@article{292,
abstract = {Retina is a paradigmatic system for studying sensory encoding: the transformation of light into spiking activity of ganglion cells. The inverse problem, where stimulus is reconstructed from spikes, has received less attention, especially for complex stimuli that should be reconstructed “pixel-by-pixel”. We recorded around a hundred neurons from a dense patch in a rat retina and decoded movies of multiple small randomly-moving discs. We constructed nonlinear (kernelized and neural network) decoders that improved significantly over linear results. An important contribution to this was the ability of nonlinear decoders to reliably separate between neural responses driven by locally fluctuating light signals, and responses at locally constant light driven by spontaneous-like activity. This improvement crucially depended on the precise, non-Poisson temporal structure of individual spike trains, which originated in the spike-history dependence of neural responses. We propose a general principle by which downstream circuitry could discriminate between spontaneous and stimulus-driven activity based solely on higher-order statistical structure in the incoming spike trains.},
author = {Botella Soler, Vicent and Deny, Stephane and Martius, Georg S and Marre, Olivier and Tkacik, Gasper},
journal = {PLoS Computational Biology},
number = {5},
publisher = {Public Library of Science},
title = {{Nonlinear decoding of a complex movie from the mammalian retina}},
doi = {10.1371/journal.pcbi.1006057},
volume = {14},
year = {2018},
}
@misc{5584,
abstract = {This package contains data for the publication "Nonlinear decoding of a complex movie from the mammalian retina" by Deny S. et al, PLOS Comput Biol (2018).
The data consists of
(i) 91 spike sorted, isolated rat retinal ganglion cells that pass stability and quality criteria, recorded on the multi-electrode array, in response to the presentation of the complex movie with many randomly moving dark discs. The responses are represented as 648000 x 91 binary matrix, where the first index indicates the timebin of duration 12.5 ms, and the second index the neural identity. The matrix entry is 0/1 if the neuron didn't/did spike in the particular time bin.
(ii) README file and a graphical illustration of the structure of the experiment, specifying how the 648000 timebins are split into epochs where 1, 2, 4, or 10 discs were displayed, and which stimulus segments are exact repeats or unique ball trajectories.
(iii) a 648000 x 400 matrix of luminance traces for each of the 20 x 20 positions ("sites") in the movie frame, with time that is locked to the recorded raster. The luminance traces are produced as described in the manuscript by filtering the raw disc movie with a small gaussian spatial kernel. },
author = {Deny, Stephane and Marre, Olivier and Botella-Soler, Vicente and Martius, Georg S and Tkacik, Gasper},
keyword = {retina, decoding, regression, neural networks, complex stimulus},
publisher = {IST Austria},
title = {{Nonlinear decoding of a complex movie from the mammalian retina}},
doi = {10.15479/AT:ISTA:98},
year = {2018},
}
@article{306,
abstract = {A cornerstone of statistical inference, the maximum entropy framework is being increasingly applied to construct descriptive and predictive models of biological systems, especially complex biological networks, from large experimental data sets. Both its broad applicability and the success it obtained in different contexts hinge upon its conceptual simplicity and mathematical soundness. Here we try to concisely review the basic elements of the maximum entropy principle, starting from the notion of ‘entropy’, and describe its usefulness for the analysis of biological systems. As examples, we focus specifically on the problem of reconstructing gene interaction networks from expression data and on recent work attempting to expand our system-level understanding of bacterial metabolism. Finally, we highlight some extensions and potential limitations of the maximum entropy approach, and point to more recent developments that are likely to play a key role in the upcoming challenges of extracting structures and information from increasingly rich, high-throughput biological data.},
author = {De Martino, Andrea and De Martino, Daniele},
journal = {Heliyon},
number = {4},
publisher = {Elsevier},
title = {{An introduction to the maximum entropy approach and its application to inference problems in biology}},
doi = {10.1016/j.heliyon.2018.e00596},
volume = {4},
year = {2018},
}
@article{457,
abstract = {Temperate bacteriophages integrate in bacterial genomes as prophages and represent an important source of genetic variation for bacterial evolution, frequently transmitting fitness-augmenting genes such as toxins responsible for virulence of major pathogens. However, only a fraction of bacteriophage infections are lysogenic and lead to prophage acquisition, whereas the majority are lytic and kill the infected bacteria. Unless able to discriminate lytic from lysogenic infections, mechanisms of immunity to bacteriophages are expected to act as a double-edged sword and increase the odds of survival at the cost of depriving bacteria of potentially beneficial prophages. We show that although restriction-modification systems as mechanisms of innate immunity prevent both lytic and lysogenic infections indiscriminately in individual bacteria, they increase the number of prophage-acquiring individuals at the population level. We find that this counterintuitive result is a consequence of phage-host population dynamics, in which restriction-modification systems delay infection onset until bacteria reach densities at which the probability of lysogeny increases. These results underscore the importance of population-level dynamics as a key factor modulating costs and benefits of immunity to temperate bacteriophages},
