Table of contents


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Focus

Focus on Next-Generation Sequencing

This focus summarizes the current state of the art in massively parallel sequencing technologies and how these platforms are changing the face of biological and biomedical research and of the sequencing business itself. With financial support from Roche, the focus will be freely available online from October 2008 to April 2009.

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Editorial

Defusing a time bomb p1051

doi:10.1038/nbt1008-1051

Researchers and their institutions need to dispel a myth about 'independent' research before the media does it for them.


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News

CD20 blockers eye crowded rheumatology market pp1053 - 1054

George S Mack

doi:10.1038/nbt1008-1053


Roche consolidates grip on anti-angiogenesis market pp1055 - 1056

Nuala Moran

doi:10.1038/nbt1008-1055


London forges £2 billion research cluster p1056

Nuala Moran

doi:10.1038/nbt1008-1056


Ark floats gene therapy's boat, for now pp1057 - 1059

Randy Osborne

doi:10.1038/nbt1008-1057


Heplisav's topline p1058

Susan Aldridge

doi:10.1038/nbt1008-1058a


Cloning shop p1058

Hayley Birch

doi:10.1038/nbt1008-1058b


FDA to steer nanotech p1060

Jeffrey L Fox

doi:10.1038/nbt1008-1060a


Plant biotech bonanza p1060

Emily Waltz

doi:10.1038/nbt1008-1060b


Plasma product companies outmuscle small recombinant players pp1060 - 1061

Peter Mitchell

doi:10.1038/nbt1008-1060c


Tysabri's troubles return p1061

Hannah Hoag

doi:10.1038/nbt1008-1061


Data Page

Trends in biotech literature 2007 p1062

Gaspar Taroncher-Oldenburg & Andrew Marshall

doi:10.1038/nbt1008-1062


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Bioentrepreneur

Building a business

Where to float? pp1063 - 1066

Nuala Moran

doi:10.1038/bioe.2008.8


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Opinion and Comment

Correspondence

Ghostbusters should only bust ghosts pp1067 - 1068

Lanie M Adamson, Mary Whitman, Adam Jacobs & Tracy E Bunting-Early

doi:10.1038/nbt1008-1067


Fuelling the 9 billion pp1068 - 1070

Wayne Martindale & Anthony Trewavas

doi:10.1038/nbt1008-1068


Allergenicity testing of GM crops pp1070 - 1071

Rob C Aalberse

doi:10.1038/nbt1008-1070


Reply to Allergenicity testing of GM crops pp1071 - 1072

doi:10.1038/nbt1008-1071


Field-evolved resistance to Bt toxins pp1072 - 1074

Willam Moar, Rick Roush, Anthony Shelton, Juan Ferré, Susan MacIntosh, B Rogers Leonard & Craig Abel

doi:10.1038/nbt1008-1072


Field-evolved resistance to Bt toxins pp1074 - 1076

doi:10.1038/nbt1008-1074


Commentary

New therapies from old medicines pp1077 - 1083

Shaw T Chen, Jinhui Dou, Robert Temple, Rajiv Agarwal, Kuei-Meng Wu & Susan Walker

doi:10.1038/nbt1008-1077

Although new botanical drugs pose many challenges for both industry and the FDA, approval of the first botanical prescription drug shows they can be successfully met.


Book Review

A timely marriage p1084

doi:10.1038/nbt1008-1084


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Features

Patents

A nail in the coffin for DNA sequence patents? pp1085 - 1086

Miles Yamanaka

doi:10.1038/nbt1008-1085

Does the recent Board decision in Ex parte Kubin mean the end for biotech patents claiming DNA sequences?


Recent patent applications in proteomics p1087

doi:10.1038/nbt1008-1087


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News and Views

Enhancing immunity to HIV through APOBEC pp1089 - 1090

Reuben S Harris

doi:10.1038/nbt1008-1089

A small molecule that interferes with HIV Vif promotes the antiviral activity of the human protein APOBEC3G.

See also: Research by Nathans et al.


From biomarkers to integrated network responses pp1090 - 1092

Uwe Sauer & Nicola Zamboni

doi:10.1038/nbt1008-1090

The ability to quantify carbon fluxes in mammalian cells is a step toward elucidating the dynamic metabolic networks associated with health and disease.

See also: Research by Munger et al.


New beta-cells from old acini pp1092 - 1093

Michael S German

doi:10.1038/nbt1008-1092

Pancreatic acinar cells have been reprogrammed in vivo into insulin-expressing cells by adenoviral delivery of three transcription factors.


