Research library: Systems biology/High-throughput
2008:
| December
| November
| October
| September
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| June
| May
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Other Years: 2004 | 2005 | 2006 | 2007
December
review
Design principles of biochemical oscillators
Béla Novák & John J. Tyson
Nature Reviews Molecular Cell Biology 9, 981–991
(December 2008); doi:10.1038/nrm2530
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research
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
Jürgen Cox & Matthias Mann
Nature Biotechnology 26, 1367–1372
(December 2008); doi:10.1038/nbt.1511
| Summary | Full Text (HTML / PDF) |
Correspondence
PhosphoPep—a database of protein phosphorylation sites in model organisms
Bernd Bodenmiller et al.
Nature Biotechnology 26, 1339–1340
(December 2008); doi:10.1038/nbt1208-1339
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article
Epitope mapping of antibodies using bacterial surface display
Johan Rockberg, John Löfblom, Barbara Hjelm, Mathias Uhlén & Stefan Ståhl
Nature Methods 5, 1039–1045
(December 2008); doi:10.1038/nmeth.1272
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news and views
On display on a bug: a systematic approach to characterize antibodies
Thomas Knorpp & Markus F Templin
Nature Methods 5, 1003–1004
(December 2008); doi:10.1038/nmeth1208-1003
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November
letter
A fast, robust and tunable synthetic gene oscillator
Jesse Stricker et al.
Nature 456, 516–519
(27 November 2008); doi:10.1038/nature07389
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article
Structure and function of a transcriptional network activated by the MAPK Hog1
Andrew P Capaldi et al.
Nature Genetics 40, 1300–1306
(November 2008); doi:10.1038/ng.235
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article
A quantitative model of transcription factor–activated gene expression
Harold D Kim & Erin K O'Shea
Nature Structural & Molecular Biology 15, 1192–1198
(November 2008); doi:10.1038/nsmb.1500
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review
Targeting and tinkering with interaction networks
Robert B Russell & Patrick Aloy
Nature Chemical Biology 4, 666–673
(November 2008); doi:10.1038/nchembio.119
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review
Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems
Patrick C. Phillips
Nature Reviews Genetics 9, 855–867
(November 2008); doi:10.1038/nrg2452
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perspective
Learning biological networks: from modules to dynamics
Richard Bonneau
Nature Chemical Biology 4, 658–664
(November 2008); doi:10.1038/nchembio.122
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commentary
Reverse engineering intracellular biochemical networks
Eli Zamir & Philippe I H Bastiaens
Nature Chemical Biology 4, 643–647
(November 2008); doi:10.1038/nchembio1108-643
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article
Functional organization of the transcriptome in human brain
Michael C Oldham et al.
Nature Neuroscience 11, 1271–1282
(November 2008); doi:10.1038/nn.2207
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news and views
What is in the brain soup?
Károly Mirnics
Nature Neuroscience 11, 1237–1238
(November 2008); doi:10.1038/nn1108-1237
| Full Text (HTML / PDF) |
article
Targeted polypharmacology: discovery of dual inhibitors of tyrosine and phosphoinositide kinases
Beth Apsel et al.
Nature Chemical Biology 4, 691–699
(November 2008); doi:10.1038/nchembio.117
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news and views
Killing two kinase families with one stone
Benoit Bilanges, Neil Torbett & Bart Vanhaesebroeck
Nature Chemical Biology 4, 648–649
(November 2008); doi:10.1038/nchembio1108-648
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article
Decision tree–driven tandem mass spectrometry for shotgun proteomics
Danielle L Swaney, Graeme C McAlister & Joshua J Coon
Nature Methods 5, 959–964
(November 2008); doi:10.1038/nmeth.1260
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October
letter
A functional RNAi screen links O-GlcNAc modification of ribosomal proteins to stress granule and processing body assembly
Takbum Ohn, Nancy Kedersha, Tyler Hickman, Sarah Tisdale & Paul Anderson
Nature Cell Biology 10, 1224–1231
(October 2008); doi:10.1038/ncb1783
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news and views
Stressed out? Make some modifications!
Angela Hilliker & Roy Parker
Nature Cell Biology 10, 1129–1130
(October 2008); doi:10.1038/ncb1008-1129
| Full Text (HTML / PDF) |
review
Next-generation DNA sequencing
Jay Shendure & Hanlee Ji
Nature Biotechnology 26, 1135–1145
(October 2008); doi:10.1038/nbt1486
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article
Somatic mutations affect key pathways in lung adenocarcinoma
Li Ding et al.
