Proteomic and interactomic insights into the molecular basis of cell functional diversity

[1]  J. Shepherd,et al.  Cycle. , 2020, The American journal of geriatric psychiatry : official journal of the American Association for Geriatric Psychiatry.

[2]  Henry Yang,et al.  Cis- and trans-regulations of pre-mRNA splicing by RNA editing enzymes influence cancer development , 2020, Nature Communications.

[3]  L. Foster,et al.  Next-generation Interactomics: Considerations for the Use of Co-elution to Measure Protein Interaction Networks* , 2019, Molecular & Cellular Proteomics.

[4]  Rongting Huang,et al.  Crosstalk of intracellular post-translational modifications in cancer. , 2019, Archives of biochemistry and biophysics.

[5]  Samie R Jaffrey,et al.  Reading, writing and erasing mRNA methylation , 2019, Nature Reviews Molecular Cell Biology.

[6]  C. Iacobucci,et al.  A Simple Cross-Linking/Mass Spectrometry Workflow to Study System-Wide Protein Interactions. , 2019, Analytical chemistry.

[7]  Ludovic C. Gillet,et al.  Integration of transcriptome, proteome and phosphoproteome data elucidates the genetic control of molecular networks , 2019, bioRxiv.

[8]  Gary D Bader,et al.  EPIC: software toolkit for elution profile-based inference of protein complexes , 2019, Nature Methods.

[9]  Sebastian A. Leidel,et al.  The epitranscriptome in translation regulation: mRNA and tRNA modifications as the two sides of the same coin? , 2019, FEBS letters.

[10]  L. Maquat,et al.  Quality and quantity control of gene expression by nonsense-mediated mRNA decay , 2019, Nature Reviews Molecular Cell Biology.

[11]  Ruedi Aebersold,et al.  A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS , 2019, bioRxiv.

[12]  Liangliang Sun,et al.  Identification and Quantification of Proteoforms by Mass Spectrometry , 2019, Proteomics.

[13]  Evan G. Williams,et al.  Multi-omic measurements of heterogeneity in HeLa cells across laboratories , 2019, Nature Biotechnology.

[14]  Brian Raught,et al.  Getting to know the neighborhood: using proximity-dependent biotinylation to characterize protein complexes and map organelles. , 2019, Current opinion in chemical biology.

[15]  Laura Trinkle-Mulcahy,et al.  Recent advances in proximity-based labeling methods for interactome mapping , 2019, F1000Research.

[16]  A. Varshavsky.  N-degron and C-degron pathways of protein degradation , 2019, Proceedings of the National Academy of Sciences.

[17]  Ruedi Aebersold,et al.  Complex‐centric proteome profiling by SEC‐SWATH‐MS , 2019, Nature Protocols.

[18]  Henning Hermjakob,et al.  Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes , 2018, Nucleic Acids Res..

[19]  Andreas Ruepp,et al.  CORUM: the comprehensive resource of mammalian protein complexes—2019 , 2018, Nucleic Acids Res..

[20]  D. Larson,et al.  Splicing heterogeneity: separating signal from noise , 2018, Genome Biology.

[21]  KL Pennington,et al.  The dynamic and stress-adaptive signaling hub of 14-3-3: emerging mechanisms of regulation and context-dependent protein–protein interactions , 2018, Oncogene.

[22]  Peer Bork,et al.  Pervasive Protein Thermal Stability Variation during the Cell Cycle , 2018, Cell.

[23]  Xiaonan Liu,et al.  An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations , 2018, Nature Communications.

[24]  L. Maquat,et al.  Nonsense-mediated mRNA Decay and Cancer. , 2018, Current opinion in genetics & development.

[25]  Lloyd M. Smith,et al.  How many human proteoforms are there? , 2018, Nature chemical biology.

[26]  U. Sauer,et al.  A Map of Protein-Metabolite Interactions Reveals Principles of Chemical Communication , 2018, Cell.

