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Melissa A. Haendel

Melissa Anne Haendel

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affiliation: Oregon State University, Linus Pauling Institute, Corvallis, OR, USA
affiliation: Oregon Health & Science University, Department of Medical Informatics and Clinical Epidemiology, Portland, OR, USA

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2024
[j52]
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  - journals/bioinformatics/CaufieldHEHJMKMRHRM24
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J. Harry Caufield, Harshad Hegde, Vincent Emonet, Nomi L. Harris, Marcin P. Joachimiak, Nicolas Matentzoglu, Hyeongsik Kim, Sierra A. T. Moxon, Justin T. Reese, Melissa A. Haendel, Peter N. Robinson, Christopher J. Mungall:
Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning. Bioinform. 40(3) (2024)
[j51]
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Sabrina Toro, Anna V. Anagnostopoulos, Susan M. Bello, Kai Lewis Blumberg, Rhiannon Cameron, Leigh Carmody, Alexander D. Diehl, Damion M. Dooley, William D. Duncan, Petra Fey, Pascale Gaudet, Nomi L. Harris, Marcin P. Joachimiak, Leila Kiani, Tiago Lubiana, Monica C. Munoz-Torres, Shawn T. O'Neil, David Osumi-Sutherland, Aleix Puig-Barbe, Justin T. Reese, Leonore Reiser, Sofia M. C. Robb, Troy Ruemping, James Seager, Eric Sid, Raymund Stefancsik, Magalie Weber, Valerie Wood, Melissa A. Haendel, Christopher J. Mungall:
Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI). J. Biomed. Semant. 15(1): 19 (2024)
[j50]
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Lauren E. Chan, Elena Casiraghi, Justin T. Reese, Quaker E. Harmon, Kevin Schaper, Harshad Hegde, Giorgio Valentini, Charles Schmitt, Alison A. Motsinger-Reif, Janet E. Hall, Christopher J. Mungall, Peter N. Robinson, Melissa A. Haendel:
Predicting nutrition and environmental factors associated with female reproductive disorders using a knowledge graph and random forests. Int. J. Medical Informatics 187: 105461 (2024)
[j49]
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Tudor Groza, J. Harry Caufield, Dylan Gration, Gareth Baynam, Melissa A. Haendel, Peter N. Robinson, Christopher J. Mungall, Justin T. Reese:
An evaluation of GPT models for phenotype concept recognition. BMC Medical Informatics Decis. Mak. 24(1): 30 (2024)
[j48]
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Shawn T. O'Neil, Charisse R. Madlock-Brown, Kenneth Wilkins, Brenda M. McGrath, Hannah E. Davis, Gina S. Assaf, Hannah Wei, Parya Zareie, Evan T. French, Johanna Loomba, Julie A. McMurry, Andrea Zhou, Christopher G. Chute, Richard A. Moffitt, Emily R. Pfaff, Yun Jae Yoo, Peter Leese, Robert F. Chew, Michael Lieberman, Melissa A. Haendel:
Finding Long-COVID: temporal topic modeling of electronic health records from the N3C and RECOVER programs. npj Digit. Medicine 7(1) (2024)
[i20]
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  - journals/corr/abs-2406-02623
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Kathleen R. Mullen, Imke Tammen, Nicolas A. Matentzoglu, Marius Mather, Christopher J. Mungall, Melissa A. Haendel, Frank W. Nicholas, Sabrina Toro, the Vertebrate Breed Ontology Consortium:
The Vertebrate Breed Ontology: Towards Effective Breed Data Standardization. CoRR abs/2406.02623 (2024)
[i19]
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  - journals/corr/abs-2411-00046
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J. Harry Caufield, Carlo Kroll, Shawn T. O'Neil, Justin T. Reese, Marcin P. Joachimiak, Harshad Hegde, Nomi L. Harris, Madan Krishnamurthy, James A. McLaughlin, Damian Smedley, Melissa A. Haendel, Peter N. Robinson, Christopher J. Mungall:
CurateGPT: A flexible language-model assisted biocuration tool. CoRR abs/2411.00046 (2024)
2023
[j47]
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  - journals/biomedsem/ChanTDMSGVMRMH23
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Lauren E. Chan, Anne E. Thessen, William D. Duncan, Nicolas Matentzoglu, Charles Schmitt, Cynthia J. Grondin, Nicole A. Vasilevsky, Julie A. McMurry, Peter N. Robinson, Christopher J. Mungall, Melissa A. Haendel:
The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond. J. Biomed. Semant. 14(1): 3 (2023)
[j46]
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  - journals/jamia/LeeseAGMPYWHCBH23
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Peter Leese, Adit Anand, Andrew T. Girvin, Amin Manna, Saaya Patel, Yun Jae Yoo, Rachel Wong, Melissa A. Haendel, Christopher G. Chute, Tellen D. Bennett, Janos G. Hajagos, Emily R. Pfaff, Richard A. Moffitt:
Clinical encounter heterogeneity and methods for resolving in networked EHR data: a study from N3C and RECOVER programs. J. Am. Medical Informatics Assoc. 30(6): 1125-1136 (2023)
[j45]
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Emily R. Pfaff, Andrew T. Girvin, Miles Crosskey, Srushti Gangireddy, Hiral Master, Wei-Qi Wei, Vern Eric Kerchberger, Mark G. Weiner, Paul A. Harris, Melissa A. Basford, Christopher Lunt, Christopher G. Chute, Richard A. Moffitt, Melissa A. Haendel:
De-black-boxing health AI: demonstrating reproducible machine learning computable phenotypes using the N3C-RECOVER Long COVID model in the All of Us data repository. J. Am. Medical Informatics Assoc. 30(7): 1305-1312 (2023)
[j44]
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Sijia Liu, Andrew Wen, Liwei Wang, Huan He, Sunyang Fu, Robert T. Miller, Andrew E. Williams, Daniel R. Harris, Ramakanth Kavuluru, Mei Liu, Noor Abu-El-Rub, Dalton Schutte, Rui Zhang, Masoud Rouhizadeh, John D. Osborne, Yongqun He, Umit Topaloglu, Stephanie S. Hong, Joel H. Saltz, Thomas Schaffter, Emily R. Pfaff, Christopher G. Chute, Tim Duong, Melissa A. Haendel, Rafael Fuentes, Peter Szolovits, Hua Xu, Hongfang Liu:
An open natural language processing (NLP) framework for EHR-based clinical research: a case demonstration using the National COVID Cohort Collaborative (N3C). J. Am. Medical Informatics Assoc. 30(12): 2036-2040 (2023)
[j43]
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Ryan T. Scott, Lauren M. Sanders, Erik L. Antonsen, Jaden J. A. Hastings, Seung-Min Park, Graham Mackintosh, Robert J. Reynolds, Adrienne L. Hoarfrost, Aenor Sawyer, Casey S. Greene, Benjamin S. Glicksberg, Corey A. Theriot, Daniel C. Berrios, Jack Miller, Joel Babdor, Richard Barker, Sergio E. Baranzini, Afshin Beheshti, Stuart J. Chalk, Guillermo M. Delgado-Aparicio, Melissa A. Haendel, Arif A. Hamid, Philip Heller, Daniel Jamieson, Katelyn J. Jarvis, John Kalantari, Kia Khezeli, Svetlana V. Komarova, Matthieu Komorowski, Prachi Kothiyal, Ashish Mahabal, Uri Manor, Héctor García Martín, Christopher E. Mason, Mona Matar, George I. Mias, Jerry G. Myers Jr., Charlotte A. Nelson, Jonathan Oribello, Patricia Parsons-Wingerter, R. K. Prabhu, Amina Ann Qutub, Jon Rask, Amanda Saravia-Butler, Suchi Saria, Nitin Kumar Singh, Michael Snyder, Frank Soboczenski, Karthik Soman, David Van Valen, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Jason H. Yang, Marinka Zitnik, Sylvain V. Costes:
