Research library: Techniques
2005:
December
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December
article
A look back: getting the message
Michael Eisenstein
Nature Methods 2, 996
(December 2005); doi:10.1038/nmeth1205-996
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research article
Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana
Ming-Tang Chen and Ron Weiss
Nature Biotechnology 23, 1551–1555
(December 2005); doi:10.1038/nbt1162
| First Paragraph | Full Text (HTML/PDF) |
protocol
Stable expression of fluorescently tagged proteins for studies of mitosis in mammalian cells
Patricia Wadsworth, Nasser M Rusan, U Serdar Tulu and Carey Fagerstrom
Nature Methods 2, 981–987
(December 2005); doi:10.1038/nmeth1205-981
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article
High-throughput screening of effective siRNAs from RNAi libraries delivered via bacterial invasion
Hui-Fen Zhao, Denis L'Abbé, Normand Jolicoeur, Meiqun Wu, Zhen Li, Zhenbao Yu and Shi-Hsiang Shen
Nature Methods 2, 967–973
(December 2005); doi:10.1038/nmeth812
| Abstract | Full Text (HTML/PDF) |
brief communication
Positional proteomics: selective recovery and analysis of N-terminal proteolytic peptides
Lucy McDonald, Duncan H L Robertson, Jane L Hurst and Robert J Beynon
Nature Methods 2, 955–957
(December 2005); doi:10.1038/nmeth811
| First Paragraph | Full Text (HTML/PDF) |
November
letter
Direct observation of base-pair stepping by RNA polymerase
Elio A. Abbondanzieri, William J. Greenleaf, Joshua W. Shaevitz, Robert Landick and Steven M. Block
Nature 438, 460–465
(24 November 2005); doi:10.1038/nature04268
| First Paragraph | Full Text (HTML / PDF) |
article
The initiation of antigen-induced B cell antigen receptor signaling viewed in living cells by fluorescence resonance energy transfer
Pavel Tolar, Hae Won Sohn and Susan K Pierce
Nature Immunology 6, 1168–1176
(November 2005); doi:10.1038/ni1262
| Abstract | Full Text (HTML/PDF) |
news and views
Unraveling B cell receptor mechanics
Jürgen Wienands
Nature Immunology 6, 1072–1074
(November 2005); doi:10.1038/ni1105-1072
| Full Text (HTML/PDF) |
review article
Genotyping errors: causes, consequences and solutions
François Pompanon, Aurélie Bonin, Eva Bellemain and Pierre Taberlet
Nature Reviews Genetics 6, 847–846
(November 2005); doi:10.1038/nrg1707
| Summary | Full Text (HTML / PDF) |
article
Structure of the E. coli protein-conducting channel bound to a translating ribosome
Kakoli Mitra, Christiane Schaffitzel, Tanvir Shaikh, Florence Tama, Simon Jenni, Charles L. Brooks III, Nenad Ban and Joachim Frank
Nature 438, 318–324
(17 November 2005); doi:10.1038/nature04133
| Summary | Full Text (HTML / PDF) |
article
Evanescent-field fluorescence-assisted lectin microarray: a new strategy for glycan profiling
Atsushi Kuno, Noboru Uchiyama, Shiori Koseki-Kuno, Youji Ebe, Seigo Takashima, Masao Yamada and Jun Hirabayashi
Nature Methods 2, 851–856
(November 2005); doi:10.1038/nmeth803
| Abstract | Full Text (HTML/PDF) |
letter
A resetting signal between Drosophila pacemakers synchronizes morning and evening activity
Dan Stoleru, Ying Peng, Pipat Nawathean and Michael Rosbash
Nature 438, 238–242
(10 November 2005); doi:10.1038/nature04192
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article
Correlative microscopy and electron tomography of GFP through photooxidation
Markus Grabenbauer, Willie J C Geerts, Julia Fernadez-Rodriguez, Andreas Hoenger, Abraham J Koster and Tommy Nilsson
Nature Methods 2, 857–862
(November 2005); doi:10.1038/nmeth806
| Abstract | Full Text (HTML/PDF) |
technical report
Second-generation shRNA libraries covering the mouse and human genome
Jose M Silva, Mamie Z Li, Ken Chang, Wei Ge, Michael C Golding, Richard J Rickles, Despina Siolas, Guang Hu, Patrick J Paddison, Michael R Schlabach, Nihar Sheth, Jeff Bradshaw, Julia Burchard, Amit Kulkarni, Guy Cavet, Ravi Sachidanandam, W Richard McCombie, Michele A Cleary, Stephen J Elledge and Gregory J Hannon
Nature Genetics 37, 1281–1288
(November 2005); doi:10.1038/ng1650
| Abstract
| Full Text (HTML / PDF) |
technical report
Probing tumor phenotypes using stable and regulated synthetic microRNA precursors
Ross A Dickins, Michael T Hemann, Jack T Zilfou, David R Simpson, Ingrid Ibarra, Gregory J Hannon and Scott W Lowe
