Research library: Systems biology/High-throughput

2007: December | November | October | September | August | July | June | May | April | March | February | January

Other Years: 2004 | 2005 | 2006 | 2008

December

letter
Isolation of rare circulating tumour cells in cancer patients by microchip technology
Sunitha Nagrath et al.
Nature 450, 1235–1239
(20 December 2007); doi:10.1038/nature06385
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November

article
Network modeling links breast cancer susceptibility and centrosome dysfunction
Miguel Angel Pujana et al.
Nature Genetics 39, 1338–1349
(November 2007); doi:10.1038/ng.2007.2
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brief communication
Semi-supervised learning for peptide identification from shotgun proteomics datasets
Lukas Käll, Jesse D Canterbury, Jason Weston, William Stafford Noble & Michael J MacCoss
Nature Methods 4, 923–925
(November 2007); doi:10.1038/nmeth1113
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review
Target deconvolution strategies in drug discovery
Georg C. Terstappen, Christina Schlüpen, Roberto Raggiaschi & Giovanni Gaviraghi
Nature Reviews Drug Discovery 6, 891–903
(November 2007); doi:10.1038/nrd2410
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October

review
Mapping protein post-translational modifications with mass spectrometry
Eric S Witze, William M Old, Katheryn A Resing & Natalie G Ahn
Nature Methods 4, 798–806
(October 2007); doi:10.1038/nmeth1100
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perspective
Activity-based protein profiling for the functional annotation of enzymes
Katherine T Barglow & Benjamin F Cravatt
Nature Methods 4, 822–827
(October 2007); doi:10.1038/nmeth1092
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article
High-throughput genetic interaction mapping in the fission yeast Schizosaccharomyces pombe
Assen Roguev, Marianna Wiren, Jonathan S Weissman & Nevan J Krogan
Nature Methods 4, 861–866
(October 2007); doi:10.1038/nmeth1098
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news and views
Fission yeast goes synthetic
Olaf Nielsen
Nature Methods 4, 777–778
(October 2007); doi:10.1038/nmeth1007-777
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article
Noninvasive optical imaging of cysteine protease activity using fluorescently quenched activity-based probes
Galia Blum, Georges von Degenfeld, Milton J Merchant, Helen M Blau & Matthew Bogyo
Nature Chemical Biology 3, 668–677
(October 2007); doi:10.1038/nchembio.2007.26
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September

letter
Structural basis for AMP binding to mammalian AMP-activated protein kinase
Bing Xiao, Richard Heath, Peter Saiu, Fiona C. Leiper, Philippe Leone, Chun Jing, Philip A. Walker, Lesley Haire, John F. Eccleston, Colin T. Davis, Stephen R. Martin, David Carling & Steven J. Gamblin
Nature 449, 496–500
(27 September 2007); doi:10.1038/nature06161
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article
Large-scale genetic fine mapping and genotype-phenotype associations implicate polymorphism in the IL2RA region in type 1 diabetes
Christopher E Lowe, Jason D Cooper, Todd Brusko, Neil M Walker, Deborah J Smyth, Rebecca Bailey, Kirsi Bourget, Vincent Plagnol, Sarah Field, Mark Atkinson, David G Clayton, Linda S Wicker & John A Todd
Nature Genetics 39, 1074–1082
(September 2007); doi:10.1038/ng2102
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review
Integrating physical and genetic maps: from genomes to interaction networks
Andreas Beyer, Sourav Bandyopadhyay & Trey Ideker
Nature Reviews Genetics 8, 699–710
(September 2007); doi:10.1038/nrg2144
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review
Beyond toothpicks: new methods for isolating mutant bacteria
A. James Link, Ki Jun Jeong & George Georgiou
Nature Reviews Microbiology 5, 680–688
(September 2007); doi:10.1038/nrmicro1715
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analysis
Ensemble modeling for analysis of cell signaling dynamics
Lars Kuepfer, Matthias Peter, Uwe Sauer & Jörg Stelling
Nature Biotechnology 25, 1001–1006
(2007); doi:10.1038/nbt1330
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brief communication
Highly efficient somatic-mutation identification using Escherichia coli mismatch-repair detection
Brock A Peters, Zhengyan Kan, Dragan Sebisanovic, Kanan Pujara, Zhiyong Wang, Peter Hong, Bernard Chow, Jeremy Stinson, Victoria E H Carlton, Thinh Q Pham, Howard Stern, Paul Waring, Kenneth J Hillan, David A Eberhard, Frederic de Sauvage, Jianbiao Zheng, Malek Faham & Somasekar Seshagiri
Nature Methods 4, 713–715
(September 2007); doi:10.1038/nmeth1081
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August

