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  1. Article ; Online: Influence of the longitudinal inclination on the speed on highways

    Hristov Borislav

    E3S Web of Conferences, Vol 263, p

    2021  Volume 04007

    Abstract: The main objective of the present paper is to investigate the influence of the longitudinal inclination of grades on the speed behavior on highways. For assessing this dependence, all uphill and downhill highway sections were considered separately in the ...

    Abstract The main objective of the present paper is to investigate the influence of the longitudinal inclination of grades on the speed behavior on highways. For assessing this dependence, all uphill and downhill highway sections were considered separately in the two travel directions and the mean values of both 85th and 15th percentile speeds were calculated for each section. In order to take into account the free speed selection, all speed limited highway sections were excluded from the study. To investigate the speed changes as a function of the longitudinal inclination, the speed differences V85 between the speeds at the end and the beginning of each individual ascending and descending section were calculated as well. The dependencies were assessed also using the “moving average” over the grades. Both methodological approaches show that the magnitude of the longitudinal inclination on uphill sections has a clear influence on the speed and on the speed differences. A significant reduction of the speed and a significant increase of the speed difference were established on ascending sections with slopes over 4%. Furthermore, it was found that the length of the ascending grades also affects the speed differences ΔV85, which increase considerably on longer uphill sections.
    Keywords Environmental sciences ; GE1-350
    Subject code 551
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher EDP Sciences
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Influence of Road Geometry on Driver’s Gaze Behavior on Motorways

    Hristov Borislav

    E3S Web of Conferences, Vol 97, p

    2019  Volume 01001

    Abstract: Driver’s gaze is a highly selective dynamic process, which ensures a precise perception of moving objects, speeds and spatial expansions in road traffic. Thus, the gaze behavior of drivers determines largely their driving behavior, and is crucial for ... ...

    Abstract Driver’s gaze is a highly selective dynamic process, which ensures a precise perception of moving objects, speeds and spatial expansions in road traffic. Thus, the gaze behavior of drivers determines largely their driving behavior, and is crucial for traffic safety. With the aid of modern technology, the gaze behavior can be precisely recorded during driving. This paper describes part of the research, which has been undertaken in order to investigate the relationship between driver’s gaze behavior and horizontal alignment geometry. It is known, that driver’s stress state and gaze concentration are not the same when steering a vehicle along straight stretches and within curves. The stress is higher in curves and this leads to an increased attention. The gaze behavior in left and right horizontal curves is characterized by certain gaze patterns, which clearly differ from each other. In this respect, appropriate investigations and analyzes have been also carried out. Different parameters have been calculated in order to assess and quantify the gaze behavior. By evaluating these parameters, the spatial and temporal concentration of the driver’s gaze as well as the intensity of information acquisition and processing have been analyzed along straight stretches, left and right horizontal curves.
    Keywords Environmental sciences ; GE1-350
    Subject code 380
    Language English
    Publishing date 2019-01-01T00:00:00Z
    Publisher EDP Sciences
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article: Systematic identification of inter-chromosomal interaction networks supports the existence of RNA factories.

    Hristov, Borislav Hrisimirov / Noble, William Stafford / Bertero, Alessandro

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Most studies of genome organization have focused on intra-chromosomal ( ...

    Abstract Most studies of genome organization have focused on intra-chromosomal (
    Language English
    Publishing date 2023-09-22
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.09.21.558852
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  4. Article ; Online: Linking cells across single-cell modalities by synergistic matching of neighborhood structure.

    Hristov, Borislav H / Bilmes, Jeffrey A / Noble, William Stafford

    Bioinformatics (Oxford, England)

    2022  Volume 38, Issue Suppl_2, Page(s) ii148–ii154

    Abstract: Motivation: A wide variety of experimental methods are available to characterize different properties of single cells in a complex biosample. However, because these measurement techniques are typically destructive, researchers are often presented with ... ...

    Abstract Motivation: A wide variety of experimental methods are available to characterize different properties of single cells in a complex biosample. However, because these measurement techniques are typically destructive, researchers are often presented with complementary measurements from disjoint subsets of cells, providing a fragmented view of the cell's biological processes. This creates a need for computational tools capable of integrating disjoint multi-omics data. Because different measurements typically do not share any features, the problem requires the integration to be done in unsupervised fashion. Recently, several methods have been proposed that project the cell measurements into a common latent space and attempt to align the corresponding low-dimensional manifolds.
    Results: In this study, we present an approach, Synmatch, which produces a direct matching of the cells between modalities by exploiting information about neighborhood structure in each modality. Synmatch relies on the intuition that cells which are close in one measurement space should be close in the other as well. This allows us to formulate the matching problem as a constrained supermodular optimization problem over neighborhood structures that can be solved efficiently. We show that our approach successfully matches cells in small real multi-omics datasets and performs favorably when compared with recently published state-of-the-art methods. Further, we demonstrate that Synmatch is capable of scaling to large datasets of thousands of cells.
    Availability and implementation: The Synmatch code and data used in this manuscript are available at https://github.com/Noble-Lab/synmatch.
    MeSH term(s) Cells
    Language English
    Publishing date 2022-09-29
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btac481
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  5. Article ; Online: Using a mobile eye-tracking technology to explore pedestrians’ gaze distribution on street space

