BIND-a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. - Gary D. Bader; Christopher W. V. Hogue (Bioinform., 2000)

BIND - The Biomolecular Interaction Network Database. - Gary D. Bader; Ian M. Donaldson; Cheryl Wolting; B. F. Francis Ouellette; Tony Pawson; Christopher W. V. Hogue (Nucleic Acids Res., 2001)

Bioinformatics: Interaction Databases. - Gary D. Bader; Christopher W. V. Hogue (Essentials of Genomics and Bioinformatics, 2002)

SeqHound: biological sequence and structure database as a platform for bioinformatics research. - Katerina Michalickova; Gary D. Bader; Michel Dumontier; Hao Lieu; Doron Betel; Ruth Isserlin; Christopher W. V. Hogue (BMC Bioinform., 2002)

An automated method for finding molecular complexes in large protein interaction networks. - Gary D. Bader; Christopher W. V. Hogue (BMC Bioinform., 2003)

PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine. - Ian M. Donaldson; Joel D. Martin; Berry de Bruijn; Cheryl Wolting; Vicki Lay; Brigitte Tuekam; Shudong Zhang; Berivan Baskin; Gary D. Bader; Katerina Michalickova; Tony Pawson; Christopher W. V. Hogue (BMC Bioinform., 2003)

BIND: the Biomolecular Interaction Network Database. - Gary D. Bader; Doron Betel; Christopher W. V. Hogue (Nucleic Acids Res., 2003)

cPath: open source software for collecting, storing, and querying biological pathways. - Ethan G. Cerami; Gary D. Bader; Benjamin E. Gross; Chris Sander (BMC Bioinform., 2006)

Pathguide: a Pathway Resource List. - Gary D. Bader; Michael P. Cary; Chris Sander (Nucleic Acids Res., 2006)

NetMatch: a Cytoscape plugin for searching biological networks. - Alfredo Ferro; Rosalba Giugno; Giuseppe Pigola; Alfredo Pulvirenti; Dmitry Skripin; Gary D. Bader; Dennis E. Shasha (Bioinform., 2007)

From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research. - Jomol P. Mathew; Barry S. Taylor; Gary D. Bader; Saiju Pyarajan; Marco Antoniotti; Arul M. Chinnaiyan; Chris Sander; Steven J. Burakoff; Bud Mishra (PLoS Comput. Biol., 2007)

Cytoscape ESP: simple search of complex biological networks. - Maital Ashkenazi; Gary D. Bader; Allan Kuchinsky; Menachem Moshelion; David J. States (Bioinform., 2008)

Cytoscape Web: an interactive web-based network browser. - Christian Tannus Lopes; Max Franz; Farzana Kazi; Sylva L. Donaldson; Quaid Morris; Gary D. Bader (Bioinform., 2010)

GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop. - Jason Montojo; Khalid Zuberi; Harold Rodriguez; Farzana Kazi; George Wright; Sylva L. Donaldson; Quaid Morris; Gary D. Bader (Bioinform., 2010)

Proteome scanning to predict PDZ domain interactions using support vector machines. - Shirley Hui; Gary D. Bader (BMC Bioinform., 2010)

An improved method for scoring protein-protein interactions using semantic similarity within the Gene Ontology. - Shobhit Jain; Gary D. Bader (BMC Bioinform., 2010)

DRYGIN: a database of quantitative genetic interaction networks in yeast. - Judice L. Y. Koh; Huiming Ding; Michael Costanzo; Anastasia Baryshnikova; Kiana Toufighi; Gary D. Bader; Chad L. Myers; Brenda J. Andrews; Charles Boone (Nucleic Acids Res., 2010)

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. - David Warde-Farley; Sylva L. Donaldson; Ovi Comes; Khalid Zuberi; Rashad Badrawi; Pauline Chao; Max Franz; Chris Grouios; Farzana Kazi; Christian Tannus Lopes; Anson Maitland; Sara Mostafavi; et al. (Nucleic Acids Res., 2010)

