Titlebook: Research in Computational Molecular Biology; 24th Annual Internat Russell Schwartz Conference proceedings 2020 Springer Nature Switzerland

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Computing the Rearrangement Distance of Natural Genomesduplicates of any marker. Therefore it still needs a delicate preprocessing of the input data in which excessive copies of unbalanced markers have to be removed..In this paper we present an algorithm solving the genomic distance problem for . genomes, in which any marker may occur an arbitrary numbe

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Deep Large-Scale Multi-task Learning Network for Gene Expression Inferencenature of gene expression data, and the existing deep models are prone to overfitting due to the lack of using the interrelations of target genes in the learning framework. To address these challenges, we formulate the gene expression inference as a multi-task learning problem and propose a novel de

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A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Setseverage advanced theoretical and architectural techniques to parallelize and decrease memory usage in calculating .-mer hitting numbers; and (ii) we build upon techniques from randomized Set Cover to select universal .-mers much faster. We implemented these innovations in PASHA, the first randomized

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Supervised Adversarial Alignment of Single-Cell RNA-seq Datast is the accuracy of cell type assignment and the second is the inability to distinguish the batch (domain). We tested the method by using the resulting representation to align several different datasets. As we show, by overcoming batch effects our method was able to correctly separate cell types,

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RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genomnucleotide sequence to compute genome-wide probabilistic scores of nucleosome and TF occupancy, for hundreds of different factors at once. . can be applied to any epigenomic dataset that provides quantitative insight into chromatin accessibility in any organism, but here we apply it to MNase-seq dat

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Representation of ,-mer Sets Using Spectrum-Preserving String Sets store a set of .-mers using an order-of-magnitude less disk space than other lossless compression tools. The second one is an exact static .-mer membership index, UST-FM, which we show improves index size by 10–44% compared to other state-of-the-art low memory indices. Our tool is publicly availabl

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Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Losshods, is . under this GDL model. We also provide a simulation study evaluating ASTRAL-multi for species tree estimation under GDL. All scripts and datasets used in this study are available on the Illinois Data Bank: ..