11 papers · ranked by Valyu relevance
Shawn Yates, Martin Lagüe, Ron Knox, Richard Cuthbert + 5 more
With the advent of next-generation marker platforms and phenomics in crop breeding programs, the volume of both the genotypic and phenotypic data produced has increased exponentially. Often the data remain underutilized if not properly collated, managed and accessed. Effective management of the data is paramount to…
Zhijie He, Cong Wang, Xudong Guo, Heyun Sun + 6 more
PE/PPE proteins, highly abundant in the Mycobacterium genome, play a vital role in virulence and immune modulation. Understanding their functions is key to comprehending the internal mechanisms of Mycobacterium. However, a lack of dedicated resources has limited research into PE/PPE proteins. Addressing this gap, we…
Yi Guo, Xiang Chen
The most important goal of pharmacogenetics research is to obtain genetic models closely related to drug efficacy in vivo and in vitro, which can be used to measure individual responses and then to assess the sensitivity and toxicity of anticancer drugs. However, these models are scattered in different pharmacogenetic…
Carol A. Soderlund
De novo transcriptome sequencing and analysis provides a way for researchers of non-model organisms to explore the differences between various conditions and species. The results are typically not definitive but will lead to new hypotheses to study. Therefore, it is important that the results be reproducible…
Lubos Molcan
Physiological processes oscillate in time. Circadian oscillations, over approximately 24-h, are very important and among the most studied. To evaluate the presence and significance of 24-h oscillations, physiological time distributed data (TDD) are often set to a cosinor model using a wide range of irregularly updated…
Olivier Sheik Amamuddy, Michael Glenister, Özlem Tastan Bishop
MDM-TASK-web is the web server for the MD-TASK and MODE-TASK software suites. It simplifies the set-up required to perform and visualize results from dynamic residue network analysis, perturbation-response scanning, dynamic cross-correlation, essential dynamics and normal mode analysis. In a nutshell, the server gives…
Jianming Zeng, Gang Li
Next-generation sequencing coupled to chromatin immunoprecipitation (ChIP-seq), DNase I hypersensitivity (DNase-seq) and the transposase-accessible chromatin assay (ATAC-seq) has generated enormous amounts of data, markedly improved our understanding of the transcriptional and epigenetic control of gene expression. To…
Fuyi Li, Cunshuo Fan, Tatiana T. Marquez-Lago, André Leier + 9 more
Post-translational modifications (PTMs) play very important roles in various cell signalling pathways and biological process. Due to PTMs’ extremely important roles, many major PTMs have been thoroughly studied, while the functional and mechanical characterization of major PTMs is well-documented in several databases.…
Dmitrii I. Sukhinin, Andreas K. Engel, Paul Manger, Claus C Hilgetag
Databases of structural connections of the mammalian brain, such as CoCoMac (cocomac.g-node.org) or BAMS (brancusi.usc.edu), are valuable resources for the analysis of brain connectivity and the modeling of brain dynamics in species such as the non-human primate or the rodent, and have also contributed to the…
Tina Sharma, Rakesh Kumar, Anshu Bhardwaj
Ab-AMR is a comprehensive repository of drug resistance mechanisms in Acinetobacter baumannii. The current version of Ab-AMR provides a drug resistance profile of 788 genomes. In order to ensure that the datasets in Ab-AMR have relevance both to the research and clinical community, standards of defining MIC…
Shichen Qiao, Chen Shen
In this study, a web database application with the Flask framework was developed to implement three types of queries and visualize the results over a bioinformatical dataset from Alfalfa (Medicago sativa). A backend SQLite database was constructed from genome FASTA, population variations, transcriptome, and annotation…