Mahesh Binzer-Panchal
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arcane-mahesh.bsky.social
Mahesh Binzer-Panchal
@arcane-mahesh.bsky.social
160 followers 400 following 22 posts
Bioinformatician at the National Bioinformatics Infrastructure Sweden ( NBIS ) and SciLifeLab.
I focus on de novo genome assembly, and pipeline development. #ReproducibleResearch with #Nextflow and #Quarto.
#OpenScience
https://github.com/mahesh-panchal
Posts Replies Media Videos
Reposted by Mahesh Binzer-Panchal
bffo.bsky.social
From @plos.org #Computational #Biology | Ten simple rules for early-career researchers supervising short-term student projects | #Education #Bioinformatics #OpenScience #PLOSCBTSR #ECR 🧪 🔓 CC/ @knaegle.bsky.social
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journals.plos.org/ploscompbiol...
Ten simple rules for early-career researchers supervising short-term student projects
Author summary Supervising undergraduate or master’s research projects is a vital aspect of academic life, offering opportunities for both student development and supervisor growth. For many early-car...
journals.plos.org
November 19, 2025 at 6:18 PM
Reposted by Mahesh Binzer-Panchal
alielw.bsky.social
Join us! 🧬🪰🎉🔬

We are currently advertising two #PhD projects to study the #evolution, #development and #genomics of sexual traits in stalk-eyed flies.

Deadline for applying is Wednesday, January 7, 2026. Get in touch for more info!
November 17, 2025 at 3:58 PM
Reposted by Mahesh Binzer-Panchal
mrtnj.bsky.social
We're hiring a PhD student to work on genomic prediction and genetic variation in farm animals.

There will be cattle, genomics, simulation, and there might be poultry.

And if you already have a PhD, consider sharing with someone who hasn't, and might be a good fit. :)

www.slu.se/en/about-slu...
PhD Student in Animal Science | slu.se
SLU - Science and Education for Sustainable Life
www.slu.se
November 17, 2025 at 2:03 PM
Reposted by Mahesh Binzer-Panchal
mickael.canouil.fr
Join me for "Mastering Quarto CLI: From Authoring to Publishing" 📈 5-6 Feb 2026

I'll help you master:
- Reproducible documents
- Multi-language workflows
- Beautiful publishing

Let's transform your data projects! www.physalia-courses.org/courses-work...

#DataScience #Quarto
Mastering Quarto CLI: From Authoring to Publishing
5th-6th February 2026
www.physalia-courses.org
October 31, 2025 at 4:52 PM
Reposted by Mahesh Binzer-Panchal
jlsteenwyk.bsky.social
Come join the Workshop on Phylogenomics in Cesky Krumlov, Czechia, from January 25 through February 7, 2026!

Applications close November 15!

#phylogenetics #evolution #genomics #ai

evomics.org/apply-worksh...
Apply: Workshop on Phylogenomics 2026 - Evolution and Genomics
Application for the 2026 Workshop on Phylogenomics Use this form to apply for the 2026 Workshop on Phylogenomics being held in Cesky Krumlov, Czechia from 25th January through 7th February, ...
evomics.org
October 29, 2025 at 7:23 PM
Reposted by Mahesh Binzer-Panchal
stephaniehicks.bsky.social
Looking for postdoctoral opportunities? ✅

Interested in working with me or any of the 30 other amazing @jhubiostat.bsky.social faculty? ✅

If yes, I encourage you to apply to our postdoc program in #DataScience and #AI in #Health and #Medicine!

🔗 apply.interfolio.com/174430

🧪🧬💻🧠
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
October 31, 2025 at 6:40 AM
Reposted by Mahesh Binzer-Panchal
stephaniehicks.bsky.social
Come work with me! @jhubiostat.bsky.social is hiring for a tenure-track Assistant Professor position 🥳 Apps due Nov 15

🔗 apply.interfolio.com/176686

🧪🧬💻🧠 #StatsSky #WomenInSTEM
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
October 31, 2025 at 6:58 AM
Reposted by Mahesh Binzer-Panchal
gonzalezlabbcn.bsky.social
Join us in Montpellier if you are interested in #evolution #genomics #adaptation #invasive species or if you want to get to know a collegial group of #Drosophila enthusiasts
droseu.bsky.social DrosEU @droseu.bsky.social · 19d
🪰 🧬16th #DrosEU2026 Workshop & Satellite #DrosophilaSuzukii Meeting Conference will take place 13–17 April 2026 in #Montpellier, France 🇫🇷.