article
Plasma membrane nanoswitches generate high-fidelity Ras signal transduction
Tianhai Tian, Angus Harding, Kerry Inder, Sarah Plowman, Robert G. Parton & John F. Hancock
Nature Cell Biology 9, 905–914
(August 2007); doi:10.1038/ncb1615
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news and views
Nanoclusters digitize Ras signalling
Anne K. Kenworthy
Nature Cell Biology 9, 875–877
(August 2007); doi:10.1038/ncb0807-875
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news and views
Gene expression analysis goes digital
Victor E Velculescu & Kenneth W Kinzler
Nature Biotechnology 25, 878–880
(August 2007); doi:10.1038/nbt0807-878
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review
Analysis of protein complexes using mass spectrometry
Anne-Claude Gingras, Matthias Gstaiger, Brian Raught & Ruedi Aebersold
Nature Reviews Molecular Cell Biology 8, 645–654
(August 2007); doi:10.1038/nrm2208
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commentary
Scaffold composition and biological relevance of screening libraries
Anang A Shelat & R Kiplin Guy
Nature Chemical Biology 3, 442–446
(August 2007); doi:10.1038/nchembio0807-442
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news and views
Computational biochemistry: Models of transition
JoAnne Stubbe
Nature 448, 762–763
(16 August 2007); doi:10.1038/448762a
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review
Mining gene expression profiles: expression signatures as cancer phenotypes
Joseph R. Nevins & Anil Potti
Nature Reviews Genetics 8, 601–609
(August 2007); doi:10.1038/nrg2137
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article
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
Gordon Robertson, Martin Hirst, Matthew Bainbridge, Misha Bilenky, Yongjun Zhao, Thomas Zeng, Ghia Euskirchen, Bridget Bernier, Richard Varhol, Allen Delaney, Nina Thiessen, Obi L Griffith, Ann He, Marco Marra, Michael Snyder & Steven Jones
Nature Methods 4, 651–657
(August 2007); doi:10.1038/nmeth1068
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news and views
ChIP-seq: welcome to the new frontier
Elaine R Mardis
Nature Methods 4, 613–614
(August 2007); doi:10.1038/nmeth0807-613
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article
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Tarjei S. Mikkelsen, Manching Ku, David B. Jaffe, Biju Issac, Erez Lieberman, Georgia Giannoukos, Pablo Alvarez, William Brockman, Tae-Kyung Kim, Richard P. Koche, William Lee, Eric Mendenhall, Aisling O'Donovan, Aviva Presser, Carsten Russ, Xiaohui Xie, Alexander Meissner, Marius Wernig, Rudolf Jaenisch, Chad Nusbaum, Eric S. Lander & Bradley E. Bernstein
Nature 448, 553–560
(2 August 2007); doi:10.1038/nature06008
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letter
Common effector processing mediates cell-specific responses to stimuli
Kathryn Miller-Jensen, Kevin A. Janes, Joan S. Brugge & Douglas A. Lauffenburger
Nature 448, 604–608
(2 August 2007); doi:10.1038/nature06001
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article
Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping
Vanessa Vermeirssen, Bart Deplancke, M Inmaculada Barrasa, John S Reece-Hoyes, H Efsun Arda, Christian A Grove, Natalia J Martinez, Reynaldo Sequerra, Lynn Doucette-Stamm, Michael R Brent & Albertha J M Walhout
Nature Methods 4, 659–664
(August 2007); doi:10.1038/nmeth1063
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perspective
Image-based chemical screening
Anne E Carpenter
Nature Chemical Biology 3, 461–465
(August 2007); doi:10.1038/nchembio.2007.15
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commentary
Reporting data from high-throughput screening of small-molecule libraries
James Inglese, Caroline E Shamu & R Kiplin Guy
Nature Chemical Biology 3, 438–441
(August 2007); doi:10.1038/nchembio0807-438
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review
High-throughput screening assays for the identification of chemical probes
James Inglese, Ronald L Johnson, Anton Simeonov, Menghang Xia, Wei Zheng, Christopher P Austin & Douglas S Auld
Nature Chemical Biology 3, 466–479
(August 2007); doi:10.1038/nchembio.2007.17
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July