[27]  Wolfgang Huber,et al.  Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues , 2017, Nucleic acids research.

[28]  M. Boutros,et al.  Phenotype databases for genetic screens in human cells. , 2017, Journal of biotechnology.

[29]  O. Delaneau,et al.  The effect of genetic variation on promoter usage and enhancer activity , 2017, Nature Communications.

[30]  Patricia Deng,et al.  The evolution and adaptation of A-to-I RNA editing , 2017, PLoS genetics.

[31]  Yigong Shi.  Mechanistic insights into precursor messenger RNA splicing by the spliceosome , 2017, Nature Reviews Molecular Cell Biology.

[32]  J. Wilusz,et al.  Non-AUG translation: a new start for protein synthesis in eukaryotes , 2017, Genes & development.

[33]  I. Dikič.  Proteasomal and Autophagic Degradation Systems. , 2017, Annual review of biochemistry.

[34]  Tao Pan,et al.  Dynamic RNA Modifications in Gene Expression Regulation , 2017, Cell.

[35]  Claire D. McWhite,et al.  Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes , 2017, Molecular systems biology.

[36]  Rosa Viner,et al.  Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification , 2017, Nature Communications.

[37]  F. Baralle,et al.  Alternative splicing as a regulator of development and tissue identity , 2017, Nature Reviews Molecular Cell Biology.

[38]  N. Gusev,et al.  Moonlighting chaperone‐like activity of the universal regulatory 14‐3‐3 proteins , 2017, The FEBS journal.

[39]  Devin K. Schweppe,et al.  Architecture of the human interactome defines protein communities and disease networks , 2017, Nature.

[40]  F. Wouters,et al.  FRET from single to multiplexed signaling events , 2017, Biophysical Reviews.

[41]  Paul M Thomas,et al.  Identification and Characterization of Human Proteoforms by Top-Down LC-21 Tesla FT-ICR Mass Spectrometry. , 2017, Journal of proteome research.

[42]  M. Tress,et al.  Alternative Splicing May Not Be the Key to Proteome Complexity. , 2017, Trends in biochemical sciences.

[43]  Nichollas E. Scott,et al.  Interactome disassembly during apoptosis occurs independent of caspase cleavage , 2017, Molecular systems biology.

[44]  Joseph S. Takahashi,et al.  Transcriptional architecture of the mammalian circadian clock , 2016, Nature Reviews Genetics.

[45]  Chuan He,et al.  Post-transcriptional gene regulation by mRNA modifications , 2016, Nature Reviews Molecular Cell Biology.

[46]  Ernesto Picardi,et al.  REDIportal: a comprehensive database of A-to-I RNA editing events in humans , 2016, Nucleic Acids Res..

[47]  B. Tian,et al.  RNA‐Seq methods for transcriptome analysis , 2017, Wiley interdisciplinary reviews. RNA.

[48]  G. Brar.  Beyond the Triplet Code: Context Cues Transform Translation , 2016, Cell.

[49]  L. Christiaen,et al.  Transcriptional Control of Developmental Cell Behaviors. , 2016, Annual review of cell and developmental biology.

[50]  Ruedi Aebersold,et al.  Mass-spectrometric exploration of proteome structure and function , 2016, Nature.

[51]  J. Harper,et al.  Proteome complexity and the forces that drive proteome imbalance , 2016, Nature.

[52]  R. Myers,et al.  Advancements in Next-Generation Sequencing. , 2016, Annual review of genomics and human genetics.

[53]  M. Ljungman,et al.  Genome stability versus transcript diversity. , 2016, DNA repair.

[54]  N. Kelleher,et al.  Progress in Top-Down Proteomics and the Analysis of Proteoforms. , 2016, Annual review of analytical chemistry.

[55]  Ludovic C. Gillet,et al.  Mass Spectrometry Applied to Bottom-Up Proteomics: Entering the High-Throughput Era for Hypothesis Testing. , 2016, Annual review of analytical chemistry.