Biomonitoring and precision health in deep space supported by artificial intelligence. Nat. Mac. Intell. 5(3): 196-207 (2023)
[j42]
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Lauren M. Sanders, Ryan T. Scott, Jason H. Yang, Amina Ann Qutub, Héctor García Martín, Daniel C. Berrios, Jaden J. A. Hastings, Jon Rask, Graham Mackintosh, Adrienne L. Hoarfrost, Stuart J. Chalk, John Kalantari, Kia Khezeli, Erik L. Antonsen, Joel Babdor, Richard Barker, Sergio E. Baranzini, Afshin Beheshti, Guillermo M. Delgado-Aparicio, Benjamin S. Glicksberg, Casey S. Greene, Melissa A. Haendel, Arif A. Hamid, Philip Heller, Daniel Jamieson, Katelyn J. Jarvis, Svetlana V. Komarova, Matthieu Komorowski, Prachi Kothiyal, Ashish Mahabal, Uri Manor, Christopher E. Mason, Mona Matar, George I. Mias, Jack Miller, Jerry G. Myers Jr., Charlotte A. Nelson, Jonathan Oribello, Seung-Min Park, Patricia Parsons-Wingerter, R. K. Prabhu, Robert J. Reynolds, Amanda Saravia-Butler, Suchi Saria, Aenor Sawyer, Nitin Kumar Singh, Michael Snyder, Frank Soboczenski, Karthik Soman, Corey A. Theriot, David Van Valen, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Marinka Zitnik, Sylvain V. Costes:
Biological research and self-driving labs in deep space supported by artificial intelligence. Nat. Mac. Intell. 5(3): 208-219 (2023)
[j41]
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  - journals/npjdm/CallahanSWZOBBBCCCDFLMMMRSTTVWZDR23
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Tiffany J. Callahan, Adrianne L. Stefanski, Jordan M. Wyrwa, Chenjie Zeng, Anna Ostropolets, Juan M. Banda, William A. Baumgartner Jr., Richard D. Boyce, Elena Casiraghi, Ben D. Coleman, Janine H. Collins, Sara J. Deakyne Davies, James A. Feinstein, Asiyah Y. Lin, Blake Martin, Nicolas A. Matentzoglu, Daniella Meeker, Justin T. Reese, Jessica Sinclair, Sanya Bathla Taneja, Katy E. Trinkley, Nicole A. Vasilevsky, Andrew E. Williams, Xingmin Aaron Zhang, Joshua C. Denny, Patrick B. Ryan, George Hripcsak, Tellen D. Bennett, Melissa A. Haendel, Peter N. Robinson, Lawrence E. Hunter, Michael G. Kahn:
Ontologizing health systems data at scale: making translational discovery a reality. npj Digit. Medicine 6 (2023)
[i18]
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  - journals/corr/abs-2302-10800
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J. Harry Caufield, Tim E. Putman, Kevin Schaper, Deepak R. Unni, Harshad Hegde, Tiffany J. Callahan, Luca Cappelletti, Sierra A. T. Moxon, Vida Ravanmehr, Seth Carbon, Lauren E. Chan, Katherina Cortes, Kent A. Shefchek, Glass Elsarboukh, James P. Balhoff, Tommaso Fontana, Nicolas Matentzoglu, Richard M. Bruskiewich, Anne E. Thessen, Nomi L. Harris, Monica C. Munoz-Torres, Melissa A. Haendel, Peter N. Robinson, Marcin P. Joachimiak, Christopher J. Mungall, Justin T. Reese:
KG-Hub - Building and Exchanging Biological Knowledge Graphs. CoRR abs/2302.10800 (2023)
[i17]
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  - journals/corr/abs-2304-02711
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J. Harry Caufield, Harshad Hegde, Vincent Emonet, Nomi L. Harris, Marcin P. Joachimiak, Nicolas Matentzoglu, HyeongSik Kim, Sierra A. T. Moxon, Justin T. Reese, Melissa A. Haendel, Peter N. Robinson, Christopher J. Mungall:
Structured prompt interrogation and recursive extraction of semantics (SPIRES): A method for populating knowledge bases using zero-shot learning. CoRR abs/2304.02711 (2023)
[i16]
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  - journals/corr/abs-2309-17169
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Tudor Groza, J. Harry Caufield, Dylan Gration, Gareth Baynam, Melissa A. Haendel, Peter N. Robinson, Chris Mungall, Justin T. Reese:
An evaluation of GPT models for phenotype concept recognition. CoRR abs/2309.17169 (2023)
[i15]
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  - journals/corr/abs-2310-03666
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Nicolas Matentzoglu, J. Harry Caufield, Harshad B. Hegde, Justin T. Reese, Sierra A. T. Moxon, Hyeongsik Kim, Nomi L. Harris, Melissa A. Haendel, Christopher J. Mungall:
MapperGPT: Large Language Models for Linking and Mapping Entities. CoRR abs/2310.03666 (2023)
[i14]
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  - journals/corr/abs-2312-10904
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Sabrina Toro, Anna V. Anagnostopoulos, Sue Bello, Kai Lewis Blumberg, Rhiannon Cameron, Leigh Carmody, Alexander D. Diehl, Damion M. Dooley, William D. Duncan, Petra Fey, Pascale Gaudet, Nomi L. Harris, Marcin P. Joachimiak, Leila Kiani, Tiago Lubiana, Monica C. Munoz-Torres, Shawn T. O'Neil, David Osumi-Sutherland, Aleix Puig, Justin P. Reese, Leonore Reiser, Sofia M. C. Robb, Troy Ruemping, James Seager, Eric Sid, Raymund Stefancsik, Magalie Weber, Valerie Wood, Melissa A. Haendel, Christopher J. Mungall:
Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI). CoRR abs/2312.10904 (2023)
2022
[j40]
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  - journals/biodb/MatentzogluBBBB22
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Nicolas Matentzoglu, James P. Balhoff, Susan M. Bello, Chris Bizon, Matthew H. Brush, Tiffany J. Callahan, Christopher G. Chute, William D. Duncan, Chris T. A. Evelo, Davera Gabriel, John Graybeal, Alasdair J. G. Gray, Benjamin M. Gyori, Melissa A. Haendel, Henriette Harmse, Nomi L. Harris, Ian Harrow, Harshad Hegde, Amelia L. Hoyt, Charles Tapley Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Köhler, Thomas Liener, Qinqin Long, James Malone, James A. McLaughlin, Julie A. McMurry, Sierra A. T. Moxon, Monica C. Munoz-Torres, David Osumi-Sutherland, James A. Overton, Bjoern Peters, Tim E. Putman, Núria Queralt-Rosinach, Kent A. Shefchek, Harold Solbrig, Anne E. Thessen, Tania Tudorache, Nicole A. Vasilevsky, Alex H. Wagner, Christopher J. Mungall:
A Simple Standard for Sharing Ontological Mappings (SSSOM). Database J. Biol. Databases Curation 2022(2022) (2022)
[j39]