    Rudenko Sergey / Danilina Nina / Hristov Borislav

    E3S Web of Conferences, Vol 263, p

    2021  Volume 05015

    Abstract: The paper deals with the question of smart sustainable city development on the example of public city street space study using a modern mobile eye-tracking technology. The article presents a methodology to obtain data on the distribution of human gaze on ...

    Abstract The paper deals with the question of smart sustainable city development on the example of public city street space study using a modern mobile eye-tracking technology. The article presents a methodology to obtain data on the distribution of human gaze on dynamic and static objects located on urban streets as well as computer technologies that are used for the acquisition and processing of data. With the help of these technologies, it is possible to study people’s behavior in dynamic environments and to obtain results describing the nature of the pedestrians’ perception of their surrounding space. The results of a survey on urban streets in Berlin using a mobile eye tracking system are shown in this paper. Based on the results of the study, a list of objects that catch people’s attention and a numerical description of the gaze distribution are presented.
    Keywords Environmental sciences ; GE1-350
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher EDP Sciences
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: uKIN Combines New and Prior Information with Guided Network Propagation to Accurately Identify Disease Genes.

    Hristov, Borislav H / Chazelle, Bernard / Singh, Mona

    Cell systems

    2020  Volume 10, Issue 6, Page(s) 470–479.e3

    Abstract: Protein interaction networks provide a powerful framework for identifying genes causal for complex genetic diseases. Here, we introduce a general framework, uKIN, that uses prior knowledge of disease-associated genes to guide, within known protein- ... ...

    Abstract Protein interaction networks provide a powerful framework for identifying genes causal for complex genetic diseases. Here, we introduce a general framework, uKIN, that uses prior knowledge of disease-associated genes to guide, within known protein-protein interaction networks, random walks that are initiated from newly identified candidate genes. In large-scale testing across 24 cancer types, we demonstrate that our network propagation approach for integrating both prior and new information not only better identifies cancer driver genes than using either source of information alone but also readily outperforms other state-of-the-art network-based approaches. We also apply our approach to genome-wide association data to identify genes functionally relevant for several complex diseases. Overall, our work suggests that guided network propagation approaches that utilize both prior and new data are a powerful means to identify disease genes. uKIN is freely available for download at: https://github.com/Singh-Lab/uKIN.
    MeSH term(s) Gene Regulatory Networks/genetics ; Humans ; Protein Interaction Maps/genetics
    Language English
    Publishing date 2020-06-24
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2854138-8
    ISSN 2405-4720 ; 2405-4712
    ISSN (online) 2405-4720
    ISSN 2405-4712
    DOI 10.1016/j.cels.2020.05.008
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  7. Article: Network-Based Coverage of Mutational Profiles Reveals Cancer Genes.

    Hristov, Borislav H / Singh, Mona

    Cell systems

    2017  Volume 5, Issue 3, Page(s) 221–229.e4

    Abstract: A central goal in cancer genomics is to identify the somatic alterations that underpin tumor initiation and progression. While commonly mutated cancer genes are readily identifiable, those that are rarely mutated across samples are difficult to ... ...

    Abstract A central goal in cancer genomics is to identify the somatic alterations that underpin tumor initiation and progression. While commonly mutated cancer genes are readily identifiable, those that are rarely mutated across samples are difficult to distinguish from the large numbers of other infrequently mutated genes. We introduce a method, nCOP, that considers per-individual mutational profiles within the context of protein-protein interaction networks in order to identify small connected subnetworks of genes that, while not individually frequently mutated, comprise pathways that are altered across (i.e., "cover") a large fraction of individuals. By analyzing 6,038 samples across 24 different cancer types, we demonstrate that nCOP is highly effective in identifying cancer genes, including those with low mutation frequencies. Overall, our work demonstrates that combining per-individual mutational information with interaction networks is a powerful approach for tackling the mutational heterogeneity observed across cancers.
    MeSH term(s) Algorithms ; Computational Biology/methods ; Computer Simulation ; Disease Progression ; Gene Regulatory Networks/genetics ; Genomics/methods ; Humans ; Mutation/genetics ; Mutation Rate ; Neoplasms/genetics ; Oncogenes/genetics ; Protein Interaction Maps/genetics
    Language English
    Publishing date 2017-09-27
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2854138-8
    ISSN 2405-4720 ; 2405-4712
    ISSN (online) 2405-4720
    ISSN 2405-4712
    DOI 10.1016/j.cels.2017.09.003
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  8. Article ; Online: Proteome-Wide Identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes.

