John D. Aitchison Institute for Systems Biology Biography Publications Institution JoVE Articles John D. Aitchison has not added a biography. If you are John D. Aitchison and would like to personalize this page please email our Author Liaison for assistance. Publications An Indicator Cell Assay for Blood-based Diagnostics PloS One. 2017 | Pubmed ID: 28594877 Combining Inferred Regulatory and Reconstructed Metabolic Networks Enhances Phenotype Prediction in Yeast PLoS Computational Biology. May, 2017 | Pubmed ID: 28520713 One-Cell Doubling Evaluation by Living Arrays of Yeast, ODELAY! G3 (Bethesda, Md.). Jan, 2017 | Pubmed ID: 27856698 Co-dependence Between Trypanosome Nuclear Lamina Components in Nuclear Stability and Control of Gene Expression Nucleic Acids Research. Sep, 2016 | Pubmed ID: 27625397 Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome Cell. Jul, 2016 | Pubmed ID: 27453469 Severe Adult Malaria is Associated with Specific PfEMP1 Adhesion Types and High Parasite Biomass Proceedings of the National Academy of Sciences of the United States of America. Jun, 2016 | Pubmed ID: 27185931 Peroxins Pex30 and Pex29 Dynamically Associate with Reticulons to Regulate Peroxisome Biogenesis from the Endoplasmic Reticulum The Journal of Biological Chemistry. Jul, 2016 | Pubmed ID: 27129769 Systematic Analysis of Yeast Proteome Reveals Peptide Detectability Factors for Mass Spectrometry Journal of Proteomics & Bioinformatics. 2015 | Pubmed ID: 26962293 The Interactome Challenge The Journal of Cell Biology. Nov, 2015 | Pubmed ID: 26572620 Corrigendum: Pan-viral Specificity of IFN-induced Genes Reveals New Roles for CGAS in Innate Immunity Nature. Sep, 2015 | Pubmed ID: 26153856 Signaling Dynamics and Peroxisomes Current Opinion in Cell Biology. Aug, 2015 | Pubmed ID: 26042681 Rapid, Optimized Interactomic Screening Nature Methods. Jun, 2015 | Pubmed ID: 25938370 Bicluster Sampled Coherence Metric (BSCM) Provides an Accurate Environmental Context for Phenotype Predictions BMC Systems Biology. 2015 | Pubmed ID: 25881257 Systems Cell Biology The Journal of Cell Biology. Sep, 2014 | Pubmed ID: 25225336 Predicting Antidisease Immunity Using Proteome Arrays and Sera from Children Naturally Exposed to Malaria Molecular & Cellular Proteomics : MCP. Oct, 2014 | Pubmed ID: 25023128 Quantitative Proteomic Analysis of Host-virus Interactions Reveals a Role for Golgi Brefeldin A Resistance Factor 1 (GBF1) in Dengue Infection Molecular & Cellular Proteomics : MCP. Nov, 2014 | Pubmed ID: 24855065 The Multifunctional Nuclear Pore Complex: a Platform for Controlling Gene Expression Current Opinion in Cell Biology. Jun, 2014 | Pubmed ID: 24657998 An Evolutionarily Conserved RNase-based Mechanism for Repression of Transcriptional Positive Autoregulation Molecular Microbiology. Apr, 2014 | Pubmed ID: 24612392 Nuclear Pore Complex Evolution: a Trypanosome Mlp Analogue Functions in Chromosomal Segregation but Lacks Transcriptional Barrier Activity Molecular Biology of the Cell. May, 2014 | Pubmed ID: 24600046 Pan-viral Specificity of IFN-induced Genes Reveals New Roles for CGAS in Innate Immunity Nature. Jan, 2014 | Pubmed ID: 24284630 Molecular Mechanisms of System Responses to Novel Stimuli Are Predictable from Public Data Nucleic Acids Research. Feb, 2014 | Pubmed ID: 24185701 Peroxisomes Take Shape Nature Reviews. Molecular Cell Biology. Dec, 2013 | Pubmed ID: 24263361 PhosphoChain: a Novel Algorithm to Predict Kinase and Phosphatase Networks from High-throughput Expression Data Bioinformatics (Oxford, England). Oct, 2013 | Pubmed ID: 23832245 Multifunctional Double-negative T Cells in Sooty Mangabeys Mediate T-helper Functions Irrespective of SIV Infection PLoS Pathogens. 