author = {Pleska, Maros and Lang, Moritz and Refardt, Dominik and Levin, Bruce and Guet, Calin C},
journal = {Nature Ecology and Evolution},
number = {2},
pages = {359 -- 366},
publisher = {Springer Nature},
title = {{Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity}},
doi = {10.1038/s41559-017-0424-z},
volume = {2},
year = {2018},
}
@article{161,
abstract = {Which properties of metabolic networks can be derived solely from stoichiometry? Predictive results have been obtained by flux balance analysis (FBA), by postulating that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization of FBA to single-cell level using maximum entropy modeling, which we extend and test experimentally. Specifically, we define for Escherichia coli metabolism a flux distribution that yields the experimental growth rate: the model, containing FBA as a limit, provides a better match to measured fluxes and it makes a wide range of predictions: on flux variability, regulation, and correlations; on the relative importance of stoichiometry vs. optimization; on scaling relations for growth rate distributions. We validate the latter here with single-cell data at different sub-inhibitory antibiotic concentrations. The model quantifies growth optimization as emerging from the interplay of competitive dynamics in the population and regulation of metabolism at the level of single cells.},
author = {De Martino, Daniele and Mc, Andersson Anna and Bergmiller, Tobias and Guet, Calin C and Tkacik, Gasper},
journal = {Nature Communications},
number = {1},
publisher = {Springer Nature},
title = {{Statistical mechanics for metabolic networks during steady state growth}},
doi = {10.1038/s41467-018-05417-9},
volume = {9},
year = {2018},
}
@article{281,
abstract = {Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here, we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for 10 transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses, but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. In particular, Dot6 encodes almost as much information as Msn2, the master regulator of the environmental stress response. Each transcription factor reports differently, and it is only their collective behavior that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change. We predict that such multidimensional representations are common in cellular decision-making.},
author = {Granados, Alejandro and Pietsch, Julian and Cepeda Humerez, Sarah A and Farquhar, Isebail and Tkacik, Gasper and Swain, Peter},
journal = {PNAS},
number = {23},
pages = {6088 -- 6093},
publisher = {National Academy of Sciences},
title = {{Distributed and dynamic intracellular organization of extracellular information}},
doi = {10.1073/pnas.1716659115},
volume = {115},
year = {2018},
}
@misc{5585,
abstract = {Mean repression values and standard error of the mean are given for all operator mutant libraries.},
author = {Igler, Claudia and Lagator, Mato and Tkacik, Gasper and Bollback, Jonathan P and Guet, Calin C},
publisher = {IST Austria},
title = {{Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring}},
doi = {10.15479/AT:ISTA:108},
year = {2018},
}
@misc{5562,
abstract = {This data was collected as part of the study [1]. It consists of preprocessed multi-electrode array recording from 160 salamander retinal ganglion cells responding to 297 repeats of a 19 s natural movie. The data is available in two formats: (1) a .mat file containing an array with dimensions “number of repeats” x “number of neurons” x “time in a repeat”; (2) a zipped .txt file containing the same data represented as an array with dimensions “number of neurons” x “number of samples”, where the number of samples is equal to the product of the number of repeats and timebins within a repeat. The time dimension is divided into 20 ms time windows, and the array is binary indicating whether a given cell elicited at least one spike in a given time window during a particular repeat. See the reference below for details regarding collection and preprocessing:
[1] Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry MJ II. Searching for Collective Behavior in a Large Network of Sensory Neurons. PLoS Comput Biol. 2014;10(1):e1003408.},
author = {Marre, Olivier and Tkacik, Gasper and Amodei, Dario and Schneidman, Elad and Bialek, William and Berry, Michael},
keyword = {multi-electrode recording, retinal ganglion cells},
publisher = {IST Austria},
title = {{Multi-electrode array recording from salamander retinal ganglion cells}},
doi = {10.15479/AT:ISTA:61},
year = {2017},
}
@article{720,