review
Gene methylation and early detection of genitourinary cancer: the road ahead
Paul Cairns
Nature Reviews Cancer 7, 531–543
(July 2007); doi:10.1038/nrc2170
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letter
A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer
David J Hunter, Peter Kraft, Kevin B Jacobs, David G Cox, Meredith Yeager, Susan E Hankinson, Sholom Wacholder, Zhaoming Wang, Robert Welch, Amy Hutchinson, Junwen Wang, Kai Yu, Nilanjan Chatterjee, Nick Orr, Walter C Willett, Graham A Colditz, Regina G Ziegler, Christine D Berg, Saundra S Buys, Catherine A McCarty, Heather Spencer Feigelson, Eugenia E Calle, Michael J Thun, Richard B Hayes, Margaret Tucker, Daniela S Gerhard, Joseph F Fraumeni, Jr, Robert N Hoover, Gilles Thomas & Stephen J Chanock
Nature Genetics 39, 870–874
(July 2007); doi:10.1038/ng2075
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news and views
ENCODE and our very busy genome
Steven Henikoff
Nature Genetics 39, 817–818
(July 2007); doi:10.1038/ng0707-817
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brief communication
A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21
David A van Heel, Lude Franke, Karen A Hunt, Rhian Gwilliam, Alexandra Zhernakova, Mike Inouye, Martin C Wapenaar, Martin C N M Barnardo, Graeme Bethel, Geoffrey K T Holmes, Con Feighery, Derek Jewell, Dermot Kelleher, Parveen Kumar, Simon Travis, Julian RF Walters, David S Sanders, Peter Howdle, Jill Swift, Raymond J Playford, William M McLaren, M Luisa Mearin, Chris J Mulder, Ross McManus, Ralph McGinnis, Lon R Cardon, Panos Deloukas & Cisca Wijmenga
Nature Genetics 39, 827–829
(July 2007); doi:10.1038/ng2058
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review
Mechanisms of specificity in protein phosphorylation
Jeffrey A. Ubersax & James E. Ferrell Jr
Nature Reviews Molecular Cell Biology 8, 530–541
(July 2007); doi:10.1038/nrm2203
| Summary | Full Text (HTML / PDF) |

perspective
Taking gene-expression profiling to the clinic: when will molecular signatures become relevant to patient care?
Christos Sotiriou & Martine J. Piccart
Nature Reviews Cancer 7, 545–553
(July 2007); doi:10.1038/nrc2173
| Summary | Full Text (HTML / PDF) |

article
A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila
Georg Dietzl, Doris Chen, Frank Schnorrer, Kuan-Chung Su, Yulia Barinova, Michaela Fellner, Beate Gasser, Kaolin Kinsey, Silvia Oppel, Susanne Scheiblauer, Africa Couto, Vincent Marra, Krystyna Keleman & Barry J. Dickson
Nature 448, 151–156
(12 July 2007); doi:10.1038/nature05954
| Summary | Full Text (HTML / PDF) |

review
Universal strategies in research and drug discovery based on protein-fragment complementation assays
Stephen W. Michnick, Po Hien Ear, Emily N. Manderson, Ingrid Remy & Eduard Stefan
Nature Reviews Drug Discovery 6, 569–582
(July 2007); doi:10.1038/nrd2311
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letter
Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes
John A Todd et al.
Nature Genetics 39, 857–864
(July 2007); doi:10.1038/ng2068
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brief communication
Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility
Miles Parkes et al.
Nature Genetics 39, 830–832
(July 2007); doi:10.1038/ng2061
| Summary | Full Text (HTML / PDF) |

news and views
Guilt beyond a reasonable doubt
David Altshuler & Mark Daly
Nature Genetics 39, 813–815
(July 2007); doi:10.1038/ng0707-813
| Summary | Full Text (HTML / PDF) |

review
The versatile worm: genetic and genomic resources for Caenorhabditis elegans research
Igor Antoshechkin & Paul W. Sternberg
Nature Reviews Genetics 8, 518–532
(July 2007); doi:10.1038/nrg2105
| Summary | Full Text (HTML / PDF) |

