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2020 – today
- 2024
[j57]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)- [c8]Augustin Toma, Ronald Xie, Steven Palayew, Gary D. Bader, Bo Wang:
WangLab at MEDIQA-M3G 2024: Multimodal Medical Answer Generation using Large Language Models. ClinicalNLP@NAACL 2024: 624-634 - [i15]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 abs/2404.14567 (2024) - 2023
- [j56]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) - [c7]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: 3292-3301 - [c6]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: 8177-8199 - [c5]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 - [i14]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 abs/2306.01859 (2023) - [i13]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 abs/2308.05864 (2023) - 2022
- [j55]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:
The reactome pathway knowledgebase 2022. Nucleic Acids Res. 50(D1): 687-692 (2022) - [c4]John M. Giorgi, Gary D. Bader, Bo Wang:
A sequence-to-sequence approach for document-level relation extraction. BioNLP@ACL 2022: 10-25 - [e1]Jun Ma, Ronald Xie, Anubha Gupta, José Guilherme de Almeida, Gary D. Bader, Bo Wang:
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. Proceedings of Machine Learning Research 212, PMLR 2022 [contents] - [i12]John M. Giorgi, Gary D. Bader, Bo Wang:
A sequence-to-sequence approach for document-level relation extraction. CoRR abs/2204.01098 (2022) - [i11]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 abs/2212.10526 (2022) - 2021
- [j54]Adrien Rougny, Vasundra Touré, John Albanese, Dagmar Waltemath, Denis Shirshov, Anatoly A. 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) - [j53]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): 3756 (2021) - [c3]John M. Giorgi, Osvald Nitski, Bo Wang, Gary D. Bader:
DeCLUTR: Deep Contrastive Learning for Unsupervised Textual Representations. ACL/IJCNLP (1) 2021: 879-895 - 2020
- [j52]John M. Giorgi, Gary D. Bader:
Towards reliable named entity recognition in the biomedical domain. Bioinform. 36(1): 280-286 (2020) - [j51]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): D489-D497 (2020) - [j50]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 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:
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578(7793): 102-111 (2020) - [j49]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): 402-408 (2020) - [j48]Thinh N. Tran, Gary D. Bader:
Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data. PLoS Comput. Biol. 16(9) (2020) - [i10]John M. Giorgi, Osvald Nitski, Gary D. Bader, Bo Wang:
DeCLUTR: Deep Contrastive Learning for Unsupervised Textual Representations. CoRR abs/2006.03659 (2020) - [i9]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: 1239 (2020)
2010 – 2019
- 2019
- [j47]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) - [i8]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 abs/1912.13415 (2019) - 2018
- [j46]John M. Giorgi, Gary D. Bader:
Transfer learning for biomedical named entity recognition with neural networks. Bioinform. 34(23): 4087-4094 (2018) - [j45]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) - [j44]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): W60-W64 (2018) - [i7]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: 800 (2018) - [i6]Brendan T. Innes, Gary D. Bader:
scClustViz - Single-cell RNAseq cluster assessment and visualization. F1000Research 7: 1522 (2018) - 2017
- [c2]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: 884-895 - 2016
- [j43]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): 309-311 (2016) - [j42]Shobhit Jain, Gary D. Bader:
Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast. Bioinform. 32(12): 1865-1872 (2016) - [j41]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) - [j40]Mohamed Helmy, Alexander Crits-Christoph, Gary D. Bader:
Ten Simple Rules for Developing Public Biological Databases. PLoS Comput. Biol. 12(11) (2016) - [j39]Alison Buchan, Eva Jurczyk, Ruth Isserlin, Gary D. Bader:
Global neuroscience and mental health research: a bibliometrics case study. Scientometrics 109(1): 515-531 (2016) - [c1]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: 155-161 - [i5]Mike Kucera, Ruth Isserlin, Arkady Arkhangorodsky, Gary D. Bader:
AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations. F1000Research 5: 1717 (2016) - 2015