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Nicolas Matentzoglu, Damien Goutte-Gattat, Shawn Zheng Kai Tan, James P. Balhoff, Seth Carbon, Anita R. Caron, William D. Duncan, Joe E. Flack, Melissa A. Haendel, Nomi L. Harris, William R. Hogan, Charles Tapley Hoyt, Rebecca C. Jackson, Hyeongsik Kim, Hüseyin Kir, Martin Larralde, Julie A. McMurry, James A. Overton, Bjoern Peters, Clare Pilgrim, Raymund Stefancsik, Sofia M. C. Robb, Sabrina Toro, Nicole A. Vasilevsky, Ramona L. Walls, Christopher J. Mungall, David Osumi-Sutherland:
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies. Database J. Biol. Databases Curation 2022(2022) (2022)
[j38]
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Emily R. Pfaff, Andrew T. Girvin, Davera Gabriel, Kristin Kostka, Michele Morris, Matvey B. Palchuk, Harold P. Lehmann, Benjamin R. C. Amor, Mark Bissell, Katie R. Bradwell, Sigfried Gold, Stephanie S. Hong, Johanna Loomba, Amin Manna, Julie A. McMurry, Emily Niehaus, Nabeel Qureshi, Anita Walden, Xiaohan Tanner Zhang, Richard L. Zhu, Richard A. Moffitt, Christopher G. Chute, William G. Adams, Shaymaa Al-Shukri, Alfred Anzalone, Ahmad Baghal, Tellen D. Bennett, Elmer V. Bernstam, Mark M. Bissell, Brian Bush, Thomas R. Campion Jr., Victor Castro, Jack Chang, Deepa D. Chaudhari, Wenjin Chen, San Chu, James J. Cimino, Keith A. Crandall, Mark Crooks, Sara J. Deakyne Davies, John Dipalazzo, David A. Dorr, Dan Eckrich, Sarah E. Eltinge, Daniel G. Fort, George Golovko, Snehil Gupta, Melissa A. Haendel, Janos G. Hajagos, David A. Hanauer, Brett M. Harnett, Ronald Horswell, Nancy Huang, Steven G. Johnson, Michael Kahn, Kamil Khanipov, Curtis Kieler, Katherine Ruiz De Luzuriaga, Sarah E. Maidlow, Ashley Martinez, Jomol Mathew, James C. McClay, Gabriel McMahan, Brian Melancon, Stéphane M. Meystre, Lucio Miele, Hiroki Morizono, Ray Pablo, Lav P. Patel, Jimmy Phuong, Daniel J. Popham, Claudia P. Pulgarin, Carlos Santos, Indra Neil Sarkar, Nancy Sazo, Soko Setoguchi, Selvin Soby, Sirisha Surampalli, Christine Suver, Uma Maheswara Reddy Vangala, Shyam Visweswaran, James von Oehsen, Kellie M. Walters, Laura K. Wiley, David A. Williams, Adrian H. Zai:
Synergies between centralized and federated approaches to data quality: a report from the national COVID cohort collaborative. J. Am. Medical Informatics Assoc. 29(4): 609-618 (2022)
[j37]
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Katie R. Bradwell, Jacob T. Wooldridge, Benjamin R. C. Amor, Tellen D. Bennett, Adit Anand, Carolyn Bremer, Yun Jae Yoo, Zhenglong Qian, Steven G. Johnson, Emily R. Pfaff, Andrew T. Girvin, Amin Manna, Emily Niehaus, Stephanie S. Hong, Xiaohan Tanner Zhang, Richard L. Zhu, Mark Bissell, Nabeel Qureshi, Joel H. Saltz, Melissa A. Haendel, Christopher G. Chute, Harold P. Lehmann, Richard A. Moffitt:
Harmonizing units and values of quantitative data elements in a very large nationally pooled electronic health record (EHR) dataset. J. Am. Medical Informatics Assoc. 29(7): 1172-1182 (2022)
[j36]
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Jason A. Thomas, Randi E. Foraker, Noa Zamstein, Jon D. Morrow, Philip R. O. Payne, Adam B. Wilcox, Melissa A. Haendel, Christopher G. Chute, Kenneth R. Gersing, Anita Walden, Tellen D. Bennett, David A. Eichmann, Justin Guinney, Warren A. Kibbe, Hongfang Liu, Emily R. Pfaff, Peter N. Robinson, Joel H. Saltz, Heidi Spratt, Justin Starren, Christine Suver, Chunlei Wu, Davera Gabriel, Stephanie S. Hong, Kristin Kostka, Harold P. Lehmann, Richard A. Moffitt, Michele Morris, Matvey B. Palchuk, Xiaohan Tanner Zhang, Richard L. Zhu, Benjamin R. C. Amor, Mark M. Bissell, Marshall Clark, Andrew T. Girvin, Adam M. Lee, Robert T. Miller, Kellie M. Walters, Yooree Chae, Connor Cook, Alexandra Dest, Racquel R. Dietz, Thomas Dillon, Patricia A. Francis, Rafael Fuentes, Alexis Graves, Andrew J. Neumann, Shawn T. O'Neil, Usman Sheikh, Andréa M. Volz, Elizabeth Zampino, Christopher P. Austin, Samuel Bozzette, Mariam Deacy, Nicole Garbarini, Michael G. Kurilla, Sam G. Michael, Joni L. Rutter, Meredith Temple-O'Connor, Katie Rebecca Bradwell, Amin Manna, Nabeel Qureshi, Mary Morrison Saltz, Julie A. McMurry, Carolyn T. Bramante, Jeremy Richard Harper, Wenndy Hernandez, Farrukh M. Koraishy, Federico Mariona, Saidulu Mattapally, Amit Saha, Satyanarayana Vedula, Yujuan Fu, Nisha Mathews, Ofer Mendelevitch:
Demonstrating an approach for evaluating synthetic geospatial and temporal epidemiologic data utility: results from analyzing >1.8 million SARS-CoV-2 tests in the United States National COVID Cohort Collaborative (N3C). J. Am. Medical Informatics Assoc. 29(8): 1350-1365 (2022)
[c27]
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  - conf/bibm/SenguptaLSBTHCH22
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Saurav Sengupta, Johanna Loomba, Suchetha Sharma, Donald E. Brown, Lorna E. Thorpe, Melissa A. Haendel, Christopher G. Chute, Stephanie S. Hong:
Analyzing historical diagnosis code data from NIH N3C and RECOVER Programs using deep learning to determine risk factors for Long Covid. BIBM 2022: 2797-2802
[c26]
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Lauren E. Chan, Jimmy Phuong, Anne E. Thessen, Stephanie S. Hong, Shahim Essaid, Melissa A. Haendel:
From Survey to Ontology, the Challenges and Opportunities in Ontologizing Questions and Answers. ICBO 2022: 1
[c25]
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Sabrina Toro, Nicolas Matentzoglu, Kathleen R. Mullen, Nicole A. Vasilevsky, Halie Rando, Melissa A. Haendel, Christopher J. Mungall, Zhi-Liang Hu, Gregoire Leroy, Imke Tammen, Frank W. Nicholas:
Classifying Animal Breeds with the Vertebrate Breed Ontology (VBO). ICBO 2022: 1-7
[i13]
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  - journals/corr/abs-2203-13906
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Deepak R. Unni, Sierra A. T. Moxon, Michael Bada, Matthew H. Brush, Richard M. Bruskiewich, Paul A. Clemons, Vlado Dancík, Michel Dumontier, Karamarie Fecho, Gustavo Glusman, Jennifer J. Hadlock, Nomi L. Harris, Arpita Joshi, Tim E. Putman, Guangrong Qin, Stephen A. Ramsey, Kent A. Shefchek, Harold Solbrig, Karthik Soman, Anne E. Thessen, Melissa A. Haendel, Chris Bizon, Christopher J. Mungall:
Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science. CoRR abs/2203.13906 (2022)
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  - journals/corr/abs-2207-02056
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Nicolas Matentzoglu, Damien Goutte-Gattat, Shawn Zheng Kai Tan, James P. Balhoff, Seth Carbon, Anita R. Caron, William D. Duncan, Joe E. Flack, Melissa A. Haendel, Nomi L. Harris, William R. Hogan, Charles Tapley Hoyt, Rebecca C. Jackson, Hyeongsik Kim, Hüseyin Kir, Martin Larralde, Julie A. McMurry, James A. Overton, Bjoern Peters, Clare Pilgrim, Raymund Stefancsik, Sofia M. C. Robb, Sabrina Toro, Nicole A. Vasilevsky, Ramona L. Walls, Christopher J. Mungall, David Osumi-Sutherland:
Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies. CoRR abs/2207.02056 (2022)
[i11]
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  - journals/corr/abs-2209-04732
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Tiffany J. Callahan, Adrianne L. Stefanski, Jordan M. Wyrwa, Chenjie Zeng, Anna Ostropolets, Juan M. Banda, William A. Baumgartner Jr., Richard D. Boyce, Elena Casiraghi, Ben D. Coleman, Janine H. Collins, Sara J. Deakyne Davies, James A. Feinstein, Melissa A. Haendel, Asiyah Y. Lin, Blake Martin, Nicolas Matentzoglu, Daniella Meeker, Justin T. Reese, Jessica Sinclair, Sanya Bathla Taneja, Katy E. Trinkley, Nicole A. Vasilevsky, Andrew E. Williams, Xingman A. Zhang, Peter N. Robinson, Patrick B. Ryan, George Hripcsak, Tellen D. Bennett, Lawrence E. Hunter, Michael G. Kahn:
Ontologizing Health Systems Data at Scale: Making Translational Discovery a Reality. CoRR abs/2209.04732 (2022)
[i10]
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Saurav Sengupta, Johanna Loomba, Suchetha Sharma, Donald E. Brown, Lorna E. Thorpe, Melissa A. Haendel, Christopher G. Chute, Stephanie S. Hong:
Analyzing historical diagnosis code data from NIH N3C and RECOVER Programs using deep learning to determine risk factors for Long Covid. CoRR abs/2210.02490 (2022)
2021
[j35]
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Lauren E. Chan, Nicole A. Vasilevsky, Anne E. Thessen, Julie A. McMurry, Melissa A. Haendel:
The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research. Database J. Biol. Databases Curation 2021 (2021)
[j34]
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Rebecca C. Jackson, Nicolas Matentzoglu, James A. Overton, Randi Vita, James P. Balhoff, Pier Luigi Buttigieg, Seth Carbon, Mélanie Courtot, Alexander D. Diehl, Damion M. Dooley, William D. Duncan, Nomi L. Harris, Melissa A. Haendel, Suzanna E. Lewis, Darren A. Natale, David Osumi-Sutherland, Alan Ruttenberg, Lynn M. Schriml, Barry Smith, Christian J. Stoeckert Jr., Nicole A. Vasilevsky, Ramona L. Walls, Jie Zheng, Christopher J. Mungall, Bjoern Peters:
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. Database J. Biol. Databases Curation 2021 (2021)
[j33]
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Melissa A. Haendel, Christopher G. Chute, Tellen D. Bennett, David A. Eichmann, Justin Guinney, Warren A. Kibbe, Philip R. O. Payne, Emily R. Pfaff, Peter N. Robinson, Joel H. Saltz, Heidi Spratt, Christine Suver, John Wilbanks, Adam B. Wilcox, Andrew E. Williams, Chunlei Wu, Clair Blacketer, Robert L. Bradford, James J. Cimino, Marshall Clark, Evan W. Colmenares, Patricia A. Francis, Davera Gabriel, Alexis Graves, Raju Hemadri, Stephanie S. Hong, George Hripcsak, Dazhi Jiao, Jeffrey G. Klann, Kristin Kostka, Adam M. Lee, Harold P. Lehmann, Lora Lingrey, Robert T. Miller, Michele Morris, Shawn N. Murphy, Karthik Natarajan, Matvey B. Palchuk, Usman Sheikh, Harold Solbrig, Shyam Visweswaran, Anita Walden, Kellie M. Walters, Griffin M. Weber, Xiaohan Tanner Zhang, Richard L. Zhu, Benjamin R. C. Amor, Andrew T. Girvin, Amin Manna, Nabeel Qureshi, Michael G. Kurilla, Sam G. Michael, Lili M. Portilla, Joni L. Rutter, Christopher P. Austin, Ken R. Gersing:
The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment. J. Am. Medical Informatics Assoc. 28(3): 427-443 (2021)
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Sebastian Köhler, Michael A. Gargano, Nicolas Matentzoglu, Leigh Carmody, David Lewis-Smith, Nicole A. Vasilevsky, Daniel Danis, Ganna Balagura, Gareth Baynam, Amy M. Brower, Tiffany J. Callahan, Christopher G. Chute, Johanna L. Est, Peter D. Galer, Shiva Ganesan, Matthias Griese, Matthias Haimel, Julia Pazmandi, Marc Hanauer, Nomi L. Harris, Michael Hartnett, Maximilian Hastreiter, Fabian Hauck, Yongqun He, Tim Jeske, Hugh Kearney, Gerhard Kindle, Christoph Klein, Katrin Knoflach, Roland Krause, David Lagorce, Julie A. McMurry, Jillian A. Miller, Monica C. Munoz-Torres, Rebecca L. Peters, Christina K. Rapp, Ana Rath, Shahmir A. Rind, Avi Z. Rosenberg, Michael M. Segal, Markus G. Seidel, Damian Smedley, Tomer Talmy, Yarlalu Thomas, Samuel A. Wiafe, Julie Xian, Zafer Yüksel, Ingo Helbig, Christopher J. Mungall, Melissa A. Haendel, Peter N. Robinson:
The Human Phenotype Ontology in 2021. Nucleic Acids Res. 49(Database-Issue): D1207-D1217 (2021)
[j31]
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Justin T. Reese, Deepak R. Unni, Tiffany J. Callahan, Luca Cappelletti, Vida Ravanmehr, Seth Carbon, Kent A. Shefchek, Benjamin M. Good, James P. Balhoff, Tommaso Fontana, Hannah Blau, Nicolas Matentzoglu, Nomi L. Harris, Monica C. Munoz-Torres, Melissa A. Haendel, Peter N. Robinson, Marcin P. Joachimiak, Christopher J. Mungall:
KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response. Patterns 2(1): 100155 (2021)
[c24]
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Lauren E. Chan, Nicole A. Vasilevsky, Anne E. Thessen, Nicolas Matentzoglu, William D. Duncan, Christopher J. Mungall, Melissa A. Haendel:
A Semantic Model Leveraging Pattern-based Ontology Terms to Bridge Environmental Exposures and Health Outcomes. ICBO 2021: 48-55
[c23]
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Nicole A. Vasilevsky, Sabrina Toro, Nicolas Matentzoglu, Dazhi Jiao, Melissa A. Haendel, Peter N. Robinson, Christopher J. Mungall:
Reclassification of Infectious Disease in the Mondo Disease Ontology. ICBO 2021: 104-109
[c22]
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Sierra A. T. Moxon, Harold Solbrig, Deepak R. Unni, Dazhi Jiao, Richard M. Bruskiewich, James P. Balhoff, Gaurav Vaidya, William D. Duncan, Harshad Hegde, Mark Miller, Matthew H. Brush, Nomi L. Harris, Melissa A. Haendel, Christopher J. Mungall:
The Linked Data Modeling Language (LinkML): A General-Purpose Data Modeling Framework Grounded in Machine-Readable Semantics. ICBO 2021: 148-151
[i9]
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Sijia Liu, Andrew Wen, Liwei Wang, Huan He, Sunyang Fu, Robert T. Miller, Andrew E. Williams, Daniel R. Harris, Ramakanth Kavuluru, Mei Liu, Noor Abu-El-Rub, Rui Zhang, John D. Osborne, Masoud Rouhizadeh, Yongqun He, Emily R. Pfaff, Christopher G. Chute, Tim Duong, Melissa A. Haendel, Rafael Fuentes, Peter Szolovits, Hua Xu, Hongfang Liu:
An Open Natural Language Processing Development Framework for EHR-based Clinical Research: A case demonstration using the National COVID Cohort Collaborative (N3C). CoRR abs/2110.10780 (2021)
[i8]