2013 | Pubmed ID: 23825945 A Role for the Nucleoporin Nup170p in Chromatin Structure and Gene Silencing Cell. Feb, 2013 | Pubmed ID: 23452847 Systematic Measurement of Transcription Factor-DNA Interactions by Targeted Mass Spectrometry Identifies Candidate Gene Regulatory Proteins Proceedings of the National Academy of Sciences of the United States of America. Feb, 2013 | Pubmed ID: 23388641 Metallochaperones Regulate Intracellular Copper Levels PLoS Computational Biology. 2013 | Pubmed ID: 23349626 Global Analysis of Condition-specific Subcellular Protein Distribution and Abundance Molecular & Cellular Proteomics : MCP. May, 2013 | Pubmed ID: 23349476 A FOXO3-IRF7 Gene Regulatory Circuit Limits Inflammatory Sequelae of Antiviral Responses Nature. Oct, 2012 | Pubmed ID: 22982991 Asymmetric Positive Feedback Loops Reliably Control Biological Responses Molecular Systems Biology. Apr, 2012 | Pubmed ID: 22531117 NUP-1 Is a Large Coiled-coil Nucleoskeletal Protein in Trypanosomes with Lamin-like Functions PLoS Biology. 2012 | Pubmed ID: 22479148 The Yeast Nuclear Pore Complex and Transport Through It Genetics. Mar, 2012 | Pubmed ID: 22419078 Nanospray FAIMS Fractionation Provides Significant Increases in Proteome Coverage of Unfractionated Complex Protein Digests Molecular & Cellular Proteomics : MCP. Dec, 2011 | Pubmed ID: 22186714 A Regression Model Approach to Enable Cell Morphology Correction in High-throughput Flow Cytometry Molecular Systems Biology. 2011 | Pubmed ID: 21952134 Mathematical Modeling of Biomolecular Network Dynamics Methods in Molecular Biology (Clifton, N.J.). 2011 | Pubmed ID: 21877294 Statistical Analysis of Dynamic Transcriptional Regulatory Network Structure Methods in Molecular Biology (Clifton, N.J.). 2011 | Pubmed ID: 21877289 Trade-off Between Responsiveness and Noise Suppression in Biomolecular System Responses to Environmental Cues PLoS Computational Biology. Jun, 2011 | Pubmed ID: 21738459 The Peroxin Pex34p Functions with the Pex11 Family of Peroxisomal Divisional Proteins to Regulate the Peroxisome Population in Yeast Molecular Biology of the Cell. May, 2011 | Pubmed ID: 21441307 Faster, Quantitative, and Accurate Precursor Acquisition Independent from Ion Count Analytical Chemistry. Mar, 2011 | Pubmed ID: 21341720 Role of the Nuclear Envelope in Genome Organization and Gene Expression Wiley Interdisciplinary Reviews. Systems Biology and Medicine. Mar-Apr, 2011 | Pubmed ID: 21305702 Environment-responsive Transcription Factors Bind Subtelomeric Elements and Regulate Gene Silencing Molecular Systems Biology. Jan, 2011 | Pubmed ID: 21206489 Expression of the Salmonella Spp. Virulence Factor SifA in Yeast Alters Rho1 Activity on Peroxisomes Molecular Biology of the Cell. Oct, 2010 | Pubmed ID: 20739463 Genome-wide Analysis of Effectors of Peroxisome Biogenesis PloS One. 2010 | Pubmed ID: 20694151 QTIPS: a Novel Method of Unsupervised Determination of Isotopic Amino Acid Distribution in SILAC Experiments Journal of the American Society for Mass Spectrometry. Aug, 2010 | Pubmed ID: 20451407 Integrated Phosphoproteomics Analysis of a Signaling Network Governing Nutrient Response and Peroxisome Induction Molecular & Cellular Proteomics : MCP. Sep, 2010 | Pubmed ID: 20395639 GINS Motion Reveals Replication Fork Progression is Remarkably Uniform Throughout the Yeast Genome Molecular Systems Biology. 2010 | Pubmed ID: 20212525 Systems Cell Biology of the Mitotic Spindle The Journal of Cell Biology. Jan, 2010 | Pubmed ID: 20065087 Dynamic Changes in the Subcellular Distribution of Gpd1p in Response to Cell Stress The Journal of Biological Chemistry. Feb, 2010 | Pubmed ID: 20026609 Histone Chaperone Chz1p Regulates H2B Ubiquitination and Subtelomeric Anti-silencing Nucleic Acids Research. Mar, 2010 | Pubmed ID: 20008511 Deterministic and Stochastic Models of Genetic Regulatory Networks Methods in Enzymology. 