2024
Ion channel classification through machine learning and protein language model embeddings.
J. Integr. Bioinform., 2024
2023
Enhanced identification of membrane transport proteins: a hybrid approach combining ProtBERT-BFD and convolutional neural networks.
J. Integr. Bioinform., July, 2023
2022
TooT-BERT-T: A BERT Approach on Discriminating Transport Proteins from Non-transport Proteins.
Proceedings of the Practical Applications of Computational Biology and Bioinformatics, 2022
TooT-BERT-C: A study on discriminating ion channels from membrane proteins based on the primary sequence's contextual representation from BERT models.
Proceedings of the 9th International Conference on Bioinformatics Research and Applications, 2022
A Study on the Application of Protein Language Models in the Analysis of Membrane Proteins.
Proceedings of the Distributed Computing and Artificial Intelligence, 2022
TooT-BERT-M: Discriminating Membrane Proteins from Non-Membrane Proteins using a BERT Representation of Protein Primary Sequences.
Proceedings of the IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 2022
Predicting the specific substrate for transmembrane transport proteins using BERT language model.
Proceedings of the IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 2022
2021
Advances in the Development of Trifluoromethoxylation Reagents.
Symmetry, 2021
2020
TooT-T: discrimination of transport proteins from non-transport proteins.
BMC Bioinform., April, 2020
BENIN: Biologically enhanced network inference.
J. Bioinform. Comput. Biol., 2020
Integrative approach for detecting membrane proteins.
BMC Bioinform., 2020
TportHMM: Predicting the substrate class of transmembrane transport proteins using profile Hidden Markov Models.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2020
2019
Ontology-based transporter substrate annotation for benchmark datasets.
Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019
2017
SynAPhy and SynAVal: Mining a Synteny-Similarity Graph to Resolve Orthology of Proteins in Fungal Genomes.
Proceedings of the 17th IEEE International Conference on Bioinformatics and Bioengineering, 2017
2016
Improving GraphChi for Large Graph Processing: Fast Radix Sort in Pre-Processing.
Proceedings of the 20th International Database Engineering & Applications Symposium, 2016
2015
mycoCLAP, the database for characterized lignocellulose-active proteins of fungal origin: resource and text mining curation support.
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Database J. Biol. Databases Curation, 2015
Computation for Genomics Knowledge Discovery.
Proceedings of the 1st IEEE/ACM International Workshop on Software Engineering for High Performance Computing in Science, 2015
Accelerating Search of Protein Sequence Databases using CUDA-Enabled GPU.
Proceedings of the Database Systems for Advanced Applications, 2015
On predicting transport proteins and their substrates for the reconstruction of metabolic networks.
Proceedings of the IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 2015
A visual spreadsheet using HTML5 for whole genome display.
Proceedings of the IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 2015
2014
SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models.
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BMC Bioinform., 2014
A review of genomic data warehousing systems.
Briefings Bioinform., 2014
2013
Pattern Language Verification in Model Driven Design.
Inf. Sci., 2013
BenchDW: a generic framework for biological data warehouse benchmarking.
Proceedings of the 28th Annual ACM Symposium on Applied Computing, 2013
An approach to controlling user models and personalization effects in recommender systems.
Proceedings of the 18th International Conference on Intelligent User Interfaces, 2013
Putting It All Together: The Design of a Pipeline for Genome-Wide Functional Annotation of Fungi in the Modern Era of "-Omics" Data and Systems Biology.
Proceedings of the Data Integration in the Life Sciences - 9th International Conference, 2013
The impact of SignalP 4.0 on the prediction of secreted proteins.
Proceedings of the 2013 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2013
2012
Semantic text mining support for lignocellulose research.
BMC Medical Informatics Decis. Mak., 2012
The EnzymeTracker: an open-source laboratory information management system for sample tracking.
BMC Bioinform., 2012
<i>ECTree</i>: an extended tree index for attributed subgraph queries.
Proceedings of the 16th International Database Engineering & Applications Symposium, 2012
Personalized semantic assistance for the curation of biochemical literature.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012
2011
Curation of characterized glycoside hydrolases of Fungal origin.
Database J. Biol. Databases Curation, 2011
Applying Linear Models to Learn Regulation Programs in a Transcription Regulatory Module Network.
Proceedings of the Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, 2011
Table-Driven Detection and Resolution of Operation-Based Merge Conflicts with Mirador.
Proceedings of the Modelling Foundations and Applications - 7th European Conference, 2011
Towards Evaluating the Impact of Semantic Support for Curating the Fungus Scientic Literature.
Proceedings of the 3rd Canadian Semantic Web Symposium (CSWS2011), 2011
An integrative approach to infer regulation programs in a transcription regulatory module network.
Proceedings of the ACM International Conference on Bioinformatics, 2011
2010
Mirador: a synthesis of model matching strategies.
Proceedings of the 1st International Workshop on Model Comparison in Practice, 2010
A regression tree-based Gibbs sampler to learn the regulation programs in a transcription regulatory module network.
Proceedings of the 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2010
Issues with the PipeAlign phylogenomics toolkit in identifying protein subfamilies.
Proceedings of the 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2010
2009
Merging of Use Case Models: Semantic Foundations.
Proceedings of the TASE 2009, 2009
Describing Pattern Languages for Checking Design Models.
Proceedings of the 16th Asia-Pacific Software Engineering Conference, 2009
2008
Tool Support for Pattern Selection and Use.
Proceedings of the International Workshop on Software Quality and Maintainability, 2008
A pipeline for 800+ shots.
Proceedings of the International Conference on Computer Graphics and Interactive Techniques, 2008
A Pattern Language Verifier for Web-Based Enterprise Applications.
Proceedings of the Model Driven Engineering Languages and Systems, 2008
2006
Semantic web infrastructure for fungal enzyme biotechnologists.
J. Web Semant., 2006
Query Optimization for a Graph Database with Visual Queries.
Proceedings of the Database Systems for Advanced Applications, 2006
A Distributed Agent System upon Semantic Web Technologies to Provide Biological Data.
Proceedings of the Canadian Semantic Web, 2006
Ontoligent Interactive Query Tool.
Proceedings of the Canadian Semantic Web, 2006
Cascaded Refactoring for Framework Development and Evolution.
Proceedings of the 17th Australian Software Engineering Conference (ASWEC 2006), 2006
Bayesian Learning for Feed-Forward Neural Network with Application to Proteomic Data: The Glycosylation Sites Detection of the Epidermal Growth Factor-Like Proteins Associated with Cancer as a Case Study.
Proceedings of the Advances in Artificial Intelligence, 2006
2005
OrfPredictor: predicting protein-coding regions in EST-derived sequences.
Nucleic Acids Res., 2005
TargetIdentifier: a webserver for identifying full-length cDNAs from EST sequences.
Nucleic Acids Res., 2005
The FungalWeb Ontology: Semantic Web Challenges in Bioinformatics and Genomics.
Proceedings of the Semantic Web - ISWC 2005, 4th International Semantic Web Conference, 2005
A graph database with visual queries for genomics.
Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January 2005, Singapore, 2005
2004
The Lord of the Rings: the visual effects that brought middle earth to the screen.
Proceedings of the International Conference on Computer Graphics and Interactive Techniques, 2004
GUPFS: The Global Unified Parallel File System Project at NERSC.
Proceedings of the 21st IEEE Conference on Mass Storage Systems and Technologies / 12th NASA Goddard Conference on Mass Storage Systems and Technologies, 2004
Refactoring Use Case Models on Episodes.
Proceedings of the 19th IEEE International Conference on Automated Software Engineering (ASE 2004), 2004
Experimental Studies of Scalability in Clustered Web Systems.
Proceedings of the 18th International Parallel and Distributed Processing Symposium (IPDPS 2004), 2004
An Efficient B+-Tree Implementation in C++ Using the STL Style.
Proceedings of the ICEIS 2004, 2004
A Prototype Tool for Use Case Refactoring.
Proceedings of the ICEIS 2004, 2004
Difficult Issues in Designing Adaptive Object Model Systems.
Proceedings of the ICEIS 2004, 2004
Proceedings of the ICEIS 2004, 2004
Use Case Refactoring: A Tool and a Case Study.
Proceedings of the 11th Asia-Pacific Software Engineering Conference (APSEC 2004), 30 November, 2004
2003
Refactoring the Scenario Specification: A Message Sequence Chart Approach.
Proceedings of the Object-Oriented Information Systems, 9th International Conference, 2003
Refactoring Use Case Models: A Case Study.
Proceedings of the ICEIS 2003, 2003
Issues in Architectural Modeling and Evolution in the Know-It-All Case Study.
Proceedings of the 10th IEEE International Conference on Engineering of Computer-Based Systems (ECBS 2003), 2003
Implementing the PostgreSQL Query Optimizer within the OPT++ Framework.
Proceedings of the 10th Asia-Pacific Software Engineering Conference (APSEC 2003), 2003
Implementing Exception Handling Policies for Workflow Management System.
Proceedings of the 10th Asia-Pacific Software Engineering Conference (APSEC 2003), 2003
Refactoring Use Case Models: The Metamodel.
Proceedings of the Computer Science 2003, 2003
2002
Architectural Refactoring in Framework Evolution: A Case Study.
Proceedings of the Generative Programming and Component Engineering, 2002
2001
Generative techniques for product lines.
ACM SIGSOFT Softw. Eng. Notes, 2001
Cascaded refactoring for framework.
Proceedings of the ACM SIGSOFT Symposium on Software Reusability: Putting Software Reuse in Context, 2001
Generative Techniques for Product Lines.
Proceedings of the 23rd International Conference on Software Engineering, 2001
Proceedings of the Object-Oriented Technology ECOOP 2001 Workshop Reader, 2001
2000
A framework for framework documentation.
ACM Comput. Surv., 2000
Three Improvements to the BLASTP Search of Genome Databases.
Proceedings of the 12th International Conference on Scientific and Statistical Database Management, 2000
1999
New results on deriving SDL specifications from MSCs.
Proceedings of the SDL '99 The Next Millennium, 1999
Developing Frameworks by Aligning Requirements, Design, and Code.
Proceedings of the Object-Oriented Technology, ECOOP'99 Workshop Reader, 1999
Reusable Strategies for Software Agents via the Subsumption.
Proceedings of the 6th Asia-Pacific Software Engineering Conference (APSEC '99), 1999
Towards OM - An Object-Oriented Implementation of Mantra.
Proceedings of the Database Systems 99, 1999
1998
Feature Interaction Detection Technique Based on Feature Assumptions.
Proceedings of the Feature Interactions in Telecommunications and Software Systems V, September 29, 1998
A Reuse Case Perspective on Documenting Frameworks.
Proceedings of the 5th Asia-Pacific Software Engineering Conference (APSEC '98), 1998
1997
A Z Specification of Use Cases: A Preliminary Report.
Proceedings of the 4th Asia-Pacific Software Engineering and International Computer Science Conference (APSEC '97 / ICSC '97), 1997
Quality and Reuse in Industrial Software Engineering.
Proceedings of the 4th Asia-Pacific Software Engineering and International Computer Science Conference (APSEC '97 / ICSC '97), 1997
1996
Software Architectures for Computer Algebra: A Case Study.
Proceedings of the Design and Implementation of Symbolic Computation Systems, 1996
Document Recognition, Semantics, and Symbolic Reasoning in Reverse Engineering of Software.
Proceedings of the Artificial Intelligence and Symbolic Mathematical Computation, 1996
1995
An Intelligent Tutoring System for the Dijkstra-Gries Methodology.
IEEE Trans. Software Eng., 1995
Easy Verification of Behavioural Subtyping in Common Cases.
Inf. Process. Lett., 1995
Formal Representation of Reusable Software Modules.
Proceedings of the 2nd Working Conference on Reverse Engineering, 1995
Retrieving Information from Data Flow Diagrams.
Proceedings of the 2nd Working Conference on Reverse Engineering, 1995
Analyzing the logical structure of data flow diagrams in software documents.
Proceedings of the Third International Conference on Document Analysis and Recognition, 1995
Intelligent Mathematical Databases.
Proceedings of the Database Systems for Advanced Applications '95, 1995
1994
A Database of Groups of Prime-power Order.
Softw. Pract. Exp., 1994
The Preliminary Design of an Object-Oriented Framework for Combinatorial Enumeration.
Proceedings of the Object-Oriented Technology for Database and Software Systems, 1994
Datalog and TwoGroups and C++.
Proceedings of the Integrating Symbolic Mathematical Computation and Artificial Intelligence, 1994
1993
The Transitive Groups of Degree Fourteen and Fifteen.
J. Symb. Comput., 1993
Specialised Theorem-Proving in an Intelligent Tutoring System for the Dijkstra-Gries Programming Methodology.
Proceedings of the Computing and Information, 1993
1992
An analysis of Atkinson's algorithm.
SIGSAM Bull., 1992
Experimental Comparison of Algorithms for Sylow Subgroups.
Proceedings of the 1992 International Symposium on Symbolic and Algebraic Computation, 1992
The Progress Towards an Intelligent Assistent - A Discussion Paper.
Proceedings of the Artificial Intelligence and Symbolic Mathematical Computation, 1992
1991
Computing Sylow Subgroups of Permutation Groups Using Homomorphic Images of Centralizers.
J. Symb. Comput., 1991
Towards a deductive database for small simple groups.
SIGSAM Bull., 1991
A Deductive Database of the Groups of Order Dividing 128.
Proceedings of the 1991 International Symposium on Symbolic and Algebraic Computation, 1991
Implementing Some Algorithms of Kantor.
Proceedings of the Applied Algebra, 1991
Fundamental Algorithms for Permutation Groups
Lecture Notes in Computer Science 559, Springer, ISBN: 3-540-54955-2, 1991
1990
Deductive Mathematical Databases - A Case Study.
Proceedings of the Statistical and Scientific Database Management, 1990
The Design of Cayley - a Language for Modern Algebra.
Proceedings of the Design and Implementation of Symbolic Computation Systems, 1990
1989
Computing in Permutation and Matrix Groups III: Sylow Subgroups.
J. Symb. Comput., 1989
1988
A Proof of Holt's Algorithm.
J. Symb. Comput., 1988
Cayley, Version 4: The User Language.
Proceedings of the Symbolic and Algebraic Computation, 1988
1987
The Suitability for Master/Slave Concurrency of Concurrent Euclid, Ada and Modula.
Softw. Pract. Exp., 1987
1986
Divide-and-conquer in computational group theory.
Proceedings of the Symposium on Symbolic and Algebraic Manipulation, 1986
1985
A General Backtrack Algorithm for the Isomorphism Problem of Combinatorial Objects.
J. Symb. Comput., 1985
Effective Computation with Group Homomorphisms.
J. Symb. Comput., 1985
An improvement to the centralizer algorithm for permutation groups.
SIGSAM Bull., 1985
1983
Computing Normalizers in Permutation Groups.
J. Algorithms, 1983
1981
Double cosets and searching small groups.
Proceedings of the Symposium on Symbolic and Algebraic Manipulation, 1981