Nature Biotechnology Contents: Volume 30 pp 1009-1150

Advertisement Hamamatsu's detectors for digital PCR and qPCR instruments allow high-speed operation, cover a wide dynamic range, and guarantee reliable results. For digital PCR systems, we offer ultrasensitive photomultiplier tubes and sCMOS cameras for fluorescence detection. For qPCR and RT-PCR systems, we offer photodiodes as low-cost detector solutions and board-level cameras as imaging solutions. TABLE OF CONTENTS November 2012 Volume 30, Issue 11 In This Issue Editorial News Bioentrepreneur Opinion and Comment Features News and Views Computational Biology Research Careers and Recruitment Advertisement COMPROMISING WHEN YOU NEED A CUSTOM PANEL FOR TARGETED ENRICHMENT? TargetRich™ custom designs enable you to capture the regions you desire, while delivering the results you need. Your research is too important to compromise. Click here to see the results and see why others are calling us about TargetRich. Call us and let us show you how our custom enrichment solutions can be a part of your solution. Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Attend Europe's most comprehensive antibody drug conjugate meeting: World ADC Frankfurt (26-28 February), to meet & network with ADC pioneers from Roche, Genentech, Bayer, Seattle Genetics, ImmunoGen, Novartis & more to maximise your ADC effectiveness, improve translation to the clinic and deliver enhanced clinical results. View Agenda - Register Now   Advertisement BIOPHARMA DEALMAKERS Company Profiles and Partnering Opportunities   Advertisement Reichert SPR Affordable Surface Plasmon Resonance Systems Reichert SPR systems are powerful analytical instruments for label-free molecular interaction analysis. Our life sciences team is ready to discuss your SPR applications. Let our team arrange a demonstration of the Reichert SPR instruments and help configure the component-based system to meet your research needs.   Advertisement New Partnering Opportunities in Alzheimer's Disease! A comprehensive interactive dashboard from Relay Technology Management. Click here for more information on Alzheimer's partnering opportunities.   Focus Top DNA Sequencing Technology Performance gains and falling costs have fueled diverse applications of high-throughput DNA sequencing. This focus issue of Nature Biotechnology summarizes the current status of these technologies as applied to life sciences and medical research. Produced with support from Ion Torrent - by Life Technologies. Table of Contents In This Issue Top In this issue   ppvii - viii doi:10.1038/nbt.2430 Editorial Top Knocking on the clinic door   p1009 doi:10.1038/nbt.2428 High-throughput sequencing for clinical purposes faces technical and quality challenges, but it's worth it. News Top Next-generation proteasome inhibitor approved in multiple myeloma   pp1011 - 1012 Alla Katsnelson doi:10.1038/nbt1112-1011 Interest resparks in RNAi   p1012 Gunjan Sinha doi:10.1038/nbt1112-1012 Miniature wireless sensors presage smart phone medicine   pp1013 - 1014 Michael Eisenstein doi:10.1038/nbt1112-1013 Deal validates DARPins   p1014 Susan Aldridge doi:10.1038/nbt1112-1014a Biosurveillance plan unveiled   p1014 Jeffrey L Fox doi:10.1038/nbt1112-1014b Calamitous HCV trial casts shadow over nucleoside drugs   pp1015 - 1016 Cormac Sheridan doi:10.1038/nbt1112-1015 Deals center on self-reported patient data services   p1016 Allison Proffitt doi:10.1038/nbt1112-1016 Commission calls for genomic privacy   p1017 Jeffrey L Fox doi:10.1038/nbt1112-1017b GM phobia spreads in South Asia   pp1017 - 1019 Killugudi Jayaraman and Hepeng Jia doi:10.1038/nbt1112-1017a Media leaps on French study claiming GM maize carcinogenicity   p1018 Anna Meldolesi doi:10.1038/nbt1112-1018 Opposition thaws for GM crops in Africa   p1019 Linda Nordling doi:10.1038/nbt1112-1019a Around the world in a month   p1019 doi:10.1038/nbt1112-1019b Biotech crowdfunding paves way for angels   p1020 Brian Orelli doi:10.1038/nbt1112-1020a Profile The New York Genome Center   pp1021 - 1022 doi:10.1038/nbt.2429 News Features The battle for sequencing supremacy   pp1023 - 1026 Michael Eisenstein doi:10.1038/nbt.2412 Which companies are leading the pack in terms of market share of the sequencing