RCAC Bioinformatics @ Purdue University
@rcac-bioinfo.bsky.social
🌐 Supporting bioinformatics research @ Purdue and beyond. 🔬 Expertise in various genomics, and data analysis for diverse species. 🚀 Computational resources, pipeline development, and researcher guidance. 📚 Tutorials, tools, community support (& more)
NEW: HiFi now brings Hi-C to #HiFisequencing with CiFi. Traditional short-read Hi-C falls short in repetitive and low-complexity regions, but #PacBio HiFi delivers with superior accuracy and lower input needs. bit.ly/4b8k10m #AGBT #AGBTGM
CiFi: Accurate long-read chromatin conformation capture with low-input requirements | bioRxiv
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
bit.ly
With #PacBio Compatible, #HiFisequencing fits seamlessly into any lab and any omics application. Visit our suite at #AGBT in Lanai Suite 289 to explore our industry partnerships and learn how PacBio technology can elevate your research. #AGBT25
New preprint featuring my favorite maize-relatives, the Andropogoneae! We sequenced the genomes of 27 species, including lemongrass, kangaroo grass, little and big bluestem, and more -- key species that shape grasslands and prairies worldwide. www.biorxiv.org/content/10.1...
🚀 EM Server Webinar: Protein Modeling with DiffModeler & DeepMainmast! 🧬 📅 Feb 5, 2025 🎙️ Dr. Daisuke Kihara, Dr. Genki Terashi, Pranav Punuru Topics: DiffModeler & DeepMainmast advanced cryo-EM protein modeling, DAQ tools, CryoREAD & more. 🔗 register: kiharalab-events-5ab900351568.herokuapp.com
EM Server
Kiharalab EM Server
em.kiharalab.org
Purdue students/staff/faculty: Join us for The Genomics Exchange, a weekly online series for bioinformatics & genomics enthusiasts! 🌟 🗓️ First session: Friday, Jan 17, 2025 ⏰ Time: 11:00 AM EST 📍 Online via Teams Register 👉: forms.office.com/r/BtHXQ1tEkQ Let’s connect & exchange ideas! 🚀
Microsoft Forms
forms.office.com
What an amazing event! The team from Purdue and the Rosen Center for Advanced Computing had a packed week! We were thrilled to have had a chance to showcase all the amazing things happening on Purdue’s campus. Thanks to everyone who helped make this week special. #BOILERUP!
Congratulations to the students from Purdue Engineering on successfully presenting their capstone project! The group worked with RCAC to develop and implement an advanced, real-time predictive maintenance system using AI and IoT sensors for RCAC's #HPC infrastructure. #TheNextGiantLeap
🚨 Purdue Libraries is hiring! 🚨 Looking for an undergrad to join a Gamification project this Spring! 🕹️ 💻 Skills: Unreal Engine, C++, Blueprints, GitHub 📍 Link to apply: hcm-us10.hr.cloud.sap/sf/jobreq?jo... Know someone who might be interested? Tag them! 🙌 #UnrealEngine #Gamedev #Purdue
🚨 Summer '25 Paid Internships! Join Purdue’s Anvil Research Experience for Undergraduates for hands-on experience in AI, bioinformatics, & data centers. $680/week + housing. Apply now: purdue.ca1.qualtrics.com/jfe/form/SV_... 🌟
Anvil REU Applications
Application submission for the Purdue Anvil REU program.
purdue.ca1.qualtrics.com
easySCF: A Tool for Enhancing Interoperability Between R and Python for Efficient Single-Cell Data Analysis https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae710/7908354 🧬🖥️🧪 https://github.com/xleizi/easySCF
AlphaFold predictions on whole genomes at a glance https://www.biorxiv.org/content/10.1101/2024.11.16.623929v2 🧬🖥️🧪
MMseqs2 Release 16 Highlights: GPU-accelerated search📄, ORF or new 6-frame translated search modes, contig taxonomy always keeps the longest ORF, bug fixes (reduced memory and higher sensitivity) and relicensed as MIT 📄 biorxiv.org/content/10.1... 💾 mmseqs.com and 🐍Bioconda 🖥️🧬🧶
Pylustrator offers an interactive interface to find the best way to present your data in a figure for publication. Added formatting and styling can be saved by automatically generated code. https://pylustrator.readthedocs.io/en/latest/ #python
annoy a bioinformatician with these simple phrases: "Can't you just use Excel?" "Isn't BLAST basically Google for DNA?" "But did you annotate it?"
