Jonathan Arnold - researchr alias

researchr

You are not signed in
Sign in
Sign up

Viewing Publication 1 - 29 from 29

2024

Phylogenetic inference of inter-population transmission rates for infectious diseasesSkylar A Gay, Gregory Ellison, Jianing Xu, Jialin Yang, Yiliang Wei, Shaoyuan Wu, Lili Yu, Christopher C. Whalen, Jonathan Arnold, Liang Liu. bib, 25(4), 2024. [doi]

2022

Ensemble Methods for Identifying RNA Operons and Regulons in the Clock Network of Neurospora CrassaAhmad Al-Omari, James Griffith, Ashley Scruse, Robert W. Robinson, Heinz-Bernd Schüttler, Jonathan Arnold. access, 10:32510-32524, 2022. [doi]

2020

RTExtract: time-series NMR spectra quantification based on 3D surface ridge trackingYue Wu, Michael T. Judge, Jonathan Arnold, Suchendra M. Bhandarkar, Arthur Edison. bioinformatics, 36(20):5068-5075, 2020. [doi]

2019

Single Cells of Neurospora Crassa Show Circadian Oscillations, Light Entrainment, Temperature Compensation, and Phase SynchronizationZhaojie 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. access, 7:49403-49417, 2019. [doi]

2018

Discovering Regulators in Post-Transcriptional Control of the Biological Clock of $Neurospora~crassa$ Using Variable Topology Ensemble Methods on GPUsAhmad Al-Omari, James Griffith, Cristian Caranica, Thiab R. Taha, Heinz-Bernd Schüttler, Jonathan Arnold. access, 6:54582-54594, 2018. [doi]

2015

Discovering Regulatory Network Topologies Using Ensemble Methods on GPGPUs With Special Reference to the Biological Clock of Neurospora crassaAhmad Al-Omari, James Griffith, Michael Judge, Thiab R. Taha, Jonathan Arnold, Heinz-Bernd Schüttler. access, 3:27-42, 2015. [doi]

Secondary structural entropy in RNA switch (Riboswitch) identificationAmirhossein Manzourolajdad, Jonathan Arnold. bmcbi, 16:133, 2015. [doi]

2013

Solving Nonlinear Systems of First Order Ordinary Differential Equations Using a Galerkin Finite Element MethodAhmad Al-Omari, Heinz-Bernd Schüttler, Jonathan Arnold, Thiab R. Taha. access, 1:408-417, 2013. [doi]

Solving Large Nonlinear Systems of First-Order Ordinary Differential Equations With Hierarchical Structure Using Multi-GPGPUs and an Adaptive Runge Kutta ODE SolverAhmad Al-Omari, Jonathan Arnold, Thiab R. Taha, Heinz-Bernd Schüttler. access, 1:770-777, 2013. [doi]

2009

KINSOLVER: A simulator for computing large ensembles of biochemical and gene regulatory networksBoanerges Aleman-Meza, Yihai Yu, Heinz-Bernd Schüttler, Jonathan Arnold, Thiab R. Taha. cma, 57(3):420-435, 2009. [doi]

2008

Likelihood of a Particular Order of Genetic Markers and the Construction of Genetic MapsS. Tewari, Jonathan Arnold, Suchendra M. Bhandarkar. jbcb, 6(1):125-162, 2008. [doi]

2007

Design and Analysis of an Efficient Recursive Linking Algorithm for Constructing Likelihood Based Genetic Maps for a Large Number of MarkersS. Tewari, Suchendra M. Bhandarkar, Jonathan Arnold. jbcb, 5(2a):201-250, 2007. [doi]

2004

Quality of service for workflows and web service processesJorge Cardoso, Amit P. Sheth, John A. Miller, Jonathan Arnold, Krys Kochut. ws, 1(3):281-308, 2004. [doi]

2003

A Parallel Genetic Algorithm for Physical Mapping of ChromosomesSuchendra M. Bhandarkar, Jinling Huang, Jonathan Arnold. csb 2003: 567-572 [doi]

IntelliGEN: A Distributed Workflow System for Discovering Protein-Protein InteractionsKrys Kochut, Jonathan Arnold, Amit P. Sheth, John A. Miller, Eileen Kraemer, Ismailcem Budak Arpinar, Jorge Cardoso. dpd, 13(1):43-72, 2003.

2002

Parallel Monte Carlo Methods for Physical Mapping of ChromosonesSuchendra M. Bhandarkar, Jonathan Arnold. csb 2002: 64 [doi]

J3DV: A Java-based 3D database visualization toolXiang Fang, John A. Miller, Jonathan Arnold. SPE, 32(5):443-463, 2002.

2001

Physical mapping with automatic capture of hybridization dataDavid Hall, Suchendra M. Bhandarkar, Jonathan Arnold, Tongzhang Jiang. bioinformatics, 17(3):205-213, 2001.

An analysis of gene-finding programs for Neurospora crassaEileen Kraemer, Jian Wang, Jinhua Guo, Samuel Hopkins, Jonathan Arnold. bioinformatics, 17(10):901-912, 2001.

2000

Parallel Computation for Chromosome Reconstruction on a Cluster of WorkstationsSuchendra M. Bhandarkar, Salem Machaka, Sanjay Shete, Jonathan Arnold. ipps 2000: 63-70 [doi]

Reconstructing distances in physical maps of chromosomes with nonoverlapping probesJohn D. Kececioglu, Sanjay Shete, Jonathan Arnold. recomb 2000: 183-192 [doi]

1998

Parallel Computing for Chromosome Reconstruction via Ordering of DNA SequencesSuchendra M. Bhandarkar, Salem Machaka, Sridhar Chirravuri, Jonathan Arnold. pc, 24(8):1177-1204, 1998.

1996

PARODS - a study of parallel algorithms for ordering DNA sequencesSuchendra M. Bhandarkar, Sridhar Chirravuri, Jonathan Arnold. bioinformatics, 12(4):269-280, 1996.

Parallel Computing of Physical Maps--A Comparative Study in SIMD and MIMD ParallelismSuchendra M. Bhandarkar, Sridhar Chirravuri, Jonathan Arnold. jcb, 3(4):503-528, 1996.

1994

ODS_BOOTSTRAP: assessing the statistical reliability of physical maps by bootstrap resamplingYuhong Wang, Rolf A. Prade, James Griffith, William E. Timberlake, Jonathan Arnold. bioinformatics, 10(6):625-634, 1994.

1993

ODS: ordering DNA sequences - a physical mapping algorithm based on simulated annealingA. Jamie Cuticchia, Jonathan Arnold, William E. Timberlake. bioinformatics, 9(2):215-219, 1993.

PCAP: probe choice and analysis package - a set of programs to aid in choosing synthetic oligomers for contig mappingA. Jamie Cuticchia, Jonathan Arnold, William E. Timberlake. bioinformatics, 9(2):201-203, 1993.

Design of an Object-Oriented Database for Reverse GeneticsKrys Kochut, Jonathan Arnold, John A. Miller, Walter D. Potter. ismb 1993: 234-242

1992

CMAP: contig mapping and analysis package, a relational database for chromosome reconstructionA. Jamie Cuticchia, Jonathan Arnold, H. Brody, William E. Timberlake. bioinformatics, 8(5):467-474, 1992.

Sign in or sign up to see more results.

runs on WebDSL