Nature Genetics 37, 1289–1295
(November 2005); doi:10.1038/ng1651
| Abstract
| Full Text (HTML / PDF) |
news and views
RNAi the natural way
Bryan R Cullen
Nature Genetics 37, 1163–1165
(November 2005); doi:10.1038/ng1105-1163
| Full Text (HTML / PDF) |
brief communication
One-step analysis of protein complexes in microliters of cell lysate
Oda Stoevesandt, Karsten Köhler, Rainer Fischer, Ian C D Johnston and Roland Brock
Nature Methods 2, 833–835
(November 2005); doi:10.1038/nmeth802
| Abstract
| Full Text (HTML / PDF) |
October
letter
Genetic isolation of transport signals directing cell surface expression
Sojin Shikano, Brian Coblitz, Haiyan Sun and Min Li
Nature Cell Biology 7, 985–992
(October 2005); doi:10.1038/ncb1297
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article
Trapped in action: direct visualization of DNA methyltransferase activity in living cells
Lothar Schermelleh, Fabio Spada, Hariharan P Easwaran, Kourosh Zolghadr, Jean B Margot, M Cristina Cardoso and Heinrich Leonhardt
Nature Methods 8, 751–756
(October 2005); doi:10.1038/nmeth794
| Abstract | Full Text (HTML/PDF) |
news and views
In living color: DNA methyltransferase caught in the act
Kornel Schuebel & Steve Baylin
Nature Methods 2, 736–738
(October 2005); doi:10.1038/nmeth1005-736
| Abstract | Full Text (HTML/PDF) |
review article
The new cytogenetics: blurring the boundaries with molecular biology
Michael R. Speicher and Nigel P. Carter
Nature Reviews Genetics 6, 782–792
(October 2005); doi:10.1038/nrg1692
| Abstract | Full Text (HTML / PDF) |
research article
Generation of functional ion-channel tools by E3 targeting
Shang-Zhong Xu, Fanning Zeng, Ming Lei, Jing Li, Bin Gao, Chenliang Xiong, Asipu Sivaprasadarao and David J Beech
Nature Biotechnology 23, 1289–1293
(October 2005); doi:10.1038/nbt1148
| Abstract | Full Text (HTML/PDF) |
news and views
Simple recipe for blocking ion channels
Christopher D Benham
Nature Biotechnology 23, 1234–1235
(October 2005); doi:10.1038/nbt1005-1234
| Full Text (HTML/PDF) |
article
Tumor-targeted, systemic delivery of therapeutic viral vectors using hitchhiking on antigen-specific T cells
Caroline Cole, Jian Qiao, Timothy Kottke, Rosa Maria Diaz, Atique Ahmed, Luis Sanchez-Perez, Gregory Brunn, Jill Thompson, John Chester and Richard G Vile
Nature Medicine 11, 1073–1081
(October 2005); doi:10.1038/nm1297
| Abstract | Full Text (HTML/PDF) |
news and views
Hitchhiker's guide to the T cell
Cliona M Rooney
Nature Medicine 11, 1051–1052
(October 2005); doi:10.1038/nm1005-1051
| Full Text (HTML/PDF) |
review article
The multiple uses of fluorescent proteins to visualize cancer in vivo
Robert M. Hoffman
Nature Reviews Cancer 5, 796–806
(October 2005); doi:10.1038/nrc1717
| Abstract | Full Text (HTML / PDF) |
article
Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis
Petra Van Damme, Lennart Martens, Jozef Van Damme, Koen Hugelier, An Staes, Joël Vandekerckhove and Kris Gevaert
Nature Methods 2, 771–777
(October 2005); doi:10.1038/nmeth792
| Abstract | Full Text (HTML/PDF) |
brief communication
Molecular dynamics imaging in micropatterned living cells
Kristiana Kandere-Grzybowska, Christopher Campbell, Yulia Komarova, Bartosz A Grzybowski and Gary G Borisy
Nature Methods 2, 739–741
(October 2005); doi:10.1038/nmeth796
| First Paragraph | Full Text (HTML/PDF) |
September
article
A streamlined platform for high-content functional proteomics of primary human specimens
Nadim Jessani, Sherry Niessen, BinQing Q Wei, Monica Nicolau, Mark Humphrey, Youngran Ji, Wonshik Han, Dong-Young Noh, John R Yates, III Stefanie S Jeffrey and Benjamin F Cravatt
Nature Methods 2, 691–697
(September 2005); doi:10.1038/nmeth778
| Abstract | Full Text (HTML/PDF) |
review article
Proteomics of organelles and large cellular structures
John R. Yates III, Annalyn Gilchrist, Kathryn E. Howell and John J. M. Bergeron
Nature Reviews Molecular Cell Biology 6, 702–714
(September 2005); doi:10.1038/nrm1711
| Abstract | Full Text (HTML / PDF) |
letter
Overexpression of an Arabidopsis thaliana ABC transporter confers kanamycin resistance to transgenic plants
Ayalew Mentewab, C Neal Stewart and Jr
Nature Biotechnology 23, 1177–1180
(September 2005); doi:10.1038/nbt1134
| First Paragraph | Full Text (HTML/PDF) |
news and views
A farewell to bacterial ARMs?