PanKB: An interactive microbial pangenome knowledgebase for research, biotechnological innovation, and knowledge mining https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae1042/7906839 🧬🖥️🧪
Tech I'm thankful for blog.stephenturner.us/p/tech-im-th... #rstats 🧬🖥️🧪
Tech I'm thankful for (2024)
Data science and bioinformatics tech I'm thankful for in 2024: tidyverse, RStudio, Positron, Bluesky, blogs, Quarto, bioRxiv, LLMs for code, Ollama, Seqera Containers, StackOverflow, ...
blog.stephenturner.us
"biology can remain hard longer than you can remain solvent" AI-first biology: five years on https://press.airstreet.com/p/ai-first-biology-five-years-on
Blackbird: structural variant detection using synthetic and low-coverage long-reads https://www.biorxiv.org/content/10.1101/2024.11.17.624011v1 🧬🖥️🧪 https://github.com/1dayac/Blackbird
Vcfexpress: flexible, rapid user-expressions to filter and format VCFs https://www.biorxiv.org/content/10.1101/2024.11.05.622129v1
Vcfexpress: flexible, rapid user-expressions to filter and format VCFs https://www.biorxiv.org/content/10.1101/2024.11.05.622129v1
Motivation: Variant Call Format (VCF) files are the standard output format for various software tool
biorxiv.org
Highly accurate assembly polishing with google/DeepPolisher & PHAROAH https://www.biorxiv.org/content/10.1101/2024.09.17.613505v1?rss=1 🧬🖥️ https://github.com/google/deeppolisher and https://github.com/miramastoras/PHARAOH
The Wild West of spike-in normalization https://www.nature.com/articles/s41587-024-02377-y (read free: https://rdcu.be/dUiGQ) 🧬🖥️ Code: https://github.com/lapatel22/spike_in_correspondence_2024
🚀 New Helixer tutorial for gene prediction! Predict genes in complex genomes like maize with 1 command—no repeatmasking, no extra data needed, all under 4 hrs! 🌽💻 Check it out: rcac-bioinformatics.readthedocs.io/en/latest/he... #Bioinformatics #Genomics #RCAC
Gene prediction using Helixer — RCAC bioinformatics tutorials
rcac-bioinformatics.readthedocs.io
I created a genomics+bioinformatics starter pack. If I left you off, *please* reply and I'll add you! go.bsky.app/B5YYBfq
Genomics+Bioinformatics Starter Pack 🧬🖥️
Join the conversation
go.bsky.app
This week's recap highlights protein design with RoseTTAFold, surveillance with wastewater sequencing, T2T human genomes, Vitessce for visualization of multimodal spatial single-cell data, and Taxometer for taxonomic classification of metagenomics contigs... blog.stephenturner.us/p/weekly-rec... 🧬🖥️
Weekly Recap (Oct 2024, part 4)
Protein design with RoseTTAFold, wastewater sequencing T2T human genomes, single-cell spatial transcriptomics, taxonomic classification, ...
blog.stephenturner.us
Cluster-efficient pangenome graph construction with @nf-co.re pangenome academic.oup.com/bioinformati...
Some of my favorite new things with data.table in #rstats (Ignore the CRAN not ok, we are working on some R C API changes still)
LncRAnalyzer: Uncovering Long Non-Coding RNAs and Exploring Gene Co-expression Patterns in Sorghum Genomics https://www.biorxiv.org/content/10.1101/2024.10.25.620275v1
LncRAnalyzer: Uncovering Long Non-Coding RNAs and Exploring Gene Co-expression Patterns in Sorghum Genomics https://www.biorxiv.org/content/10.1101/2024.10.25.620275v1
Sorghum (Sorghum bicolor L. Moench) is a versatile crop with significant phenotypic and genetic dive
biorxiv.org
🚀 Welcome to RCAC Bioinformatics! We’re here to support bioinformatics research with resources, expertise, and custom pipelines. Follow us for updates, tutorials, and collaboration opportunities! 🧬💻 #Bioinformatics #RCAC