sector? Michael Eisenstein reports. Direct-to-consumer genomics reinvents itself   pp1027 - 1029 Malorye Allison doi:10.1038/nbt.2409 By putting its foot in the door at the FDA, can 23andMe reinvigorate direct-to-consumer genomics? Malorye Allison investigates. Advertisement Staring at complex Omics data sets? A partnership between Waters and Nonlinear Dynamics is ready to help you visualize data and extract reliable results: the Waters Omics Research Plaform with TransOmics Informatics. Nonlinear's software unlocks the potential of content-rich data generated by Waters' ion mobility MS technology in proteomics and metabolomics experiments. Bioentrepreneur Top Building a business Stranger in a strange land?   pp1030 - 1032 Bassil Dahiyat doi:10.1038/nbt.2352 Opinion and Comment Top Correspondence Assuring the quality of next-generation sequencing in clinical laboratory practice   pp1033 - 1036 Amy S Gargis, Lisa Kalman, Meredith W Berry, David P Bick, David P Dimmock, Tina Hambuch, Fei Lu, Elaine Lyon, Karl V Voelkerding, Barbara A Zehnbauer, Richa Agarwala, Sarah F Bennett, Bin Chen, Ephrem L H Chin, John G Compton, Soma Das, Daniel H Farkas, Matthew J Ferber, Birgit H Funke, Manohar R Furtado, Lilia M Ganova-Raeva, Ute Geigenmuller, Sandra J Gunselman, Madhuri R Hegde, Philip L F Johnson, Andrew Kasarskis, Shashikant Kulkarni, Thomas Lenk, C S Jonathan Liu, Megan Manion, Teri A Manolio, Elaine R Mardis, Jason D Merker, Mangalathu S Rajeevan, Martin G Reese, Heidi L Rehm, Birgitte B Simen, Joanne M Yeakley, Justin M Zook and Ira M Lubin doi:10.1038/nbt.2403 NGS analyses by visualization with Trackster   pp1036 - 1039 Jeremy Goecks, Nate Coraor, The Galaxy Team, Anton Nekrutenko and James Taylor doi:10.1038/nbt.2404 Proteomics-directed cloning of circulating antiviral human monoclonal antibodies   pp1039 - 1043 Shuji Sato, Sean A Beausoleil, Lana Popova, Jason G Beaudet, Ravi K Ramenani, Xiaowu Zhang, James S Wieler, Sandra M Schieferl, Wan Cheung Cheung and Roberto D Polakiewicz doi:10.1038/nbt.2406 Analyzing the association of SCNA boundaries with replication timing   pp1043 - 1045 Sven Bilke and Yevgeniy Gindin doi:10.1038/nbt.2415 Analyzing the association of SCNA boundaries with replication timing   pp1045 - 1046 Subhajyoti De and Franziska Michor doi:10.1038/nbt.2414 Features DNA goes to court   pp1047 - 1053 Caitlin Smith, Stephen Strauss and Laura DeFrancesco doi:10.1038/nbt.2408 DNA profiling is playing a growing role in solving crimes, identifying victims of natural and unnatural disasters and even tracking diplomats. Some forensic experts are looking to advances in genome technologies to gain further ground against criminals. Patents Advances in DNA sequencing lead to patent disputes   pp1054 - 1058 Christopher M Holman doi:10.1038/nbt.2407 Will next-generation DNA sequencing technologies be hindered or helped by today's more aggressive patent acquisition and enforcement practices? Recent patent applications in sequencing   p1059 doi:10.1038/nbt.2426 Advertisement   Human and Mouse Exome NGS  $798/each, guaranteed coverage    RNA-Seq from $798: 20 million  guaranteed reads  4-6 weeks, fastest turnaround time in the industry    http://www.otogenetics.com/    News and Views Top Insulating gene circuits from context by RNA processing   pp1061 - 1062 Caleb J Bashor and James J Collins doi:10.1038/nbt.2411 Two studies find that programmable RNA-processing tools counter the problem of context-dependence in the construction of synthetic biology circuits. See also: Research by Lou et al. Single-stranded siRNAs for in vivo gene silencing   p1063 Markus Elsner doi:10.1038/nbt.2413 The implications of ENCODE for diagnostics   pp1064 - 1065 Eugene Fratkin, Sivan Bercovici and Dietrich A Stephan doi:10.1038/nbt.2418 Large-scale functional genomics data coupled with whole-genome sequencing will lead to improved diagnostic assays. Uniting ENCODE with genome-wide proteomics   pp1065 - 1067 Young-Ki Paik and William S Hancock doi:10.1038/nbt.2416 An important goal of future omics research is to determine how the annotated regions of the genome control the production of protein isoforms. Research Highlights   p1067 doi:10.1038/nbt.2423 News and Views Feature Genome sequencing in clinical microbiology   