We look forward to connecting with colleagues across Europe to discuss new research in #Drosophila #genomics #evolution & #CitizenScience +info 👉 droseu.net
October 31, 2025 at 5:59 PM
Reposted by Mahesh Binzer-Panchal
jfy133.genomic.social.ap.brid.gy
❓ Do you develop a #nextflow pipeline for #metagenomics, #metataxonomics, #metatranscriptomics, #metaproteomics, etc?

🧑‍💻 I'm looking for #bioinformatics developers to give demos of their #opensource pipelines to the scientific community in a ‘Meta-*omics Nextflow pipeline community exhibition […]
Original post on genomic.social
genomic.social
September 16, 2025 at 6:31 AM
Reposted by Mahesh Binzer-Panchal
suvimake.bsky.social
Genetic variation is the key to species resilience, enabling populations to adapt to changing environmental conditions. Our research group will take a deep dive into the variation present in the genes encoding for central roles of the immune system. www.slu.se/en/news/2025...
The price of perfection: Opting out of variety - a danger to animal immunity and survival | slu.se
For thousands of years, humans have been controlling the breeding of dogs, horses and farm animals. Despite the benefits, this has led to unexpectedly high risks for the animals. With knowledge from r...
www.slu.se
September 12, 2025 at 11:10 AM
Reposted by Mahesh Binzer-Panchal
nf-co.re
New blog post! Introducing nf-core Advisories
https://nf-co.re/blog/2025/advisories/
August 21, 2025 at 11:01 AM
Reposted by Mahesh Binzer-Panchal
interprodb.bsky.social
InterProScan 6 (beta) is here 🎉
A Nextflow-powered, containerised overhaul for scalable, reproducible protein annotation—decoupled software/data, automated data handling, and smoother runs across HPC and cloud.
Feedback welcome!
github.com/ebi-pf-team/...
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InterProScan 6 (beta) Nextflow - Containerised - Reproducible outputs Start with FASTA file InterProScan workflow: Annotate proteins (and nucleotides) with families, domains & sites Select analyses (e.g. Pfam, PANTHER, CDD, NCBIFAM...) Optional: GO and pathway annotations Output formats: JSON, TSV, XML, GFF3
August 8, 2025 at 9:32 AM
Reposted by Mahesh Binzer-Panchal
bffo.bsky.social
From @plos.org #Computational #Biology | Fundamentals of FAIR biomedical data analyses in the cloud using custom pipelines | #Bioinformatics #FAIR #Cloud #Education #OpenScience #Nextflow #WDL #CWL 🧬 🖥️ 🧪 🔓
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journals.plos.org/ploscompbiol...
Fundamentals of FAIR biomedical data analyses in the cloud using custom pipelines
As the biomedical data ecosystem increasingly embraces the findable, accessible, interoperable, and reusable (FAIR) data principles to publish multimodal datasets to the cloud, opportunities for cloud...
journals.plos.org
July 19, 2025 at 7:43 PM
Reposted by Mahesh Binzer-Panchal
mireyaplass.bsky.social
I’m really happy to present #SCALPEL, a new #Nextflow tool to quantify transcript isoforms at the single-cell level using conventional 3’ scRNA-seq data #scRNA-seq #single-cell #tools #isoforms
www.nature.com/articles/s41...
Quantification of transcript isoforms at the single-cell level using SCALPEL - Nature Communications
Single-cell RNA-seq facilitates the study of transcriptome diversity in individual cells. Here, authors introduce a tool for isoform quantification at the single-cell level using 3’ scRNA-seq data, co...
www.nature.com
July 14, 2025 at 10:31 AM
Reposted by Mahesh Binzer-Panchal
bffo.bsky.social
From @drvgmartinacosta.bsky.social & colleagues in @plos.org #Computational #Biology | Ten simple rules for faculty members building just and equitable environments in academic science | #Education #PLOSCBTSR 🧬 🖥️ 🧪 🔓
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journals.plos.org/ploscompbiol...
Ten simple rules for faculty members building just and equitable environments in academic science
journals.plos.org
July 8, 2025 at 5:58 PM
Reposted by Mahesh Binzer-Panchal
mberacochea.bsky.social
We have just released a new version of the Microbiome Informatics metagenomes assembler pipeline - github.com/EBI-Metageno.... Jenny Mattock benchmarked a new contigs cleaning process that Sonya Ochkalova implemented. Great team effort with > 100 comments in the PR. #nextflow @mgnifydb.bsky.social
Release v3.0.0 · EBI-Metagenomics/miassembler
Massive work from @ochkalova and @jmattock5 What's Changed Add --iontorrent by @KateSakharova in #40 Increase memory for CANU LR by @KateSakharova in #41 Add more time to CANU LR by @KateSakharova...
github.com
June 18, 2025 at 4:14 PM
Reposted by Mahesh Binzer-Panchal
christinaernst.bsky.social
Used EMBL-EBI data resources to find, analyse, or archive your data? 🧬

Now’s your turn: tell us how you’ve used them + why they matter.

