Related papers: Genome organization: experiments and modelling
The computational modeling of genetic regulatory networks is now common place, either by fitting a system to experimental data or by exploring the behaviour of abstract systems with the aim of identifying underlying principles. This paper…
Nowadays, due to the increasing amount of experimental data obtained by sequencing, the most interest is focused on determining the functions and characteristics of its individual parts of the genome instead of determining the nucleotide…
In multicellular organisms, cells coordinate their activities through cell-cell communication (CCC), which is crucial for development, tissue homeostasis, and disease progression. Recent advances in single-cell and spatial omics…
A (personal) experimental summary of the Hard Probes 2010 conference is presented.
This paper introduces reproducible research, and explains its importance, benefits and challenges. Some important tools for conducting reproducible research in Transportation Research are also introduced. Moreover, the source code for…
We propose a stochastic model for gene transcription coupled to DNA supercoiling, where we incorporate the experimental observation that polymerases create supercoiling as they unwind the DNA helix, and that these enzymes bind more…
The emergence and popularization of online social networks suddenly made available a large amount of data from social organization, interaction and human behavior. All this information opens new perspectives and challenges to the study of…
The rapid advance of DNA sequencing technologies has yielded databases of thousands of genomes. To search and index these databases effectively, it is important that we take advantage of the similarity between those genomes. Several authors…
Interpreting the effects of variants within the human genome and proteome is essential for analysing disease risk, predicting medication response, and developing personalised health interventions. Due to the intrinsic similarities between…
We present here our introduction to the contributed volume "Quantum Theory: Informational Foundations and Foils", Springer Netherlands (2016). It highlights recent trends in quantum foundations and offers an overview of the contributions…
With the boom in modern software development, open-source software has become an integral part of various industries, driving progress in computer science. However, the immense complexity and diversity of the open-source ecosystem also pose…
We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have…
The organization of cells within tissues plays a vital role in various biological processes, including development and morphogenesis. As a result, understanding how cells self-organize in tissues has been an active area of research. In our…
This paper investigates differences in characteristics across publication types for aging-related genetic research. We utilized bibliometric data for five model species retrieved from authoritative databases including PubMed. Publications…
Genetic algorithms are a well-known method for tackling the problem of variable selection. As they are non-parametric and can use a large variety of fitness functions, they are well-suited as a variable selection wrapper that can be applied…
This paper reports about experiments with GermaNet as a resource within domain specific document analysis. The main question to be answered is: How is the coverage of GermaNet in a specific domain? We report about results of a field test of…
The following is an amalgamation of four preprints and some computer programs which together represent the current state of our investigations of higher order links. This investigation was motivated by questions discussed and raised in the…
In this paper we deepen and enlarge the reflection on the possible advantages of a knockoff approach to genome wide association studies (Sesia et al., 2018), starting from the discussions in Bottolo & Richardson (2019); Jewell & Witten…
Genomic data visualization is essential for interpretation and hypothesis generation as well as a valuable aid in communicating discoveries. Visual tools bridge the gap between algorithmic approaches and the cognitive skills of…
Numerous research studies have been investigated on proxy signatures over the last decade. This survey reviews the research progress on proxy signatures, analyzes a few notable proposals, and provides an overall remark of these proposals.