[{"page":"5893 - 5904","publist_id":"4389","year":"2011","month":"04","intvolume":"        31","date_published":"2011-04-20T00:00:00Z","publisher":"Society for Neuroscience","date_updated":"2021-01-12T06:57:56Z","issue":"16","title":"NMDA receptors in hippocampal GABAergic synapses and their role in nitric oxide signaling","author":[{"full_name":"Szabadits, Eszter","last_name":"Szabadits","first_name":"Eszter"},{"full_name":"Cserép, Csaba","first_name":"Csaba","last_name":"Cserép"},{"last_name":"Szonyi","first_name":"András","full_name":"Szonyi, András"},{"first_name":"Yugo","last_name":"Fukazawa","full_name":"Fukazawa, Yugo"},{"full_name":"Ryuichi Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"},{"full_name":"Watanabe, Masahiko","first_name":"Masahiko","last_name":"Watanabe"},{"last_name":"Itohara","first_name":"Shigeyoshi","full_name":"Itohara, Shigeyoshi"},{"last_name":"Freund","first_name":"Tamás","full_name":"Freund, Tamás F"},{"last_name":"Nyíri","first_name":"Gábor","full_name":"Nyíri, Gábor"}],"doi":"10.1523/JNEUROSCI.5938-10.2011","publication_status":"published","publication":"Journal of Neuroscience","extern":1,"citation":{"chicago":"Szabadits, Eszter, Csaba Cserép, András Szonyi, Yugo Fukazawa, Ryuichi Shigemoto, Masahiko Watanabe, Shigeyoshi Itohara, Tamás Freund, and Gábor Nyíri. “NMDA Receptors in Hippocampal GABAergic Synapses and Their Role in Nitric Oxide Signaling.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2011. <a href=\"https://doi.org/10.1523/JNEUROSCI.5938-10.2011\">https://doi.org/10.1523/JNEUROSCI.5938-10.2011</a>.","ista":"Szabadits E, Cserép C, Szonyi A, Fukazawa Y, Shigemoto R, Watanabe M, Itohara S, Freund T, Nyíri G. 2011. NMDA receptors in hippocampal GABAergic synapses and their role in nitric oxide signaling. Journal of Neuroscience. 31(16), 5893–5904.","short":"E. Szabadits, C. Cserép, A. Szonyi, Y. Fukazawa, R. Shigemoto, M. Watanabe, S. Itohara, T. Freund, G. Nyíri, Journal of Neuroscience 31 (2011) 5893–5904.","ieee":"E. Szabadits <i>et al.</i>, “NMDA receptors in hippocampal GABAergic synapses and their role in nitric oxide signaling,” <i>Journal of Neuroscience</i>, vol. 31, no. 16. Society for Neuroscience, pp. 5893–5904, 2011.","ama":"Szabadits E, Cserép C, Szonyi A, et al. NMDA receptors in hippocampal GABAergic synapses and their role in nitric oxide signaling. <i>Journal of Neuroscience</i>. 2011;31(16):5893-5904. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.5938-10.2011\">10.1523/JNEUROSCI.5938-10.2011</a>","mla":"Szabadits, Eszter, et al. “NMDA Receptors in Hippocampal GABAergic Synapses and Their Role in Nitric Oxide Signaling.” <i>Journal of Neuroscience</i>, vol. 31, no. 16, Society for Neuroscience, 2011, pp. 5893–904, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.5938-10.2011\">10.1523/JNEUROSCI.5938-10.2011</a>.","apa":"Szabadits, E., Cserép, C., Szonyi, A., Fukazawa, Y., Shigemoto, R., Watanabe, M., … Nyíri, G. (2011). NMDA receptors in hippocampal GABAergic synapses and their role in nitric oxide signaling. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.5938-10.2011\">https://doi.org/10.1523/JNEUROSCI.5938-10.2011</a>"},"volume":31,"type":"journal_article","abstract":[{"text":"GABAergic inhibition plays a central role in the control of pyramidal cell ensemble activities; thus, any signaling mechanism that regulates inhibition is able to fine-tune network patterns. Here, we provide evidence that the retrograde nitric oxide (NO)- cGMP cascade triggered by NMDA receptor (NMDAR) activation plays a role in the control of hippocampal GABAergic transmission in mice. GABAergic synapses express neuronal nitric oxide synthase (nNOS) postsynaptically and NO receptors (NO-sensitive guanylyl cyclase) in the presynaptic terminals. We hypothesized that-similar to glutamatergic synapses-the Ca 2+ transients required to activate nNOS were provided by NMDA receptor activation. Indeed, administration of 5 μm NMDA induced a robust nNOS-dependent cGMP production in GABAergic terminals, selectively in the CA1 and CA3c areas. Furthermore, using preembedding, postembedding, and SDS-digested freeze-fracture replica immunogold labeling, we provided quantitative immunocytochemical evidence that NMDAR subunits GluN1, GluN2A, and GluN2B were present in most somatic GABAergic synapses postsynaptically. These data indicate that NMDARs can modulate hippocampal GABAergic inhibition via NO- cGMP signaling in an activity-dependent manner and that this effect is subregion specific in the mouse hippocampus.","lang":"eng"}],"date_created":"2018-12-11T11:58:06Z","_id":"2512","day":"20","status":"public","quality_controlled":0},{"year":"2011","publist_id":"4388","page":"744 - 749","title":"The SK2-long isoform directs synaptic localization and function of SK2-containing channels","author":[{"full_name":"Allen, Duane H","last_name":"Allen","first_name":"Duane"},{"first_name":"Chris","last_name":"Bond","full_name":"Bond, Chris T"},{"full_name":"Luján, Rafael","last_name":"Luján","first_name":"Rafael"},{"full_name":"Ballesteros-Merino, Carmen","first_name":"Carmen","last_name":"Ballesteros Merino"},{"first_name":"Michael","last_name":"Lin","full_name":"Lin, Michael T"},{"first_name":"Kang","last_name":"Wang","full_name":"Wang, Kang"},{"full_name":"Klett, Nathan","first_name":"Nathan","last_name":"Klett"},{"first_name":"Masahiko","last_name":"Watanabe","full_name":"Watanabe, Masahiko"},{"orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Ryuichi Shigemoto"},{"full_name":"Stackman, Robert W","last_name":"Stackman","first_name":"Robert"},{"first_name":"James","last_name":"Maylie","full_name":"Maylie, James G"},{"last_name":"Adelman","first_name":"John","full_name":"Adelman, John P"}],"issue":"6","date_updated":"2021-01-12T06:57:56Z","publisher":"Nature Publishing Group","date_published":"2011-06-01T00:00:00Z","intvolume":"        14","month":"06","publication":"Nature Neuroscience","publication_status":"published","doi":"10.1038/nn.2832","day":"01","status":"public","quality_controlled":0,"date_created":"2018-12-11T11:58:07Z","_id":"2513","abstract":[{"text":"SK2-containing channels are expressed in the postsynaptic density (PSD) of dendritic spines on mouse hippocampal area CA1 pyramidal neurons and influence synaptic responses, plasticity and learning. The Sk2 gene (also known as Kcnn2) encodes two isoforms that differ only in the length of their N-terminal domains. SK2-long (SK2-L) and SK2-short (SK2-S) are coexpressed in CA1 pyramidal neurons and likely form heteromeric channels. In mice lacking SK2-L (SK2-S only mice), SK2-S-containing channels were expressed in the extrasynaptic membrane, but were excluded from the PSD. The SK channel contribution to excitatory postsynaptic potentials was absent in SK2-S only mice and was restored by SK2-L re-expression. Blocking SK channels increased the amount of long-term potentiation induced in area CA1 in slices from wild-type mice but had no effect in slices from SK2-S only mice. Furthermore, SK2-S only mice outperformed wild-type mice in the novel object recognition task. These results indicate that SK2-L directs synaptic SK2-containing channel expression and is important for normal synaptic signaling, plasticity and learning. ","lang":"eng"}],"type":"journal_article","volume":14,"citation":{"short":"D. Allen, C. Bond, R. Luján, C. Ballesteros Merino, M. Lin, K. Wang, N. Klett, M. Watanabe, R. Shigemoto, R. Stackman, J. Maylie, J. Adelman, Nature Neuroscience 14 (2011) 744–749.","ista":"Allen D, Bond C, Luján R, Ballesteros Merino C, Lin M, Wang K, Klett N, Watanabe M, Shigemoto R, Stackman R, Maylie J, Adelman J. 2011. The SK2-long isoform directs synaptic localization and function of SK2-containing channels. Nature Neuroscience. 14(6), 744–749.","ieee":"D. Allen <i>et al.</i>, “The SK2-long isoform directs synaptic localization and function of SK2-containing channels,” <i>Nature Neuroscience</i>, vol. 14, no. 6. Nature Publishing Group, pp. 744–749, 2011.","ama":"Allen D, Bond C, Luján R, et al. The SK2-long isoform directs synaptic localization and function of SK2-containing channels. <i>Nature Neuroscience</i>. 