Here is a list of my publications to date. The abstracts can be accessed by clicking the show abstract element below each title.

T. Teșileanu, B. Ölveczky, V. Balasubramanian.
Rules and mechanisms for efficient twostage learning in neural circuits.
eLife 6: e20944 (2017) [arXiv:1608.08040]
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Trialanderror learning requires evaluating variable actions and reinforcing successful variants. In songbirds, vocal exploration is induced by LMAN, the output of a basal gangliarelated circuit that also contributes a corrective bias to the vocal output. This bias is gradually consolidated in RA, a motor cortex analogue downstream of LMAN. We develop a new model of such twostage learning. Using stochastic gradient descent, we derive how the activity in ‘tutor’ circuits (e.g., LMAN) should match plasticity mechanisms in ‘student’ circuits (e.g., RA) to achieve efficient learning. We further describe a reinforcement learning framework through which the tutor can build its teaching signal. We show that mismatches between the tutor signal and the plasticity mechanism can impair learning. Applied to birdsong, our results predict the temporal structure of the corrective bias from LMAN given a plasticity rule in RA. Our framework can be applied predictively to other paired brain areas showing twostage learning.

S. Bradde, M. Vucelja, T. Teșileanu, V. Balasubramanian.
Dynamics of adaptive immunity against phage in bacterial populations.
PLoS Comput. Biol. 13(4): e1005486 (2017) [arXiv:1510.06082]
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The CRISPR (clustered regularly interspaced short palindromic repeats) mechanism allows bacteria to adaptively defend against phages by acquiring short genomic sequences (spacers) that target specific sequences in the viral genome. We propose a population dynamical model where immunity can be both acquired and lost. The model predicts regimes where bacterial and phage populations can coexist, others where the populations exhibit damped oscillations, and still others where one population is driven to extinction. Our model considers two key parameters: (1) ease of acquisition and (2) spacer effectiveness in conferring immunity. Analytical calculations and numerical simulations show that if spacers differ mainly in ease of acquisition, or if the probability of acquiring them is sufficiently high, bacteria develop a diverse population of spacers. On the other hand, if spacers differ mainly in their effectiveness, their final distribution will be highly peaked, akin to a “winnertakeall” scenario, leading to a specialized spacer distribution. Bacteria can interpolate between these limiting behaviors by actively tuning their overall acquisition probability.

T. Teșileanu, L. J. Colwell, and S. Leibler.
Protein sectors: statistical coupling analysis versus conservation.
PLoS Comput. Biol. 11(2): e1004091 (2015) [arXiv:1405.7081]
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Statistical coupling analysis (SCA) is a method for analyzing multiple sequence alignments that was used to identify groups of coevolving residues termed “sectors”. The method applies spectral analysis to a matrix obtained by combining correlation information with sequence conservation. It has been asserted that the protein sectors identified by SCA are functionally significant, with different sectors controlling different biochemical properties of the protein. Here we reconsider the available experimental data and note that it involves almost exclusively proteins with a single sector. We show that in this case sequence conservation is the dominating factor in SCA, and can alone be used to make statistically equivalent functional predictions. Therefore, we suggest shifting the experimental focus to proteins for which SCA identifies several sectors. Correlations in protein alignments, which have been shown to be informative in a number of independent studies, would then be less dominated by sequence conservation.

A. Melnikov, A. Murugan, X. Zhang, T. Teșileanu, L. Wang, P. Rogov, S. Feizi, A. Gnirke, C. G. Callan Jr., J. B. Kinney, M. Kellis, E. S. Lander, and T. S. Mikkelsen.
Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay.
Nature Biotechnology 30, 271277 (2012)
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Learning to read and write the transcriptional regulatory code is of central importance to progress in genetic analysis and engineering. Here we describe a massively parallel reporter assay (MPRA) that facilitates the systematic dissection of transcriptional regulatory elements. In MPRA, microarraysynthesized DNA regulatory elements and unique sequence tags are cloned into plasmids to generate a library of reporter constructs. These constructs are transfected into cells and tag expression is assayed by highthroughput sequencing. We apply MPRA to compare >27,000 variants of two inducible enhancers in human cells: a synthetic cAMPregulated enhancer and the virusinducible interferonβ enhancer. We first show that the resulting data define accurate maps of functional transcription factor binding sites in both enhancers at singlenucleotide resolution. We then use the data to train quantitative sequenceactivity models (QSAMs) of the two enhancers. We show that QSAMs from two cellular states can be combined to design enhancer variants that optimize potentially conflicting objectives, such as maximizing induced activity while minimizing basal activity.

