Gary D. Bader - RankMe

85 papers A* 2Misc 1Journal 75Unranked 5

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Approaches to identify scenarios for data science implementations within healthcare settings: recommendations based on experiences at multiple academic institutions. Frontiers Digit. Health 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
2025	J	`jnl`	RETINA: Reconstruction-based pre-trained enhanced TransUNet for electron microscopy segmentation on the CEM500K dataset. PLoS Comput. Biol. Cheng Xing, Ronald Xie, Gary D. Bader
2025	J	`jnl`	Towards Applying Large Language Models to Complement Single-Cell Foundation Models. CoRR Steven Palayew, Bo Wang, Gary D. Bader
2024	J	`jnl`	Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024. J. Integr. Bioinform. Martin Golebiewski, Gary D. Bader, Padraig Gleeson, Thomas E. Gorochowski, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath, Falk Schreiber
2024	—	`conf`	WangLab at MEDIQA-M3G 2024: Multimodal Medical Answer Generation using Large Language Models. ClinicalNLP@NAACL Augustin Toma, Ronald Xie, Steven Palayew, Gary D. Bader, Bo Wang
2024	J	`jnl`	WangLab at MEDIQA-M3G 2024: Multimodal Medical Answer Generation using Large Language Models. CoRR Ronald Xie, Steven Palayew, Augustin Toma, Gary D. Bader, Bo Wang
2023	J	`jnl`	Cytoscape.js 2023 update: a graph theory library for visualization and analysis. Bioinform. Max Franz, Christian Tannus Lopes, Dylan Fong, Mike Kucera, Manfred Cheung, Metin Can Siper, Gerardo Huck, Yue Dong, Selçuk Onur Sümer, Gary D. Bader
2023	A*	`conf`	MAESTER: Masked Autoencoder Guided Segmentation at Pixel Resolution for Accurate, Self-Supervised Subcellular Structure Recognition. CVPR Ronald Xie, Kuan Pang, Gary D. Bader, Bo Wang
2023	—	`conf`	Open Domain Multi-document Summarization: A Comprehensive Study of Model Brittleness under Retrieval. EMNLP (Findings) John M. Giorgi, Luca Soldaini, Bo Wang, Gary D. Bader, Kyle Lo, Lucy Lu Wang, Arman Cohan
2023	J	`jnl`	Spatially Resolved Gene Expression Prediction from H&E Histology Images via Bi-modal Contrastive Learning. CoRR Ronald Xie, Kuan Pang, Gary D. Bader, Bo Wang
2023	A*	`conf`	Spatially Resolved Gene Expression Prediction from Histology Images via Bi-modal Contrastive Learning. NeurIPS Ronald Xie, Kuan Pang, Sai Chung, Catia Perciani, Sonya MacParland, Bo Wang, Gary D. Bader
2023	J	`jnl`	The Multi-modality Cell Segmentation Challenge: Towards Universal Solutions. CoRR Jun Ma, Ronald Xie, Shamini Ayyadhury, Cheng Ge, Anubha Gupta, Ritu Gupta, Song Gu, Yao Zhang, Gihun Lee, Joonkee Kim, Wei Lou, Haofeng Li, Eric Upschulte, Timo Dickscheid, José Guilherme de Almeida, Yixin Wang, Lin Han, Xin Yang, Marco Labagnara, Sahand Jamal Rahi, Carly Kempster, Alice Pollitt, Leon Espinosa, Tâm Mignot, Jan Moritz Middeke, Jan-Niklas Eckardt, Wangkai Li, Zhaoyang Li, Xiaochen Cai, Bizhe Bai, Noah F. Greenwald, David Van Valen, Erin Weisbart, Beth A. Cimini, Zhuoshi Li, Chao Zuo, Oscar Brück, Gary D. Bader, Bo Wang
2022	—	`conf`	A sequence-to-sequence approach for document-level relation extraction. BioNLP@ACL John M. Giorgi, Gary D. Bader, Bo Wang
2022	J	`jnl`	A sequence-to-sequence approach for document-level relation extraction. CoRR John M. Giorgi, Gary D. Bader, Bo Wang
2022	J	`jnl`	Exploring the Challenges of Open Domain Multi-Document Summarization. CoRR John M. Giorgi, Luca Soldaini, Bo Wang, Gary D. Bader, Kyle Lo, Lucy Lu Wang, Arman Cohan
2022	—	`ed.`	Proceedings of The Cell Segmentation Challenge in Multi-modality High-Resolution Microscopy Images, Competitions in Neural Information Processing Systems, December 7, 2022, New Orleans, LA, USA Cell Segmentation Challenge @ NeurIPS Jun Ma, Ronald Xie, Anubha Gupta, José Guilherme de Almeida, Gary D. Bader, Bo Wang
2022	J	`jnl`	The reactome pathway knowledgebase 2022. Nucleic Acids Res. 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, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary D. Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio
2021	J	`jnl`	A flexible search system for high-accuracy identification of biological entities and molecules. J. Open Source Softw. Max Franz, Jeffrey V. Wong, Metin Can Siper, Christian Dallago, John M. Giorgi, Emek Demir, Chris Sander, Gary D. Bader
2021	—	`conf`	DeCLUTR: Deep Contrastive Learning for Unsupervised Textual Representations. ACL/IJCNLP (1) John M. Giorgi, Osvald Nitski, Bo Wang, Gary D. Bader
2021	J	`jnl`	SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. Briefings Bioinform. Adrien Rougny, Vasundra Touré, John Albanese, Dagmar Waltemath, Denis Shirshov, Anatoly A. Sorokin, Gary D. Bader, Michael L. Blinov, Alexander Mazein
2020	J	`jnl`	A reference map of the human binary protein interactome. Nat. 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, Meaghan Daley, Steven Deimling, Alice Desbuleux, Amélie Dricot, Marinella Gebbia, Madeleine F. Hardy, Nishka Kishore, Jennifer J. Knapp, István A. Kovács, Irma Lemmens, Miles W. Mee, Joseph C. Mellor, Carl Pollis, Carles Pons, Aaron D. Richardson, Sadie Schlabach, Bridget Teeking, Anupama Yadav, Mariana Babor, Dawit Balcha, Omer Basha, Christian Bowman-Colin, Suet-Feung Chin, Soon-gang Choi, Claudia Colabella, Georges Coppin, Cassandra D'Amata, David De Ridder, Steffi De Rouck, Miquel Duran-Frigola, Hanane Ennajdaoui, Florian Goebels, Liana Goehring, Anjali Gopal, Ghazal Haddad, Elodie Hatchi, Mohamed Helmy, Yves Jacob, Yoseph Kassa, Serena Landini, Roujia Li, Natascha van Lieshout, Andrew MacWilliams, Dylan Markey, Joseph N. Paulson, Sudharshan Rangarajan, John Rasla, Ashyad Rayhan, Thomas Rolland, Adriana San-Miguel, Yun Shen, Dayag Sheykhkarimli, Gloria M. Sheynkman, Eyal Simonovsky, Murat Tasan, Alexander Tejeda, Vincent Tropepe, Jean-Claude Twizere, Yang Wang, Robert J. Weatheritt, Jochen Weile, Yu Xia, Xinping Yang, Esti Yeger Lotem, Quan Zhong, Patrick Aloy, Gary D. Bader, Javier De Las Rivas, Suzanne Gaudet, Tong Hao, Janusz Rak, Jan Tavernier, David E. Hill, Marc Vidal, Frederick P. Roth, Michael A. Calderwood
2020	J	`jnl`	Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 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, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel González-Pérez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, André Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jüri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Núria López-Bigas, Gary D. Bader, Jonathan Barenboim, Rameen Beroukhim, Søren Brunak, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, J. Lynn Fink, Joan Frigola, Carlo Gambacorti Passerini, Dale W. Garsed, Gad Getz, Ivo Glynne Gut, David Haan, Arif Ozgun Harmanci, Mohamed Helmy, Ermin Hodzic, José M. G. Izarzugaza, Jong K. Kim, Jan O. Korbel, Erik Larsson, Shantao Li, Xiaotong Li, Shaoke Lou, Kathleen Marchal, Iñigo Martincorena, Alexander Martínez-Fundichely, Patrick D. McGillivray, William Meyerson, Ferran Muiños, Marta Paczkowska, Kiejung Park, Jakob Skou Pedersen, Tirso Pons, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Carlota Rubio-Perez, Süleyman Cenk Sahinalp, Leonidas Salichos, Mark Shackleton, Raunak Shrestha, Alfonso Valencia, Miguel Vazquez, Lieven P. C. Verbeke, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak, Joachim Weischenfeldt, Guanming Wu, Jun Yu, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, Kadir C. Akdemir, Eva G. Alvarez, Adrian Baez-Ortega, Paul C. Boutros, David D. L. Bowtell, Benedikt Brors, Kathleen H. Burns, Kin Chan, Isidro Cortés-Ciriano, Ana Dueso-Barroso, Andrew J. Dunford, Paul A. Edwards, Xavier Estivill, Dariush Etemadmoghadam, Milana Frenkel-Morgenstern, Dmitry A. Gordenin, Barbara Hutter, David T. W. Jones, Young Seok Ju, Marat D. Kazanov, Leszek J. Klimczak, Youngil Koh, Eunjung Alice Lee, Jake June-Koo Lee, Andy G. Lynch, Geoff MacIntyre, Florian Markowetz, Matthew Meyerson, Satoru Miyano, Fabio C. P. Navarro, Stephan Ossowski, Peter J. Park, John V. Pearson, Montserrat Puiggròs, Karsten Rippe, Steven A. Roberts, Bernardo Rodriguez-Martin, Ralph Scully, David Torrents, Izar Villasante, Nicola Waddell, Jeremiah A. Wala, Lixing Yang, Sung-Soo Yoon, Jorge Zamora
