Experimental characterization of the human non-sequence-specific nucleic acid interactome

[1]  P. Bork,et al.  Experimental characterization of the human non-sequence-specific nucleic acid interactome , 2013, Genome Biology.

[2]  K. Kuroiwa,et al.  YB-1 suppression induces STAT3 proteolysis and sensitizes renal cancer to interferon-α , 2013, Cancer Immunology, Immunotherapy.

[3]  J. Steitz,et al.  The "Observer Effect" in genome-wide surveys of protein-RNA interactions. , 2013, Molecular cell.

[4]  Giulio Superti-Furga,et al.  Structural basis for viral 5′-PPP-RNA recognition by human IFIT proteins , 2013, Nature.

[5]  P. Sorensen,et al.  Identification and quantification of newly synthesized proteins translationally regulated by YB-1 using a novel Click-SILAC approach. , 2012, Journal of proteomics.

[6]  J. Steitz,et al.  Association of Argonaute proteins and microRNAs can occur after cell lysis. , 2012, RNA.

[7]  K. Duff,et al.  Contrasting Pathology of the Stress Granule Proteins TIA-1 and G3BP in Tauopathies , 2012, The Journal of Neuroscience.

[8]  Norman E. Davey,et al.  Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins , 2012, Cell.

[9]  A. Bosserhoff,et al.  MAPK and PI3K/AKT mediated YB‐1 activation promotes melanoma cell proliferation which is counteracted by an autoregulatory loop , 2012, Experimental dermatology.

[10]  Rafael C. Jimenez,et al.  The IntAct molecular interaction database in 2012 , 2011, Nucleic Acids Res..

[11]  L. Ovchinnikov,et al.  Interplay between Y-box-binding protein 1 (YB-1) and poly(A) binding protein (PABP) in specific regulation of YB-1 mRNA translation , 2011, RNA biology.

[12]  G. Superti-Furga,et al.  IFIT1 is an antiviral protein that recognizes 5′-triphosphate RNA , 2011, Nature Immunology.

[13]  Karl Mechtler,et al.  General statistical modeling of data from protein relative expression isobaric tags. , 2011, Journal of proteome research.

[14]  D. Söll,et al.  HSPC117 Is the Essential Subunit of a Human tRNA Splicing Ligase Complex , 2011, Science.

[15]  Giulio Superti-Furga,et al.  Initial characterization of the human central proteome , 2011, BMC Systems Biology.

[16]  J. Greenblatt,et al.  Molecular Systems Biology 6; Article number 448; doi:10.1038/msb.2010.104 Citation: Molecular Systems Biology 6:448 , 2022 .

[17]  Supriyo De,et al.  Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information , 2010, BMC Medical Genomics.

[18]  S. Blackshaw,et al.  Profiling the Human Protein-DNA Interactome Reveals ERK2 as a Transcriptional Repressor of Interferon Signaling , 2009, Cell.

[19]  Matthias Mann,et al.  Unbiased RNA–protein interaction screen by quantitative proteomics , 2009, Proceedings of the National Academy of Sciences.

[20]  Juan M. Vaquerizas,et al.  A census of human transcription factors: function, expression and evolution , 2009, Nature Reviews Genetics.

[21]  D. Figeys,et al.  A Novel Proteomics Approach for the Discovery of Chromatin-associated Protein Networks*S , 2009, Molecular & Cellular Proteomics.

[22]  G. Superti-Furga,et al.  An orthogonal proteomic-genomic screen identifies AIM2 as a cytoplasmic DNA sensor for the inflammasome , 2009, Nature Immunology.

[23]  Sandhya Rani,et al.  Human Protein Reference Database—2009 update , 2008, Nucleic Acids Res..

[24]  Matthew R. Laird,et al.  Protein Protein Interaction Network Evaluation for Identifying Potential Drug Targets , 2009 .

