New tool from me: I wrote a local aligner that can do approximate reference-based alignment and find genes in a query microbial genome, without a separate indexing step or any temporary disk space usage.

Written fully in Rust and there will be a browser version out later: https://github.com/tmaklin/kbo 1/3

#rust #rustlang #bioinformatics

GitHub - tmaklin/kbo: Spectral Burrows-Wheeler transform accelerated local alignment search.

Spectral Burrows-Wheeler transform accelerated local alignment search. - tmaklin/kbo

^GitHub

Our new preprint on the impact of protein phosphorylation on structures is now out!

Protein phosphorylation is a key regulator of cellular processes.It's ubiquitous, yet the function and relevance of most phosphosites is unknown. Understanding phosphosite function requires elucidating the structural mechanisms through which it acts. (1)

https://www.biorxiv.org/content/10.1101/2024.10.18.617420v1?med=mas

@bioinformatics @strucbio #bioinformatics #protein #StructuralBiology

Global comparative structural analysis of responses to protein phosphorylation

Post-translational modifications (PTMs), particularly protein phosphorylation, are key regulators of cellular processes, impacting numerous aspects of protein activity.

^bioRxiv

Profile and Binomica Labs registered on archaea.bio!

I'll be doing a lot more Halobacteria & Halococcus work in the near future, looking forward to sharing some interesting notes

https://www.archaea.bio/profiles/sung-won-lim

#microbiology #archaea #bioinformatics

Sung won Lim

Independent researcher at Binomica Labs (Queens, NYC), and a remote adjunct researcher in Kyle lab at University of New Hampshire. 

^{Sung won Lim (archaea.bio)}

The SplitsTree App: interactive analysis and visualization using phylogenetic trees and networks

https://www.nature.com/articles/s41592-024-02406-3

#evolution #bioinformatics

The SplitsTree App: interactive analysis and visualization using phylogenetic trees and networks - Nature Methods

Nature Methods - The SplitsTree App: interactive analysis and visualization using phylogenetic trees and networks

^Nature

PhD Student in Virology/Bionformatics

Otto von Guericke Universität Magdeburg

The project will investigate genomic features in DVG and DI formation in #enteroviruses using #molecular biology and #bioinformatics.

See the full job description on jobRxiv: https://jobrxiv.org/job/otto-von-guericke-universitat-magdeburg-27778-phd-student-in-virology-bionformatics/?feed_id=...
https://jobrxiv.org/job/otto-von-guericke-universitat-magdeburg-27778-phd-student-in-virology-bionformatics/?feed_id=81269

PhD Student in Virology/Bionformatics

Post a job in 3min, or find thousands of job offers like this one at jobRxiv!

^jobRxiv

Funded PhD Position in metagenomics of environmental films

Texas Tech University

Exciting funded PhD opportunity studying metagenomics of environmental films

See the full job description on jobRxiv: https://jobrxiv.org/job/texas-tech-university-27778-funded-phd-position-in-metagenomics-of-environmental-films/?feed_id=79057

#biofilms #bioinformatics #biology #metag...
https://jobrxiv.org/job/texas-tech-university-27778-funded-phd-position-in-metagenomics-of-environmental-films/?feed_id=79057

Funded PhD Position in metagenomics of environmental films

Post a job in 3min, or find thousands of job offers like this one at jobRxiv!

^jobRxiv

1) Want to know how much of your metagenome is eukaryotic? No references? No problem. We developed SingleM microbial fraction (SMF) and ran it on 250k metagenomes https://www.biorxiv.org/content/10.1101/2024.05.16.594470v1.

If you know what Eukaryotes are there, you can filter reads by mapping to their genomes. However, often you don’t know what’s in your sample, or the euk doesn’t have a genome.