The Biomolecular Interaction Network Database in PSI-MI 2.5. - Ruth Isserlin; Rashad Badrawi; Gary D. Bader (Database J. Biol. Databases Curation, 2011)

A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway. - Rajesh Raju; Lavanya Balakrishnan; Vishalakshi Nanjappa; Mitali Bhattacharjee; Derese Getnet; Babylakshmi Muthusamy; Joji Kurian Thomas; Jyoti Sharma; B. Abdul Rahiman; H. C. Harsha; Subramanian Shankar; T. S. Keshava Prasad; et al. (Database J. Biol. Databases Curation, 2011)

NetSlim: high-confidence curated signaling maps. - Rajesh Raju; Vishalakshi Nanjappa; Lavanya Balakrishnan; Aneesha Radhakrishnan; Joji Kurian Thomas; Jyoti Sharma; Maozhen Tian; Shyam Mohan Palapetta; Tejaswini Subbannayya; Nirujogi Raja Sekhar; Babylakshmi Muthusamy; Renu Goel; et al. (Database J. Biol. Databases Curation, 2011)

A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequence. - Xiaojian Shao; Chris Soon Heng Tan; Courtney Voss; Shawn S. C. Li; Naiyang Deng; Gary D. Bader (Bioinform., 2011)

clusterMaker: a multi-algorithm clustering plugin for Cytoscape. - John H. Morris; Leonard Apeltsin; Aaron M. Newman; Jan Baumbach; Tobias Wittkop; Gang Su; Gary D. Bader; Thomas E. Ferrin (BMC Bioinform., 2011)

Pathway Commons, a web resource for biological pathway data. - Ethan G. Cerami; Benjamin E. Gross; Emek Demir; Igor V. Rodchenkov; Özgün Babur; Nadia Anwar; Nikolaus Schultz; Gary D. Bader; Chris Sander (Nucleic Acids Res., 2011)

Protein Complexes are Central in the Yeast Genetic Landscape. - Magali Michaut; Anastasia Baryshnikova; Michael Costanzo; Chad L. Myers; Brenda J. Andrews; Charles Boone; Gary D. Bader (PLoS Comput. Biol., 2011)

WordCloud: a Cytoscape plugin to create a visual semantic summary of networks. - Layla Oesper; Daniele Merico; Ruth Isserlin; Gary D. Bader (Source Code Biol. Medicine, 2011)

Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study. - Mohammed Alshalalfa; Gary D. Bader; Anna Goldenberg; Quaid Morris; Reda Alhajj (BMC Syst. Biol., 2012)

Multiple Genetic Interaction Experiments Provide Complementary Information Useful for Gene Function Prediction. - Magali Michaut; Gary D. Bader (PLoS Comput. Biol., 2012)

GeStoDifferent: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process. - Marco Antoniotti; Gary D. Bader; Giulio Caravagna; Silvia Crippa; Alex Graudenzi; Giancarlo Mauri (Bioinform., 2013)

Cytoscape App Store. - Samad Lotia; Jason Montojo; Yue Dong; Gary D. Bader; Alexander R. Pico (Bioinform., 2013)

The BioPAX Validator. - Igor V. Rodchenkov; Emek Demir; Chris Sander; Gary D. Bader (Bioinform., 2013)

Predicting PDZ domain mediated protein interactions from structure. - Shirley Hui; Xiang Xing; Gary D. Bader (BMC Bioinform., 2013)

GeneMANIA Prediction Server 2013 Update. - Khalid Zuberi; Max Franz; Harold Rodriguez; Jason Montojo; Christian Tannus Lopes; Gary D. Bader; Quaid Morris (Nucleic Acids Res., 2013)

Using Biological Pathway Data with Paxtools. - Emek Demir; Özgün Babur; Igor V. Rodchenkov; Bülent Arman Aksoy; Ken I. Fukuda; Benjamin E. Gross; Selçuk Onur Sümer; Gary D. Bader; Chris Sander (PLoS Comput. Biol., 2013)

HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery. - Alvin Leung 001; Gary D. Bader; Jüri Reimand (Bioinform., 2014)

Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results. - Ruth Isserlin; Daniele Merico; Veronique Voisin; Gary D. Bader (F1000Research, 2014)

The Cytoscape app article collection. - Alexander R. Pico; Gary D. Bader; Barry Demchak; Oriol Guitart Pla; Timothy Hull; William J. R. Longabaugh; Christian Tannus Lopes; Samad Lotia; Piet Molenaar; Jason Montojo; John H. Morris; Keiichiro Ono; et al. (F1000Research, 2014)

Erratum to: Inferring interaction type in gene regulatory networks using co-expression data. - Pegah Khosravi; Vahid H. Gazestani; Leila Pirhaji; Brian Law; Mehdi Sadeghi; Gary D. Bader; Bahram Goliaei (Algorithms Mol. Biol., 2015)

Inferring interaction type in gene regulatory networks using co-expression data. - Pegah Khosravi; Vahid H. Gazestani; Leila Pirhaji; Brian Law; Mehdi Sadeghi; Bahram Goliaei; Gary D. Bader (Algorithms Mol. Biol., 2015)

Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli. - James Vlasblom; Khalid Zuberi; Harold Rodriguez; Roland Arnold; Alla Gagarinova; Viktor Deineko; Ashwani Kumar; Elisa Leung; Kamran Rizzolo; Bahram Samanfar; Luke Chang; Sadhna Phanse; et al. (Bioinform., 2015)

Social Network: a Cytoscape app for visualizing co-publication networks. - Victor Kofia; Ruth Isserlin; Alison Buchan; Gary D. Bader (F1000Research, 2015)

NetMatchStar: an enhanced Cytoscape network querying app. - Fabio Rinnone; Giovanni Micale; Vincenzo Bonnici; Gary D. Bader; Dennis E. Shasha; Alfredo Ferro; Alfredo Pulvirenti; Rosalba Giugno (F1000Research, 2015)

Specifications of Standards in Systems and Synthetic Biology. - Falk Schreiber; Gary D. Bader; Martin Golebiewski; Michael Hucka; Benjamin Kormeier; Nicolas Le Novère; Chris J. Myers; David P. Nickerson; Björn Sommer 001; Dagmar Waltemath; Stephan Weise (J. Integr. Bioinform., 2015)

SyQUAL: a platform for qualitative modelling and simulation of biological systems. - Rosario Distefano; Nickolas Goncharenko; Franco Fummi; Rosalba Giugno; Gary D. Bader; Nicola Bombieri (HLDVT, 2016)

Cytoscape.js: a graph theory library for visualisation and analysis. - Max Franz; Christian Tannus Lopes; Gerardo Huck; Yue Dong; Selçuk Onur Sümer; Gary D. Bader (Bioinform., 2016)

Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast. - Shobhit Jain; Gary D. Bader (Bioinform., 2016)

AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations. - Mike Kucera; Ruth Isserlin; Arkady Arkhangorodsky; Gary D. Bader (F1000Research, 2016)

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. - Falk Schreiber; Gary D. Bader; Padraig Gleeson; Martin Golebiewski; Michael Hucka; Nicolas Le Novère; Chris J. Myers; David P. Nickerson; Björn Sommer 001; Dagmar Waltemath (J. Integr. Bioinform., 2016)

Ten Simple Rules for Developing Public Biological Databases. - Mohamed Helmy; Alexander Crits-Christoph; Gary D. Bader (PLoS Comput. Biol., 2016)

Global neuroscience and mental health research: a bibliometrics case study. - Alison Buchan; Eva Jurczyk; Ruth Isserlin; Gary D. Bader (Scientometrics, 2016)

A brief history of COMBINE. - Chris J. Myers; Gary D. Bader; Padraig Gleeson; Martin Golebiewski; Michael Hucka; Nicolas Le Novère; David P. Nickerson; Falk Schreiber; Dagmar Waltemath (WSC, 2017)

