van Oudenaarden, Alexander - Department of Physics, Massachusetts Institute of Technology (MIT)

• 02004006008001000 02004006008001000
• Molecular Cell Genome-wide Dissection of MicroRNA Functions
• Systems Biology 7.32 / 7.81J / 8.591J Problem Set 5 Assigned: 11.17.09
• 458 Cell 140, February 19, 2010 2010 Elsevier Inc. and LeDoux, 2004), whereas the Rac
• Giant higher harmonic generation in mesoscopic metal wires and rings interrupted by tunnel junctions
• 7.32/7.81J/8.591J Systems Biology A. van Oudenaarden MIT November 200971 XI Local excitation, global inhibition models
• Developmental Cell, Vol. 9, 565571, October, 2005, Copyright 2005 by Elsevier Inc. DOI 10.1016/j.devcel.2005.08.014 Short ArticleA System of Counteracting
• nature genetics volume 31 may 2002 69 Regulation of noise in the expression of a single gene
• Nature Macmillan Publishers Ltd 1998 Magneto-electric
• www.sciencemag.org/cgi/content/full/327/5972/1522/DC1 Supporting Online Material for
• Supplementary Figure 1: Design of experiment and sucrose metabolism in yeast. Sucrose is hydrolyzed by the enzyme invertase in the periplasmic space between the
• VOLUME 77, NUMBER 20 P H Y S I C A L R E V I E W L E T T E R S 11 NOVEMBER 1996 One-Dimensional Localization of Quantum Vortices in Disordered Josephson Junction Arrays
• tainty, or otherwise, about them. But there's a catch: The computational demands of these
• 7.32/7.81J/8.591J Systems Biology A. van Oudenaarden MIT October 200948 VIII Modeling Escherichia coli chemotaxis
• 7.32/7.81J/8.591J Systems Biology A. van Oudenaarden MIT October 200938 VII Biological Oscillators
• Supplementary Figure 1 | Strategy for long-term culturing and follow-up of monoclonal populations. Schematic with representative images and immuno-staining demonstrating the long term-culturing strategy. a, In the
• 7.32/7.81J/8.591J Systems Biology A. van Oudenaarden MIT October 200922 IV Positive feedback and multistability
• Probing polymerization forces by using actin-propelled lipid vesicles
• L E T T E R S NATURE CELL BIOLOGY VOLUME 6 | NUMBER 5 | MAY 2004 451
• Elevated ATPase Activity of KaiC Applies a Circadian Checkpoint on Cell
• Motility of Escherichia coli cells in clusters formed by chemotactic aggregation
• 610 Cell 140, March 5, 2010 2010 Elsevier Inc. enzymes, only a few appear to interact
• Supplemental Information SUPPLEMENTAL REFERENCES
• Systems Biology 7.32 / 7.81 / 8.591 Problem Set 3 Assigned: 10.21.09
• SUPPLEMENTARY INFORMATION 1www.nature.com/nature
• Quantitative Time-Lapse Fluorescence Microscopy
• N E W S A N D V I E W S 146 VOLUME 39 | NUMBER 2 | FEBRUARY 2007 | NATURE GENETICS
• The phenomenon of incomplete penetrance --whereby organisms
• Stochastic Simulation using Systems Biology Recitation 8
• Enhancement of cellular memory by reducing stochastic transitions Supplementary Information
• Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes
• One-dimensional Mott localization of quantum vortices in Josephson-junction arrays A. van Oudenaarden, B. van Leeuwen, M. P. M. Robbens, and J. E. Mooij
• Systems Biology 7.32 / 7.81J / 8.591J Problem Set 4 Assigned: 11.03.09
• 7.32/7.81J/8.591J Systems Biology A. van Oudenaarden MIT November 200967 X Diffusion
• Growth landscape formed by perception and import of glucose in yeast
• Supporting Information Khalil et al. 10.1073/pnas.0904715106
• Biomimetic Systems for Studying Actin-Based Motility
• 7.32/7.81J/8.591J Systems Biology A. van Oudenaarden MIT October 200932 V Synthetic genetic switches
• Stochastic switching as a survival strategy in fluctuating environments
• SYSTEMS MICROBIOLOGY `A living cell as a wellstirred bioreactor'
• 19. Arnheim, N., Treco, D., Taylor, B. & Eicher, E. M. Distribution of ribosomal gene length variants among mouse chromosomes. Proc. Natl Acad. Sci. USA 79, 46774680 (1982).
• VOLUME 76, NUMBER 26 P H Y S I C A L R E V I E W L E T T E R S 24 JUNE 1996 One-Dimensional Mott Insulator Formed by Quantum Vortices in Josephson Junction Arrays
• NEWS AND VIEWS Single cell resolution in regulation of gene expression
• SUPPLEMENTARY INFORMATION 1www.nature.com/nature
• Brief report TheJournalofClinicalInvestigation http://www.jci.org
• Supplementary Information Stochastic gene expression out-of-steady-state in the cyanobacterial circadian clock
• Lim and van Oudenaarden Supplementary Methods
• Caenorhabditis elegans aristaless/Arx gene alr-1 restricts variable gene expression
• exaggeration in all populations. There is no direct and necessary
• Supporting Online Materials for Pedraza et al. Noise propagation in gene networks
• Systems Biology 7.32 / 7.81J / 8.591J Problem Set 2 Assigned: 10.07.09
• Stochastic gene expression out-of-steady-state in the cyanobacterial circadian clock
• One of the most astounding findings of the Human Genome Project was that our genome contains as many
• 7.32/7.81J/8.591J Systems Biology A. van Oudenaarden MIT October 200942 A second study describes the development of a genetic oscillator based on the
• Supplemental Data October 2005 Developmental Cell
• Leading Edge 216 Cell 135, October 17, 2008 2008 Elsevier Inc.