abstract = {Advances in multi-unit recordings pave the way for statistical modeling of activity patterns in large neural populations. Recent studies have shown that the summed activity of all neurons strongly shapes the population response. A separate recent finding has been that neural populations also exhibit criticality, an anomalously large dynamic range for the probabilities of different population activity patterns. Motivated by these two observations, we introduce a class of probabilistic models which takes into account the prior knowledge that the neural population could be globally coupled and close to critical. These models consist of an energy function which parametrizes interactions between small groups of neurons, and an arbitrary positive, strictly increasing, and twice differentiable function which maps the energy of a population pattern to its probability. We show that: 1) augmenting a pairwise Ising model with a nonlinearity yields an accurate description of the activity of retinal ganglion cells which outperforms previous models based on the summed activity of neurons; 2) prior knowledge that the population is critical translates to prior expectations about the shape of the nonlinearity; 3) the nonlinearity admits an interpretation in terms of a continuous latent variable globally coupling the system whose distribution we can infer from data. Our method is independent of the underlying system’s state space; hence, it can be applied to other systems such as natural scenes or amino acid sequences of proteins which are also known to exhibit criticality.},
author = {Humplik, Jan and Tkacik, Gasper},
issn = {1553734X},
journal = {PLoS Computational Biology},
number = {9},
publisher = {Public Library of Science},
title = {{Probabilistic models for neural populations that naturally capture global coupling and criticality}},
doi = {10.1371/journal.pcbi.1005763},
volume = {13},
year = {2017},
}
@article{725,
abstract = {Individual computations and social interactions underlying collective behavior in groups of animals are of great ethological, behavioral, and theoretical interest. While complex individual behaviors have successfully been parsed into small dictionaries of stereotyped behavioral modes, studies of collective behavior largely ignored these findings; instead, their focus was on inferring single, mode-independent social interaction rules that reproduced macroscopic and often qualitative features of group behavior. Here, we bring these two approaches together to predict individual swimming patterns of adult zebrafish in a group. We show that fish alternate between an “active” mode, in which they are sensitive to the swimming patterns of conspecifics, and a “passive” mode, where they ignore them. Using a model that accounts for these two modes explicitly, we predict behaviors of individual fish with high accuracy, outperforming previous approaches that assumed a single continuous computation by individuals and simple metric or topological weighing of neighbors’ behavior. At the group level, switching between active and passive modes is uncorrelated among fish, but correlated directional swimming behavior still emerges. Our quantitative approach for studying complex, multi-modal individual behavior jointly with emergent group behavior is readily extensible to additional behavioral modes and their neural correlates as well as to other species.},
author = {Harpaz, Roy and Tkacik, Gasper and Schneidman, Elad},
issn = {00278424},
journal = {PNAS},
number = {38},
pages = {10149 -- 10154},
publisher = {National Academy of Sciences},
title = {{Discrete modes of social information processing predict individual behavior of fish in a group}},
doi = {10.1073/pnas.1703817114},
volume = {114},
year = {2017},
}
@article{1104,
abstract = {In the early visual system, cells of the same type perform the same computation in different places of the visual field. How these cells code together a complex visual scene is unclear. A common assumption is that cells of a single-type extract a single-stimulus feature to form a feature map, but this has rarely been observed directly. Using large-scale recordings in the rat retina, we show that a homogeneous population of fast OFF ganglion cells simultaneously encodes two radically different features of a visual scene. Cells close to a moving object code quasilinearly for its position, while distant cells remain largely invariant to the object's position and, instead, respond nonlinearly to changes in the object's speed. We develop a quantitative model that accounts for this effect and identify a disinhibitory circuit that mediates it. Ganglion cells of a single type thus do not code for one, but two features simultaneously. This richer, flexible neural map might also be present in other sensory systems.},
author = {Deny, Stephane and Ferrari, Ulisse and Mace, Emilie and Yger, Pierre and Caplette, Romain and Picaud, Serge and Tkacik, Gasper and Marre, Olivier},
issn = {20411723},
journal = {Nature Communications},
number = {1},
publisher = {Nature Publishing Group},
title = {{Multiplexed computations in retinal ganglion cells of a single type}},
doi = {10.1038/s41467-017-02159-y},
volume = {8},
year = {2017},
}
@article{548,
