22 papers · ranked by Valyu relevance
Apostolos Dimitromanolakis, Jingxiong Xu, Agnieszka Krol, Laurent Briollais
'Laurent Briollais'] Background Simulation of genetic variants data is frequently required for the evaluation of statistical methods in the fields of human and animal genetics. Although a number of high-quality genetic simulators have been developed, many of them require advanced knowledge in population genetics or in…
Zhenhua Yu, Fang Du, Rongjun Ban, Yuanwei Zhang
Background A number of simulators have been developed for emulating next-generation sequencing data by incorporating known errors such as base substitutions and indels. However, their practicality may be degraded by functional and runtime limitations. Particularly, the positional and genomic contextual information is…
Jia-Xing Yue, Gianni Liti
Simulated genomes with pre-defined and random genomic variants can be very useful for benchmarking genomic and bioinformatics analyses. Here we introduce simuG, a lightweight tool for simulating the full-spectrum of genomic variants (SNPs, INDELs, CNVs, inversions and translocations) for any organisms (including…
Umit Akkose, Ogun Adebali
Sequence content is heterogeneous throughout genomes. Therefore, Genome-wide NGS reads biased towards specific nucleotide profiles are affected by the genome-wide heterogeneous nucleotide distribution. Boquila generates sequences that mimic the nucleotide profile of true reads, which can be used to correct the…
Swetansu Pattnaik, Saurabh Gupta, Arjun A Rao, Binay Panda
Background The rapid advancements in the field of genome sequencing are aiding our understanding on many biological systems. In the last five years, computational biologists and bioinformatics specialists have come up with newer, better and more efficient tools towards the discovery, analysis and interpretation of…
Ren-Hua Chung, Chen-Yu Kang
We have developed OmicsSIMLA, which simulates multi-omics data (i.e., genomics, epigenomics, transcriptomics, and proteomics data) with disease status. OmicsSIMLA simulates multiple types of omics data while the relationships between different types of omics data and the relationships between the omics data and the…
Ren-Hua Chung, Chung-Chin Shih
Background Association studies based on next-generation sequencing (NGS) technology have become popular, and statistical association tests for NGS data have been developed rapidly. A flexible tool for simulating sequence data in either unrelated case-control or family samples with different disease and quantitative…
Callum Burnard, Alban Mancheron, William Ritchie
A publicly available human genome serves as both a valuable resource for researchers and a potential risk to the individual who provided the genome. Many actors with selfish intentions could exploit it to extract information about the donor’s health or that of their relatives. Recent efforts have employed artificial…
Fathima Nuzla Ismail, Shanika Amarasoma
—Next-generation sequencing (NGS) is a pivotal technique in genome sequencing due to its high throughput, rapid results, cost-effectiveness, and enhanced accuracy. Its significance extends across various domains, playing a crucial role in identifying genetic variations and exploring genomic complexity. NGS finds…
M. Elise Lauterbur, Maria Izabel A. Cavassim, Ariella L. Gladstein, Graham Gower + 38 more
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of…
Swetansu Pattnaik, Saurabh Gupta, Arjun A. Rao, Binay Panda
We report SInC (SNV, Indel and CNV) simulator and read generator, an open-source tool capable of simulating biological variants taking into account a platform-specific error model. SInC is capable of simulating and generating single- and paired-end reads with user-defined insert size with high efficiency compared to…
Peiyu Xu, Shenni Liang, Andrew Hahn, Vivian Zhao + 11 more
Infectious disease dynamics are driven by the complex interplay of epidemiological, ecological, and evolutionary processes. Accurately modeling these interactions is crucial for understanding pathogen spread and informing public health strategies. However, existing simulators often fail to capture the dynamic interplay…
Kaleigh Riggs, Huann‐Sheng Chen, Melissa Rotunno, Bing Li + 3 more
'Naoko I. Simonds' 'Leah E. Mechanic' 'Bo Peng'] Title: Abstract In silico simulations play an indispensable role in the development and application of statistical models and methods for genetic studies. Simulation tools allow for the evaluation of methods and investigation of models in a controlled manner. With the…
Callum Burnard, Alban Mancheron, William Ritchie
A publicly available human genome is both valuable to researchers and a risk for its donor. Many actors could exploit it to extract information about the donor’s health or that of their relatives. Recent efforts have employed artificial intelligence models to simulate genomic data, aiming to create synthetic datasets…
Michael J. Burns, Rafael Della Coletta, Samuel B. Fernandes, Martin O. Bohn + 2 more
The use of computational and data-driven approaches to accelerate and optimize breeding programs is becoming common practice among plant breeders. Simulations allow breeders to evaluate potential changes in breeding schemes in a time– and cost-efficient manner. However, accurately simulating traits that match empirical…
Teddy Lazebnik, Liron Simon-Keren
Genome data are crucial in modern medicine, offering significant potential for diagnosis and treatment. Thanks to technological advancements, many millions of healthy and diseased genomes have already been sequenced; however, obtaining the most suitable data for a specific study, and specifically for validation…
Jiaying Lai, YunZhou Liu, Robert B. Scharpf, Rachel Karchin
Most neoplastic tumors originate from a single cell, and their evolution can be genetically traced through lineages characterized by common alterations such as small somatic mutations (SSMs), copy number alterations (CNAs), structural variants (SVs), and aneuploidies. Due to the complexity of these alterations in most…
M. Johnsson
This paper will argue that one of the biggest challenges for livestock genomics is to make whole-genome sequencing and functional genomics applicable to breeding practice. It discusses potential explanations for why it is so difficult to consistently improve the accuracy of genomic prediction by means of wholegenome…
Authors not listed
Protein conformational landscapes contain the functionally relevant information useful for understanding biological processes. Mapping out conformational landscapes provides valuable insights into protein behaviors and biological phenomena, and has relevance to therapeutic design. While experimental structural biology…
Authors not listed
Computational simulations of biomolecules provide a wealth of information about the thermodynamic landscape of biologically important systems, kinetics of important cellular processes, and the biophysical basis of life. Despite the ubiquity of molecular simulations in biophysical literature, major challenges persist…
Gopal Sarma, Victor Faúndez
Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems, a diverse array of biological systems have been the target of large-scale…
HANIYEH ABDOLLAHZADEH, Tonya Peeples, Mohammad Shahcheraghi
DNA-based nanomaterials have shown great potential in numerous applications, thanks to their unique properties including DNA's various molecular interactions, programmability, and versatility with biological modules. Meanwhile, the DNA origami platforms have shown promise in the creation of drug carriers. This…