Anthony J. Kusalik

62 papers B 2C 4Misc 3Journal 26Unranked 22

Year	Rank	Type	Title / Venue / Authors
2024	—	`conf`	Discovering Knowledge Embedded in Gene Set Databases: A Mathematical Modelling Approach. ICCBB Katie L. Ovens, Ebunoluwa Makinde, Samuel Horovatin, Elham Rezaei, Alan M. Rosenberg, Lingling Jin, Ian McQuillan, Anthony J. Kusalik, Farhad Maleki
2023	J	`jnl`	NMTF-DTI: A Nonnegative Matrix Tri-factorization Approach With Multiple Kernel Fusion for Drug-Target Interaction Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. Ali Akbar Jamali, Anthony J. Kusalik, Fang-Xiang Wu
2021	J	`jnl`	EPIphany - A Platform for Analysis and Visualization of Peptide Immunoarray Data. Frontiers Bioinform. Zoe Parker Cates, Antonio Facciuolo, Daniel J. Hogan, Philip J. Griebel, Scott Napper, Anthony J. Kusalik
2020	J	`jnl`	MDIPA: a microRNA-drug interaction prediction approach based on non-negative matrix factorization. Bioinform. Ali Akbar Jamali, Anthony J. Kusalik, Fang-Xiang Wu
2019	J	`jnl`	Antimicrobial resistance genetic factor identification from whole-genome sequence data using deep feature selection. BMC Bioinform. Jin-Hong Shi, Yan Yan, Matthew G. Links, Longhai Li, Jo-Anne R. Dillon, Michael Horsch, Anthony J. Kusalik
2019	J	`jnl`	Effects of input data quantity on genome-wide association studies (GWAS). Int. J. Data Min. Bioinform. Yan Yan, Connor Burbridge, Jin-Hong Shi, Juxin Liu, Anthony J. Kusalik
2019	—	`conf`	Gene Set Databases: A Fountain of Knowledge or a Siren Call? BCB Farhad Maleki, Katie L. Ovens, Ian McQuillan, Elham Rezaei, Alan M. Rosenberg, Anthony J. Kusalik
2019	—	`conf`	Gene Set Overlap: An Impediment to Achieving High Specificity in Over-representation Analysis. BIOINFORMATICS Farhad Maleki, Anthony J. Kusalik
2019	J	`jnl`	Measuring consistency among gene set analysis methods: A systematic study. J. Bioinform. Comput. Biol. Farhad Maleki, Katie L. Ovens, Daniel J. Hogan, Elham Rezaei, Alan M. Rosenberg, Anthony J. Kusalik
2019	—	`conf`	Method Choice in Gene Set Analysis Has Important Consequences for Analysis Outcome. BIOINFORMATICS Farhad Maleki, Katie L. Ovens, Elham Rezaei, Alan M. Rosenberg, Anthony J. Kusalik
2018	—	`conf`	Comparing Four Genome-Wide Association Study (GWAS) Programs with Varied Input Data Quantity. BIBM Yan Yan, Connor Burbridge, Jin-Hong Shi, Juxin Liu, Anthony J. Kusalik
2018	—	`conf`	Sample Size and Reproducibility of Gene Set Analysis. BIBM Farhad Maleki, Katie L. Ovens, Ian McQuillan, Anthony J. Kusalik
2017	J	`jnl`	NovoExD: De novo Peptide Sequencing for ETD/ECD Spectra. IEEE ACM Trans. Comput. Biol. Bioinform. Yan Yan, Anthony J. Kusalik, Fang-Xiang Wu
2015	J	`jnl`	Case study: using sequence homology to identify putative phosphorylation sites in an evolutionarily distant species (honeybee). Briefings Bioinform. Brett Trost, Scott Napper, Anthony J. Kusalik
2014	J	`jnl`	A better sequence-read simulator program for metagenomics. BMC Bioinform. Stephen Johnson, Brett Trost, Jeffrey R. Long, Vanessa Pittet, Anthony J. Kusalik
2014	J	`jnl`	Equivalent input produces different output in the UniFrac significance test. BMC Bioinform. Jeffrey R. Long, Vanessa Pittet, Brett Trost, Qingxiang Yan, David Vickers, Monique Haakensen, Anthony J. Kusalik
2014	—	`conf`	NovoGMET: De Novo Peptide Sequencing Using Graphs with Multiple Edge Types (GMET) for ETD/ECD Spectra. ISBRA Yan Yan, Anthony J. Kusalik, Fang-Xiang Wu
