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Deyou Zheng
Department of Neurology, Albert Einstein College of Medicine, United States of America

Faculty Member: Structural Biology > Structural Genomics [ since 3 December 2002 ]
[ Evaluations ]
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Evaluations

Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling.
Hu S, Xie Z, …, Qian J, Zhu H
Cell 2009 Oct 30 139(3):610-22 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Zhong Yao and Rony Seger / Sourav Bandyopadhyay and Trey Ideker / Günter Mayer / Deyou Zheng / Clifford Harding
Evaluated 30 Nov 2009

Personalized copy number and segmental duplication maps using next-generation sequencing.
Alkan C, Kidd JM, …, Gibbs RA, Eichler EE
Nat Genet 2009 Oct 41(10):1061-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Deyou Zheng
Evaluated 16 Nov 2009

MicroRNA-mediated switching of chromatin-remodelling complexes in neural development.
Yoo AS, Staahl BT, Chen L, Crabtree GR
Nature 2009 Jul 30 460(7255):642-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Deyou Zheng
Evaluated 10 Aug 2009

mRNA-Seq whole-transcriptome analysis of a single cell.
Tang F, Barbacioru C, …, Lao K, Surani MA
Nat Methods 2009 May 6(5):377-82 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Deyou Zheng
Evaluated 15 May 2009

Species-specific transcription in mice carrying human chromosome 21.
Wilson MD, Barbosa-Morais NL, …, Tavaré S, Odom DT
Science 2008 Oct 17 322(5900):434-8 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Yoav Gilad / Kenneth Zaret / Deyou Zheng / Jose M. Jimenez-Gomez and Julin Maloof / Reza Kalhor and Lin Chen / Evi Soutoglou and Tom Misteli / Heng Zhu
Evaluated 27 Oct 2008

Integration of external signaling pathways with the core transcriptional network in embryonic stem cells.
Chen X, Xu H, …, Wei CL, Ng HH
Cell 2008 Jun 13 133(6):1106-17 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Deyou Zheng / Lin Chen
Evaluated 23 Jul 2008

The chemical genomic portrait of yeast: uncovering a phenotype for all genes.
Hillenmeyer ME, Fung E, …, Nislow C, Giaever G
Science 2008 Apr 18 320(5874):362-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Manyuan Long / Ramon Serrano / Deyou Zheng
Evaluated 28 May 2008

Consistent blind protein structure generation from NMR chemical shift data.
Shen Y, Lange O, …, Baker D, Bax A
Proc Natl Acad Sci U S A 2008 Mar 25 105(12):4685-90 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Antonio Rosato / Gottfried Otting / Deyou Zheng / Torleif Härd / Mikael Akke / Dorothee Kern
Evaluated 21 Apr 2008

SCFbeta-TRCP controls oncogenic transformation and neural differentiation through REST degradation.
Westbrook TF, Hu G, …, Harper JW, Elledge SJ
Nature 2008 Mar 20 452(7185):370-4 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Deyou Zheng
Evaluated 26 Mar 2008

Control of chromosome stability by the beta-TrCP-REST-Mad2 axis.
Guardavaccaro D, Frescas D, …, Hernando E, Pagano M
Nature 2008 Mar 20 452(7185):365-9 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Deyou Zheng
Evaluated 26 Mar 2008

Polymorphic Y chromosomes harbor cryptic variation with manifold functional consequences.
Lemos B, Araripe LO, Hartl DL
Science 2008 Jan 4 319(5859):91-3 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Deyou Zheng
Evaluated 15 Jan 2008

Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D.
Perocchi F, Xu Z, Clauder-Münster S, Steinmetz LM
Nucleic Acids Res 2007 35(19):e128 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Deyou Zheng
Evaluated 24 Oct 2007

