Review
Biochemistry & Molecular Biology
Ashish Kumar Singh, Felix Mueller-Planitz
Summary: Eukaryotes form nucleosome particles by associating their genomes with histone proteins, which regulate and protect genetic information. These nucleosomes often assemble into evenly spaced arrays, covering significant portions of the genome, with a high degree of conservation throughout the eukaryotic domain. Various factors like transcription, nucleosome remodelers, DNA sequence, and histone density play roles in the formation of these arrays, with unanswered questions remaining about their biogenesis and cellular functions.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Computer Science, Hardware & Architecture
Jianli Jin, Lifang Feng, Jianping Wang, Danyang Chen, Huimin Lu
Summary: This article introduces the architecture and multiplexing methods of visible light positioning systems, as well as the application of a new signature code. By discussing the decomposition of received signal strengths and the adaptive positioning mechanism, it demonstrates the potential superior performance in a large-scale IoT environment.
IEEE WIRELESS COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Kun Fang, Junbai Wang, Lu Liu, Victor X. Jin
Summary: This review surveys computational methods for mapping higher-resolution nucleosome and higher-order chromatin architectures. It discusses methods and tools for nucleosome detection, identification of 3D chromatin domains and interactions, integration of multi-omics data with Hi-C data, and advancements in single-cell (sc)Hi-C data analysis.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Erinija Pranckeviciene, Sergey Hosid, Indiras Maziukas, Ilya Ioshikhes
Summary: Nucleosomes are essential for DNA packing in eukaryotes and play a major role in gene regulation. Researchers have developed a software package for nucleosome DNA sequence analysis and mapping, which will facilitate in-depth studies of gene regulatory mechanisms by computational biologists.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Astrid Lancrey, Alexandra Joubert, Evelyne Duvernois-Berthet, Etienne Routhier, Saurabh Raj, Agnes Thierry, Marta Sigarteu, Loic Ponger, Vincent Croquette, Julien Mozziconacci, Jean-Baptiste Boule
Summary: The artificial 601 DNA sequence is effective in positioning nucleosomes in vitro, but its application in vivo is limited and depends on the chromosomal context.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Engineering, Electrical & Electronic
Nianqi Tang, Yunghsiang S. Han
Summary: This paper proposes a new decoding algorithm for Reed-Solomon codes, which has the best computational complexity and smallest constant factor achieved to date. Comparing with existing methods, the new algorithm shows significant advantage in terms of computational complexity when decoding practical RS codes. Moreover, it has a regular architecture and is suitable for hardware implementation.
IEEE TRANSACTIONS ON COMMUNICATIONS
(2022)
Article
Computer Science, Information Systems
Hengjia Wei
Summary: This paper proposes new explicit constructions and efficient locating algorithms for robust positioning patterns, improving upon previous results. It presents explicit constructions for both constant fraction of errors and constant number of errors, along with efficient locating algorithms.
IEEE TRANSACTIONS ON INFORMATION THEORY
(2022)
Article
Computer Science, Information Systems
Debashreet Das, C. R. Tripathy, P. K. Tripathy, M. R. Kabat
Summary: This paper proposes a Genetic Algorithm-based method for optimizing the reliability of computational grids under cost and bandwidth constraints. The method is shown to be more efficient than existing methods through illustration and implementation on Grid networks.
JOURNAL OF KING SAUD UNIVERSITY-COMPUTER AND INFORMATION SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Guo-Sheng Han, Qi Li, Ying Li
Summary: This study proposes three new deep learning models for nucleosome positioning and finds a better performing integrated model. The models can effectively extract local features and base order features of DNA sequences, providing valuable practical applications.
Article
Biochemical Research Methods
Hiroaki Kato, Mitsuhiro Shimizu, Takeshi Urano
Summary: Chemical map-based statistical models, demonstrated through the nuCpos software package, offer superior accuracy in predicting nucleosome positioning compared to MNase-seq-based methods. This approach allows for reasonable prediction of nucleosome occupancy that aligns with in vivo observations and is not affected by A/T nucleotide frequency. The method also successfully predicts effects of genetic alterations on nucleosome positioning.
BMC BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
A. Sannia, A. Giordano, N. Lo Gullo, C. Mastroianni, F. Plastina
Summary: We present a classical-quantum hybrid approach that improves the performance of a learning agent in decision making by quadratic factor. The approach utilizes a quantum routine on a quantum computer to encode probability distributions, which are then employed in reinforcement learning to drive action choices. The routine is suitable for scenarios with a large but finite number of actions requiring probability distribution with extensive support. The performance of the routine is evaluated in terms of computational complexity, quantum resource requirements, and accuracy. An algorithm for exploiting the routine in Q-learning is also designed.
SCIENTIFIC REPORTS
(2023)
Article
Physics, Multidisciplinary
Francisco Braga, Helena Sofia Pinto
Summary: This article presents a system that uses a 3D model of a sculpture to compose music. The hypothesis of cross-domain mapping as an approach to model inspiration is raised. The semantic meaning of the sculpture is not directly used, and a more abstract approach is adopted. The use of a Genetic Algorithm leads to promising results with higher musical interest.
Review
Construction & Building Technology
Graziella Laignel, Nicolas Pozin, Xavier Geffrier, Loukas Delevaux, Florian Brun, Bastien Dolla
Summary: This method automatically generates multiple apartment layouts that meet architectural and functional constraints, demonstrating feasibility and efficiency within around 1 minute.