Philip A Rea
Nature Biotechnology 23, 1085–1087
(September 2005); doi:10.1038/nbt0905-1085
| Full Text (HTML/PDF) |
article
Determination of absolute protein numbers in single synapses by a GFP-based calibration technique
Yoshiko Sugiyama, Izumi Kawabata, Kenji Sobue and Shigeo Okabe
Nature Methods 2, 677–684
(September 2005); doi:10.1038/nmeth783
| Abstract | Full Text (HTML/PDF) |
news and views
Synthetic chemistry: Glycosylation with a twist
Sabine L. Flitsch
Nature 437, 201–202
(08 September 2005); doi:10.1038/437201a
| Full Text (HTML / PDF) |
brief communication
Gene expression profiling in single cells within tissue
Paola Capodieci, Michael Donovan, Heidi Buchinsky, Yusuf Jeffers, Carlos Cordon-Cardo, William Gerald, Jon Edelson, Shailesh M Shenoy and Robert H Singer
Nature Methods 2, 663–665
(September 2005); doi:10.1038/nmeth786
| First Paragraph | Full Text (HTML/PDF) |
August
review article
Breast cancer metastasis: markers and models
Britta Weigelt, Johannes L. Peterse and Laura J. van't Veer
Nature Reviews Cancer 5, 591–602
(August 2005); doi:10.1038/nrc1670
| Abstract | Full Text (HTML / PDF) |
research article
In vivo imaging platform for tracking immunotherapeutic cells
Eric T Ahrens, Rafael Flores, Hongyan Xu and Penelope A Morel
Nature Biotechnology 23, 983–987
(August 2005); doi:10.1038/nbt1121
| First Paragraph | Full Text (HTML/PDF) |
news and views
Hot spot MRI emerges from the background
Jeff W M Bulte
Nature Biotechnology 23, 945–946
(August 2005); doi:10.1038/nbt0805-945
| Full Text (HTML/PDF) |
article
Real-time imaging of ligand-induced IKK activation in intact cells and in living mice
Shimon Gross and David Piwnica-Worms
Nature Methods 2, 607–614
(August 2005); doi:10.1038/nmeth779
| Abstract | Full Text (HTML/PDF) |
letter
A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors
Xiangdong Meng, Michael H Brodsky and Scot A Wolfe
Nature Biotechnology 23, 988–994
(August 2005); doi:10.1038/nbt1120
| First Paragraph | Full Text (HTML/PDF) |
news and views
Discovering DNA regulatory elements with bacteria
Martha L Bulyk
Nature Biotechnology 23, 942–944
(August 2005); doi:10.1038/nbt0805-942
| Full Text (HTML/PDF) |
July
review article
Design and development of polymers for gene delivery
Daniel W. Pack, Allan S. Hoffman, Suzie Pun and Patrick S. Stayton
Nature Reviews Drug Discovery 4, 581–593
(July 2005); doi:10.1038/nrd1775
| Abstract | Full Text (HTML / PDF) |
article
Enzymatic detection of protein translocation
Tom S Wehrman, Clayton L Casipit, Nevin M Gewertz and Helen M Blau
Nature
Methods 2, 521–527
(July 2005);
doi:10.1038/nmeth771
| Abstract | Full Text
(HTML/PDF)
brief communications
Colony filtration blot: a new screening method for soluble protein expression in Escherichia coli
Tobias Cornvik, Sue-Li Dahlroth, Audur Magnusdottir, Maria Dolores Herman, Rosemarie Knaust, Monica Ekberg and Pär Nordlund
Nature Methods 2, 507–509
(July 2005); doi:10.1038/nmeth767
| Abstract | Full Text (HTML/PDF) |
letter
Nicotine reinforcement and cognition restored by targeted expression of nicotinic receptors
U. Maskos, B. E. Molles, S. Pons, M. Besson, B. P. Guiard, J.-P. Guilloux, A. Evrard, P. Cazala, A. Cormier, M. Mameli-Engvall, N. Dufour, I. Cloëz-Tayarani, A.-P. Bemelmans, J. Mallet, A. M. Gardier, V. David, P. Faure, S. Granon and J.-P. Changeux
Nature 436, 103–107
(07 July 2005); doi:10.1038/nature03694
| First Paragraph | Full Text (HTML / PDF) |
letter
Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma
Levi A. Garraway, Hans R. Widlund, Mark A. Rubin, Gad Getz, Aaron J. Berger, Sridhar Ramaswamy, Rameen Beroukhim, Danny A. Milner, Scott R. Granter, Jinyan Du, Charles Lee, Stephan N. Wagner, Cheng Li, Todd R. Golub , David L. Rimm, Matthew L. Meyerson , David E. Fisher and William R. Sellers
Nature 436, 117–122
(07 July 2005); doi:10.1038/nature03664
| First Paragraph | Full Text (HTML / PDF) |
brief communications
Multiphoton excitation-evoked chromophore-assisted laser inactivation using green fluorescent protein
Takuji Tanabe, Masahito Oyamada, Katsumasa Fujita, Ping Dai, Hideo Tanaka and Tetsuro Takamatsu