Nature 455, 1069–1075
(23 October 2008); doi:10.1038/nature07423
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article
Comprehensive genomic characterization defines human glioblastoma genes and core pathways
The Cancer Genome Atlas Research Network
Nature 455, 1061–1068
(23 October 2008); doi:10.1038/nature07385
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review
Modelling and analysis of gene regulatory networks
Guy Karlebach & Ron Shamir
Nature Reviews Molecular Cell Biology 9, 770–780
(October 2008); doi:10.1038/nrm2503
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review
The potential and challenges of nanopore sequencing
Daniel Branton et al.
Nature Biotechnology 26 1146–1153
(October 2008); doi:10.1038/nbt.1495
| Summary | Full Text (HTML / PDF) |
review
Thirty years of Alzheimer's disease genetics: the implications of systematic meta-analyses
Lars Bertram & Rudolph E. Tanzi
Nature Reviews Neuroscience 9, 768–778
(October 2008); doi:10.1038/nrn2494
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perspective
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
Markus J Herrgård et al.
Nature Biotechnology 26, 1155–1160
(October 2008); doi:10.1038/nbt1492
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article
Systems-level metabolic flux profiling identifies fatty acid synthesis as a target for antiviral therapy
Joshua Munger et al.
Nature Biotechnology 26, 1179–1186
(October 2008); doi:10.1038/nbt.1500
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news and views
From biomarkers to integrated network responses
Uwe Sauer & Nicola Zamboni
Nature Biotechnology 26, 1090–1092
(October 2008); doi:10.1038/nbt1008-1090
| Full Text (HTML / PDF) |
perspective
Trends in large-scale mouse mutagenesis: from genetics to functional genomics
Yoichi Gondo
Nature Reviews Genetics 9, 803–810
(October 2008); doi:10.1038/nrg2431
| Summary | Full Text (HTML / PDF) |
September
review
Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges
Lincoln D. Stein
Nature Reviews Genetics 9, 678–688
(September 2008); doi:10.1038/nrg2414
| Summary | Full Text (HTML / PDF) |
research
Predicting PDZ domain–peptide interactions from primary sequences
Jiunn R Chen, Bryan H Chang, John E Allen, Michael A Stiffler & Gavin MacBeath
Nature Biotechnology 26, 1041–1045
(September 2008); doi:10.1038/nbt.1489
| Summary | Full Text (HTML / PDF) |
perspective
Molecular eco-systems biology: towards an understanding of community function
Jeroen Raes & Peer Bork
Nature Reviews Microbiology 6, 693–699
(September 2008); doi:10.1038/nrmicro1935
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article
Identification of genes that regulate epithelial cell migration using an siRNA screening approach
Kaylene J. Simpson et al.
Nature Cell Biology 10, 1027–1038
(September 2008); doi:10.1038/ncb1762
| Summary | Full Text (HTML / PDF) |
article
β-Lactone probes identify a papain-like peptide ligase in Arabidopsis thaliana
Zheming Wang et al.
Nature Chemical Biology 4, 557–563
(September 2008); doi:10.1038/nchembio.104
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news and views
Unexpected N-terminal editing: a cysteine protease that cuts and pastes
Isaac Carrico
Nature Chemical Biology 4, 525–526
(September 2008); doi:10.1038/nchembio0908-525
| Full Text (HTML / PDF) |
review
Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges
Lincoln D. Stein
Nature Reviews Genetics 9, 678–688
(September 2008); doi:10.1038/nrg2414
| Summary | Full Text (HTML / PDF) |
article
High-throughput, quantitative analyses of genetic interactions in E. coli
Athanasios Typas et al.
Nature Methods 5, 781–787
(September 2008); doi:10.1038/nmeth.1240
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article
eSGA: E. coli synthetic genetic array analysis
Gareth Butland et al.
Nature Methods 5, 789–795
(September 2008); doi:10.1038/nmeth.1239
| Summary | Full Text (HTML / PDF) |
news and views
Sex to the rescue
Thomas J Silhavy & Zemer Gitai
Nature Methods 5, 759–760
(September 2008); doi:10.1038/nmeth0908-759
| Full Text (HTML / PDF) |
August
letter
Metabolic gene regulation in a dynamically changing environment
Matthew R. Bennett et al.
Nature 454, 1119–1122
(28 August 2008); doi:10.1038/nature07211
| Summary | Full Text (HTML / PDF) |
news and views
Systems biology: Reverse engineering the cell
Nicholas T. Ingolia & Jonathan S. Weissman
Nature 454, 1059–1062
(28 August 2008); doi:10.1038/4541059a
| Full Text (HTML / PDF) |
commentary
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
Chris F Taylor et al.