[56]  Evan G. Williams,et al.  Systems proteomics of liver mitochondria function , 2016, Science.

[57]  J. McPherson,et al.  Coming of age: ten years of next-generation sequencing technologies , 2016, Nature Reviews Genetics.

[58]  R. Aebersold,et al.  On the Dependency of Cellular Protein Levels on mRNA Abundance , 2016, Cell.

[59]  L. Vasiljeva,et al.  The regulation and functions of the nuclear RNA exosome complex , 2016, Nature Reviews Molecular Cell Biology.

[60]  Zengyou He,et al.  Protein Inference. , 2016, Advances in experimental medicine and biology.

[61]  H. Mirzaei,et al.  Modern Proteomics – Sample Preparation, Analysis and Practical Applications , 2016, Advances in Experimental Medicine and Biology.

[62]  Brian Raught,et al.  A Dynamic Protein Interaction Landscape of the Human Centrosome-Cilium Interface , 2015, Cell.

[63]  Aviv Regev,et al.  Comparative analysis of gene regulatory networks: from network reconstruction to evolution. , 2015, Annual review of cell and developmental biology.

[64]  Marco Y. Hein,et al.  A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances , 2015, Cell.

[65]  Greg W. Clark,et al.  Panorama of ancient metazoan macromolecular complexes , 2015, Nature.

[66]  Qingfei Jiang,et al.  RNA rewriting, recoding, and rewiring in human disease. , 2015, Trends in molecular medicine.

[67]  Edward L. Huttlin,et al.  The BioPlex Network: A Systematic Exploration of the Human Interactome , 2015, Cell.

[68]  D. Rio,et al.  Mechanisms and Regulation of Alternative Pre-mRNA Splicing. , 2015, Annual review of biochemistry.

[69]  S. Teichmann,et al.  Structure, dynamics, assembly, and evolution of protein complexes. , 2015, Annual review of biochemistry.

[70]  M. Snyder,et al.  High-throughput sequencing technologies. , 2015, Molecular cell.

[71]  Nichollas E. Scott,et al.  Development of a computational framework for the analysis of protein correlation profiling and spatial proteomics experiments. , 2015, Journal of proteomics.

[72]  P. Hoen,et al.  Alternative mRNA transcription, processing, and translation: insights from RNA sequencing , 2015 .

[73]  Maxwell R. Mumbach,et al.  Dynamic profiling of the protein life cycle in response to pathogens , 2015, Science.

[74]  Sharad Kumar,et al.  Old, new and emerging functions of caspases , 2014, Cell Death and Differentiation.

[75]  Henning Hermjakob,et al.  The complex portal - an encyclopaedia of macromolecular complexes , 2014, Nucleic Acids Res..

[76]  P. ’. ‘t Hoen,et al.  Alternative mRNA transcription, processing, and translation: insights from RNA sequencing. , 2015, Trends in genetics : TIG.

[77]  Bridget E. Begg,et al.  A Proteome-Scale Map of the Human Interactome Network , 2014, Cell.

[78]  G. Drewes,et al.  Tracking cancer drugs in living cells by thermal profiling of the proteome , 2014, Science.

[79]  A. Oliveira,et al.  Global analysis of protein structural changes in complex proteomes , 2014, Nature Biotechnology.

[80]  P. Sharp,et al.  Building Robust Transcriptomes with Master Splicing Factors , 2014, Cell.

[81]  C. Thermes,et al.  Ten years of next-generation sequencing technology. , 2014, Trends in genetics : TIG.

[82]  Evan G. Williams,et al.  Multilayered Genetic and Omics Dissection of Mitochondrial Activity in a Mouse Reference Population , 2014, Cell.

[83]  Jeffrey R. Whiteaker,et al.  Proteogenomic characterization of human colon and rectal cancer , 2014, Nature.

[84]  B. Kuster,et al.  Mass-spectrometry-based draft of the human proteome , 2014, Nature.