June

article
Genome-wide association study identifies novel breast cancer susceptibility loci
Douglas F. Easton, et al.
Nature 447, 1087–1093
(28 June 2007); doi:10.1038/nature05887
| Summary | Full Text (HTML / PDF) |

review
Chronic myeloid leukaemia as a model of disease evolution in human cancer
Junia V. Melo & David J. Barnes
Nature Reviews Cancer 7, 441–453
(June 2007); doi:10.1038/nrc2147
| Summary | Full Text (HTML / PDF) |

article
MMTV insertional mutagenesis identifies genes, gene families and pathways involved in mammary cancer
Vassiliki Theodorou, Melanie A Kimm, Mandy Boer, Lodewyk Wessels, Wendy Theelen, Jos Jonkers & John Hilkens
Nature Genetics 39, 759–769
(June 2007); doi:10.1038/ng2034
| Summary | Full Text (HTML / PDF) |

review
Exploring genetic interactions and networks with yeast
Charles Boone, Howard Bussey & Brenda J. Andrews
Nature Reviews Genetics 8, 437–449
(June 2007); doi:10.1038/nrg2085
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article
A semisynthetic epitope for kinase substrates
Jasmina J Allen, Manqing Li, Craig S Brinkworth, Jennifer L Paulson, Dan Wang, Anette Hübner, Wen-Hai Chou, Roger J Davis, Alma L Burlingame, Robert O Messing, Carol D Katayama, Stephen M Hedrick & Kevan M Shokat
Nature Methods 4, 511–516
(June 2007); doi:10.1038/nmeth1048
| Summary | Full Text (HTML / PDF) |

article
Chromosomally unstable mouse tumours have genomic alterations similar to diverse human cancers
Richard S. Maser, Bhudipa Choudhury, Peter J. Campbell, Bin Feng, Kwok-Kin Wong, Alexei Protopopov, Jennifer O'Neil, Alejandro Gutierrez, Elena Ivanova, Ilana Perna, Eric Lin, Vidya Mani, Shan Jiang, Kate McNamara, Sara Zaghlul, Sarah Edkins, Claire Stevens, Cameron Brennan, Eric S. Martin, Ruprecht Wiedemeyer, Omar Kabbarah, Cristina Nogueira, Gavin Histen, Jon Aster, Marc Mansour, Veronique Duke, Letizia Foroni, Adele K. Fielding, Anthony H. Goldstone, Jacob M. Rowe, Yaoqi A. Wang, A. Thomas Look, Michael R. Stratton, Lynda Chin, P. Andrew Futreal & Ronald A. DePinho
Nature 447, 966–971
(21 June 2007); doi:10.1038/nature05886
| Summary | Full Text (HTML / PDF) |

article
Generation of functional hemangioblasts from human embryonic stem cells
Shi-Jiang Lu, Qiang Feng, Sergio Caballero, Yu Chen, Malcolm A S Moore, Maria B Grant & Robert Lanzaamp;
Nature Methods 4, 501–509
(June 2007); doi:10.1038/nmeth1041
| Summary | Full Text (HTML / PDF) |

article
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
The ENCODE Project Consortium Analysis Coordination Chromatin and Replication Genes and Transcripts Integrated Analysis and Manuscript Preparation Management Group Multi-species Sequence Analysis Transcriptional Regulatory Elements UCSC Genome Browser Variation NISC Comparative Sequencing Program Baylor College of Medicine, Human Genome Sequencing Center Washington University Genome Sequencing Center Broad Institute Children's Hospital Oakland Research Institute
Nature 447, 799–816
(14 June 2007); doi:10.1038/nature05874
| Summary | Full Text (HTML / PDF) |

brief communication
Pervasive combinatorial modification of histone H3 in human cells
Benjamin A Garcia, James J Pesavento, Craig A Mizzen & Neil L Kelleher
Nature Methods 4, 487–489
(June 2007); doi:10.1038/nmeth1052
| Summary | Full Text (HTML / PDF) |

brief communication
Microgram-scale protein structure determination by NMR
James M Aramini, Paolo Rossi, Clemens Anklin, Rong Xiao & Gaetano T Montelione
Nature Methods 4, 491–493
(June 2007); doi:10.1038/nmeth1051
| Summary | Full Text (HTML / PDF) |

article
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls
The Wellcome Trust Case Control Consortium
Nature 447, 661–678
(7 June 2007); doi:10.1038/nature05911
| Summary | Full Text (HTML / PDF) |

news and views
Genomics: Guilt by association
Anne M. Bowcock
Nature 447, 645–646
(7 June 2007); doi:10.1038/447645a
| Full Text (HTML / PDF) |

letter
Rewiring cellular morphology pathways with synthetic guanine nucleotide exchange factors
Brian J. Yeh, Robert J. Rutigliano, Anrica Deb, Dafna Bar-Sagi & Wendell A. Lim
Nature 447, 596–600
(31 May 2007); doi:10.1038/nature05851
| Summary | Full Text (HTML / PDF) |

review
Network motifs: theory and experimental approaches
Uri Alon
Nature Reviews Genetics 7, 450–461
(June 2007); doi:10.1038/nrg2102
| Summary | Full Text (HTML / PDF) |