2020	J	`jnl`	DeCLUTR: Deep Contrastive Learning for Unsupervised Textual Representations. CoRR John M. Giorgi, Osvald Nitski, Gary D. Bader, Bo Wang
2020	J	`jnl`	Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. Nucleic Acids Res. 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, Jonah Dlin, Qizhi Wen, Caitlin O'Callaghan, Wanxin Li, Geoffrey Elder, Peter T. Smith, Christian Dallago, Ethan Cerami, Benjamin Gross, Ugur Dogrusoz, Emek Demir, Gary D. Bader, Chris Sander
2020	J	`jnl`	Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data. PLoS Comput. Biol. Thinh N. Tran, Gary D. Bader
2020	J	`jnl`	Towards reliable named entity recognition in the biomedical domain. Bioinform. John M. Giorgi, Gary D. Bader
2020	J	`jnl`	netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks. F1000Research 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
2019	J	`jnl`	End-to-end Named Entity Recognition and Relation Extraction using Pre-trained Language Models. CoRR John M. Giorgi, Xindi Wang, Nicola Sahar, Won Young Shin, Gary D. Bader, Bo Wang
2019	J	`jnl`	Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. J. Integr. Bioinform. Falk Schreiber, Björn Sommer, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Dagmar Waltemath
2018	J	`jnl`	GeneMANIA update 2018. Nucleic Acids Res. Max Franz, Harold Rodriguez, Christian Tannus Lopes, Khalid Zuberi, Jason Montojo, Gary D. Bader, Quaid Morris
2018	J	`jnl`	Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. J. Integr. Bioinform. 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, Dagmar Waltemath
2018	J	`jnl`	The Cytoscape Automation app article collection. F1000Research 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, Benno Schwikowski, Piet Molenaar, Trey Ideker
2018	J	`jnl`	Transfer learning for biomedical named entity recognition with neural networks. Bioinform. John M. Giorgi, Gary D. Bader
2018	J	`jnl`	scClustViz - Single-cell RNAseq cluster assessment and visualization. F1000Research Brendan T. Innes, Gary D. Bader
2017	Misc	`conf`	A brief history of COMBINE. WSC Chris J. Myers, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novère, David P. Nickerson, Falk Schreiber, Dagmar Waltemath
2016	J	`jnl`	AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations. F1000Research Mike Kucera, Ruth Isserlin, Arkady Arkhangorodsky, Gary D. Bader
2016	J	`jnl`	Cytoscape.js: a graph theory library for visualisation and analysis. Bioinform. Max Franz, Christian Tannus Lopes, Gerardo Huck, Yue Dong, Selçuk Onur Sümer, Gary D. Bader
2016	J	`jnl`	Global neuroscience and mental health research: a bibliometrics case study. Scientometrics Alison Buchan, Eva Jurczyk, Ruth Isserlin, Gary D. Bader
2016	J	`jnl`	Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast. Bioinform. Shobhit Jain, Gary D. Bader
2016	J	`jnl`	Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. J. Integr. Bioinform. Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novère, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath
2016	—	`conf`	SyQUAL: a platform for qualitative modelling and simulation of biological systems. HLDVT Rosario Distefano, Nickolas Goncharenko, Franco Fummi, Rosalba Giugno, Gary D. Bader, Nicola Bombieri
2016	J	`jnl`	Ten Simple Rules for Developing Public Biological Databases. PLoS Comput. Biol. Mohamed Helmy, Alexander Crits-Christoph, Gary D. Bader
2015	J	`jnl`	Erratum to: Inferring interaction type in gene regulatory networks using co-expression data. Algorithms Mol. Biol. Pegah Khosravi, Vahid H. Gazestani, Leila Pirhaji, Brian Law, Mehdi Sadeghi, Gary D. Bader, Bahram Goliaei