Nature Methods 2, 503–505
(July 2005); doi:10.1038/nmeth770
| Abstract | Full Text (HTML/PDF) |
article
EGFP as your targeted 'hitman'
Oded Tour
Nature Methods 2, 491–492
(July 2005); doi:10.1038/nmeth0705-491
| Abstract | Full Text (HTML/PDF) |
June
research article
Rapid generation of specific antibodies by enhanced homologous recombination
Hidetaka Seo, Mieko Masuoka, Hiromu Murofushi, Shunichi Takeda, Takehiko Shibata and Kunihiro Ohta
Nature Biotechnology 23, 731–735
(June 2005); doi:10.1038/nbt1092
| First Paragraph | Full Text (HTML/PDF) |
research article
Intein-based biosynthetic incorporation of unlabeled protein tags into isotopically labeled proteins for NMR studies
Sara Züger and Hideo Iwai
Nature Biotechnology 23, 736–740
(June 2005); doi:10.1038/nbt1097
| First Paragraph | Full Text (HTML/PDF) |
article
A Tn7-based broad-range bacterial cloning and expression system
Kyoung-Hee Choi, Jared B Gaynor, Kimberly G White, Carolina Lopez, Catharine M Bosio, RoxAnn R Karkhoff-Schweizer and Herbert P Schweizer
Nature Methods 2, 443–448
(June 2005); doi:10.1038/nmeth765
| Abstract | Full Text (HTML/PDF) |
research article
A molecular ruler based on plasmon coupling of single gold and silver nanoparticles
Carsten Sönnichsen, Björn M Reinhard, Jan Liphardt and A Paul Alivisatos
Nature Biotechnology 23, 741–745
(June 2005); doi:10.1038/nbt1100
| First Paragraph | Full Text (HTML/PDF) |
news and views
Plasmon coupling measures up
C Shad Thaxton and Chad A Mirkin
Nature Biotechnology 23, 681–682
(June 2005); doi:10.1038/nbt0605-681
| Full Text (HTML/PDF) |
research article
Characterization and culture of human embryonic stem cells
Lisa M Hoffman and Melissa K Carpenter
Nature Biotechnology 23, 699–708
(June 2005); doi:10.1038/nbt1102
| Abstract | Full Text (HTML/PDF) |
brief communication
An inducible translocation strategy to rapidly activate and inhibit small GTPase signaling pathways
Takanari Inoue, Won Do Heo, Joshua S Grimley, Thomas J Wandless and Tobias Meyer
Nature Methods 2, 415–418
(June 2005); doi:10.1038/nmeth763
| Abstract | Full Text (HTML/PDF) |
letter
MicroRNA expression profiles classify human cancers
Jun Lu , Gad Getz, Eric A. Miska , Ezequiel Alvarez-Saavedra, Justin Lamb, David Peck, Alejandro Sweet-Cordero, Benjamin L. Ebert, Raymond H. Mak, Adolfo A. Ferrando, James R. Downing, Tyler Jacks, H. Robert Horvitz and Todd R. Golub
Nature 435, 834–838
(09 June 2005); doi:10.1038/nature03702
| First Paragraph | Full Text (HTML / PDF) |
research article
A high-throughput assay for assessing the cell permeability of combinatorial libraries
Peng Yu, Bo Liu and Thomas Kodadek
Nature Biotechnology 23, 746–751
(June 2005); doi:10.1038/nbt1099
| First Paragraph | Full Text (HTML/PDF) |
article
Highly efficient molecular delivery into mammalian cells using carbon nanotube spearing
Dong Cai, Jennifer M Mataraza, Zheng-Hong Qin, Zhongping Huang, Jianyu Huang, Thomas C Chiles, David Carnahan, Kris Kempa and Zhifeng Ren
Nature Methods 2, 449–454
(June 2005); doi:10.1038/nmeth761
| First Paragraph | Full Text (HTML/PDF) |
review article
Miniaturization in functional genomics and proteomics
Sascha Sauer, Bodo M. H. Lange, Johan Gobom, Lajos Nyarsik, Harald Seitz and Hans Lehrach
Nature Reviews Genetics 6, 465–476
(June 2005); doi:10.1038/nrg1618
| Summary | Full Text (HTML / PDF) |
article
Reverse MAPPIT: screening for protein-protein interaction modifiers in mammalian cells
Sven Eyckerman, Irma Lemmens, Dominiek Catteeuw, Annick Verhee, Joel Vandekerckhove, Sam Lievens and Jan Tavernier
Nature Methods 2, 427–433
(June 2005); doi:10.1038/nmeth760
| Abstract | Full Text (HTML/PDF) |
news and views
Perturbing interactions
Stuart Milstein and Marc Vidal
Nature Methods 2, 412–414
(June 2005); doi:10.1038/nmeth0605-412
| Abstract | Full Text (HTML/PDF) |
May
research article
Quantitative mouse brain proteomics using culture-derived isotope tags as internal standards
Yasushi Ishihama, Toshitaka Sato, Tsuyoshi Tabata, Norimasa Miyamoto, Koji Sagane, Takeshi Nagasu and Yoshiya Oda
Nature Biotechnology 23, 617–621