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Nicolas Matentzoglu, James P. Balhoff, Susan M. Bello, Chris Bizon, Matthew H. Brush, Tiffany J. Callahan, Christopher G. Chute, William D. Duncan, Chris T. A. Evelo, Davera Gabriel, John Graybeal, Alasdair J. G. Gray, Benjamin M. Gyori, Melissa A. Haendel, Henriette Harmse, Nomi L. Harris, Ian Harrow, Harshad Hegde, Amelia L. Hoyt, Charles Tapley Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Köhler, Thomas Liener, Qinqin Long, James Malone, James A. McLaughlin, Julie A. McMurry, Sierra A. T. Moxon, Monica C. Munoz-Torres, David Osumi-Sutherland, James A. Overton, Bjoern Peters, Tim E. Putman, Núria Queralt-Rosinach, Kent A. Shefchek, Harold Solbrig, Anne E. Thessen, Tania Tudorache, Nicole A. Vasilevsky, Alex H. Wagner, Christopher J. Mungall:
A Simple Standard for Sharing Ontological Mappings (SSSOM). CoRR abs/2112.07051 (2021)
[i7]
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Ryan T. Scott, Erik L. Antonsen, Lauren M. Sanders, Jaden J. A. Hastings, Seung-Min Park, Graham Mackintosh, Robert J. Reynolds, Adrienne L. Hoarfrost, Aenor Sawyer, Casey S. Greene, Benjamin S. Glicksberg, Corey A. Theriot, Daniel C. Berrios, Jack Miller, Joel Babdor, Richard Barker, Sergio E. Baranzini, Afshin Beheshti, Stuart J. Chalk, Guillermo M. Delgado-Aparicio, Melissa A. Haendel, Arif A. Hamid, Philip Heller, Daniel Jamieson, Katelyn J. Jarvis, John Kalantari, Kia Khezeli, Svetlana V. Komarova, Matthieu Komorowski, Prachi Kothiyal, Ashish Mahabal, Uri Manor, Héctor García Martín, Christopher E. Mason, Mona Matar, George I. Mias, Jerry G. Myers Jr., Charlotte A. Nelson, Jonathan Oribello, Patricia Parsons-Wingerter, R. K. Prabhu, Amina Ann Qutub, Jon Rask, Amanda Saravia-Butler, Suchi Saria, Nitin Kumar Singh, Frank Soboczenski, Michael Snyder, Karthik Soman, David Van Valen, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Jason H. Yang, Marinka Zitnik, Sylvain V. Costes:
Beyond Low Earth Orbit: Biomonitoring, Artificial Intelligence, and Precision Space Health. CoRR abs/2112.12554 (2021)
[i6]
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  - journals/corr/abs-2112-12582
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Lauren M. Sanders, Jason H. Yang, Ryan T. Scott, Amina Ann Qutub, Héctor García Martín, Daniel C. Berrios, Jaden J. A. Hastings, Jon Rask, Graham Mackintosh, Adrienne L. Hoarfrost, Stuart J. Chalk, John Kalantari, Kia Khezeli, Erik L. Antonsen, Joel Babdor, Richard Barker, Sergio E. Baranzini, Afshin Beheshti, Guillermo M. Delgado-Aparicio, Benjamin S. Glicksberg, Casey S. Greene, Melissa A. Haendel, Arif A. Hamid, Philip Heller, Daniel Jamieson, Katelyn J. Jarvis, Svetlana V. Komarova, Matthieu Komorowski, Prachi Kothiyal, Ashish Mahabal, Uri Manor, Christopher E. Mason, Mona Matar, George I. Mias, Jack Miller, Jerry G. Myers Jr., Charlotte A. Nelson, Jonathan Oribello, Seung-Min Park, Patricia Parsons-Wingerter, R. K. Prabhu, Robert J. Reynolds, Amanda Saravia-Butler, Suchi Saria, Aenor Sawyer, Nitin Kumar Singh, Frank Soboczenski, Michael Snyder, Karthik Soman, Corey A. Theriot, David Van Valen, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Marinka Zitnik, Sylvain V. Costes:
Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving Labs. CoRR abs/2112.12582 (2021)
2020
[j30]
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William D. Duncan, Thankam Thyvalikakath, Melissa A. Haendel, Carlo Torniai, Pedro Hernández, Mei Song, Amit Acharya, Daniel J. Caplan, Titus Schleyer, Alan Ruttenberg:
Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology. J. Biomed. Semant. 11(1): 8 (2020)
[j29]
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Kent A. Shefchek, Nomi L. Harris, Michael A. Gargano, Nicolas Matentzoglu, Deepak R. Unni, Matthew H. Brush, Dan Keith, Tom Conlin, Nicole A. Vasilevsky, Xingmin Aaron Zhang, James P. Balhoff, Larry Babb, Susan M. Bello, Hannah Blau, Yvonne M. Bradford, Seth Carbon, Leigh Carmody, Lauren E. Chan, Valentina Cipriani, Alayne Cuzick, Maria G. Della Rocca, Nathan A. Dunn, Shahim Essaid, Petra Fey, Christian A. Grove, Jean-Philippe F. Gourdine, Ada Hamosh, Midori A. Harris, Ingo Helbig, Maureen E. Hoatlin, Marcin P. Joachimiak, Simon Jupp, Kenneth B. Lett, Suzanna E. Lewis, Craig McNamara, Zoë May Pendlington, Clare Pilgrim, Tim E. Putman, Vida Ravanmehr, Justin T. Reese, Erin Rooney Riggs, Sofia M. C. Robb, Paola Roncaglia, James Seager, Erik Segerdell, Morgan Similuk, Andrea L. Storm, Courtney Thaxon, Anne E. Thessen, Julius O. B. Jacobsen, Julie A. McMurry, Tudor Groza, Sebastian Köhler, Damian Smedley, Peter N. Robinson, Christopher J. Mungall, Melissa A. Haendel, Monica C. Munoz-Torres, David Osumi-Sutherland:
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 48(Database-Issue): D704-D715 (2020)
[j28]
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Anne E. Thessen, Ramona L. Walls, Lars Vogt, Jessica Singer, Robert Warren, Pier Luigi Buttigieg, James P. Balhoff, Christopher J. Mungall, Deborah L. McGuinness, Brian J. Stucky, Matthew J. Yoder, Melissa A. Haendel:
Transforming the study of organisms: Phenomic data models and knowledge bases. PLoS Comput. Biol. 16(11) (2020)
[c21]
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Justin Guinney, Subha Madhavan, Melissa A. Haendel, Alex H. Wagner, Ratna R. Thangudu:
Global research consortia and data harmonization projects drive the clinical interpretation of cancers. AMIA 2020
[c20]
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Nicole A. Vasilevsky, Shahim Essaid, Nicolas Matentzoglu, Nomi L. Harris, Melissa A. Haendel, Peter N. Robinson, Christopher J. Mungall:
Mondo Disease Ontology: Harmonizing Disease Concepts Across the World (short paper). ICBO/ODLS 2020: 1-2

2010 – 2019

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2019
[j27]
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Jean-Philippe F. Gourdine, Matthew H. Brush, Nicole A. Vasilevsky, Kent A. Shefchek, Sebastian Köhler, Nicolas Matentzoglu, Monica C. Munoz-Torres, Julie A. McMurry, Xingmin Aaron Zhang, Peter N. Robinson, Melissa A. Haendel:
Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery. Database J. Biol. Databases Curation 2019: baz114 (2019)
[j26]