2009 | Pubmed ID: 19897099 A Role for the Karyopherin Kap123p in Microtubule Stability Traffic (Copenhagen, Denmark). Nov, 2009 | Pubmed ID: 19761543 Myosin-driven Peroxisome Partitioning in S. Cerevisiae The Journal of Cell Biology. Aug, 2009 | Pubmed ID: 19687257 A Noncanonical Bromodomain in the AAA ATPase Protein Yta7 Directs Chromosomal Positioning and Barrier Chromatin Activity Molecular and Cellular Biology. Sep, 2009 | Pubmed ID: 19581291 Role of the Histone Variant H2A.Z/Htz1p in TBP Recruitment, Chromatin Dynamics, and Regulated Expression of Oleate-responsive Genes Molecular and Cellular Biology. May, 2009 | Pubmed ID: 19273605 Regulation of Peroxisome Dynamics Current Opinion in Cell Biology. Feb, 2009 | Pubmed ID: 19188056 Control of Transcriptional Variability by Overlapping Feed-forward Regulatory Motifs Biophysical Journal. Oct, 2008 | Pubmed ID: 18621837 Systems Biology at the Institute for Systems Biology Briefings in Functional Genomics & Proteomics. Jul, 2008 | Pubmed ID: 18579616 Saccharomyces Cerevisiae Yta7 Regulates Histone Gene Expression Genetics. May, 2008 | Pubmed ID: 18493054 Genome-wide Analysis of Signaling Networks Regulating Fatty Acid-induced Gene Expression and Organelle Biogenesis The Journal of Cell Biology. Apr, 2008 | Pubmed ID: 18426976 Identifying Bona Fide Components of an Organelle by Isotope-coded Labeling of Subcellular Fractions : an Example in Peroxisomes Methods in Molecular Biology (Clifton, N.J.). 2008 | Pubmed ID: 18370030 Cell Biology: Pore Puzzle Nature. Nov, 2007 | Pubmed ID: 18046388 Comprehensive Analysis of Diverse Ribonucleoprotein Complexes Nature Methods. Nov, 2007 | Pubmed ID: 17922018 Transcriptional Responses to Fatty Acid Are Coordinated by Combinatorial Control Molecular Systems Biology. 2007 | Pubmed ID: 17551510 The Role of Karyopherins in the Regulated Sumoylation of Septins The Journal of Cell Biology. Apr, 2007 | Pubmed ID: 17403926 Yng1 PHD Finger Binding to H3 Trimethylated at K4 Promotes NuA3 HAT Activity at K14 of H3 and Transcription at a Subset of Targeted ORFs Molecular Cell. Dec, 2006 | Pubmed ID: 17157260 Studying Nuclear Protein Import in Yeast Methods (San Diego, Calif.). Aug, 2006 | Pubmed ID: 16979507 Dual Feedback Loops in the GAL Regulon Suppress Cellular Heterogeneity in Yeast Nature Genetics. Sep, 2006 | Pubmed ID: 16936734 Expression and Functional Profiling Reveal Distinct Gene Classes Involved in Fatty Acid Metabolism Molecular Systems Biology. 2006 | Pubmed ID: 16738555 The Peroxisomal Membrane Protein Inp2p is the Peroxisome-specific Receptor for the Myosin V Motor Myo2p of Saccharomyces Cerevisiae Developmental Cell. May, 2006 | Pubmed ID: 16678774 Pex19p Binds Pex30p and Pex32p at Regions Required for Their Peroxisomal Localization but Separate from Their Peroxisomal Targeting Signals The Journal of Biological Chemistry. May, 2006 | Pubmed ID: 16551610 The Dynamin-like Protein Vps1p of the Yeast Saccharomyces Cerevisiae Associates with Peroxisomes in a Pex19p-dependent Manner The Journal of Biological Chemistry. May, 2006 | Pubmed ID: 16520372 The Mobile Nucleoporin Nup2p and Chromatin-bound Prp20p Function in Endogenous NPC-mediated Transcriptional Control The Journal of Cell Biology. Dec, 2005 | Pubmed ID: 16365162 A Data Integration Methodology for Systems Biology Proceedings of the National Academy of Sciences of the United States of America. Nov, 2005 | Pubmed ID: 16301537 A Data Integration Methodology for Systems Biology: Experimental Verification Proceedings of the National Academy of Sciences of the United States of America. Nov, 2005 | Pubmed ID: 16301536 Interactions Between Mad1p and the Nuclear Transport Machinery in the Yeast Saccharomyces Cerevisiae Molecular Biology of the Cell. Sep, 2005 | Pubmed ID: 16000377 Inp1p is a Peroxisomal Membrane Protein Required for Peroxisome Inheritance in Saccharomyces Cerevisiae The Journal of Cell Biology. Jun, 2005 | Pubmed ID: 15928207 Proteomic and Genomic Characterization of Chromatin Complexes at a Boundary The Journal of Cell Biology. Apr, 2005 | Pubmed ID: 15824130 Nop53p is a Novel Nucleolar 60S Ribosomal Subunit Biogenesis Protein The Biochemical Journal. Jun, 2005 | Pubmed ID: 15686447 Quantitative Mass Spectrometry Reveals a Role for the GTPase Rho1p in Actin Organization on the Peroxisome Membrane The Journal of Cell Biology. Dec, 2004 | Pubmed ID: 15596542 Characterization of Karyopherin Cargoes Reveals Unique Mechanisms of Kap121p-mediated Nuclear Import Molecular and Cellular Biology. Oct, 2004 | Pubmed ID: 15367670 Pex30p, Pex31p, and Pex32p Form a Family of Peroxisomal Integral Membrane Proteins Regulating Peroxisome Size and Number in Saccharomyces Cerevisiae Molecular Biology of the Cell. Feb, 2004 | Pubmed ID: 14617799 Cell Cycle Regulated Transport Controlled by Alterations in the Nuclear Pore Complex Cell. Dec, 2003 | Pubmed ID: 14697200 Virtual Gating and Nuclear Transport: the Hole Picture Trends in Cell Biology. Dec, 2003 | Pubmed ID: 14624840 Pex11-related Proteins in Peroxisome Dynamics: a Role for the Novel Peroxin Pex27p in Controlling Peroxisome Size and Number in Saccharomyces Cerevisiae Molecular Biology of the Cell. Oct, 2003 | Pubmed ID: 14517321 Utp8p is an Essential Intranuclear Component of the Nuclear TRNA Export Machinery of Saccharomyces Cerevisiae The Journal of Biological Chemistry. Aug, 2003 | Pubmed ID: 12794079 Inventories to Insights The Journal of Cell Biology. May, 2003 | Pubmed ID: 12743099 YHR150w and YDR479c Encode Peroxisomal Integral Membrane Proteins Involved in the Regulation of Peroxisome Number, Size, and Distribution in Saccharomyces Cerevisiae The Journal of Cell Biology. Apr, 2003 | Pubmed ID: 12707309 Karyopherins in Nuclear Pore Biogenesis: a Role for Kap121p in the Assembly of Nup53p into Nuclear Pore Complexes The Journal of Cell Biology. Oct, 2002 | Pubmed ID: 12403813 Approaching Complete Peroxisome Characterization by Gas-phase Fractionation Electrophoresis. Sep, 2002 | Pubmed ID: 12298092 Transcriptome Profiling to Identify Genes Involved in Peroxisome Assembly and Function The Journal of Cell Biology. Jul, 2002 | Pubmed ID: 12135984 Kap121p-mediated Nuclear Import is Required for Mating and Cellular Differentiation in Yeast Molecular and Cellular Biology. Apr, 2002 | Pubmed ID: 11909949 A Tense Time for the Nuclear Envelope Cell. Feb, 2002 | Pubmed ID: 11853664 ओडेलेय: खमीर विकास के बहु-पैरामीटर मात्राकरण के लिए एक बड़े पैमाने पर विधि Thurston Herricks1, Fred D. Mast1,2, Song Li1, John D. Aitchison1,2 1Institute for Systems Biology, 2Center for Infectious Disease Research JoVE 55879 Biologie फैटी एसिड में मात्रात्मक Phosphoproteomics प्रेरित Saccharomyces cerevisiae Ramsey A. Saleem1, John D. Aitchison1 1Institute for Systems Biology JoVE 1474 Biologie
ओडेलेय: खमीर विकास के बहु-पैरामीटर मात्राकरण के लिए एक बड़े पैमाने पर विधि Thurston Herricks1, Fred D. Mast1,2, Song Li1, John D. Aitchison1,2 1Institute for Systems Biology, 2Center for Infectious Disease Research JoVE 55879 Biologie
फैटी एसिड में मात्रात्मक Phosphoproteomics प्रेरित Saccharomyces cerevisiae Ramsey A. Saleem1, John D. Aitchison1 1Institute for Systems Biology JoVE 1474 Biologie