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333 results on '"Bonev, Boyan"'

4. Innate immune memory after brain injury drives inflammatory cardiac dysfunction

Author

Simats, Alba, Zhang, Sijia, Messerer, Denise, Chong, Faye, Beşkardeş, Sude, Chivukula, Aparna Sharma, Cao, Jiayu, Besson-Girard, Simon, Montellano, Felipe A., Morbach, Caroline, Carofiglio, Olga, Ricci, Alessio, Roth, Stefan, Llovera, Gemma, Singh, Rashween, Chen, Yiming, Filser, Severin, Plesnila, Nikolaus, Braun, Christian, Spitzer, Hannah, Gokce, Ozgun, Dichgans, Martin, Heuschmann, Peter U., Hatakeyama, Kinta, Beltrán, Eduardo, Clauss, Sebastian, Bonev, Boyan, Schulz, Christian, and Liesz, Arthur

Published
2024
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5. Regulation of single-cell genome organization into TADs and chromatin nanodomains

Author

Szabo, Quentin, Donjon, Axelle, Jerković, Ivana, Papadopoulos, Giorgio L, Cheutin, Thierry, Bonev, Boyan, Nora, Elphège P, Bruneau, Benoit G, Bantignies, Frédéric, and Cavalli, Giacomo

Subjects
Human Genome, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Animals, Cell Differentiation, Cell Line, Chromatin, Chromosome Painting, Drosophila, Embryonic Stem Cells, In Situ Hybridization, Fluorescence, Male, Mice, Mice, Inbred C57BL, Molecular Conformation, Nanostructures, Nuclear Microscopy, Protein Domains, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

The genome folds into a hierarchy of three-dimensional structures within the nucleus. At the sub-megabase scale, chromosomes form topologically associating domains (TADs)1-4. However, how TADs fold in single cells is elusive. Here, we reveal TAD features inaccessible to cell population analysis by using super-resolution microscopy. TAD structures and physical insulation associated with their borders are variable between individual cells, yet chromatin intermingling is enriched within TADs compared to adjacent TADs in most cells. The spatial segregation of TADs is further exacerbated during cell differentiation. Favored interactions within TADs are regulated by cohesin and CTCF through distinct mechanisms: cohesin generates chromatin contacts and intermingling while CTCF prevents inter-TAD contacts. Furthermore, TADs are subdivided into discrete nanodomains, which persist in cells depleted of CTCF or cohesin, whereas disruption of nucleosome contacts alters their structural organization. Altogether, these results provide a physical basis for the folding of individual chromosomes at the nanoscale.

Published
2020

8. PASCAL Boundaries: A Class-Agnostic Semantic Boundary Dataset

Author

Premachandran, Vittal, Bonev, Boyan, and Yuille, Alan L.

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

In this paper, we address the boundary detection task motivated by the ambiguities in current definition of edge detection. To this end, we generate a large database consisting of more than 10k images (which is 20x bigger than existing edge detection databases) along with ground truth boundaries between 459 semantic classes including both foreground objects and different types of background, and call it the PASCAL Boundaries dataset, which will be released to the community. In addition, we propose a novel deep network-based multi-scale semantic boundary detector and name it Multi-scale Deep Semantic Boundary Detector (M-DSBD). We provide baselines using models that were trained on edge detection and show that they transfer reasonably to the task of boundary detection. Finally, we point to various important research problems that this dataset can be used for.

Published
2015

9. Ground-truth dataset and baseline evaluations for image base-detail separation algorithms

Author

Dong, Xuan, Bonev, Boyan, Li, Weixin, Qiu, Weichao, Chen, Xianjie, and Yuille, Alan

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Base-detail separation is a fundamental computer vision problem consisting of modeling a smooth base layer with the coarse structures, and a detail layer containing the texture-like structures. One of the challenges of estimating the base is to preserve sharp boundaries between objects or parts to avoid halo artifacts. Many methods have been proposed to address this problem, but there is no ground-truth dataset of real images for quantitative evaluation. We proposed a procedure to construct such a dataset, and provide two datasets: Pascal Base-Detail and Fashionista Base-Detail, containing 1000 and 250 images, respectively. Our assumption is that the base is piecewise smooth and we label the appearance of each piece by a polynomial model. The pieces are objects and parts of objects, obtained from human annotations. Finally, we proposed a way to evaluate methods with our base-detail ground-truth and we compared the performances of seven state-of-the-art algorithms., Comment: This paper has been withdrawn by the author due to some un-proper examples

