Anthony J. Kusalik

Publication Activity (10 Years)

Years Active: 1984-2023
Publications (10 Years): 12

Top Topics

Negative Matrix Factorization

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Ali Akbar Jamali, Anthony J. Kusalik, Fang-Xiang Wu
NMTF-DTI: A Nonnegative Matrix Tri-factorization Approach With Multiple Kernel Fusion for Drug-Target Interaction Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (1) (2023)
Zoe Parker Cates, Antonio Facciuolo, Daniel J. Hogan, Philip J. Griebel, Scott Napper, Anthony J. Kusalik
EPIphany - A Platform for Analysis and Visualization of Peptide Immunoarray Data. Frontiers Bioinform. 1 (2021)
Ali Akbar Jamali, Anthony J. Kusalik, Fang-Xiang Wu
MDIPA: a microRNA-drug interaction prediction approach based on non-negative matrix factorization. Bioinform. 36 (20) (2020)
Farhad Maleki, Anthony J. Kusalik
Gene Set Overlap: An Impediment to Achieving High Specificity in Over-representation Analysis. BIOINFORMATICS (2019)
Yan Yan, Connor Burbridge, Jin-Hong Shi, Juxin Liu, Anthony J. Kusalik
Effects of input data quantity on genome-wide association studies (GWAS). Int. J. Data Min. Bioinform. 22 (1) (2019)
Farhad Maleki, Katie L. Ovens, Ian McQuillan, Elham Rezaei, Alan M. Rosenberg, Anthony J. Kusalik
Gene Set Databases: A Fountain of Knowledge or a Siren Call? BCB (2019)
Jin-Hong Shi, Yan Yan, Matthew G. Links, Longhai Li, Jo-Anne R. Dillon, Michael Horsch, Anthony J. Kusalik
Antimicrobial resistance genetic factor identification from whole-genome sequence data using deep feature selection. BMC Bioinform. (15) (2019)
Farhad Maleki, Katie L. Ovens, Elham Rezaei, Alan M. Rosenberg, Anthony J. Kusalik
Method Choice in Gene Set Analysis Has Important Consequences for Analysis Outcome. BIOINFORMATICS (2019)
Farhad Maleki, Katie L. Ovens, Daniel J. Hogan, Elham Rezaei, Alan M. Rosenberg, Anthony J. Kusalik
Measuring consistency among gene set analysis methods: A systematic study. J. Bioinform. Comput. Biol. 17 (5) (2019)
Yan Yan, Connor Burbridge, Jin-Hong Shi, Juxin Liu, Anthony J. Kusalik
Comparing Four Genome-Wide Association Study (GWAS) Programs with Varied Input Data Quantity. BIBM (2018)
Farhad Maleki, Katie L. Ovens, Ian McQuillan, Anthony J. Kusalik
Sample Size and Reproducibility of Gene Set Analysis. BIBM (2018)
Yan Yan, Anthony J. Kusalik, Fang-Xiang Wu
NovoExD: De novo Peptide Sequencing for ETD/ECD Spectra. IEEE ACM Trans. Comput. Biol. Bioinform. 14 (2) (2017)
Brett Trost, Scott Napper, Anthony J. Kusalik
Case study: using sequence homology to identify putative phosphorylation sites in an evolutionarily distant species (honeybee). Briefings Bioinform. 16 (5) (2015)
Yan Yan, Anthony J. Kusalik, Fang-Xiang Wu
NovoGMET: De Novo Peptide Sequencing Using Graphs with Multiple Edge Types (GMET) for ETD/ECD Spectra. ISBRA (2014)
Stephen Johnson, Brett Trost, Jeffrey R. Long, Vanessa Pittet, Anthony J. Kusalik
A better sequence-read simulator program for metagenomics. BMC Bioinform. 15 (S-9) (2014)
Yan Yan, Anthony J. Kusalik, Fang-Xiang Wu
NovoPair: De novo peptide sequencing for tandem mass spectra pair. BIBM (2014)
Jeffrey R. Long, Qingxiang Yan, Brett Trost, Anthony J. Kusalik
The UniFrac significance test generates different outputs given semantically equivalent inputs. BCB (2014)
Jeffrey R. Long, Vanessa Pittet, Brett Trost, Qingxiang Yan, David Vickers, Monique Haakensen, Anthony J. Kusalik
Equivalent input produces different output in the UniFrac significance test. BMC Bioinform. 15 (2014)
Brett Trost, Ryan Arsenault, Philip J. Griebel, Scott Napper, Anthony J. Kusalik
DAPPLE: a pipeline for the homology-based prediction of phosphorylation sites. Bioinform. 29 (13) (2013)
Yan Yan, Anthony J. Kusalik, Fang-Xiang Wu
A multi-edge graph based de novo peptide sequencing method for HCD spectra. BIBM (2013)
Brett Trost, Anthony J. Kusalik
Computational phosphorylation site prediction in plants using random forests and organism-specific instance weights. Bioinform. 29 (6) (2013)
Brett Trost, Anthony J. Kusalik
Computational prediction of eukaryotic phosphorylation sites. Bioinform. 27 (21) (2011)
Giovanni Capone, Giuseppe Novello, Candida Fasano, Brett Trost, Mikelis G. Bickis, Anthony J. Kusalik, Darja Kanduc
The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand. BMC Bioinform. 11 (2010)
Chushin Koh, Fang-Xiang Wu, Gopalan Selvaraj, Anthony J. Kusalik
