A non-parameter Ising model for network-based identification of differentially expressed genes in recurrent breast cancer patients. - Xumeng Li; F. Alex Feltus; Xiaoqian Sun; James Zijun Wang; Feng Luo 001 (BIBM, 2010)

Effectively Integrating Information Content and Structural Relationship to Improve the GO-based Similarity Measure Between Proteins. - Bo Li 036; Feng Luo 001; James Z. Wang 002; F. Alex Feltus; Jizhong Zhou (BIOCOMP, 2010)

Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases. - Lacey-Anne Sanderson; Stephen P. Ficklin; Chun-Huai Cheng; Sook Jung; F. Alex Feltus; Kirstin E. Bett; Dorrie Main (Database J. Biol. Databases Curation, 2013)

Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study. - F. Alex Feltus; Stephen P. Ficklin; Scott M. Gibson; Melissa C. Smith (BMC Syst. Biol., 2013)

OSG-KINC: High-throughput gene co-expression network construction using the open science grid. - William L. Poehlman; Mats Rynge; D. Balamurugan; Nicholas Mills; Frank Alex Feltus (BIBM, 2017)

Big Data Smart Socket (BDSS): a system that abstracts data transfer habits from end users. - Nicholas A. Watts; Frank Alex Feltus (Bioinform., 2017)

NDN-SCI for managing large scale genomics data. - Susmit Shannigrahi; Chengyu Fan; Christos Papadopoulos; F. Alex Feltus (ICN, 2018)

Maximizing the performance of scientific data transfer by optimizing the interface between parallel file systems and advanced research networks. - Nicholas Mills; F. Alex Feltus; Walter B. Ligon III (Future Gener. Comput. Syst., 2018)

Integrity Protection for Scientific Workflow Data: Motivation and Initial Experiences. - Mats Rynge; Karan Vahi; Ewa Deelman; Anirban Mandal; Ilya Baldin; Omkar Bhide; Randy W. Heiland; Von Welch; Raquel Hill; William L. Poehlman; F. Alex Feltus (PEARC, 2019)

GPU Implementation of Pairwise Gaussian Mixture Models for Multi-Modal Gene Co-Expression Networks. - Benjamin T. Shealy; Josh J. R. Burns; Melissa C. Smith; F. Alex Feltus; Stephen P. Ficklin (IEEE Access, 2019)

Growing and cultivating the forest genomics database, TreeGenes. - Taylor Falk; Nic Herndon; Emily S. Grau; Sean Buehler; Peter Richter 001; Sumaira Zaman; Eliza M. Baker; Risharde Ramnath; Stephen P. Ficklin; Margaret Staton; Frank Alex Feltus; Sook Jung; et al. (Database J. Biol. Databases Curation, 2019)

Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases. - Shawna Spoor; Chun-Huai Cheng; Lacey-Anne Sanderson; Bradford Condon; Abdullah Almsaeed; Ming Chen; Anthony Bretaudeau; Helena Rasche; Sook Jung; Dorrie Main; Kirstin E. Bett; Margaret Staton; et al. (Database J. Biol. Databases Curation, 2019)

Cellular State Transformations using Generative Adversarial Networks. - Colin Targonski; Benjamin T. Shealy; Melissa C. Smith; F. Alex Feltus (CoRR, 2019)

Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases. - Shawna Spoor; Connor Wytko; Brian Soto; Ming Chen; Abdullah Almsaeed; Bradford Condon; Nic Herndon; Heidi Hough; Sook Jung; Meg Staton; Jill L. Wegrzyn; Dorrie Main; et al. (Database J. Biol. Databases Curation, 2020)

Cellular State Transformations Using Deep Learning for Precision Medicine Applications. - Colin Targonski; M. Reed Bender; Benjamin T. Shealy; Benafsh Husain; Bill Paseman; Melissa C. Smith; F. Alex Feltus (Patterns, 2020)

Designing Hydra with Centralized versus Decentralized Control: A Comparative Study. - Siqi Liu; Varun Patil; Tianyuan Yu; Alexander Afanasyev; Frank Alex Feltus; Susmit Shannigrahi; Lixia Zhang 001 (IWCI@CoNEXT, 2021)

Intelligent Resource Provisioning for Scientific Workflows and HPC. - Benjamin T. Shealy; F. Alex Feltus; Melissa C. Smith (WORKS, 2021)

Named Data Networking for Genomics Data Management and Integrated Workflows. - Cameron Ogle; David Reddick; Coleman McKnight; Tyler Biggs; Rini Pauly; Stephen P. Ficklin; F. Alex Feltus; Susmit Shannigrahi (Frontiers Big Data, 2021)

Case Study of Attribute Based Access Control for Genomics Data Using Named Data Networking. - David Reddick; F. Alex Feltus; Susmit Shannigrahi (CCNC, 2022)

WiP: AABAC - Automated Attribute Based Access Control for Genomics Data. - David Reddick; Justin Presley; Frank Alex Feltus; Susmit Shannigrahi (SACMAT, 2022)

Addressing noise in co-expression network construction. - Josh J. R. Burns; Benjamin T. Shealy; Mitchell S. Greer; John A. Hadish; Matthew McGowan; Tyler Biggs; Melissa C. Smith; F. Alex Feltus; Stephen P. Ficklin (Briefings Bioinform., 2022)

GEMmaker: process massive RNA-seq datasets on heterogeneous computational infrastructure. - John A. Hadish; Tyler Biggs; Benjamin T. Shealy; M. Reed Bender; Coleman McKnight; Connor Wytko; Melissa C. Smith; F. Alex Feltus; Loren A. Honaas; Stephen P. Ficklin (BMC Bioinform., 2022)

AABAC - Automated Attribute Based Access Control for Genomics Data. - David Reddick; Justin Presley; F. Alex Feltus; Susmit Shannigrahi (CoRR, 2022)

Hydra - A Federated Data Repository over NDN. - Justin Presley; Xi Wang; Tym Brandel; Xusheng Ai; Proyash Podder; Tianyuan Yu; Varun Patil; Lixia Zhang 001; Alex Afanasyev; F. Alex Feltus; Susmit Shannigrahi (CoRR, 2022)

GNSGA: A Decentralized Data Replication Algorithm for Big Science Data. - Xi Wang; Xusheng Ai; F. Alex Feltus; Susmit Shannigrahi (IFIP Networking, 2023)

Hydra: A Scalable Decentralized P2P Storage Federation for Large Scientific Datasets. - Justin Presley; Xi Wang; Xusheng Ai; Tianyuan Yu; Tym Brandel; Proyash Podder; Varun Patil; Alex Afanasyev; F. Alex Feltus; Lixia Zhang 001; Susmit Shannigrahi (ICNC, 2024)

GEMDiff: a diffusion workflow bridges between normal and tumor gene expression states: a breast cancer case study. - Xusheng Ai; Melissa C. Smith; F. Alex Feltus (Briefings Bioinform., 2025)