RNA expression analysis was performed on the corpus luteum tissue at five time points after prostaglandin F2 alpha treatment of midcycle cows using an Affymetrix Bovine Gene v1 Array. The normalized linear microarray data was uploaded to the NCBI GEO repository (GSE94069). Subsequent statistical analysis determined differentially expressed transcripts ± 1.5-fold change from saline control with P ≤ 0.05. Gene ontology of differentially expressed transcripts was annotated by DAVID and Panther. Physiological characteristics of the study animals are presented in a figure. Bioinformatic analysis by Ingenuity Pathway Analysis was curated, compiled, and presented in tables. A dataset comparison with similar microarray analyses was performed and bioinformatics analysis by Ingenuity Pathway Analysis, DAVID, Panther, and String of differentially expressed genes from each dataset as well as the differentially expressed genes common to all three datasets were curated, compiled, and presented in tables. Finally, a table comparing four bioinformatics tools' predictions of functions associated with genes common to all three datasets is presented. These data have been further analyzed and interpreted in the companion article "Early transcriptome responses of the bovine mid-cycle corpus luteum to prostaglandin F2 alpha includes cytokine signaling". Resources in this dataset:Resource Title: Supporting information as Excel spreadsheets and tables. File Name: Web Page, url: http://www.sciencedirect.com/science/article/pii/S2352340917304031?via=ihub#s0070

The graph shows the number of articles published in the discipline of ^.

Framing the investigation of diverse cancers as a machine learning problem has recently shown significant potential in multi-omics analysis and cancer research. Empowering these successful machine learning models are the high-quality training datasets with sufficient data volume and adequate preprocessing. However, while there exist several public data portals including The Cancer Genome Atlas (TCGA) multi-omics initiative or open-bases such as the LinkedOmics, these databases are not off-the-shelf for existing machine learning models. we propose MLOmics, an open cancer multi-omics database aiming at serving better the development and evaluation of bioinformatics and machine learning models. MLOmics contains 8,314 patient samples covering all 32 cancer types with four omics types, stratified features, and extensive baselines. Complementary support for downstream analysis and bio-knowledge linking are also included to support interdisciplinary analysis.

In recent years, the explosion of genomic data and bioinformatic tools has been accompanied by a growing conversation around reproducibility of results and usability of software. However, the actual state of the body of bioinformatics software remains largely unknown. The purpose of this paper is to investigate the state of source code in the bioinformatics community, specifically looking at relationships between code properties, development activity, developer communities, and software impact. To investigate these issues, we curated a list of 1,720 bioinformatics repositories on GitHub through their mention in peer-reviewed bioinformatics articles. Additionally, we included 23 high-profile repositories identified by their popularity in an online bioinformatics forum. We analyzed repository metadata, source code, development activity, and team dynamics using data made available publicly through the GitHub API, as well as article metadata. We found key relationships within our dataset, including: certain scientific topics are associated with more active code development and higher community interest in the repository; most of the code in the main dataset is written in dynamically typed languages, while most of the code in the high-profile set is statically typed; developer team size is associated with community engagement and high-profile repositories have larger teams; the proportion of female contributors decreases for high-profile repositories and with seniority level in author lists; and, multiple measures of project impact are associated with the simple variable of whether the code was modified at all after paper publication. In addition to providing the first large-scale analysis of bioinformatics code to our knowledge, our work will enable future analysis through publicly available data, code, and methods. Code to generate the dataset and reproduce the analysis is provided under the MIT license at https://github.com/pamelarussell/github-bioinformatics. Data are available at https://doi.org/10.17605/OSF.IO/UWHX8.

Table. 1. Recent Bioinformatics Tools for Discovery, Prediction, and Analysis of Natural Product Pathways. (2020–2024).

List of Top Authors of Bioinformatics and Biology Insights sorted by articles.

List of Top Authors of Genomics, Proteomics and Bioinformatics sorted by articles.

List of Top Authors of Current Protocols in Bioinformatics sorted by articles.

