108 citations · 199 across the 12 of their papers we have counts for
12 papers
Benchmarking and Evaluation of AI Models in Biology: Outcomes and Recommendations from the CZI Virtual Cells Workshop
Elizabeth Fahsbender, Alma Andersson, Jeremy Ash +32
Artificial intelligence holds immense promise for transforming biology, yet a lack of standardized, cross domain, benchmarks undermines our ability to build robust, trustworthy mod…
Product Manifold Representations for Learning on Biological Pathways
Daniel McNeela, Frederic Sala, Anthony Gitter
Machine learning models that embed graphs in non-Euclidean spaces have shown substantial benefits in a variety of contexts, but their application has not been studied extensively i…
Current and future directions in network biology
Marinka Zitnik, Michelle M. Li, Aydin Wells +34
Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseas…
A Text-guided Protein Design Framework
Shengchao Liu, Yanjing Li, Zhuoxinran Li +10
Current AI-assisted protein design mainly utilizes protein sequential and structural information. Meanwhile, there exists tremendous knowledge curated by humans in the text format…
Graph algorithms for predicting subcellular localization at the pathway level
Chris S. Magnano, Anthony Gitter
Protein subcellular localization is an important factor in normal cellular processes and disease. While many protein localization resources treat it as static, protein localization…
An Open-Publishing Response to the COVID-19 Infodemic
Halie M. Rando, Simina M. Boca, Lucy D'Agostino McGowan +7
The COVID-19 pandemic catalyzed the rapid dissemination of papers and preprints investigating the disease and its associated virus, SARS-CoV-2. The multifaceted nature of COVID-19…
Identification and Development of Therapeutics for COVID-19
Halie M. Rando, Nils Wellhausen, Soumita Ghosh +21
After emerging in China in late 2019, the novel Severe acute respiratory syndrome-like coronavirus 2 (SARS-CoV-2) spread worldwide and as of early 2021, continues to significantly…
Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure
Halie M. Rando, Adam L. MacLean, Alexandra J. Lee +31
The novel coronavirus SARS-CoV-2, which emerged in late 2019, has since spread around the world and infected hundreds of millions of people with coronavirus disease 2019 (COVID-19)…
Bayes Optimal Informer Sets for Early-Stage Drug Discovery
Peng Yu, Spencer S. Ericksen, Anthony Gitter +1
An important experimental design problem in early-stage drug discovery is how to prioritize available compounds for testing when very little is known about the target protein. Info…
Inferring Signaling Pathways with Probabilistic Programming
David Merrell, Anthony Gitter
Cells regulate themselves via dizzyingly complex biochemical processes called signaling pathways. These are usually depicted as a network, where nodes represent proteins and edges…
Unsupervised learning of transcriptional regulatory networks via latent tree graphical models
Anthony Gitter, Furong Huang, Ragupathyraj Valluvan +2
Gene expression is a readily-observed quantification of transcriptional activity and cellular state that enables the recovery of the relationships between regulators and their targ…
A New Computationally Efficient Measure of Topological Redundancy of Biological and Social Networks
Reka Albert, Bhaskar DasGupta, Anthony Gitter +5
It is well-known that biological and social interaction networks have a varying degree of redundancy, though a consensus of the precise cause of this is so far lacking. In this pap…