NEW PREPRINT The increasingly popular class imbalance approaches (such as SMOTE) for risk prediction modeling: they are likely to do more harm than good arxiv.org/abs/2202.09101

Graph Neural Networks beyond Weisfeiler-Lehman and vanilla Message Passing by Michael Bronstein @ICLR2025 🇸🇬 in Towards Data Science towardsdatascience.com/graph-neural-n…

A great opportunity for a programmer in the group of Janani Ravi! Anyone looking for a great person to work with, Janani is it! careers.msu.edu/en-us/job/5097…

I just published in Towards Data Science Cross-Entropy, Negative Log-Likelihood, and All That Jazz towardsdatascience.com/cross-entropy-…

Geo Geo Pertea presented part 1/2 of "Robust #normalization and transformation techniques for constructing gene #coexpression networks" Lots of awesome background information and critical thinking! #RNAseq #bioinformatics 📜 doi.org/10.1186/s13059… 🎥 youtu.be/eR73cV6mmuY

Automating PyPI releases with Github Actions caktusgroup.com/blog/2021/02/1…

Bioinformatics too often relies on general-purpose CPUs when GPUs and other specialized hardware are more suited to the task. If you agree, please 👍 my BEDTools feature request github.com/arq5x/bedtools…

Today Ma'ayan Lab updated the augmented ASCT+B gene set library in #Enrichr maayanlab.cloud/Enrichr/ The library was created from Human BioMolecular Atlas Program (HuBMAP) hubmapconsortium.github.io/ccf-asct-repor… This library has marker genes for 777 human cell types augmented with #RNAseq data from #ARCHS4 maayanlab.cloud/archs4/

Our review ⁦Waisman Center⁩ for NICHD IDDRC special issue on computational neuroscience. We envision machine learning for data analysis & modeling in emerging research on intellectual and developmental disabilities! jneurodevdisorders.biomedcentral.com/articles/10.11…

🎉Happy to share that our group (Krishnan Lab) will be moving to CU Anschutz Medical Campus CU School of Medicine in Aug! We'll join the new Center for Health AI @ CU Anschutz, where I'll be an Associate Professor. It has been a great run at MSU and we are thrilled about what our future holds at CU! 🧵1/5

LaTeX style files for LoG 2022 are now available 📝 Abstract deadline: 9th September, 2022 - 38 days to go! CFP has all the details: logconference.org/cfp/

If you don’t want someone sending emails at 8pm, do you also not want them doing therapy at 4pm or feeding their kids at 12pm? Or is everyone supposed to just fit everything neatly into a 9-5 workday?

Pipeline release! nf-core/sarek v3.0.2 (Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing) See the changelog: github.com/nf-core/sarek/…

Pipeline release! nf-core/rnaseq v3.9 (RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.) See the changelog: github.com/nf-core/rnaseq…

Pipeline release! nf-core/chipseq v2.0.0 (ChIP-seq peak-calling, QC and differential analysis pipeline.) See the changelog: github.com/nf-core/chipse…

Pipeline release! nf-core/scrnaseq v2.1.0 (A single-cell RNAseq pipeline for 10X genomics data) See the changelog: github.com/nf-core/scrnas…

A network-based approach for isolating the chronic inflammation gene signatures underlying complex diseases towards finding new treatment opportunities frontiersin.org/articles/10.33…

Pipeline release! nf-core/cutandrun v3.0 (Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.) See the changelog: github.com/nf-core/cutand…

Pipeline release! nf-core/atacseq v2.0 (ATAC-seq peak-calling, QC and differential analysis pipeline) See the changelog: github.com/nf-core/atacse…

🎇 We're one of 20 finalists for the DataWorks! Prize for our work on: Removing metadata barriers to promote data reuse Methods that address unstructured & missing metadata that are barriers to discovering & reusing public omics data. Learn more & VOTE! herox.com/dataworks/roun…