Gary D. Bader

Publication Activity (10 Years)

Years Active: 2000-2024
Publications (10 Years): 36

Top Topics

Gene Regulatory

Biological Databases

Named Entity Recognition

Gene Expression

Top Venues

J. Integr. Bioinform.

Publications

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
Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024. J. Integr. Bioinform. 21 (1) (2024)
Ronald Xie, Steven Palayew, Augustin Toma, Gary D. Bader, Bo Wang
WangLab at MEDIQA-M3G 2024: Multimodal Medical Answer Generation using Large Language Models. CoRR (2024)
John M. Giorgi, Luca Soldaini, Bo Wang, Gary D. Bader, Kyle Lo, Lucy Lu Wang, Arman Cohan
Open Domain Multi-document Summarization: A Comprehensive Study of Model Brittleness under Retrieval. EMNLP (Findings) (2023)
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
The Multi-modality Cell Segmentation Challenge: Towards Universal Solutions. CoRR (2023)
Ronald Xie, Kuan Pang, Gary D. Bader, Bo Wang
Spatially Resolved Gene Expression Prediction from H&E Histology Images via Bi-modal Contrastive Learning. CoRR (2023)
Ronald Xie, Kuan Pang, Gary D. Bader, Bo Wang
MAESTER: Masked Autoencoder Guided Segmentation at Pixel Resolution for Accurate, Self-Supervised Subcellular Structure Recognition. CVPR (2023)
Max Franz, Christian Tannus Lopes, Dylan Fong, Mike Kucera, Manfred Cheung, Metin Can Siper, Gerardo Huck, Yue Dong, Selçuk Onur Sümer, Gary D. Bader
Cytoscape.js 2023 update: a graph theory library for visualization and analysis. Bioinform. 39 (1) (2023)
Ronald Xie, Kuan Pang, Sai Chung, Catia Perciani, Sonya MacParland, Bo Wang, Gary D. Bader
Spatially Resolved Gene Expression Prediction from Histology Images via Bi-modal Contrastive Learning. NeurIPS (2023)
John M. Giorgi, Luca Soldaini, Bo Wang, Gary D. Bader, Kyle Lo, Lucy Lu Wang, Arman Cohan
Exploring the Challenges of Open Domain Multi-Document Summarization. CoRR (2022)
John M. Giorgi, Gary D. Bader, Bo Wang
A sequence-to-sequence approach for document-level relation extraction. BioNLP@ACL (2022)
John M. Giorgi, Gary D. Bader, Bo Wang
A sequence-to-sequence approach for document-level relation extraction. CoRR (2022)
Max Franz, Jeffrey V. Wong, Metin Can Siper, Christian Dallago, John M. Giorgi, Emek Demir, Chris Sander, Gary D. Bader
A flexible search system for high-accuracy identification of biological entities and molecules. J. Open Source Softw. 6 (67) (2021)
John M. Giorgi, Osvald Nitski, Bo Wang, Gary D. Bader
DeCLUTR: Deep Contrastive Learning for Unsupervised Textual Representations. ACL/IJCNLP (1) (2021)
Adrien Rougny, Vasundra Touré, John Albanese, Dagmar Waltemath, Denis Shirshov, Anatoly Sorokin, Gary D. Bader, Michael L. Blinov, Alexander Mazein
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. Briefings Bioinform. 22 (5) (2021)
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 Gonzalez-Perez, 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 G. Gut, David Haan, Arif O. 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
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578 (7793) (2020)
John M. Giorgi, Gary D. Bader
Towards reliable named entity recognition in the biomedical domain. Bioinform. 36 (1) (2020)
John M. Giorgi, Osvald Nitski, Gary D. Bader, Bo Wang
DeCLUTR: Deep Contrastive Learning for Unsupervised Textual Representations. CoRR (2020)
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
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. Nucleic Acids Res. 48 (Database-Issue) (2020)
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
netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks. F1000Research 9 (2020)
Thinh N. Tran, Gary D. Bader
Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data. PLoS Comput. Biol. 16 (9) (2020)
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
A reference map of the human binary protein interactome. Nat. 580 (7803) (2020)
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
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. J. Integr. Bioinform. 16 (2) (2019)
John M. Giorgi, Xindi Wang, Nicola Sahar, Won Young Shin, Gary D. Bader, Bo Wang
End-to-end Named Entity Recognition and Relation Extraction using Pre-trained Language Models. CoRR (2019)
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
The Cytoscape Automation app article collection. F1000Research 7 (2018)
Max Franz, Harold Rodriguez, Christian Tannus Lopes, Khalid Zuberi, Jason Montojo, Gary D. Bader, Quaid Morris
