hipFG: high-throughput harmonization and integration pipeline for functional genomics data.
Bioinform., November, 2023
Omnibus and robust deconvolution scheme for bulk RNA sequencing data integrating multiple single-cell reference sets and prior biological knowledge.
Bioinform., 2022
SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants.
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Bioinform., 2020
VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project.
Bioinform., 2019
VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project.
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Bioinform., 2019
DASHR 2.0: integrated database of human small non-coding RNA genes and mature products.
Bioinform., 2019
SPAR: small RNA-seq portal for analysis of sequencing experiments.
Nucleic Acids Res., 2018
Integrative DNA copy number detection and genotyping from sequencing and array-based platforms.
Bioinform., 2018
Functional annotation of genomic variants in studies of late-onset Alzheimer's disease.
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Bioinform., 2018
DASHR: database of small human noncoding RNAs.
Nucleic Acids Res., 2016
A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer).
BMC Bioinform., 2016
PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.
J. Comput. Biol., 2015
HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements.
Bioinform., 2015
DRAW+SneakPeek: Analysis workflow and quality metric management for DNA-seq experiments.
Bioinform., 2013
SAVoR: a server for sequencing annotation and visualization of RNA structures.
Nucleic Acids Res., 2012
DACTAL: divide-and-conquer trees (almost) without alignments.
Bioinform., 2012
The Impact of Multiple Protein Sequence Alignment on Phylogenetic Estimation.
IEEE ACM Trans. Comput. Biol. Bioinform., 2011
Invited: Multiclass RNA function classification using next-generation sequencing.
Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, 2011
Correcting population stratification in genetic association studies using a phylogenetic approach.
Bioinform., 2010
A Bayesian approach to efficient differential allocation for resampling-based significance testing.
BMC Bioinform., 2009
Distance-based genome rearrangement phylogeny.
Proceedings of the Mathematics of Evolution and Phylogeny., 2007
Reconstructing Chromosomal Evolution.
SIAM J. Comput., 2006
Weighted isotonic regression under the <i>L</i><sub>1</sub> norm.
Proceedings of the Seventeenth Annual ACM-SIAM Symposium on Discrete Algorithms, 2006
Dense subgraph computation via stochastic search: application to detect transcriptional modules.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006
Transcriptional Target Prediction Using Qualitative Reasoning.
Proceedings of the 28th International Conference of the IEEE Engineering in Medicine and Biology Society, 2006
Phylogenetic Networks: Properties and Relationship to Trees and Clusters.
Trans. Comp. Sys. Biology, 2005
An Interaction-Dependent Model for Transcription Factor Binding.
Proceedings of the Systems Biology and Regulatory Genomics, 2005
Enhanced position weight matrices using mixture models.
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005
Phylogenetic Networks, Trees, and Clusters.
Proceedings of the Computational Science, 2005
RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer.
Proceedings of the Computing and Combinatorics, 11th Annual International Conference, 2005
Improving Genome Rearrangement Phylogeny Using Sequence-Style Parsimony.
Proceedings of the Fifth IEEE International Symposium on Bioinformatic and Bioengineering (BIBE 2005), 2005
Genome Identification and Classification by Short Oligo Arrays.
Proceedings of the Algorithms in Bioinformatics, 4th International Workshop, 2004
Analyzing the Order of Items in Manuscripts of <i>The Canterbury Tales</i>.
Comput. Humanit., 2003
Steps toward accurate reconstructions of phylogenies from gene-order data.
J. Comput. Syst. Sci., 2002
Toward New Software for Computational Phylogenetics.
Computer, 2002
Genome Rearrangement Phylogeny Using Weighbor.
Proceedings of the Algorithms in Bioinformatics, Second International Workshop, 2002
Fast Phylogenetic Methods for the Analysis of Genome Rearrangement Data: An Empirical Study.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002
Statistically based postprocessing of phylogenetic analysis by clustering.
Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology, 2002
Exact-IEBP: A New Technique for Estimating Evolutionary Distances between Whole Genomes.
Proceedings of the Algorithms in Bioinformatics, First International Workshop, 2001
Estimating true evolutionary distances between genomes.
Proceedings of the Proceedings on 33rd Annual ACM Symposium on Theory of Computing, 2001
New approaches for reconstructing phylogenies from gene order data.
Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001
A New Fast Heuristic for Computing the Breakpoint Phylogeny and Experimental Phylogenetic Analyses of Real and Synthetic Data.
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000