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Sebastian Köhler, Leigh Carmody, Nicole A. Vasilevsky, Julius O. B. Jacobsen, Daniel Danis, Jean-Philippe F. Gourdine, Michael A. Gargano, Nomi L. Harris, Nicolas Matentzoglu, Julie A. McMurry, David Osumi-Sutherland, Valentina Cipriani, James P. Balhoff, Tom Conlin, Hannah Blau, Gareth Baynam, Richard Palmer, Dylan Gratian, Hugh J. S. Dawkins, Michael Segal, Anna C. Jansen, Ahmed Muaz, Willie H. Chang, Jenna Bergerson, Stanley J. F. Laulederkind, Zafer Yüksel, Sergi Beltran, Alexandra F. Freeman, Panagiotis I. Sergouniotis, Daniel Durkin, Andrea L. Storm, Marc Hanauer, Michael Brudno, Susan M. Bello, Murat Sincan, Kayli Rageth, Matthew T. Wheeler, Renske Oegema, Halima Lourghi, Maria G. Della Rocca, Rachel Thompson, Francisco Castellanos, James Priest, Charlotte Cunningham-Rundles, Ayushi Hegde, Ruth C. Lovering, Catherine Hajek, Annie Olry, Luigi Notarangelo, Morgan Similuk, Xingmin Aaron Zhang, David Gómez-Andrés, Hanns Lochmüller, Hélène Dollfus, Sergio Rosenzweig, Shruti Marwaha, Ana Rath, Kathleen Sullivan, Cynthia L. Smith, Joshua D. Milner, Dorothée Leroux, Cornelius F. Boerkoel, Amy Klion, Melody C. Carter, Tudor Groza, Damian Smedley, Melissa A. Haendel, Chris Mungall, Peter N. Robinson:
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Res. 47(Database-Issue): D1018-D1027 (2019)
[j25]
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Xingmin Aaron Zhang, Amy Yates, Nicole A. Vasilevsky, Jean-Philippe F. Gourdine, Tiffany J. Callahan, Leigh C. Carmody, Daniel Danis, Marcin P. Joachimiak, Vida Ravanmehr, Emily R. Pfaff, James Champion, Kimberly Robasky, Hao Xu, Karamarie Fecho, Nephi A. Walton, Richard L. Zhu, Justin Ramsdill, Christopher J. Mungall, Sebastian Köhler, Melissa A. Haendel, Clement J. McDonald, Daniel J. Vreeman, David B. Peden, Tellen D. Bennett, James A. Feinstein, Blake Martin, Adrianne L. Stefanski, Lawrence E. Hunter, Christopher G. Chute, Peter N. Robinson:
Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery. npj Digit. Medicine 2 (2019)
[j24]
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Y. Amy Tang, Klemens Pichler, Anja Füllgrabe, Jane Lomax, James Malone, Monica C. Munoz-Torres, Drashtti Vasant, Eleanor Williams, Melissa A. Haendel:
Ten quick tips for biocuration. PLoS Comput. Biol. 15(5) (2019)
[i5]
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Kristi L. Holmes, Nicole A. Vasilevsky, Marijane White, Matthew H. Brush, Lisa O'Keefe, Karen Gutzman, Melissa A. Haendel:
Architecting Attribution: expanding the scope of academic credit. RO 2019
2018
[c19]
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Jean-Philippe F. Gourdine, Nicole A. Vasilevsky, Lilly Winfree, Matthew H. Brush, Melissa A. Haendel:
Expanding the Molecular Glycophenotype Ontology to include model organisms and acquired diseases. ICBO 2018
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Pankaj Jaiswal, Laurel Cooper, Melissa A. Haendel, Christopher J. Mungall:
Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), Corvallis, Oregon, USA, August 7-10, 2018. CEUR Workshop Proceedings 2285, CEUR-WS.org 2018 [contents]
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Kristi L. Holmes, Karen Gutzman, Patricia Smith, David Eichmann, Melissa A. Haendel:
Making it count: a computational approach to attribution. RO 2018
2017
[j23]
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Michael Bada, Nicole A. Vasilevsky, William A. Baumgartner Jr., Melissa A. Haendel, Lawrence E. Hunter:
Gold-standard ontology-based anatomical annotation in the CRAFT Corpus. Database J. Biol. Databases Curation 2017: bax087 (2017)
[j22]
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Violeta Ilik, Michael Conlon, Graham Triggs, Marijane White, Muhammad Javed, Matthew H. Brush, Karen Gutzman, Shahim Essaid, Paul Friedman, Simon Porter, Martin Szomszor, Melissa Anne Haendel, David Eichmann, Kristi L. Holmes:
OpenVIVO: Transparency in Scholarship. Frontiers Res. Metrics Anal. 2: 12 (2017)
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Christopher J. Mungall, Julie A. McMurry, Sebastian Köhler, James P. Balhoff, Charles D. Borromeo, Matthew H. Brush, Seth Carbon, Tom Conlin, Nathan A. Dunn, Mark Engelstad, Erin Foster, Jean-Philippe F. Gourdine, Julius O. B. Jacobsen, Dan Keith, Bryan Laraway, Suzanna E. Lewis, Jeremy NguyenXuan, Kent A. Shefchek, Nicole A. Vasilevsky, Zhou Yuan, Nicole L. Washington, Harry Hochheiser, Tudor Groza, Damian Smedley, Peter N. Robinson, Melissa A. Haendel:
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 45(Database-Issue): D712-D722 (2017)
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Sebastian Köhler, Nicole A. Vasilevsky, Mark Engelstad, Erin Foster, Julie A. McMurry, Ségolène Aymé, Gareth Baynam, Susan M. Bello, Cornelius F. Boerkoel, Kym M. Boycott, Michael Brudno, Orion J. Buske, Patrick F. Chinnery, Valentina Cipriani, Laureen E. Connell, Hugh J. S. Dawkins, Laura E. DeMare, Andrew Devereau, Bert B. A. de Vries, Helen V. Firth, Kathleen Freson, Daniel Greene, Ada Hamosh, Ingo Helbig, Courtney Hum, Johanna Jähn, Roger James, Roland Krause, Stanley J. F. Laulederkind, Hanns Lochmüller, Gholson J. Lyon, Soichi Ogishima, Annie Olry, Willem H. Ouwehand, Nikolas Pontikos, Ana Rath, Franz Schaefer, Richard H. Scott, Michael Segal, Panagiotis I. Sergouniotis, Richard Sever, Cynthia L. Smith, Volker Straub, Rachel Thompson, Catherine Turner, Ernest Turro, Marijcke W. M. Veltman, Tom Vulliamy, Jing Yu, Julie von Ziegenweidt, Andreas Zankl, Stephan Züchner, Tomasz Zemojtel, Julius O. B. Jacobsen, Tudor Groza, Damian Smedley, Christopher J. Mungall, Melissa A. Haendel, Peter N. Robinson:
The Human Phenotype Ontology in 2017. Nucleic Acids Res. 45(Database-Issue): D865-D876 (2017)
[c18]
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James P. Balhoff, Matthew H. Brush, Laura Christopherson, Sherri de Coronado, Gilberto Fragoso, Melissa A. Haendel, Christopher J. Mungall, Kimberly Robasky, Nicole A. Vasilevsky, Lawrence W. Wright:
Tailoring the NCI Thesaurus for Use in The OBO Library. ICBO 2017
[c17]
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Nicole A. Vasilevsky, James P. Balhoff, Christopher J. Mungall, David Osumi-Sutherland, Sebastian Köhler, Susan M. Bello, Cynthia L. Smith, Peter N. Robinson, Melissa A. Haendel:
Aligning the Human Phenotype and Mammalian Phenotype Ontology using Dead Simple Ontology Design Patterns. ICBO 2017
2016
[j19]
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Alexander D. Diehl, Terrence F. Meehan, Yvonne M. Bradford, Matthew H. Brush, Wasila M. Dahdul, David S. Dougall, Yongqun He, David Osumi-Sutherland, Alan Ruttenberg, Sirarat Sarntivijai, Ceri E. Van Slyke, Nicole A. Vasilevsky, Melissa A. Haendel, Judith A. Blake, Christopher J. Mungall:
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. J. Biomed. Semant. 7: 44 (2016)
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Anita E. Bandrowski, Matthew H. Brush, Jeffrey S. Grethe, Melissa A. Haendel, David N. Kennedy, Sean L. Hill, Patrick R. Hof, Maryann E. Martone, Maaike Pols, Serena S. Tan, Nicole L. Washington, Elena V. Zudilova-Seinstra, Nicole A. Vasilevsky:
