On Parallel Search of DNA Sequence Databases. - Xiaojun Guan; Richard J. Mural; Reinhold Mann; Edward C. Uberbacher (PP, 1991)

An Improved System for Exon Recognition and Gene Modeling in Human DNA Sequence. - Yin Xu; J. Ralph Einstein; Richard J. Mural; Manesh J. Shah; Edward C. Uberbacher (ISMB, 1994)

Constructing gene models from accurately predicted exons: an application of dynamic programming. - Ying Xu 001; Richard J. Mural; Edward C. Uberbacher (Comput. Appl. Biosci., 1994)

Use of Neural Networks for Prediction of Graft Failure following Liver Transplantation. - Sherri Matis; Howard Doyle; Ignazio Marino; Richard J. Mural; Edward C. Uberbacher (CBMS, 1995)

Sequence comparison on a cluster of workstations using the PVM system. - Xiaojun Guan; Richard J. Mural; Edward C. Uberbacher (IPPS, 1995)

Predicting Protein Folding Classes without Overly Relying on Homology. - Mark Craven; Richard J. Mural; Loren J. Hauser; Edward C. Uberbacher (ISMB, 1995)

Correcting sequencing errors in DNA coding regions using a dynamic programming approach. - Ying Xu 001; Richard J. Mural; Edward C. Uberbacher (Comput. Appl. Biosci., 1995)

Gene Prediction by Pattern Recognition and Homology Search. - Ying Xu 001; Edward C. Uberbacher (ISMB, 1996)

Alignments of DNA and protein sequences containing frameshift errors. - Xiaojun Guan; Edward C. Uberbacher (Comput. Appl. Biosci., 1996)

A polynomial-time algorithm for a class of protein threading problems. - Ying Xu 001; Edward C. Uberbacher (Comput. Appl. Biosci., 1996)

Detection of RNA Polymerase II Promoters and Polyadenylation Sites in Human DNA Sequence. - Sherri Matis; Ying Xu 001; Manesh J. Shah; Xiaojun Guan; J. Ralph Einstein; Richard J. Mural; Edward C. Uberbacher (Comput. Chem., 1996)

An Iterative Algorithm for Correcting Sequencing Errors in DNA Coding Regions. - Ying Xu 001; Richard J. Mural; Edward C. Uberbacher (J. Comput. Biol., 1996)

GRAIL: a multi-agent neural network system for gene identification. - Ying Xu 001; Richard J. Mural; J. Ralph Einstein; Manesh B. Shah; Edward C. Uberbacher (Proc. IEEE, 1996)

Inferring Gene Structures in Genomic Sequences Using Pattern Recognition and Expressed Sequence Tags. - Ying Xu 001; Richard J. Mural; Edward C. Uberbacher (ISMB, 1997)

Reference-based gene model prediction on DNA contigs (extended abstract). - Ying Xu 001; Edward C. Uberbacher (RECOMB, 1997)

2D image segmentation using minimum spanning trees. - Ying Xu 001; Edward C. Uberbacher (Image Vis. Comput., 1997)

Automated Gene Identification in Large-Scale Genomic Sequences. - Ying Xu 001; Edward C. Uberbacher (J. Comput. Biol., 1997)

A new method for modeling and solving the protein fold recognition problem (extended abstract). - Ying Xu 001; Dong Xu 002; Edward C. Uberbacher (RECOMB, 1998)

An Efficient Computational Method for Globally Optimal Threading. - Ying Xu 001; Dong Xu 002; Edward C. Uberbacher (J. Comput. Biol., 1998)

A segmentation algorithm for noisy images: Design and evaluation. - Ying Xu 001; Victor Olman; Edward C. Uberbacher (Pattern Recognit. Lett., 1998)

Sequence-structure specificity of a knowledge based energy function at the secondary structure level. - Dong Xu 002; Michael A. Unseren; Ying Xu 001; Edward C. Uberbacher (Bioinform., 2000)

Stepping Up the Pace of Discovery: the Genomes to Life Program. - Marvin Frazier; David Thomassen; Aristides Patrinos; Gary Johnson; Carl Edward Oliver; Edward C. Uberbacher (CSB, 2003)

A Computational Method for Assessing Peptide-Identification Reliability in Tandem Mass Spectrometry Analysis with SEQUEST. - Jane Razumovskaya; Victor Olman; Dong Xu 002; Edward C. Uberbacher; Nathan Verberkmoes; Ying Xu 001 (CSB, 2003)

Computing for the DOE Genomes to Life Program. - Edward C. Uberbacher; David Thomassen; Aristides Patrinos; Gary Johnson; Carl Edward Oliver; Marvin Frazier (CSB, 2003)

Background rareness-based iterative multiple sequence alignment algorithm for regulatory element detection. - Chandrasegaran Narasimhan; Philip F. LoCascio; Edward C. Uberbacher (Bioinform., 2003)

Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions. - Tatiana V. Karpinets; Margaret F. Romine; Denise Schmoyer; Guruprasad Kora; Mustafa H. Syed; Michael R. Leuze; Margrethe H. Serres; Byung-Hoon Park; Nagiza F. Samatova; Edward C. Uberbacher (Database J. Biol. Databases Curation, 2010)

Gene and translation initiation site prediction in metagenomic sequences. - Doug Hyatt; Philip F. LoCascio; Loren J. Hauser; Edward C. Uberbacher (Bioinform., 2012)

BESC knowledgebase public portal. - Mustafa H. Syed; Tatiana V. Karpinets; Morey Parang; Michael R. Leuze; Byung-Hoon Park; Doug Hyatt; Steven D. Brown; Steve Moulton; Michael D. Galloway; Edward C. Uberbacher (Bioinform., 2012)

MicroRNAs Form Triplexes with Double Stranded DNA at Sequence-Specific Binding Sites; a Eukaryotic Mechanism via which microRNAs Could Directly Alter Gene Expression. - Steven W. Paugh; David R. Coss; Ju Bao; Lucas T. Laudermilk; Christy R. Grace; Antonio M. Ferreira; M. Brett Waddell; Granger Ridout; Deanna Naeve; Michael R. Leuze; Philip F. LoCascio; John C. Panetta; et al. (PLoS Comput. Biol., 2016)