C. P. Herzog, I. R. Klebanov, S. S. Pufu, and T. Teșileanu.
Multimatrix models and triSasaki Einstein spaces.
Phys. Rev. D 83, 046001 (2011) [arXiv:1011.5487]
show abstract
Localization methods reduce the path integrals in N ≥ 2 supersymmetric ChernSimons gauge theories on S^{3} to multimatrix integrals. A recent evaluation of such a twomatrix integral for the N = 6 superconformal U(N) × U(N) ABJM theory produced detailed agreement with the AdS/CFT correspondence, explaining, in particular, the N^{3/2} scaling of the free energy. We study a class of pmatrix integrals describing N = 3 superconformal U(N)^{p} ChernSimons gauge theories. We present a simple method that allows us to evaluate the eigenvalue densities and the free energies in the large N limit keeping the ChernSimons levels k_{i} fixed. The dual Mtheory backgrounds are AdS_{4} × Y, where Y are sevendimensional triSasaki Einstein spaces specified by the k_{i}. The gravitational free energy scales inversely with the square root of the volume of Y. We find a general formula for the pmatrix free energies that agrees with the available results for volumes of the triSasaki Einstein spaces Y, thus providing a thorough test of the corresponding AdS_{4}/CFT_{3} dualities. This formula is consistent with the Seiberg duality conjectured for ChernSimons gauge theories.

I. R. Klebanov, S. S. Pufu, and T. Teșileanu.
Membranes with topological charge and AdS_{4}/CFT_{3} correspondence.
Phys. Rev. D 81, 125011 (2010) [arXiv:1004.0413]
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If the second Betti number b_{2} of a SasakiEinstein manifold Y^{7} does not vanish, then Mtheory on AdS_{4} × Y^{7} possesses “topological” U(1)^{b2} gauge symmetry. The corresponding Abelian gauge fields come from threeform fluctuations with one index in AdS_{4} and the other two in Y^{7}. We find black membrane solutions carrying one of these U(1) charges. In the zero temperature limit, our solutions interpolate between AdS_{4} × Y^{7} in the UV and AdS_{2} × R^{2} × squashed Y^{7} in the IR. In fact, the AdS_{2} × R^{2} × squashed Y^{7} background is by itself a solution of the supergravity equations of motion. These solutions do not appear to preserve any supersymmetry. We search for their possible instabilities and do not find any. We also discuss the meaning of our charged membrane backgrounds in a dual quiver ChernSimons gauge theory with a global U(1) charge density. Finally, we present a simple analytic solution which has the same IR but different UV behavior. We reduce this solution to type IIA string theory, and perform Tduality to type IIB. The type IIB metric turns out to be a product of the squashed Y^{7} and the extremal BTZ black hole. We discuss an interpretation of this type IIB background in terms of the (1+1)dimensional CFT on D3branes partially wrapped over the squashed Y^{7}.

C. P. Herzog, I. R. Klebanov, S. S. Pufu, and T. Teșileanu.
Emergent quantum nearcriticality from baryonic black branes.
JHEP 1003, 093 (2010) [arXiv:0911.0400]
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We find new black 3brane solutions describing the “conifold gauge theory” at nonzero temperature and baryonic chemical potential. Of particular interest is the lowtemperature limit where we find a new kind of weakly curved nearhorizon geometry; it is a warped product AdS_{2} × R^{3} × T^{1,1} with warp factors that are powers of the logarithm of the AdS radius. Thus, our solution encodes a new type of emergent quantum nearcriticality. We carry out some stability checks for our solutions. We also set up a consistent ansatz for baryonic black 2branes of Mtheory that are asymptotic to AdS_{4} × Q^{1,1,1}.

S. S. Gubser, C. P. Herzog, S. S. Pufu, and T. Teșileanu.
Superconductors from Superstrings.
Phys. Rev. Lett. 103, 141601 (2009) [arXiv:0907.3510]
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We establish that in a large class of strongly coupled 3+1 dimensional N = 1 quiver conformal field theories with gravity duals, adding a chemical potential for the Rcharge leads to the existence of superfluid states in which a chiral primary operator of the schematic form O = λλ+W condenses. Here λ is a gluino and W is the superpotential. Our argument is based on the construction of a consistent truncation of type IIB supergravity that includes a U(1) gauge field and a complex scalar.

R. C. Helling, P. Schupp, and T. Teșileanu.
CMB statistical anisotropy, multipole vectors and the influence of the dipole.
Phys. Rev. D 74, 063004 (2006) [arXiv:astroph/0603594]
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A simple algorithm which gives the multipole vectors in terms of the roots of a polynomial is given. We find that the reported alignment of the low l multipole vectors can be summarised as an antialignment of these with the dipole direction. This antialignment is not only present in l = 2 and 3 but also for l = 5 and higher. This alignment is likely due to nonlinearity in the data processing. Our results are based on the three year WMAP data, we also list corresponding results for the first year data.

T. Teșileanu and H. MeyerOrtmanns.
Competition of Languages and their Hamming Distance.
International Journal of Modern Physics C 17, issue 3 (2006) [arXiv:physics/0508229]
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We consider the spreading and competition of languages that are spoken by a population of individuals. The individuals can change their mother tongue during their lifespan, pass on their language to their offspring and finally die. The languages are described by bitstrings, their mutual difference is expressed in terms of their Hamming distance. Language evolution is determined by mutation and adaptation rates. In particular we consider the case where the replacement of a language by another one is determined by their mutual Hamming distance. As a function of the mutation rate we find a sharp transition between a scenario with one dominant language and fragmentation into many language clusters. The transition is also reflected in the Hamming distance between the two languages with the largest and second to largest number of speakers. We also consider the case where the population is localized on a square lattice and the interaction of individuals is restricted to a certain geometrical domain. Here it is again the Hamming distance that plays an essential role in the final fate of a language of either surviving or being extinct.