Jonathan P. Arnold

32 papers A 2B 1Journal 26Unranked 3
YearRankTypeTitle / Venue / Authors
2025 J jnl
MINE: a new way to design genetics experiments for discovery.
Briefings Bioinform.
Isaac Torres, Shufan Zhang, Amanda Bouffier, Michael Skaro, Yue Wu, Lauren Stupp, Jonathan P. Arnold, Y. Anny Chung, Heinz-Bernd Schüttler
2022 J jnl
Ensemble Methods for Identifying RNA Operons and Regulons in the Clock Network of Neurospora Crassa.
IEEE Access
Ahmad Al-Omari, James Griffith, Ashley Scruse, Robert W. Robinson, Heinz-Bernd Schüttler, Jonathan P. Arnold
2020 J jnl
RTExtract: time-series NMR spectra quantification based on 3D surface ridge tracking.
Bioinform.
Yue Wu, Michael T. Judge, Jonathan P. Arnold, Suchendra M. Bhandarkar, Arthur Edison
2019 J jnl
Single Cells of Neurospora Crassa Show Circadian Oscillations, Light Entrainment, Temperature Compensation, and Phase Synchronization.
IEEE Access
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 P. Arnold
2018 J jnl
Discovering Regulators in Post-Transcriptional Control of the Biological Clock of $Neurospora~crassa$ Using Variable Topology Ensemble Methods on GPUs.
IEEE Access
Ahmad Al-Omari, James Griffith, Cristian Caranica, Thiab R. Taha, Heinz-Bernd Schüttler, Jonathan P. Arnold
2015 J jnl
Discovering Regulatory Network Topologies Using Ensemble Methods on GPGPUs With Special Reference to the Biological Clock of Neurospora crassa.
IEEE Access
Ahmad Al-Omari, James Griffith, Michael T. Judge, Thiab R. Taha, Jonathan P. Arnold, Heinz-Bernd Schüttler
2015 J jnl
Secondary structural entropy in RNA switch (Riboswitch) identification.
BMC Bioinform.
Amirhossein Manzourolajdad, Jonathan P. Arnold
2013 J jnl
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
Ahmad Al-Omari, Jonathan P. Arnold, Thiab R. Taha, Heinz-Bernd Schüttler
2013 J jnl
Solving Nonlinear Systems of First Order Ordinary Differential Equations Using a Galerkin Finite Element Method.
IEEE Access
Ahmad Al-Omari, Heinz-Bernd Schüttler, Jonathan P. Arnold, Thiab R. Taha
2009 J jnl
KINSOLVER: A simulator for computing large ensembles of biochemical and gene regulatory networks.
Comput. Math. Appl.
Boanerges Aleman-Meza, Yihai Yu, Heinz-Bernd Schüttler, Jonathan P. Arnold, Thiab R. Taha
2008 J jnl
Likelihood of a Particular Order of Genetic Markers and the Construction of Genetic Maps.
J. Bioinform. Comput. Biol.
Susanta Tewari, Jonathan P. Arnold, Suchendra M. Bhandarkar
2007 J jnl
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.
Susanta Tewari, Suchendra M. Bhandarkar, Jonathan P. Arnold
2004 J jnl
Quality of service for workflows and web service processes.
J. Web Semant.
Jorge Cardoso, Amit P. Sheth, John A. Miller, Jonathan P. Arnold, Krys J. Kochut
2003 — conf
A Parallel Genetic Algorithm for Physical Mapping of Chromosomes.
CSB
Suchendra M. Bhandarkar, Jinling Huang, Jonathan P. Arnold
2003 J jnl
IntelliGEN: A Distributed Workflow System for Discovering Protein-Protein Interactions.
Distributed Parallel Databases
Krys J. Kochut, Jonathan P. Arnold, Amit P. Sheth, John A. Miller, Eileen T. Kraemer, Ismailcem Budak Arpinar, Jorge Cardoso
2002 J jnl
J3DV: A Java-based 3D database visualization tool.
Softw. Pract. Exp.
Xiang Fang, John A. Miller, Jonathan P. Arnold
2002 — conf
Parallel Monte Carlo Methods for Physical Mapping of Chromosones.
CSB
Suchendra M. Bhandarkar, Jonathan P. Arnold
2001 J jnl
An analysis of gene-finding programs for Neurospora crassa.
Bioinform.
Eileen T. Kraemer, Jian Wang, Jinhua Guo, Samuel Hopkins, Jonathan P. Arnold
2001 J jnl
Physical mapping with automatic capture of hybridization data.
Bioinform.
David Hall, Suchendra M. Bhandarkar, Jonathan P. Arnold, Tongzhang Jiang
2000 A conf
Parallel Computation for Chromosome Reconstruction on a Cluster of Workstations.
IPDPS
Suchendra M. Bhandarkar, Salem Machaka, Sanjay Shete, Jonathan P. Arnold
2000 B conf
Reconstructing distances in physical maps of chromosomes with nonoverlapping probes.
RECOMB
John D. Kececioglu, Sanjay Shete, Jonathan P. Arnold
1998 J jnl
Parallel Computing for Chromosome Reconstruction via Ordering of DNA Sequences.
Parallel Comput.
Suchendra M. Bhandarkar, Salem Machaka, Sridhar Chirravuri, Jonathan P. Arnold
1996 J jnl
PARODS - a study of parallel algorithms for ordering DNA sequences.
Comput. Appl. Biosci.
Suchendra M. Bhandarkar, Sridhar Chirravuri, Jonathan P. Arnold
1996 J jnl
Parallel Computing of Physical Maps--A Comparative Study in SIMD and MIMD Parallelism.
J. Comput. Biol.
Suchendra M. Bhandarkar, Sridhar Chirravuri, Jonathan P. Arnold
1994 J jnl
ODS_BOOTSTRAP: assessing the statistical reliability of physical maps by bootstrap resampling.
Comput. Appl. Biosci.
Yuhong Wang, Rolf A. Prade, James Griffith, William E. Timberlake, Jonathan P. Arnold
1993 — conf
A neural network model based on differential-algebraic equations for nonlinear programming.
ICNN
Momiao Xiong, Jonathan P. Arnold, Hubert J. Chen
1993 A conf
Design of an Object-Oriented Database for Reverse Genetics.
ISMB
Krys J. Kochut, Jonathan P. Arnold, John A. Miller, Walter D. Potter
1993 J jnl
ODS: ordering DNA sequences - a physical mapping algorithm based on simulated annealing.
Comput. Appl. Biosci.
A. Jamie Cuticchia, Jonathan P. Arnold, William E. Timberlake
1993 J jnl
PCAP: probe choice and analysis package - a set of programs to aid in choosing synthetic oligomers for contig mapping.
Comput. Appl. Biosci.
A. Jamie Cuticchia, Jonathan P. Arnold, William E. Timberlake
1992 J jnl
CMAP: contig mapping and analysis package, a relational database for chromosome reconstruction.
Comput. Appl. Biosci.
A. Jamie Cuticchia, Jonathan P. Arnold, H. Brody, William E. Timberlake
1988 J jnl
Herbert O. Yardley, Gangbuster.
Cryptologia
Jonathan P. Arnold
1986 J jnl
A comprehensive package for DNA sequence analysis in FORTRAN IV for the PDP-11.
Nucleic Acids Res.
Jonathan P. Arnold, Virginia K. Eckenrode, Klaus Lemke, Gregory J. Phillips, Stephen W. Schaeffer