(May 2005); doi:10.1038/nbt1086
| First Paragraph | Full Text (HTML/PDF) |
research article
Enzyme family-specific and activity-based screening of chemical libraries using enzyme microarrays
Daniel P Funeriu, Jörg Eppinger, Lucile Denizot, Masato Miyake and Jun Miyake
Nature Biotechnology 23, 622–627
(May 2005); doi:10.1038/nbt1090
| First Paragraph | Full Text (HTML/PDF) |
article
Quantitative analysis of gene expression in living adult neural stem cells by gene trapping
John R Scheel, Jasodhara Ray, Fred H Gage and Carrolee Barlow
Nature Methods 2, 363–370
(May 2005); doi:10.1038/nmeth755
| Abstract | Full Text (HTML/PDF) |
letter
Combinatorial microRNA target predictions
Azra Krek, Dominic Grün, Matthew N Poy, Rachel Wolf, Lauren Rosenberg, Eric J Epstein, Philip MacMenamin, Isabelle da Piedade, Kristin C Gunsalus, Markus Stoffel and Nikolaus Rajewsky
Nature Genetics 37, 495–500
(May 2005); doi:10.1038/ng1536
| First Paragraph | Full Text (HTML/PDF) |
research article
Gene knockdown by large circular antisense for high-throughput functional genomics
Yun-Han Lee, Ik-Jae Moon, Bin Hur, Jeong-Hoh Park, Kil-Hwan Han, Seok-Yong Uhm, Yong-Joo Kim, Koo-Jeong Kang, Jong-Wook Park, Young-Bae Seu, Young-Ho Kim and Jong-Gu Park
Nature Biotechnology 23, 591–599
(May 2005); doi:10.1038/nbt1089
| Abstract | Full Text (HTML/PDF) |
article
Monitoring macromolecular complexes involved in the chaperonin-assisted protein folding cycle by mass spectrometry
Esther van Duijn, Patrick J Bakkes, Ron M A Heeren, Robert H H van den Heuvel, Harm van Heerikhuizen, Saskia M van der Vies and Albert J R Heck
Nature Methods 2, 371–376
(May 2005); doi:10.1038/nmeth753
| Abstract | Full Text (HTML/PDF) |
news and views
Watching and weighting—chaperone complexes in action
Carol V Robinson
Nature Methods 2, 331–332
(May 2005); doi:10.1038/nmeth0505-331
| Abstract | Full Text (HTML/PDF) |
article
Epistasis analysis with global transcriptional phenotypes
Nancy Van Driessche, Janez Demsar, Ezgi O Booth, Paul Hill, Peter Juvan, Blaz Zupan, Adam Kuspa and Gad Shaulsky
Nature Genetics 37, 471–477
(May 2005); doi:10.1038/ng1545
| Abstract | Full Text (HTML/PDF) |
news and views
Universal epistasis analysis
Timothy R Hughes
Nature Genetics 37, 457–458
(May 2005); doi:10.1038/ng0505-457
| Full Text (HTML/PDF) |
analysis
Systematic interpretation of genetic interactions using protein networks
Ryan Kelley and Trey Ideker
Nature Biotechnology 23, 561–566
(May 2005); doi:10.1038/nbt1096
| Abstract | Full Text (HTML/PDF) |
research article
Baculovirus as versatile vectors for protein expression in insect and mammalian cells
Thomas A Kost, J Patrick Condreay and Donald L Jarvis
Nature Biotechnology 23, 567–575
(May 2005); doi:10.1038/nbt1095
| Abstract | Full Text (HTML/PDF) |
perspective
Neural stem cells and neurospheres — re-evaluating the relationship
Brent A Reynolds and Rodney L Rietze
Nature Methods 2, 333–336
(May 2005); doi:10.1038/nmeth758
| Abstract | Full Text (HTML/PDF) |
article
Independence and reproducibility across microarray platforms
Jennie E Larkin, Bryan C Frank, Haralambos Gavras, Razvan Sultana and John Quackenbush
Nature Methods 2, 337–344
(May 2005); doi:10.1038/nmeth757
| Abstract | Full Text (HTML/PDF) |
article
Multiple-laboratory comparison of microarray platforms
Rafael A Irizarry, Daniel Warren, Forrest Spencer, Irene F Kim, Shyam Biswal, Bryan C Frank, Edward Gabrielson, Joe G N Garcia, Joel Geoghegan, Gregory Germino, Constance Griffin, Sara C Hilmer, Eric Hoffman, Anne E Jedlicka, Ernest Kawasaki, Francisco Martínez-Murillo, Laura Morsberger, Hannah Lee, David Petersen, John Quackenbush, Alan Scott, Michael Wilson, Yanqin Yang, Shui Qing Ye and Wayne Yu
Nature Methods 2, 345–350
(May 2005); doi:10.1038/nmeth756
| Abstract | Full Text (HTML/PDF) |
article
Standardizing global gene expression analysis between laboratories and across platforms
Members of the Toxicogenomics Research Consortium: B.K. Weis
Nature Methods 2, 351–356
(May 2005); doi:10.1038/nmeth754
| Abstract | Full Text (HTML/PDF) |
news and views
Of fish and chips