Published
2015

10. Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila

Author

Ciabrelli, Filippo, Comoglio, Federico, Fellous, Simon, Bonev, Boyan, Ninova, Maria, Szabo, Quentin, Xuéreb, Anne, Klopp, Christophe, Aravin, Alexei, Paro, Renato, Bantignies, Frédéric, and Cavalli, Giacomo

Subjects
Biological Sciences, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Animals, Animals, Genetically Modified, Chromatin, Drosophila Proteins, Drosophila melanogaster, Epigenesis, Genetic, Gene Expression Regulation, Developmental, Histone-Lysine N-Methyltransferase, Histones, In Situ Hybridization, Fluorescence, Lysine, Male, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Transgenerational epigenetic inheritance (TEI) describes the transmission of alternative functional states through multiple generations in the presence of the same genomic DNA sequence. Very little is known about the principles and the molecular mechanisms governing this type of inheritance. Here, by transiently enhancing 3D chromatin interactions, we established stable and isogenic Drosophila epilines that carry alternative epialleles, as defined by differential levels of Polycomb-dependent trimethylation of histone H3 Lys27 (forming H3K27me3). After being established, epialleles can be dominantly transmitted to naive flies and can induce paramutation. Importantly, epilines can be reset to a naive state by disruption of chromatin interactions. Finally, we found that environmental changes modulate the expressivity of the epialleles, and we extended our paradigm to naturally occurring phenotypes. Our work sheds light on how nuclear organization and Polycomb group (PcG) proteins contribute to epigenetically inheritable phenotypic variability.

Published
2017

12. Statistical sentiment analysis performance in Opinum

Author

Bonev, Boyan, Ramírez-Sánchez, Gema, and Rojas, Sergio Ortiz

Subjects
Computer Science - Computation and Language
Abstract

The classification of opinion texts in positive and negative is becoming a subject of great interest in sentiment analysis. The existence of many labeled opinions motivates the use of statistical and machine-learning methods. First-order statistics have proven to be very limited in this field. The Opinum approach is based on the order of the words without using any syntactic and semantic information. It consists of building one probabilistic model for the positive and another one for the negative opinions. Then the test opinions are compared to both models and a decision and confidence measure are calculated. In order to reduce the complexity of the training corpus we first lemmatize the texts and we replace most named-entities with wildcards. Opinum presents an accuracy above 81% for Spanish opinions in the financial products domain. In this work we discuss which are the most important factors that have impact on the classification performance.

Published
2013

14. Innate immune memory after brain injury drives inflammatory cardiac dysfunction

Author

Simats, Alba, primary, Zhang, Sijia, additional, Messerer, Denise, additional, Cao, Jiayu, additional, Chong, Faye, additional, Besson-Girard, Simon, additional, Carofiglio, Olga, additional, Filser, Severin, additional, Plesnila, Nikolaus, additional, Braun, Christian, additional, Gokce, Ozgun, additional, Dichgans, Martin, additional, Hatakeyama, Kinta, additional, Bonev, Boyan, additional, Beltran, Eduardo, additional, Schulz, Christian, additional, and Liesz, Arthur, additional

Published
2023
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16. The role of microRNA-9 in vertebrate neural development

Author

Bonev, Boyan and Papalopulu, Athanasia

Subjects
570, oscillations, Neurogenesis, Development, microRNA, Hes1, heterogeneity
Abstract