Unveiling viral enablers pp1093 - 1094

Yueh-Ming Loo & Michael Gale, Jr

doi:10.1038/nbt1008-1093

Global RNA interference screens uncover the host genes that support infection by HIV, West Nile virus and influenza virus.


Research Highlights p1095

doi:10.1038/nbt1008-1095


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Editorial

Next-generation sequencing

Prepare for the deluge p1099

doi:10.1038/nbt1008-1099

The gobs of data produced by next-generation sequencing are a key problem limiting wider adoption.


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News

Next-generation sequencing

Profile: Rade Drmanac p1100

Laura DeFrancesco

doi:10.1038/nbt1008-1100

Launching the world's first commercial human genome sequencing center is currently the 'unreasonable' career ambition of sequencing-by-hybridization pioneer Rade Drmanac.


News Features

Next-generation sequencing

Fixing the front end pp1101 - 1104

Ken Garber

doi:10.1038/nbt1008-1101

One bottleneck in next-generation sequencing is genomic sample selection. As research groups tackle the problem, companies are seizing a market opportunity. Ken Garber reports.


Next-generation sequencing

What price personal genome exploration? pp1105 - 1108

Jeffrey L Fox

doi:10.1038/nbt1008-1105

Companies offering direct-to-consumer genomic information face tough questions about who regulates them, where they fit in health care and how to value their services. What will it take to move them from niche services to a broader customer base? Jeffrey Fox reports.


Next-generation sequencing

The sequencing shakeup pp1109 - 1112

Amy Coombs

doi:10.1038/nbt1008-1109

Deep sequencing technology could soon be competitive with certain array applications. But the jury remains out on which of the myriad platforms will have the greatest impact and broadest application. Amy Coombs investigates.


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Opinion and Comment

Commentary

Next-generation sequencing

How to get genomes at one ten-thousandth the cost pp1113 - 1115

Jeffery A Schloss

doi:10.1038/nbt1008-1113

The NHGRI's Advanced DNA Sequencing Technology program is spearheading the development of platforms that will bring routine whole-genome sequencing closer to reality.


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Research

Perspectives

Next-generation sequencing

The development and impact of 454 sequencing pp1117 - 1124

Jonathan M Rothberg & John H Leamon

doi:10.1038/nbt1485


Next-generation sequencing

What would you do if you could sequence everything? pp1125 - 1133

Avak Kahvejian, John Quackenbush & John F Thompson

doi:10.1038/nbt1494


Reviews

Next-generation sequencing

Next-generation DNA sequencing pp1135 - 1145

Jay Shendure & Hanlee Ji

doi:10.1038/nbt1486


Next-generation sequencing

The potential and challenges of nanopore sequencing pp1146 - 1153

Daniel Branton, David W Deamer, Andre Marziali, Hagan Bayley, Steven A Benner, Thomas Butler, Massimiliano Di Ventra, Slaven Garaj, Andrew Hibbs, Xiaohua Huang, Stevan B Jovanovich, Predrag S Krstic, Stuart Lindsay, Xinsheng Sean Ling, Carlos H Mastrangelo, Amit Meller, John S Oliver, Yuriy V Pershin, J Michael Ramsey, Robert Riehn, Gautam V Soni, Vincent Tabard-Cossa, Meni Wanunu, Matthew Wiggin & Jeffery A Schloss

doi:10.1038/nbt.1495


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Computational Biology

Perspective

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology pp1155 - 1160

Markus J Herrgård, Neil Swainston, Paul Dobson, Warwick B Dunn, K Yalçin Arga, Mikko Arvas, Nils Blüthgen, Simon Borger, Roeland Costenoble, Matthias Heinemann, Michael Hucka, Nicolas Le Novère, Peter Li, Wolfram Liebermeister, Monica L Mo, Ana Paula Oliveira, Dina Petranovic, Stephen Pettifer, Evangelos Simeonidis, Kieran Smallbone, Irena Spasié, Dieter Weichart, Roger Brent, David S Broomhead, Hans V Westerhoff, Betül Kürdar, Merja Penttilä, Edda Klipp, Bernhard Ø Palsson, Uwe Sauer, Stephen G Oliver, Pedro Mendes, Jens Nielsen & Douglas B Kell

doi:10.1038/nbt1492


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Research

Articles

Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum pp1161 - 1168

Marco A van den Berg, Richard Albang, Kaj Albermann, Jonathan H Badger, Jean-Marc Daran, Arnold J M Driessen, Carlos Garcia-Estrada, Natalie D Fedorova, Diana M Harris, Wilbert H M Heijne, Vinita Joardar, Jan A K W Kiel, Andriy Kovalchuk, Juan F Martín, William C Nierman, Jeroen G Nijland, Jack T Pronk, Johannes A Roubos, Ida J van der Klei, Noël N M E van Peij, Marten Veenhuis, Hans von Döhren, Christian Wagner, Jennifer Wortman & Roel A L Bovenberg

doi:10.1038/nbt.1498

Penicillins and derived beta-lactam antibiotics are essential in healthcare. To gain more insight into penicillin synthesis van den Berg and colleagues sequence and analyze the genome and transcriptome of the filamentous fungus Penicillium chrysogenum.


Notch signaling respecifies the hemangioblast to a cardiac fate pp1169 - 1178

Vincent C Chen, Robert Stull, Daniel Joo, Xin Cheng & Gordon Keller

doi:10.1038/nbt.1497

The development of effective methods for generating cardiomyocytes from embryonic stem cells may prove useful in cell replacement therapies and drug screening. Chen et al. show that activation of Notch signaling efficiently converts hematopoietic progenitors derived from mouse embryonic stem cells into cardiovascular progenitors that give rise to large numbers of cardiomyocytes.


Systems-level metabolic flux profiling identifies fatty acid synthesis as a target for antiviral therapy pp1179 - 1186

Joshua Munger, Bryson D Bennett, Anuraag Parikh, Xiao-Jiang Feng, Jessica McArdle, Herschel A Rabitz, Thomas Shenk & Joshua D Rabinowitz

doi:10.1038/nbt.1500

Munger et al. show that infection with human cytomegalovirus upregulates fatty acid biosynthesis and that pharmacological inhibition of this pathway inhibits replication of both this virus and influenza A. This approach, the first to reliably map major carbon fluxes in mammalian cells, extends the promise of metabolomics from diagnostic applications to identification of new therapeutic concepts.

See also: News and Views by Sauer & Zamboni


Letter

Small-molecule inhibition of HIV-1 Vif pp1187 - 1192

Robin Nathans, Hong Cao, Natalia Sharova, Akbar Ali, Mark Sharkey, Ruzena Stranska, Mario Stevenson & Tariq M Rana

doi:10.1038/nbt.1496

The HIV-1 protein Vif, which promotes degradation of the host cell's antiviral APOBEC3 proteins, has yet to be targeted for therapeutic intervention. Nathans et al. use a high-throughput fluorescence screen to identify a small molecule that inhibits HIV replication in cultured cells by antagonizing Vif in an APOBEC3-dependent manner.

See also: News and Views by Harris


Corrigenda

Corrigendum: Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina) p1193

Diego Martinez, Randy M Berka, Bernard Henrissat, Markku Saloheimo, Mikko Arvas, Scott E Baker, Jarod Chapman, Olga Chertkov, Pedro M Coutinho, Dan Cullen, Etienne G J Danchin, Igor V Grigoriev, Paul Harris, Melissa Jackson, Christian P Kubicek, Cliff S Han, Isaac Ho, Luis F Larrondo, Alfredo Lopez de Leon, Jon K Magnuson, Sandy Merino, Monica Misra, Beth Nelson, Nicholas Putnam, Barbara Robbertse, Asaf A Salamov, Monika Schmoll, Astrid Terry, Nina Thayer, Ann Westerholm-Parvinen, Conrad L Schoch, Jian Yao, Ravi Barabote, Mary Anne Nelson, Chris Detter, David Bruce, Cheryl R Kuske, Gary Xie, Paul Richardson, Daniel S Rokhsar, Susan M Lucas, Edward M Rubin, Nigel Dunn-Coleman, Michael Ward & Thomas S Brettin

doi:10.1038/nbt1008-1193a


Corrigendum: Public biotech 2007—the numbers p1193

Stacy Lawrence & Riku Lähteenmäki

doi:10.1038/nbt1008-1193b


Corrigendum: Predicting PDZ domain–peptide interactions from primary sequences p1193

Jiunn R Chen, Bryan H Chang, John E Allen, Michael A Stiffler & Gavin MacBeath

doi:10.1038/nbt1008-1193c


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Naturejobs

Careers and Recruitment

So you want to be a venture capitalist? pp1195 - 1196

Jason Brown

doi:10.1038/nbt1008-1195

Venture capitalists have a key role in the translation of scientific innovation from idea to commercial reality.


People

People p1198

doi:10.1038/nbt1008-1198


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