Search Results - "Lizana, Ludvig"

Modelling chromosome-wide target search by Hedström, Lucas, Lizana, Ludvig

“…Abstract The most common gene regulation mechanism is when a transcription factor (TF) protein binds to a regulatory sequence to increase or decrease RNA…”
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Mapping robust multiscale communities in chromosome contact networks by Holmgren, Anton, Bernenko, Dolores, Lizana, Ludvig

“…To better understand DNA’s 3D folding in cell nuclei, researchers developed chromosome capture methods such as Hi-C that measure the contact frequencies…”
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Mapping the semi-nested community structure of 3D chromosome contact networks by Bernenko, Dolores, Lee, Sang Hoon, Stenberg, Per, Lizana, Ludvig

“…Mammalian DNA folds into 3D structures that facilitate and regulate genetic processes such as transcription, DNA repair, and epigenetics. Several insights…”
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Fractal and Knot-Free Chromosomes Facilitate Nucleoplasmic Transport by Kim, Yeonghoon, Lizana, Ludvig, Jeon, Jae-Hyung

“…Chromosomes in the nucleus assemble into hierarchies of 3D domains that, during interphase, share essential features with a knot-free condensed polymer known…”
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A simple method to calculate first-passage time densities with arbitrary initial conditions by Nyberg, Markus, Ambjörnsson, Tobias, Lizana, Ludvig

“…Numerous applications all the way from biology and physics to economics depend on the density of first crossings over a boundary. Motivated by the lack of…”
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Highly interacting regions of the human genome are enriched with enhancers and bound by DNA repair proteins by Sobhy, Haitham, Kumar, Rajendra, Lewerentz, Jacob, Lizana, Ludvig, Stenberg, Per

“…In specific cases, chromatin clearly forms long-range loops that place distant regulatory elements in close proximity to transcription start sites, but we have…”
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Exploring 3D community inconsistency in human chromosome contact networks by Bernenko, Dolores, Lee, Sang Hoon, Lizana, Ludvig

“…Abstract Researchers have developed chromosome capture methods such as Hi-C to better understand DNA’s 3D folding in nuclei. The Hi-C method captures contact…”
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Severe slowing-down and universality of the dynamics in disordered interacting many-body systems: ageing and ultraslow diffusion by Sanders, Lloyd P, Lomholt, Michael A, Lizana, Ludvig, Fogelmark, Karl, Metzler, Ralf, Ambjörnsson, Tobias

“…Low-dimensional, many-body systems are often characterized by ultraslow dynamics. We study a labelled particle in a generic system of identical particles with…”
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Mapping the spectrum of 3D communities in human chromosome conformation capture data by Lee, Sang Hoon, Kim, Yeonghoon, Lee, Sungmin, Durang, Xavier, Stenberg, Per, Jeon, Jae-Hyung, Lizana, Ludvig

“…Several experiments show that the three dimensional (3D) organization of chromosomes affects genetic processes such as transcription and gene regulation. To…”
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The scaffolding function of LSD1 controls DNA methylation in mouse ESCs by Malla, Sandhya, Kumari, Kanchan, García-Prieto, Carlos A., Caroli, Jonatan, Nordin, Anna, Phan, Trinh T. T., Bhattarai, Devi Prasad, Martinez-Gamero, Carlos, Dorafshan, Eshagh, Stransky, Stephanie, Álvarez-Errico, Damiana, Saiki, Paulina Avovome, Lai, Weiyi, Lyu, Cong, Lizana, Ludvig, Gilthorpe, Jonathan D., Wang, Hailin, Sidoli, Simone, Mateus, Andre, Lee, Dung-Fang, Cantù, Claudio, Esteller, Manel, Mattevi, Andrea, Roman, Angel-Carlos, Aguilo, Francesca

“…Lysine-specific histone demethylase 1 (LSD1), which demethylates mono- or di- methylated histone H3 on lysine 4 (H3K4me1/2), is essential for early…”
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Many-body effects on tracer particle diffusion with applications for single-protein dynamics on DNA by Ahlberg, Sebastian, Ambjörnsson, Tobias, Lizana, Ludvig

“…30% of the DNA in E. coli bacteria is covered by proteins. Such a high degree of crowding affects the dynamics of generic biological processes (e.g. gene…”
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Modeling protein target search in human chromosomes by Nyberg, Markus, Ambjörnsson, Tobias, Stenberg, Per, Lizana, Ludvig

“…Several processes in the cell, such as gene regulation, start when key proteins recognize and bind to short DNA sequences. However, as these sequences can be…”
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Effects of City-Size Heterogeneity on Epidemic Spreading in a Metapopulation: A Reaction-Diffusion Approach by Lund, Halvor, Lizana, Ludvig, Simonsen, Ingve

“…We review and introduce a generalized reaction-diffusion approach to epidemic spreading in a metapopulation modeled as a complex network. The metapopulation…”
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Modeling the spatial dynamics of culture spreading in the presence of cultural strongholds by Lizana, Ludvig, Mitarai, Namiko, Sneppen, Kim, Nakanishi, Hiizu

“…Cultural competition has throughout our history shaped and reshaped the geography of boundaries between humans. Language and culture are intimately connected…”
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Structural correlations in bacterial metabolic networks by Bernhardsson, Sebastian, Gerlee, Philip, Lizana, Ludvig

“…Evolution of metabolism occurs through the acquisition and loss of genes whose products acts as enzymes in metabolic reactions, and from a presumably simple…”
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Foundation of fractional Langevin equation: harmonization of a many-body problem by Lizana, Ludvig, Ambjörnsson, Tobias, Taloni, Alessandro, Barkai, Eli, Lomholt, Michael A

“…In this study we derive a single-particle equation of motion, from first principles, starting out with a microscopic description of a tracer particle in a…”
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Controlling Enzymatic Reactions by Geometry in a Biomimetic Nanoscale Network by Sott, Kristin, Lobovkina, Tatsiana, Lizana, Ludvig, Tokarz, Michal, Bauer, Brigitte, Konkoli, Zoran, Orwar, Owe

“…We demonstrate that a transition from a compact geometry (sphere) to a structured geometry (several spheres connected by nanoconduits) in nanotube−vesicle…”
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Polycomb proteins translate histone methylation to chromatin folding by Lizana, Ludvig, Nahali, Negar, Schwartz, Yuri B.

“…Epigenetic repression often involves covalent histone modifications. Yet, how the presence of a histone mark translates into changes in chromatin structure…”
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Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps by Kumar, Rajendra, Sobhy, Haitham, Stenberg, Per, Lizana, Ludvig

“…Hi-C experiments generate data in form of large genome contact maps (Hi-C maps). These show that chromosomes are arranged in a hierarchy of three-dimensional…”
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Genomic 3D compartments emerge from unfolding mitotic chromosomes by Kumar, Rajendra, Lizana, Ludvig, Stenberg, Per

“…The 3D organisation of the genome in interphase cells is not a randomly folded polymer. Rather, experiments show that chromosomes arrange into a network of 3D…”
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