High-resolution profiling of histone methylations in the human genome.
Barski A, Cuddapah S, …, Chepelev I, Zhao K
Cell 2007 May 18 129(4):823-37 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Steven Henikoff / Xing Wang Deng / Michael Meisterernst / Deyou Zheng / Magdalena Zernicka-Goetz
Evaluated 29 Jun 2007

Genome-wide mapping of in vivo protein-DNA interactions.
Johnson DS, Mortazavi A, Myers RM, Wold B
Science 2007 Jun 8 316(5830):1497-502 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Jim Maher / John Jaenike / Deyou Zheng / Ulf Pettersson / Gabriele Varani / Magdalena Zernicka-Goetz
Evaluated 29 Jun 2007

Developmentally regulated piRNA clusters implicate MILI in transposon control.
Aravin AA, Sachidanandam R, …, Fejes-Toth K, Hannon GJ
Science 2007 May 4 316(5825):744-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Deyou Zheng
Evaluated 14 May 2007

An RNA map predicting Nova-dependent splicing regulation.
Ule J, Stefani G, …, Blencowe BJ, Darnell RB
Nature 2006 Nov 30 444(7119):580-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Donald Rio / Deyou Zheng / Andrea Barta
Evaluated 13 Dec 2006

Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale.
Herring CD, Raghunathan A, …, Cantor CR, Palsson BØ
Nat Genet 2006 Dec 38(12):1406-12 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Deyou Zheng
Evaluated 28 Nov 2006

The dynamic energy landscape of dihydrofolate reductase catalysis.
Boehr DD, McElheny D, Dyson HJ, Wright PE
Science 2006 Sep 15 313(5793):1638-42 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Deyou Zheng / Mitsuhiko Ikura / Andrea Mattevi
Evaluated 25 Sep 2006

An RNA gene expressed during cortical development evolved rapidly in humans.
Pollard KS, Salama SR, …, Vanderhaeghen P, Haussler D
Nature 2006 Sep 14 443(7108):167-72 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Kevan A Martin / John Abrams / Deyou Zheng / Andrew Feinberg / Rafael Zardoya / Ali H. Brivanlou / Robert Sapolsky / Gabriele Varani / Christopher A. Walsh
Evaluated 29 Aug 2006


Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise.
Newman JR, Ghaemmaghami S, …, DeRisi JL, Weissman JS
Nature 2006 Jun 15 441(7095):840-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Deyou Zheng / Jurg Bahler
Evaluated 20 Jun 2006

Independent evolution of bitter-taste sensitivity in humans and chimpanzees.
Wooding S, Bufe B, …, Weiss RB, Bamshad MJ
Nature 2006 Apr 13 440(7086):930-4 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Deyou Zheng
Evaluated 2 May 2006

3' UTR seed matches, but not overall identity, are associated with RNAi off-targets.
Birmingham A, Anderson EM, …, Marshall WS, Khvorova A
Nat Methods 2006 Mar 3(3):199-204 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Norbert Perrimon / Michael Kiebler / Deyou Zheng / Jeff Woessner
Evaluated 22 Mar 2006

Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile.
Schuldiner M, Collins SR, …, Weissman JS, Krogan NJ
Cell 2005 Nov 4 123(3):507-19 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Andrew Emili / Deyou Zheng / Jef Boeke / Jurg Bahler
Evaluated 6 Feb 2006

A simple physical model for scaling in protein-protein interaction networks.
Deeds EJ, Ashenberg O, Shakhnovich EI
Proc Natl Acad Sci U S A 2006 Jan 10 103(2):311-6 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Nick Grishin / Deyou Zheng
Evaluated 3 Feb 2006

Comparisons of NMR spectral quality and success in crystallization demonstrate that NMR and X-ray crystallography are complementary methods for small protein structure determination.
Snyder DA, Chen Y, …, Hunt J, Montelione GT
J Am Chem Soc 2005 Nov 30 127(47):16505-11 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Deyou Zheng / Thomas Szyperski
Evaluated 6 Dec 2005