abstract = {In this work maximum entropy distributions in the space of steady states of metabolic networks are considered upon constraining the first and second moments of the growth rate. Coexistence of fast and slow phenotypes, with bimodal flux distributions, emerges upon considering control on the average growth (optimization) and its fluctuations (heterogeneity). This is applied to the carbon catabolic core of Escherichia coli where it quantifies the metabolic activity of slow growing phenotypes and it provides a quantitative map with metabolic fluxes, opening the possibility to detect coexistence from flux data. A preliminary analysis on data for E. coli cultures in standard conditions shows degeneracy for the inferred parameters that extend in the coexistence region.},
author = {De Martino, Daniele},
issn = {24700045},
journal = {Physical Review E},
number = {6},
publisher = {American Physiological Society},
title = {{Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes}},
doi = {10.1103/PhysRevE.96.060401},
volume = {96},
year = {2017},
}
@article{613,
abstract = {Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment. This integrated platform broadly enables experiments that bridge individual and population behaviors. We demonstrate: (i) population structuring by independent closed-loop control of gene expression in many individual cells, (ii) cell-cell variation control during antibiotic perturbation, (iii) hybrid bio-digital circuits in single cells, and freely specifiable digital communication between individual bacteria. These examples showcase the potential for real-time integration of theoretical models with measurement and control of many individual cells to investigate and engineer microbial population behavior.},
author = {Chait, Remy P and Ruess, Jakob and Bergmiller, Tobias and Tkacik, Gasper and Guet, Calin C},
issn = {20411723},
journal = {Nature Communications},
number = {1},
publisher = {Nature Publishing Group},
title = {{Shaping bacterial population behavior through computer interfaced control of individual cells}},
doi = {10.1038/s41467-017-01683-1},
volume = {8},
year = {2017},
}
@article{947,
abstract = {Viewing the ways a living cell can organize its metabolism as the phase space of a physical system, regulation can be seen as the ability to reduce the entropy of that space by selecting specific cellular configurations that are, in some sense, optimal. Here we quantify the amount of regulation required to control a cell's growth rate by a maximum-entropy approach to the space of underlying metabolic phenotypes, where a configuration corresponds to a metabolic flux pattern as described by genome-scale models. We link the mean growth rate achieved by a population of cells to the minimal amount of metabolic regulation needed to achieve it through a phase diagram that highlights how growth suppression can be as costly (in regulatory terms) as growth enhancement. Moreover, we provide an interpretation of the inverse temperature β controlling maximum-entropy distributions based on the underlying growth dynamics. Specifically, we show that the asymptotic value of β for a cell population can be expected to depend on (i) the carrying capacity of the environment, (ii) the initial size of the colony, and (iii) the probability distribution from which the inoculum was sampled. Results obtained for E. coli and human cells are found to be remarkably consistent with empirical evidence.},
author = {De Martino, Daniele and Capuani, Fabrizio and De Martino, Andrea},
issn = {24700045},
journal = { Physical Review E Statistical Nonlinear and Soft Matter Physics },
number = {1},
publisher = {American Institute of Physics},
title = {{Quantifying the entropic cost of cellular growth control}},
doi = {10.1103/PhysRevE.96.010401},
volume = {96},
year = {2017},
}
@article{959,
abstract = {In this work it is shown that scale-free tails in metabolic flux distributions inferred in stationary models are an artifact due to reactions involved in thermodynamically unfeasible cycles, unbounded by physical constraints and in principle able to perform work without expenditure of free energy. After implementing thermodynamic constraints by removing such loops, metabolic flux distributions scale meaningfully with the physical limiting factors, acquiring in turn a richer multimodal structure potentially leading to symmetry breaking while optimizing for objective functions.},
author = {De Martino, Daniele},
issn = {24700045},
journal = { Physical Review E Statistical Nonlinear and Soft Matter Physics },
number = {6},
pages = {062419},
publisher = {American Institute of Physics},
title = {{Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics}},
doi = {10.1103/PhysRevE.95.062419},
volume = {95},
year = {2017},
}
@inproceedings{652,