AUTOMATION IN CONSTRUCTION
(2021)
Article
Biophysics
Leo S. McCormack, Artem K. Efremov, Jie Yan
Summary: Research has found that proteins on finite-size DNA form oscillatory patterns, influenced by the DNA length and the proteins' binding cooperativity. The geometric characteristics of protein patterns are not significantly affected by small variations in proteins' affinity to DNA due to sequence heterogeneity. Competition between different types of proteins for binding to DNA leads to diverse and complex alternating positioning of the proteins.
BIOPHYSICAL JOURNAL
(2021)
Article
Multidisciplinary Sciences
Cesar Diaz-Celis, Cristhian Canari-Chumpitaz, Robert P. Sosa, Juan P. Castillo, Meng Zhang, Enze Cheng, Andy Q. Chen, Michael Vien, Jeong Hoon Kim, Bibiana Onoa, Carlos Bustamante
Summary: DNA unwrapping and disassembly of nucleosomes play a crucial role in genomic access and transcription regulation. This study, using high-resolution optical tweezers and single-molecule FRET detection, reveals the asymmetry in nucleosome unwrapping and identifies the DNA segments involved in the process. It also suggests the stochastic disassembly of nucleosomes into hexasomes and tetrasomes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Artur Kaczmarczyk, Abdollah Allahverdi, Thomas B. Brouwer, Lars Nordenskiold, Nynke H. Dekker, John van Noort
JOURNAL OF BIOLOGICAL CHEMISTRY
(2017)
Article
Chemistry, Physical
J. A. J. Wondergem, H. Schiessel, M. Tompitak
JOURNAL OF CHEMICAL PHYSICS
(2017)
Meeting Abstract
Biophysics
Bram Henneman, Clara Van Emmerik, Thomas Brouwer, Ramon A. Van der Valk, Nancy Kirolos, Hugo Van Ingen, John Van Noort, Remus T. Dame
BIOPHYSICAL JOURNAL
(2018)
Article
Biophysics
Babette E. de Jong, Thomas B. Brouwer, Artur Kaczmarczyk, Bert Visscher, John van Noortt
BIOPHYSICAL JOURNAL
(2018)
Meeting Abstract
Biophysics
Lars Nordenskiold, Aghil Soman, Nikolay Korolev, Surya Wahyu, Sook Yi Wong, Chong Wai Liew, Simon Lattmann, Hsian Ling Teo, John Van Noort, Daniela Rhodes
BIOPHYSICAL JOURNAL
(2019)
Editorial Material
Biology
Babette E. de Jong, John van Noort
Article
Biophysics
Thomas B. Brouwer, Nicolaas Hermans, John van Noort
BIOPHYSICAL JOURNAL
(2020)
Article
Multidisciplinary Sciences
Artur Kaczmarczyk, He Meng, Orkide Ordu, John van Noort, Nynke H. Dekker
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Gabriela Arias-Alpizar, Li Kong, Redmar C. Vlieg, Alexander Rabe, Panagiota Papadopoulou, Michael S. Meijer, Sylvestre Bonnet, Stefan Vogel, John van Noort, Alexander Kros, Frederick Campbell
NATURE COMMUNICATIONS
(2020)
Article
Materials Science, Biomaterials
Elena A. Egorova, Gabriela Arias-Alpizar, Redmar C. Vlieg, Gert S. Gooris, Joke A. Bouwstra, John van Noort, Alexander Kros, Aimee L. Boyle
Summary: Gold nanorods (GNRs) are versatile nanoparticles with unique optical properties, making them ideal for applications such as photothermal cancer therapy and biosensing. However, the ligands used for stabilizing GNRs during synthesis are toxic, necessitating the use of biocompatible stabilizing coatings. Thiolated peptide amphiphiles (PAs) were found to be effective GNR stabilizers, forming thin and stable coatings under physiological conditions. These PA-coated GNRs showed no cytotoxicity in vitro and their behavior and cellular interactions could be visualized in real time using two-photon microscopy in zebrafish embryos.
JOURNAL OF MATERIALS CHEMISTRY B
(2022)
Article
Multidisciplinary Sciences
Nikolay Korolev, Anatoly Zinchenko, Aghil Soman, Qinming Chen, Sook Yi Wong, Nikolay Berezhnoy, Rajib Basak, Johan R. C. van der Maarel, John van Noort, Lars Nordenskiold
Summary: This study investigates the mechanical properties and interactions between nucleosome clutches in large topologically associated domains (TADs) at the single-molecule level. The results show that TAD-sized chromatin fibers have similar mechanical properties to shorter fibers, and there are also large rupture events. Although arrays of native human DNA, lambda-phage DNA, and '601' DNA differ slightly in reconstitution yield and nucleosome stability, the global structural and mechanical properties of the fibers are similar.
SCIENTIFIC REPORTS
(2022)
Meeting Abstract
Biophysics
Redmar C. Vlieg, Chris L. W. Kettenis, John van Noort
BIOPHYSICAL JOURNAL
(2018)
Meeting Abstract
Biophysics
Thomas B. Brouwer, Artur Kaczmarczyk, Nicolaas Hermans, Margherita Botto, John van Noort
BIOPHYSICAL JOURNAL
(2018)
Article
Biochemical Research Methods
Marco Tompitak, Gerard T. Barkema, Helmut Schiessel
BMC BIOINFORMATICS
(2017)
Article
Biophysics
Marco Tompitak, Cedric Vaillant, Helmut Schiessel
BIOPHYSICAL JOURNAL
(2017)