2015	J	`jnl`	Inferring interaction type in gene regulatory networks using co-expression data. Algorithms Mol. Biol. Pegah Khosravi, Vahid H. Gazestani, Leila Pirhaji, Brian Law, Mehdi Sadeghi, Bahram Goliaei, Gary D. Bader
2015	J	`jnl`	NetMatchStar: an enhanced Cytoscape network querying app. F1000Research Fabio Rinnone, Giovanni Micale, Vincenzo Bonnici, Gary D. Bader, Dennis E. Shasha, Alfredo Ferro, Alfredo Pulvirenti, Rosalba Giugno
2015	J	`jnl`	Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Bioinform. James Vlasblom, Khalid Zuberi, Harold Rodriguez, Roland Arnold, Alla Gagarinova, Viktor Deineko, Ashwani Kumar, Elisa Leung, Kamran Rizzolo, Bahram Samanfar, Luke Chang, Sadhna Phanse, Ashkan Golshani, Jack Greenblatt, Walid A. Houry, Andrew Emili, Quaid Morris, Gary D. Bader, Mohan Babu
2015	J	`jnl`	Social Network: a Cytoscape app for visualizing co-publication networks. F1000Research Victor Kofia, Ruth Isserlin, Alison Buchan, Gary D. Bader
2015	J	`jnl`	Specifications of Standards in Systems and Synthetic Biology. J. Integr. Bioinform. Falk Schreiber, Gary D. Bader, Martin Golebiewski, Michael Hucka, Benjamin Kormeier, Nicolas Le Novère, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath, Stephan Weise
2014	J	`jnl`	Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results. F1000Research Ruth Isserlin, Daniele Merico, Veronique Voisin, Gary D. Bader
2014	J	`jnl`	HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery. Bioinform. Alvin Leung, Gary D. Bader, Jüri Reimand
2014	J	`jnl`	The Cytoscape app article collection. F1000Research 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, Benno Schwikowski, David Welker, Trey Ideker
2013	J	`jnl`	Cytoscape App Store. Bioinform. Samad Lotia, Jason Montojo, Yue Dong, Gary D. Bader, Alexander R. Pico
2013	J	`jnl`	GeStoDifferent: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process. Bioinform. Marco Antoniotti, Gary D. Bader, Giulio Caravagna, Silvia Crippa, Alex Graudenzi, Giancarlo Mauri
2013	J	`jnl`	GeneMANIA Prediction Server 2013 Update. Nucleic Acids Res. Khalid Zuberi, Max Franz, Harold Rodriguez, Jason Montojo, Christian Tannus Lopes, Gary D. Bader, Quaid Morris
2013	J	`jnl`	Predicting PDZ domain mediated protein interactions from structure. BMC Bioinform. Shirley Hui, Xiang Xing, Gary D. Bader
2013	J	`jnl`	The BioPAX Validator. Bioinform. Igor V. Rodchenkov, Emek Demir, Chris Sander, Gary D. Bader
2013	J	`jnl`	Using Biological Pathway Data with Paxtools. PLoS Comput. Biol. Emek Demir, Özgün Babur, Igor V. Rodchenkov, Bülent Arman Aksoy, Ken I. Fukuda, Benjamin E. Gross, Selçuk Onur Sümer, Gary D. Bader, Chris Sander
2012	J	`jnl`	Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study. BMC Syst. Biol. Mohammed Alshalalfa, Gary D. Bader, Anna Goldenberg, Quaid Morris, Reda Alhajj
2012	J	`jnl`	Multiple Genetic Interaction Experiments Provide Complementary Information Useful for Gene Function Prediction. PLoS Comput. Biol. Magali Michaut, Gary D. Bader
2011	J	`jnl`	A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway. Database J. Biol. Databases Curation 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, S. Sujatha Mohan, Gary D. Bader, Mohan R. Wani, Akhilesh Pandey
2011	J	`jnl`	A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequence. Bioinform. Xiaojian Shao, Chris Soon Heng Tan, Courtney Voss, Shawn S. C. Li, Naiyang Deng, Gary D. Bader
2011	J	`jnl`	NetSlim: high-confidence curated signaling maps. Database J. Biol. Databases Curation 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, Yashwanth Subbannayya, Deepthi Telikicherla, Mitali Bhattacharjee, Sneha M. Pinto, Nazia Syed, Srinivas Manda Srikanth, Gajanan J. Sathe, Sartaj Ahmad, Sandip N. Chavan, Ghantasala S. Sameer Kumar, Arivusudar Marimuthu, T. S. Keshava Prasad, H. C. Harsha, B. Abdul Rahiman, Osamu Ohara, Gary D. Bader, S. Sujatha Mohan, William P. Schiemann, Akhilesh Pandey
2011	J	`jnl`	Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. Ethan G. Cerami, Benjamin E. Gross, Emek Demir, Igor V. Rodchenkov, Özgün Babur, Nadia Anwar, Nikolaus Schultz, Gary D. Bader, Chris Sander