abstract = {We present an approach that enables robots to self-organize their sensorimotor behavior from scratch without providing specific information about neither the robot nor its environment. This is achieved by a simple neural control law that increases the consistency between external sensor dynamics and internal neural dynamics of the utterly simple controller. In this way, the embodiment and the agent-environment coupling are the only source of individual development. We show how an anthropomorphic tendon driven arm-shoulder system develops different behaviors depending on that coupling. For instance: Given a bottle half-filled with water, the arm starts to shake it, driven by the physical response of the water. When attaching a brush, the arm can be manipulated into wiping a table, and when connected to a revolvable wheel it finds out how to rotate it. Thus, the robot may be said to discover the affordances of the world. When allowing two (simulated) humanoid robots to interact physically, they engage into a joint behavior development leading to, for instance, spontaneous cooperation. More social effects are observed if the robots can visually perceive each other. Although, as an observer, it is tempting to attribute an apparent intentionality, there is nothing of the kind put in. As a conclusion, we argue that emergent behavior may be much less rooted in explicit intentions, internal motivations, or specific reward systems than is commonly believed.},
author = {Der, Ralf and Martius, Georg S},
isbn = {978-150905069-7},
location = {Cergy-Pontoise, France},
publisher = {IEEE},
title = {{Dynamical self consistency leads to behavioral development and emergent social interactions in robots}},
doi = {10.1109/DEVLRN.2016.7846789},
year = {2017},
}
@article{823,
abstract = {The resolution of a linear system with positive integer variables is a basic yet difficult computational problem with many applications. We consider sparse uncorrelated random systems parametrised by the density c and the ratio α=N/M between number of variables N and number of constraints M. By means of ensemble calculations we show that the space of feasible solutions endows a Van-Der-Waals phase diagram in the plane (c, α). We give numerical evidence that the associated computational problems become more difficult across the critical point and in particular in the coexistence region.},
author = {Colabrese, Simona and De Martino, Daniele and Leuzzi, Luca and Marinari, Enzo},
issn = {17425468},
journal = { Journal of Statistical Mechanics: Theory and Experiment},
number = {9},
publisher = {IOPscience},
title = {{Phase transitions in integer linear problems}},
doi = {10.1088/1742-5468/aa85c3},
volume = {2017},
year = {2017},
}
@article{943,
abstract = {Like many developing tissues, the vertebrate neural tube is patterned by antiparallel morphogen gradients. To understand how these inputs are interpreted, we measured morphogen signaling and target gene expression in mouse embryos and chick ex vivo assays. From these data, we derived and validated a characteristic decoding map that relates morphogen input to the positional identity of neural progenitors. Analysis of the observed responses indicates that the underlying interpretation strategy minimizes patterning errors in response to the joint input of noisy opposing gradients. We reverse-engineered a transcriptional network that provides a mechanistic basis for the observed cell fate decisions and accounts for the precision and dynamics of pattern formation. Together, our data link opposing gradient dynamics in a growing tissue to precise pattern formation.},
author = {Zagórski, Marcin P and Tabata, Yoji and Brandenberg, Nathalie and Lutolf, Matthias and Tkacik, Gasper and Bollenbach, Tobias and Briscoe, James and Kicheva, Anna},
issn = {00368075},
journal = {Science},
number = {6345},
pages = {1379 -- 1383},
publisher = {American Association for the Advancement of Science},
title = {{Decoding of position in the developing neural tube from antiparallel morphogen gradients}},
doi = {10.1126/science.aam5887},
volume = {356},
year = {2017},
}
@article{955,
abstract = {Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components.},
author = {Friedlander, Tamar and Prizak, Roshan and Barton, Nicholas H and Tkacik, Gasper},
issn = {20411723},
journal = {Nature Communications},
number = {1},
publisher = {Nature Publishing Group},
title = {{Evolution of new regulatory functions on biophysically realistic fitness landscapes}},
doi = {10.1038/s41467-017-00238-8},
volume = {8},
year = {2017},
}
@article{993,
abstract = {In real-world applications, observations are often constrained to a small fraction of a system. Such spatial subsampling can be caused by the inaccessibility or the sheer size of the system, and cannot be overcome by longer sampling. Spatial subsampling can strongly bias inferences about a system’s aggregated properties. To overcome the bias, we derive analytically a subsampling scaling framework that is applicable to different observables, including distributions of neuronal avalanches, of number of people infected during an epidemic outbreak, and of node degrees. We demonstrate how to infer the correct distributions of the underlying full system, how to apply it to distinguish critical from subcritical systems, and how to disentangle subsampling and finite size effects. Lastly, we apply subsampling scaling to neuronal avalanche models and to recordings from developing neural networks. We show that only mature, but not young networks follow power-law scaling, indicating self-organization to criticality during development.},
author = {Levina (Martius), Anna and Priesemann, Viola},
issn = {20411723},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{Subsampling scaling}},
doi = {10.1038/ncomms15140},
volume = {8},
year = {2017},
}