#metagenomics #bioinformatics #genomics #microbiomes #microbialecology

Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns

Metagenomes often contain many reads derived from eukaryotes. However, there is usually no reliable method for estimating the prevalence of non-microbial reads in a metagenome, forcing many analysis techniques to make the often-faulty assumption that…

^bioRxiv

"Indexing All Life's Known Biological #Sequences" https://www.biorxiv.org/content/10.1101/2020.10.01.322164v3

"In this work, we take advantage of recently developed, very efficient data structures and algorithms for representing sequence sets. We make Petabases of DNA sequences across all clades of life, including viruses, bacteria, fungi, plants, animals, and humans, fully searchable and make the indexes available to the research community"

#bioinformatics #database

Indexing All Life's Known Biological Sequences

The amount of biological sequencing data available in public repositories is growing exponentially, forming an invaluable biomedical research resource.

^bioRxiv

Hello sugar people of the . My former collegue Bernard Henrissat now in 🇩🇰 is looking for a #PhD student in a Marie Sklodowska-Curie 🇪🇺 training network to work with him at the Technical University of Denmark. More info:
https://euraxess.ec.europa.eu/jobs/201030
The deadline for application is May 31st, 2024 and the job will start in November.

Skills desired: #bioinformatics, general biology (++ #carbohydrates) and fluency in 🇬🇧.
Eligibility: the candidate should not have worked in 🇩🇰 before.

Call for 9 PhD fellowships within the MSCA DN project GLYCO-N: GLYCOprotein N-glycosylation from non-life to eukaryotes a Doctoral Network to expand the knowledge on a ubiquitous posttranslational modification of proteins.

Introduction:

^EURAXESS

There's a new minimap2 release with ONT specific accurate long reads setting. Looking forward to giving it a test run!

https://github.com/lh3/minimap2/releases/tag/v2.27

#bioinformatics #microbiology

Release Minimap2-2.27 (r1193) · lh3/minimap2

Notable changes to minimap2: New feature: added the lr:hq preset for accurate long reads at ~1% error rate. This was suggested by Oxford Nanopore developers (#1127). It is not clear if this prese...

^GitHub

Looking for some suggestions - I'm working with Archaeal genomic regions whose optimally fitting model seems to be Tamura-Nei (https://doi.org/10.1093/oxfordjournals.molbev.a040023).

Would it be too much to suspect the Archaeal region is under similar types of evolutionary pressure?

#archaea #microbiology #evolution #phylogenetics #bioinformatics

Large language models improve annotation of prokaryotic viral proteins

https://www.nature.com/articles/s41564-023-01584-8

#virology #viruses #bioinformatics #genomics

Large language models improve annotation of prokaryotic viral proteins - Nature Microbiology

Ocean viral proteome annotations are expanded by a machine learning approach that is not reliant on sequence homology and can annotate sequences not homologous to those seen in training.

^Nature

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

https://www.nature.com/articles/s41587-023-02100-3

#genomics #bioinformatics

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy - Nature Biotechnology

Nature Biotechnology - Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

^Nature

Gotta check these out!

Robust, scalable, and informative clustering for diverse biological networks

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03062-0

#bioinformatics #genomics #genetics #statistics

Robust, scalable, and informative clustering for diverse biological networks - Genome Biology

Clustering molecular data into informative groups is a primary step in extracting robust conclusions from big data.

^{BioMed Central}

Stowers is starting up a paid training program for bioinformatics, please share with anyone who might be interested in something like that! (in Kansas City)

https://www.stowers.org/gradschool/computational-biology-scholars

#bioinformatics

Computational Biology Scholars

The mission of The Graduate School of the Stowers Institute for Medical Research is to prepare a superb cadre of predoctoral researchers from around the world for the pursuit of innovative and creative investigations in the biological sciences.

^Turnstyle

If anyone is looking for the WGCNA tutorials while the Horvath's lab website has been down for a while, there's a Dropbox link with all the tutorials here: https://bioinformatics.stackexchange.com/a/21886

#bioinformatics

Where to access the WGCNA tutorial documents: Horvath lab site down

I am currently using the WGCNA package for some analysis and it seems the Horvath lab site is down. Does anyone know of anywhere else I can access the tutorial documents?

^{Bioinformatics Stack Exchange}

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

At my workplace, we're looking into how we can support the processing of very large datasets in R. It would be wonderful if some bioinformaticians could answer a couple of questions to direct us to the problem points.