Gavin Sherlock
Nature Methods 2, 329–330
(May 2005); doi:10.1038/nmeth0505-329
| Abstract | Full Text (HTML/PDF) |
April
research article
Enrichment and analysis of peptide subsets using fluorous affinity tags and mass spectrometry
Scott M Brittain, Scott B Ficarro, Ansgar Brock and Eric C Peters
Nature Biotechnology 23, 463–468
(April 2005); doi:10.1038/nbt1076
| First Paragraph | Full Text (HTML/PDF) |
article
In vivo protein biotinylation for identification of organ-specific antigens accessible from the vasculature
Jascha-N Rybak, Anna Ettorre, Brigitte Kaissling, Raffaella Giavazzi, Dario Neri and Giuliano Elia
Nature Methods 2, 291–298
(April 2005); doi:10.1038/nmeth745
| Abstract | Full Text (HTML/PDF) |
letters to nature
Visualizing the mechanical activation of Src
Yingxiao Wang, Elliot L. Botvinick, Yihua Zhao, Michael W. Berns , Shunichi Usami, Roger Y. Tsien and Shu Chien
Nature 434, 1040–1045
(21 April 2005); doi:10.1038/nature03469
| First Paragraph | Full Text (HTML / PDF) |
article
Prediction and validation of the distinct dynamics of transient and sustained ERK activation
Satoru Sasagawa, Yu-ichi Ozaki, Kazuhiro Fujita and Shinya Kuroda
Nature Cell Biology 7, 365–373
(April 2005); doi:10.1038/ncb1233
| Abstract | Full Text (HTML/PDF) |
news and views
Directing NGF's actions: it's a Rap
Philip J. S. Stork
Nature Cell Biology 7, 338–339
(April 2005); doi:10.1038/ncb0405-338
| Full Text (HTML/PDF) |
article
Reverse engineering of regulatory networks in human B cells
Katia Basso, Adam A Margolin, Gustavo Stolovitzky, Ulf Klein, Riccardo Dalla-Favera and Andrea Califano
Nature Genetics 37, 382–390
(April 2005); doi:10.1038/ng1532
| Abstract | Full Text (HTML/PDF) |
research article
Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA
Adam D Judge, Vandana Sood, Janet R Shaw, Dianne Fang, Kevin McClintock and Ian MacLachlan
Nature Biotechnology 23, 457–462
(April 2005); doi:10.1038/nbt1081
| First Paragraph | Full Text (HTML/PDF) |
brief communication
In vivo protein labeling with trimethoprim conjugates: a flexible chemical tag
Lawrence W Miller, Yunfei Cai, Michael P Sheetz and Virginia W Cornish
Nature methods 2, 255–357
(April 2005); doi:10.1038/nmeth749
| Abstract | Full Text (HTML/PDF) |
brief communication
The hESC line Envy expresses high levels of GFP in all differentiated progeny
Magdaline Costa, Mirella Dottori, Elizabeth Ng, Susan M Hawes, Koula Sourris, Pegah Jamshidi, Martin F Pera, Andrew G Elefanty and Edouard G Stanley
Nature Methods 2, 259–260
(April 2005); doi:10.1038/nmeth748
| Abstract | Full Text (HTML/PDF) |
research article
Extracellular secretion of polypeptides using a modified Escherichia coli flagellar secretion apparatus
Katariina Majander, Lena Anton, Jenni Antikainen, Hannu Lång, Mirko Brummer, Timo K Korhonen and Benita Westerlund-Wikström
Nature Biotechnology 23, 475–481
(April 2005); doi:10.1038/nbt1077
| First Paragraph | Full Text (HTML/PDF) |
article
A multiplexed homogeneous fluorescence-based assay for protein kinase activity in cell lysates
Melissa D Shults, Kevin A Janes, Douglas A Lauffenburger and Barbara Imperiali
Nature Methods 2, 277–284
(April 2005); doi:10.1038/nmeth747
| Abstract | Full Text (HTML/PDF) |
news and views
Measuring kinase activity: finding needles in a haystack
Benjamin E Turk
Nature Methods 2, 251–252
(April 2005); doi:10.1038/nmeth0405-251
| Abstract | Full Text (HTML/PDF) |
article
Photo-leucine and photo-methionine allow identification of protein-protein interactions in living cells
Monika Suchanek, Anna Radzikowska and Christoph Thiele
Nature Methods 2, 261–268
(April 2005); doi:10.1038/nmeth752
| Abstract | Full Text (HTML/PDF) |
research article
Pulse proteolysis: A simple method for quantitative determination of protein stability and ligand binding
Chiwook Park and Susan Marqusee
Nature Methods 2, 207–212
(March 2005); doi:10.1038/nmeth740
| Abstract | Full Text (HTML/PDF) |
March
research article
Evolutionary optimization of fluorescent proteins for intracellular FRET
Annalee W Nguyen and Patrick S Daugherty
Nature Biotechnology 23, 355–360
