Article
Multidisciplinary Sciences
Hanna Kranas, Irina Tuszynska, Bartek Wilczynski
Summary: HiCEnterprise is the first freely available software tool for the identification of long-range chromatin contacts, implementing four different statistical tests and user-friendly functions for input, output, and visualization. It is crucial for proper statistical analysis and open access to the research community.
Article
Biochemical Research Methods
Jingzhe Lu, Xu Wang, Keyong Sun, Xun Lan
Summary: Chrom-Lasso is a linear regression model-based method for Hi-C data analysis that removes complex biases and enhances the identification of functional interactions. This approach demonstrates advantages in detecting functional important interactions, dynamic changes, and the consistency between genes expression and chromatin interactions.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Kristina M. Garske, Caroline Comenho, David Z. Pan, Marcus Alvarez, Karen Mohlke, Markku Laakso, Kirsi H. Pietilainen, Paivi Pajukanta
Summary: This study demonstrates the importance of long range chromosomal interactions (LRIs) in adipogenesis, showing that LRIs increase throughout the differentiation process and mark developmental regions of the genome.
Article
Biochemical Research Methods
Itunu G. Osuntoki, Andrew Harrison, Hongsheng Dai, Yanchun Bao, Nicolae Radu Zabet
Summary: Motivation: Several computational and statistical methods have been developed to analyze Hi-C data, but most of them do not consider the dependency in the data. Results: In this study, we present a novel statistical method called ZipHiC, which uses a hidden Markov random field model and Approximate Bayesian Computation to detect enriched contacts in Hi-C data. ZipHiC outperforms existing tools, provides insights into biases in Hi-C data, and identifies functional biological roles. Additionally, it corrects biases in micro-C datasets compared to similar Hi-C experiments.
Article
Biochemical Research Methods
Mikhail D. Magnitov, Azat K. Garaev, Alexander Tyakht, Sergey Ulianov, Sergey Razin
Summary: This study developed a tool called Pentad for analyzing changes in chromatin compartmentalization. By applying Pentad to existing Hi-C datasets, the tool can reliably detect redistribution of contact frequency in chromatin compartments and assess alterations in compartment strength.
BMC BIOINFORMATICS
(2022)
Article
Optics
Yifan Hong, Andrew Lucas
Summary: An efficient protocol for quantum state transfer using Hamiltonian dynamics with long-range interactions is described. The time to transfer n qubits a large distance is proportional to the square root of n. The fidelity of multiqubit state transfer process remains finite even without error correction, in the presence of uncorrelated random errors in coupling constants.
Article
Genetics & Heredity
Elizabeth H. Finn, Tom Misteli
Summary: The organization of the human genome within the cell nucleus is non-random, with interactions between genomic loci depending on their location. These interactions are cell-type specific and correlated with local chromatin type.
Article
Biochemical Research Methods
Erle M. Holgersen, Andrea Gillespie, Olivia C. Leavy, Joseph S. Baxter, Alisa Zvereva, Gareth Muirhead, Nichola Johnson, Orsolya Sipos, Nicola H. Dryden, Laura R. Broome, Yi Chen, Igor Kozin, Frank Dudbridge, Olivia Fletcher, Syed Haider
Summary: The CHiCANE toolkit presented in this protocol is specialized for the analysis and meaningful interpretation of CHi-C assays, aiding in the identification of regulatory interactions mediating gene expression changes and performing downstream analysis.
Article
Biotechnology & Applied Microbiology
Michel van Kempen, Stephanie S. Kim, Charlotte Tumescheit, Milot Mirdita, Jeongjae Lee, Cameron L. M. Gilchrist, Johannes Soeding, Martin Steinegger
Summary: Foldseek aligns the structure of a query protein against a database by representing the tertiary amino acid interactions as sequences over a structural alphabet. It improves computation time by four to five orders of magnitude, with sensitivities of 86%, 88%, and 133% compared to Dali, TM-align, and CE, respectively. Foldseek significantly speeds up protein structural search.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Minhyuk Park, Stefan Ivanovic, Gillian Chu, Chengze Shen, Tandy Warnow
Summary: UPP2 is an improvement on UPP, with a fast technique for selecting HMMs in the ensemble, achieving the same accuracy as UPP but with reduced runtime.