Transfer learning for biomedical named entity recognition with neural networks. - John M. Giorgi; Gary D. Bader (Bioinform., 2018)

The Cytoscape Automation app article collection. - Barry Demchak; David Otasek; Alexander R. Pico; Gary D. Bader; Keiichiro Ono; Brett Settle; Eric Sage; John H. Morris; William J. R. Longabaugh; Christian Tannus Lopes; Michael Kucera; Adam Treister; et al. (F1000Research, 2018)

scClustViz - Single-cell RNAseq cluster assessment and visualization. - Brendan T. Innes; Gary D. Bader (F1000Research, 2018)

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. - Falk Schreiber; Gary D. Bader; Padraig Gleeson; Martin Golebiewski; Michael Hucka; Sarah M. Keating; Nicolas Le Novère; Chris J. Myers; David P. Nickerson; Björn Sommer 001; Dagmar Waltemath (J. Integr. Bioinform., 2018)

GeneMANIA update 2018. - Max Franz; Harold Rodriguez; Christian Tannus Lopes; Khalid Zuberi; Jason Montojo; Gary D. Bader; Quaid Morris (Nucleic Acids Res., 2018)

End-to-end Named Entity Recognition and Relation Extraction using Pre-trained Language Models. - John M. Giorgi; Xindi Wang 001; Nicola Sahar; Won Young Shin; Gary D. Bader; Bo Wang 044 (CoRR, 2019)

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. - Falk Schreiber; Björn Sommer 001; Gary D. Bader; Padraig Gleeson; Martin Golebiewski; Michael Hucka; Sarah M. Keating; Matthias König 003; Chris J. Myers; David P. Nickerson; Dagmar Waltemath (J. Integr. Bioinform., 2019)

Towards reliable named entity recognition in the biomedical domain. - John M. Giorgi; Gary D. Bader (Bioinform., 2020)

netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks. - Shraddha Pai; Philipp Weber; Ruth Isserlin; Hussam Kaka; Shirley Hui; Muhammad Ahmad Shah; Luca Giudice; Rosalba Giugno; Anne Krogh Nøhr; Jan Baumbach; Gary D. Bader (F1000Research, 2020)

Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. - Igor V. Rodchenkov; Ozgun Babur; Augustin Luna; Bülent Arman Aksoy; Jeffrey V. Wong; Dylan Fong; Max Franz; Metin Can Siper; Manfred Cheung; Michael Wrana; Harsh Mistry; Logan Mosier; et al. (Nucleic Acids Res., 2020)

A reference map of the human binary protein interactome. - Katja Luck; Dae-Kyum Kim; Luke Lambourne; Kerstin Spirohn; Bridget E. Begg; Wenting Bian; Ruth Brignall; Tiziana Cafarelli; Francisco J. Campos-Laborie; Benoît Charloteaux; Dong-Sic Choi; Atina G. Coté; et al. (Nat., 2020)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - Esther Rheinbay; Morten Muhlig Nielsen; Federico Abascal; Jeremiah Wala; Ofer Shapira; Grace Tiao; Henrik Hornshøj; Julian M. Hess; Randi Istrup Juul; Ziao Lin; Lars Feuerbach; Radhakrishnan Sabarinathan; et al. (Nat., 2020)

Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data. - Thinh N. Tran; Gary D. Bader (PLoS Comput. Biol., 2020)

DeCLUTR: Deep Contrastive Learning for Unsupervised Textual Representations. - John M. Giorgi; Osvald Nitski; Bo Wang 044; Gary D. Bader (ACL/IJCNLP (1), 2021)

SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. - Adrien Rougny; Vasundra Touré; John Albanese; Dagmar Waltemath; Denis Shirshov; Anatoly A. Sorokin; Gary D. Bader; Michael L. Blinov; Alexander Mazein (Briefings Bioinform., 2021)