(March 2005); doi:10.1038/nbt1066
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cresearch article
Protein photo-cross-linking in mammalian cells by site-specific incorporation of a photoreactive amino acid
Nobumasa Hino, Yuko Okazaki, Takatsugu Kobayashi, Akiko Hayashi, Kensaku Sakamoto and Shigeyuki Yokoyama
Nature Methods 2, 201–206
(March 2005); doi:10.1038/nmeth739
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research article
Programmable ligand-controlled riboregulators of eukaryotic gene expression
Travis S Bayer and Christina D Smolke
Nature Biotechnology 23, 337–343
(March 2005); doi:10.1038/nbt1069
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news and views
Plug-and-play with RNA
Farren J Isaacs and James J Collins
Nature Biotechnology 23, 306–307
(March 2005); doi:10.1038/nbt0305-306
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brief communication
Stem cell proliferative history in tissue revealed by temporal halogenated thymidine analog discrimination
Christopher J Vega and Daniel A Peterson
Nature Methods 2, 167–169
(March 2005); doi:10.1038/nmeth741
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A FlAsH-based FRET approach to determine G protein-coupled receptor activation in living cells
Carsten Hoffmann, Guido Gaietta, Moritz Bünemann, Stephen R Adams, Silke Oberdorff-Maass, Björn Behr, Jean-Pierre Vilardaga, Roger Y Tsien, Mark H Ellisman and Martin J Lohse
Nature Methods 2, 171–176
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Real-time monitoring of receptor and G-protein interactions in living cells
Céline Galés, R Victor Rebois, Mireille Hogue, Phan Trieu, Andreas Breit, Terence E Hébert, 3 and Michel Bouvier
Nature Methods 2, 177–184
(March 2005); doi:10.1038/nmeth743
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New eyes to see texture in ligand efficacy
Terry P Kenakin
Nature Methods 2, 163–164
(March 2005); doi:10.1038/nmeth0305-163.html
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technical report
MAGIC, an in vivo genetic method for the rapid construction of recombinant DNA molecules
Mamie Z Li and Stephen J Elledge
Nature Genetics 37, 311–319
(March 2005); doi:10.1038/ng1505
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A new method for C-terminal sequence analysis in the proteomic era
Bart Samyn, Kjell Sergeant, Pedro Castanheira, Carlos Faro and Jozef Van Beeumen
Nature Methods 2, 193–200
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Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy
Dong-Ho Kim, Mark A Behlke, Scott D Rose, Mi-Sook Chang, Sangdun Choi and John J Rossi
Nature Biotechnology 23, 222–226
(February 2005); doi:10.1038/nbt1051
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letter
Synthetic shRNAs as potent RNAi triggers
Despina Siolas, Cara Lerner, Julja Burchard, Wei Ge, Peter S Linsley, Patrick J Paddison, Gregory J Hannon and Michele A Cleary
Nature Biotechnology 23, 227–231
(February 2005); doi:10.1038/nbt1052
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Dicing with siRNA
Bryan R.G. Williams
Nature Biotechnology 23, 181–182
(February 2005); doi:10.1038/nbt0205-181
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research article
Biosynthetic labeling of RNA with uracil phosphoribosyltransferase allows cell-specific microarray analysis of mRNA synthesis and decay
Michael D Cleary, Christopher D Meiering, Eric Jan, Rebecca Guymon and John C Boothroyd
Nature Biotechnology 23, 232–237
(February 2005); doi:10.1038/nbt1061
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A window on the dynamics of biological switches
Michael Bittner
Nature Biotechnology 23, 183–184
(February 2005); doi:10.1038/nbt0205-183
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An extracellular matrix microarray for probing cellular differentiation
Christopher J Flaim, Shu Chien and Sangeeta N Bhatia
Nature Methods 2, 119–125
(February 2005); doi:10.1038/nmeth736
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review article
DNA supercoiling — a global transcriptional regulator for enterobacterial growth?
