Research in Computational Molecular Biology

Boosting alignment accuracy by adaptive local realignment.- A concurrent subtractive assembly approach for identification of disease associated sub-meta-genomes.- A flow procedure for the linearization of genome variation graphs.- Dynamic alignment-free and reference-free read compression.- A fast approximate algorithm for mapping long reads to large reference databases.- Determining the consistency of resolved triplets and fan triplets.- Progressive calibration and averaging for tandem mass spectrometry statistical confidence estimation: Why settle for a single decoy.- Resolving multi-copy duplications de novo using polyploid phasing.- A Bayesian active learning experimental design for inferring signaling networks.- BBK* (Branch and Bound over K*): A provable and efficient ensemble-based algorithm to optimize stability and binding affinity over large sequence spaces.- Super-bubbles, ultra-bubbles and cacti.- EPR-dictionaries: A practical and fast data structure for constant time searches in unidirectional and bidirectional FM indices.- A Bayesian framework for estimating cell type composition from DNA methylation without the need for methylation reference.- Towards recovering Allele-specific cancer genome graphs.- Using stochastic approximation techniques to efficiently construct confidence intervals for heritability.- Improved search of large transcriptomic sequencing databases using split sequence bloom trees.- All some sequence bloom trees.- Longitudinal genotype-phenotype association study via temporal structure auto-learning predictive model.- Improving imputation accuracy by inferring causal variants in genetic studies.- The copy-number tree mixture deconvolution problem and applications to multi-sample bulk sequencing tumor data.- Quantifying the impact of non-coding variants on transcription factor-DNA binding.- aBayesQR: A Bayesian method for reconstruction of viral populations characterized by low diversity.- BeWith: A between-within method for module