Cold Spring Harbor Laboratory

Exploring transcriptomic and genomic latent variable correction approaches in differential expression analysis

Abstract Background Differential expression analysis is a central tool for studying the biological processes altered in human diseases via transcriptomic signatures. However, transcriptomic datasets are systematically confounded by latent variables from two distinct sources: unme...

Reciprocal connections dynamically build consensus between neocortical areas

Abstract The neocortex is organized into specialized areas. Although computations within individual areas have been well studied, it is unclear how these regions function collectively and reconcile potential conflicts to form coherent percepts and decisions. We investigated the j...

Psilocybin prevents chemotherapy-induced peripheral neuropathy through mitochondrial trafficking preservation

Chemotherapy-induced peripheral neuropathy (CIPN) is a disabling, often irreversible toxicity that affects millions of patients, limits life-saving cancer therapy, and lacks proven treatment. In this work, we show that as little as two doses of psilocybin before chemotherapy dura...

Gaugefixer: overcoming parameter non-identifiability in models of sequence-function relationships

Background: Mathematical models that describe sequence-function relationships are widely used in computational biology. A key challenge when interpreting these models is that their parameters are not uniquely determined, i.e., many different parameter choices can encode the same...

The combination of morphogenic regulators BABY BOOM and GRF ‐ GIF improves maize transformation efficiency and promotes leaf regeneration

Summary Transformation is an indispensable tool for plant genetics and functional genomics. Although stable transformation in maize is no longer a major obstacle, there remains a need for accessible and efficient methods for academic laboratories. Here, we present the GGB system,...

A dependency map enhanced with next-generation 3D cancer models

Despite advances in precision oncology, effective personalized treatments are still lacking for most patients with cancer1. The Cancer Dependency Map (DepMap) accelerates this field by systematically identifying cancer vulnerabilities in diverse preclinical models. Data from over...

A compendium of next-generation patient-derived models for diverse cancers

Abstract The development of new therapeutics and the validation of pathogenetic cancer mechanisms require representative laboratory models 1,2 . However, existing collections represent only a fraction of the diversity observed in human cancer 2–4 . Recent technologies have enable...