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by Jiang, Yuxiang and Oron, Tal Ronnen and Clark, Wyatt T and Bankapur, Asma R and Anea, D', Daniel and Lepore, Rosalba and Funk, Christopher S and Kahanda, Indika and Verspoor, Karin M and Ben-Hur, Asa and Koo, Da Chen Emily and Penfold-Brown, Duncan and Shasha, Dennis and Youngs, Noah and Bonneau, Richard and Lin, Alexana and Sahraeian, Sayed M.E and Martelli, Pier Luigi and ti, Giuseppe and Casadio, Rita and Cao, Renzhi and Zhong, Zhaolong and Cheng, Jianlin and Altenhoff, Aian and Skunca, Nives and Dessimoz, Christophe and Dogan, Tunca and Hakala, Kai and Kaewphan, Suwisa and Mehryary, Farrokh and Salakoski, Tapio and Ginter, Filip and Fang, Hai and Smithers, Ben and Oates, Matt and Gough, Julian and Törönen, Petri and Koskinen, Patrik and Holm, Liisa and Chen, Ching Tai and Hsu, Wen Lian and Bryson, Kevin and Cozzetto, Domenico and Minneci, Federico and Jones, David T and Chapman, Samuel and BKC, Dukka and Khan, Ishita K and Kihara, Daisuke and Ofer, Dan and Rappoport, Nadav and Stern, Amos and Cibrian-Uhalte, Elena and Denny, Paul and Foulger, Rebecca E and Hieta, Reija and Legge, Duncan and Lovering, Ruth C and Magrane, Michele and Melidoni, Anna N and Mutowo-Meullenet, Prudence and Pichler, Klemens and Shypitsyna, Aleksana and Li, Biao and Zakeri, Pooya and ElShal, Sarah and Tranchevent, Léon Charles and Das, Sayoni and Dawson, Natalie L and Lee, David and Lees, Jonathan G and Sillitoe, Ian and Bhat, Prajwal and Nepusz, Tamás and Romero, Alfonso E and Sasidharan, Rajkumar and Yang, Haixuan and Paccanaro, Alberto and Gillis, Jesse and Sedeño-Cortés, Aiana E and Pavlidis, Paul and Feng, Shou and Cejuela, Juan M and Goldberg, Tatyana and Hamp, Tobias and Richter, Lothar and Salamov, Asaf and Gabaldon, Toni and Marcet-Houben, Marina and Supek, Fran and Gong, Qingtian and Ning, Wei and Zhou, Yuanpeng and Tian, Weidong and Falda, Marco and Fontana, Paolo and Lavezzo, Enrico and Toppo, Stefano and Ferrari, Carlo and Giollo, Manuel and ...
Genome Biology, ISSN 1474-7596, 2016, Volume 17, Issue 1, p. 184
Journal Article
F1000Research, ISSN 2046-1402, 2015, Volume 4, pp. 1 - 20
The human phenotype ontology (HPO) was recently developed as a standardized vocabulary for describing the phenotype abnormalities associated with human... 
Bioinformatics | Genomics | Proteins | Problems | Genotype & phenotype | Phenotypes | Annotations | Ontology | Disease | Genes | Computer applications | Data processing | Software | Genomes
Journal Article
IEEE/ACM Transactions on Computational Biology and Bioinformatics, ISSN 1545-5963, 09/2019, Volume 16, Issue 5, pp. 1424 - 1435
We consider the problem of identifying regions within a pan-genome De Bruijn graph that are traversed by many sequence paths. We define such regions and the... 
visualization | Itemsets | Sociology | Genomics | Clustering algorithms | classification | Bioinformatics | Statistics | Pan-genomics | ALGORITHM | BIOCHEMICAL RESEARCH METHODS | STATISTICS & PROBABILITY | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | MATHEMATICS, INTERDISCIPLINARY APPLICATIONS | SEQUENCE
Journal Article
GENOME BIOLOGY, ISSN 1474-760X, 11/2019, Volume 20, Issue 1, pp. 1 - 23
Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational... 
CANDIDA-ALBICANS | Critical assessment | Community challenge | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | Protein function prediction | GENETICS & HEREDITY | Biofilm | LIBRARY | Long-term memory | ONTOLOGY | GENERATION | IDENTIFICATION | Databases | Distributed, Parallel, and Cluster Computing | Bioinformatics | Machine Learning | Artificial Intelligence | Computer Science
Journal Article
01/2016, ISBN 1369048777
Proteins are the workhorses of life, and identifying their functions is a very important biological problem. The function of a protein can be loosely defined... 
Bioinformatics
Dissertation
GigaScience, ISSN 2047-217X, 2015, Volume 4, Issue 1, p. 41
Background: The recently held Critical Assessment of Function Annotation challenge (CAFA2) required its participants to submit predictions for a large number... 
Support vector machines | Automated function prediction | Gene Ontology | Machine learning | MULTIDISCIPLINARY SCIENCES | Proteins - physiology | Databases, Protein
Journal Article
Proceedings of the 3rd International Workshop on metamorphic testing, ISSN 0270-5257, 05/2018, pp. 26 - 33
Bioinformatics software plays a very important role in making critical decisions within many areas including medicine and health care. However, most of the... 
software testing | biomedical natural language processing | metamorphic testing | bioinformatics | Software testing | Text recognition | Metamorphic testing | Biological system modeling | Biomedical Natural Language Processing | Hidden Markov models | Tools | Software | Bioinformatics | Testing
Conference Proceeding
Database, ISSN 1758-0463, 01/2018, Volume 2018, Issue 2018
The text-mining services for kinome curation track, part of BioCreative VI, proposed a competition to assess the effectiveness of text mining to perform... 
Protein Kinases - metabolism | Data Mining | Humans | Periodicals as Topic | Databases, Factual
Journal Article
Journal of Biomedical Semantics, ISSN 2041-1480, 03/2015, Volume 6, Issue 1, p. 9
Most computational methods that predict protein function do not take advantage of the large amount of information contained in the biomedical literature. In... 
Text mining | Biomedical concept recognition | Protein function prediction | MATHEMATICAL & COMPUTATIONAL BIOLOGY
Journal Article
Proceedings of the 10th International Conference on Bioinformatics and Computational Biology, BICOB 2018, 2018, Volume 2018-
Conference Proceeding
by Jiang, Yuxiang and Oron, Ronnen Tal and Clark, T Wyatt and Bankapur, R Asma and D’Andrea, Daniel and Lepore, Rosalba and Funk, S Christopher and Kahanda, Indika and Verspoor, M Karin and Ben-Hur, Asa and Koo, Emily Da Chen and Penfold-Brown, Duncan and Shasha, Dennis and Youngs, Noah and Bonneau, Richard and Lin, Alexandra and Sahraeian, E Sayed M and Martelli, Luigi Pier and Profiti, Giuseppe and Casadio, Rita and Cao, Renzhi and Zhong, Zhaolong and Cheng, Jianlin and Altenhoff, Adrian and Skunca, Nives and Dessimoz, Christophe and Dogan, Tunca and Hakala, Kai and Kaewphan, Suwisa and Mehryary, Farrokh and Salakoski, Tapio and Ginter, Filip and Fang, Hai and Smithers, Ben and Oates, Matt and Gough, Julian and Törönen, Petri and Koskinen, Patrik and Holm, Liisa and Chen, Ching-Tai and Hsu, Wen-Lian and Bryson, Kevin and Cozzetto, Domenico and Minneci, Federico and Jones, T David and Chapman, Samuel and BKC, Dukka and Khan, K Ishita and Kihara, Daisuke and Ofer, Dan and Rappoport, Nadav and Stern, Amos and Cibrian-Uhalte, Elena and Denny, Paul and Foulger, E Rebecca and Hieta, Reija and Legge, Duncan and Lovering, C Ruth and Magrane, Michele and Melidoni, N Anna and Mutowo-Meullenet, Prudence and Pichler, Klemens and Shypitsyna, Aleksandra and Li, Biao and Zakeri, Pooya and ElShal, Sarah and Tranchevent, Léon-Charles and Das, Sayoni and Dawson, L Natalie and Lee, David and Lees, G Jonathan and Sillitoe, Ian and Bhat, Prajwal and Nepusz, Tamás and Romero, E Alfonso and Sasidharan, Rajkumar and Yang, Haixuan and Paccanaro, Alberto and Gillis, Jesse and Sedeño-Cortés, E Adriana and Pavlidis, Paul and Feng, Shou and Cejuela, M Juan and Goldberg, Tatyana and Hamp, Tobias and Richter, Lothar and Salamov, Asaf and Gabaldon, Toni and Marcet-Houben, Marina and Supek, Fran and Gong, Qingtian and Ning, Wei and Zhou, Yuanpeng and Tian, Weidong and Falda, Marco and Fontana, Paolo and Lavezzo, Enrico and Toppo, Stefano and Ferrari, Carlo and Giollo, Manuel and ...
ISSN 1474-7596, 2016
Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular... 
disease gene prioritization | protein function prediction
Journal Article
Proceedings of the 10th International Conference on Bioinformatics and Computational Biology, BICOB 2018, 2018, Volume 2018-
Conference Proceeding
PEERJ COMPUTER SCIENCE, ISSN 2376-5992, 11/2019, Volume 5, p. e233
Background. MicroRNAs (miRNAs) play a vital role as post-transcriptional regulators in gene expression. Experimental determination of miRNA sequence and... 
ab initio | CRITERIA | YIELD | COMPUTER SCIENCE, INFORMATION SYSTEMS | Systematic review | CLASSIFICATION | STRUCTURE-SEQUENCE FEATURES | GENOME | COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE | PREDICTION | Plant | BIOGENESIS | ANNOTATION | MIRNA | Machine learning | REAL | microRNA | COMPUTER SCIENCE, THEORY & METHODS
Journal Article
Proceedings of the 8th ACM International Conference on bioinformatics, computational biology,and health informatics, 08/2017, pp. 60 - 66
Automated Protein Function Prediction is the task of automatically predicting functional annotations for a protein based on gold-standard annotations derived... 
hierarchical multilabel classification | structured support vector machines | incomplete labels | automated protein function prediction | Incomplete labels | Structured support vector machines | Hierarchical multilabel classification | Automated Protein Function Prediction
Conference Proceeding
by Zhou, Naihui and Jiang, Yuxiang and Bergquist, Timothy R and Lee, Alexandra J and Kacsoh, Balint Z and Crocker, Alex W and Lewis, Kimberley A and Georghiou, George and Nguyen, Huy N and Hamid, Md Nafiz and Davis, Larry and Dogan, Tunca and Atalay, Volkan and Rifaioglu, Ahmet S and Dalkıran, Alperen and Cetin Atalay, Rengul and Zhang, Chengxin and Hurto, Rebecca L and Freddolino, Peter L and Zhang, Yang and Bhat, Prajwal and Supek, Fran and Fernández, José M and Gemovic, Branislava and Perovic, Vladimir R and Davidović, Radoslav S and Sumonja, Neven and Veljkovic, Nevena and Asgari, Ehsaneddin and Mofrad, Mohammad R K and Profiti, Giuseppe and Savojardo, Castrense and Martelli, Pier Luigi and Casadio, Rita and Boecker, Florian and Schoof, Heiko and Kahanda, Indika and Thurlby, Natalie and McHardy, Alice C and Renaux, Alexandre and Saidi, Rabie and Gough, Julian and Freitas, Alex A and Antczak, Magdalena and Fabris, Fabio and Wass, Mark N and Hou, Jie and Cheng, Jianlin and Wang, Zheng and Romero, Alfonso E and Paccanaro, Alberto and Yang, Haixuan and Goldberg, Tatyana and Zhao, Chenguang and Holm, Liisa and Törönen, Petri and Medlar, Alan J and Zosa, Elaine and Borukhov, Itamar and Novikov, Ilya and Wilkins, Angela and Lichtarge, Olivier and Chi, Po-Han and Tseng, Wei-Cheng and Linial, Michal and Rose, Peter W and Dessimoz, Christophe and Vidulin, Vedrana and Dzeroski, Saso and Sillitoe, Ian and Das, Sayoni and Lees, Jonathan Gill and Jones, David T and Wan, Cen and Cozzetto, Domenico and Fa, Rui and Torres, Mateo and Warwick Vesztrocy, Alex and Rodriguez, Jose Manuel and Tress, Michael L and Frasca, Marco and Notaro, Marco and Grossi, Giuliano and Petrini, Alessandro and Re, Matteo and Valentini, Giorgio and Mesiti, Marco and Roche, Daniel B and Reeb, Jonas and Ritchie, David W and Aridhi, Sabeur and Alborzi, Seyed Ziaeddin and Devignes, Marie-Dominique and Koo, Da Chen Emily and Bonneau, Richard and Gligorijević, Vladimir and Barot, Meet and Fang, Hai and Toppo, Stefano and Lavezzo, Enrico and ...
Genome biology, 11/2019, Volume 20, Issue 1, p. 244
The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of... 
Candida albicans - genetics | Locomotion | Genome, Bacterial | Animals | Biofilms | Genome, Fungal | Pseudomonas aeruginosa - genetics | Memory, Long-Term | Humans | Molecular Sequence Annotation - trends | Molecular Sequence Annotation - methods | Drosophila melanogaster - genetics
Journal Article
Association for Engineering Education - Engineering Library Division Papers, 06/2019
Writing exercises may be used in problem-centric STEM-based courses to identify common misconceptions held by the writer as well as to probe their... 
Evaluation | Automation | Motivation | Students | Circuits | Feedback | Machine learning | Writing | Risk | Natural language processing | At risk students | Workload
Conference Proceeding
02/2018
Bioinformatics software plays a very important role in making critical decisions within many areas including medicine and health care. However, most of the... 
Computer Science - Software Engineering
Journal Article
Proceedings of the 8th ACM International Conference on bioinformatics, computational biology,and health informatics, 08/2017, pp. 89 - 97
We consider the problem of identifying regions within a pan-genome de Bruijn graph that are traversed by many sequence paths. We define such regions and the... 
classification | pan-genomics | visualization | Visualization | Classification | Pan-genomics
Conference Proceeding
04/2019
Proteins are the workhorses of life and gaining insight on their functions is of paramount importance for applications such as drug design. However, the... 
Journal Article
2019 IEEE International Conference On Artificial Intelligence Testing (AITest), 04/2019, pp. 140 - 148
Proteins are the workhorses of life and gaining insight on their functions is of paramount importance for applications such as drug design. However, the... 
Proteins | Protein engineering | protein function prediction | metamorphic testing | supervised learning | Tools | Ontologies | Genetics | Bioinformatics | Testing
Conference Proceeding
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