The Resource Identification Initiative: A Cultural Shift in Publishing. Neuroinformatics 14(2): 169-182 (2016)
[c16]
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Michael Bada, Nicole A. Vasilevsky, Melissa A. Haendel, Lawrence Hunter:
Gold-Standard Ontology-Based Annotation of Concepts in Biomedical Text in the CRAFT Corpus: Updates and Extensions. ICBO/BioCreative 2016
[c15]
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Matthew H. Brush, Kent A. Shefchek, Melissa A. Haendel:
SEPIO: A Semantic Model for the Integration and Analysis of Scientific Evidence. ICBO/BioCreative 2016
[c14]
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Jean-Philippe F. Gourdine, Thomas O. Metz, David Koeller, Matthew H. Brush, Melissa A. Haendel:
Building a Molecular Glyco-phenotype Ontology to Decipher Undiagnosed Diseases. ICBO/BioCreative 2016
[c13]
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Nicole A. Vasilevsky, Mark Engelstad, Erin Foster, Chris Mungall, Peter N. Robinson, Sebastian Köhler, Melissa A. Haendel:
Enhancing the Human Phenotype Ontology for Use by the Layperson. ICBO/BioCreative 2016
[c12]
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Marijane White, Matthew H. Brush, Shahim Essaid, Robin Champieux, Adrienne Zell, Melissa A. Haendel, Colin Grove, Syeda Momina Tabish, David Eichmann:
Enhancing SciENcv through Semantic Research Profile Integration with the VIVO-ISF Ontology. ICBO/BioCreative 2016
[c11]
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Melissa A. Haendel, Maricel G. Kann, Nicole L. Washington:
Session Introduction. PSB 2016: 93-95
2015
[j17]
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Christopher Ochs, Yehoshua Perl, James Geller, Melissa A. Haendel, Matthew H. Brush, Sivaram Arabandi, Samson W. Tu:
Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network. J. Biomed. Informatics 56: 127-144 (2015)
[j16]
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Joan Starr, Eleni Castro, Mercè Crosas, Michel Dumontier, Robert R. Downs, Ruth E. Duerr, Laurel L. Haak, Melissa A. Haendel, Iván Herman, Simon Hodson, Joe Hourclé, John Ernest Kratz, Jennifer Lin, Lars Holm Nielsen, Amy Nurnberger, Stefan Pröll, Andreas Rauber, Simone Sacchi, Arthur P. Smith, Michael Taylor, Tim Clark:
Achieving human and machine accessibility of cited data in scholarly publications. PeerJ Comput. Sci. 1: e1 (2015)
[i3]
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Anita E. Bandrowski, Matthew H. Brush, Jeffrey S. Grethe, Melissa A. Haendel, David N. Kennedy, Sean L. Hill, Patrick R. Hof, Maryann E. Martone, Maaike Pols, Serena S. Tan, Nicole L. Washington, Elena V. Zudilova-Seinstra, Nicole A. Vasilevsky:
The Resource Identification Initiative: A cultural shift in publishing. F1000Research 4: 134 (2015)
[i2]
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Joan Starr, Eleni Castro, Mercè Crosas, Michel Dumontier, Robert R. Downs, Ruth E. Duerr, Laurel L. Haak, Melissa A. Haendel, Iván Herman, Simon Hodson, Joe Hourclé, John Ernest Kratz, Jennifer Lin, Lars Holm Nielsen, Amy Nurnberger, Stefan Pröll, Andreas Rauber, Simone Sacchi, Arthur P. Smith, Michael Taylor, Tim Clark:
Achieving human and machine accessibility of cited data in scholarly publications. PeerJ Prepr. 3: e697 (2015)
2014
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Ceri E. Van Slyke, Yvonne M. Bradford, Monte Westerfield, Melissa A. Haendel:
The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio. J. Biomed. Semant. 5: 12 (2014)
[j14]
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Robert Hoehndorf, Dietrich Rebholz-Schuhmann, Melissa A. Haendel, Robert Stevens:
Thematic series on biomedical ontologies in JBMS: challenges and new directions. J. Biomed. Semant. 5: 15 (2014)
[j13]
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Melissa A. Haendel, James P. Balhoff, Frederic B. Bastian, David C. Blackburn, Judith A. Blake, Yvonne M. Bradford, Aurélie Comte, Wasila M. Dahdul, Thomas Dececchi, Robert E. Druzinsky, Terry F. Hayamizu, Nizar Ibrahim, Suzanna E. Lewis, Paula M. Mabee, Anne Niknejad, Marc Robinson-Rechavi, Paul C. Sereno, Christopher J. Mungall:
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J. Biomed. Semant. 5: 21 (2014)
[j12]
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Wasila M. Dahdul, Hong Cui, Paula M. Mabee, Christopher J. Mungall, David Osumi-Sutherland, Ramona L. Walls, Melissa A. Haendel:
Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. J. Biomed. Semant. 5: 34 (2014)
[j11]
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Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Terrence F. Meehan, Alexander D. Diehl, Uma D. Vempati, Stephan C. Schürer, Chao Pang, James Malone, Helen E. Parkinson, Yue Liu, Terue Takatsuki, Kaoru Saijo, Hiroshi Masuya, Yukio Nakamura, Matthew H. Brush, Melissa A. Haendel, Jie Zheng, Christian J. Stoeckert Jr., Bjoern Peters, Christopher J. Mungall, Thomas E. Carey, David J. States, Brian D. Athey, Yongqun He:
CLO: The cell line ontology. J. Biomed. Semant. 5: 37 (2014)
[j10]
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Robert W. Thacker, Maria Díaz, Adeline Kerner, Régine Vignes-Lebbe, Erik Segerdell, Melissa A. Haendel, Christopher J. Mungall:
The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology. J. Biomed. Semant. 5: 39 (2014)
[j9]
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Anika Oellrich, Sebastian Köhler, Nicole L. Washington, Chris Mungall, Suzanna Lewis, Melissa A. Haendel, Peter N. Robinson, Damian Smedley:
The influence of disease categories on gene candidate predictions from model organism phenotypes. J. Biomed. Semant. 5(S-1): S4 (2014)
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Jessica D. Tenenbaum, Susanna-Assunta Sansone, Melissa A. Haendel:
A sea of standards for omics data: sink or swim? J. Am. Medical Informatics Assoc. 21(2): 200-203 (2014)
[j7]
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Sebastian Köhler, Sandra C. Doelken, Christopher J. Mungall, Sebastian Bauer, Helen V. Firth, Isabelle Bailleul-Forestier, Graeme C. M. Black, Danielle L. Brown, Michael Brudno, Jennifer Campbell, David R. FitzPatrick, Janan T. Eppig, Andrew P. Jackson, Kathleen Freson, Marta Gîrdea, Ingo Helbig, Jane A. Hurst, Johanna Jähn, Laird G. Jackson, Anne M. Kelly, David H. Ledbetter, Sahar Mansour, Christa L. Martin, Celia Moss, Andrew D. Mumford, Willem H. Ouwehand, Soo-Mi Park, Erin Rooney Riggs, Richard H. Scott, Sanjay Sisodiya, Steven Van Vooren, Ronald J. Wapner, Andrew O. M. Wilkie, Caroline F. Wright, Anneke T. Vulto-van Silfhout, Nicole de Leeuw, Bert B. A. de Vries, Nicole L. Washington, Cynthia L. Smith, Monte Westerfield, Paul N. Schofield, Barbara J. Ruef, Georgios V. Gkoutos, Melissa A. Haendel, Damian Smedley, Suzanna E. Lewis, Peter N. Robinson:
