The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common
Fund program that catalogs how human cells globally respond to chemical, genetic, and …

Summary Illustrations of Neural Network architectures are often time-consuming to produce,
and machine learning researchers all too often find themselves constructing these diagrams …

A central goal of genetics is to define the relationships between genotypes and phenotypes.
High-content phenotypic screens such as Perturb-seq (CRISPR-based screens with single-…

There is a pressing need to identify therapeutic targets in tumors with low mutation rates
such as the malignant pediatric brain tumor medulloblastoma. To address this challenge, we …

Answer ALS is a biological and clinical resource of patient-derived, induced pluripotent
stem (iPS) cell lines, multi-omic data derived from iPS neurons and longitudinal clinical and …

Neurodegenerative diseases are challenging for systems biology because of the lack of
reliable animal models or patient samples at early disease stages. Induced pluripotent stem …

The Prize-collecting Steiner Forest (PCSF) problem is NP-hard, requiring extreme computational
effort to find exact solutions for large inputs. We introduce a new heuristic algorithm for …

When analyzing biological data, it can be helpful to consider gene sets, or predefined groups
of biologically related genes. Methods exist for identifying gene sets that are differential …

We introduce Graph-Sparse Logistic Regression, a new algorithm for classification for the
case in which the support should be sparse but connected on a graph. We val- idate this …

Neurodegenerative diseases present a challenge for systems biology, due to the lack of
reliable animal models and the difficulties in obtaining samples from patients at early stages of …