GeneMANIA update 2018. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
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
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. J. Integr. Bioinform. 15 (1) (2018)
Brendan T. Innes, Gary D. Bader
scClustViz - Single-cell RNAseq cluster assessment and visualization. F1000Research 7 (2018)
John M. Giorgi, Gary D. Bader
Transfer learning for biomedical named entity recognition with neural networks. Bioinform. 34 (23) (2018)
Chris J. Myers, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novère, David P. Nickerson, Falk Schreiber, Dagmar Waltemath
A brief history of COMBINE. WSC (2017)
Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novère, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. J. Integr. Bioinform. 13 (3) (2016)
Mohamed Helmy, Alexander Crits-Christoph, Gary D. Bader
Ten Simple Rules for Developing Public Biological Databases. PLoS Comput. Biol. 12 (11) (2016)
Alison Buchan, Eva Jurczyk, Ruth Isserlin, Gary D. Bader
Global neuroscience and mental health research: a bibliometrics case study. Scientometrics 109 (1) (2016)
Rosario Distefano, Nickolas Goncharenko, Franco Fummi, Rosalba Giugno, Gary D. Bader, Nicola Bombieri
SyQUAL: a platform for qualitative modelling and simulation of biological systems. HLDVT (2016)
Max Franz, Christian Tannus Lopes, Gerardo Huck, Yue Dong, Selçuk Onur Sümer, Gary D. Bader
Cytoscape.js: a graph theory library for visualisation and analysis. Bioinform. 32 (2) (2016)
Shobhit Jain, Gary D. Bader
Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast. Bioinform. 32 (12) (2016)
Mike Kucera, Ruth Isserlin, Arkady Arkhangorodsky, Gary D. Bader
AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations. F1000Research 5 (2016)
Pegah Khosravi, Vahid H. Gazestani, Leila Pirhaji, Brian Law, Mehdi Sadeghi, Bahram Goliaei, Gary D. Bader
Inferring interaction type in gene regulatory networks using co-expression data. Algorithms Mol. Biol. 10 (2015)
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
Specifications of Standards in Systems and Synthetic Biology. J. Integr. Bioinform. 12 (2) (2015)
Pegah Khosravi, Vahid H. Gazestani, Leila Pirhaji, Brian Law, Mehdi Sadeghi, Gary D. Bader, Bahram Goliaei
Erratum to: Inferring interaction type in gene regulatory networks using co-expression data. Algorithms Mol. Biol. 10 (2015)
Victor Kofia, Ruth Isserlin, Alison Buchan, Gary D. Bader
Social Network: a Cytoscape app for visualizing co-publication networks. F1000Research 4 (2015)
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
. Bioinform. 31 (3) (2015)
Fabio Rinnone, Giovanni Micale, Vincenzo Bonnici, Gary D. Bader, Dennis E. Shasha, Alfredo Ferro, Alfredo Pulvirenti, Rosalba Giugno
NetMatchStar: an enhanced Cytoscape network querying app. F1000Research 4 (2015)
Alvin Leung, Gary D. Bader, Jüri Reimand
HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery. Bioinform. 30 (15) (2014)
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
The Cytoscape app article collection. F1000Research 3 (2014)
Ruth Isserlin, Daniele Merico, Veronique Voisin, Gary D. Bader
Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results. F1000Research 3 (2014)
Igor V. Rodchenkov, Emek Demir, Chris Sander, Gary D. Bader
The BioPAX Validator. Bioinform. 29 (20) (2013)
Khalid Zuberi, Max Franz, Harold Rodriguez, Jason Montojo, Christian Tannus Lopes, Gary D. Bader, Quaid Morris
GeneMANIA Prediction Server 2013 Update. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Emek Demir, Özgün Babur, Igor V. Rodchenkov, Bülent Arman Aksoy, Ken I. Fukuda, Benjamin E. Gross, Selçuk Onur Sümer, Gary D. Bader, Chris Sander
Using Biological Pathway Data with Paxtools. PLoS Comput. Biol. 9 (9) (2013)
Shirley Hui, Xiang Xing, Gary D. Bader
Predicting PDZ domain mediated protein interactions from structure. BMC Bioinform. 14 (2013)
Marco Antoniotti, Gary D. Bader, Giulio Caravagna, Silvia Crippa, Alex Graudenzi, Giancarlo Mauri
GeStoDifferent: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process. Bioinform. 29 (4) (2013)
Samad Lotia, Jason Montojo, Yue Dong, Gary D. Bader, Alexander R. Pico
Cytoscape App Store. Bioinform. 29 (10) (2013)
Magali Michaut, Gary D. Bader
Multiple Genetic Interaction Experiments Provide Complementary Information Useful for Gene Function Prediction. PLoS Comput. Biol. 8 (6) (2012)
Mohammed Alshalalfa, Gary D. Bader, Anna Goldenberg, Quaid Morris, Reda Alhajj
Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study. BMC Syst. Biol. 6 (2012)
Magali Michaut, Anastasia Baryshnikova, Michael Costanzo, Chad L. Myers, Brenda J. Andrews, Charles Boone, Gary D. Bader
Protein Complexes are Central in the Yeast Genetic Landscape. PLoS Comput. Biol. 7 (2) (2011)
Ethan G. Cerami, Benjamin E. Gross, Emek Demir, Igor V. Rodchenkov, Özgün Babur, Nadia Anwar, Nikolaus Schultz, Gary D. Bader, Chris Sander
Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 39 (Database-Issue) (2011)
Ruth Isserlin, Rashad Badrawi, Gary D. Bader
The Biomolecular Interaction Network Database in PSI-MI 2.5. Database J. Biol. Databases Curation 2011 (2011)
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
A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway. Database J. Biol. Databases Curation 2011 (2011)
Layla Oesper, Daniele Merico, Ruth Isserlin, Gary D. Bader
WordCloud: a Cytoscape plugin to create a visual semantic summary of networks. Source Code Biol. Medicine 6 (2011)
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
NetSlim: high-confidence curated signaling maps. Database J. Biol. Databases Curation 2011 (2011)
John H. Morris, Leonard Apeltsin, Aaron M. Newman, Jan Baumbach, Tobias Wittkop, Gang Su, Gary D. Bader, Thomas E. Ferrin
clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinform. 12 (2011)
Xiaojian Shao, Chris S. H. Tan, Courtney Voss, Shawn S. C. Li, Naiyang Deng, Gary D. Bader
A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequence. Bioinform. 27 (3) (2011)
Christian Tannus Lopes, Max Franz, Farzana Kazi, Sylva L. Donaldson, Quaid Morris, Gary D. Bader
Cytoscape Web: an interactive web-based network browser. Bioinform. 26 (18) (2010)
Judice L. Y. Koh, Huiming Ding, Michael Costanzo, Anastasia Baryshnikova, Kiana Toufighi, Gary D. Bader, Chad L. Myers, Brenda J. Andrews, Charles Boone
DRYGIN: a database of quantitative genetic interaction networks in yeast. Nucleic Acids Res. 38 (Database-Issue) (2010)
Shirley Hui, Gary D. Bader
Proteome scanning to predict PDZ domain interactions using support vector machines. BMC Bioinform. 11 (2010)
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
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Shobhit Jain, Gary D. Bader
An improved method for scoring protein-protein interactions using semantic similarity within the Gene Ontology. BMC Bioinform. 11 (2010)
Jason Montojo, Khalid Zuberi, Harold Rodriguez, Farzana Kazi, George Wright, Sylva L. Donaldson, Quaid Morris, Gary D. Bader
GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop. Bioinform. 26 (22) (2010)
Maital Ashkenazi, Gary D. Bader, Allan Kuchinsky, Menachem Moshelion, David J. States
Cytoscape ESP: simple search of complex biological networks. Bioinform. 24 (12) (2008)
Jomol P. Mathew, Barry S. Taylor, Gary D. Bader, Saiju Pyarajan, Marco Antoniotti, Arul M. Chinnaiyan, Chris Sander, Steven J. Burakoff, Bud Mishra
From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research. PLoS Comput. Biol. 3 (2) (2007)
Alfredo Ferro, Rosalba Giugno, Giuseppe Pigola, Alfredo Pulvirenti, Dmitry Skripin, Gary D. Bader, Dennis E. Shasha
NetMatch: a Cytoscape plugin for searching biological networks. Bioinform. 23 (7) (2007)
Ethan G. Cerami, Gary D. Bader, Benjamin E. Gross, Chris Sander
cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinform. 7 (2006)
Gary D. Bader, Michael P. Cary, Chris Sander
Pathguide: a Pathway Resource List. Nucleic Acids Res. 34 (Database-Issue) (2006)
Gary D. Bader, Doron Betel, Christopher W. V. Hogue
BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res. 31 (1) (2003)
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
PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine. BMC Bioinform. 4 (2003)
Gary D. Bader, Christopher W. V. Hogue
An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinform. 4 (2003)
Katerina Michalickova, Gary D. Bader, Michel Dumontier, Hao Lieu, Doron Betel, Ruth Isserlin, Christopher W. V. Hogue
SeqHound: biological sequence and structure database as a platform for bioinformatics research. BMC Bioinform. 3 (2002)
Gary D. Bader, Ian M. Donaldson, Cheryl Wolting, B. F. Francis Ouellette, Tony Pawson, Christopher W. V. Hogue
BIND - The Biomolecular Interaction Network Database. Nucleic Acids Res. 29 (1) (2001)
Gary D. Bader, Christopher W. V. Hogue
BIND-a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. Bioinform. 16 (5) (2000)