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APS March Meeting 2010 Focus Session on Physics of Behavior -- From Molecules to OrganismsA remote control for the C. elegans nervous systemAbout our work
Adler et al., 2000Aspen Center for Physics: Physics of BehaviorAutomated Probing and Inference of Analytical Models for Metabolic Network Dynamics
Bandaru et al., 2011Bel and Nemenman, 2009
Bel et al, 2010
Bel et al., 2010Bialek et al., 2001aBialek et al., 2001b
Block one: Biological information processing is probabilistic
CNS Clinic 2012: Dynamic ClampingCNS Clinic 2012: Information theory for understanding the neural code
CNS Clinic 2012: Ins and outs of script programming with GenesisCNS Clinic 2012: Model fitting with neural data: Stories from the trenchesCNS Clinic 2012: Principal Components Analysis of neural and behavioral data
CNS Clinic 2012: Spike train analysisCalendar: Travel and VisitorsCell fate determination dynamics in bacteria
Cell order in bacterial swarms arises from reversals of moving directionCheong et al., 2011Collective decisions among bacterial viruses
Computational Neuroscience Methods Clinic, 2012Conference OrganizationDe Ronde et al., 2009
Diagnostics using microarray dataDresigmeyer et al., 2008E. coli chemoreceptor: mesoscopic model
Edwards et al., 2007Entropy EstimationEntropy estimation methods
Establishing causalityExploring neural code in natural environmentsFirst q-bio Conference: Employment board
First q-bio Conference: ParticipantsFirst q-bio Conference: ProgramFirst q-bio Conference: Program Details
First q-bio Summer School:Participants
First q-bio Summer School: ClassroomsFirst q-bio Summer School: Gene Regulation
First q-bio Summer School: Other Topics in Biological ModelingFirst q-bio Summer School: ParticipantsFirst q-bio Summer School: Program
First q-bio Summer School: School HotelFirst q-bio Summer School: Signal Transduction MechanismsFirst q-bio Summer School: Stochasticity in Biochemistry and Systems Biology
First q-bio Summer School Program
First q bio Summer School Program
Gintautas et al., 2011
Group seminar / Journal clubHigh-resolution, long-term characterization of bacterial motility using optical tweezersHoly and Nemenman, 2002
Http://cnls.lanl.gov/q-bio/wiki/index.php/First q-bio Summer School Program
Ilya NemenmanInformation Bottleneck Method
Information processing in biological systems
Information transmission in biological systems
Installing Octave on your PC and Mac
Interactive LearningIssuesKominis and Nemenman, 1997
Lab MembersLearning, adaptation, and adaptive behaviors
Learning and Adaptation
Margolin et al., 2004bMargolin et al., 2006aMargolin et al., 2006b
Margolin et al., 2010Mechanisms of adaptation to stimulus statistics in neuronal systemsMichaelis-Menten reaction: pump current and other stochastic effects
Minkevich and Nemenman, 1995aMinkevich and Nemenman, 1995bMugler et al., 2008
Mugler et al., 2009
Mugler et al. 2009
Munsky et al., 2009
Naud et al., 1999Nemenman, 2004Nemenman, 2005
Nemenman, 2011
Nemenman, 2011a
Nemenman, 2011b
Nemenman, 2012
Nemenman-IEEEIT
Nemenman-filtering
Nemenman Research Group at Emory University
Nemenman and Bialek, 2002Nemenman and Silbergleit, 1999
Nemenman and WigginsNemenman et al.Nemenman et al., 2002
Nemenman et al., 2004
Nemenman et al., 2007
Nemenman et al., 2007a
Nemenman et al., 2008Nemenman et al., 2008aNemenman et al., 2009
Nemenman et al., 2010Nemenman et al., 2011
Neural coding
NewsOpen positionsOptimality in Bacterial Chemotaxis
Otwinowski et al., 2011P53 regulation
Personal
Personal PagesPh. D. Thesis
Physic 511A, 2012: Graduate Electrodynamics
Physic 511A: Graduate Electrodynamics
Physics 380, 2010: Basic Probability TheoryPhysics 380, 2010: Coding Theorems
Physics 380, 2010: Fourier AnalysisPhysics 380, 2010: Information, Gambling, and Population BiologyPhysics 380, 2010: Information Processing in Biology
Physics 380, 2010: Information TheoryPhysics 380, 2010: IntroductionPhysics 380, 2010: Linear Response Theory