2014	—	`conf`	NovoPair: De novo peptide sequencing for tandem mass spectra pair. BIBM Yan Yan, Anthony J. Kusalik, Fang-Xiang Wu
2014	—	`conf`	The UniFrac significance test generates different outputs given semantically equivalent inputs. BCB Jeffrey R. Long, Qingxiang Yan, Brett Trost, Anthony J. Kusalik
2013	—	`conf`	A multi-edge graph based de novo peptide sequencing method for HCD spectra. BIBM Yan Yan, Anthony J. Kusalik, Fang-Xiang Wu
2013	J	`jnl`	Computational phosphorylation site prediction in plants using random forests and organism-specific instance weights. Bioinform. Brett Trost, Anthony J. Kusalik
2013	J	`jnl`	DAPPLE: a pipeline for the homology-based prediction of phosphorylation sites. Bioinform. Brett Trost, Ryan Arsenault, Philip J. Griebel, Scott Napper, Anthony J. Kusalik
2011	J	`jnl`	Computational prediction of eukaryotic phosphorylation sites. Bioinform. Brett Trost, Anthony J. Kusalik
2010	J	`jnl`	The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand. BMC Bioinform. Giovanni Capone, Giuseppe Novello, Candida Fasano, Brett Trost, Mikelis G. Bickis, Anthony J. Kusalik, Darja Kanduc
2009	J	`jnl`	Using a State-Space Model and Location Analysis to Infer Time-Delayed Regulatory Networks. EURASIP J. Bioinform. Syst. Biol. Chushin Koh, Fang-Xiang Wu, Gopalan Selvaraj, Anthony J. Kusalik
2006	J	`jnl`	Determination of the minimum number of microarray experiments for discovery of gene expression patterns. BMC Bioinform. Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik
2006	—	`conf`	On Determination of Minimum Sample Size for Discovery of Temporal Gene Expression Patterns. IMSCCS (1) Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik
2006	J	`jnl`	Optimally-connected Hidden Markov Models for Predicting Mhc-binding Peptides. J. Bioinform. Comput. Biol. Chenhong Zhang, Mikelis G. Bickis, Fang-Xiang Wu, Anthony J. Kusalik
2005	J	`jnl`	Dynamic Model-based Clustering for Time-course Gene Expression Data. J. Bioinform. Comput. Biol. Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik
2005	Misc	`conf`	Genetic Weighted K-means for Large-Scale Clustering Problems. FLAIRS Fang-Xiang Wu, Anthony J. Kusalik, Wen-Jun Zhang
2004	—	`conf`	A. Genetic Algorithm for Inferring Time Delays in Gene Regulatory Networks. CSB Fang-Xiang Wu, Anthony J. Kusalik, Wen-Jun Zhang
2004	C	`conf`	Model-Based Clustering with Genes Expression Dynamics for Time-Course Gene Expression Data. BIBE Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik
2004	Misc	`conf`	Modeling Gene Expression from Microarray Expression Data with State-Space Equations. Pacific Symposium on Biocomputing Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik
2004	—	`conf`	State-Space Model for Gene Regulatory Networks with Time Delays. CSB Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik
2003	Misc	`conf`	A Genetic K-means Clustering Algorithm Applied to Gene Expression Data. AI Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik
2003	C	`conf`	An Algorithm to Reconstruct a Target DNA Sequence from Its Spectrum Connected at a Given Level. BIBE Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik
2003	C	`conf`	Determination of the Minimum Sample Size in Microarray Experiments to Cluster Genes Using K-means Clustering. BIBE Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik
2001	J	`jnl`	Proceedings of the Eleventh Workshop on Logic Programming Environments (WLPE'01) CoRR Anthony J. Kusalik
