genehackJul 22, 2025

Since the current …everything has folks a little on edge about .gov websites going down, be aware that #NCBI (hosts of #Pubmed, #GenBank, and other important #biomed database sites) will be offline from this Friday evening into the weekend.

(Consider re-sharing if you have an audience that would appreciate knowing.)

https://ncbiinsights.ncbi.nlm.nih.gov/2025/07/08/ncbi-website-maintenance-july-26th/

NCBI Website Maintenance - Beginning July 25th - NCBI Insights

On Friday, July 25th, starting at 9:00 PM EDT, we’ll be performing essential maintenance on the NLM data center. This upgrade is critical to ensure the continued reliability and stability of our services. We anticipate this planned outage will last 24 hours or more. During this time, users may experience interrupted access or degraded performance … Continue reading NCBI Website Maintenance — Beginning July 25th →

NCBI Insights
Moreno ColaiacovoFeb 11, 2025

Questo articolo di @HelenBranswell (purtroppo dietro paywall) esprime la preoccupazione che hanno tanti scienziati nel mondo: la possibilità che #Trump rimuova i database di sequenze #Genbank e SRA, da sempre punto di riferimento per la ricerca biomedica. 🧬

Certo gli stessi dati sono archiviati anche nei database di ENA e DDBJ, ma si tratta di risorse che pochi conoscono. Se le banche dati americane dovessero sparire, sarebbe un problema serio per tutti!

https://www.statnews.com/2025/02/10/genbank-sra-nih-genetic-databases-trump-impact/

Amid shakeup in U.S. science, researchers express alarm over integrity of key genetic databases

Amid a shakeup in U.S. science, researchers are expressing alarm over the integrity of key genetic databases overseen by the NIH.

STAT
J of Systematics and EvolutionJan 19, 2025
Meet PyNCBIminer!
This open-source, user-friendly software automates the assembly of large #DNA data sets from #GenBank for #phylogenetic reconstruction using the supermatrix method--and eliminates the need for large local #databases!
https://doi.org/10.1111/jse.13155
@WileyEcolEvol
#JSE #bioinformatics #BioinformaticsTools
Teresita Porter 🙋🏻‍♀️Oct 19, 2024

Taxonomy Identifiers (TaxId) for Biodiversity Genomics: a guide to getting TaxId for submission of data to public databases

https://wellcomeopenresearch.org/articles/9-591

#preprint #taxonomy #databases #INSCD #genbank #ENA #DDBJ

Show threadCharles PlessyAug 26, 2024
Our genome assembly was published back-to-back in Genome Biology and Evolution with the work of Yael Klirs and her co-authors (https://doi.org/10.1093/gbe/evae181), and our results are in very good agreement. I am very glad that it happened, because some of the features of #Oikopleura dioica's mitogenome were difficult to accept for #GenBank curators. I hope that our publications will lead them to revise their point of view and accept our gene annotation.
Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss

Abstract. Sequencing the mitochondrial genome of the tunicate Oikopleura dioica is a challenging task due to the presence of long poly-A/T homopolymer stre

OUP Academic
Giuseppe MichieliMay 25, 2024

#US #CDC: Technical #Update: #Summary #Analysis of #Genetic #Sequence of a HPAI A(#H5N1) Virus Identified in a #Human in #Michigan, https://www.cdc.gov/flu/avianflu/spotlights/2023-2024/h5n1-technical-update-may-24-2024.html

This analysis supports conclusion that overall #risk to general public associated with the ongoing HPAI A(H5N1) #outbreak has not changed and remains low at this time. #Genome of the virus identified from patient in Michigan (A/Michigan/90/2024) is publicly posted in #GISAID (EPI_ISL_19162802) and has been submitted to #GenBank.

Technical Update: Summary Analysis of the Genetic Sequence of a Highly

This is a technical summary of an analysis of the genomic sequence of the virus identified in the Michigan case of highly pathogenic avian influenza (HPAI) A(H5N1) virus infection.

Centers for Disease Control and Prevention
idw_onlineMay 8, 2024
Projekt koordiniert von @jki_bund will Öko-Linsenanbau in Deutschland wiederbeleben. Dazu muss die #Linse züchterisch bzgl Winterhärte, Ertrag verbessert werden. Umfangreiche Testung mit regionalen Landsorten & #Genbank -Sortimenten @LeibnizIPK geplant.
https://nachrichten.idw-online.de/2024/05/08/neues-projekt-will-linsenanbau-in-deutschland-wiederbeleben
Neues Projekt will Linsenanbau in Deutschland wiederbeleben

Matt WillemsenJan 21, 2024
First SARS-CoV-2 genome was deposited in U.S. database earlier than previously known
https://www.science.org/content/article/first-sars-cov-2-genome-deposited-us-database-earlier-than-previously-known #SARS—CoV—2 #genome #GenBank #NIH #china
Teresita Porter 🙋🏻‍♀️Dec 15, 2023

DNA sequences from type specimens and type strains - how to increase their number and improve their annotation in NCBI GenBank and related databases

https://doi.org/10.1093/sysbio/syad068

#mycology #fungi #prokaryotes #eukaryotes #TypeSpecimens #TypeStrains #NCBI #GenBank #sequence #databases

DNA sequences from type specimens and type strains – how to increase their number and improve their annotation in NCBI GenBank and related databases

Abstract. Scientific names permit humans and search engines to access knowledge about the biodiversity that surrounds us, and names linked to DNA sequences are

OUP Academic
Teresita Porter 🙋🏻‍♀️Nov 29, 2023

Database resources of the National Center for Biotechnology Information

https://doi.org/10.1093/nar/gkad1044

#ReferenceSequence #Databases #NCBI #GenBank #PubMed #SRA #RefSeq #Taxonomy #bioinformatics

Database resources of the National Center for Biotechnology Information

Abstract. The National Center for Biotechnology Information (NCBI) provides online information resources for biology, including the GenBank® nucleic acid sequen

OUP Academic