Physics 380, 2010: Random WalksPhysics 380, 2011: Block four: AdaptationPhysics 380, 2011: Block one: Biological information processing is probabilistic
Physics 380, 2011: Block three: Dynamical Information ProcessingPhysics 380, 2011: Block two: Information theory in biological signalingPhysics 380, 2011: Homework 1
Physics 380, 2011: Homework 10Physics 380, 2011: Homework 2Physics 380, 2011: Homework 3
Physics 380, 2011: Homework 4Physics 380, 2011: Homework 5Physics 380, 2011: Homework 6
Physics 380, 2011: Homework 7Physics 380, 2011: Homework 8Physics 380, 2011: Homework 9
Physics 380, 2011: Homewrok 1
Physics 380, 2011: Homewrok 2
Physics 380, 2011: Information Processing in Biology
Physics 380, 2011: Lecture 1Physics 380, 2011: Lecture 10Physics 380, 2011: Lecture 11
Physics 380, 2011: Lecture 12Physics 380, 2011: Lecture 13Physics 380, 2011: Lecture 14
Physics 380, 2011: Lecture 15Physics 380, 2011: Lecture 16Physics 380, 2011: Lecture 17
Physics 380, 2011: Lecture 18Physics 380, 2011: Lecture 19Physics 380, 2011: Lecture 2
Physics 380, 2011: Lecture 20Physics 380, 2011: Lecture 21Physics 380, 2011: Lecture 22
Physics 380, 2011: Lecture 23Physics 380, 2011: Lecture 24Physics 380, 2011: Lecture 25
Physics 380, 2011: Lecture 26Physics 380, 2011: Lecture 27Physics 380, 2011: Lecture 3
Physics 380, 2011: Lecture 4Physics 380, 2011: Lecture 5Physics 380, 2011: Lecture 6
Physics 380, 2011: Lecture 7Physics 380, 2011: Lecture 8Physics 380, 2011: Lecture 9
Physics 380, 2011: Lectures 5-6
Physics 380, 2012: Homework 11Physics 380, 2012: Homework 12
Physics 511A, 2011: Chapter 1, Volume 2. The principle of relativityPhysics 511A, 2012: Chapter 1, Volume 8. Electrostatics of conductorsPhysics 511A, 2012: Chapter 2, Volume 2. Relativistic mechanics
Physics 511A, 2012: Chapter 2, Volume 8. Electrostatics of dielectricPhysics 511A, 2012: Chapter 3, Volume 2. Charges in electromagnetic fieldPhysics 511A, 2012: Chapter 3, Volume 8. Steady current
Physics 511A, 2012: Chapter 4, Volume 2. Electromagnetic field equationsPhysics 511A, 2012: Chapter 4, Volume 8. Static magnetic fieldPhysics 511A, 2012: Chapter 5, Volume 2. Constant electromagnetic fields
Physics 511A, 2012: Chapter 6, Volume 2. Electromagnetic wavesPhysics 511A, 2012: Chapter 7, Volume 2. Propagation of lightPhysics 511A, 2012: Chapter 8, Volume 2. The field of moving charges
Physics 511A, 2012: Chapter 9, Volume 2. Radiation of electromagnetic wavesPhysics 511A, 2012: Graduate ElectrodynamicsPhysics 511A, 2012: Waves in media
PresentationsProfessional
Project Pages
ProjectsPublicationsPublications/Bandaru et al., 2010
Publications about our researchRBC Metabolic NetworkReconstructing the behavior of walking fruit flies
Relational networksResearch InterestsReverse-engineering algorithms benchmarks
Reverse engineering cellular networksSilbergleit et al., 2003aSilbergleit et al., 2003b
Simpler methods for High Throughput Data analysisSinitsyn and Nemenman, 2007Sinitsyn and Nemenman, 2007a
Sinitsyn and Nemenman, 2010
Sinitsyn et al, 2008
Sinitsyn et al, 2009
Sinitsyn et al., 2009Smart Thoughts From Smart People
Stochastic biochemical networks
Stochastic biochemistry
Stochastic biochemstry
Stochastic dynamics on biological networks
Stochastic path integral
Stochasticity biochemstry
Stochasticity in regulatory networks
Tanase-Nicola and Nemenman, 2011TeachingTemperature control of molecular circuit switch responsible for virulent phenotype expression in uropathogenic Escherichia coli
Test pagesTeuscher et al, 2008The Berry phase in stochastic kinetics
The emergence of stereotyped behaviors in C. elegansThermal impulse response and the temperature preference of Escherichia coliTools and approximations for stochastic analysis
Travel plans
Visual neural computationWang et al., 2005
Wang et al., 2006Wang et al., 2007Wang et al., 2009
Wei et al., 2011Wiggins and Nemenman, 2003Ziv et al., 2007
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