2001	—	`ed.`	Proceedings of the Eleventh Workshop on Logic Programming Environments (WLPE'01), Paphos, Cyprus, December 1, 2001 LPE Anthony J. Kusalik
2000	J	`jnl`	Area-Efficient VLSI Layouts for Binary Hypercubes. IEEE Trans. Computers Alpesh Patel, Anthony J. Kusalik, Carl McCrosky
1999	C	`conf`	An Implementation Architecture for Orthogonally Persistent Deductive Object-Oriented Database Systems. IDEAS Mohammad Ashrafuzzaman, Anthony J. Kusalik
1999	—	`conf`	Preface. WLPE@ICLP Mireille Ducassé, Anthony J. Kusalik, Germán Puebla
1999	—	`ed.`	Tenth Workshop on Logic Programming Environments, WLPE 1999, in connection with the International Conference on Logic Programming, ICLP 1999, Las Cruces, New Mexico, USA, Nobember 29, 1999 WLPE@ICLP Mireille Ducassé, Anthony J. Kusalik, Germán Puebla
1998	J	`jnl`	Icola - Incremental Constraint-Based Graphics for Visualization. Constraints An Int. J. Gregory M. Oster, Anthony J. Kusalik
1997	J	`jnl`	Application of a Multi-Structure Neural Network (MSNN) to Sorting Pistachio Nuts. Int. J. Neural Syst. Ahmad Ghazanfari, Anthony J. Kusalik, Joseph Irudayaraj
1997	—	`ed.`	Proceedings of the 8th Workshop on Logic Programming Environments, LPE '97, post-conference workshop at ICLP 1997, Leuven, Belgium, July 11, 1997 LPE Anthony J. Kusalik, Mireille Ducassé, Ulrich Neumerkel
1997	—	`conf`	Resolving Color Conflicts During Color Unification. LPE Anthony J. Kusalik, Eric Neufeld
1997	B	`conf`	Visual Metaphors fro Understanding Logic Program Execution. Graphics Interface Eric Neufeld, Anthony J. Kusalik, Michael Dobrohoczki
1996	—	`conf`	Colour Tagging for Prolog Visualization (Poster Abstract). JICSLP Michael Dobrohoczki, Anthony J. Kusalik, Eric Neufeld
1996	—	`conf`	Visualizing Parallel Logic Program Execution for Performance Tuning. JICSLP Anthony J. Kusalik, Steven D. Prestwich
1995	—	`ed.`	Proceedings of the 7th Workshop on Logic Programming Environments, LPR '95, in conjunction with ILPS '95, Portland, Oregon, USA, December 8, 1995 LPE Markus P. J. Fromherz, Marc Kirschenbaum, Anthony J. Kusalik
1994	—	`conf`	High-Level Visualisation of Parallel Logic Program Execution. PARLE Steven D. Prestwich, Anthony J. Kusalik
1993	—	`conf`	A Constraint-Based Declarative Display Description Language for Visualization. LPE Anthony J. Kusalik, Gregory M. Oster
1993	—	`conf`	Programmer-Oriented Visualization of Parallel Logic Program Execution. LPE Anthony J. Kusalik, Steven D. Prestwich
1993	B	`conf`	Towards Generalized Visualization Support for Logic Programming. ICLP Anthony J. Kusalik, Gregory M. Oster
1990	—	`ed.`	Proceedings of the ICLP 1990 Workshop on Logic Programming Environments, Eilat, Israel, June 16, 1990. Technical Report, ECRC IR-LP-31-25 LPE Mireille Ducassé, Anna-Maria Emde, Anthony J. Kusalik, Jacob Levy
1990	J	`jnl`	Secondary storage in a concurrent logic programming environment. J. Syst. Softw. Anthony J. Kusalik
1988	—	`conf`	Improving First-Class Array Expressions Using Prolog. ICLP/SLP Carl McCrosky, Anthony J. Kusalik
1986	—	`conf`	A Logical Treatment of Secondary Storage. SLP Ian T. Foster, Anthony J. Kusalik
1986	J	`jnl`	Specification and Initialization of a Logic Computer System. New Gener. Comput. Anthony J. Kusalik
1984	J	`jnl`	Bounded-Wait Merge in Shapiro's Concurrent Prolog. New Gener. Comput. Anthony J. Kusalik
1984	J	`jnl`	Serialization of Process Reduction in Concurrent Prolog. New Gener. Comput. Anthony J. Kusalik