2011;14(6):744-749. doi:<a href=\"https://doi.org/10.1038/nn.2832\">10.1038/nn.2832</a>","chicago":"Allen, Duane, Chris Bond, Rafael Luján, Carmen Ballesteros Merino, Michael Lin, Kang Wang, Nathan Klett, et al. “The SK2-Long Isoform Directs Synaptic Localization and Function of SK2-Containing Channels.” <i>Nature Neuroscience</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/nn.2832\">https://doi.org/10.1038/nn.2832</a>.","apa":"Allen, D., Bond, C., Luján, R., Ballesteros Merino, C., Lin, M., Wang, K., … Adelman, J. (2011). The SK2-long isoform directs synaptic localization and function of SK2-containing channels. <i>Nature Neuroscience</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nn.2832\">https://doi.org/10.1038/nn.2832</a>","mla":"Allen, Duane, et al. “The SK2-Long Isoform Directs Synaptic Localization and Function of SK2-Containing Channels.” <i>Nature Neuroscience</i>, vol. 14, no. 6, Nature Publishing Group, 2011, pp. 744–49, doi:<a href=\"https://doi.org/10.1038/nn.2832\">10.1038/nn.2832</a>."},"extern":1},{"author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös","full_name":"László Erdös"},{"first_name":"Antti","last_name":"Knowles","full_name":"Knowles, Antti"}],"title":"Quantum diffusion and eigenfunction delocalization in a random band matrix model","issue":"2","date_updated":"2021-01-12T06:59:15Z","publisher":"Springer","date_published":"2011-04-01T00:00:00Z","month":"04","intvolume":"       303","year":"2011","publist_id":"4175","page":"509 - 554","day":"01","quality_controlled":0,"status":"public","date_created":"2018-12-11T11:59:14Z","_id":"2717","abstract":[{"text":"We consider Hermitian and symmetric random band matrices H in d ≥ 1 dimensions. The matrix elements H xy, indexed by, are independent, uniformly distributed random variables if {pipe}x-y{pipe} is less than the band width W, and zero otherwise. We prove that the time evolution of a quantum particle subject to the Hamiltonian H is diffusive on time scales. We also show that the localization length of the eigenvectors of H is larger than a factor W d/6 times the band width. All results are uniform in the size of the matrix. ","lang":"eng"}],"type":"journal_article","volume":303,"citation":{"apa":"Erdös, L., &#38; Knowles, A. (2011). Quantum diffusion and eigenfunction delocalization in a random band matrix model. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-011-1204-2\">https://doi.org/10.1007/s00220-011-1204-2</a>","mla":"Erdös, László, and Antti Knowles. “Quantum Diffusion and Eigenfunction Delocalization in a Random Band Matrix Model.” <i>Communications in Mathematical Physics</i>, vol. 303, no. 2, Springer, 2011, pp. 509–54, doi:<a href=\"https://doi.org/10.1007/s00220-011-1204-2\">10.1007/s00220-011-1204-2</a>.","ama":"Erdös L, Knowles A. Quantum diffusion and eigenfunction delocalization in a random band matrix model. <i>Communications in Mathematical Physics</i>. 2011;303(2):509-554. doi:<a href=\"https://doi.org/10.1007/s00220-011-1204-2\">10.1007/s00220-011-1204-2</a>","short":"L. Erdös, A. Knowles, Communications in Mathematical Physics 303 (2011) 509–554.","ista":"Erdös L, Knowles A. 2011. Quantum diffusion and eigenfunction delocalization in a random band matrix model. Communications in Mathematical Physics. 303(2), 509–554.","ieee":"L. Erdös and A. Knowles, “Quantum diffusion and eigenfunction delocalization in a random band matrix model,” <i>Communications in Mathematical Physics</i>, vol. 303, no. 2. Springer, pp. 509–554, 2011.","chicago":"Erdös, László, and Antti Knowles. “Quantum Diffusion and Eigenfunction Delocalization in a Random Band Matrix Model.” <i>Communications in Mathematical Physics</i>. Springer, 2011. <a href=\"https://doi.org/10.1007/s00220-011-1204-2\">https://doi.org/10.1007/s00220-011-1204-2</a>."},"extern":1,"publication":"Communications in Mathematical Physics","doi":"10.1007/s00220-011-1204-2","publication_status":"published"},{"publist_id":"4126","page":"75 - 119","year":"2011","publisher":"Springer","intvolume":"       185","month":"07","date_published":"2011-07-01T00:00:00Z","issue":"1","author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"László Erdös"},{"full_name":"Schlein, Benjamin","first_name":"Benjamin","last_name":"Schlein"},{"full_name":"Yau, Horng-Tzer","last_name":"Yau","first_name":"Horng"}],"title":"Universality of random matrices and local relaxation flow","date_updated":"2021-01-12T06:59:32Z","publication_status":"published","doi":"10.1007/s00222-010-0302-7","publication":"Inventiones Mathematicae","type":"journal_article","abstract":[{"text":"Consider the Dyson Brownian motion with parameter β, where β=1,2,4 corresponds to the eigenvalue flows for the eigenvalues of symmetric, hermitian and quaternion self-dual ensembles. For any β≥1, we prove that the relaxation time to local equilibrium for the Dyson Brownian motion is bounded above by N -ζ for some ζ&gt; 0. The proof is based on an estimate of the entropy flow of the Dyson Brownian motion w. r. t. a &quot;pseudo equilibrium measure&quot;. As an application of this estimate, we prove that the eigenvalue spacing statistics in the bulk of the spectrum for N×N symmetric Wigner ensemble is the same as that of the Gaussian Orthogonal Ensemble (GOE) in the limit N→∞. The assumptions on the probability distribution of the matrix elements of the Wigner ensemble are a subexponential decay and some minor restriction on the support.","lang":"eng"}],"citation":{"apa":"Erdös, L., Schlein, B., &#38; Yau, H. (2011). Universality of random matrices and local relaxation flow. <i>Inventiones Mathematicae</i>. Springer. <a href=\"https://doi.org/10.1007/s00222-010-0302-7\">https://doi.org/10.1007/s00222-010-0302-7</a>","mla":"Erdös, László, et al. “Universality of Random Matrices and Local Relaxation Flow.” <i>Inventiones Mathematicae</i>, vol. 185, no. 1, Springer, 2011, pp. 75–119, doi:<a href=\"https://doi.org/10.1007/s00222-010-0302-7\">10.1007/s00222-010-0302-7</a>.","ieee":"L. Erdös, B. Schlein, and H. Yau, “Universality of random matrices and local relaxation flow,” <i>Inventiones Mathematicae</i>, vol. 185, no. 1. Springer, pp. 75–119, 2011.","ista":"Erdös L, Schlein B, Yau H. 2011. Universality of random matrices and local relaxation flow. Inventiones Mathematicae. 185(1), 75–119.","short":"L. Erdös, B. Schlein, H. Yau, Inventiones Mathematicae 185 (2011) 75–119.","ama":"Erdös L, Schlein B, Yau H. Universality of random matrices and local relaxation flow. <i>Inventiones Mathematicae</i>. 2011;185(1):75-119. doi:<a href=\"https://doi.org/10.1007/s00222-010-0302-7\">10.1007/s00222-010-0302-7</a>","chicago":"Erdös, László, Benjamin Schlein, and Horng Yau. “Universality of Random Matrices and Local Relaxation Flow.” <i>Inventiones Mathematicae</i>. Springer, 2011. <a href=\"https://doi.org/10.1007/s00222-010-0302-7\">https://doi.org/10.1007/s00222-010-0302-7</a>."},"extern":1,"volume":185,"day":"01","status":"public","quality_controlled":0,"date_created":"2018-12-11T11:59:29Z","_id":"2764"},{"title":"Universality of Wigner random matrices: A survey of recent results","author":[{"full_name":"László Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","orcid":"0000-0001-5366-9603"}],"issue":"3","date_updated":"2019-04-26T07:22:20Z","publisher":"IOP Publishing Ltd.","date_published":"2011-01-01T00:00:00Z","month":"01","intvolume":"        66","year":"2011","publist_id":"4125","page":"507 - 626","status":"public","day":"01","quality_controlled":0,"date_created":"2018-12-11T11:59:29Z","_id":"2765","abstract":[{"lang":"eng","text":"This is a study of the universality of spectral statistics for large random matrices. Considered are N×N symmetric, Hermitian, or quaternion self-dual random matrices with independent identically distributed entries (Wigner matrices), where the probability distribution of each matrix element is given by a measure v with zero expectation and with subexponential decay. The main result is that the correlation functions of the local eigenvalue statistics in the bulk of the spectrum coincide with those of the Gaussian Orthogonal Ensemble (GOE), the Gaussian Unitary Ensemble (GUE), and the Gaussian Symplectic Ensemble (GSE), respectively, in the limit as N → ∞. This approach is based on a study of the Dyson Brownian motion via a related new dynamics, the local relaxation flow. As a main input, it is established that the density of the eigenvalues converges to the Wigner semicircle law, and this holds even down to the smallest possible scale. Moreover, it is shown that the eigenvectors are completely delocalized. These results hold even without the condition that the matrix elements are identically distributed: only independence is used. In fact, for the matrix elements of the Green function strong estimates are given that imply that the local statistics of any two ensembles in the bulk are identical if the first four moments of the matrix elements match. Universality at the spectral edges requires matching only two moments. A Wigner-type estimate is also proved, and it is shown that the eigenvalues repel each other on arbitrarily small scales."