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 42(Database-Issue): 966-974 (2014)
2013
[j6]
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Cecilia N. Arighi, Ben Carterette, K. Bretonnel Cohen, Martin Krallinger, W. John Wilbur, Petra Fey, Robert J. Dodson, Laurel Cooper, Ceri E. Van Slyke, Wasila M. Dahdul, Paula M. Mabee, Donghui Li, Bethany R. Harris, Marc Gillespie, Silvia Jimenez, Phoebe M. Roberts, Lisa Matthews, Kevin G. Becker, Harold J. Drabkin, Susan M. Bello, Luana Licata, Andrew Chatr-aryamontri, Mary L. Schaeffer, Julie Park, Melissa A. Haendel, Kimberly Van Auken, Yuling Li, Juancarlos Chan, Hans-Michael Müller, Hong Cui, James P. Balhoff, Chi-Yang Wu, Zhiyong Lu, Chih-Hsuan Wei, Catalina O. Tudor, Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan, Juan Miguel Cejuela, Pratibha Dubey, Cathy H. Wu:
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database J. Biol. Databases Curation 2013 (2013)
[j5]
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Terrence F. Meehan, Nicole A. Vasilevsky, Christopher J. Mungall, David S. Dougall, Melissa A. Haendel, Judith A. Blake, Alexander D. Diehl:
Ontology based molecular signatures for immune cell types via gene expression analysis. BMC Bioinform. 14: 263 (2013)
[c10]
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Carlo Torniai, Shahim Essaid, Brian Lowe, Jon Corson-Rikert, Melissa A. Haendel:
Finding common ground: integrating the eagle-i and VIVO ontologies. ICBO 2013: 46-49
[c9]
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Shahim Essaid, Carlo Torniai, Melissa A. Haendel:
Enabling semantic search in a bio-specimen repository. ICBO 2013: 50-53
[c8]
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Matthew H. Brush, Chris Mungall, Nicole L. Washington, Melissa A. Haendel:
What's in a Genotype?: An Ontological Characterization for Integration of Genetic Variation Data. ICBO 2013: 105-108
[c7]
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Matthew H. Brush, Jie Zheng, Yongqun He, Sirarat Sarntivijai, Bjoern Peters, Alexander D. Diehl, Christian J. Stoeckert Jr., Melissa A. Haendel:
Alignment of Cultured Cell Modeling Across OBO Foundry Ontologies: Key Outcomes, Insights. ICBO 2013: 120
[c6]
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Melissa A. Haendel, Carlo Torniai, Nicole A. Vasilevsky, Scott Hoffmann, Daniela Bourges-Waldegg:
eagle-i: ontology-driven federated search and data entry tools for discovering biomedical research resources. ICBO 2013: 130-131
2012
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Nicole A. Vasilevsky, Tenille Johnson, Karen Corday, Carlo Torniai, Matthew H. Brush, Erik Segerdell, Melanie Wilson, Chris Shaffer, David Robinson, Melissa A. Haendel:
Research resources: curating the new eagle-i discovery system. Database J. Biol. Databases Curation 2012 (2012)
2011
[c5]
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Matthew H. Brush, Nicole A. Vasilevsky, Carlo Torniai, Tenille Johnson, Chris Shaffer, Melissa A. Haendel:
Developing a Reagent Application Ontology within the OBO Foundry Framework. ICBO 2011
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Stella Mitchell, Carlo Torniai, Brian Lowe, Jon Corson-Rikert, Melanie Wilson, Mansoor Ahmed, Shanshan Chen, Ying Ding, Nicholas Rejack, Melissa A. Haendel:
Aligning Research Resource and Researcher Representation: The eagle-i and VIVO Use Case. ICBO 2011
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Chris Mungall, David Anderson, Anita E. Bandrowski, Brian A. Canada, Andrew Chatr-aryamontri, Keith C. Cheng, P. Michael Conn, Kara Dolinski, Mark H. Ellisman, Janan T. Eppig, Jeffrey S. Grethe, Joseph W. Kemnitz, Shawn Iadonato, Stephen D. Larson, Charles Magness, Maryann E. Martone, Mike Tyers, Carlo Torniai, Olga G. Troyanskaya, Judith Turner, Monte Westerfield, Melissa A. Haendel:
An Ontology-Based Approach to Linking Model Organisms and Resources to Human Diseases. ICBO 2011
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Christopher J. Mungall, Melissa A. Haendel, Amelia Ireland, Shahid Manzoor, Terry Meehan, David Osumi-Sutherland, Carlo Torniai, Alexander D. Diehl:
Modularization for the Cell Ontology. ICBO 2011
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Carlo Torniai, Matthew H. Brush, Nicole A. Vasilevsky, Erik Segerdell, Melanie Wilson, Tenille Johnson, Karen Corday, Chris Shaffer, Melissa A. Haendel:
Developing an Application Ontology for Biomedical Resource Annotation and Retrieval: Challenges and Lessons Learned. ICBO 2011

2000 – 2009

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2008
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Judy Sprague, Leyla Bayraktaroglu, Yvonne M. Bradford, Tom Conlin, Nathan A. Dunn, David Fashena, Ken Frazer, Melissa A. Haendel, Douglas G. Howe, Jonathan Knight, Prita Mani, Sierra A. T. Moxon, Christian Pich, Sridhar Ramachandran, Kevin Schaper, Erik Segerdell, Xiang Shao, Amy Singer, Peiran Song, Brock Sprunger, Ceri E. Van Slyke, Monte Westerfield:
The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res. 36(Database-Issue): 768-772 (2008)
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Melissa A. Haendel, Fabian Neuhaus, David Osumi-Sutherland, Paula M. Mabee, José L. V. Mejino Jr., Chris Mungall, Barry Smith:
CARO - The Common Anatomy Reference Ontology. Anatomy Ontologies for Bioinformatics 2008: 327-349
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Nicole L. Washington, M. Gibson, Chris Mungall, Michael Ashburner, Georgios V. Gkoutos, Monte Westerfield, Melissa A. Haendel, Suzanna E. Lewis:
NLP and Phenotypes: using Ontologies to link Human Diseases to Animal Models. Ontologies and Text Mining for Life Sciences 2008
2007
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John Day-Richter, Midori A. Harris, Melissa A. Haendel, Suzanna Lewis:
OBO-Edit - an ontology editor for biologists. Bioinform. 23(16): 2198-2200 (2007)
2006
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Judy Sprague, Leyla Bayraktaroglu, Dave Clements, Tom Conlin, David Fashena, Ken Frazer, Melissa A. Haendel, Douglas G. Howe, Prita Mani, Sridhar Ramachandran, Kevin Schaper, Erik Segerdell, Peiran Song, Brock Sprunger, Sierra Taylor, Ceri E. Van Slyke, Monte Westerfield:
The Zebrafish Information Network: the zebrafish model organism database. Nucleic Acids Res. 34(Database-Issue): 581-585 (2006)

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