Publications by authors named "Lenore Cowen"

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Memory-efficient, accelerated protein interaction inference with blocked, multi-GPU D-SCRIPT.
Daniel E Schäffer, Samuel Sledzieski, Lenore Cowen, Bonnie Berger

Bioinformatics· October 2025

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Decoding the Functional Interactome of Non-Model Organisms with PHILHARMONIC.
Samuel Sledzieski, Charlotte Versavel, Rohit Singh, Faith Ocitti, Kapil Devkota, Lenore Cowen

bioRxiv· August 2025

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Approximate IsoRank for Scalable and Functionally Meaningful Cross-Species Alignments of Protein Interaction Networks.
Kapil Devkota, Anselm Blumer, Xiaozhe Hu, Lenore Cowen

J Comput Biol· October 2024

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Current and future directions in network biology.
Marinka Zitnik, Michelle M Li, Aydin Wells, Kimberly Glass, Deisy Morselli Gysi, Lenore Cowen

Bioinform Adv· August 2024

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Insulin signaling and pharmacology in humans and in corals.
Meghana Hosahalli Shivananda Murthy, Paniz Jasbi, Whitney Lowe, Lokender Kumar, Monsurat Olaosebikan, Lenore Cowen

PeerJ· February 2024

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Characterizing transcriptomic responses to sediment stress across location and morphology in reef-building corals.
Jill Ashey, Hailey McKelvie, John Freeman, Polina Shpilker, Lauren H Zane, Lenore Cowen

PeerJ· February 2024

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TT3D: Leveraging precomputed protein 3D sequence models to predict protein-protein interactions.
Samuel Sledzieski, Kapil Devkota, Rohit Singh, Lenore Cowen, Bonnie Berger

Bioinformatics· November 2023

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Contrastive learning in protein language space predicts interactions between drugs and protein targets.
Rohit Singh, Samuel Sledzieski, Bryan Bryson, Lenore Cowen, Bonnie Berger

Proc Natl Acad Sci U S A· June 2023

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Transfer of knowledge from model organisms to evolutionarily distant non-model organisms: The coral Pocillopora damicornis membrane signaling receptome.
Lokender Kumar, Nathanael Brenner, Samuel Sledzieski, Monsurat Olaosebikan, Liza M Roger, Lenore Cowen

PLoS One· February 2023

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Evaluation of fluorescence-based viability stains in cells dissociated from scleractinian coral Pocillopora damicornis.
Liza M Roger, Yaa Adarkwa Darko, Tytus Bernas, Frances White, Monsurat Olaosebikan, Lenore Cowen

Sci Rep· September 2022

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Majority Vote Cascading: A Semi-Supervised Framework for Improving Protein Function Prediction.
John Lazarsfeld, Jonathan Rodriguez, Mert Erden, Yuelin Liu, Lenore J Cowen

IEEE/ACM Trans Comput Biol Bioinform· August 2022

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Bioinformatics of Corals: Investigating Heterogeneous Omics Data from Coral Holobionts for Insight into Reef Health and Resilience.
Lenore J Cowen, Hollie M Putnam

Annu Rev Biomed Data Sci· August 2022

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MEDFORD: A human- and machine-readable metadata markup language.
Polina Shpilker, John Freeman, Hailey McKelvie, Jill Ashey, Jay-Miguel Fonticella, Lenore Cowen

Database (Oxford)· August 2022

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GLIDER: function prediction from GLIDE-based neighborhoods.
Kapil Devkota, Henri Schmidt, Matt Werenski, James M Murphy, Mert Erden, Lenore J Cowen

Bioinformatics· June 2022

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Topsy-Turvy: integrating a global view into sequence-based PPI prediction.
Rohit Singh, Kapil Devkota, Samuel Sledzieski, Bonnie Berger, Lenore Cowen

Bioinformatics· June 2022

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Cognitive cascades: How to model (and potentially counter) the spread of fake news.
Nicholas Rabb, Lenore Cowen, Jan P de Ruiter, Matthias Scheutz

PLoS One· February 2022

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Bioengineered models of Parkinson's disease using patient-derived dopaminergic neurons exhibit distinct biological profiles in a 3D microenvironment.
Nicholas J Fiore, Yosif M Ganat, Kapil Devkota, Rebecca Batorsky, Ming Lei, Lenore J Cowen

Cell Mol Life Sci· January 2022

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D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions.
Samuel Sledzieski, Rohit Singh, Lenore Cowen, Bonnie Berger

Cell Syst· October 2021

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MUNDO: protein function prediction embedded in a multispecies world.
Victor Arsenescu, Kapil Devkota, Mert Erden, Polina Shpilker, Matthew Werenski, Lenore J Cowen

Bioinform Adv· September 2021

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Bioinformatics of corals: Investigating heterogeneous omics data from coral holobionts for insight into reef health and resillience.
Lenore J Cowen, Judith Klein-Seetharaman, Hollie Putnam

Pac Symp Biocomput· April 2021

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GLIDE: combining local methods and diffusion state embeddings to predict missing interactions in biological networks.
Kapil Devkota, James M Murphy, Lenore J Cowen

Bioinformatics· July 2020

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Cell shape, and not 2D migration, predicts extracellular matrix-driven 3D cell invasion in breast cancer.
Janani P Baskaran, Anna Weldy, Justinne Guarin, Gabrielle Munoz, Polina H Shpilker, Lenore Cowen

APL Bioeng· June 2020

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Assessment of network module identification across complex diseases.
Sarvenaz Choobdar, Mehmet E Ahsen, Jake Crawford, Mattia Tomasoni, Tao Fang, Lenore J Cowen

Nat Methods· September 2019

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Retraction Note: detangling PPI networks to uncover functionally meaningful clusters.
Sarah Hall-Swan, Jake Crawford, Rebecca Newman, Lenore J Cowen

BMC Syst Biol· November 2018

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Detangling PPI networks to uncover functionally meaningful clusters.
Sarah Hall-Swan, Jake Crawford, Rebecca Newman, Lenore J Cowen

BMC Syst Biol· March 2018

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