We're hoping that we can publish something out of this that will be helpful to everyone in the field: https://forms.office.com/r/jNd2cbEZkh

#rstats #bioinformatics

Come work with us! I have a PhD position available to help understand which mutations in the non-coding parts of coding transcripts have functional consequences in Stem Cells.

We will using genome wide mesaurement of the effect of variation in miRNA binding sites to address when vairation causes changes in regulation and when it doesn't.

Mixed wetlab, bioinformatics and statistics project.

https://www.findaphd.com/phds/project/white-rose-bbsrc-dtp-how-can-we-identify-variants-in-untranslated-rna-that-affect-stem-cells/?p160958

#phdPosition #PhD #bioinformatics #UTR #miRNA #genetics

White Rose BBSRC DTP: How can we identify variants in untranslated RNA that affect stem-cells at University of Sheffield on FindAPhD.com

PhD Project - White Rose BBSRC DTP: How can we identify variants in untranslated RNA that affect stem-cells at University of Sheffield, listed on FindAPhD.com

^{www.FindAPhD.com}

Very happy to share our new publication in PLOS ONE:

KIPEs3: Automatic annotation of biosynthesis pathways
https://doi.org/10.1371/journal.pone.0294342

Excellent work by Andreas Rempel (Bielefeld University) and Nancy Choudhary (@PuckerLab @tubraunschweig #Bioinformatics #OpenAccess

#bioawk is a command-line gem; it’s an extension of awk that auto-assigns variables for BED, SAM, VCF, GFF, and FASTX[AQ] format files, speeding up routine tasks.

For FASTX:
$1:name
$2:seq
$3:qual (FASTQ only)
$4:comment

Found in @vsbuffalo’s great #Bioinformatics Data Skills.

PhylteR: efficient identification of outlier sequences in phylogenomic datasets.

PhylteR can automatically identify sequences likely to be hidden paralogs or horizontally transferred genes in very large datasets. Removing those sequences therefore reduces noise in downstream analyses.

Available as an R package on CRAN or as docker and singularity images.

Package:

https://cran.r-project.org/web/packages/phylter/index.html

Paper:

https://doi.org/10.1093/molbev/msad234

#Phylogeny #Genomics #bioinformatics #Phylogenomics

#PhD positions available in my group for Fall 2024 - projects focusing on #GiantVirus diversity and #evolution. Opportunities for both molecular wet-lab and #bioinformatics research.

The lab is fun, supportive, and inclusive, and we have many cool new viruses we are studying, so come join us!

Please boost and spread the word!

https://jobrxiv.org/job/virginia-tech-27778-funded-phd-position/

PhD position in viral evolution and diversity

Post a job in 3min, or find thousands of job offers like this one at jobRxiv!

^jobRxiv

Registrations are now open for the 2nd edition of the course "Analysis of Prokaryotic Pangenomes" with @jomcinerney & Alan Beavan.

Check it out: https://physalia-courses.org/courses-workshops/prokaritotic-pangenomes/

#Pangenomes #Bioinformatics

Anyone have advice on how to get the Spades genome assembler to use less memory?

#Spades #bioinformatics

https://github.com/ablab/spades

GitHub - ablab/spades: SPAdes Genome Assembler

SPAdes Genome Assembler. Contribute to ablab/spades development by creating an account on GitHub.

^GitHub

I wrote a short guide on how to build both alignment-free and reference-based prokaryote phylogenetic trees from SNP alignments without using snippy, check it out

https://www.bacpop.org/guides/building_trees_with_ska/

#bioinformatics #genomics

After months of work I'm so happy that our new preprint is online!

Profiling the expression of #transportome genes in #cancer: a systematic approach.
https://www.biorxiv.org/content/10.1101/2023.07.18.549498v1

It's a bit unfinished but it's by design! We want and need #feedback from #bioinformatics and #physiology people to move forward. I've tried to follow #openscience principles, so the pipeline is completely autonomous, containerized and the code for the paper is there, included in the repos!

Profiling the Expression of Transportome Genes in cancer: A systematic approach

The transportome, the -omic layer encompassing all Ion Channels and Transporters (ICTs), is crucial for cell physiology. It is therefore reasonable to hypothesize a role of the transportome in disease, and in particular in cancer.

^bioRxiv