BioExtract Server, a Web-based workflow enabling system, leveraging iPlant collaborative resources. - Carol Lushbough; Etienne Z. Gnimpieba; Rion Dooley (CLUSTER, 2013)

Bioinformatics Knowledge Transmission (training, learning, and teaching): overview and flexible comparison of computer based training approaches. - Etienne Z. Gnimpieba; Douglas M. Jennewein; Luke Fuhrman; Carol Lushbough (CoRR, 2013)

RNA-seq gene and transcript expression analysis using the BioExtract server and iPlant collaborative. - Etienne Z. Gnimpieba; Abalo Chango; Carol M. Lushbough (BCB, 2014)

Heuristic parallelizable algorithm for similarity based biosystems comparison. - Mathialakan Thavappiragasam; Carol M. Lushbough; Etienne Z. Gnimpieba (BCB, 2014)

Automatic biosystems comparison using semantic and name similarity. - Mathialakan Thavappiragasam; Carol M. Lushbough; Etienne Z. Gnimpieba (BCB, 2014)

Pheno2GRN: a workflow for phenotype to gene network study and reverse engineering comparison. - Nick Weinandt; Laura M. Jackson; Etienne Z. Gnimpieba; Carol Lushbough (BCB, 2014)

SBMLDock: Docker Driven Systems Biology Tool Development and Usage. - Etienne Z. Gnimpieba; Mathialakan Thavappiragasam; Abalo Chango; Bill Conn; Carol M. Lushbough (CMSB, 2015)

Life science data analysis workflow development using the bioextract server leveraging the iPlant collaborative cyberinfrastructure. - Carol M. Lushbough; Etienne Z. Gnimpieba; Rion Dooley (Concurr. Comput. Pract. Exp., 2015)

NanoStringBioNet: Integrated R framework for bioscience knowledge discovery from NanoString nCounter data. - Mariah M. Hoffman; Carrie J. Minette; Shanta M. Messerli; Ratan D. Bhardwaj; Etienne Z. Gnimpieba (BIBM, 2017)

Bio-TDS: bioscience query tool discovery system. - Etienne Z. Gnimpieba; Menno S. VanDiermen; Shayla M. Gustafson; Bill Conn; Carol M. Lushbough (Nucleic Acids Res., 2017)

GenNER - A highly scalable and optimal NER method for text-based gene and protein recognition. - Ernest Basile Fotseu Fotseu; Thierry Kongne Nembot; Rajesh Kumar Sani; Venkataramana Gadhamshetty; Etienne Z. Gnimpieba; Alain Bertrand Bomgni (BIBM, 2021)

Automatic Extension of Medical Subject Headings (MeSH) Thesaurus to Emerging Research. - William Gasper; Jiahao Ma; Dario Ghersi; Etienne Z. Gnimpieba; Venkataramana Gadhamshetty; Parvathi Chundi (BIBM, 2021)

Prediction of essential genes in G20 using machine learning model. - Thierry Kongne Nembot; Ernest Basile Fotseu Fotseu; Rajesh Kumar Sani; Etienne Z. Gnimpieba; Carol Lushbough; Alain Bertrand Bomgni (BIBM, 2021)

Integration of text mining and biological network analysis to access essential genes in Desulfovibrio alaskensis G20. - Priya Saxena; Abhilash Kumar Tripathi; Payal Thakur; Shailabh Rauniyar; Vinoj Gopalakrishnan; Ram Nageena Singh; Mathew A. Olakunle; Etienne Z. Gnimpieba; Rajesh Kumar Sani (BIBM, 2021)

Identifying genes involved in biocorrosion from the literature using text-mining. - Payal Thakur; Shailabh Rauniyar; Abhilash Kumar Tripathi; Priya Saxena; Vinoj Gopalakrishnan; Ram Nageena Singh; Mathew A. Olakunle; Etienne Z. Gnimpieba; Rajesh Kumar Sani (BIBM, 2021)

Discovery of genes associated with sulfate-reducing bacteria biofilm using text mining and biological network analysis. - Abhilash Kumar Tripathi; Priya Saxena; Payal Thakur; Shailabh Rauniyar; Vinoj Gopalakrishnan; Ram Nageena Singh; Mathew A. Olakunle; Etienne Z. Gnimpieba; Rajesh Kumar Sani (BIBM, 2021)