May

letter
Genetic reconstruction of a functional transcriptional regulatory network
Zhanzhi Hu, Patrick J Killion & Vishwanath R Iyer
Nature Genetics 39, 683–687
(May 2007); doi:10.1038/ng2012
| Summary | Full Text (HTML / PDF) |

article
A high-quality catalog of the Drosophila melanogaster proteome
Erich Brunner, Christian H Ahrens, Sonali Mohanty, Hansruedi Baetschmann, Sandra Loevenich, Frank Potthast, Eric W Deutsch, Christian Panse, Ulrik de Lichtenberg, Oliver Rinner, Hookeun Lee, Patrick G A Pedrioli, Johan Malmstrom, Katja Koehler, Sabine Schrimpf, Jeroen Krijgsveld, Floyd Kregenow, Albert J R Heck, Ernst Hafen, Ralph Schlapbach & Ruedi Aebersold
Nature Biotechnology 25, 576–583
(May 2007); doi:10.1038/nbt1300
| Summary | Full Text (HTML / PDF) |

brief communication
Quantitative proteomic assessment of very early cellular signaling events
Joern Dengjel, Vyacheslav Akimov, Jesper V Olsen, Jakob Bunkenborg, Matthias Mann, Blagoy Blagoev & Jens S Andersen
Nature Biotechnology 25, 566–568
(May 2007); doi:10.1038/nbt1301
| Summary | Full Text (HTML / PDF) |

perspective
Towards zoomable multidimensional maps of the cell
Zhenjun Hu, Joe Mellor, Jie Wu, Minoru Kanehisa, Joshua M Stuart & Charles DeLisi
Nature Biotechnology 25, 547–554
(May 2007); doi:10.1038/nbt1304
| Summary | Full Text (HTML / PDF) |

article
Chemoselective probes for metabolite enrichment and profiling
Erin E Carlson & Benjamin F Cravatt
Nature Methods 4, 429–435
(May 2007); doi:10.1038/nmeth1038
| Summary | Full Text (HTML / PDF) |

news and views
High-throughput screening flows along
Hicham Fenniri & Ramon Alvarez-Puebla
Nature Chemical Biology 3, 247–249
(May 2007); doi:10.1038/nchembio0507-247
| Summary | Full Text (HTML / PDF) |

news and views
Autism: highly heritable but not inherited
Arthur L Beaudet
Nature Methods 13, 534–536
(May 2007); doi:10.1038/nm0507-534
| Summary | Full Text (HTML / PDF) |

letter
Estrogen receptor alpha (ESR1) gene amplification is frequent in breast cancer
Frederik Holst, Phillip R Stahl, Christian Ruiz, Olaf Hellwinkel, Zeenath Jehan, Marc Wendland, Annette Lebeau, Luigi Terracciano, Khawla Al-Kuraya, Fritz Jänicke, Guido Sauter & Ronald Simon
Nature Genetics 39, 655–660
(May 2007); doi:10.1038/ng2006
| Summary | Full Text (HTML / PDF) |

review
Biology by numbers: mathematical modelling in developmental biology
Claire J. Tomlin & Jeffrey D. Axelrod
Nature Reviews Genetics 8, 331–340
(May 2007); doi:10.1038/nrg2098
| Summary | Full Text (HTML / PDF) |

article
High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons
Patrick T McGrath, Honglak Lee, Li Zhang, Antonio A Iniesta, Alison K Hottes, Meng How Tan, Nathan J Hillson, Ping Hu, Lucy Shapiro & Harley H McAdams
Nature Biotechnology 25, 584–592
(May 2007); doi:10.1038/nbt1294
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article
Image-based multivariate profiling of drug responses from single cells
Lit-Hsin Loo, Lani F Wu & Steven J Altschuler
Nature Methods 4, 445–453
(May 2007); doi:10.1038/nmeth1032
| Summary | Full Text (HTML / PDF) |

brief communication
Ligand interaction scan: a general method for engineering ligand-sensitive protein alleles
Oran Erster, Miriam Eisenstein & Mordechai Liscovitch
Nature Methods 4, 393–395
(May 2007); doi:10.1038/nmeth1046
| Summary | Full Text (HTML / PDF) |