Article
Computer Science, Interdisciplinary Applications
Anirban Pal
Summary: This study introduces a fast and efficient computational methodology for estimating the cohesive-repulsive energies and forces between fiber segments in fibrous systems, providing an accurate simulation of their behavior.
ENGINEERING COMPUTATIONS
(2021)
Article
Physics, Multidisciplinary
Huaizhi Wu, Xin-Yu Lin, Zong-Xing Ding, Shi-Biao Zheng, Igor Lesanovsky, Weibin Li
Summary: We propose a Rydberg molecule dressing scheme that can generate strong and long-range interactions at selective distances. By coupling ground-state atoms off-resonantly to two interacting Rydberg atoms on an attractive molecular curve, we can control the ratio of dressed interaction to dephasing rate at large atomic separations. This scheme enables the fast generation of spin squeezing and provides a new route for studying complex many-body dynamics and realizing quantum information processing with non-convex long-range interactions.
SCIENCE CHINA-PHYSICS MECHANICS & ASTRONOMY
(2022)
Article
Genetics & Heredity
Taylor M. Lagler, Armen Abnousi, Ming Hu, Yuchen Yang, Yun Li
Summary: The study introduces a novel approach called HiC-ACT that aims to improve the detection of chromatin interactions by utilizing information from neighboring chromatin interactions. By post-processing results from methods assuming independence, HiC-ACT enhances sensitivity, controls type I error, and is computationally efficient. The approach shows advantages in detecting interactions with lower signal-to-noise ratio and similar epigenetic signatures, and exhibits higher correlation with known enhancers compared to existing methods Fit-Hi-C/FitHiC2.
AMERICAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Genetics & Heredity
Rui Sun, Shuangtao Li, Linlin Chang, Jing Dong, Chuanfei Zhong, Hongli Zhang, Lingzhi Wei, Yongshun Gao, Guixia Wang, Yuntao Zhang, Jian Sun
Summary: In this study, a high-quality chromosome-level genome assembly of Fragaria pentaphylla was generated, providing fundamental molecular resources for evolutionary studies, breeding efforts, and exploring the unique biological characteristics of F. pentaphylla. Phylogenetic and chromosome syntenic analysis revealed its close relationship with F. nubicola.
FRONTIERS IN GENETICS
(2022)
Article
Biochemical Research Methods
Huiling Liu, Wenxiu Ma
Summary: In this study, we introduced the scHiCDiff software tool that can detect differential chromatin interactions (DCIs) from single-cell Hi-C data using both nonparametric tests and parametric models. We thoroughly evaluated the scHiCDiff methods on simulated and real data, and our results demonstrated that scHiCDiff, especially the zero-inflated negative binomial model option, can effectively detect reliable and consistent single-cell DCIs between two conditions, thereby facilitating the study of cell type-specific variations of chromatin structures at the single-cell level.
Article
Biochemistry & Molecular Biology
Sufang Cheng, Huirong Mao, Yezhao Ruan, Cong Wu, Zheng Xu, Guoliang Hu, Xiaoquan Guo, Caiying Zhang, Huabin Cao, Ping Liu
BIOLOGICAL TRACE ELEMENT RESEARCH
(2020)
Article
Integrative & Complementary Medicine
Jian Chen, Yaqing Mao, Chenghong Xing, Ruiming Hu, Zheng Xu, Huabin Cao, Junrong Luo
EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE
(2020)
Article
Plant Sciences
Xiuru Dai, Zheng Xu, Zhikai Liang, Xiaoyu Tu, Silin Zhong, James C. Schnable, Pinghua Li
Article
Environmental Sciences
Yanyu Xiao, Xibang Zheng, Guyue Li, Changming Zhou, Cong Wu, Zheng Xu, Guoliang Hu, Xiaoquan Guo, Lin Li, Huabin Cao, Vincent Latigo, Ping Liu
ENVIRONMENTAL POLLUTION
(2020)
Article
Biochemistry & Molecular Biology
Leina Lu, Xiaoxiao Liu, Wei-Kai Huang, Paola Giusti-Rodriguez, Jian Cui, Shanshan Zhang, Wanying Xu, Zhexing Wen, Shufeng Ma, Jonathan D. Rosen, Zheng Xu, Cynthia F. Bartels, Riki Kawaguchi, Ming Hu, Peter C. Scacheri, Zhili Rong, Yun Li, Patrick F. Sullivan, Hongjun Song, Guo-li Ming, Yan Li, Fulai Jin
Article
Critical Care Medicine
Jianfeng Xie, Wenjuan Wu, Shusheng Li, Yu Hu, Ming Hu, Jinxiu Li, Yi Yang, Tingrong Huang, Kun Zheng, Yishan Wang, Hanyujie Kang, Yingzi Huang, Li Jiang, Wei Zhang, Ming Zhong, Ling Sang, Xia Zheng, Chun Pan, Ruiqiang Zheng, Xuyan Li, Zhaohui Tong, Haibo Qiu, Bin Du
INTENSIVE CARE MEDICINE
(2020)
Article
Agriculture, Dairy & Animal Science
Sufang Cheng, Xin Liu, Pei Liu, Guyue Li, Xiaoquan Guo, Guoliang Hu, Lin Li, Cong Wu, Zheng Xu, Qi Zhou, Jialin Jiang, Shixian Luo, Huajun Huang, Ping Liu
Summary: Broiler ascites syndrome is a metabolic disorder observed worldwide in fast-growing broilers, with pulmonary arterial remodeling being a key step. This study analyzed SNP loci of genes associated with pulmonary artery remodeling in AS progression, shedding light on the molecular mechanism underlying AS progression.