NMR and X-ray crystallography, complementary tools in structural proteomics of small proteins.
Yee AA, Savchenko A, …, Edwards AM, Arrowsmith CH
J Am Chem Soc 2005 Nov 30 127(47):16512-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Deyou Zheng / Thomas Szyperski
Evaluated 6 Dec 2005

Cis-trans isomerization at a proline opens the pore of a neurotransmitter-gated ion channel.
Lummis SC, Beene DL, …, Broadhurst RW, Dougherty DA
Nature 2005 Nov 10 438(7065):248-52 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Deyou Zheng / Thomas Kodadek
Evaluated 18 Nov 2005

NMR data collection and analysis protocol for high-throughput protein structure determination.
Liu G, Shen Y, …, Montelione GT, Szyperski T
Proc Natl Acad Sci U S A 2005 Jul 26 102(30):10487-92 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Gottfried Otting / Deyou Zheng
Evaluated 3 Nov 2005

Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset.
Choe SE, Boutros M, …, Church GM, Halfon MS
Genome Biol 2005 6(2):R16 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Jose Luis Riechmann / Deyou Zheng
Evaluated 15 Aug 2005

G-matrix Fourier transform NOESY-based protocol for high-quality protein structure determination.
Shen Y, Atreya HS, Liu G, Szyperski T
J Am Chem Soc 2005 Jun 29 127(25):9085-99 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Deyou Zheng
Evaluated 30 Jun 2005

Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles.
Gilad Y, Rifkin SA, …, Gerstein M, White KP
Genome Res 2005 May 15(5):674-80 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Deyou Zheng
Evaluated 18 May 2005

Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments.
Johnson JM, Edwards S, Shoemaker D, Schadt EE
Trends Genet 2005 Feb 21(2):93-102 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Deyou Zheng
Evaluated 22 Mar 2005

From ORFeome to biology: a functional genomics pipeline.
Wiemann S, Arlt D, …, Sültmann H, Poustka A
Genome Res 2004 Oct 14(10B):2136-44 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Deyou Zheng
Evaluated 3 Dec 2004

Megabase deletions of gene deserts result in viable mice.
Nóbrega MA, Zhu Y, …, Afzal V, Rubin EM
Nature 2004 Oct 21 431(7011):988-93 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Jim Thomas / Deyou Zheng / Marie-Angele Grandbastien / Andrew S McCallion
Evaluated 29 Oct 2004

The prokaryotic selenoproteome.
Kryukov GV, Gladyshev VN
EMBO Rep 2004 May 5(5):538-43 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Deyou Zheng
Evaluated 6 May 2004

The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor.
Yang H, Yang M, …, Hilgenfeld R, Rao Z
Proc Natl Acad Sci U S A 2003 Nov 11 100(23):13190-5 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Deyou Zheng
Evaluated 18 Nov 2003

Using a neural network and spatial clustering to predict the location of active sites in enzymes.
Gutteridge A, Bartlett GJ, Thornton JM
J Mol Biol 2003 Jul 18 330(4):719-34 [abstract on PubMed] [related articles] [order article]
Selected by | Deyou Zheng
Evaluated 20 Aug 2003

Comprehensive identification of human bZIP interactions with coiled-coil arrays.
Newman JR, Keating AE
Science 2003 Jun 27 300(5628):2097-101 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Deyou Zheng / E Neil G Marsh
Evaluated 3 Jul 2003

Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS.
Herrmann T, Güntert P, Wüthrich K
J Biomol NMR 2002 Nov 24(3):171-89 [abstract on PubMed] [related articles] [order article]
Selected by | Deyou Zheng / Antonio Rosato
Evaluated 24 Jan 2003

Transmembrane helix predictions revisited.
Chen CP, Kernytsky A, Rost B
Protein Sci 2002 Dec 11(12):2774-91 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Deyou Zheng / Rolf Apweiler
Evaluated 17 Dec 2002

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