2011	J	`jnl`	Protein Complexes are Central in the Yeast Genetic Landscape. PLoS Comput. Biol. Magali Michaut, Anastasia Baryshnikova, Michael Costanzo, Chad L. Myers, Brenda J. Andrews, Charles Boone, Gary D. Bader
2011	J	`jnl`	The Biomolecular Interaction Network Database in PSI-MI 2.5. Database J. Biol. Databases Curation Ruth Isserlin, Rashad Badrawi, Gary D. Bader
2011	J	`jnl`	WordCloud: a Cytoscape plugin to create a visual semantic summary of networks. Source Code Biol. Medicine Layla Oesper, Daniele Merico, Ruth Isserlin, Gary D. Bader
2011	J	`jnl`	clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinform. John H. Morris, Leonard Apeltsin, Aaron M. Newman, Jan Baumbach, Tobias Wittkop, Gang Su, Gary D. Bader, Thomas E. Ferrin
2010	J	`jnl`	An improved method for scoring protein-protein interactions using semantic similarity within the Gene Ontology. BMC Bioinform. Shobhit Jain, Gary D. Bader
2010	J	`jnl`	Cytoscape Web: an interactive web-based network browser. Bioinform. Christian Tannus Lopes, Max Franz, Farzana Kazi, Sylva L. Donaldson, Quaid Morris, Gary D. Bader
2010	J	`jnl`	DRYGIN: a database of quantitative genetic interaction networks in yeast. Nucleic Acids Res. Judice L. Y. Koh, Huiming Ding, Michael Costanzo, Anastasia Baryshnikova, Kiana Toufighi, Gary D. Bader, Chad L. Myers, Brenda J. Andrews, Charles Boone
2010	J	`jnl`	GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop. Bioinform. Jason Montojo, Khalid Zuberi, Harold Rodriguez, Farzana Kazi, George Wright, Sylva L. Donaldson, Quaid Morris, Gary D. Bader
2010	J	`jnl`	Proteome scanning to predict PDZ domain interactions using support vector machines. BMC Bioinform. Shirley Hui, Gary D. Bader
2010	J	`jnl`	The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res. 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, Jason Montojo, Quentin Shao, George Wright, Gary D. Bader, Quaid Morris
2008	J	`jnl`	Cytoscape ESP: simple search of complex biological networks. Bioinform. Maital Ashkenazi, Gary D. Bader, Allan Kuchinsky, Menachem Moshelion, David J. States
2007	J	`jnl`	From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research. PLoS Comput. Biol. Jomol P. Mathew, Barry S. Taylor, Gary D. Bader, Saiju Pyarajan, Marco Antoniotti, Arul M. Chinnaiyan, Chris Sander, Steven J. Burakoff, Bud Mishra
2007	J	`jnl`	NetMatch: a Cytoscape plugin for searching biological networks. Bioinform. Alfredo Ferro, Rosalba Giugno, Giuseppe Pigola, Alfredo Pulvirenti, Dmitry Skripin, Gary D. Bader, Dennis E. Shasha
2006	J	`jnl`	Pathguide: a Pathway Resource List. Nucleic Acids Res. Gary D. Bader, Michael P. Cary, Chris Sander
2006	J	`jnl`	cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinform. Ethan G. Cerami, Gary D. Bader, Benjamin E. Gross, Chris Sander
2003	J	`jnl`	An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinform. Gary D. Bader, Christopher W. V. Hogue
2003	J	`jnl`	BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res. Gary D. Bader, Doron Betel, Christopher W. V. Hogue
2003	J	`jnl`	PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine. BMC Bioinform. 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
2002	—	`ch.`	Bioinformatics: Interaction Databases. Essentials of Genomics and Bioinformatics Gary D. Bader, Christopher W. V. Hogue
2002	J	`jnl`	SeqHound: biological sequence and structure database as a platform for bioinformatics research. BMC Bioinform. Katerina Michalickova, Gary D. Bader, Michel Dumontier, Hao Lieu, Doron Betel, Ruth Isserlin, Christopher W. V. Hogue
2001	J	`jnl`	BIND - The Biomolecular Interaction Network Database. Nucleic Acids Res. Gary D. Bader, Ian M. Donaldson, Cheryl Wolting, B. F. Francis Ouellette, Tony Pawson, Christopher W. V. Hogue
2000	J	`jnl`	BIND-a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. Bioinform. Gary D. Bader, Christopher W. V. Hogue