[25]  S. Batzoglou,et al.  Genome-Wide Analysis of Transcription Factor Binding Sites Based on ChIP-Seq Data , 2008, Nature Methods.

[26]  Kai-Wei Chang,et al.  RNA-binding proteins in human genetic disease. , 2008, Trends in genetics : TIG.

[27]  T. Mikkelsen,et al.  Genome-scale DNA methylation maps of pluripotent and differentiated cells , 2008, Nature.

[28]  P. Robinson,et al.  Walking the interactome for prioritization of candidate disease genes. , 2008, American journal of human genetics.

[29]  Yoshihiro Yamanishi,et al.  KEGG for linking genomes to life and the environment , 2007, Nucleic Acids Res..

[30]  K. Dolinski,et al.  The BioGRID Interaction Database: 2008 update , 2007, Nucleic Acids Res..

[31]  A. Mortazavi,et al.  Genome-Wide Mapping of in Vivo Protein-DNA Interactions , 2007, Science.

[32]  Dustin E. Schones,et al.  High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.

[33]  A. Baines.  A FERM-adjacent (FA) region defines a subset of the 4.1 superfamily and is a potential regulator of FERM domain function , 2006, BMC Genomics.

[34]  Z. Weng,et al.  A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome , 2006, Cell.

[35]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt): an expanding universe of protein information , 2005, Nucleic Acids Res..

[36]  Robert D. Finn,et al.  Pfam: clans, web tools and services , 2005, Nucleic Acids Res..

[37]  M. Andrulis,et al.  The Y-box binding protein YB-1 is associated with progressive disease and mediates survival and drug resistance in multiple myeloma. , 2005, Blood.

[38]  Yusuke Nakamura,et al.  ICBP90, an E2F-1 target, recruits HDAC1 and binds to methyl-CpG through its SRA domain , 2004, Oncogene.

[39]  Simon C. Potter,et al.  An overview of Ensembl. , 2004, Genome research.

[40]  Luana Licata,et al.  Searching the MINT Database for Protein Interaction Information , 2003, Current protocols in bioinformatics.

[41]  A. Masselot,et al.  OLAV: Towards high‐throughput tandem mass spectrometry data identification , 2003, Proteomics.

[42]  David Botstein,et al.  Promoter-specific binding of Rap1 revealed by genome-wide maps of protein–DNA association , 2001, Nature Genetics.

[43]  G. Church,et al.  Exploring the DNA-binding specificities of zinc fingers with DNA microarrays , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[44]  D. Botstein,et al.  Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF , 2001, Nature.

[45]  P. Brown,et al.  Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase. , 2000, Molecular cell.

[46]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[47]  D. N. Perkins,et al.  Probability‐based protein identification by searching sequence databases using mass spectrometry data , 1999, Electrophoresis.

[48]  M. Wilm,et al.  Rapid Protein Sequencing by Tandem Mass Spectrometry and cDNA Cloning of p20-CGGBP , 1997, The Journal of Biological Chemistry.

[49]  Walter Fontana,et al.  Fast folding and comparison of RNA secondary structures , 1994 .

[50]  M. Nissen,et al.  The A.T-DNA-binding domain of mammalian high mobility group I chromosomal proteins. A novel peptide motif for recognizing DNA structure. , 1990, The Journal of biological chemistry.

[51]  J. S. Jiménez.  Protein-DNA interaction at the origin of neurological diseases: a hypothesis. , 2010, Journal of Alzheimer's disease : JAD.

[52]  M. Mann,et al.  A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements. , 2009, Genome research.

[53]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[54]  Ioannis Xenarios,et al.  DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions , 2002, Nucleic Acids Res..

[55]  John J. Wyrick,et al.  Genome-wide location and function of DNA binding proteins. , 2000, Science.

[56]  B. Dörken,et al.  Nuclear localization and increased levels of transcription factor YB-1 in primary human breast cancers are associated with intrinsic MDR1 gene expression , 1997, Nature Medicine.

[57]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .