I put the NCBI My Bibliography link on my ORCID page.
November 7, 2026 at 9:37 PM
I put the NCBI My Bibliography link on my ORCID page.
My postdoc was very proud of himself for making an AI agent that searches PubMed for him daily, and so I showed him my NCBI "Saved Searches" that have been running on a schedule for the last twenty years, anyway, progress. Oh, but his agent gives summaries of the articles! You mean... abstracts?
November 6, 2026 at 6:44 PM
My postdoc was very proud of himself for making an AI agent that searches PubMed for him daily, and so I showed him my NCBI "Saved Searches" that have been running on a schedule for the last twenty years, anyway, progress. Oh, but his agent gives summaries of the articles! You mean... abstracts?
honestly just pubmed or ncbi and if i’m lazy wikipedia. it can get dry and i’m pretty sure the cookie trackers think i have every mental illness on earth by now but it works and it’s fun on the whole
November 6, 2026 at 1:28 AM
honestly just pubmed or ncbi and if i’m lazy wikipedia. it can get dry and i’m pretty sure the cookie trackers think i have every mental illness on earth by now but it works and it’s fun on the whole
Fun w/ AI coding - trivial effort to build web assembly (WASM) for old tools. Took my gradschool C code hack of yn00 - a fast tabular output of pairwise Ka,Ks - to rust and added full ML codeml pairwise. Runs in your browser, no webserver. hyphaltip.github.io/subopt-kaks/
kaks dN/dS
Estimate dN/dS (Ka/Ks) for coding sequences in the browser: Yang-Nielsen 2000, Nei-Gojobori 1986 and codeml-style pairwise maximum likelihood, all 27 NCBI genetic codes. Nothing leaves your computer.
hyphaltip.github.io
November 6, 2026 at 7:35 AM
Fun w/ AI coding - trivial effort to build web assembly (WASM) for old tools. Took my gradschool C code hack of yn00 - a fast tabular output of pairwise Ka,Ks - to rust and added full ML codeml pairwise. Runs in your browser, no webserver. hyphaltip.github.io/subopt-kaks/
Orbit: Reproducible Agentic Workflow Development with Cloud Execution Included (Poster 126, live demo). Nekrutenko, Cain & Baker demo Orbit live: a desktop app that plans, runs and publishes analyses on Galaxy + NCBI Datasets, across TACC/Jetstream2/ACCESS-CI. ##CSHLdata26 (8/8)
November 5, 2026 at 10:03 PM
Orbit: Reproducible Agentic Workflow Development with Cloud Execution Included (Poster 126, live demo). Nekrutenko, Cain & Baker demo Orbit live: a desktop app that plans, runs and publishes analyses on Galaxy + NCBI Datasets, across TACC/Jetstream2/ACCESS-CI. ##CSHLdata26 (8/8)
Any link there? www.ncbi.nlm.nih.gov/datasets/tax...
(Seems I'm falling into a rabbit hole...)
(Seems I'm falling into a rabbit hole...)
November 5, 2026 at 7:37 AM
Any link there? www.ncbi.nlm.nih.gov/datasets/tax...
(Seems I'm falling into a rabbit hole...)
(Seems I'm falling into a rabbit hole...)
I would love to know the story behind this naming... www.ncbi.nlm.nih.gov/datasets/tax...
November 5, 2026 at 6:25 AM
I would love to know the story behind this naming... www.ncbi.nlm.nih.gov/datasets/tax...
Authors published a paper in Biorxiv, they used NCBI Genome in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #STMpublishing
www.biorxiv.org
November 5, 2026 at 1:00 PM
Authors published a paper in Biorxiv, they used NCBI Genome in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #STMpublishing
Is anyone having trouble accessing fasta sequences on ncbi right now or is it just me? I keep getting this:
November 2, 2026 at 10:14 PM
Is anyone having trouble accessing fasta sequences on ncbi right now or is it just me? I keep getting this:
Authors published a paper in Biorxiv, they used NCBI Sequence Read A in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #methodsmatter
www.biorxiv.org
November 4, 2026 at 1:00 PM
Authors published a paper in Biorxiv, they used NCBI Sequence Read A in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #methodsmatter
CRV Science Labs ⚗️
🌳 Permo-Carboniferous–Cenozoic Lepidoptera Genomic Radiation, Angiosperm-Coupled Ditrysia & Papilionoidea Time-Tree, and COX1 DNA Barcode Resolution vs. Deep-Node Saturation Boundaries — A 72-taxon, …
https://crvscience.com/labs/discoveries/lepidoptera-ditrysia-timetree-cox1-gap
🌳 Permo-Carboniferous–Cenozoic Lepidoptera Genomic Radiation, Angiosperm-Coupled Ditrysia & Papilionoidea Time-Tree, and COX1 DNA Barcode Resolution vs. Deep-Node Saturation Boundaries — A 72-taxon, …
https://crvscience.com/labs/discoveries/lepidoptera-ditrysia-timetree-cox1-gap
CRV Science Labs ⚗️
🌳 Permo-Carboniferous–Cenozoic Lepidoptera Genomic Radiation, Angiosperm-Coupled Ditrysia & Papilionoidea Time-Tree, and COX1 DNA Barcode Resolution vs. Deep-Node Saturation Boundaries — A 72-taxon, 1,078,183 bp (1.08 Mb across 92 NCBI RefSeq/GenBank sequence records) Dual-Pass …
crvscience.com
November 6, 2026 at 3:52 AM
CRV Science Labs ⚗️
🌳 Permo-Carboniferous–Cenozoic Lepidoptera Genomic Radiation, Angiosperm-Coupled Ditrysia & Papilionoidea Time-Tree, and COX1 DNA Barcode Resolution vs. Deep-Node Saturation Boundaries — A 72-taxon, …
https://crvscience.com/labs/discoveries/lepidoptera-ditrysia-timetree-cox1-gap
🌳 Permo-Carboniferous–Cenozoic Lepidoptera Genomic Radiation, Angiosperm-Coupled Ditrysia & Papilionoidea Time-Tree, and COX1 DNA Barcode Resolution vs. Deep-Node Saturation Boundaries — A 72-taxon, …
https://crvscience.com/labs/discoveries/lepidoptera-ditrysia-timetree-cox1-gap
Vertical lollipop timeline listing years down the side, with bar length showing annual publications on microglial senescence in neurodegeneration research.
#MicroglialSenescence #Neuroinflammation #AlzheimerDisease #DiseaseAssociatedMicroglia #Bibliometrics #NeurodegenerationResearch #Gliobiology
#MicroglialSenescence #Neuroinflammation #AlzheimerDisease #DiseaseAssociatedMicroglia #Bibliometrics #NeurodegenerationResearch #Gliobiology
![Figure: Microglial senescence papers have climbed steeply since 2000
I am sharing a bibliometric view of how the literature linking microglia, ageing or senescence, and neurodegeneration has developed. The chart is a vertical year-ladder lollipop timeline: each year from 2000 to 2025 is a rung, stem length is proportional to the annual PubMed record count, and the peak year is accented.
Data come from PubMed (NCBI E-utilities) using microglia[tiab] AND (senescence[tiab] OR senescent[tiab] OR aging[tiab] OR ageing[tiab]) AND (neurodegeneration[tiab] OR Alzheimer[tiab]), yielding 1,658 records in total, and these counts reflect indexing and query wording, not research effort or quality.
The series begins at 3 records in 2000 and reaches 197 in 2025, which is also the peak year. That corresponds to a 65.7-fold increase, with a mean annual growth of 18.2%. The rise is steady rather than driven by a single outlier year, which is why the ladder form is useful: the lengthening stems make the cumulative shift readable without smoothing.
The increase is temporally associated with a broader conceptual shift in the field. Microglia are increasingly described in terms of replicative exhaustion, CDKN2A-linked cell cycle arrest, the senescence-associated secretory phenotype, impaired phagocytic clearance and altered lipid handling, alongside disease-associated microglial states. Whether these descriptions converge on a single senescent phenotype or reflect partially overlapping activation programmes is not something this record count can resolve. The query also captures papers that use ageing as a covariate rather than as a mechanistic variable, so precision for true senescence studies is likely imperfect.
Open questions for colleagues: how should keyword-based retrieval be reconciled with marker-based definitions of senescent microglia, and would restricting to title or abstract mentions of specific effectors change the trajectory?](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:cmhgqrx4smzujdep5355m3rb/bafkreigvtghn6mco6k437ax53tbtka5cuuh4ku5paq3qv7odx6zjbeqp64)
![Figure: Microglial senescence papers have climbed steeply since 2000
I am sharing a bibliometric view of how the literature linking microglia, ageing or senescence, and neurodegeneration has developed. The chart is a vertical year-ladder lollipop timeline: each year from 2000 to 2025 is a rung, stem length is proportional to the annual PubMed record count, and the peak year is accented.
Data come from PubMed (NCBI E-utilities) using microglia[tiab] AND (senescence[tiab] OR senescent[tiab] OR aging[tiab] OR ageing[tiab]) AND (neurodegeneration[tiab] OR Alzheimer[tiab]), yielding 1,658 records in total, and these counts reflect indexing and query wording, not research effort or quality.
The series begins at 3 records in 2000 and reaches 197 in 2025, which is also the peak year. That corresponds to a 65.7-fold increase, with a mean annual growth of 18.2%. The rise is steady rather than driven by a single outlier year, which is why the ladder form is useful: the lengthening stems make the cumulative shift readable without smoothing.
The increase is temporally associated with a broader conceptual shift in the field. Microglia are increasingly described in terms of replicative exhaustion, CDKN2A-linked cell cycle arrest, the senescence-associated secretory phenotype, impaired phagocytic clearance and altered lipid handling, alongside disease-associated microglial states. Whether these descriptions converge on a single senescent phenotype or reflect partially overlapping activation programmes is not something this record count can resolve. The query also captures papers that use ageing as a covariate rather than as a mechanistic variable, so precision for true senescence studies is likely imperfect.
Open questions for colleagues: how should keyword-based retrieval be reconciled with marker-based definitions of senescent microglia, and would restricting to title or abstract mentions of specific effectors change the trajectory?](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:cmhgqrx4smzujdep5355m3rb/bafkreidcirevdpfmsonmlna2t7k2smtmcrym7pr7xsz46xrlfdmicje67q)
November 2, 2026 at 5:35 PM
Vertical lollipop timeline listing years down the side, with bar length showing annual publications on microglial senescence in neurodegeneration research.
#MicroglialSenescence #Neuroinflammation #AlzheimerDisease #DiseaseAssociatedMicroglia #Bibliometrics #NeurodegenerationResearch #Gliobiology
#MicroglialSenescence #Neuroinflammation #AlzheimerDisease #DiseaseAssociatedMicroglia #Bibliometrics #NeurodegenerationResearch #Gliobiology
CRV Science Labs ⚗️
🦠 Hierarchical Antimicrobial Resistance, Porin Disruption & Mobile HGT Island Calibration: Benchmarking Against NCBI AMRFinderPlus — We implement and calibrate a 5-stage native Rust Hierarchical Antimicrobial Resista…
https://crvscience.com/labs/discoveries/amr-hgt-amrfinderplus
🦠 Hierarchical Antimicrobial Resistance, Porin Disruption & Mobile HGT Island Calibration: Benchmarking Against NCBI AMRFinderPlus — We implement and calibrate a 5-stage native Rust Hierarchical Antimicrobial Resista…
https://crvscience.com/labs/discoveries/amr-hgt-amrfinderplus
CRV Science Labs ⚗️
🦠 Hierarchical Antimicrobial Resistance, Porin Disruption & Mobile HGT Island Calibration: Benchmarking Against NCBI AMRFinderPlus — We implement and calibrate a 5-stage native Rust Hierarchical Antimicrobial Resistance (AMR), Point-Mutation, Porin-Disruption, and Horizontal Gen…
crvscience.com
November 1, 2026 at 9:31 AM
CRV Science Labs ⚗️
🦠 Hierarchical Antimicrobial Resistance, Porin Disruption & Mobile HGT Island Calibration: Benchmarking Against NCBI AMRFinderPlus — We implement and calibrate a 5-stage native Rust Hierarchical Antimicrobial Resista…
https://crvscience.com/labs/discoveries/amr-hgt-amrfinderplus
🦠 Hierarchical Antimicrobial Resistance, Porin Disruption & Mobile HGT Island Calibration: Benchmarking Against NCBI AMRFinderPlus — We implement and calibrate a 5-stage native Rust Hierarchical Antimicrobial Resista…
https://crvscience.com/labs/discoveries/amr-hgt-amrfinderplus
Progress and disparities in fungal genomics in the long-read era
->Nature | More on "Fungal genomics and long-read sequencing" at BigEarthData.ai
->Nature | More on "Fungal genomics and long-read sequencing" at BigEarthData.ai
Progress and disparities in fungal genomics in the long-read era
Goffeau, A. et al. Life with 6000 genes. Science 274, 563–567 (1996). Birren, B. W., Fink, G. & Lander, E. Fungal Genome Initiative: White Paper Developed by the Fungal Research Community https://www.broadinstitute.org/files/shared/fungi/fgi/FGI_01_whitepaper_2002.pdf (2002). National Center for Biotechnology Information (NCBI). National Library of Medicine (US), National Center for Biotechnology Information https://www.ncbi.nlm.nih.gov/ (1988). Grigoriev, I. V. et al. MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res. 42, D699–D704 (2014). Marks, R. A., Hotaling, S., Frandsen, P. B. & VanBuren, R. Representation and participation across 20 years of plant genome sequencing. Nat. Plants 7, 1571–1578 (2021). Hotaling, S., Kelley, J. L. & Frandsen, P. B. Toward a genome sequence for every animal: Where are we now? Proc. Natl Acad. Sci. USA 118, e2109019118 (2021). Hotaling, S. et al. Long reads are revolutionizing 20 years of insect genome sequencing. Genome Biol. Evol. 13, evab138 (2021). Niego, A. G. T. et al. The contribution of fungi to the global economy. Fungal Divers. 121, 95–137 (2023). Simões, D., de Andrade, E. & Sabino, R. Fungi in a One Health perspective. Encyclopedia 3, 900–918 (2023). Sarhan, M. S., Abdalrahem, A., Maixner, F. & Fuchsberger, C. De novo assembly of complete circular mitochondrial genomes from...
www.nature.com
November 3, 2026 at 12:47 PM
Sigh. Really hoping none of this nonsense carries over into the core of NCBI redesign.
October 28, 2026 at 3:47 PM
Sigh. Really hoping none of this nonsense carries over into the core of NCBI redesign.
Mascot Newsletter, October 2026
Mascot Distiller skill for AI assistants: develop your own quantitation reports.
SOX3 is a leading candidate gene for a rare form of X-linked Charcot–Marie–Tooth neuropathy.
New NCBI Taxonomy site.
www.matrixscience.com/nl/202610/ne...
#proteomics #massspec
Mascot Distiller skill for AI assistants: develop your own quantitation reports.
SOX3 is a leading candidate gene for a rare form of X-linked Charcot–Marie–Tooth neuropathy.
New NCBI Taxonomy site.
www.matrixscience.com/nl/202610/ne...
#proteomics #massspec
October 29, 2026 at 11:13 AM
Mascot Newsletter, October 2026
Mascot Distiller skill for AI assistants: develop your own quantitation reports.
SOX3 is a leading candidate gene for a rare form of X-linked Charcot–Marie–Tooth neuropathy.
New NCBI Taxonomy site.
www.matrixscience.com/nl/202610/ne...
#proteomics #massspec
Mascot Distiller skill for AI assistants: develop your own quantitation reports.
SOX3 is a leading candidate gene for a rare form of X-linked Charcot–Marie–Tooth neuropathy.
New NCBI Taxonomy site.
www.matrixscience.com/nl/202610/ne...
#proteomics #massspec
Work by @rociomozo.bsky.social, @andreailla.bsky.social (also an undergrad in the lab at the time), and @fonamental.bsky.social at @ibe-barcelona.bsky.social. Isolates are cryobanked, 16S sequences on NCBI 🙌 Paper 📄 doi.org/10.1007/s002...
Culture and Isolation of Bacteria Associated with Mediterranean Corals - Microbial Ecology
Corals harbor a diverse bacterial community that facilitates adaptation and sustains their health. In coral holobiont research, culture-independent approaches have transformed the existing paradigm. M...
doi.org
October 27, 2026 at 2:11 PM
Work by @rociomozo.bsky.social, @andreailla.bsky.social (also an undergrad in the lab at the time), and @fonamental.bsky.social at @ibe-barcelona.bsky.social. Isolates are cryobanked, 16S sequences on NCBI 🙌 Paper 📄 doi.org/10.1007/s002...
