13 papers · ranked by Valyu relevance
Jiaxian Shen, Fangqiong Ling, Erica M. Hartmann
As the scientific literature grows exponentially and research becomes increasingly interdisciplinary, accurate and high-throughput reference deduplication is vital in evidence synthesis studies (e.g., systematic reviews, meta-analyses) to ensure the completeness of datasets while reducing the manual screening burden.…
Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf
Ontologies are widely used in biomedicine for the annotation and standardization of data. One of the main roles of ontologies is to provide structured background knowledge within a domain as well as a set of labels, synonyms, and definitions for the classes within a domain. The two types of information provided by…
Negacy D. Hailu, Michael Bada, Asmelash Teka Hadgu, Lawrence E. Hunter
the automated identification of mentions of ontological concepts in natural language texts is a central task in biomedical information extraction. Despite more than a decade of effort, performance in this task remains below the level necessary for many applications. recently, applications of deep learning in natural…
John A. Bachman, Benjamin M. Gyori, Peter K. Sorger
A major challenge in analyzing large phosphoproteomic datasets is that information on phosphorylating kinases and other upstream regulators is limited to a small fraction of phosphosites. One approach to addressing this problem is to aggregate and normalize information from all available information sources, including…
Michael B. Cole, Davide Risso, Allon Wagner, David DeTomaso + 4 more
Systematic measurement biases make data normalization an essential preprocessing step in single-cell RNA sequencing (scRNA-seq) analysis. There may be multiple, competing considerations behind the assessment of normalization performance, some of them study-specific. Because normalization can have a large impact on…
Li Lin, Minfang Song, Yong Jiang, Xiaojing Zhao + 2 more
Normalization with respect to sequencing depth is a crucial step in single-cell RNA sequencing preprocessing. Most methods normalize data using the whole transcriptome based on the assumption that the majority of transcriptome remains constant and are unable to detect drastic changes of the transcriptome. Here, we…
Lis Arend, Klaudia Adamowicz, Johannes R. Schmidt, Yuliya Burankova + 7 more
Despite the significant progress in accuracy and reliability in mass spectrometry technology, as well as the development of strategies based on isotopic labeling or internal standards in recent decades, systematic biases originating from non-biological factors remain a significant challenge in data analysis. In…
Zhenfeng Wu, Weixiang Liu, Haishuo Ji, Deshui Yu + 4 more
Data normalization is a crucial step in the gene expression analysis as it determines the validity of its downstream analyses. Although many metrics has been designed to evaluate the relative success of these methods, the results by different metrics did not show consistency. Based on the previous work, we designed a…
Diem-Trang T. Tran, Aditya Bhaskara, Matthew Might, Balagurunathan Kuberan
The use of RNA-sequencing has garnered much attention in the recent years for characterizing and understanding various biological systems. However, it remains a major challenge to gain insights from a large number of RNA-seq experiments collectively, due to the normalization problem. Current normalization methods are…
Meng Wang, Lihua Jiang, Ruiqi Jian, Joanne Y. Chan + 3 more
Data normalization is an important step in processing proteomics data generated in mass spectrometry (MS) experiments, which aims to reduce sample-level variation and facilitate comparisons of samples. Previously published methods for normalization primarily depend on the assumption that the distribution of protein…
Ramyar Molania, Johann A. Gagnon-Bartsch, Alexander Dobrovic, Terence P Speed
The Nanostring nCounter gene expression assay uses molecular barcodes and single molecule imaging to detect and count hundreds of unique transcripts in a single reaction. These counts need to be normalized to adjust for the amount of sample, variations in assay efficiency, and other factors. Most users adopt the…
Annie W. Shieh, Sandeep K. Bansal, Zhen Zuo, Sidney H. Wang
Acute cellular stress is known to induce a global reduction in protein translation through suppression of cap dependent translation. However, selective translation in response to acute stress has been shown to play important roles in regulating the stress response. An accurate transcriptome-wide profile of acute…
Diogo de Jesus Soares Machado, Camilla Reginatto De Pierri, Letícia Graziela Costa Santos, Leonardo Scapin + 4 more
The large amount of existing textual data justifies the development of new text mining tools. Bioinformatics tools can be brought to Text Mining, increasing the arsenal of resources. Here, we present BIOTEXT, a package of strategies for converting natural language text into biological-like information data, providing a…