McCombie, Bicheng Yang, Gengyun Zhang, Huanming Yang, Jun Wang, Charles Spillane, Douglas R Cook, Gregory D May, Xun Xu and Scott A Jackson doi:10.1038/nbt.2022 Pigeonpea is an important protein source in many developing countries, but limited genetic resources have constrained its improvement. The draft genome sequence of pigeonpea, the first for a nonindustrial crop and for a grain legume, should facilitate molecular breeding efforts to improve yields for subsistence farmers. Abstract | Full Text | PDF Genome architectures revealed by tethered chromosome conformation capture and population-based modeling pp90 - 98 Reza Kalhor, Harianto Tjong, Nimanthi Jayathilaka, Frank Alber and Lin Chen doi:10.1038/nbt.2057 Genome function is influenced by the three-dimensional organization of chromosomes. Kalhor et al. experimentally detect low-frequency intra- and interchromosomal interactions previously obscured by noise and use these data to model the genome architectures of populations of cells. Abstract | Full Text | PDF See also: News and Views by Misteli Letter Targeted RNA sequencing reveals the deep complexity of the human transcriptome pp99 - 104 Tim R Mercer, Daniel J Gerhardt, Marcel E Dinger, Joanna Crawford, Cole Trapnell, Jeffrey A Jeddeloh, John S Mattick and John L Rinn doi:10.1038/nbt.2024 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. First paragraph | Full Text | PDF Resources Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes pp105 - 111 Xun Xu, Xin Liu, Song Ge, Jeffrey D Jensen, Fengyi Hu, Xin Li, Yang Dong, Ryan N Gutenkunst, Lin Fang, Lei Huang, Jingxiang Li, Weiming He, Guojie Zhang, Xiaoming Zheng, Fumin Zhang, Yingrui Li, Chang Yu, Karsten Kristiansen, Xiuqing Zhang, Jian Wang, Mark Wright, Susan McCouch, Rasmus Nielsen, Jun Wang and Wen Wang doi:10.1038/nbt.2050 A catalog of genetic variation in a crop species facilitates marker-assisted breeding, gene mapping and analysis of elite traits. Xu et al. resequenced 40 cultivated and 10 wild rice accessions to >15 [times] coverage, yielding 6.5 million single-nucleotide polymorphisms and 808,000 small insertions and deletions. Abstract | Full Text | PDF Errata Top Erratum: In defense of life sciences venture investing p112 Bruce L Booth and Bijan Salehizadeh doi:10.1038/nbt0112-112a Full Text | PDF Erratum: Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells p112 Kitai Kim, Rui Zhao, Akiko Doi, Kitwa Ng, Juli Unternaehrer, Patrick Cahan, Huo Hongguang, Yuin-Han Loh, Martin J Aryee, M William Lensch, Hu Li, James J Collins, Andrew P Feinberg and George Q Daley doi:10.1038/nbt0112-112b Full Text | PDF Erratum: Move over ZFNs p112 Laura DeFrancesco doi:10.1038/nbt0112-112c Full Text | PDF Corrigenda Top Corrigendum: Biotechs follow big pharma lead back into academia p112 Jim Kling doi:10.1038/nbt0112-112d Full Text | PDF Corrigendum: New models emerge for commercializing university assets p112 Nuala Moran doi:10.1038/nbt0112-112e Full Text | PDF Corrigendum: Drugmakers use real-world patient data to calibrate product development p112 Cormac Sheridan doi:10.1038/nbt0112-112f Full Text | PDF Careers and Recruitment Top Broadening PhD curricula pp113 - 114 Nathan L Vanderford doi:10.1038/nbt.2091 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. Full Text | PDF People People p116 doi:10.1038/nbt.2097 Full Text | PDF Top Advertisement Miami 2012 Winter Symposium: Nanotechnology in Biomedicine February 26-29, 2012 • Miami, FL, USA The 45th Miami Winter Symposium will bring together leaders in the field to discuss breakthroughs in new nanomaterials and the challenges in translating these materials into products for the clinic and laboratory. For more information and to register, visit: www.nature.com/natureconferences/miami/mws2012   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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