Evolutionary dynamics of the glycoprotein (gp) gene of Zaire Ebolavirus strains and its implications across Africa
Evolutionary dynamics of the glycoprotein (gp) gene of Zaire Ebolavirus strains and its implications across Africa
Twenty seven viral sequences were acquired from the National Center for Biotechnology Information GenBank (NCBI GenBank) and analyzed them using multiple alignments with the Fast Fourier Transform (MAFFT), and Molecular Evolutionary Genetics Analysis (MEGA) programs. The purpose of this study was to examine the genetic variation in the glycoprotein (gp) gene among Zaire ebolavirus (ZEBOV) strains. We identified 347 mutations with a high single nucleotide polymorphism (SNP) frequency at positions 2008, 2038, 2221, 2267, and 2271.
dlvr.it
October 29, 2026 at 10:45 PM
Evolutionary dynamics of the glycoprotein (gp) gene of Zaire Ebolavirus strains and its implications across Africa
man... I'm just trying to find some sequences, I didn't come here for megacringe
October 26, 2026 at 1:26 PM
man... I'm just trying to find some sequences, I didn't come here for megacringe
Has anyone had recent contact with NCBI regarding genome submissions? I've got some that I want released for an accepted paper, but have had zero luck getting a response to requests for immediate release.
October 26, 2026 at 2:01 PM
Has anyone had recent contact with NCBI regarding genome submissions? I've got some that I want released for an accepted paper, but have had zero luck getting a response to requests for immediate release.
My logo is drawn from the first bases of the public human mitochondrial reference sequence (rCRS), not anyone's own DNA. G A T C A sets the shape, turn and size of the four frames.
No randomness: same input, same mark.
#CreativeCoding #GenerativeArt #CodeArt
No randomness: same input, same mark.
#CreativeCoding #GenerativeArt #CodeArt
![The HYSTERON logo beside the data it is drawn from, on a dark navy background. Left: four nested rounded-square frames, alternating yellow and blue, each turned at a slightly different angle, with a small white figure-eight at the centre. Right: the heading drawn from a public DNA reference, human mitochondrial genome, rCRS (NCBI NC_012920.1), bases 1–64 of 16,569. Below, the 64 letters in four rows of 16, starting GATCACAGGTCTATCA; the first five, GATCA, are yellow, with the digits 2 0 3 1 0 under them. Then A=0 C=1 G=2 T=3 and a short code excerpt: for each of four frames, the exponent n = 2.5 + d[i], the rotation from a running sum of the digits, and the size step 0.70 + 0.03 times the next digit. A comment reads: centre, a figure-eight (lemniscate), no randomness.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:hwq7f7qsvneg2po5swjm3fcr/bafkreicintejhjrsr354prkdcitrdpwfda4bw32qrmohpolexwwhmwz5e4)
October 29, 2026 at 6:41 PM
My logo is drawn from the first bases of the public human mitochondrial reference sequence (rCRS), not anyone's own DNA. G A T C A sets the shape, turn and size of the four frames.
No randomness: same input, same mark.
#CreativeCoding #GenerativeArt #CodeArt
No randomness: same input, same mark.
#CreativeCoding #GenerativeArt #CodeArt
@chrmosimann.bsky.social Twelve ways to misspell Homo sapiens, every one of them canon at NCBI. Your last rejected manuscript just got promoted.
October 26, 2026 at 12:21 PM
@chrmosimann.bsky.social Twelve ways to misspell Homo sapiens, every one of them canon at NCBI. Your last rejected manuscript just got promoted.
If you ever suffer from imposter syndrome,look at how experts posted human genome information at NCBI:
#SpellingMatters #Genomics #devbio #evodevo 👫
#SpellingMatters #Genomics #devbio #evodevo 👫
October 23, 2026 at 4:29 PM
If you ever suffer from imposter syndrome,look at how experts posted human genome information at NCBI:
#SpellingMatters #Genomics #devbio #evodevo 👫
#SpellingMatters #Genomics #devbio #evodevo 👫