Modeling Transcription Factor Binding Sites with Gibbs Sampling and Minimum Description Length Encoding. - Jonathan Schug; G. Christian Overton (ISMB, 1997)

Stability and reachability analysis of a hybrid model of luminescence in the marine bacterium Vibrio fischeri. - Calin Belta; Jonathan Schug; Thao Dang 001; Vijay Kumar 001; George J. Pappas; Harvey Rubin; Paul Dunlap (CDC, 2001)

A relational schema for both array-based and SAGE gene expression experiments. - Christian J. Stoeckert Jr.; Angel D. Pizarro; Elisabetta Manduchi; M. Gibson; Brian P. Brunk; Jonathan Crabtree; Jonathan Schug; Shai Shen-Orr; G. Christian Overton (Bioinform., 2001)

K2/Kleisli and GUS: Experiments in integrated access to genomic data sources. - Susan B. Davidson; Jonathan Crabtree; Brian P. Brunk; Jonathan Schug; Val Tannen; G. Christian Overton; Christian J. Stoeckert Jr. (IBM Syst. J., 2001)

Visual Programming for Modeling and Simulation of Biomolecular Regulatory Networks. - Rajeev Alur; Calin Belta; Franjo Ivancic; Vijay Kumar 001; Harvey Rubin; Jonathan Schug; Oleg Sokolsky; Jonathan Webb (HiPC, 2002)

Modeling and analyzing biomolecular networks. - Rajeev Alur; Calin Belta; Vijay Kumar 001; Max Mintz; George J. Pappas; Harvey Rubin; Jonathan Schug (Comput. Sci. Eng., 2002)

PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished). - Amit Bahl; Brian P. Brunk; Ross L. Coppel; Jonathan Crabtree; Sharon J. Diskin; Martin J. Fraunholz; Gregory R. Grant; Dinesh Gupta; Robert L. Huestis; Jessica C. Kissinger; Philip Labo; Li Li; et al. (Nucleic Acids Res., 2002)

PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data. - Amit Bahl; Brian P. Brunk; Jonathan Crabtree; Martin J. Fraunholz; Bindu Gajria; Gregory R. Grant; Hagai Ginsburg; Dinesh Gupta; Jessica C. Kissinger; Philip Labo; Li Li; Matthew D. Mailman; et al. (Nucleic Acids Res., 2003)

Data Integration and Pattern-Finding in Biological Sequence with TESS's Annotation Grammar and Extraction Language (AnGEL). - Jonathan Schug; Max Mintz; Christian J. Stoeckert Jr. (DILS, 2007)

EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes. - Joan M. Mazzarelli; John Brestelli; Regina K. Gorski; Junmin Liu; Elisabetta Manduchi; Deborah F. Pinney; Jonathan Schug; Peter White; Klaus H. Kaestner; Christian J. Stoeckert Jr. (Nucleic Acids Res., 2007)

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). - Gregory R. Grant; Michael H. Farkas; Angel D. Pizarro; Nicholas F. Lahens; Jonathan Schug; Brian P. Brunk; Christian J. Stoeckert Jr.; John B. Hogenesch; Eric A. Pierce (Bioinform., 2011)

Mitochondrial Genome Sequence Analysis: A custom bioinformatics pipeline substantially improves Affymetrix MitoChip v2.0 call rate and accuracy. - Hongbo M. Xie; Juan C. Perin; Theodore G. Schurr; Matthew C. Dulik; Sergey I. Zhadanov; Joseph A. Baur; Michael P. King; Emily Place; Colleen Clarke; Michael Grauer; Jonathan Schug; Avni Santani; et al. (BMC Bioinform., 2011)

Tissue-specific regulation of mouse MicroRNA genes in endoderm-derived tissues. - Yan Gao; Jonathan Schug; Lindsay B. McKenna; John Le Lay; Klaus H. Kaestner; Linda E. Greenbaum (Nucleic Acids Res., 2011)

Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus. - David E. Condon; Phu V. Tran; Yu-Chin Lien; Jonathan Schug; Michael K. Georgieff; Rebecca A. Simmons; Kyoung-Jae Won (BMC Bioinform., 2018)