}],"type":"review","volume":66,"extern":1,"citation":{"chicago":"Erdös, László. “Universality of Wigner Random Matrices: A Survey of Recent Results.” <i>Russian Mathematical Surveys</i>. IOP Publishing Ltd., 2011. <a href=\"https://doi.org/10.1070/RM2011v066n03ABEH004749\">https://doi.org/10.1070/RM2011v066n03ABEH004749</a>.","short":"L. Erdös, Russian Mathematical Surveys 66 (2011) 507–626.","ieee":"L. Erdös, “Universality of Wigner random matrices: A survey of recent results,” <i>Russian Mathematical Surveys</i>, vol. 66, no. 3. IOP Publishing Ltd., pp. 507–626, 2011.","ista":"Erdös L. 2011. Universality of Wigner random matrices: A survey of recent results. Russian Mathematical Surveys. 66(3), 507–626.","ama":"Erdös L. Universality of Wigner random matrices: A survey of recent results. <i>Russian Mathematical Surveys</i>. 2011;66(3):507-626. doi:<a href=\"https://doi.org/10.1070/RM2011v066n03ABEH004749\">10.1070/RM2011v066n03ABEH004749</a>","mla":"Erdös, László. “Universality of Wigner Random Matrices: A Survey of Recent Results.” <i>Russian Mathematical Surveys</i>, vol. 66, no. 3, IOP Publishing Ltd., 2011, pp. 507–626, doi:<a href=\"https://doi.org/10.1070/RM2011v066n03ABEH004749\">10.1070/RM2011v066n03ABEH004749</a>.","apa":"Erdös, L. (2011). Universality of Wigner random matrices: A survey of recent results. <i>Russian Mathematical Surveys</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1070/RM2011v066n03ABEH004749\">https://doi.org/10.1070/RM2011v066n03ABEH004749</a>"},"publication":"Russian Mathematical Surveys","publication_status":"published","main_file_link":[{"open_access":"0","url":"http://arxiv.org/abs/1004.0861"}],"doi":"10.1070/RM2011v066n03ABEH004749"},{"publisher":"Birkhäuser","date_published":"2011-11-01T00:00:00Z","month":"11","intvolume":"        12","title":"Quantum diffusion and delocalization for band matrices with general distribution","author":[{"full_name":"László Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","orcid":"0000-0001-5366-9603"},{"first_name":"Antti","last_name":"Knowles","full_name":"Knowles, Antti"}],"issue":"7","date_updated":"2021-01-12T06:59:33Z","publist_id":"4124","page":"1227 - 1319","year":"2011","abstract":[{"lang":"eng","text":"We consider Hermitian and symmetric random band matrices H in d ≥ dimensions. The matrix elements Hxy, indexed by x,y ∈ Λ ⊂ ℤd are independent and their variances satisfy σ2xy:= E{pipe}Hxy{pipe}2 = W-d f((x-y)/W for some probability density f. We assume that the law of each matrix element Hxy is symmetric and exhibits subexponential decay. We prove that the time evolution of a quantum particle subject to the Hamiltonian H is diffusive on time scales ≪ Wd/3. We also show that the localization length of the eigenvectors of H is larger than a factor Wd/6 times the band width W. All results are uniform in the size {pipe}Λ{pipe} of the matrix. This extends our recent result (Erdo{double acute}s and Knowles in Commun. Math. Phys., 2011) to general band matrices. As another consequence of our proof we show that, for a larger class of random matrices satisfying Σx σ2xy for all y, the largest eigenvalue of H is bounded with high probability by 2+M-2/3+e{open} for any e{open} &gt; 0, where M:= 1/(maxx,y σ2xy)."}],"type":"journal_article","volume":12,"citation":{"chicago":"Erdös, László, and Antti Knowles. “Quantum Diffusion and Delocalization for Band Matrices with General Distribution.” <i>Annales Henri Poincare</i>. Birkhäuser, 2011. <a href=\"https://doi.org/10.1007/s00023-011-0104-5\">https://doi.org/10.1007/s00023-011-0104-5</a>.","ama":"Erdös L, Knowles A. Quantum diffusion and delocalization for band matrices with general distribution. <i>Annales Henri Poincare</i>. 2011;12(7):1227-1319. doi:<a href=\"https://doi.org/10.1007/s00023-011-0104-5\">10.1007/s00023-011-0104-5</a>","ista":"Erdös L, Knowles A. 2011. Quantum diffusion and delocalization for band matrices with general distribution. Annales Henri Poincare. 12(7), 1227–1319.","short":"L. Erdös, A. Knowles, Annales Henri Poincare 12 (2011) 1227–1319.","ieee":"L. Erdös and A. Knowles, “Quantum diffusion and delocalization for band matrices with general distribution,” <i>Annales Henri Poincare</i>, vol. 12, no. 7. Birkhäuser, pp. 1227–1319, 2011.","mla":"Erdös, László, and Antti Knowles. “Quantum Diffusion and Delocalization for Band Matrices with General Distribution.” <i>Annales Henri Poincare</i>, vol. 12, no. 7, Birkhäuser, 2011, pp. 1227–319, doi:<a href=\"https://doi.org/10.1007/s00023-011-0104-5\">10.1007/s00023-011-0104-5</a>.","apa":"Erdös, L., &#38; Knowles, A. (2011). Quantum diffusion and delocalization for band matrices with general distribution. <i>Annales Henri Poincare</i>. Birkhäuser. <a href=\"https://doi.org/10.1007/s00023-011-0104-5\">https://doi.org/10.1007/s00023-011-0104-5</a>"},"extern":1,"status":"public","day":"01","quality_controlled":0,"date_created":"2018-12-11T11:59:29Z","_id":"2766","publication":"Annales Henri Poincare","publication_status":"published","doi":"10.1007/s00023-011-0104-5"},{"doi":"10.1126/science.1203223","publication_status":"published","publication":"Science","day":"08","status":"public","quality_controlled":0,"_id":"2799","date_created":"2018-12-11T11:59:39Z","type":"journal_article","abstract":[{"text":"Shear flows undergo a sudden transition from laminar to turbulent motion as the velocity increases, and the onset of turbulence radically changes transport efficiency and mixing properties. Even for the well-studied case of pipe flow, it has not been possible to determine at what Reynolds number the motion will be either persistently turbulent or ultimately laminar. We show that in pipes, turbulence that is transient at low Reynolds numbers becomes sustained at a distinct critical point. Through extensive experiments and computer simulations, we were able to identify and characterize the processes ultimately responsible for sustaining turbulence. In contrast to the classical Landau-Ruelle-Takens view that turbulence arises from an increase in the temporal complexity of fluid motion, here, spatial proliferation of chaotic domains is the decisive process and intrinsic to the nature of fluid turbulence.","lang":"eng"}],"extern":1,"citation":{"short":"K. Avila, D. Moxey, A. De Lózar, M. Avila, D. Barkley, B. Hof, Science 333 (2011) 192–196.","ista":"Avila K, Moxey D, De Lózar A, Avila M, Barkley D, Hof B. 2011. The onset of turbulence in pipe flow. Science. 333(6039), 192–196.","ieee":"K. Avila, D. Moxey, A. De Lózar, M. Avila, D. Barkley, and B. Hof, “The onset of turbulence in pipe flow,” <i>Science</i>, vol. 333, no. 6039. American Association for the Advancement of Science, pp. 192–196, 2011.","ama":"Avila K, Moxey D, De Lózar A, Avila M, Barkley D, Hof B. The onset of turbulence in pipe flow. <i>Science</i>. 2011;333(6039):192-196. doi:<a href=\"https://doi.org/10.1126/science.1203223\">10.1126/science.1203223</a>","chicago":"Avila, Kerstin, David Moxey, Alberto De Lózar, Marc Avila, Dwight Barkley, and Björn Hof. “The Onset of Turbulence in Pipe Flow.” <i>Science</i>. American Association for the Advancement of Science, 2011. <a href=\"https://doi.org/10.1126/science.1203223\">https://doi.org/10.1126/science.1203223</a>.","apa":"Avila, K., Moxey, D., De Lózar, A., Avila, M., Barkley, D., &#38; Hof, B. (2011). The onset of turbulence in pipe flow. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1203223\">https://doi.org/10.1126/science.1203223</a>","mla":"Avila, Kerstin, et al. “The Onset of Turbulence in Pipe Flow.” <i>Science</i>, vol. 333, no. 6039, American Association for the Advancement of Science, 2011, pp. 192–96, doi:<a href=\"https://doi.org/10.1126/science.1203223\">10.1126/science.1203223</a>."