article
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
Tarjei S. Mikkelsen, Matthew J. Wakefield, Bronwen Aken, Chris T. Amemiya, Jean L. Chang, Shannon Duke, Manuel Garber, Andrew J. Gentles, Leo Goodstadt, Andreas Heger, Jerzy Jurka, Michael Kamal, Evan Mauceli, Stephen M. J. Searle, Ted Sharpe, Michelle L. Baker, Mark A. Batzer, Panayiotis V. Benos, Katherine Belov, Michele Clamp, April Cook, James Cuff, Radhika Das, Lance Davidow, Janine E. Deakin, Melissa J. Fazzari, Jacob L. Glass, Manfred Grabherr, John M. Greally, Wanjun Gu, Timothy A. Hore, Gavin A. Huttley, Michael Kleber, Randy L. Jirtle, Edda Koina, Jeannie T. Lee, Shaun Mahony, Marco A. Marra, Robert D. Miller, Robert D. Nicholls, Mayumi Oda, Anthony T. Papenfuss, Zuly E. Parra, David D. Pollock, David A. Ray, Jacqueline E. Schein, Terence P. Speed, Katherine Thompson, John L. VandeBerg, Claire M. Wade, Jerilyn A. Walker, Paul D. Waters, Caleb Webber, Jennifer R. Weidman, Xiaohui Xie, Michael C. ZodyBroad Institute Genome Sequencing Platform and Broad Institute Whole Genome Assembly Team and , Jennifer A. Marshall Graves, Chris P. Ponting, Matthew Breen, Paul B. Samollow, Eric S. Lander & Kerstin Lindblad-Toh
Nature 447, 167–177
(10 May 2007); doi:10.1038/nature05805
| Summary | Full Text (HTML / PDF) |

letter
Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24
Julius Gudmundsson, Patrick Sulem, Andrei Manolescu, Laufey T Amundadottir, Daniel Gudbjartsson, Agnar Helgason, Thorunn Rafnar, Jon T Bergthorsson, Bjarni A Agnarsson, Adam Baker, Asgeir Sigurdsson, Kristrun R Benediktsdottir, Margret Jakobsdottir, Jianfeng Xu, Thorarinn Blondal, Jelena Kostic, Jielin Sun, Shyamali Ghosh, Simon N Stacey, Magali Mouy, Jona Saemundsdottir, Valgerdur M Backman, Kristleifur Kristjansson, Alejandro Tres, Alan W Partin, Marjo T Albers-Akkers, Javier Godino-Ivan Marcos, Patrick C Walsh, Dorine W Swinkels, Sebastian Navarrete, Sarah D Isaacs, Katja K Aben, Theresa Graif, John Cashy, Manuel Ruiz-Echarri, Kathleen E Wiley, Brian K Suarez, J Alfred Witjes, Mike Frigge, Carole Ober, Eirikur Jonsson, Gudmundur V Einarsson, Jose I Mayordomo, Lambertus A Kiemeney, William B Isaacs, William J Catalona, Rosa B Barkardottir, Jeffrey R Gulcher, Unnur Thorsteinsdottir, Augustine Kong & Kari Stefansson
Nature Genetics 39, 631–637
(May 2007); doi:10.1038/ng1999
| Summary | Full Text (HTML / PDF) |

letter
Multiple regions within 8q24 independently affect risk for prostate cancer
Christopher A Haiman, Nick Patterson, Matthew L Freedman, Simon R Myers, Malcolm C Pike, Alicja Waliszewska, Julie Neubauer, Arti Tandon, Christine Schirmer, Gavin J McDonald, Steven C Greenway, Daniel O Stram, Loic Le Marchand, Laurence N Kolonel, Melissa Frasco, David Wong, Loreall C Pooler, Kristin Ardlie, Ingrid Oakley-Girvan, Alice S Whittemore, Kathleen A Cooney, Esther M John, Sue A Ingles, David Altshuler, Brian E Henderson & David Reich
Nature Genetics 39, 638–644
(May 2007); doi:10.1038/ng2015
| Summary | Full Text (HTML / PDF) |

letter
Genome-wide association study of prostate cancer identifies a second risk locus at 8q24
Meredith Yeager, Nick Orr, Richard B Hayes, Kevin B Jacobs, Peter Kraft, Sholom Wacholder, Mark J Minichiello, Paul Fearnhead, Kai Yu, Nilanjan Chatterjee, Zhaoming Wang, Robert Welch, Brian J Staats, Eugenia E Calle, Heather Spencer Feigelson, Michael J Thun, Carmen Rodriguez, Demetrius Albanes, Jarmo Virtamo, Stephanie Weinstein, Fredrick R Schumacher, Edward Giovannucci, Walter C Willett, Geraldine Cancel-Tassin, Olivier Cussenot, Antoine Valeri, Gerald L Andriole, Edward P Gelmann, Margaret Tucker, Daniela S Gerhard, Joseph F Fraumeni, Jr, Robert Hoover, David J Hunter, Stephen J Chanock & Gilles Thomas
Nature Genetics 39, 645–649
(May 2007); doi:10.1038/ng2022
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news and views
Multiple prostate cancer risk variants on 8q24
John S Witte
Nature Genetics 39, 577
(May 2007); doi:10.1038/ng0507-579
| Summary | Full Text (HTML / PDF) |

research
A risk-based bioanalytical strategy for the assessment of antibody immune responses against biological drugs
Gopi Shankar, Charles Pendley & Kathryn E Stein
Nature Biotechnology 25, 555–561
(May 2007); doi:10.1038/nbt1303
| Summary | Full Text (HTML / PDF) |

brief communication
A yeast two-hybrid smart-pool-array system for protein-interaction mapping
Fulai Jin, Larisa Avramova, Jing Huang & Tony Hazbun
Nature Methods 4, 405–407
(May 2007); doi:10.1038/nmeth1042
| Summary | Full Text (HTML / PDF) |

April

article
A module of negative feedback regulators defines growth factor signaling
Ido Amit, Ami Citri, Tal Shay, Yiling Lu, Menachem Katz, Fan Zhang, Gabi Tarcic, Doris Siwak, John Lahad, Jasmine Jacob-Hirsch, Ninette Amariglio, Nora Vaisman, Eran Segal, Gideon Rechavi, Uri Alon, Gordon B Mills, Eytan Domany & Yosef Yarden
Nature Genetics 39, 503–512
(April 2007); doi:10.1038/ng1987
| Summary | Full Text (HTML / PDF) |

commentary
Recommendations of the 2006 Human Variome Project meeting
Richard G.H. Cotton
Nature Genetics 39, 433–436
(April 2007); doi:10.1038/ng2024
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article
Genome-wide resources of endoribonuclease-prepared short interfering RNAs for specific loss-of-function studies
Ralf Kittler, Vineeth Surendranath, Anne-Kristin Heninger, Mikolaj Slabicki, Mirko Theis, Gabriele Putz, Kristin Franke, Antonio Caldarelli, Hannes Grabner, Karol Kozak, Jan Wagner, Effi Rees, Bernd Korn, Corina Frenzel, Christoph Sachse, Birte Sönnichsen, Jie Guo, Janell Schelter, Julja Burchard, Peter S Linsley, Aimee L Jackson, Bianca Habermann & Frank Buchholz
Nature Methods 4, 337–344
(April 2007); doi:10.1038/nmeth1025
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review
Cancer epigenomics: DNA methylomes and histone-modification maps
Manel Esteller
Nature Reviews Genetics 8, 286–298
(April 2007); doi:10.1038/nrg2005
| Summary | Full Text (HTML / PDF) |

letter
Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map
Sean R. Collins, Kyle M. Miller, Nancy L. Maas, Assen Roguev, Jeffrey Fillingham, Clement S. Chu, Maya Schuldiner, Marinella Gebbia, Judith Recht, Michael Shales, Huiming Ding, Hong Xu, Junhong Han, Kristin Ingvarsdottir, Benjamin Cheng, Brenda Andrews, Charles Boone, Shelley L. Berger, Phil Hieter, Zhiguo Zhang, Grant W. Brown, C. James Ingles, Andrew Emili, C. David Allis, David P. Toczyski, Jonathan S. Weissman, Jack F. Greenblatt & Nevan J. Krogan
Nature 446, 806–810
(11 April 2007); doi:10.1038/nature05649
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March

perspective
Beyond standardization: dynamic software infrastructures for systems biology
Morris A. Swertz and Ritsert C. Jansen
Nature Reviews Genetics 8, 235–243
(March 2007); doi:10.1038/nrg2048
| Summary | Full Text (HTML / PDF) |