Article
Biochemistry & Molecular Biology
Qi Zhang, Zheng Xu, Yutong Lai
Summary: The study introduces an empirical Bayes approach (EBHiC) for peak detection from Hi-C data, providing flexible over-dispersion modeling by including true interaction intensities as latent variables.
STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY
(2021)
Article
Mathematics
Zheng Xu
Summary: This paper proposes estimation methods for logistic regression based on individual-level predictors and aggregate-level responses. Likelihood of logistic models in this situation is derived and estimators with different optimization methods are proposed. Simulation studies and a real data-based study are conducted to evaluate and compare the performance of the different estimators.
Article
Mathematics
Zheng Xu, Song Yan, Cong Wu, Qing Duan, Sixia Chen, Yun Li
Summary: This study developed NGS data-based methods for association studies, filling the gap in the literature. Simulation studies showed that NGS data-based methods have better performance than genotype-based methods for handling binary and count responses, especially when sequencing depth is low.
Article
Mathematics
Zheng Xu
Summary: This paper extends methods for testing the association between a continuous response variable and a group of common or rare genetic variants without the need for genotype calling. The proposed NGS data-based methods, derived from a linear model framework, show better statistical power compared to genotype-based methods, with improved performance as sequencing depth increases.
Article
Mathematics, Interdisciplinary Applications
Zheng Xu, Song Yan, Shuai Yuan, Cong Wu, Sixia Chen, Zifang Guo, Yun Li
Summary: Sequencing-based genetic association analysis typically involves creating genotype calls from sequence data and then performing association tests. This study proposes a computationally efficient two-stage approach which screens single-nucleotide polymorphisms (SNPs) in the first stage using a rapid maximum likelihood (ML)-based method directly on sequence data, and then evaluates the selected SNPs in the second stage by performing association tests on genotypes from multi-sample linkage disequilibrium (LD)-aware calling. Simulation and real data-based studies demonstrate that this approach can save computational costs by 80% while still achieving over 90% power compared to the traditional method of genotyping all markers.
Article
Mathematics, Interdisciplinary Applications
Sixia Chen, Alexandra May Woodruff, Janis Campbell, Sara Vesely, Zheng Xu, Cuyler Snider
Summary: Nonprobability samples are commonly used in various fields such as public health, economics, education, and political polls. However, naive estimates based on nonprobability samples may suffer from serious selection bias. Mass imputation methods have been shown to effectively improve the representativeness of nonprobability samples.
Article
Ecology
A. E. Saak, T. Wang, Z. Xu, D. Kolady, J. D. Ulrich-Schad, D. Clay
Summary: The study found that it takes 5-10 years for conservation tillage to be profitable, with higher adoption and positive outcomes in areas with less precipitation. Adoption subsidies should decrease with duration of usage in adopted areas, and monetary incentives may be needed in areas with higher rainfall to encourage conservation tillage adoption.
JOURNAL OF SOIL AND WATER CONSERVATION
(2021)
Article
Agronomy
Chenyong Miao, Alejandro Pages, Zheng Xu, Eric Rodene, Jinliang Yang, James C. Schnable