},"volume":333,"year":"2011","publist_id":"4090","page":"192 - 196","issue":"6039","title":"The onset of turbulence in pipe flow","author":[{"full_name":"Avila, Kerstin","first_name":"Kerstin","last_name":"Avila"},{"full_name":"Moxey, David","last_name":"Moxey","first_name":"David"},{"full_name":"de Lózar, Alberto","last_name":"De Lózar","first_name":"Alberto"},{"last_name":"Avila","first_name":"Marc","full_name":"Avila, Marc"},{"full_name":"Barkley, Dwight","last_name":"Barkley","first_name":"Dwight"},{"full_name":"Björn Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"}],"date_updated":"2021-01-12T06:59:47Z","publisher":"American Association for the Advancement of Science","month":"07","intvolume":"       333","date_published":"2011-07-08T00:00:00Z"},{"page":"193 - 204","publist_id":"4089","year":"2011","date_published":"2011-08-25T00:00:00Z","month":"08","intvolume":"       681","publisher":"Cambridge University Press","date_updated":"2021-01-12T06:59:48Z","author":[{"last_name":"Samanta","first_name":"Devranjan","full_name":"Samanta, Devranjan"},{"last_name":"De Lózar","first_name":"Alberto","full_name":"de Lózar, Alberto"},{"last_name":"Hof","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Björn Hof"}],"title":"Experimental investigation of laminar turbulent intermittency in pipe flow","publication":"Journal of Fluid Mechanics","publication_status":"published","doi":"10.1017/jfm.2011.189","volume":681,"extern":1,"citation":{"apa":"Samanta, D., De Lózar, A., &#38; Hof, B. (2011). Experimental investigation of laminar turbulent intermittency in pipe flow. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2011.189\">https://doi.org/10.1017/jfm.2011.189</a>","mla":"Samanta, Devranjan, et al. “Experimental Investigation of Laminar Turbulent Intermittency in Pipe Flow.” <i>Journal of Fluid Mechanics</i>, vol. 681, Cambridge University Press, 2011, pp. 193–204, doi:<a href=\"https://doi.org/10.1017/jfm.2011.189\">10.1017/jfm.2011.189</a>.","ama":"Samanta D, De Lózar A, Hof B. Experimental investigation of laminar turbulent intermittency in pipe flow. <i>Journal of Fluid Mechanics</i>. 2011;681:193-204. doi:<a href=\"https://doi.org/10.1017/jfm.2011.189\">10.1017/jfm.2011.189</a>","ista":"Samanta D, De Lózar A, Hof B. 2011. Experimental investigation of laminar turbulent intermittency in pipe flow. Journal of Fluid Mechanics. 681, 193–204.","short":"D. Samanta, A. De Lózar, B. Hof, Journal of Fluid Mechanics 681 (2011) 193–204.","ieee":"D. Samanta, A. De Lózar, and B. Hof, “Experimental investigation of laminar turbulent intermittency in pipe flow,” <i>Journal of Fluid Mechanics</i>, vol. 681. Cambridge University Press, pp. 193–204, 2011.","chicago":"Samanta, Devranjan, Alberto De Lózar, and Björn Hof. “Experimental Investigation of Laminar Turbulent Intermittency in Pipe Flow.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2011. <a href=\"https://doi.org/10.1017/jfm.2011.189\">https://doi.org/10.1017/jfm.2011.189</a>."},"abstract":[{"text":"In shear flows, turbulence first occurs in the form of localized structures (puffs/spots) surrounded by laminar fluid. We here investigate such spatially intermittent flows in a pipe experiment showing that turbulent puffs have a well-defined interaction distance, which sets their minimum spacing as well as the maximum observable turbulent fraction. Two methodologies are employed. Starting from a laminar flow, puffs are first created by locally injecting a jet of fluid through the pipe wall. When the perturbation is applied periodically at low frequencies, as expected, a regular sequence of puffs is observed where the puff spacing is given by the ratio of the mean flow speed to the perturbation frequency. At large frequencies however puffs are found to interact and annihilate each other. Varying the perturbation frequency, an interaction distance is determined which sets the highest possible turbulence fraction. This enables us to establish an upper bound for the friction factor in the transitional regime, which provides a well-defined link between the Blasius and the Hagen-Poiseuille friction laws. In the second set of experiments, the Reynolds number is reduced suddenly from fully turbulent to the intermittent regime. The resulting flow reorganizes itself to a sequence of constant size puffs which, unlike in Couette and Taylor–Couette flow are randomly spaced. The minimum distance between the turbulent patches is identical to the puff interaction length. The puff interaction length is found to be in agreement with the wavelength of regular stripe and spiral patterns in plane Couette and Taylor–Couette flow.","lang":"eng"}],"type":"journal_article","date_created":"2018-12-11T11:59:40Z","_id":"2800","day":"25","quality_controlled":0,"status":"public"},{"date_published":"2011-09-01T00:00:00Z","alternative_title":["Journal of Physics: Conference Series"],"month":"09","intvolume":"       318","publisher":"IOP Publishing Ltd.","date_updated":"2019-04-26T07:22:20Z","author":[{"full_name":"Holzner, Markus","first_name":"Markus","last_name":"Holzner"},{"last_name":"Avila","first_name":"Marc","full_name":"Avila, Marc"},{"first_name":"Alberto","last_name":"De Lózar","full_name":"de Lózar, Alberto"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Björn Hof"}],"title":"A Lagrangian approach to the interface velocity of turbulent puffs in pipe flow","issue":"5","publist_id":"4088","conference":{"name":"ETC13: European Turbulence Conference"},"year":"2011","volume":318,"citation":{"apa":"Holzner, M., Avila, M., De Lózar, A., &#38; Hof, B. (2011). A Lagrangian approach to the interface velocity of turbulent puffs in pipe flow (Vol. 318). Presented at the ETC13: European Turbulence Conference, IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1742-6596/318/5/052031\">https://doi.org/10.1088/1742-6596/318/5/052031</a>","mla":"Holzner, Markus, et al. <i>A Lagrangian Approach to the Interface Velocity of Turbulent Puffs in Pipe Flow</i>. Vol. 318, no. 5, IOP Publishing Ltd., 2011, doi:<a href=\"https://doi.org/10.1088/1742-6596/318/5/052031\">10.1088/1742-6596/318/5/052031</a>.","ista":"Holzner M, Avila M, De Lózar A, Hof B. 2011. A Lagrangian approach to the interface velocity of turbulent puffs in pipe flow. ETC13: European Turbulence Conference, Journal of Physics: Conference Series, vol. 318.","short":"M. Holzner, M. Avila, A. De Lózar, B. Hof, in:, IOP Publishing Ltd., 2011.","ieee":"M. Holzner, M. Avila, A. De Lózar, and B. Hof, “A Lagrangian approach to the interface velocity of turbulent puffs in pipe flow,” presented at the ETC13: European Turbulence Conference, 2011, vol. 318, no. 5.","ama":"Holzner M, Avila M, De Lózar A, Hof B. A Lagrangian approach to the interface velocity of turbulent puffs in pipe flow. In: Vol 318. IOP Publishing Ltd.; 2011. doi:<a href=\"https://doi.org/10.1088/1742-6596/318/5/052031\">10.1088/1742-6596/318/5/052031</a>","chicago":"Holzner, Markus, Marc Avila, Alberto De Lózar, and Björn Hof. “A Lagrangian Approach to the Interface Velocity of Turbulent Puffs in Pipe Flow,” Vol. 318. IOP Publishing Ltd., 2011. <a href=\"https://doi.org/10.1088/1742-6596/318/5/052031\">https://doi.org/10.1088/1742-6596/318/5/052031</a>."},"extern":1,"abstract":[{"lang":"eng","text":"Turbulent puffs in pipe flow are characterized by a sharp laminar-turbulent interface at the trailing edge and a more diffused leading interface. It is known that these laminar-turbulent interfaces propagate at a speed that is approximately equal to the flow rate. Our results from direct numerical simulation show that, locally, the interface velocity relative to the fluid (i) counteracts the advection due to the laminar velocity profile so that the puff can preserve its characteristic overall shape, (ii) is very small in magnitude, but involves a large interface area so that the global propagation velocity relative to the mean flow can be large and (iii) is determined by both inertial and viscous effects. The analysis provides some new insights into the mechanisms that sustain or expand localized turbulence and might be relevant for the design of new control strategies."}],"type":"conference","_id":"2801","date_created":"2018-12-11T11:59:40Z","status":"public","quality_controlled":0,"day":"01","publication_status":"published","doi":"10.1088/1742-6596/318/5/052031"},{"year":"2011","page":"10 - 16","publist_id":"3894","date_updated":"2021-01-12T07:00:23Z","title":"Sending mixed messages: Auxin-cytokinin crosstalk in roots","author":[{"last_name":"Bishopp","first_name":"Anthony","full_name":"Bishopp, Anthony"},{"full_name":"Eva Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739","last_name":"Benková"},{"full_name":"Helariutta, Ykä","first_name":"Ykä","last_name":"Helariutta"}],"issue":"1","date_published":"2011-02-01T00:00:00Z","intvolume":"        14","month":"02","publisher":"Elsevier","publication":"Current Opinion in Plant Biology","doi":"10.1016/j.pbi.2010.08.014","publication_status":"published","date_created":"2018-12-11T12:00:03Z","_id":"2871","day":"01","quality_controlled":0,"status":"public","volume":14,"citation":{"mla":"Bishopp, Anthony, et al. “Sending Mixed Messages: Auxin-Cytokinin Crosstalk in Roots.” <i>Current Opinion in Plant Biology</i>, vol. 14, no. 1, Elsevier, 2011, pp. 10–16, doi:<a href=\"https://doi.org/10.1016/j.pbi.2010.08.014\">10.1016/j.pbi.2010.08.014</a>.","apa":"Bishopp, A., Benková, E., &#38; Helariutta, Y. (2011). Sending mixed messages: Auxin-cytokinin crosstalk in roots. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2010.08.014\">https://doi.org/10.1016/j.pbi.2010.08.014</a>","chicago":"Bishopp, Anthony, Eva Benková, and Ykä Helariutta. “Sending Mixed Messages: Auxin-Cytokinin Crosstalk in Roots.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.pbi.2010.08.014\">https://doi.org/10.1016/j.pbi.2010.08.014</a>.","short":"A. Bishopp, E. Benková, Y. Helariutta, Current Opinion in Plant Biology 14 (2011) 10–16.","ieee":"A. Bishopp, E. Benková, and Y. Helariutta, “Sending mixed messages: Auxin-cytokinin crosstalk in roots,” <i>Current Opinion in Plant Biology</i>, vol. 14, no. 1. Elsevier, pp. 10–16, 2011.","ista":"Bishopp A, Benková E, Helariutta Y. 2011. Sending mixed messages: Auxin-cytokinin crosstalk in roots. Current Opinion in Plant Biology. 14(1), 10–16.","ama":"Bishopp A, Benková E, Helariutta Y. Sending mixed messages: Auxin-cytokinin crosstalk in roots. <i>Current Opinion in Plant Biology</i>. 2011;14(1):10-16. doi:<a href=\"https://doi.org/10.1016/j.pbi.2010.08.014\">10.1016/j.pbi.2010.08.014</a>"},"extern":1,"abstract":[{"lang":"eng","text":"Despite their relatively simple appearance, roots are incredibly complex organs that are highly adapted to differing environments. Many aspects of root development are co-ordinated by subtle spatial differences in the concentrations of the phytohormones auxin and cytokinin. Events from the formation of a root during embryogenesis to the determination of the network of lateral roots are controlled by interactions between these hormones. Recently, interactions have been defined where auxin signaling promotes the expression of cytokinin signaling inhibitors, cytokinin signaling promotes the expression of auxin signaling inhibitors and finally where cytokinin signaling regulates the complex network of auxin transport proteins to position zones of high auxin signaling. We are witnessing a period of discovery in which we are beginning to understand how these hormonal pathways communicate to regulate root formation."}],"type":"journal_article"},{"publication":"Plant Journal","publication_status":"published","doi":"10.1111/j.1365-313X.2011.04621.x","abstract":[{"text":"The apical hook develops in the upper part of the hypocotyl when seeds buried in the soil germinate, and serves to protect cotyledons and the shoot apical meristem from possible damage caused by pushing through the soil. The curvature is formed through differential cell growth that occurs at the two opposite sides of the hypocotyl, and it is established by a gradient of auxin activity and refined by the coordinated action of auxin and ethylene. Here we show that gibberellins (GAs) promote hook development through the transcriptional regulation of several genes of the ethylene and auxin pathways in Arabidopsis. The level of GA activity determines the speed of hook formation and the extent of the curvature during the formation phase independently of ethylene, probably by modulating auxin transport and response through HLS1, PIN3, and PIN7. Moreover, GAs cooperate with ethylene in preventing hook opening, in part through the induction of ethylene production mediated by ACS5/ETO2 and ACS8.","lang":"eng"}],"type":"journal_article","volume":67,"citation":{"mla":"Gallego Bartolomé, Javier, et al. “Hierarchy of Hormone Action Controlling Apical Hook Development in Arabidopsis.” <i>Plant Journal</i>, vol. 67, no. 4, Wiley-Blackwell, 2011, pp. 622–34, doi:<a href=\"https://doi.org/10.1111/j.1365-313X.2011.04621.x\">10.1111/j.1365-313X.2011.04621.x</a>.","apa":"Gallego Bartolomé, J., Arana, M., Vandenbussche, F., Žádníková, P., Minguet, E., Guardiola, V., … Blázquez, M. (2011). Hierarchy of hormone action controlling apical hook development in Arabidopsis. <i>Plant Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1365-313X.2011.04621.x\">https://doi.org/10.1111/j.1365-313X.2011.04621.x</a>","chicago":"Gallego Bartolomé, Javier, María Arana, Filip Vandenbussche, Petra Žádníková, Eugenio Minguet, Vicente Guardiola, Dominique Van Der Straeten, Eva Benková, David Alabadí, and Miguel Blázquez. “Hierarchy of Hormone Action Controlling Apical Hook Development in Arabidopsis.” <i>Plant Journal</i>. Wiley-Blackwell, 2011. <a href=\"https://doi.org/10.1111/j.1365-313X.2011.04621.x\">https://doi.org/10.1111/j.1365-313X.2011.04621.x</a>.","ama":"Gallego Bartolomé J, Arana M, Vandenbussche F, et al. Hierarchy of hormone action controlling apical hook development in Arabidopsis. <i>Plant Journal</i>. 2011;67(4):622-634. doi:<a href=\"https://doi.org/10.1111/j.1365-313X.2011.04621.x\">10.1111/j.1365-313X.2011.04621.x</a>","ieee":"J. Gallego Bartolomé <i>et al.</i>, “Hierarchy of hormone action controlling apical hook development in Arabidopsis,” <i>Plant Journal</i>, vol. 67, no. 4. Wiley-Blackwell, pp. 622–634, 2011.","ista":"Gallego Bartolomé J, Arana M, Vandenbussche F, Žádníková P, Minguet E, Guardiola V, Van Der Straeten D, Benková E, Alabadí D, Blázquez M. 2011. Hierarchy of hormone action controlling apical hook development in Arabidopsis. Plant Journal. 67(4), 622–634.","short":"J. Gallego Bartolomé, M. Arana, F. Vandenbussche, P. Žádníková, E. Minguet, V. Guardiola, D. Van Der Straeten, E. Benková, D. Alabadí, M. Blázquez, Plant Journal 67 (2011) 622–634."},"extern":1,"day":"01","status":"public","quality_controlled":0,"_id":"2874","date_created":"2018-12-11T12:00:04Z","publist_id":"3891","page":"622 - 634","year":"2011","publisher":"Wiley-Blackwell","date_published":"2011-08-01T00:00:00Z","month":"08","intvolume":"        67","title":"Hierarchy of hormone action controlling apical hook development in Arabidopsis","author":[{"full_name":"Gallego-Bartolomé, Javier","last_name":"Gallego Bartolomé","first_name":"Javier"},{"full_name":"Arana, María V","first_name":"María","last_name":"Arana"},{"first_name":"Filip","last_name":"Vandenbussche","full_name":"Vandenbussche, Filip"},{"full_name":"Žádníková, Petra","first_name":"Petra","last_name":"Žádníková"},{"full_name":"Minguet, Eugenio G","first_name":"Eugenio","last_name":"Minguet"},{"full_name":"Guardiola, Vicente","first_name":"Vicente","last_name":"Guardiola"},{"full_name":"Van Der Straeten, Dominique","last_name":"Van Der Straeten","first_name":"Dominique"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Eva Benková"},{"full_name":"Alabadí, David","last_name":"Alabadí","first_name":"David"},{"last_name":"Blázquez","first_name":"Miguel","full_name":"Blázquez, Miguel A"}],"issue":"4","date_updated":"2021-01-12T07:00:24Z"},{"quality_controlled":0,"status":"public","day":"01","_id":"2897","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T12:00:13Z","type":"journal_article","volume":6,"extern":1,"citation":{"short":"T. Paixao, R. Azevedo, PLoS Computational Biology 6 (2011).","ista":"Paixao T, Azevedo R. 2011. Redundancy and the Evolution of Cis Regulatory Element Multiplicity. PLoS Computational Biology. 6(7).","ieee":"T. Paixao and R. Azevedo, “Redundancy and the Evolution of Cis Regulatory Element Multiplicity,” <i>PLoS Computational Biology</i>, vol. 6, no. 7. Public Library of Science, 2011.","ama":"Paixao T, Azevedo R. Redundancy and the Evolution of Cis Regulatory Element Multiplicity. <i>PLoS Computational Biology</i>. 2011;6(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1000848\">10.1371/journal.pcbi.1000848</a>","chicago":"Paixao, Tiago, and Ricardo Azevedo. “Redundancy and the Evolution of Cis Regulatory Element Multiplicity.” <i>PLoS Computational Biology</i>. Public Library of Science, 2011. <a href=\"https://doi.org/10.1371/journal.pcbi.1000848\">https://doi.org/10.1371/journal.pcbi.1000848</a>.","apa":"Paixao, T., &#38; Azevedo, R. (2011). Redundancy and the Evolution of Cis Regulatory Element Multiplicity. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1000848\">https://doi.org/10.1371/journal.pcbi.1000848</a>","mla":"Paixao, Tiago, and Ricardo Azevedo. “Redundancy and the Evolution of Cis Regulatory Element Multiplicity.” <i>PLoS Computational Biology</i>, vol. 6, no. 7, Public Library of Science, 2011, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1000848\">10.1371/journal.pcbi.1000848</a>."