nature.com/articles/s4158… fast and sensitive detection of protein homologs combining pretraining and fine-tuning. This makes so much sense.

Great to see this out there, wonderful to have contributed to this position paper and huge thanks to Dr. Tijana Milenkovic and Marinka Zitnik for leading this effort!

An updated preprint reveals how scientists at Recursion & @Genentech make digital #maps of #biology – scaling genetic perturbation techniques w/ high-dimensional assays such as cellular microscopy & RNA sequencing to create “maps” that both capture known biological relationships

An updated benchmark of scATAC-seq pipelines: genomebiology.biomedcentral.com/articles/10.11… See also from 2019. genomebiology.biomedcentral.com/articles/10.11…

genomebiology.biomedcentral.com/articles/10.11… looks very interesting..

Position-dependent function of human sequence-specific transcription factors with HOMER2 nature.com/articles/s4158…

We’re opening a researcher position in my group for a machine learning-focused computational biologist! calicolabs.com/careers/?gh_ji…

For evolutionary biologists interested in tracing genomes back to their ancient ancestors, we’ve developed EdgeHOG—a tool that reconstructs ancestral gene orders at an unprecedented scale and speed. #Genomics #EvolutionaryBiology #EdgeHOG Thread!

Excited to be co-teaching another edition of Computational Network Biology in Fall2024 with Anthony Gitter! compnetbiocourse.discovery.wisc.edu

#MLCB2024 will be streamed live from YouTube this week (Thursday and Friday). Get the link from here: mlcb.github.io

Want to learn how transformers and large-language models can help to organize&understand single cell profiles? Led by Artur Szałata, we review current such approaches in single cell genomics and give perspectives towards foundation models etc. nature.com/articles/s4159…

Using Hi-C to detect SVs and 3D genome alteration in matched diagnosis vs. relapse B-ALL. Very interesting work! Congratulations Iannis Aifantis Aristotelis Tsirigos and Bill Carroll and all the authors! nature.com/articles/s4146…

Paper and Book Recommendations Mingyao Li: “The ‘Point of Significance’ column by Naomi Altman in Nature Methods.” Rafael Irizarry: “The book ‘Practical Statistics for Medical Research’ by Doug- las G. Altman.” 10/

NIH finally allocates funding for improving and maintaining software. - R03, budget $300k over 2 yrs - Due 12/4/24; 6/4/25 - RFA-OD-24-010 - Building Sustainable Software Tools for Open Science grants.nih.gov/grants/guide/r…

Proud of our Herculean-effort paper on "Current and future directions in network biology" published in Bioinformatics Advances. I hope it helps inspire current researchers and attract new talent to the field. Link to the paper (including the figure shown below): academic.oup.com/bioinformatics…

"[T]o fellow #PhD students who may be feeling overwhelmed by the plethora of opportunities and demands, remember the power of sitting still. Creating space for yourself isn’t a sign of falling behind; it’s a way to focus on what truly matters to you." bit.ly/3TneVpG