Andrew Travers and Georgi Muskhelishvili
Nature Reviews Microbiology 3, 157–169
(February 2005); doi:10.1038/nrmicro1088
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Functional annotation and network reconstruction through cross-platform integration of microarray data
Xianghong Jasmine Zhou, Ming-Chih J Kao, Haiyan Huang, Angela Wong, Juan Nunez-Iglesias, Michael Primig, Oscar M Aparicio, Caleb E Finch, Todd E Morgan and Wing Hung Wong
Nature Biotechnology 23, 238–243
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A family of phosphodiesterase inhibitors discovered by cocrystallography and scaffold-based drug design
Graeme L Card, Landy Blasdel, Bruce P England, Chao Zhang, Yoshihisa Suzuki, Sam Gillette, Daniel Fong, Prabha N Ibrahim, Dean R Artis, Gideon Bollag, Michael V Milburn, Sung-Hou Kim, Joseph Schlessinger and Kam Y J Zhang
Nature Biotechnology 23, 201–207
(February 2005); doi:10.1038/nbt1059
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A new school for screening
Harren Jhoti
Nature Biotechnology 23, 184–186
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Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation
Patrick Ng, Chia-Lin Wei, Wing-Kin Sung, Kuo Ping Chiu, Leonard Lipovich, Chin Chin Ang, Sanjay Gupta, Atif Shahab, Azmi Ridwan, Chee Hong Wong, Edison T Liu and Yijun Ruan
Nature Methods 2, 105–111
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Transcriptome PETs: A genome's best friends
Brock A Peters and Victor E Velculescu
Nature Methods 2, 93–94
(February 2005); doi:10.1038/nmeth0205-93
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Site-specific labeling of cell surface proteins with biophysical probes using biotin ligase
Irwin Chen, Mark Howarth, Weiying Lin & Alice Y Ting
Nature Methods 2, 99–104
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Coordinate dual-gene transgenesis by lentiviral vectors carrying synthetic bidirectional promoters
Mario Amendola, Mary Anna Venneri, Alessandra Biffi, Elisa Vigna and Luigi Naldini
Nature Biotechnology 23, 108–116
(January 2005); doi:10.1038/nbt1049
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Protein tagging and detection with engineered self-assembling fragments of green fluorescent protein
Stéphanie Cabantous, Thomas C Terwilliger and Geoffrey S Waldo
Nature Biotechnology 23, 102–107
(January 2005); doi:10.1038/nbt1044
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LAMP, a new imaging assay of gap junctional communication unveils that Ca2+ influx inhibits cell coupling
Kenneth Dakin, YuRui Zhao and Wen-Hong Li
Nature Methods 2, 55–62
(January 2005); doi:10.1038/nmeth730
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Illuminating gap junctions
David C Spray
Nature Methods 2, 12–14
(January 2005); doi:10.1038/nmeth0105-12
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Immunoaffinity profiling of tyrosine phosphorylation in cancer cells
John Rush, Albrecht Moritz, Kimberly A Lee, Ailan Guo, Valerie L Goss, Erik J Spek, Hui Zhang, Xiang-Ming Zha, Roberto D Polakiewicz and Michael J Comb
Nature Biotechnology 23, 94–101
(January 2005); doi:10.1038/nbt1046
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An enriched look at tyrosine phosphorylation
Thomas P Conrads and Timothy D Veenstra
Nature Biotechnology 23, 36–37
(January 2005); doi:10.1038/nbt0105-36
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Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment
Jonghwan Kim, Akshay A Bhinge, Xochitl C Morgan and Vishwanath R Iyer
Nature Methods 2, 47–53
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Microfluidic sorting of mammalian cells by optical force switching
Mark M Wang, Eugene Tu, Daniel E Raymond, Joon Mo Yang, Haichuan Zhang, Norbert Hagen, Bob Dees, Elinore M Mercer, Anita H Forster, Ilona Kariv, Philippe J Marchand and William F Butler
Nature Biotechnology 23, 83–87
(January 2005); doi:10.1038/nbt1050
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Polyene-lipids: A new tool to image lipids
Lars Kuerschner, Christer S Ejsing, Kim Ekroos, Andrej Shevchenko, Kurt I Anderson and Christoph Thiele
Nature Methods 2, 39–45
(January 2005); doi:10.1038/nmeth728
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Brilliant lipids
Gerrit van Meer and Rob M J Liskamp
Nature Methods 2, 14–15
(January 2005); doi:10.1038/nmeth0105-14
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review article
Kinomics: methods for deciphering the kinome
Sam A Johnson and Tony Hunter
Nature Methods 2, 17–25
(January 2005); doi:10.1038/nmeth731
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Using protein-DNA chimeras to detect and count small numbers of molecules
Ian Burbulis, Kumiko Yamaguchi, Andrew Gordon, Robert Carlson and Roger Brent
Nature Methods 2, 31–37
(January 2005); doi:10.1038/nmeth729
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Tadpoles by the tail
Garry P Nolan
Nature Methods 2, 11–12
(January 2005); doi:10.1038/nmeth0105-11
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The invertor knock-in conditional chromosomal translocation mimic
Alan Forster, Richard Pannell, Lesley F Drynan, Rosalind Codrington, Angelika Daser, Markus Metzler, M Natividad Lobato and Terence H Rabbitts
Nature Methods 2, 27–30
(January 2005); doi:10.1038/nmeth727
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