Attention model-based and multi-organism driven gene recognition from text: application to a microbial biofilm organism set. - Alain Bertrand Bomgni; Ernest Basile Fotseu Fotseu; Daril Raoul Kengne Wambo; Rajesh Kumar Sani; Carol Lushbough; Etienne Z. Gnimpieba (BIBM, 2022)

U-Net Based Image Segmentation Techniques for Development of Non-Biocidal Fouling-Resistant Ultra-Thin Two-dimensional (2D) Coatings. - Bichar Dip Shrestha Gurung; Ramesh Devadig; Tuyen Do; Venkataramana Gadhamshetty; Etienne Z. Gnimpieba (BIBM, 2022)

Using BASIN-ML for Machine Learning-Based Statistical Analysis and Reporting for Biofilm Datasets. - Sam Haas; Timothy W. Hartman; Bichar Dip Shrestha Gurung; Tuyen Do; Rajesh Kumar Sani; Venkataramana Gadhamshetty; Etienne Z. Gnimpieba (BIBM, 2022)

Title: Challenges in single cells sequencing Microbial community and biofilm: A case of Oleidesulfovibrio alaskensis G20 NGS protocol. - Ram Nageena Singh; Etienne Z. Gnimpieba; Rajesh Kumar Sani (BIBM, 2022)

Fine-tuning a pre-trained Transformers-based model for gene name entity recognition in biomedical text using a customized dataset: case of Desulfovibrio vulgaris Hildenborough. - Alain Bertrand Bomgni; Dialo Abdala; Bichar Dip Shrestha Gurung; Marcellin Julius Antonio Nkenlifack; Venkataramana Gadhamshetty; Etienne Z. Gnimpieba (BIBM, 2023)

NLPADADE: Leveraging Natural Language Processing for Automated Detection of Adverse Drug Effects. - Alain Bertrand Bomgni; Claude Epiphanie Mbotchack Ngale; Shiva Aryal; Marcellin Julius Antonio Nkenlifack; Venkataramana Gadhamshetty; Etienne Z. Gnimpieba (BIBM, 2023)

Computational methods for biofouling and corrosion-resistant graphene nanocomposites. A transdisciplinary approach. - Ramesh Devadig; Bichar Dip Shrestha Gurung; Etienne Z. Gnimpieba; Bharath Jasthi; Venkataramana Gadhamshetty (BIBM, 2023)

Utilizing XGBoost for the Prediction of Material Corrosion Rates from Embedded Tabular Data using Large Language Model. - Tuyen Do; Bichar Dip Shrestha Gurung; Shiva Aryal; Anup Khanal; Sandeep Chataut; Venkataramana Gadhamshetty; Carol Lushbough; Etienne Z. Gnimpieba (BIBM, 2023)

Transformer in Microbial Image Analysis: A Comparative Exploration of TransUNet, UNet, and DoubleUNet for SEM Image Segmentation. - Bichar Dip Shrestha Gurung; Anup Khanal; Timothy W. Hartman; Tuyen Do; Sandeep Chataut; Carol Lushbough; Venkataramana Gadhamshetty; Etienne Z. Gnimpieba (BIBM, 2023)

SIMPL - An Application for Cell and Microbe Tracking Using Machine Learning. - Sam Haas; Bichar Dip Shrestha Gurung; Timothy W. Hartman; Tuyen Do; Etienne Z. Gnimpieba (BIBM, 2023)

Genome wide computational prediction and analysis of noncoding genome of corrosive biofilm forming Oleidesulfovibrio alaskensis G20. - Ram Nageena Singh; Etienne Z. Gnimpieba; Rajesh Kumar Sani (BIBM, 2023)

ESPINA: efficient and secured protocol for emerging IoT network applications. - Alain Bertrand Bomgni; Garrik Brel Jagho Mdemaya; Hafiz Munsub Ali; David R. Gnimpieba Zanfack; Etienne Z. Gnimpieba (Clust. Comput., 2023)

