Titlebook: Research in Computational Molecular Biology; 23rd Annual Internat Lenore J. Cowen Conference proceedings 2019 Springer Nature Switzerland A

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Identifying Clinical Terms in Free-Text Notes Using Ontology-Guided Machine Learning,has a large impact on electronic health record analysis. The mining of such terms is complicated by the broad use of synonyms and non-standard terms in medical documents. Here we presented a machine learning model for concept recognition in large unstructured text which optimizes the use of ontologi

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: Differentially Methylated Region Detection with Change Point Models,that are differentially methylated (DMRs) between different conditions. Many methods have been developed, which focus primarily on the setting of two-group comparison. We develop a DMR detecting method . for WGBS data, which is applicable for a wide range of experimental designs beyond the two-group

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On the Complexity of Sequence to Graph Alignment,ntations. Aligning sequences to graphs is a fundamental operation on several types of sequence graphs (variation graphs, assembly graphs, pan-genomes, etc.) and their biological applications. Though research on sequence to graph alignments is nascent, it can draw from related work on pattern matchin

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Minimization-Aware Recursive , (,): A Novel, Provable Algorithm that Accelerates Ensemble-Based Pro. The previous state of the art, iMinDEE-.-., computes provable .-approximations to partition functions of protein states (e.g., bound vs. unbound) by computing provable, admissible pairwise-minimized energy lower bounds on protein conformations and using the . enumeration algorithm to return a gap-

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Sparse Binary Relation Representations for Genome Graph Annotation,mand. In recent research, several graph data structures have been proposed to represent large sets of sequencing data and to allow for efficient querying of sequences. In particular, the concept of labeled de Bruijn graphs has been explored by several groups. While there has been good progress towar

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Efficient Construction of a Complete Index for Pan-Genomics Read Alignment,ng databases containing thousands of genomes. To understand why, it helps to examine the main components of the FM-index in more detail, which is a rank data structure over the Burrows-Wheeler Transform (.) of the string that will allow us to find the interval in the string’s suffix array (.) contai

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