Jonathan Arnold

Publication Activity (10 Years)

Years Active: 1992-2024
Publications (10 Years): 6

Top Topics

Prediction Accuracy

Infectious Disease

Ensemble Methods

Top Venues

Briefings Bioinform.

Publications

Skylar A Gay, Gregory Ellison, Jianing Xu, Jialin Yang, Yiliang Wei, Shaoyuan Wu, Lili Yu, Christopher C. Whalen, Jonathan Arnold, Liang Liu
Phylogenetic inference of inter-population transmission rates for infectious diseases. Briefings Bioinform. 25 (4) (2024)
Yue Wu, Michael T. Judge, Jonathan Arnold, Suchendra M. Bhandarkar, Arthur Edison
RTExtract: time-series NMR spectra quantification based on 3D surface ridge tracking. Bioinform. 36 (20) (2020)
Zhaojie Deng, Jia Hwei Cheong, Cristian Caranica, Lingyun Wu, Xiao Qiu, Michael T. Judge, Brooke Hull, Carmen Rodriguez, James Griffith, Ahmad Al-Omari, Sam Arsenault, Heinz-Bernd Schüttler, Leidong Mao, Jonathan Arnold
Single Cells of Neurospora Crassa Show Circadian Oscillations, Light Entrainment, Temperature Compensation, and Phase Synchronization. IEEE Access 7 (2019)
Ahmad Al-Omari, James Griffith, Cristian Caranica, Thiab R. Taha, Heinz-Bernd Schüttler, Jonathan Arnold
Discovering Regulators in Post-Transcriptional Control of the Biological Clock of $Neurospora~crassa$ Using Variable Topology Ensemble Methods on GPUs. IEEE Access 6 (2018)
Amirhossein Manzourolajdad, Jonathan Arnold
Secondary structural entropy in RNA switch (Riboswitch) identification. BMC Bioinform. 16 (2015)
Ahmad Al-Omari, James Griffith, Michael T. Judge, Thiab R. Taha, Jonathan Arnold, Heinz-Bernd Schüttler
Discovering Regulatory Network Topologies Using Ensemble Methods on GPGPUs With Special Reference to the Biological Clock of Neurospora crassa. IEEE Access 3 (2015)
Ahmad Al-Omari, Heinz-Bernd Schüttler, Jonathan Arnold, Thiab R. Taha
Solving Nonlinear Systems of First Order Ordinary Differential Equations Using a Galerkin Finite Element Method. IEEE Access 1 (2013)
Ahmad Al-Omari, Jonathan Arnold, Thiab R. Taha, Heinz-Bernd Schüttler
Solving Large Nonlinear Systems of First-Order Ordinary Differential Equations With Hierarchical Structure Using Multi-GPGPUs and an Adaptive Runge Kutta ODE Solver. IEEE Access 1 (2013)
Boanerges Aleman-Meza, Yihai Yu, Heinz-Bernd Schüttler, Jonathan Arnold, Thiab R. Taha
KINSOLVER: A simulator for computing large ensembles of biochemical and gene regulatory networks. Comput. Math. Appl. 57 (3) (2009)
Susanta Tewari, Jonathan Arnold, Suchendra M. Bhandarkar
Likelihood of a Particular Order of Genetic Markers and the Construction of Genetic Maps. J. Bioinform. Comput. Biol. 6 (1) (2008)
Susanta Tewari, Suchendra M. Bhandarkar, Jonathan Arnold
Design and Analysis of an Efficient Recursive Linking Algorithm for Constructing Likelihood Based Genetic Maps for a Large Number of Markers. J. Bioinform. Comput. Biol. 5 (2a) (2007)
Jorge Cardoso, Amit P. Sheth, John A. Miller, Jonathan Arnold, Krys J. Kochut
Quality of service for workflows and web service processes. J. Web Semant. 1 (3) (2004)
Krys J. Kochut, Jonathan Arnold, Amit P. Sheth, John A. Miller, Eileen T. Kraemer, Ismailcem Budak Arpinar, Jorge Cardoso
IntelliGEN: A Distributed Workflow System for Discovering Protein-Protein Interactions. Distributed Parallel Databases 13 (1) (2003)
Suchendra M. Bhandarkar, Jinling Huang, Jonathan Arnold
A Parallel Genetic Algorithm for Physical Mapping of Chromosomes. CSB (2003)
Xiang Fang, John A. Miller, Jonathan Arnold
J3DV: A Java-based 3D database visualization tool. Softw. Pract. Exp. 32 (5) (2002)
Suchendra M. Bhandarkar, Jonathan Arnold
Parallel Monte Carlo Methods for Physical Mapping of Chromosones. CSB (2002)
David Hall, Suchendra M. Bhandarkar, Jonathan Arnold, Tongzhang Jiang
Physical mapping with automatic capture of hybridization data. Bioinform. 17 (3) (2001)
Eileen T. Kraemer, Jian Wang, Jinhua Guo, Samuel Hopkins, Jonathan Arnold
An analysis of gene-finding programs for Neurospora crassa. Bioinform. 17 (10) (2001)
John D. Kececioglu, Sanjay Shete, Jonathan Arnold
Reconstructing distances in physical maps of chromosomes with nonoverlapping probes. RECOMB (2000)
Suchendra M. Bhandarkar, Salem Machaka, Sanjay Shete, Jonathan Arnold
Parallel Computation for Chromosome Reconstruction on a Cluster of Workstations. IPDPS (2000)
Suchendra M. Bhandarkar, Salem Machaka, Sridhar Chirravuri, Jonathan Arnold
Parallel Computing for Chromosome Reconstruction via Ordering of DNA Sequences. Parallel Comput. 24 (8) (1998)
Suchendra M. Bhandarkar, Sridhar Chirravuri, Jonathan Arnold
PARODS - a study of parallel algorithms for ordering DNA sequences. Comput. Appl. Biosci. 12 (4) (1996)
Suchendra M. Bhandarkar, Sridhar Chirravuri, Jonathan Arnold
Parallel Computing of Physical Maps--A Comparative Study in SIMD and MIMD Parallelism. J. Comput. Biol. 3 (4) (1996)
Yuhong Wang, Rolf A. Prade, James Griffith, William E. Timberlake, Jonathan Arnold
ODS_BOOTSTRAP: assessing the statistical reliability of physical maps by bootstrap resampling. Comput. Appl. Biosci. 10 (6) (1994)
Krys J. Kochut, Jonathan Arnold, John A. Miller, Walter D. Potter
Design of an Object-Oriented Database for Reverse Genetics. ISMB (1993)
Momiao Xiong, Jonathan Arnold, Hubert J. Chen
A neural network model based on differential-algebraic equations for nonlinear programming. ICNN (1993)
A. Jamie Cuticchia, Jonathan Arnold, William E. Timberlake
PCAP: probe choice and analysis package - a set of programs to aid in choosing synthetic oligomers for contig mapping. Comput. Appl. Biosci. 9 (2) (1993)
A. Jamie Cuticchia, Jonathan Arnold, William E. Timberlake
ODS: ordering DNA sequences - a physical mapping algorithm based on simulated annealing. Comput. Appl. Biosci. 9 (2) (1993)
A. Jamie Cuticchia, Jonathan Arnold, H. Brody, William E. Timberlake
CMAP: contig mapping and analysis package, a relational database for chromosome reconstruction. Comput. Appl. Biosci. 8 (5) (1992)