MultiHop optimal time complexity clustering for emerging IoT applications. - Yann Brice Chebu Mtopi; Alain Bertrand Bomgni; Hafiz Munsub Ali; David R. Gnimpieba Zanfack; Waleed Ejaz; Clémentin Tayou Djamégni; Etienne Zohim Gnimpieba (Clust. Comput., 2023)

Toward Fine-Tuning Large Language Models in Ontology of Microbial Phenotypes Construction. - Anushuya Baidya; Tuyen Do; Etienne Z. Gnimpieba (BIBM, 2024)

AIM-HKR: AI-Driven Molecular Retrosynthesis Using Heterogeneous Knowledge Representations. - Alain Bertrand Bomgni; Ribot Fleury Téné Ceskoutsé; Kevin Jordan Njike Njingang; Thomas Bouétou Bouétou; Venkataramana Gadhamshetty; Etienne Gnimpieba Zohim (BIBM, 2024)

NFB-Checker: An AI/ML-Powered Microorganism Nitrogen Fixation Susceptibility Prediction from Gene Collection. - Tuyen Do; Shiva Aryal; Bichar Dip Shrestha Gurung; Diing D. M. Agany; Nick Klein; Ruanbao Zhou; Rajesh Kumar Sani; Etienne Z. Gnimpieba (BIBM, 2024)

Efficient Prediction of Protein-Ligand Binding Using ESM-2 and Mol2vec with Random Forest Model. - Bichar Dip Shrestha Gurung; Manish Rayamajhi; Anushuya Baidya; Owen Growney; Helena Naomie Dongmo Mafo; Yun-Seok Choi; Etienne Z. Gnimpieba (BIBM, 2024)

Enhancing Sulphate Reducing Bacteria Clustering by Implementing UMAP on Raman Spectroscopy Data. - Md Hasanur Rahman 004; Bichar Dip Shrestha Gurung; Manoj Tripathi; Alan Dalton; Venkataramana Gadhamshetty; Etienne Z. Gnimpieba (BIBM, 2024)

Applying the DeepSeqDock Harmonization Framework on Pseudomonas Aeruginosa Bacterial Biofilm Data. - Corey Zhao; Bichar Dip Shrestha Gurung; Timothy W. Hartman; Tuyen Do; Mariah M. Hoffman; Etienne Z. Gnimpieba (BIBM, 2024)

Biofilm marker discovery with cloud-based dockerized metagenomics analysis of microbial communities. - Etienne Z. Gnimpieba; Timothy W. Hartman; Tuyen Do; Jessica Zylla; Shiva Aryal; Samuel J. Haas; Diing D. M. Agany; Bichar Dip Shrestha Gurung; Valena Doe; Zelaikha B. Yosufzai; Daniel Pan; Ross Campbell; et al. (Briefings Bioinform., 2024)

Sub-clustering based recommendation system for stroke patient: Identification of a specific drug class for a given patient. - Ribot Fleury T. Ceskoutsé; Alain Bertrand Bomgni; David R. Gnimpieba Zanfack; Diing D. M. Agany; Thomas Bouétou Bouétou; Etienne Gnimpieba Zohim (Comput. Biol. Medicine, 2024)

Comparative Study of Domain Driven Terms Extraction Using Large Language Models. - Sandeep Chataut; Tuyen Do; Bichar Dip Shrestha Gurung; Shiva Aryal; Anup Khanal; Carol Lushbough; Etienne Z. Gnimpieba (CoRR, 2024)

Leveraging Multi-AI Agents for Cross-Domain Knowledge Discovery. - Shiva Aryal; Tuyen Do; Bisesh Heyojoo; Sandeep Chataut; Bichar Dip Shrestha Gurung; Venkataramana Gadhamshetty; Etienne Z. Gnimpieba (CoRR, 2024)

HeteroKGRep: Heterogeneous Knowledge Graph based Drug Repositioning. - Ribot Fleury T. Ceskoutsé; Alain Bertrand Bomgni; David R. Gnimpieba Zanfack; Diing D. M. Agany; Thomas Bouétou Bouétou; Etienne Gnimpieba Zohim (Knowl. Based Syst., 2024)