Nature Biotechnology 26, 889–896
(August 2008); doi:10.1038/nbt0808-889
| Summary | Full Text (HTML / PDF) |
review
Pseudoreceptor models in drug design: bridging ligand- and receptor-based virtual screening
Yusuf Tanrikulu & Gisbert Schneider
Nature Reviews Drug Discovery 7, 667–677
(August 2008); doi:10.1038/nrd2615
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review
Building the cell: design principles of cellular architecture
Susanne M. Rafelski & Wallace F. Marshall
Nature Reviews Molecular Cell Biology 9, 593–602
(August 2008); doi:10.1038/nrm2460
| Summary | Full Text (HTML / PDF) |
article
A comprehensive strategy enabling high-resolution functional analysis of the yeast genome
David K Breslow et al.
Nature Methods 5, 711–718
(August 2008); doi:10.1038/nmeth.1234
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article
A potent mechanism-inspired O-GlcNAcase inhibitor that blocks phosphorylation of tau in vivo
Scott A Yuzwa et al.
Nature Chemical Biology 4, 483–490
(August 2008); doi:10.1038/nchembio.96
| Summary | Full Text (HTML / PDF) |
news and views
Turning down tau phosphorylation
Peter M Fischer
Nature Chemical Biology 4, 448–449
(August 2008); doi:10.1038/nchembio0808-448
| Full Text (HTML / PDF) |
article
An integrated platform of genomic assays reveals small-molecule bioactivities
Shawn Hoon et al.
Nature Chemical Biology 4, 498–506
(August 2008); doi:10.1038/nchembio.100
| Summary | Full Text (HTML / PDF) |
July
review
The art and design of genetic screens: RNA interference
Michael Boutros & Julie Ahringer
Nature Reviews Genetics 9, 554–566
(July 2008); doi:10.1038/nrg2364
| Summary | Full Text (HTML / PDF) |
article
Stem cell transcriptome profiling via massive-scale mRNA sequencing
Nicole Cloonan et al.
Nature Methods 5, 613–619
(July 2008); doi:10.1038/nmeth.1223
| Summary | Full Text (HTML / PDF) |
article
Functional immobilization of signaling proteins enables control of stem cell fate
Kristin Alberti et al.
Nature Methods 5, 645–650
(July 2008); doi:10.1038/nmeth.1222
| Summary | Full Text (HTML / PDF) |
article
Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks
Jun Zhu et al.
Nature Genetics 40, 854–861
doi:10.1038/ng.167
| Summary | Full Text (HTML / PDF) |
article
Automated on-chip rapid microscopy, phenotyping and sorting of C. elegans
Kwanghun Chung, Matthew M Crane & Hang Lu
Nature Methods 5, 637–643
(July 2008); doi:10.1038/nmeth.1227
| Summary | Full Text (HTML / PDF) |
news and views
Microfluidics: streamlining discovery in worm biology
S Elizabeth Hulme, Sergey S Shevkoplyas & Aravinthan Samuel
Nature Methods 5, 589–590
(July 2008); doi:10.1038/nmeth0708-589
| Full Text (HTML / PDF) |
article
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer & Barbara Wold
Nature Methods 5, 621–628
(July 2008); doi:10.1038/nmeth.1226
| Summary | Full Text (HTML / PDF) |
news and views
The beginning of the end for microarrays?
Jay Shendure
Nature Methods 5, 585–587
(July 2008); doi:10.1038/nmeth0708-585
| Full Text (HTML / PDF) |
June
letter
Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype
Helene R. McMurray et al.
Nature 453, 1112–1116
(19 June 2008); doi:10.1038/nature06973
| Summary | Full Text (HTML / PDF) |
news and views
Cancer: Deconstructing oncogenesis
Ji Luo & Stephen J. Elledge
Nature 453, 995–996
(19 June 2008); doi:10.1038/453995a
| Full Text (HTML / PDF) |
perspective
The Mouse Tumor Biology database
Debra M. Krupke, Dale A. Begley, John P. Sundberg, Carol J. Bult & Janan T. Eppig
Nature Reviews Cancer 8, 459–465
(June 2008); doi:10.1038/nrc2390
| Summary | Full Text (HTML / PDF) |
article
Gene expression signatures and small-molecule compounds link a protein kinase to Plasmodium falciparum motility
Nobutaka Kato et al.