[85]  Gary D Bader,et al.  A draft map of the human proteome , 2014, Nature.

[86]  D. Bentley.  Coupling mRNA processing with transcription in time and space , 2014, Nature Reviews Genetics.

[87]  P. Bickel,et al.  System wide analyses have underestimated protein abundances and the importance of transcription in mammals , 2012, PeerJ.

[88]  Leonard J Foster,et al.  Protein correlation profiling-SILAC to study protein-protein interactions. , 2014, Methods in molecular biology.

[89]  Yuval Peres,et al.  Separating signal from noise , 2013, ArXiv.

[90]  Ludovic C. Gillet,et al.  Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system , 2013, Nature Methods.

[91]  Trey Ideker,et al.  Genotype to phenotype via network analysis. , 2013, Current opinion in genetics & development.

[92]  R. Milo.  What is the total number of protein molecules per cell volume? A call to rethink some published values , 2013, BioEssays : news and reviews in molecular, cellular and developmental biology.

[93]  M. Selbach,et al.  Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation , 2013, Cell.

[94]  Amber L. Couzens,et al.  The CRAPome: a Contaminant Repository for Affinity Purification Mass Spectrometry Data , 2013, Nature Methods.

[95]  R. Aebersold,et al.  The protein interaction landscape of the human CMGC kinase group. , 2013, Cell reports.

[96]  Eric W. Deutsch,et al.  A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis , 2013, Nature.

[97]  J. Bujnicki,et al.  MODOMICS: a database of RNA modification pathways—2013 update , 2012, Nucleic Acids Res..

[98]  Marianna Aprile,et al.  RNA-Seq and human complex diseases: recent accomplishments and future perspectives , 2012, European Journal of Human Genetics.

[99]  S. Stamm,et al.  Function of alternative splicing. , 2013, Gene.

[100]  D. Tollervey,et al.  Transcriptome-wide Analysis of Exosome Targets , 2012, Molecular cell.

[101]  R. Aebersold,et al.  Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells , 2012, Cell.

[102]  Mark H. Ellisman,et al.  Engineered ascorbate peroxidase as a genetically-encoded reporter for electron microscopy , 2012, Nature Biotechnology.

[103]  Andrei L. Turinsky,et al.  A Census of Human Soluble Protein Complexes , 2012, Cell.

[104]  L. Foster,et al.  A high-throughput approach for measuring temporal changes in the interactome , 2012, Nature Methods.

[105]  E. Gottlieb,et al.  Rocking cell metabolism: revised functions of the key glycolytic regulator PKM2 in cancer. , 2012, Trends in biochemical sciences.

[106]  Bernhard Kuster,et al.  Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present , 2012, Analytical and Bioanalytical Chemistry.

[107]  Alex Bateman,et al.  Tissue-Specific Splicing of Disordered Segments that Embed Binding Motifs Rewires Protein Interaction Networks , 2012, Molecular cell.

[108]  Brian Burke,et al.  A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells , 2012, The Journal of cell biology.

[109]  M. Tinti,et al.  The capture of phosphoproteins by 14-3-3 proteins mediates actions of insulin , 2011, Trends in Endocrinology & Metabolism.

[110]  Richard D. LeDuc,et al.  Mapping Intact Protein Isoforms in Discovery Mode Using Top Down Proteomics , 2011, Nature.

[111]  Christodoulos A. Floudas,et al.  Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database , 2011, Scientific reports.

[112]  Carol A. Bocchini,et al.  A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®) , 2011, Human mutation.

[113]  M. Selbach,et al.  Global quantification of mammalian gene expression control , 2011, Nature.

[114]  Adam P. Arkin,et al.  Network News: Innovations in 21st Century Systems Biology , 2011, Cell.

[115]  C. Ghigna,et al.  Alternative splicing and muscular dystrophy , 2010, RNA biology.

[116]  Hans-Werner Mewes,et al.  CORUM: the comprehensive resource of mammalian protein complexes , 2007, Nucleic Acids Res..