},"publication":"PLoS Computational Biology","doi":"10.1371/journal.pcbi.1000848","publication_status":"published","title":"Redundancy and the Evolution of Cis Regulatory Element Multiplicity","author":[{"full_name":"Tiago Paixao","orcid":"0000-0003-2361-3953","last_name":"Paixao","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Azevedo","first_name":"Ricardo","full_name":"Azevedo, Ricardo B"}],"issue":"7","date_updated":"2021-01-12T07:00:33Z","publisher":"Public Library of Science","acknowledgement":"TFs regulate gene expression by binding to specific sequences in the promoter regions of their target genes. Promoters often contain multiple copies of the same TF binding sites. How does this multiplicity evolve? One possibility is that individuals with multiple, redundant binding sites have higher fitness. However, nonadaptive processes are also likely to be important. Here, we develop a mathematical model of the evolution of TF binding sites to help us disentangle how different evolutionary mechanisms contribute to the evolution of binding site redundancy and multiplicity. We show that recombination is expected to promote the evolution of multiple binding sites. This prediction is corroborated by genome-wide data from yeast. Another important factor in the evolution of multiplicity predicted in our analysis is TF promiscuity, that is, the ability of a TF to bind to multiple sequences. In addition, our analysis indicated that direct selection can have large effects on the evolution of redundancy and multiplicity. Data from yeast identified selection for changes in expression level as a candidate mechanism for the evolution of multiple binding sites. We conclude that, although selection may play a major role in the evolution of multiplicity in regulatory regions, nonadaptive forces can also lead to high levels of multiplicity.","date_published":"2011-01-01T00:00:00Z","month":"01","intvolume":"         6","year":"2011","publist_id":"3861"},{"date_updated":"2021-01-12T07:00:33Z","author":[{"full_name":"Tiago Paixao","last_name":"Paixao","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago"},{"first_name":"Sujal","last_name":"Phadke","full_name":"Phadke, Sujal S"},{"full_name":"Azevedo, Ricardo B","first_name":"Ricardo","last_name":"Azevedo"},{"full_name":"Zufall, Rebecca A","last_name":"Zufall","first_name":"Rebecca"}],"title":"Sex ratio evolution under probabilistic sex determination","issue":"7","date_published":"2011-03-01T00:00:00Z","intvolume":"        65","month":"03","publisher":"Wiley-Blackwell","year":"2011","page":"2050 - 2060","publist_id":"3860","_id":"2898","date_created":"2018-12-11T12:00:13Z","day":"01","status":"public","quality_controlled":0,"volume":65,"extern":1,"citation":{"mla":"Paixao, Tiago, et al. “Sex Ratio Evolution under Probabilistic Sex Determination.” <i>Evolution; International Journal of Organic Evolution</i>, vol. 65, no. 7, Wiley-Blackwell, 2011, pp. 2050–60, doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2011.01266.x\">10.1111/j.1558-5646.2011.01266.x</a>.","apa":"Paixao, T., Phadke, S., Azevedo, R., &#38; Zufall, R. (2011). Sex ratio evolution under probabilistic sex determination. <i>Evolution; International Journal of Organic Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1558-5646.2011.01266.x\">https://doi.org/10.1111/j.1558-5646.2011.01266.x</a>","chicago":"Paixao, Tiago, Sujal Phadke, Ricardo Azevedo, and Rebecca Zufall. “Sex Ratio Evolution under Probabilistic Sex Determination.” <i>Evolution; International Journal of Organic Evolution</i>. Wiley-Blackwell, 2011. <a href=\"https://doi.org/10.1111/j.1558-5646.2011.01266.x\">https://doi.org/10.1111/j.1558-5646.2011.01266.x</a>.","ista":"Paixao T, Phadke S, Azevedo R, Zufall R. 2011. Sex ratio evolution under probabilistic sex determination. Evolution; International Journal of Organic Evolution. 65(7), 2050–2060.","ieee":"T. Paixao, S. Phadke, R. Azevedo, and R. Zufall, “Sex ratio evolution under probabilistic sex determination,” <i>Evolution; International Journal of Organic Evolution</i>, vol. 65, no. 7. Wiley-Blackwell, pp. 2050–2060, 2011.","short":"T. Paixao, S. Phadke, R. Azevedo, R. Zufall, Evolution; International Journal of Organic Evolution 65 (2011) 2050–2060.","ama":"Paixao T, Phadke S, Azevedo R, Zufall R. Sex ratio evolution under probabilistic sex determination. <i>Evolution; International Journal of Organic Evolution</i>. 2011;65(7):2050-2060. doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2011.01266.x\">10.1111/j.1558-5646.2011.01266.x</a>"},"abstract":[{"text":"Sex allocation theory has been remarkably successful at explaining the prevalence of even sex ratios in natural populations and at identifying specific conditions that can result in biased sex ratios. Much of this theory focuses on parental sex determination (SD) strategies. Here, we consider instead the evolutionary causes and consequences of mixed offspring SD strategies, in which the genotype of an individual determines not its sex, but the probability of developing one of multiple sexes. We find that alleles specifying mixed offspring SD strategies can generally outcompete alleles that specify pure strategies, but generate constraints that may prevent a population from reaching an even sex ratio. We use our model to analyze sex ratios in natural populations of Tetrahymena thermophila, a ciliate with seven sexes determined by mixed SD alleles. We show that probabilistic SD is sufficient to account for the occurrence of skewed sex ratios in natural populations of T. thermophila, provided that their effective population sizes are small. Our results highlight the importance of genetic drift in sex ratio evolution and suggest that mixed offspring SD strategies should be more common than currently thought.","lang":"eng"}],"type":"journal_article","publication":"Evolution; International Journal of Organic Evolution","publication_status":"published","doi":"10.1111/j.1558-5646.2011.01266.x"},{"year":"2011","publist_id":"3815","author":[{"last_name":"Vicente","first_name":"Sara","full_name":"Vicente, Sara"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov"},{"full_name":"Rother, Carsten","first_name":"Carsten","last_name":"Rother"}],"title":"Graph-cut Based Image Segmentation with Connectivity Priors","date_updated":"2021-01-12T07:00:43Z","publisher":"Massachusetts Institute of Technology Press","date_published":"2011-01-01T00:00:00Z","month":"01","publication":"Markov Random Fields for Vision and Image Processing","publication_status":"published","quality_controlled":0,"day":"01","status":"public","_id":"2922","date_created":"2018-12-11T12:00:21Z","editor":[{"first_name":"Andrew","last_name":"Blake","full_name":"Blake, Andrew"},{"first_name":"Pushmeet","last_name":"Kohli","full_name":"Kohli, Pushmeet"},{"full_name":"Rother, Carsten","first_name":"Carsten","last_name":"Rother"}],"type":"book_chapter","citation":{"apa":"Vicente, S., Kolmogorov, V., &#38; Rother, C. (2011). Graph-cut Based Image Segmentation with Connectivity Priors. In A. Blake, P. Kohli, &#38; C. Rother (Eds.), <i>Markov Random Fields for Vision and Image Processing</i>. Massachusetts Institute of Technology Press.","mla":"Vicente, Sara, et al. “Graph-Cut Based Image Segmentation with Connectivity Priors.” <i>Markov Random Fields for Vision and Image Processing</i>, edited by Andrew Blake et al., Massachusetts Institute of Technology Press, 2011.","ieee":"S. Vicente, V. Kolmogorov, and C. Rother, “Graph-cut Based Image Segmentation with Connectivity Priors,” in <i>Markov Random Fields for Vision and Image Processing</i>, A. Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology Press, 2011.","ista":"Vicente S, Kolmogorov V, Rother C. 2011.Graph-cut Based Image Segmentation with Connectivity Priors. In: Markov Random Fields for Vision and Image Processing. .","short":"S. Vicente, V. Kolmogorov, C. Rother, in:, A. Blake, P. Kohli, C. Rother (Eds.), Markov Random Fields for Vision and Image Processing, Massachusetts Institute of Technology Press, 2011.","ama":"Vicente S, Kolmogorov V, Rother C. Graph-cut Based Image Segmentation with Connectivity Priors. In: Blake A, Kohli P, Rother C, eds. <i>Markov Random Fields for Vision and Image Processing</i>. Massachusetts Institute of Technology Press; 2011.","chicago":"Vicente, Sara, Vladimir Kolmogorov, and Carsten Rother. “Graph-Cut Based Image Segmentation with Connectivity Priors.” In <i>Markov Random Fields for Vision and Image Processing</i>, edited by Andrew Blake, Pushmeet Kohli, and Carsten Rother. Massachusetts Institute of Technology Press, 2011."