Nature Chemical Biology 4, 347–356
(June 2008); doi:10.1038/nchembio.87
| Summary | Full Text (HTML / PDF) |
news and views
Stopping malaria parasites dead in their tracks
Christian D Doerig
Nature Chemical Biology 4, 334–335
(June 2008); doi:10.1038/nchembio0608-3340
| Full Text (HTML / PDF) |
letter
Global control of cell-cycle transcription by coupled CDK and network oscillators
David A. Orlando et al.
Nature 453, 944–947
(12 June 2008); doi:10.1038/nature06955
| Summary | Full Text (HTML / PDF) |
article
Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites
Oliver Schilling & Christopher M Overall
Nature Biotechnology 26, 685–694
(June 2008); doi:10.1038/nbt1408
| Summary | Full Text (HTML / PDF) |
news and views
Proteases' prime targets revealed
Scott L Diamond & Doron Greenbaum
Nature Biotechnology 26, 652–653
(June 2008); doi:10.1038/nbt0608-652
| Summary | Full Text (HTML / PDF) |
May
letter
Functional genomic screen reveals genes involved in lipid-droplet formation and utilization
Yi Guo et al.
Nature 453, 657–661
(29 May 2008); doi:10.1038/nature06928
| Summary | Full Text (HTML / PDF) |
article
Stromal gene expression predicts clinical outcome in breast cancer
Greg Finak et al.
Nature Medicine 14, 518–527
(May 2008); doi:10.1038/nm1764
| Summary | Full Text (HTML / PDF) |
perpective
High-throughput kinase profiling as a platform for drug discovery
David M. Goldstein, Nathanael S. Gray & Patrick P. Zarrinkar
Nature Reviews Drug Discovery 7, 391–397
(May 2008); doi:10.1038/nrd2541
| Summary | Full Text (HTML / PDF) |
article
Novel targets for Huntington's disease in an mTOR-independent autophagy pathway
Andrea Williams et al.
Nature Chemical Biology 5, 295–305
(May 2008); doi:10.1038/nchembio.79
| Summary | Full Text (HTML / PDF) |
letter
Hierarchical structure and the prediction of missing links in networks
Aaron Clauset, Cristopher Moore & M. E. J. Newman
Nature 453, 98–101
(1 May 2008); doi:10.1038/nature06830
| Summary | Full Text (HTML / PDF) |
news and views
Networks: Teasing out the missing links
Sid Redner
Nature 453, 47–47
(1 May 2008); doi:10.1038/453047a
| Full Text (HTML / PDF) |
letter
Genome-wide screen reveals APC-associated RNAs enriched in cell protrusions
Stavroula Mili, Konstadinos Moissoglu & Ian G. Macara
Nature 453, 115–114
(1 May 2008); doi:10.1038/nature06888
| Summary | Full Text (HTML / PDF) |
analysis
An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors
Ittai Ben-Porath et al.
Nature Genetics 40, 499–507
(May 2008); doi:10.1038/ng.127
| Summary | Full Text (HTML / PDF) |
article
BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals
Ina Poser et al.
Nature Methods 5, 409–415
(May 2008); doi:10.1038/nmeth.1199
| Summary | Full Text (HTML / PDF) |
article
BAC to the future: functional genomics in mammals
Assen Roguev & Nevan J Krogan
Nature Methods 5, 383–384
(May 2008); doi:10.1038/nmeth0508-383
| Summary | Full Text (HTML / PDF) |
April
letter
A deadenylation negative feedback mechanism governs meiotic metaphase arrest
Eulàlia Belloc & Raúl Méndez
Nature 452, 1017–1021
(24 April 2008); doi:10.1038/nature06809
| Summary | Full Text (HTML / PDF) |
article
MicroRNAs accurately identify cancer tissue origin
Nitzan Rosenfeld et al.