Using a State-Space Model and Location Analysis to Infer Time-Delayed Regulatory Networks. EURASIP J. Bioinform. Syst. Biol. 2009 (2009)
Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik
On Determination of Minimum Sample Size for Discovery of Temporal Gene Expression Patterns. IMSCCS (1) (2006)
Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik
Determination of the minimum number of microarray experiments for discovery of gene expression patterns. BMC Bioinform. 7 (S-4) (2006)
Chenhong Zhang, Mikelis G. Bickis, Fang-Xiang Wu, Anthony J. Kusalik
Optimally-connected Hidden Markov Models for Predicting Mhc-binding Peptides. J. Bioinform. Comput. Biol. 4 (5) (2006)
Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik
Dynamic Model-based Clustering for Time-course Gene Expression Data. J. Bioinform. Comput. Biol. 3 (4) (2005)
Fang-Xiang Wu, Anthony J. Kusalik, Wen-Jun Zhang
Genetic Weighted K-means for Large-Scale Clustering Problems. FLAIRS Conference (2005)
Fang-Xiang Wu, Anthony J. Kusalik, Wen-Jun Zhang
A. Genetic Algorithm for Inferring Time Delays in Gene Regulatory Networks. CSB (2004)
Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik
Modeling Gene Expression from Microarray Expression Data with State-Space Equations. Pacific Symposium on Biocomputing (2004)
Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik
State-Space Model for Gene Regulatory Networks with Time Delays. CSB (2004)
Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik
Model-Based Clustering with Genes Expression Dynamics for Time-Course Gene Expression Data. BIBE (2004)
Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik
A Genetic K-means Clustering Algorithm Applied to Gene Expression Data. Canadian Conference on AI (2003)
Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik
Determination of the Minimum Sample Size in Microarray Experiments to Cluster Genes Using K-means Clustering. BIBE (2003)
Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik
An Algorithm to Reconstruct a Target DNA Sequence from Its Spectrum Connected at a Given Level. BIBE (2003)
Anthony J. Kusalik
Proceedings of the Eleventh Workshop on Logic Programming Environments (WLPE'01) CoRR (2001)
Alpesh Patel, Anthony J. Kusalik, Carl McCrosky
Area-Efficient VLSI Layouts for Binary Hypercubes. IEEE Trans. Computers 49 (2) (2000)
Mohammad Ashrafuzzaman, Anthony J. Kusalik
An Implementation Architecture for Orthogonally Persistent Deductive Object-Oriented Database Systems. IDEAS (1999)
Mireille Ducassé, Anthony J. Kusalik, Germán Puebla
Preface. Electron. Notes Theor. Comput. Sci. 30 (4) (1999)
Gregory M. Oster, Anthony J. Kusalik
Icola - Incremental Constraint-Based Graphics for Visualization. Constraints An Int. J. 3 (1) (1998)
Eric Neufeld, Anthony J. Kusalik, Michael Dobrohoczki
Visual Metaphors fro Understanding Logic Program Execution. Graphics Interface (1997)
Ahmad Ghazanfari, Anthony J. Kusalik, Joseph Irudayaraj
Application of a Multi-Structure Neural Network (MSNN) to Sorting Pistachio Nuts. Int. J. Neural Syst. 8 (1) (1997)
Anthony J. Kusalik, Eric Neufeld
Resolving Color Conflicts During Color Unification. LPE (1997)
Michael Dobrohoczki, Anthony J. Kusalik, Eric Neufeld
Colour Tagging for Prolog Visualization (Poster Abstract). JICSLP (1996)
Anthony J. Kusalik, Steven D. Prestwich
Visualizing Parallel Logic Program Execution for Performance Tuning. JICSLP (1996)
Steven D. Prestwich, Anthony J. Kusalik
High-Level Visualisation of Parallel Logic Program Execution. PARLE (1994)
Anthony J. Kusalik, Steven D. Prestwich
Programmer-Oriented Visualization of Parallel Logic Program Execution. LPE (1993)
Anthony J. Kusalik, Gregory M. Oster
Towards Generalized Visualization Support for Logic Programming. ICLP (1993)
Anthony J. Kusalik, Gregory M. Oster
A Constraint-Based Declarative Display Description Language for Visualization. LPE (1993)
Anthony J. Kusalik
Secondary storage in a concurrent logic programming environment. J. Syst. Softw. 11 (1) (1990)
Carl McCrosky, Anthony J. Kusalik
Improving First-Class Array Expressions Using Prolog. ICLP/SLP (1988)
Ian T. Foster, Anthony J. Kusalik
A Logical Treatment of Secondary Storage. SLP (1986)
Anthony J. Kusalik
Specification and Initialization of a Logic Computer System. New Gener. Comput. 4 (2) (1986)
Anthony J. Kusalik
Serialization of Process Reduction in Concurrent Prolog. New Gener. Comput. 2 (3) (1984)
Anthony J. Kusalik
Bounded-Wait Merge in Shapiro's Concurrent Prolog. New Gener. Comput. 2 (2) (1984)