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Single-cell multi-omics analysis reveals cooperative transcription factors for gene regulation in oligodendrocytes biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

Pleased to be organizing RSGDREAM2024 with Ferhat Ay and Aly Azeem Khan in Madison! Deadline to submit abstracts for talks & posters fast approaching (Aug 2nd)! Come to Madison to share and learn more about regulatory genomics and systems biology and DREAM challenges!

Great locally attended #rsgdream2024 UW–Madison & shared our ongoing work on #brain #generegulation

Thrilled to attend #SfN24! Sharing unpublished work, incl. #neuroAI research. Looking forward to your comments & feedback!

Our new VAPOR learns VAE-subspace-specific ODEs to decouple temporally or spatially gene expression dynamics in co-occurring biological processes

Our NeuroTD, a novel deep learning approach, integrates multi-modalities, siamese neural networks & time-frequency domain alignments to reveal temporal relationships, time delays & causal links in neural activities, behavior & gene expression! #NeuroAI

Online now: Protocol for comparative gene expression data analysis between brains and organoids using a cloud-based web app dlvr.it/TFzYts #protocol #starprotocols #cellpress

Please come to our #ASHG24 poster Board 1031F Nov 8 using interpretable deep learning analysis on single-cell multiomics for transcription factor cooperativity in #oligodendrocyte #generegulation

Our integrated graph neural network & ensemble learning model PASCode enables phenotypic scoring & subtyping analyses of single cells w/ applications to clinical phenotypes & neuropsychiatric symptoms #Alzheimers #PsychAD

Our iBrainMap model integrates Knowledge-Guided Graph Neural Network with network diffusion to enable personalized single-cell functional genomic analysis and molecular subtyping of individuals w/ applications to #Alzheimers #PsychAD

Interested to pursue PhD or MS in Biomedical Data Science? The UW Madison BDS program will have a virtual open house this Tuesday, Nov 12th, 11:00 am CST! Visit biostat.wiscweb.wisc.edu/education/pros… for more details.

Our new preprint intro COSIME: Cooperative multi-view integration and Scalable and Interpretable Model Explainer biorxiv.org/content/10.110…

Our preprint intro ARTEMIS, a novel generative model to unravel cellular dynamics incl. gene expression, population changes & perturbations. We showcase it by pancreatic beta-cell differentiation, zebrafish embryogenesis & lung cancer EMT Sayali Alatkar biorxiv.org/content/10.110…

CoTF-reg reveals cooperative transcription factors in oligodendrocyte gene regulation using single-cell multi-omics: Communications Biology, Published online: 05 February 2025; doi:10.1038/s42003-025-07570-6The authors introduce coTF-reg, an analytical… nature.com/articles/s4200…

Our new ML work Waisman Center Communications Biology integrates multi-omics data and quantifies transcription factor cooperativity for oligodendrocyte gene regulation at the single-cell level waisman.wisc.edu/2025/02/12/new…

Online now: Multimodal analyses reveal genes driving electrophysiological maturation of neurons in the primate prefrontal cortex dlvr.it/TKtVpD

Multimodal analyses help understand cell-type gene regulation for early neuronal electrophysiology & autism. An interdisciplinary journey Waisman Center since pandemic from raw data to machine learning to experimental validation! waisman.wisc.edu/2025/05/22/gen…

Our ARTEMIS Sayali Alatkar is published in #ISMBECCB2025 proceedings! It integrates VAE, diffusion & optimal transport to predict continuous dynamics of gene expression, cell populations & perturbations. academic.oup.com/bioinformatics…

Thrilled to attend #ISMBECCB2025 in Liverpool, UK. We have two talks on Tuesday, July 22: NETRem Saniya Khullar at 12:20 pm in NetBio Room 01B & ARTEMIS Sayali Alatkar at 3:40 pm in SysMod Room 01C. Happy to catch up!

Tracking how cells change over time is nearly impossible with today’s technology, but the lab of Daifeng Wang has developed a new machine learning algorithm called ARTEMIS that can predict the continuous changes in cell populations over time. Check it out! waisman.wisc.edu/2025/07/29/mee…