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2020 – today
- 2025
[j58]Jessica Gliozzo, Mauricio Soto Gomez, Valentina Guarino, Arturo Bonometti, Alberto Cabri, Emanuele Cavalleri, Justin T. Reese, Peter N. Robinson, Marco Mesiti, Giorgio Valentini, Elena Casiraghi:
Intrinsic-dimension analysis for guiding dimensionality reduction and data fusion in multi-omics data processing. Artif. Intell. Medicine 160: 103049 (2025)- 2024
- [j57]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) - [j56]Anando Sen, Victoria Hedley, Eva Degraeuwe, Steven Hirschfeld, Ronald Cornet, Ramona Walls, John Owen, Peter N. Robinson, Edward G. Neilan, Thomas Liener, Giovanni Nisato, Neena Modi, Simon Woodworth, Avril Palmeri, Ricarda Gaentzsch, Melissa Walsh, Teresa Berkery, Joanne Lee, Laura Persijn, Kasey Baker, Kristina An Haack, Sonia Segovia Simon, Julius O. B. Jacobsen, Giorgio Reggiardo, Melissa A. Kirwin, Jessie Trueman, Claudia Pansieri, Donato Bonifazi, Sinéad Nally, Fedele Bonifazi, Rebecca Leary, Volker Straub:
Learning from conect4children: A Collaborative Approach towards Standardisation of Disease-Specific Paediatric Research Data. Data 9(4): 55 (2024) - [j55]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) - [j54]Guy Karlebach, Peter N. Robinson:
Computing Minimal Boolean Models of Gene Regulatory Networks. J. Comput. Biol. 31(2): 117-127 (2024) - [j53]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) - [c18]Marco Nicolini, Dario Malchiodi, Alberto Cabri, Emanuele Cavalleri, Marco Mesiti, Alberto Paccanaro, Peter N. Robinson, Justin T. Reese, Elena Casiraghi, Giorgio Valentini:
Fine-Tuning of Conditional Transformers Improves the Generation of Functionally Characterized Proteins. BIOSTEC (1) 2024: 561-568 - [c17]Emanuele Cavalleri, Mauricio Soto Gomez, Ali Pashaeibarough, Dario Malchiodi, J. Harry Caufield, Justin T. Reese, Christopher J. Mungall, Peter N. Robinson, Elena Casiraghi, Giorgio Valentini, Marco Mesiti:
Initial achievements in relation extraction from RNA-focused scientific papers. SEBD 2024: 61-69 - [c16]Emanuele Cavalleri, Mauricio Soto Gomez, Ali Pashaeibarough, Dario Malchiodi, J. Harry Caufield, Justin T. Reese, Chris Mungall, Peter N. Robinson, Elena Casiraghi, Giorgio Valentini, Marco Mesiti:
SPIREX: Improving LLM-based relation extraction from RNA-focused scientific literature using graph machine learning. VLDB Workshops 2024 - [i11]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
- [j52]Guy Karlebach, Leigh Carmody, Jagadish Chandrabose Sundaramurthi, Elena Casiraghi, Peter Hansen, Justin T. Reese, Christopher J. Mungall, Giorgio Valentini, Peter N. Robinson:
An expectation-maximization framework for comprehensive prediction of isoform-specific functions. Bioinform. 39(4) (2023) - [j51]Tudor Groza, Honghan Wu, Marcel E. Dinger, Daniel Danis, Coleman Hilton, Anita Bagley, Jon R. Davids, Ling Luo, Zhiyong Lu, Peter N. Robinson:
Term-BLAST-like alignment tool for concept recognition in noisy clinical texts. Bioinform. 39(12) (2023) - [j50]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) - [j49]Giorgio Valentini, Dario Malchiodi, Jessica Gliozzo, Marco Mesiti, Mauricio Soto Gomez, Alberto Cabri, Justin T. Reese, Elena Casiraghi, Peter N. Robinson:
The promises of large language models for protein design and modeling. Frontiers Bioinform. 3 (2023) - [j48]Elena Casiraghi, Rachel Wong, Margaret Hall, Ben D. Coleman, Marco Notaro, Michael D. Evans, Jena S. Tronieri, Hannah Blau, Bryan Laraway, Tiffany J. Callahan, Lauren E. Chan, Carolyn T. Bramante, John B. Buse, Richard A. Moffitt, Til Sturmer, Steven G. Johnson, Yu Raymond Shao, Justin T. Reese, Peter N. Robinson, Alberto Paccanaro, Giorgio Valentini, Jared D. Huling, Kenneth Wilkins:
A method for comparing multiple imputation techniques: A case study on the U.S. national COVID cohort collaborative. J. Biomed. Informatics 139: 104295 (2023) - [j47]Luca Cappelletti, Tommaso Fontana, Elena Casiraghi, Vida Ravanmehr, Tiffany J. Callahan, Carlos Cano, Marcin P. Joachimiak, Christopher J. Mungall, Peter N. Robinson, Justin T. Reese, Giorgio Valentini:
GRAPE for fast and scalable graph processing and random-walk-based embedding. Nat. Comput. Sci. 3(6): 552-568 (2023) - [j46]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) - [c15]Luca Cappelletti, Stefano Taverni, Tommaso Fontana, Marcin P. Joachimiak, Justin T. Reese, Peter N. Robinson, Elena Casiraghi, Giorgio Valentini:
Degree-Normalization Improves Random-Walk-Based Embedding Accuracy in PPI Graphs. IWBBIO (2) 2023: 372-383 - [i10]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) - [i9]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) - [i8]Tiffany J. Callahan, Ignacio J. Tripodi, Adrianne L. Stefanski, Luca Cappelletti, Sanya Bathla Taneja, Jordan M. Wyrwa, Elena Casiraghi, Nicolas A. Matentzoglu, Justin T. Reese, Jonathan C. Silverstein, Charles Tapley Hoyt, Richard D. Boyce, Scott A. Malec, Deepak R. Unni, Marcin P. Joachimiak, Peter N. Robinson, Christopher J. Mungall, Emanuele Cavalleri, Tommaso Fontana, Giorgio Valentini, Marco Mesiti, Lucas A. Gillenwater, Brook E. Santangelo, Nicole A. Vasilevsky, Robert Hoehndorf, Tellen D. Bennett, Patrick B. Ryan, George Hripcsak, Michael G. Kahn, Michael Bada, William A. Baumgartner Jr., Lawrence E. Hunter:
An Open-Source Knowledge Graph Ecosystem for the Life Sciences. CoRR abs/2307.05727 (2023) - [i7]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) - [i6]Emanuele Cavalleri, Alberto Cabri, Mauricio Soto Gomez, Sara Bonfitto, Paolo Perlasca, Jessica Gliozzo, Tiffany J. Callahan, Justin T. Reese, Peter N. Robinson, Elena Casiraghi, Giorgio Valentini, Marco Mesiti:
RNA-KG: An ontology-based knowledge graph for representing interactions involving RNA molecules. CoRR abs/2312.00183 (2023) - 2022
- [j45]Julius O. B. Jacobsen, Catherine Kelly, Valentina Cipriani, Peter N. Robinson, Damian Smedley:
Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases. Briefings Bioinform. 23(5) (2022) - [j44]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) - [j43]Shankai Yan, Ling Luo, Po-Ting Lai, Daniel Veltri, Andrew J. Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N. Robinson, Zhiyong Lu:
PhenoRerank: A re-ranking model for phenotypic concept recognition pre-trained on human phenotype ontology. J. Biomed. Informatics 129: 104059 (2022) - [j42]Robin Steinhaus, Peter N. Robinson, Dominik Seelow:
FABIAN-variant: predicting the effects of DNA variants on transcription factor binding. Nucleic Acids Res. 50(W1): 322-329 (2022) - [j41]Robin Steinhaus, Sebastian Proft, Evelyn Seelow, Tobias Schalau, Peter N. Robinson, Dominik Seelow:
Deep phenotyping: symptom annotation made simple with SAMS. Nucleic Acids Res. 50(W1): 677-681 (2022) - [c14]Guy Karlebach, Peter N. Robinson:
Computing Minimal Boolean Models of Gene Regulatory Networks. BIBM 2022: 2519-2525 - [c13]Alessandro Petrini, Marco Notaro, Jessica Gliozzo, Tiziana Castrignanò, Peter N. Robinson, Elena Casiraghi, Giorgio Valentini:
ParSMURF-NG: A Machine Learning High Performance Computing System for the Analysis of Imbalanced Big Omics Data. AIAI Workshops 2022: 424-435 - [i5]Elena Casiraghi, Rachel Wong, Margaret Hall, Ben D. Coleman, Marco Notaro, Michael D. Evans, Jena S. Tronieri, Hannah Blau, Bryan Laraway, Tiffany J. Callahan, Lauren E. Chan, Carolyn T. Bramante, John B. Buse, Richard A. Moffitt, Til Sturmer, Steven G. Johnson, Yu Raymond Shao, Justin T. Reese, Peter N. Robinson, Alberto Paccanaro, Giorgio Valentini, Jared D. Huling, Kenneth Wilkins:
Tell Bennet, Christopher Chute, Peter DeWitt, Kenneth Gersing, Andrew Girvin, Melissa Haendel, Jeremy Harper, Janos Hajagos, Stephanie Hong, Emily Pfaff, Jane Reusch, Corneliu Antoniescu, Kimberly Robaski: A Methodological Framework for the Comparative Evaluation of Multiple Imputation Methods: Multiple Imputation of Race, Ethnicity and Body Mass Index in the U.S. National COVID Cohort Collaborative. CoRR abs/2206.06444 (2022) - [i4]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) - 2021
- [j40]Ling Luo, Shankai Yan, Po-Ting Lai, Daniel Veltri, Andrew J. Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N. Robinson, Zhiyong Lu:
PhenoTagger: a hybrid method for phenotype concept recognition using human phenotype ontology. Bioinform. 37(13): 1884-1890 (2021) - [j39]Marco Notaro, Marco Frasca, Alessandro Petrini, Jessica Gliozzo, Elena Casiraghi, Peter N. Robinson, Giorgio Valentini:
HEMDAG: a family of modular and scalable hierarchical ensemble methods to improve Gene Ontology term prediction. Bioinform. 37(23): 4526-4533 (2021) - [j38]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) - [j37]Alice Scarabelli, Massimo Zilocchi, Elena Casiraghi, Pierangelo Fasani, Guido Giovanni Plensich, Alessandro Andrea Esposito, Elvira Stellato, Alessandro Petrini, Justin T. Reese, Peter N. Robinson, Giorgio Valentini, Gianpaolo Carrafiello:
Abdominal Computed Tomography Imaging Findings in Hospitalized COVID-19 Patients: A Year-Long Experience and Associations Revealed by Explainable Artificial Intelligence. J. Imaging 7(12): 258 (2021) - [j36]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) - [j35]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) - [c12]Feifan Liu, Noha Sharafeldin, Vithal Madhira, Katie R. Bradwell, Qianqian Song, Benjamin Bates, Yu R. Shao, Jing Su, Alfred Anzalone, Timothym Bergquist, Sarah Cutrona, Ben S. Gerber, Peter N. Robinson, Justin Guinney, Umit Topaloglu:
COVID-19 Mortality Prediction among Patients with Cancer Using a Large National Cohort. AMIA 2021 - [c11]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 - [i3]Giorgio Valentini, Elena Casiraghi, Luca Cappelletti, Vida Ravanmehr, Tommaso Fontana, Justin T. Reese, Peter N. Robinson:
Het-node2vec: second order random walk sampling for heterogeneous multigraphs embedding. CoRR abs/2101.01425 (2021) - [i2]Luca Cappelletti, Tommaso Fontana, Elena Casiraghi, Vida Ravanmehr, Tiffany J. Callahan, Marcin P. Joachimiak, Christopher J. Mungall, Peter N. Robinson, Justin T. Reese, Giorgio Valentini:
GraPE: fast and scalable Graph Processing and Embedding. CoRR abs/2110.06196 (2021) - 2020
- [j34]Elena Casiraghi, Dario Malchiodi, Gabriella Trucco, Marco Frasca, Luca Cappelletti, Tommaso Fontana, Alessandro Andrea Esposito, Emanuele Avola, Alessandro Jachetti, Justin T. Reese, Alessandro Rizzi, Peter N. Robinson, Giorgio Valentini:
Explainable Machine Learning for Early Assessment of COVID-19 Risk Prediction in Emergency Departments. IEEE Access 8: 196299-196325 (2020) - [j33]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) - [c10]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 - [i1]Ling Luo, Shankai Yan, Po-Ting Lai, Daniel Veltri, Andrew J. Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N. Robinson, Zhiyong Lu:
PhenoTagger: A Hybrid Method for Phenotype Concept Recognition using Human Phenotype Ontology. CoRR abs/2009.08478 (2020)
2010 – 2019
- 2019
- [j32]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) - [j31]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) - [j30]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) - [c9]Leigh C. Carmody, Xingmin Aaron Zhang, Nicole A. Vasilevsky, Christopher J. Mungall, Nicolas Matentzoglu, Peter N. Robinson:
Medical Action Ontology (MAxO). ICBO 2019: 1 - 2017
- [j29]Verena Heinrich, Tom Kamphans, Stefan Mundlos, Peter N. Robinson, Peter M. Krawitz:
A likelihood ratio-based method to predict exact pedigrees for complex families from next-generation sequencing data. Bioinform. 33(1): 72-78 (2017) - [j28]Marco Notaro, Max Schubach, Peter N. Robinson, Giorgio Valentini:
Prediction of Human Phenotype Ontology terms by means of hierarchical ensemble methods. BMC Bioinform. 18(1): 449:1-449:18 (2017) - [j27]Tobias Penzkofer, Marten Jäger, Marek Figlerowicz, Richard Badge, Stefan Mundlos, Peter N. Robinson, Tomasz Zemojtel:
L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes. Nucleic Acids Res. 45(Database-Issue): D68-D73 (2017) - [j26]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) - [j25]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) - [c8]Marco Notaro, Max Schubach, Marco Frasca, Marco Mesiti, Peter N. Robinson, Giorgio Valentini:
Ensembling Descendant Term Classifiers to Improve Gene - Abnormal Phenotype Predictions. CIBB 2017: 70-80 - [c7]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
- [j24]Anika Oellrich, Nigel Collier, Tudor Groza, Dietrich Rebholz-Schuhmann, Nigam Shah, Olivier Bodenreider, Mary Regina Boland, Ivo I. Georgiev, Hongfang Liu, Kevin M. Livingston, Augustin Luna, Ann-Marie Mallon, Prashanti Manda, Peter N. Robinson, Gabriella Rustici, Michelle Simon, Liqin Wang, Rainer Winnenburg, Michel Dumontier:
The digital revolution in phenotyping. Briefings Bioinform. 17(5): 819-830 (2016) - [c6]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 - 2015
- [j23]Nigel Collier, Tudor Groza, Damian Smedley, Peter N. Robinson, Anika Oellrich, Dietrich Rebholz-Schuhmann:
PhenoMiner: from text to a database of phenotypes associated with OMIM diseases. Database J. Biol. Databases Curation 2015 (2015) - [j22]Tudor Groza, Sebastian Köhler, Sandra C. Doelken, Nigel Collier, Anika Oellrich, Damian Smedley, Francisco M. Couto, Gareth Baynam, Andreas Zankl, Peter N. Robinson:
Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora. Database J. Biol. Databases Curation 2015 (2015) - [j21]Léon Kuchenbecker, Mikalai Nienen, Jochen Hecht, Avidan U. Neumann, Nina Babel, Knut Reinert, Peter N. Robinson:
IMSEQ - a fast and error aware approach to immunogenetic sequence analysis. Bioinform. 31(18): 2963-2971 (2015) - [j20]Na Zhu, Verena Heinrich, Thorsten Dickhaus, Jochen Hecht, Peter N. Robinson, Stefan Mundlos, Tom Kamphans, Peter M. Krawitz:
Strategies to improve the performance of rare variant association studies by optimizing the selection of controls. Bioinform. 31(22): 3577-3583 (2015) - [j19]Tudor Groza, Tania Tudorache, Peter N. Robinson, Andreas Zankl:
Capturing domain knowledge from multiple sources: the rare bone disorders use case. J. Biomed. Semant. 6: 21 (2015) - [c5]Giorgio Valentini, Sebastian Köhler, Matteo Ré, Marco Notaro, Peter N. Robinson:
Prediction of Human Gene - Phenotype Associations by Exploiting the Hierarchical Structure of the Human Phenotype Ontology. IWBBIO (1) 2015: 66-77 - [c4]Peter N. Robinson, Marco Frasca, Sebastian Köhler, Marco Notaro, Matteo Re, Giorgio Valentini:
A Hierarchical Ensemble Method for DAG-Structured Taxonomies. MCS 2015: 15-26 - 2014
- [j18]Damian Smedley, Sebastian Köhler, Johanna Christina Czeschik, Joanna S. Amberger, Carol A. Bocchini, Ada Hamosh, Julian Veldboer, Tomasz Zemojtel, Peter N. Robinson:
Walking the interactome for candidate prioritization in exome sequencing studies of Mendelian diseases. Bioinform. 30(22): 3215-3222 (2014) - [j17]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) - [j16]Aaron J. Masino, Elizabeth T. Dechene, Matthew C. Dulik, Alisha Wilkens, Nancy B. Spinner, Ian D. Krantz, Jeffrey W. Pennington, Peter N. Robinson, Peter S. White:
Clinical phenotype-based gene prioritization: an initial study using semantic similarity and the human phenotype ontology. BMC Bioinform. 15: 248 (2014) - [j15]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
- [j14]Damian Smedley, Anika Oellrich, Sebastian Köhler, Barbara J. Ruef, Monte Westerfield, Peter N. Robinson, Suzanna Lewis, Christopher J. Mungall:
PhenoDigm: analyzing curated annotations to associate animal models with human diseases. Database J. Biol. Databases Curation 2013 (2013) - [c3]Julien Grosjean, Tayeb Merabti, Lina Fatima Soualmia, Catherine Letord, Jean Charlet, Peter N. Robinson, Stéfan Jacques Darmoni:
Integrating the Human Phenotype Ontology into HeTOP Terminology-Ontology Server. MedInfo 2013: 961 - 2012
- [j13]Sebastian Bauer, Sebastian Köhler, Marcel H. Schulz, Peter N. Robinson:
Bayesian ontology querying for accurate and noise-tolerant semantic searches. Bioinform. 28(19): 2502-2508 (2012) - [j12]Maria Taboada, Diego Martínez Hernández, Belén Pilo, Adriano Jiménez-Escrig, Peter N. Robinson, María Jesús Sobrido:
Querying phenotype-genotype relationships on patient datasets using semantic web technology: the example of cerebrotendinous xanthomatosis. BMC Medical Informatics Decis. Mak. 12: 78 (2012) - 2011
- [j11]Christian Rödelsperger, Peter M. Krawitz, Sebastian Bauer, Jochen Hecht, Abigail W. Bigham, Michael Bamshad, Birgit Jonske de Condor, Michal R. Schweiger, Peter N. Robinson:
Identity-by-descent filtering of exome sequence data for disease-gene identification in autosomal recessive disorders. Bioinform. 27(6): 829-836 (2011) - [j10]Sebastian Bauer, Peter N. Robinson, Julien Gagneur:
Model-based gene set analysis for Bioconductor. Bioinform. 27(13): 1882-1883 (2011) - [j9]Sebastian Köhler, Sebastian Bauer, Chris Mungall, Gabriele Carletti, Cynthia L. Smith, Paul N. Schofield, Georgios V. Gkoutos, Peter N. Robinson:
Improving ontologies by automatic reasoning and evaluation of logical definitions. BMC Bioinform. 12: 418 (2011) - [j8]Marcel H. Schulz, Sebastian Köhler, Sebastian Bauer, Peter N. Robinson:
Exact score distribution computation for ontological similarity searches. BMC Bioinform. 12: 441 (2011) - 2010
- [j7]Peter M. Krawitz, Christian Rödelsperger, Marten Jäger, Luke Jostins, Sebastian Bauer, Peter N. Robinson:
Microindel detection in short-read sequence data. Bioinform. 26(6): 722-729 (2010)
2000 – 2009
- 2009
- [c2]Marcel H. Schulz, Sebastian Köhler, Sebastian Bauer, Martin Vingron, Peter N. Robinson:
Exact Score Distribution Computation for Similarity Searches in Ontologies. WABI 2009: 298-309 - 2008
- [j6]Sebastian Bauer, Steffen Grossmann, Martin Vingron, Peter N. Robinson:
Ontologizer 2.0 - a multifunctional tool for GO term enrichment analysis and data exploration. Bioinform. 24(14): 1650-1651 (2008) - [j5]Marcel H. Schulz, Sebastian Bauer, Peter N. Robinson:
The generalised k-Truncated Suffix Tree for time-and space-efficient searches in multiple DNA or protein sequences. Int. J. Bioinform. Res. Appl. 4(1): 81-95 (2008) - 2007
- [j4]Steffen Grossmann, Sebastian Bauer, Peter N. Robinson, Martin Vingron:
Improved detection of overrepresentation of Gene-Ontology annotations with parent-child analysis. Bioinform. 23(22): 3024-3031 (2007) - 2006
- [j3]Christoph Gille, Peter N. Robinson:
HotSwap for bioinformatics: A STRAP tutorial. BMC Bioinform. 7: 64 (2006) - [j2]Bradley J. Beattie, Peter N. Robinson:
Binary State Pattern Clustering: A Digital Paradigm for Class and Biomarker Discovery in Gene Microarray Studies of Cancer. J. Comput. Biol. 13(5): 1114-1130 (2006) - [c1]Steffen Grossmann, Sebastian Bauer, Peter N. Robinson, Martin Vingron:
An Improved Statistic for Detecting Over-Represented Gene Ontology Annotations in Gene Sets. RECOMB 2006: 85-98 - 2004
- [j1]Peter N. Robinson, Andreas Wollstein, Ulrike Böhme, Bradley J. Beattie:
Ontologizing gene-expression microarray data: characterizing clusters with Gene Ontology. Bioinform. 20(6): 979-981 (2004)
Coauthor Index
Tiffany Callahan
aka: Tiffany J. Callahan
aka: Tiffany J. Callahan
Nicolas Matentzoglu
aka: Nicolas A. Matentzoglu
aka: Nicolas A. Matentzoglu
Chris Mungall
aka: Christopher J. Mungall
aka: Christopher J. Mungall
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