[117]  James A. Wells,et al.  Small-Molecule Activators of a Proenzyme , 2009, Science.

[118]  R. Aebersold,et al.  Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans , 2009, Nature.

[119]  Julie M. Sahalie,et al.  An experimentally derived confidence score for binary protein-protein interactions , 2008, Nature Methods.

[120]  B. Frey,et al.  Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing , 2008, Nature Genetics.

[121]  Eric T. Wang,et al.  Alternative Isoform Regulation in Human Tissue Transcriptomes , 2008, Nature.

[122]  J. Yates,et al.  Mass spectrometry for proteomics. , 2008, Current opinion in chemical biology.

[123]  Emmanuel D Levy,et al.  Evolution and dynamics of protein interactions and networks. , 2008, Current opinion in structural biology.

[124]  Ming Dong,et al.  A "tagless" strategy for identification of stable protein complexes genome-wide by multidimensional orthogonal chromatographic separation and iTRAQ reagent tracking. , 2008, Journal of proteome research.

[125]  Qiang Gao,et al.  Toward chromatographic analysis of interacting protein networks. , 2008, Journal of chromatography. A.

[126]  Octave Noubibou Doudieu,et al.  CORUM: the comprehensive resource of mammalian protein complexes , 2007, Nucleic Acids Res..

[127]  Hagen Blankenburg,et al.  The implications of alternative splicing in the ENCODE protein complement , 2007, Proceedings of the National Academy of Sciences.

[128]  Tyson A. Clark,et al.  Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. , 2007, Genes & development.

[129]  R. Ellis,et al.  Molecular chaperones: assisting assembly in addition to folding. , 2006, Trends in biochemical sciences.

[130]  Yukio Kawahara,et al.  A-to-I RNA Editing and Human Disease , 2006, RNA biology.

[131]  Marcin Feder,et al.  MODOMICS: a database of RNA modification pathways , 2005, Nucleic Acids Res..

[132]  Sylvie Garneau-Tsodikova,et al.  Protein posttranslational modifications: the chemistry of proteome diversifications. , 2005, Angewandte Chemie.

[133]  S. Stamm,et al.  Function of Alternative Splicing , 2004 .

[134]  Andreas Beyer,et al.  Post-transcriptional Expression Regulation in the Yeast Saccharomyces cerevisiae on a Genomic Scale*S , 2004, Molecular & Cellular Proteomics.

[135]  E. Lander,et al.  Finishing the euchromatic sequence of the human genome , 2004 .

[136]  J. Bonfield,et al.  Finishing the euchromatic sequence of the human genome , 2004, Nature.

[137]  Graham Bell,et al.  Phenotypic consequences of 1,000 generations of selection at elevated CO2 in a green alga , 2004, Nature.

[138]  X. Puente,et al.  Human and mouse proteases: a comparative genomic approach , 2003, Nature Reviews Genetics.

[139]  R. Aebersold,et al.  Mass spectrometry-based proteomics , 2003, Nature.

[140]  T. Hunter,et al.  The Protein Kinase Complement of the Human Genome , 2002, Science.

[141]  Chang‐Deng Hu,et al.  Visualization of interactions among bZIP and Rel family proteins in living cells using bimolecular fluorescence complementation. , 2002, Molecular cell.

[142]  A. Furger,et al.  Integrating mRNA Processing with Transcription , 2002, Cell.

[143]  T. Hunter,et al.  Oncogenic kinase signalling , 2001, Nature.

[144]  J. Hopfield,et al.  From molecular to modular cell biology , 1999, Nature.

[145]  R. Benne.  The long and the short of it , 1996, Nature.

[146]  R. B. Loftfield.  THE FREQUENCY OF ERRORS IN PROTEIN BIOSYNTHESIS. , 1963, The Biochemical journal.

[147]  G. Beadle,et al.  Genetic Control of Biochemical Reactions in Neurospora , 1941 .