Top papers from last week: - Predicting transcriptional responses to novel chemical perturbations using deep generative model for drug discovery: nature.com/articles/s4146… - Metagenomics-Toolkit: The Flexible and Efficient Cloud-Based Metagenomics Workflow featuring Machine…

Train a protein structure flow-matching model that can be conditioned by atomic coordinates and then use it to design enzymes based on active site geometry specified by density functional theory.

Can synthetic receptors be engineered to detect soluble factors and enable precise control of cell therapies while minimizing off-target effects? (From David Baker's lab) @Nature @roybal_lab "Engineered receptors for soluble cellular communication and disease sensing" •…

How can we effectively analyze and visualize massive protein sequence datasets to better understand protein evolution and function? @ourANU @biorxivpreprint "Exploring large protein sequence space through homology- and representation-based hierarchical clustering" • This…

Can a novel hashing-based approach change how we search for similar protein structures while dramatically reducing computational costs? @njuniversity @arxiv "Hashing for Protein Structure Similarity Search" • Protein structure similarity search (PSSS) is crucial but current…

What if we could better understand which cells actually respond to CRISPR genetic modifications in pooled screens, separating them from cells that appear unaffected despite expressing guide RNAs? @insitro @arxiv "Modeling variable guide efficiency in pooled CRISPR screens with…

How can we overcome the technical barriers in comparing living and fixed brain tissue imaging? @Stanford @Princeton @PNASNews "BIFROST: A method for registering diverse imaging datasets of the Drosophila brain" • The paper addresses a fundamental challenge in neuroscience:…

What genetic factors influence the shape of our hearts, and how might this impact cardiovascular health? @NatureComms @KingsCollegeLon "Genetic basis of right and left ventricular heart shape" • In a new study of 45,683 UK Biobank participants, researchers investigated how…

Can theta oscillations in the prefrontal cortex really help us anticipate and adapt to conflicting situations in our environment? @UDD_cl @NatureComms "Lateral prefrontal theta oscillations causally drive a computational mechanism underlying conflict expectation and adaptation"…

What biomarkers could help predict organ-specific metastasis in lung cancer before it occurs, potentially improving patient outcomes? @NatureComms @UCAS1978 "Multi-omics with dynamic network biomarker algorithm prefigures organ-specific metastasis of lung adenocarcinoma" •…

AlphaFold2 enables accurate deorphanization of ligands to single-pass receptors | @CellSystemsCP - Use AlphaFold2/ParallelFold to screen single-pass transmembrane receptor interactions with secreted protein ligands - Build comprehensive libraries of 1,107 receptors and 1,862…

MMSeq2 on CUDA cores! MSA retrievals could get super fast now

Can language models trained on evolutionary data better identify disease-causing variants in non-coding DNA regions? @harvardmed @broadinstitute "LOL-EVE: Predicting Promoter Variant Effects from Evolutionary Sequences" • Scientists have made progress in predicting protein…

Can artificial intelligence help doctors better identify and analyze spinal metastases to improve treatment decisions and patient outcomes?@medrxivpreprint @Harvard @BIDMChealth "An Open Annotated Dataset and Baseline Machine Learning Model for Segmentation of Vertebrae with…

Can epigenetic signatures distinguish between Primary Age-Related Tauopathy (PART) and Alzheimer's Disease (AD), and predict tau pathology severity to help understand disease mechanisms and progression?@medrxivpreprint "Epigenetic signatures of regional tau pathology and…

Can deep learning algorithms accurately quantify Paneth cell density in intestinal tissue to predict Crohn's disease outcomes and reduce the time-intensive manual counting process currently required? @eBioMedicine @UW "Development of a deep learning algorithm for Paneth cell…

What blood-based protein biomarkers could effectively screen for tuberculosis disease, potentially meeting WHO's target of 90% sensitivity and 70% specificity for point-of-care testing?@ASMicrobiology "Host blood protein biomarkers to screen for tuberculosis disease: a…

Can a simple, low-cost device using LAMP (Loop-mediated isothermal Amplification) and machine learning accurately detect antibiotic resistance genes in bacterial infections? @UCalgaryMed @ASMicrobiology "A novel machine-learning aided platform for rapid detection of urine ESBLs…

Can brain activity patterns during memory formation help protect against Alzheimer's disease symptoms, even in the presence of significant brain pathology? "Cognitive reserve against Alzheimer’s pathology is linked to brain activity during memory formation" @NatureComms @DZNE_en…

What molecular mechanisms drive the complex interactions between cancer cells and stromal cells in pancreatic cancer's tumor microenvironment, and how can this knowledge lead to better therapeutic strategies? "Clinical functional proteomics of intercellular signalling in…

Can a task-agnostic exoskeleton controller effectively assist humans across diverse movement patterns while reducing metabolic cost and joint work? "Task-agnostic exoskeleton control via biological joint moment estimation"@nature @BostonDynamics @gatechengineers • A research…