Nature Biotechnology 26, 462–469
(April 2008); doi:10.1038/nbt1392
| Summary | Full Text (HTML / PDF) |
news and views
Cancer biomarker profiling with microRNAs
Stefanie S Jeffrey
Nature Biotechnology 26, 400–401
(April 2008); doi:10.1038/nbt0408-400
| Summary | Full Text (HTML / PDF) |
review
High-throughput electrophysiology: an emerging paradigm for ion-channel screening and physiology
John Dunlop, Mark Bowlby, Ravikumar Peri, Dmytro Vasilyev & Robert Arias
Nature Reviews Drug Discovery 7, 358–368
(April 2008); doi:10.1038/nrd2552
| Summary | Full Text (HTML / PDF) |
brief communication
A quantitative analysis software tool for mass spectrometry-based proteomics
Sung Kyu Park, John D Venable, Tao Xu & John R Yates III
Nature Methods 5, 319–322
(April 2008); doi:10.1038/nmeth.1195
| Summary | Full Text (HTML / PDF) |
review
Mining the plasma proteome for cancer biomarkers
Samir M. Hanash, Sharon J. Pitteri & Vitor M. Faca
Nature 452, 571–579
(3 April 2008); doi:10.1038/nature06916
| Summary | Full Text (HTML / PDF) |
brief communication
Evolutionary plasticity of genetic interaction networks
Julia Tischler, Ben Lehner & Andrew G Fraser
Nature Genetics 40, 390–391
(April 2008); doi:10.1038/ng.114
| Summary | Full Text (HTML / PDF) |
article
Identification of small molecules rescuing fragile X syndrome phenotypes in Drosophila
Shuang Chang, Steven M Bray, Zigang Li, Daniela C Zarnescu, Chuan He, Peng Jin & Stephen T Warren
Nature Chemical Biology 4, 256–263
(April 2008); doi:10.1038/nchembio.78
| Summary | Full Text (HTML / PDF) |
March
article
Homogeneous reporter system enables quantitative functional assessment of multiple transcription factors
Sergei Romanov et al.
Nature Methods 5, 253–260
(March 2008); doi:10.1038/nmeth.1186
| Summary | Full Text (HTML / PDF) |
resources
Large-scale chemical dissection of mitochondrial function
Bridget K Wagner et al.
Nature Biotechnology 26, 343–351
(March 2008); doi:10.1038/nbt1387
| Summary | Full Text (HTML / PDF) |
news and views
A toolkit for the cell's powerhouse
Eric A Schon
Nature Biotechnology 26, 294–296
(March 2008); doi:10.1038/nbt0308-294
| Summary | Full Text (HTML / PDF) |
February
article
Proteomic analysis of active multiple sclerosis lesions reveals therapeutic targets
May H. Han et al.
Nature 451, 1076–1081
(28 February 2008); doi:10.1038/nature06559
| Summary | Full Text (HTML / PDF) |
article
A forward chemical genetic screen reveals an inhibitor of the Mre11–Rad50–Nbs1 complex
Aude Dupré et al.
Nature Chemical Biology 4, 119–125
(February 2008); doi:10.1038/nchembio.63
| Summary | Full Text (HTML / PDF) |
news and views
Small molecule versus DNA repair nanomachine
James T Stivers
Nature Chemical Biology 4, 86–88
(February 2008); doi:10.1038/nchembio0208-86
| Full Text (HTML / PDF) |
article
High-content single-cell drug screening with phosphospecific flow cytometry
Peter O Krutzik, Janelle M Crane, Matthew R Clutter & Garry P Nolan
Nature Chemical Biology 4, 132–142
(February 2008); doi:10.1038/nchembio.2007.59
| Summary | Full Text (HTML / PDF) |
scientific report
CARM1 promotes adipocyte differentiation by coactivating PPARγ
Neelu Yadav et al.
EMBO Reports 9, 193–198
(February 2008); doi:10.1038/sj.embor.7401151
| Summary | Full Text (HTML / PDF) |
perspective
New surveyor tools for charting microbial metabolic maps
Rainer Breitling, Dennis Vitkup & Michael P. Barrett
Nature Reviews Microbiology 6, 156–161
(February 2008); doi:10.1038/nrmicro1797
| Summary | Full Text (HTML / PDF) |
January
letter
A quantitative analysis of kinase inhibitor selectivity
Mazen W Karaman et al.
Nature Biotechnology 26, 127–132
(January 2008); doi:10.1038/nbt1358
| Summary | Full Text (HTML / PDF) |
review
Coupling and coordination in gene expression processes: a systems biology view
Suzanne Komili & Pamela A. Silver
Nature Reviews Genetics 9, 38–48
(January 2008); doi:10.1038/nrg2223
| Summary | Full Text (HTML / PDF) |
article
Dorsomorphin inhibits BMP signals required for embryogenesis and iron metabolism
Paul B Yu et al.
Nature Chemical Biology 4, 33–41
(January 2008); doi:10.1038/nchembio.2007.54
| Summary | Full Text (HTML / PDF) |
news and views
Small-molecule dissection of BMP signaling
Gregory J Anderson & Deepak Darshan
Nature Chemical Biology 4, 15–16
(January 2008); doi:10.1038/nchembio0108-15
| Full Text (HTML / PDF) |
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