pp1068 - 1071 Jacqueline Z-M Chan, Mark J Pallen, Beryl Oppenheim and Chrystala Constantinidou doi:10.1038/nbt.2410 High-throughput sequencing is being adopted to characterize microbial pathogens and track their evolution and spread. Biotechnology JOBS of the week Professor of Sustainable Feedstocks and Industrial Biotechnology Warwick University PhD Graduate Program - Pharmaceutical Biotechnology University of Illinois at Chicago Tenure Track Faculty Position in Plant Science / Plant Biotechnology Agricultural Biotechnology Research Center More Science jobs from Biotechnology EVENT 2nd Biotechnology World Congress February 18-21, 2013 Dubai, UAE More science events from Computational Biology Top Perspective Protein structure prediction from sequence variation   pp1072 - 1080 Debora S Marks, Thomas A Hopf and Chris Sander doi:10.1038/nbt.2419 Q&A Genome interpretation and assembly[mdash]recent progress and next steps   pp1081 - 1083 H. Craig Mak doi:10.1038/nbt.2425 Ten experts discuss innovations needed to analyze the millions of genomes soon to be sequenced. Research Top Reviews The expanding scope of DNA sequencing   pp1084 - 1094 Jay Shendure and Erez Lieberman Aiden doi:10.1038/nbt.2421 Interpreting noncoding genetic variation in complex traits and human disease   pp1095 - 1106 Lucas D Ward and Manolis Kellis doi:10.1038/nbt.2422 Mapping recently identified nucleotide variants in the genome and transcriptome   pp1107 - 1116 Chun-Xiao Song, Chengqi Yi and Chuan He doi:10.1038/nbt.2398 Pharmacogenomics in clinical practice and drug development   pp1117 - 1124 Andrew R Harper and Eric J Topol doi:10.1038/nbt.2424 Articles Systematic identification of synergistic drug pairs targeting HIV   pp1125 - 1130 Xu Tan, Long Hu, Lovelace J Luquette III, Geng Gao, Yifang Liu, Hongjing Qu, Ruibin Xi, Zhi John Lu, Peter J Park and Stephen J Elledge doi:10.1038/nbt.2391 Tan et al. use a multiplex screening method to systematically evaluate [sim]500,000 drug pairs assembled from a collection of 1,000 FDA-approved or clinically tested compounds, and identify drugs that synergize to inhibit HIV replication. Engineering a thermoregulated intein-modified xylanase into maize for consolidated lignocellulosic biomass processing   pp1131 - 1136 Binzhang Shen, Xueguang Sun, Xiao Zuo, Taran Shilling, James Apgar, Mary Ross, Oleg Bougri, Vladimir Samoylov, Matthew Parker, Elaina Hancock, Hector Lucero, Benjamin Gray, Nathan A Ekborg, Dongcheng Zhang, Jeremy C Schley Johnson, Gabor Lazar and R Michael Raab doi:10.1038/nbt.2402 To facilitate the conversion of maize into biofuels, Shen et al. equip the plant with a thermoregulated intein-modified xylanase that does not compromise yield and allows cell-wall degradation at high temperatures. Letters Ribozyme-based insulator parts buffer synthetic circuits from genetic context   pp1137 - 1142 Chunbo Lou, Brynne Stanton, Ying-Ja Chen, Brian Munsky and Christopher A Voigt doi:10.1038/nbt.2401 Lou et al. find that sequences between promoters and regulated genes in synthetic circuits cause unpredictable gene expression, and they identify and characterize insulator parts that cleave untranslated regions present in circuits to overcome this problem. See also: News and Views by Bashor & Collins Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy   pp1143 - 1148 Jeffrey D Martell, Thomas J Deerinck, Yasemin Sancak, Thomas L Poulos, Vamsi K Mootha, Gina E Sosinsky, Mark H Ellisman and Alice Y Ting doi:10.1038/nbt.2375 Martell et al. engineer APEX, a protein tag for electron microscopy that does not require light activation, enabling the imaging of subcellular protein localization in large or thick sections. Careers and Recruitment Top Third-quarter biotech job picture   p1149 Michael Francisco doi:10.1038/nbt.2417 People People   p1150 doi:10.1038/nbt.2420 Advertisement TRADE SECRETS A Nature Network blog byBIOENTREPRENEUR Brought to you by Nature Biotechnology Access the insights, advice and commentary from scientists and entrepreneurs building biotech sectors around the world. Join the global dialogue on life science entrepreneurship: http://blogs.nature.com/trade_secrets   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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