    Hollin, Thomas / Abel, Steven / Banks, Charles / Hristov, Borislav / Prudhomme, Jacques / Hales, Kianna / Florens, Laurence / Stafford Noble, William / Le Roch, Karine G

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 1365

    Abstract: Ribonucleoprotein complexes are composed of RNA, RNA-dependent proteins (RDPs) and RNA-binding proteins (RBPs), and play fundamental roles in RNA regulation. However, in the human malaria parasite, Plasmodium falciparum, identification and ... ...

    Abstract Ribonucleoprotein complexes are composed of RNA, RNA-dependent proteins (RDPs) and RNA-binding proteins (RBPs), and play fundamental roles in RNA regulation. However, in the human malaria parasite, Plasmodium falciparum, identification and characterization of these proteins are particularly limited. In this study, we use an unbiased proteome-wide approach, called R-DeeP, a method based on sucrose density gradient ultracentrifugation, to identify RDPs. Quantitative analysis by mass spectrometry identifies 898 RDPs, including 545 proteins not yet associated with RNA. Results are further validated using a combination of computational and molecular approaches. Overall, this method provides the first snapshot of the Plasmodium protein-protein interaction network in the presence and absence of RNA. R-DeeP also helps to reconstruct Plasmodium multiprotein complexes based on co-segregation and deciphers their RNA-dependence. One RDP candidate, PF3D7_0823200, is functionally characterized and validated as a true RBP. Using enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP-seq), we demonstrate that this protein interacts with various Plasmodium non-coding transcripts, including the var genes and ap2 transcription factors.
    MeSH term(s) Humans ; RNA/metabolism ; Plasmodium falciparum/genetics ; Plasmodium falciparum/metabolism ; Proteome/metabolism ; RNA-Binding Proteins/metabolism ; Plasmodium/genetics
    Chemical Substances RNA (63231-63-0) ; Proteome ; RNA-Binding Proteins
    Language English
    Publishing date 2024-02-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-45519-1
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  9. Article ; Online: Measuring significant changes in chromatin conformation with ACCOST.

    Cook, Kate B / Hristov, Borislav H / Le Roch, Karine G / Vert, Jean Philippe / Noble, William Stafford

    Nucleic acids research

    2020  Volume 48, Issue 5, Page(s) 2303–2311

    Abstract: Chromatin conformation assays such as Hi-C cannot directly measure differences in 3D architecture between cell types or cell states. For this purpose, two or more Hi-C experiments must be carried out, but direct comparison of the resulting Hi-C matrices ... ...

    Abstract Chromatin conformation assays such as Hi-C cannot directly measure differences in 3D architecture between cell types or cell states. For this purpose, two or more Hi-C experiments must be carried out, but direct comparison of the resulting Hi-C matrices is confounded by several features of Hi-C data. Most notably, the genomic distance effect, whereby contacts between pairs of genomic loci that are proximal along the chromosome exhibit many more Hi-C contacts that distal pairs of loci, dominates every Hi-C matrix. Furthermore, the form that this distance effect takes often varies between different Hi-C experiments, even between replicate experiments. Thus, a statistical confidence measure designed to identify differential Hi-C contacts must accurately account for the genomic distance effect or risk being misled by large-scale but artifactual differences. ACCOST (Altered Chromatin COnformation STatistics) accomplishes this goal by extending the statistical model employed by DEseq, re-purposing the 'size factors,' which were originally developed to account for differences in read depth between samples, to instead model the genomic distance effect. We show via analysis of simulated and real data that ACCOST provides unbiased statistical confidence estimates that compare favorably with competing methods such as diffHiC, FIND and HiCcompare. ACCOST is freely available with an Apache license at https://bitbucket.org/noblelab/accost.
    MeSH term(s) Animals ; Cell Line ; Chromatin/chemistry ; Chromatin/metabolism ; DNA/chemistry ; DNA/metabolism ; Epistasis, Genetic ; Epithelial Cells/cytology ; Epithelial Cells/metabolism ; Genetic Loci ; Genome ; Humans ; Lymphocytes/cytology ; Lymphocytes/metabolism ; Mice ; Molecular Conformation ; Plasmodium falciparum/genetics ; Software ; Sporozoites/genetics ; Trophozoites/genetics
    Chemical Substances Chromatin ; DNA (9007-49-2)
    Language English
    Publishing date 2020-03-23
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkaa069
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  10. Book ; Online ; Thesis: Untersuchung des Blickverhaltens von Kraftfahrern auf Autobahnen

    Hristov, Borislav

    2010  

    Author's details Borislav Hristov
    Language German
    Size Online-Ressource
    Document type Book ; Online ; Thesis
    Thesis / German Habilitation thesis Techn. Univ., Fak. Verkehrswiss., Diss.--Dresden, 2010
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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