},"extern":1},{"author":[{"full_name":"Kumar, M Pawan","first_name":"M Pawan","last_name":"Kumar"},{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov"},{"full_name":"Torr, Philip H","first_name":"Philip","last_name":"Torr"}],"title":"Analyzing Convex Relaxations for MAP Estimation","date_updated":"2021-01-12T07:00:43Z","publisher":"Massachusetts Institute of Technology Press","date_published":"2011-01-01T00:00:00Z","month":"01","year":"2011","publist_id":"3814","quality_controlled":0,"status":"public","day":"01","date_created":"2018-12-11T12:00:21Z","_id":"2923","editor":[{"full_name":"Blake, Andrew","first_name":"Andrew","last_name":"Blake"},{"full_name":"Kohli, Pushmeet","last_name":"Kohli","first_name":"Pushmeet"},{"first_name":"Carsten","last_name":"Rother","full_name":"Rother, Carsten"}],"type":"book_chapter","citation":{"apa":"Kumar, M. P., Kolmogorov, V., &#38; Torr, P. (2011). Analyzing Convex Relaxations for MAP Estimation. In A. Blake, P. Kohli, &#38; C. Rother (Eds.), <i>Markov Random Fields for Vision and Image Processing</i>. Massachusetts Institute of Technology Press.","mla":"Kumar, M. Pawan, et al. “Analyzing Convex Relaxations for MAP Estimation.” <i>Markov Random Fields for Vision and Image Processing</i>, edited by Andrew Blake et al., Massachusetts Institute of Technology Press, 2011.","ama":"Kumar MP, Kolmogorov V, Torr P. Analyzing Convex Relaxations for MAP Estimation. In: Blake A, Kohli P, Rother C, eds. <i>Markov Random Fields for Vision and Image Processing</i>. Massachusetts Institute of Technology Press; 2011.","ieee":"M. P. Kumar, V. Kolmogorov, and P. Torr, “Analyzing Convex Relaxations for MAP Estimation,” in <i>Markov Random Fields for Vision and Image Processing</i>, A. Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology Press, 2011.","short":"M.P. Kumar, V. Kolmogorov, P. Torr, in:, A. Blake, P. Kohli, C. Rother (Eds.), Markov Random Fields for Vision and Image Processing, Massachusetts Institute of Technology Press, 2011.","ista":"Kumar MP, Kolmogorov V, Torr P. 2011.Analyzing Convex Relaxations for MAP Estimation. In: Markov Random Fields for Vision and Image Processing. .","chicago":"Kumar, M Pawan, Vladimir Kolmogorov, and Philip Torr. “Analyzing Convex Relaxations for MAP Estimation.” In <i>Markov Random Fields for Vision and Image Processing</i>, edited by Andrew Blake, Pushmeet Kohli, and Carsten Rother. Massachusetts Institute of Technology Press, 2011."},"extern":1,"publication":"Markov Random Fields for Vision and Image Processing","publication_status":"published"},{"title":"Bilayer Segmentation of Video","author":[{"full_name":"Criminisi, Antonio","first_name":"Antonio","last_name":"Criminisi"},{"full_name":"Cross, Geoffrey","last_name":"Cross","first_name":"Geoffrey"},{"full_name":"Blake, Andrew","last_name":"Blake","first_name":"Andrew"},{"full_name":"Vladimir Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov"}],"date_updated":"2021-01-12T07:00:43Z","publisher":"Massachusetts Institute of Technology Press","month":"01","date_published":"2011-01-01T00:00:00Z","year":"2011","publist_id":"3813","status":"public","day":"01","quality_controlled":0,"editor":[{"last_name":"Blake","first_name":"Andrew","full_name":"Blake, Andrew"},{"full_name":"Kohli, Pushmeet","first_name":"Pushmeet","last_name":"Kohli"},{"full_name":"Rother, Carsten","first_name":"Carsten","last_name":"Rother"}],"date_created":"2018-12-11T12:00:22Z","_id":"2924","type":"book_chapter","citation":{"apa":"Criminisi, A., Cross, G., Blake, A., &#38; Kolmogorov, V. (2011). Bilayer Segmentation of Video. In A. Blake, P. Kohli, &#38; C. Rother (Eds.), <i>Markov Random Fields for Vision and Image Processing</i>. Massachusetts Institute of Technology Press.","mla":"Criminisi, Antonio, et al. “Bilayer Segmentation of Video.” <i>Markov Random Fields for Vision and Image Processing</i>, edited by Andrew Blake et al., Massachusetts Institute of Technology Press, 2011.","ieee":"A. Criminisi, G. Cross, A. Blake, and V. Kolmogorov, “Bilayer Segmentation of Video,” in <i>Markov Random Fields for Vision and Image Processing</i>, A. Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology Press, 2011.","ista":"Criminisi A, Cross G, Blake A, Kolmogorov V. 2011.Bilayer Segmentation of Video. In: Markov Random Fields for Vision and Image Processing. .","short":"A. Criminisi, G. Cross, A. Blake, V. Kolmogorov, in:, A. Blake, P. Kohli, C. Rother (Eds.), Markov Random Fields for Vision and Image Processing, Massachusetts Institute of Technology Press, 2011.","ama":"Criminisi A, Cross G, Blake A, Kolmogorov V. Bilayer Segmentation of Video. In: Blake A, Kohli P, Rother C, eds. <i>Markov Random Fields for Vision and Image Processing</i>. Massachusetts Institute of Technology Press; 2011.","chicago":"Criminisi, Antonio, Geoffrey Cross, Andrew Blake, and Vladimir Kolmogorov. “Bilayer Segmentation of Video.” In <i>Markov Random Fields for Vision and Image Processing</i>, edited by Andrew Blake, Pushmeet Kohli, and Carsten Rother. Massachusetts Institute of Technology Press, 2011."},"extern":1,"publication_status":"published","publication":"Markov Random Fields for Vision and Image Processing"},{"publication_status":"published","publication":"Markov Random Fields for Vision and Image Processing","citation":{"chicago":"Rother, Carsten, Vladimir Kolmogorov, Yuri Boykov, and Andrew Blake. “Interactive Foreground Extraction Using Graph Cut.” In <i>Markov Random Fields for Vision and Image Processing</i>, edited by Andrew Blake, Pushmeet Kohli, and Carsten Rother. Massachusetts Institute of Technology Press, 2011.","short":"C. Rother, V. Kolmogorov, Y. Boykov, A. Blake, in:, A. Blake, P. Kohli, C. Rother (Eds.), Markov Random Fields for Vision and Image Processing, Massachusetts Institute of Technology Press, 2011.","ista":"Rother C, Kolmogorov V, Boykov Y, Blake A. 2011.Interactive Foreground Extraction using graph cut. In: Markov Random Fields for Vision and Image Processing. .","ieee":"C. Rother, V. Kolmogorov, Y. Boykov, and A. Blake, “Interactive Foreground Extraction using graph cut,” in <i>Markov Random Fields for Vision and Image Processing</i>, A. Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology Press, 2011.","ama":"Rother C, Kolmogorov V, Boykov Y, Blake A. Interactive Foreground Extraction using graph cut. In: Blake A, Kohli P, Rother C, eds. <i>Markov Random Fields for Vision and Image Processing</i>. Massachusetts Institute of Technology Press; 2011.","mla":"Rother, Carsten, et al. “Interactive Foreground Extraction Using Graph Cut.” <i>Markov Random Fields for Vision and Image Processing</i>, edited by Andrew Blake et al., Massachusetts Institute of Technology Press, 2011.","apa":"Rother, C., Kolmogorov, V., Boykov, Y., &#38; Blake, A. (2011). Interactive Foreground Extraction using graph cut. In A. Blake, P. Kohli, &#38; C. Rother (Eds.), <i>Markov Random Fields for Vision and Image Processing</i>. Massachusetts Institute of Technology Press."},"extern":1,"type":"book_chapter","editor":[{"last_name":"Blake","first_name":"Andrew","full_name":"Blake, Andrew"},{"first_name":"Pushmeet","last_name":"Kohli","full_name":"Kohli, Pushmeet"},{"last_name":"Rother","first_name":"Carsten","full_name":"Rother, Carsten"}],"_id":"2925","date_created":"2018-12-11T12:00:22Z","status":"public","quality_controlled":0,"day":"01","publist_id":"3812","year":"2011","month":"01","date_published":"2011-01-01T00:00:00Z","publisher":"Massachusetts Institute of Technology Press","date_updated":"2021-01-12T07:00:44Z","author":[{"full_name":"Rother, Carsten","last_name":"Rother","first_name":"Carsten"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov"},{"full_name":"Boykov, Yuri","last_name":"Boykov","first_name":"Yuri"},{"full_name":"Blake, Andrew","last_name":"Blake","first_name":"Andrew"}],"title":"Interactive Foreground Extraction using graph cut"},{"publication_status":"published","publication":"Markov Random Fields for Vision and Image Processing","day":"22","status":"public","quality_controlled":0,"editor":[{"last_name":"Blake","first_name":"Andrew","full_name":"Blake, Andrew"},{"full_name":"Kohli, Pushmeet","first_name":"Pushmeet","last_name":"Kohli"},{"last_name":"Rother","first_name":"Carsten","full_name":"Rother, Carsten"}],"_id":"2935","date_created":"2018-12-11T12:00:26Z","type":"book_chapter","citation":{"ista":"Boykov Y, Kolmogorov V. 2011.Basic graph cut algorithms. In: Markov Random Fields for Vision and Image Processing. , 31–50.","ieee":"Y. Boykov and V. Kolmogorov, “Basic graph cut algorithms,” in <i>Markov Random Fields for Vision and Image Processing</i>, A. Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology Press, 2011, pp. 31–50.","short":"Y. Boykov, V. Kolmogorov, in:, A. Blake, P. Kohli, C. Rother (Eds.), Markov Random Fields for Vision and Image Processing, Massachusetts Institute of Technology Press, 2011, pp. 31–50.","ama":"Boykov Y, Kolmogorov V. Basic graph cut algorithms. In: Blake A, Kohli P, Rother C, eds. <i>Markov Random Fields for Vision and Image Processing</i>. Massachusetts Institute of Technology Press; 2011:31-50.","chicago":"Boykov, Yuri, and Vladimir Kolmogorov. “Basic Graph Cut Algorithms.” In <i>Markov Random Fields for Vision and Image Processing</i>, edited by Andrew Blake, Pushmeet Kohli, and Carsten Rother, 31–50. Massachusetts Institute of Technology Press, 2011.","apa":"Boykov, Y., &#38; Kolmogorov, V. (2011). Basic graph cut algorithms. In A. Blake, P. Kohli, &#38; C. Rother (Eds.), <i>Markov Random Fields for Vision and Image Processing</i> (pp. 31–50). Massachusetts Institute of Technology Press.","mla":"Boykov, Yuri, and Vladimir Kolmogorov. “Basic Graph Cut Algorithms.” <i>Markov Random Fields for Vision and Image Processing</i>, edited by Andrew Blake et al., Massachusetts Institute of Technology Press, 2011, pp. 31–50."},"extern":1,"year":"2011","publist_id":"3801","page":"31 - 50","title":"Basic graph cut algorithms","author":[{"full_name":"Boykov, Yuri","first_name":"Yuri","last_name":"Boykov"},{"full_name":"Vladimir Kolmogorov","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T07:39:53Z","publisher":"Massachusetts Institute of Technology Press","month":"07","date_published":"2011-07-22T00:00:00Z"},{"author":[{"last_name":"Fienberg","first_name":"Stephen","full_name":"Fienberg, Stephen E"},{"first_name":"Aleksandra","last_name":"Slavkovic","full_name":"Slavkovic, Aleksandra"},{"orcid":"0000-0002-7008-0216","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","full_name":"Caroline Uhler"}],"title":"Privacy Preserving GWAS Data Sharing","date_updated":"2021-01-12T07:40:05Z","publisher":"IEEE","month":"01","date_published":"2011-01-01T00:00:00Z","year":"2011","conference":{"name":"Proceedings of the 11th IEEE International Conference on Data Mining"},"publist_id":"3766","day":"01","status":"public","quality_controlled":0,"_id":"2960","date_created":"2018-12-11T12:00:34Z","type":"conference","abstract":[{"lang":"eng","text":"Traditional statistical methods for the confidentiality protection for statistical databases do not scale well to deal with GWAS (genome-wide association studies) databases and external information on them. The more recent concept of differential privacy, introduced by the cryptographic community, is an approach which provides a rigorous definition of privacy with meaningful privacy guarantees in the presence of arbitrary external information. Building on such notions, we propose new methods to release aggregate GWAS data without compromising an individual's privacy. We present methods for releasing differentially private minor allele frequencies, chi-square statistics and p-values. We compare these approaches on simulated data and on a GWAS study of canine hair length involving 685 dogs. We also propose a privacy-preserving method for finding genome-wide associations based on a differentially private approach to penalized logistic regression."}],"extern":1,"citation":{"mla":"Fienberg, Stephen, et al. <i>Privacy Preserving GWAS Data Sharing</i>. IEEE, 2011, doi:<a href=\"https://doi.org/10.1109/ICDMW.2011.140\">10.1109/ICDMW.2011.140</a>.","apa":"Fienberg, S., Slavkovic, A., &#38; Uhler, C. (2011). Privacy Preserving GWAS Data Sharing. Presented at the Proceedings of the 11th IEEE International Conference on Data Mining, IEEE. <a href=\"https://doi.org/10.1109/ICDMW.2011.140\">https://doi.org/10.1109/ICDMW.2011.140</a>","chicago":"Fienberg, Stephen, Aleksandra Slavkovic, and Caroline Uhler. “Privacy Preserving GWAS Data Sharing.” IEEE, 2011. <a href=\"https://doi.org/10.1109/ICDMW.2011.140\">https://doi.org/10.1109/ICDMW.2011.140</a>.","short":"S. Fienberg, A. Slavkovic, C. Uhler, in:, IEEE, 2011.","ieee":"S. Fienberg, A. Slavkovic, and C. Uhler, “Privacy Preserving GWAS Data Sharing,” presented at the Proceedings of the 11th IEEE International Conference on Data Mining, 2011.","ista":"Fienberg S, Slavkovic A, Uhler C. 2011. Privacy Preserving GWAS Data Sharing. Proceedings of the 11th IEEE International Conference on Data Mining.","ama":"Fienberg S, Slavkovic A, Uhler C. Privacy Preserving GWAS Data Sharing. In: IEEE; 2011. doi:<a href=\"https://doi.org/10.1109/ICDMW.2011.140\">10.1109/ICDMW.2011.140</a>"},"publication_status":"published","doi":"10.1109/ICDMW.2011.140"},{"publist_id":"3764","page":"36 - 53","year":"2011","acknowledgement":"Anna-Sapfo Malaspinas is supported by a Janggen-Poehn Fellowship. Caroline Uhler is supported by an International Fulbright Science and Technology Fellowship.","publisher":"Public Knowledge Project","intvolume":"         2","month":"01","date_published":"2011-01-01T00:00:00Z","issue":"1","title":"Detecting epistasis via Markov bases","oa":1,"author":[{"last_name":"Malaspinas","first_name":"Anna","full_name":"Malaspinas, Anna-Sapfo "},{"orcid":"0000-0002-7008-0216","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","full_name":"Caroline Uhler"}],"date_updated":"2021-01-12T07:40:05Z","publication_status":"published","doi":"http://dx.doi.org/10.18409/jas.v2i1.27","main_file_link":[{"url":"http://arxiv.org/abs/1006.4929","open_access":"1"}],"publication":"Journal of Algebraic Statistics","type":"journal_article","abstract":[{"text":"Rapid research progress in genotyping techniques have allowed large genome-wide association studies. Existing methods often focus on determining associations between single loci and a specic phenotype. However, a particular phenotype is usually the result of complex relationships between multiple loci and the environment. In this paper, we describe a two-stage method for detecting epistasis by combining the traditionally used single-locus search with a search for multiway interactions. Our method is based on an extended version of Fisher's exact test. To\nperform this test, a Markov chain is constructed on the space of multidimensional contingency tables using the elements of a Markov basis as moves. We test our method on simulated data and compare it to a two-stage logistic regression method and to a fully Bayesian method, showing that we are able to detect the interacting loci when other methods fail to do so. Finally, we apply our method to a genome-wide data set consisting of 685 dogs and identify epistasis associated with canine hair length for four pairs of single nucleotide polymorphisms (SNPs).","lang":"eng"}],"extern":1,"citation":{"mla":"Malaspinas, Anna, and Caroline Uhler. “Detecting Epistasis via Markov Bases.” <i>Journal of Algebraic Statistics</i>, vol. 2, no. 1, Public Knowledge Project, 2011, pp. 36–53, doi:<a href=\"http://dx.doi.org/10.18409/jas.v2i1.27\">http://dx.doi.org/10.18409/jas.v2i1.27</a>.","apa":"Malaspinas, A., &#38; Uhler, C. (2011). Detecting epistasis via Markov bases. <i>Journal of Algebraic Statistics</i>. Public Knowledge Project. <a href=\"http://dx.doi.org/10.18409/jas.v2i1.27\">http://dx.doi.org/10.18409/jas.v2i1.27</a>","chicago":"Malaspinas, Anna, and Caroline Uhler. “Detecting Epistasis via Markov Bases.” <i>Journal of Algebraic Statistics</i>. Public Knowledge Project, 2011. <a href=\"http://dx.doi.org/10.18409/jas.v2i1.27\">http://dx.doi.org/10.18409/jas.v2i1.27</a>.","ama":"Malaspinas A, Uhler C. Detecting epistasis via Markov bases. <i>Journal of Algebraic Statistics</i>. 2011;2(1):36-53. doi:<a href=\"http://dx.doi.org/10.18409/jas.v2i1.27\">http://dx.doi.org/10.18409/jas.v2i1.27</a>","short":"A. Malaspinas, C. Uhler, Journal of Algebraic Statistics 2 (2011) 36–53.","ieee":"A. Malaspinas and C. Uhler, “Detecting epistasis via Markov bases,” <i>Journal of Algebraic Statistics</i>, vol. 2, no. 1. Public Knowledge Project, pp. 36–53, 2011.","ista":"Malaspinas A, Uhler C. 2011. Detecting epistasis via Markov bases. Journal of Algebraic Statistics. 2(1), 36–53."},"volume":2,"status":"public","day":"01","quality_controlled":0,"date_created":"2018-12-11T12:00:34Z","_id":"2961"}]