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Items tagged with: bioinformatics

RE: genomic.social/@lwpembleton/11…

Love tinkering with #Linux? Enjoyed #biology and #genetics at uni? Come work with us and turn that passion into a career.
#genomics #bioinformatics #FediHire #jobs #RStats #agriculture #nz #science

Luke Pembleton (@lwpembleton@genomic.social)

🧬 We're hiring a Bioinformatician in NZ! Come work with me and our global R&D team at Barenbrug. Ideal for an early‑career researcher or recent grad who loves coding, #genomics and solving cool biological problems.
Luke Pembleton (genomic.social)
#linux #science #biology #Jobs #bioinformatics #rstats #agriculture #genomics #genetics #fedihire #NZ

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Are you passionate about computational biology and the evolution of specialized plant metabolism?

We invite highly motivated and experienced students and early-career researchers to join @PuckerLab in Bonn for a visiting research stay. This is a great opportunity to gain hands-on experience, exchange ideas, and work in a collaborative and supportive scientific environment with excellent computational resources.

More details and contact information:
izmb.uni-bonn.de/en/pbb/contac…

#Bioinformatics

Contact

IZMB
#bioinformatics @PuckerLab

Heng Li: hlilab.github.io/vacancies

"We are looking for a postdoctoral fellow to develop high-performance algorithms for sequence alignment, pangenome representation, application of pangenome data structures, or other projects the applicant may propose. A qualified candidate is expected to be proficient in a high-performance language such as C, C++ or Rust, and have rich research experiences in #bioinformatics and computational genomics."

#job

HLi Lab - Vacancies

Openings
hlilab.github.io
#Job #bioinformatics

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Anyone know what software is used to generate these amino acid sequence alignments figures?
#bioinformatics
#bioinformatics

#bioinformatics

#bioinformatics

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#bioinformatics #microbiology #assembly question. I'm looking through some new archaeal genome assemblies, and some of the species show perfect assembly output except in one plasmid - always in about 1k different contigs of braided alternate paths but graph together nonetheless. Is this a biological signature of something?
#bioinformatics #microbiology #assembly

Postdoc job opportunity! We're looking for early career researcher in evolutionary genomics to study the relation between intra-specific gene expression variability, polymorphism, and macro-evolutionary rates. We have all of the data in 3 fishes and amphioxus, just waiting for your expertise and enthusiasm!
tinyurl.com/3aewk286
#EvoDevo #MolecularEvolution #bioinformatics #PopulationGenomics #RNAseq #PostDoc

Opportunités de carrière : Postdoctoral position in evolutionary genomics (22280)

tinyurl.com
#bioinformatics #evodevo #postdoc #rnaseq #MolecularEvolution #PopulationGenomics

Excited to announce our article, "EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals" was just published in Nature Communications!

We demonstrate that it's possible to infer how genes work together using only sequencing data by leveraging correlated signals of evolution. Check it out at the link below!

#genomics #bioinformatics #rstats #genetics #evolution #biology

nature.com/articles/s41467-025…

EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals - Nature Communications

Despite having structures for most proteins, we still do not know their function. Here, authors introduce EvoWeaver, a de novo method to identify genes working together using evolutionary information.
Nature
#Evolution #biology #bioinformatics #rstats #genomics #genetics

#bioinformatics #biological

What do #nanopore #sequencing #bioinformatics folks think about this one? New preprint on hashing raw nanopore signals and using them directly for de-novo assembly.

arxiv.org/abs/2503.02997v1

Hypothetical blow5-to-assembly pipe would be interesting, though figuring it out is way out of my depth.

Enabling Fast, Accurate, and Efficient Real-Time Genome Analysis via New Algorithms and Techniques

The advent of high-throughput sequencing technologies has revolutionized genome analysis by enabling the rapid and cost-effective sequencing of large genomes.
arXiv.org
#bioinformatics #nanopore #sequencing

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New shitty reality:
Every time #NCBI is #down you wonder whether it's permanent or not.

Just now the whole nih.gov is not resolving from two different locations I have access to.
Also:
downdetector.com/status/nih/

And just in time when I decided to do some #bioinformatics work 1AM on Sat^W Sunday.

#nih

#bioinformatics #NIH #down #NCBI

#bioinformatics

#science #Evolution #bacteria #bioinformatics #genomics

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: 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
#Rust #bioinformatics #rustlang

[New paper]: Two subtle problems with over-representation analysis.
ORA is a type of enrichment analysis that analyses over-represented functional categories in gene lists. These tools have accumulated ~190k citations, but they have subtly different behaviours. Here we unpack the differences and investigate two subtle problems in some implementations, which may have negatively impacted those 190k research papers.
doi.org/10.1093/bioadv/vbae159
#genomics #bioinformatics
#bioinformatics #genomics

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)

biorxiv.org/content/10.1101/20…

@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
#bioinformatics #protein #structuralbiology @StrucBio group @bioinformatics group

#bioinformatics #microbiology #archaea

#Evolution #bioinformatics

#bioinformatics #molecular #enteroviruses

#biology #bioinformatics #metag #biofilms

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 biorxiv.org/content/10.1101/20….

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
#bioinformatics #genomics #MicrobialEcology #metagenomics #microbiomes

"Indexing All Life's Known Biological #Sequences" biorxiv.org/content/10.1101/20…

"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
#bioinformatics #database #sequences

#bioinformatics #cbw1999 #25yearsofcbw #oldbioinformaticsthings

#bioinformatics

#bioinformatics #microbiology

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[New preprint] Direction-aware functional class scoring enrichment analysis of Infinium DNA methylation data
#Genomics #Epigenetics #Bioinformatics
In this article we outline a refined method for pathway enrichment of infinium array data that is more sensitive and precise as compared to existing over-representation approaches. Feedback welcome.
biorxiv.org/content/10.1101/20…

Direction-aware functional class scoring enrichment analysis of Infinium DNA methylation data

Infinium Methylation BeadChip arrays remain one of the most popular platforms for epigenome-wide association studies, but tools for downstream pathway analysis have their limitations.
bioRxiv
#bioinformatics #genomics #epigenetics

#Evolution #bioinformatics #microbiology #archaea #phylogenetics

#bioinformatics #genomics #viruses #virology

#bioinformatics #genomics

#bioinformatics #statistics #genomics #genetics

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)

stowers.org/gradschool/computa…

#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
#bioinformatics

#bioinformatics #microbiology

#bioinformatics

#bioinformatics #taxonomy #referencesequence #databases #NCBI #Genbank #PubMed #sra #refseq

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: forms.office.com/r/jNd2cbEZkh

#rstats #bioinformatics

#bioinformatics #rstats

#opensource #bioinformatics @BOSC

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.

findaphd.com/phds/project/whit…

#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
#bioinformatics #PhD #phdPosition #genetics #utr #miRNA

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Very happy to share our new publication in PLOS ONE:

KIPEs3: Automatic annotation of biosynthesis pathways
doi.org/10.1371/journal.pone.0…

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

KIPEs3: Automatic annotation of biosynthesis pathways

Flavonoids and carotenoids are pigments involved in stress mitigation and numerous other processes. Both pigment classes can contribute to flower and fruit coloration.
doi.org
#OpenAccess #bioinformatics @TU Braunschweig @PuckerLab

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