- [j38]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: 23 (2015) - [j37]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: 25 (2015) - [j36]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:
Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli. Bioinform. 31(3): 306-310 (2015) - [j35]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) - [i4]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: 479 (2015) - [i3]Victor Kofia, Ruth Isserlin, Alison Buchan, Gary D. Bader:
Social Network: a Cytoscape app for visualizing co-publication networks. F1000Research 4: 481 (2015) - 2014
- [j34]Alvin Leung, Gary D. Bader, Jüri Reimand:
HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery. Bioinform. 30(15): 2230-2232 (2014) - [i2]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: 138 (2014) - [i1]Ruth Isserlin, Daniele Merico, Veronique Voisin, Gary D. Bader:
Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results. F1000Research 3: 141 (2014) - 2013
- [j33]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): 513-514 (2013) - [j32]Samad Lotia, Jason Montojo, Yue Dong, Gary D. Bader, Alexander R. Pico:
Cytoscape App Store. Bioinform. 29(10): 1350-1351 (2013) - [j31]Igor V. Rodchenkov, Emek Demir, Chris Sander, Gary D. Bader:
The BioPAX Validator. Bioinform. 29(20): 2659-2660 (2013) - [j30]Shirley Hui, Xiang Xing, Gary D. Bader:
Predicting PDZ domain mediated protein interactions from structure. BMC Bioinform. 14: 27 (2013) - [j29]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): 115-122 (2013) - [j28]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) - 2012
- [j27]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: 112 (2012) - [j26]Magali Michaut, Gary D. Bader:
Multiple Genetic Interaction Experiments Provide Complementary Information Useful for Gene Function Prediction. PLoS Comput. Biol. 8(6) (2012) - 2011
- [j25]Ruth Isserlin, Rashad Badrawi, Gary D. Bader:
The Biomolecular Interaction Network Database in PSI-MI 2.5. Database J. Biol. Databases Curation 2011 (2011) - [j24]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) - [j23]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) - [j22]Xiaojian Shao, Chris Soon Heng 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): 383-390 (2011) - [j21]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: 436 (2011) - [j20]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): 685-690 (2011) - [j19]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) - [j18]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: 7 (2011) - 2010
- [j17]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): 2347-2348 (2010) - [j16]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): 2927-2928 (2010) - [j15]Shirley Hui, Gary D. Bader:
Proteome scanning to predict PDZ domain interactions using support vector machines. BMC Bioinform. 11: 507 (2010) - [j14]Shobhit Jain, Gary D. Bader:
An improved method for scoring protein-protein interactions using semantic similarity within the Gene Ontology. BMC Bioinform. 11: 562 (2010) - [j13]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): 502-507 (2010) - [j12]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): 214-220 (2010)
2000 – 2009
- 2008
- [j11]Maital Ashkenazi, Gary D. Bader, Allan Kuchinsky, Menachem Moshelion, David J. States:
Cytoscape ESP: simple search of complex biological networks. Bioinform. 24(12): 1465-1466 (2008) - 2007
- [j10]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): 910-912 (2007) - [j9]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) - 2006
- [j8]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: 497 (2006) - [j7]Gary D. Bader, Michael P. Cary, Chris Sander:
Pathguide: a Pathway Resource List. Nucleic Acids Res. 34(Database-Issue): 504-506 (2006) - 2003
- [j6]Gary D. Bader, Christopher W. V. Hogue:
An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinform. 4: 2 (2003) - [j5]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: 11 (2003) - [j4]Gary D. Bader, Doron Betel, Christopher W. V. Hogue:
BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res. 31(1): 248-250 (2003) - 2002
- [j3]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: 32 (2002) - [p1]Gary D. Bader, Christopher W. V. Hogue:
Bioinformatics: Interaction Databases. Essentials of Genomics and Bioinformatics 2002: 363-379 - 2001
- [j2]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): 242-245 (2001) - 2000
- [j1]Gary D. Bader, Christopher W. V. Hogue:
BIND-a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. Bioinform. 16(5): 465-477 (2000)
Coauthor Index
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