review
High-throughput electronic biology: mining information for drug discovery
William Loging, Lee Harland and Bryn Williams-Jones
Nature Reviews Drug Discovery 6, 220–230
(March 2007); doi:10.1038/nrd2265
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article
An integrated mass spectrometric and computational framework for the analysis of protein interaction networks
Oliver Rinner, Lukas N. Mueller, Martin Hubálek, Markus Müller, Matthias Gstaiger & Ruedi Aebersold
Nature Biotechnology 25, 345 - 352
(March 2007); doi:10.1038/nbt1289
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article
Patterns of somatic mutation in human cancer genomes
Christopher Greenman et al.
Nature 446, 153–158
(8 March 2007); doi:10.1038/nature05610
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news and views
Cancer: Drivers and passengers
Daniel A. Haber and Jeff Settleman
Nature 446, 145–146
(8 March 2007); doi:10.1038/446145a
| Summary | Full Text (HTML / PDF) |

letter
Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate
Silvia D. M. Santos, Peter J. Verveer & Philippe I. H. Bastiaens
Nature Cell Biology 9, 324–330
(March 2007); doi:10.1038/ncb1543
| Summary | Full Text (HTML / PDF) |

news and views
Untangling the signalling wires
Boris N. Kholodenko
Nature Cell Biology 9, 247–249
(March 2007); doi:10.1038/ncb0307-247
| Summary | Full Text (HTML / PDF) |

analysis
A human phenome-interactome network of protein complexes implicated in genetic disorders
Kasper Lage, E Olof Karlberg, Zenia M Størling, Páll Í Ólason, Anders G Pedersen, Olga Rigina, Anders M Hinsby, Zeynep Tümer, Flemming Pociot, Niels Tommerup, Yves Moreau & Søren Brunak
Nature Biotechnology 25, 309–316
(March 2007); doi:10.1038/nbt1295
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perspective
Darwinian medicine: a case for cancer
Mel Greaves
Nature Reviews Cancer 7, 213–221
(March 2007); doi:10.1038/nrc2071
| Summary | Full Text (HTML / PDF) |

February

article
Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88
Herman J Pel et al.
Nature Biotechnology 25, 221–231
(February 2007); doi:10.1038/nbt1282
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news and views
The genome of an industrial workhorse
Dan Cullen
Nature Biotechnology 25, 189–190
(February 2007); doi:10.1038/nbt0207-189
| Summary | Full Text (HTML / PDF) |

letter
Bioinformatic discovery of novel bioactive peptides
Richard J Edwards, Niamh Moran, Marc Devocelle, Aoife Kiernan, Gerardene Meade, William Signac, Martina Foy, Stephen D E Park, Eimear Dunne, Dermot Kenny and Denis C Shields
Nature Chemical Biology 3, 108–112
(February 2007); doi:10.1038/nchembio854
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January

article
Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
Peng Lu, Christine Vogel, Rong Wang, Xin Yao & Edward M Marcotte
Nature Biotechnology 25, 117–124
(January 2007); doi:10.1038/nbt1270
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letter
Computational prediction of proteotypic peptides for quantitative proteomics
Parag Mallick, Markus Schirle, Sharon S Chen, Mark R Flory, Hookeun Lee, Daniel Martin, Jeffrey Ranish, Brian Raught, Robert Schmitt, Thilo Werner, Bernhard Kuster & Ruedi Aebersold
Nature Biotechnology 25, 125–131
(January 2007); doi:10.1038/nbt1275
| First Paragraph | Full Text (HTML / PDF) |

news and views
Peptides you can count on
John JM Bergeron & Michael Hallett
Nature Biotechnology 25, 61–62
(January 2007); doi:10.1038/nbt0107-61
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article
Imaging cellular network dynamics in three dimensions using fast 3D laser scanning
Werner Göbel, Björn M Kampa & Fritjof Helmchen
Nature Methods 4, 73–79
(January 2007); doi:10.1038/nmeth989
| Summary | Full Text (HTML / PDF) |

article
Genome-wide atlas of gene expression in the adult mouse brain
Ed S. Lein et al.
Nature 445, 168–176
(11 January 2007); doi:10.1038/nature05453
| Summary | Full Text (HTML / PDF) |

letter
A systems biology analysis of the Drosophila phagosome
L. M. Stuart, J. Boulais, G. M. Charriere, E. J. Hennessy, S. Brunet, I. Jutras, G. Goyette, C. Rondeau, S. Letarte, H. Huang, P. Ye, F. Morales, C. Kocks, J. S. Bader, M. Desjardins and R. A. B. Ezekowitz
Nature 445, 95–101
(4 January 2007); doi:10.1038/nature05380
| First Paragraph | Full Text (HTML / PDF) |

review
Computational prediction of cancer-gene function
Pingzhao Hu, Gary Bader, Dennis A. Wigle and Andrew Emili
Nature Reviews Cancer 7, 23–34
(January 2007); doi:10.1038/nrc2036
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