The BAltic Gene Set gene catalogue v1.1 encompasses 66,530,673 genes.The 66 million genes are based on metagenomic data from Alneberg at al. (2020) from 124 seawater samples, that span the salinity and oxygen gradients of the Baltic Sea and capture seasonal dynamics at two locations. To obtain the gene catalogue, we used a mix-assembly approach described in Delgado et al. (2022).The gene catalogue has been functionally and taxonomically annotated, using the Mix-assembly Gene Catalog pipeline (https://github.com/EnvGen/mix_assembly_pipeline). The taxonomy annotation was performed using Mmseqs21 and CAT3.Here you find representative mix-assembly gene and protein sequences, and different types of annotations for the proteins. Also, contigs for the co-assembly are included (see Delgado et al. 2022), gene and protein sequences from each individual assembly and the co-assembly, and a table containing the genes in each of the clusters. See README for details.When using the BAGSv1.1 gene catalogue, please cite:1. Delgado LF, Andersson AF. Evaluating metagenomic assembly approaches for biome-specific gene catalogues. Microbiome 10, 72 (2022)2. Alneberg J, Bennke C, Beier S, Bunse C, Quince C, Ininbergs K, Riemann L, Ekman M, Jürgens K, Labrenz M, Pinhassi J, Andersson AF (2020) Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes. Commun Biol 3, 119 (2020)

This collection contains an example MINUTE-ChIP dataset to run minute pipeline on, provided as supporting material to help users understand the results of a MINUTE-ChIP experiment from raw data to a primary analysis that yields the relevant files for downstream analysis along with summarized QC indicators. Example primary non-demultiplexed FASTQ files provided here were used to generate GSM5493452-GSM5493463 (H3K27m3) and GSM5823907-GSM5823918 (Input), deposited on GEO with the minute pipeline all together under series GSE181241. For more information about MINUTE-ChIP, you can check the publication relevant to this dataset: Kumar, Banushree, et al. "Polycomb repressive complex 2 shields naïve human pluripotent cells from trophectoderm differentiation." Nature Cell Biology 24.6 (2022): 845-857. If you want more information about the minute pipeline, there is a public biorXiv and a GitHub repository and official documentation.

List of Top Authors of Advances in Bioinformatics sorted by articles.

These are the reference genomes against which we assessed reads and consensus sequences.

Data about Phakopsora pachyrhizi, causative agent of soybean rust. Genomics and Bioinformatics Research Unit, Stoneville, MS. Resources in this dataset:Resource Title: All supplemental files. File Name: AllSupplementalFiles.zipResource Description: Word, Excel, and JAVA files Resource Title: Data dictionary for BMC Genomics P. pachyrhizi Supplemental Data. File Name: Data Dictionary - BMC Genomics P. pachyrhizi Supplemental Data.csv

Index file corresponding to BAM file http://figshare.com/articles/Example_BAM_file/1460736

Simulation results comparing the topconfects R package to other methods, to accompany a paper describing to topconfects method. The topconfects method finds confidently large differential gene expression effect sizes while correcting for multiple testing.

List of protein, disease, and compartment mentions per article

This record contains the data (references, reads, assemblies) used in the analyses for the Trycycler paper.

List of Top Authors of BMC Bioinformatics sorted by articles.

zipped folder containing 6340 files. Each file represents one genome with the filename as its GCF ID (NCBI accession id). The files contain repeat positions relative to oriC with + and - signs represent the repeat position in right and left replichore. Every repeat pair is separated by '||' symbol.

Autotransporters are secreted proteins that are assembled into the outer membrane of bacterial cells. The passenger domains of autotransporters are crucial for bacterial pathogenesis, with some remaining attached to the bacterial surface while others are released by proteolysis. An enigma remains as to whether autotransporters should be considered a class of secretion system, or simply a class of substrate with peculiar requirements for their secretion. We sought to establish a sensitive search protocol that could identify and characterize diverse autotransporters from bacterial genome sequence data. The new sequence analysis pipeline identified more than 1500 autotransporter sequences from diverse bacteria, including numerous species of Chlamydiales and Fusobacteria as well as all classes of Proteobacteria. Interrogation of the proteins revealed that there are numerous classes of passenger domains beyond the known proteases, adhesins and esterases. In addition the barrel-domain-a characteristic feature of autotransporters-was found to be composed from seven conserved sequence segments that can be arranged in multiple ways in the tertiary structure of the assembled autotransporter. One of these conserved motifs overlays the targeting information required for autotransporters to reach the outer membrane. Another conserved and diagnostic motif maps to the linker region between the passenger domain and barrel-domain, indicating it as an important feature in the assembly of autotransporters.