It takes 15 mins and helps keep these services open and free for all.

👉 tinyurl.com/bdf73zpp
Closes 16 July

#opendata #FAIRdata
June 17, 2025 at 8:00 PM
Reposted by Mahesh Binzer-Panchal
science.ninja
My time as a Bioinformatics Staff scientist at CalTech is coming to a close and I am looking for the next thing. If you need someone with plenty of experience in sequencing analysis, and pipeline building (Nextflow), please connect. I'm hoping to go back to industry but open to anything interesting.
June 6, 2025 at 6:40 PM
Reposted by Mahesh Binzer-Panchal
stephenturner.us
Colora: A Snakemake Workflow for Complete Chromosome-scale De Novo Genome Assembly www.biorxiv.org/content/10.1... 🧬🖥️ github.com/LiaOb21/colora
June 5, 2025 at 8:02 PM
arcane-mahesh.bsky.social
Some useful advice for sample collection to generate a reference genome.

academic.oup.com/gigascience/...
Best-practice guidance for Earth BioGenome Project sample collection and processing: progress and challenges in biodiverse reference genome creation
Abstract. The Earth BioGenome Project has the extremely ambitious goal of generating, at scale, high-quality reference genomes across the entire Tree of Li
academic.oup.com
June 2, 2025 at 10:54 AM
Reposted by Mahesh Binzer-Panchal
nf-co.re
You might know that @nf-co.re is crazy about @nextflow.io pipelines, but did you know that we're also mad about laptop stickers? 😆

We have a whole web page dedicated to them where you can see the whole collection so far: nf-co.re/stickers
May 28, 2025 at 10:08 AM
Reposted by Mahesh Binzer-Panchal
smllmp.bsky.social
New short blog: Setting up the @nextflow.io Language Server (LSP) with NeoVim livesys.se/posts/nextfl...
Setting up the Nextflow Language Server (LSP) with NeoVim | Living Systems_
livesys.se
May 16, 2025 at 9:43 PM
Reposted by Mahesh Binzer-Panchal
lauritzthamsen.org
1/4: If you are at #IEEE #CCGrid 2025 in #Tromsø next week, catch Jonathan, Fabian, and Kathleen (@westkath.bsky.social) presenting joint work! 📰🧵👇

#CCGrid #distributed #sustainable #cloud #computing #research #Spark #Nextflow
A slide listing our three contributions to the 25th IEEE International Symposium on Cluster, Cloud and Internet Computing (CCGrid 2025): - Wednesday, 21 May, 11 am (SSP2 session on Software Systems and Platforms – Cloud Continuum): Flora: Efficient Cloud Resource Selection for Big Data Processing via Job Classification (full paper) - Thursday, 22 May, 2 pm (SSP5 session on Software Systems and Platforms – Workflows and Workloads): WOW: Workflow-Aware Data Movement and Task Scheduling for Dynamic Scientific Workflows (full paper) - Wednesday, 21 May, 11 am (SIT2 session on Sustainable IT Systems): Exploring the Potential of Carbon-Aware Execution for Scientific Workflows (short paper)
May 16, 2025 at 12:59 PM
Reposted by Mahesh Binzer-Panchal
seqera.io
We’ve just dropped some powerful new @nextflow.io features as part of the 25.04 release, all designed to enhance clarity, control, and collaboration in workflow development. 🎉

💡Learn more: hubs.la/Q03mQ2_10
May 15, 2025 at 6:25 PM
Reposted by Mahesh Binzer-Panchal
camillemrcht.bsky.social
In this (rebutted) grant proposal I wrote that I thought we could see circular RNAs with Vizitig, despite being hard to detect and with low expression. Guess what? Looks very much like a circular RNA to me 😎 (in TET2 gene, human co-assembled cancer RNA-seq samples).
May 6, 2025 at 5:49 PM