During neural development proliferating cells in the ventricular zone undergo repeated self-renewal to maintain the progenitor pool or, alternatively exit the cell cycle and differentiate into neurons. This process is regulated by the coordination of cell intrinsic signals and regional and temporal specific external cues which determine the type and the amount of neurons generated. After a neural progenitor has committed to differentiation the process of balancing internal and external signals continues during maturation to guide the initiation, elongation and branching of the axon. One major remaining question is how biological regulation can be integrated with the developmental context to produce a specific outcome. Here, I show that microRNAs and particularly, microRNA-9 (miR-9) plays a very important role in vertebrate neural development; a role, which is highly dependent on the context. In X. tropicalis, miR-9 reveals regional specific progenitor heterogeneity - it is required for cell cycle exit and differentiation throughout the neural tube, but forebrain progenitors additionally, and uniquely, require miR-9 for their survival. I have shown that the major miR-9 target in this context is the hairy and enhancer of split gene hairy1. When miR-9 is absent, hairy1 domain expands and selectively activates different signaling pathways in the forebrain and the hindbrain, culminating in the regional specific differences we observed. In the mouse, the homologue of hairy1 - Hes1 expression is oscillatory which is essential for progenitor maintenance. I have shown that Hes1 is also a subject of miR-9 regulation, which, in this context, is necessary for maintaining the oscillations. Furthermore, miR-9 is also regulated by Hes1, which leads to opposite-phase oscillations of miR-9 primary transcripts, but step-wise accumulation of the mature miR-9 form due to its stability. I propose that miR-9 levels act as output to measure the number of Hes1 cycles and at certain critical threshold levels this leads to dampening of the oscillations and allows progenitors to differentiate. MiR-9 is also expressed in differentiated neurons in the forebrain, where its function is completely unknown. We have shown that in this context it promotes axon branching and inhibits axon growth through the microtubule-associated protein 1B (MAP1B). We have also provided evidence that brain-derived neurotrophic factor (BDNF) can modulate this process by regulating miR-9 levels in the axon. Overall, these findings contribute to our understanding of neural development and provide novel explanation of how to cell fate decisions are integrated with context-specific signals to generate a specific outcome.

Published
2012

17. Conformational analysis and interaction of the Staphylococcus aureus transmembrane peptidase AgrB with its AgrD propeptide substrate

Author

Bardelang, Philip, primary, Murray, Ewan J., additional, Blower, Isobel, additional, Zandomeneghi, Sara, additional, Goode, Alice, additional, Hussain, Rohanah, additional, Kumari, Divya, additional, Siligardi, Giuliano, additional, Inoue, Katsuaki, additional, Luckett, Jeni, additional, Doutch, James, additional, Emsley, Jonas, additional, Chan, Weng C., additional, Hill, Philip, additional, Williams, Paul, additional, and Bonev, Boyan B., additional

Published
2023
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20. Quantum vs Classical Ranking in Segment Grouping

Author

Escolano, Francisco, Bonev, Boyan, Hancock, Edwin R., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Fränti, Pasi, editor, Brown, Gavin, editor, Loog, Marco, editor, Escolano, Francisco, editor, and Pelillo, Marcello, editor

Published
2014
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21. A Fast and Simple Algorithm for Producing Candidate Regions

Author

Bonev, Boyan, Yuille, Alan L., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Fleet, David, editor, Pajdla, Tomas, editor, Schiele, Bernt, editor, and Tuytelaars, Tinne, editor

Published
2014
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23. TurboTensors for Entropic Image Comparison

Author

Escolano, Francisco, Hancock, Edwin R., Bonev, Boyan, Lozano, Miguel Angel, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Kropatsch, Walter G., editor, Artner, Nicole M., editor, Haxhimusa, Yll, editor, and Jiang, Xiaoyi, editor

Published
2013
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24. Heat Flow-Thermodynamic Depth Complexity in Directed Networks

Author

Escolano, Francisco, Bonev, Boyan, Hancock, Edwin R., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Gimel’farb, Georgy, editor, Hancock, Edwin, editor, Imiya, Atsushi, editor, Kuijper, Arjan, editor, Kudo, Mineichi, editor, Omachi, Shinichiro, editor, Windeatt, Terry, editor, and Yamada, Keiji, editor

Published
2012
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25. Information-Geometric Graph Indexing from Bags of Partial Node Coverages

Author

Escolano, Francisco, Bonev, Boyan, Lozano, Miguel A., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Jiang, Xiaoyi, editor, Ferrer, Miquel, editor, and Torsello, Andrea, editor

Published
2011
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26. High-Dimensional Spectral Feature Selection for 3D Object Recognition Based on Reeb Graphs

Author

Bonev, Boyan, Escolano, Francisco, Giorgi, Daniela, Biasotti, Silvia, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Hancock, Edwin R., editor, Wilson, Richard C., editor, Windeatt, Terry, editor, Ulusoy, Ilkay, editor, and Escolano, Francisco, editor

