Search results for "Supplementary data"
showing 10 items of 15 documents
REGGAE : a novel approach for the identification of key transcriptional regulators
2019
Abstract Motivation Transcriptional regulators play a major role in most biological processes. Alterations in their activities are associated with a variety of diseases and in particular with tumor development and progression. Hence, it is important to assess the effects of deregulated regulators on pathological processes. Results Here, we present REGulator-Gene Association Enrichment (REGGAE), a novel method for the identification of key transcriptional regulators that have a significant effect on the expression of a given set of genes, e.g. genes that are differentially expressed between two sample groups. REGGAE uses a Kolmogorov–Smirnov-like test statistic that implicitly combines assoc…
Insights into how nucleotide supplements enhance the peroxidase-mimicking DNAzyme activity of the G-quadruplex/hemin system
2012
Since the initial discovery of the catalytic capability of short DNA fragments, this peculiar enzyme-like property (termed DNAzyme) has continued to garner much interest in the scientific community because of the virtually unlimited applications in developing new molecular devices. Alongside the exponential rise in the number of DNAzyme applications in the last past years, the search for convenient ways to improve its overall efficiency has only started to emerge. Credence has been lent to this strategy by the recent demonstration that the quadruplex-based DNAzyme proficiency can be enhanced by ATP supplements. Herein, we have made a further leap along this path, trying first of all to deci…
Epigenomic k-mer dictionaries: shedding light on how sequence composition influences in vivo nucleosome positioning
2014
Abstract Motivation: Information-theoretic and compositional analysis of biological sequences, in terms of k-mer dictionaries, has a well established role in genomic and proteomic studies. Much less so in epigenomics, although the role of k-mers in chromatin organization and nucleosome positioning is particularly relevant. Fundamental questions concerning the informational content and compositional structure of nucleosome favouring and disfavoring sequences with respect to their basic building blocks still remain open. Results: We present the first analysis on the role of k-mers in the composition of nucleosome enriched and depleted genomic regions (NER and NDR for short) that is: (i) exhau…
Clima subártico para os primeiros Homo sapiens na Europa
2021
Description
Corrigendum to “Global frequency and intensity analysis of the ν10/ν7/ν4/ν12 band system of 12C2H4 at 10 μm using the D2h top data system” [J. Quant.…
2017
Abstract This corrigendum provides a new version of one of the 3 supplementary data files associated with the article A. Alkadrou et al., J. Quant. Spectrosc. Radiat. Transf. 182 (2016) 158–171, namely the HITRAN-formatted linelist generated as described in section 5 of the article. Indeed, the K a and K c labels of the upper levels of a number of transitions belonging to the ν 10 , ν 7 and ν 4 bands listed in this supplementary data file were found to be incorrect. The linelist provided with this corrigendum corrects these erroneous assignments, and provides K a and K c labels for all the upper levels.
Abrupt Alnus population decline at the end of the first millennium CE in Europe - The event ecology, possible causes and implications
2019
The study, based on the examination of 70 published and unpublished pollen profiles from Poland and supplementary data from the surrounding regions, shows that an abrupt, episodic Alnus population decline at the end of the first millennium CE was a much more widespread event than has been previously reported, spanning large areas of the temperate and boreal zones in Europe. The data from Poland suggest that the decline was roughly synchronous and most likely occurred between the 9th and 10th centuries, with strong indications for the 10th century. The pollen data indicate that human impacts were not a major factor in the event. Instead, we hypothesize that one or a series of abrupt climatic…
Long read alignment based on maximal exact match seeds
2012
Abstract Motivation: The explosive growth of next-generation sequencing datasets poses a challenge to the mapping of reads to reference genomes in terms of alignment quality and execution speed. With the continuing progress of high-throughput sequencing technologies, read length is constantly increasing and many existing aligners are becoming inefficient as generated reads grow larger. Results: We present CUSHAW2, a parallelized, accurate, and memory-efficient long read aligner. Our aligner is based on the seed-and-extend approach and uses maximal exact matches as seeds to find gapped alignments. We have evaluated and compared CUSHAW2 to the three other long read aligners BWA-SW, Bowtie2 an…
NeoFox: annotating neoantigen candidates with neoantigen features
2020
Abstract Summary The detection and prediction of true neoantigens is of great importance for the field of cancer immunotherapy. Wesearched the literature for proposed neoantigen features and integrated them into a toolbox called NEOantigen Feature toolbOX (NeoFox). NeoFox is an easy-to-use Python package that enables the annotation of neoantigen candidates with 16 neoantigen features. Availability and implementation NeoFox is freely available as an open source Python package released under the GNU General Public License (GPL) v3 license at https://github.com/TRON-Bioinformatics/neofox. Supplementary information Supplementary data are available at Bioinformatics online.
IntelliPy: a GUI for analyzing IntelliCage data
2021
Abstract Summary The IntelliCage systems offer the possibility to conduct long-term behavioral experiments on mice in social groups without human intervention. Although this setup provides new findings, only about 150 studies with the IntelliCage system have been published in the last two decades, which is also caused by the challenging problems of processing and handling the large and heterogeneous amounts of captured data. This application note introduces the Python-GUI IntelliPy, especially designed for users not very experienced in using programming languages. IntelliPy allows users to quickly analyze the IntelliCage output in a user-friendly way, thus making the systems more accessible…
LipiDisease: associate lipids to diseases using literature mining
2021
Abstract Summary Lipids exhibit an essential role in cellular assembly and signaling. Dysregulation of these functions has been linked with many complications including obesity, diabetes, metabolic disorders, cancer and more. Investigating lipid profiles in such conditions can provide insights into cellular functions and possible interventions. Hence the field of lipidomics is expanding in recent years. Even though the role of individual lipids in diseases has been investigated, there is no resource to perform disease enrichment analysis considering the cumulative association of a lipid set. To address this, we have implemented the LipiDisease web server. The tool analyzes millions of recor…