• S12 | Vol.8 No.4s | april2011 | nature methodS Supplement High-throughput measurements of gene expression
• Available online at www.sciencedirect.com Coupling cellular oscillators--circadian and cell division cycles
• C H A P T E R S E V E N T E E N Imaging Single mRNA
• dynamic phase diagram of possible behav-iours of the filaments. Just how universal this
• Transcript counting in single cells reveals dynamics of rDNA transcription
• Supplementary Figure S1: Plot of total cell fluorescence versus RNA in the cell. Total cell fluorescence is directly proportional to the RNA count in the cells and can be used to
• Molecular Cell, Volume 38 Supplemental Information
• Variability in gene expression underlies incomplete penetrance
• Snowdrift game dynamics and facultative cheating , Hyun Youk1
• the top of the atmosphere of a planet or star. The notion that the ratio E/T might deter-
• Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as
• Imaging individual mRNA molecules using multiple
• nature | methods Imaging individual mRNA molecules using multiple singly
• The Frequency Dependence of Osmo-Adaptation in
• www.sciencemag.org/cgi/content/full/319/5862/483/DC1 Supporting Online Material for
• Power-Limited Contraction Dynamics of Vorticella convallaria: An Ultrafast Biological Spring
• Heritable Stochastic Switching Revealed by Single-Cell Genealogy
• SUPPLEMENTARY INFORMATION HERITABLE STOCHASTIC SWITCHING REVEALED BY
• shown that a phosphate anion of type 1 (the same as that used by Hamilton et al.; see the
• Molecular Cell MicroRNA-Mediated Feedback and Feedforward
• A multistep epigenetic switch enables the stable inheritance of DNA methylation states
• Leading Edge 650 Cell 126, August 25, 2006 2006 Elsevier Inc.
• Cellular asymmetry and individuality in directional sensing
• NEWS AND VIEWS Exciting fluctuations: monitoring competence
• Predicting stochastic gene expression dynamics in single cells
• Supplementary Note Contributions of low molecule number and chromosomal positioning
• Actin Polymerization: Forcing Flat Faces Forward
• Copyright 2004 by the Genetics Society of America Stochastic Gene Expression in Fluctuating Environments
• Elastic Instability in Growing Yeast Colonies Baochi Nguyen,* Arpita Upadhyaya,y
• Multistability in the lactose utilization network of
• Intrinsic noise in gene regulatory networks Mukund Thattai and Alexander van Oudenaarden*
• news and views NATURE CELL BIOLOGY | VOL 1 | DECEMBER 1999 | cellbio.nature.com E197
• 7.32/7.81J/8.591J Systems Biology A. van Oudenaarden MIT September 20097 II Equilibrium binding and cooperativity
• Systems Biology 7.32 / 7.81 / 8.591 Problem Set 1 Assigned: 09.23.09
• 7.32/7.81J/8.591J Systems Biology A. van Oudenaarden MIT October 200928 IV. 2. Multistability in the lactose utilization network of Escherichia coli
• 7.32/7.81J/8.591J Systems Biology A. van Oudenaarden MIT October 200956 IX Stochastic Chemical Kinetics
• serum (Omega Scientific) in RPMI 1640 with 10 mM HEPES buffer, 2 mM l-glutamine, penicillin and 100 mg ml21
• Single-Molecule Approaches to Stochastic Gene Expression
• gene expression at single-cell resolution. For example, the intestine of C. elegans is formed
• A Systems-Level Analysis of Perfect Adaptation in Yeast Osmoregulation
• identified cornichon homologs 2 and 3 (2), because CKAMP44 also slows AMPAR deactivation,
• Cell, Volume 138 A Systems-Level Analysis of Perfect
• 15 7.32/7.81J/8.591J Systems Biology B. Pando, J. Li, & A. van Oudenaarden MIT September 2009 III Ultrasensitivity and thresholding by molecular titration
• RNA sequencing reveals two major classes of gene expression levels in metazoan cells
• Shankar Mukherji, Margaret S. Ebert, Grace X. Zheng, John S. Tsang, Phillip A. Sharp, and Alexander van Oudenaarden
• A Novel Sperm-Delivered Toxin Causes Late-Stage Embryo Lethality and Transmission Ratio Distortion in
• 2915RESEARCH ARTICLE INTRODUCTION
• 854 VOLUME 43 | NUMBER 9 | SEPTEMBER 2011 Nature GeNetics A rt i c l e s
• The thrombospondin repeat containing protein MIG-21 controls a leftright asymmetric Wnt signaling response in migrating C. elegans neuroblasts
• S UPP LE ME NTARY INFORMATION WWW.NATURE.COM/NATURECELLBIOLOGY 1
• T E C H N I C A L R E P O R T Single-molecule transcript counting of stem-cell
• Molecular Cell Single-Cell Analysis Reveals that Noncoding RNAs
• Supplemental Information EXTENDED EXPERIMENTAL PROCEDURES
• The Caenorhabditis elegans Synthetic Multivulva Genes Prevent Ras Pathway Activation by Tightly Repressing
• Slug and Sox9 Cooperatively Determine the Mammary Stem Cell State
• Supplemental Information EXTENDED EXPERIMENTAL PROCEDURES
• Optimality in the Development of Intestinal Crypts
• When Noisy Neighbors Are a Blessing: Analysis of Gene Expression Noise
• An RNA Reset Button Alex C. Tuck1 and David Tollervey1,*
• Molecular Cell, Volume 45 Supplemental Information
• T E C H N I C A L R E P O R T Single-molecule transcript counting of stem-cell