Published
2010
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27. Entropy-Based Variational Scheme for Fast Bayes Learning of Gaussian Mixtures

Author

Peñalver, Antonio, Escolano, Francisco, Bonev, Boyan, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Hancock, Edwin R., editor, Wilson, Richard C., editor, Windeatt, Terry, editor, Ulusoy, Ilkay, editor, and Escolano, Francisco, editor

Published
2010
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28. Constellations and the Unsupervised Learning of Graphs

Author

Bonev, Boyan, Escolano, Francisco, Lozano, Miguel A., Suau, Pablo, Cazorla, Miguel A., Aguilar, Wendy, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Escolano, Francisco, editor, and Vento, Mario, editor

Published
2007
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31. Self-training and Co-training Applied to Spanish Named Entity Recognition

Author

Kozareva, Zornitsa, Bonev, Boyan, Montoyo, Andres, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Carbonell, Jaime G., editor, Siekmann, Jörg, editor, Gelbukh, Alexander, editor, de Albornoz, Álvaro, editor, and Terashima-Marín, Hugo, editor

Published
2005
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44. Behaviour and interactions of proteins and peptides with and within membranes; from simple models to cellular membranes: general discussion

Author

Aguilar, Mibel, primary, Al Nahas, Kareem, additional, Barrera, Francisco, additional, Bassereau, Patricia, additional, Bastos, Margarida, additional, Beales, Paul, additional, Bechinger, Burkhard, additional, Bonev, Boyan, additional, Brand, Izabella, additional, Chattopadhyay, Amitabha, additional, DeGrado, William, additional, Fuchs, Patrick, additional, Garcia Saez, Ana J., additional, Hoogenboom, Bart, additional, Kapoor, Shobhna, additional, Milán Rodríguez, Paula, additional, Molloy, Justin, additional, O’Shea, Paul, additional, Pabst, Georg, additional, Pal, Sreetama, additional, Rice, Amy, additional, Roux, Aurelien, additional, Sanderson, John, additional, Seddon, John, additional, Tamm, Lukas K., additional, and Vijayakumar, Aishwarya, additional

Published
2021
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45. Theoretical and experimental studies of complex peptide–membrane systems: general discussion

Author

Aguilar, Mibel, primary, Al Nahas, Kareem, additional, Barrera, Francisco, additional, Bassereau, Patricia, additional, Bastos, Margarida, additional, Beales, Paul, additional, Bechinger, Burkhard, additional, Bonev, Boyan, additional, Brand, Izabella, additional, Chattopadhyay, Amitabha, additional, Clarke, Ronald J., additional, DeGrado, William, additional, Deplazes, Evelyne, additional, Garcia Saez, Ana J., additional, Hoogenboom, Bart, additional, Lund, Reidar, additional, Milán Rodríguez, Paula, additional, O’Shea, Paul, additional, Pabst, Georg, additional, Pal, Sreetama, additional, Roux, Aurélien, additional, Sanderson, John, additional, Semeraro, Enrico Federico, additional, Sengupta, Durba, additional, Siegel, David P., additional, van 't Hag, Leonie, additional, Vijayakumar, Aishwarya, additional, and Zoranić, Larisa, additional

Published
2021
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47. Peptide–membrane interactions and biotechnology; enabling next-generation synthetic biology: general discussion

Author

Aguilar, Mibel, primary, Bassereau, Patricia, additional, Bastos, Margarida, additional, Beales, Paul, additional, Bechinger, Burkhard, additional, Bonev, Boyan, additional, Brand, Izabella, additional, Chalouhi, Edward, additional, Clarke, Ronald J., additional, Deplazes, Evelyne, additional, Fraternali, Franca, additional, Fuchs, Patrick, additional, Hoogenboom, Bart, additional, Lund, Reidar, additional, Mahmoudi, Najet, additional, Milán Rodríguez, Paula, additional, O’Shea, Paul, additional, Pabst, Georg, additional, Pal, Sreetama, additional, Rice, Amy, additional, Sanderson, John, additional, Seddon, John, additional, Sengupta, Durba, additional, Siegel, David P., additional, Srivastava, Anand, additional, Utterström, Johanna, additional, Vácha, Robert, additional, van ’t Hag, Leonie, additional, Vijayakumar, Aishwarya, additional, and Zoranić, Larisa, additional

Published
2021
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