A flexible search system for high-accuracy identification of biological entities and molecules. - Max Franz; Jeffrey V. Wong; Metin Can Siper; Christian Dallago; John M. Giorgi; Emek Demir; Chris Sander; Gary D. Bader (J. Open Source Softw., 2021)

A sequence-to-sequence approach for document-level relation extraction. - John M. Giorgi; Gary D. Bader; Bo Wang 044 (BioNLP@ACL, 2022)

Exploring the Challenges of Open Domain Multi-Document Summarization. - John M. Giorgi; Luca Soldaini; Bo Wang 044; Gary D. Bader; Kyle Lo; Lucy Lu Wang; Arman Cohan (CoRR, 2022)

The reactome pathway knowledgebase 2022. - Marc Gillespie; Bijay Jassal; Ralf Stephan; Marija Milacic; Karen Rothfels; Andrea Senff-Ribeiro; Johannes Griss; Cristoffer Sevilla; Lisa Matthews; Chuqiao Gong; Chuan Deng; Thawfeek M. Varusai; et al. (Nucleic Acids Res., 2022)

MAESTER: Masked Autoencoder Guided Segmentation at Pixel Resolution for Accurate, Self-Supervised Subcellular Structure Recognition. - Ronald Xie; Kuan Pang; Gary D. Bader; Bo Wang 044 (CVPR, 2023)

Open Domain Multi-document Summarization: A Comprehensive Study of Model Brittleness under Retrieval. - John M. Giorgi; Luca Soldaini; Bo Wang 044; Gary D. Bader; Kyle Lo; Lucy Lu Wang; Arman Cohan (EMNLP (Findings), 2023)

Spatially Resolved Gene Expression Prediction from Histology Images via Bi-modal Contrastive Learning. - Ronald Xie; Kuan Pang; Sai Chung; Catia Perciani; Sonya MacParland; Bo Wang 044; Gary D. Bader (NeurIPS, 2023)

Spatially Resolved Gene Expression Prediction from H&E Histology Images via Bi-modal Contrastive Learning. - Ronald Xie; Kuan Pang; Gary D. Bader; Bo Wang 044 (CoRR, 2023)

The Multi-modality Cell Segmentation Challenge: Towards Universal Solutions. - Jun Ma 016; Ronald Xie; Shamini Ayyadhury; Cheng Ge; Anubha Gupta; Ritu Gupta; Song Gu; Yao Zhang 010; Gihun Lee; Joonkee Kim; Wei Lou; Haofeng Li; et al. (CoRR, 2023)

Cytoscape.js 2023 update: a graph theory library for visualization and analysis. - Max Franz; Christian Tannus Lopes; Dylan Fong; Mike Kucera; Manfred Cheung; Metin Can Siper; Gerardo Huck; Yue Dong; Selçuk Onur Sümer; Gary D. Bader (Bioinform., 2023)

WangLab at MEDIQA-M3G 2024: Multimodal Medical Answer Generation using Large Language Models. - Augustin Toma; Ronald Xie; Steven Palayew; Gary D. Bader; Bo Wang 044 (ClinicalNLP@NAACL, 2024)

Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024. - Martin Golebiewski; Gary D. Bader; Padraig Gleeson; Thomas E. Gorochowski; Sarah M. Keating; Matthias König 003; Chris J. Myers; David P. Nickerson; Björn Sommer 001; Dagmar Waltemath; Falk Schreiber (J. Integr. Bioinform., 2024)

Approaches to identify scenarios for data science implementations within healthcare settings: recommendations based on experiences at multiple academic institutions. - Lillian Sung; Michael Brudno; Michael C. W. Caesar; Amol A. Verma; Brad Buchsbaum; Ravi Retnakaran; Vasily Giannakeas; Azadeh Kushki; Gary D. Bader; Helen Lasthiotakis; Muhammad Mamdani; Lisa Strug (Frontiers Digit. Health, 2025)

Towards Applying Large Language Models to Complement Single-Cell Foundation Models. - Steven Palayew; Bo Wang 044; Gary D. Bader (CoRR, 2025)