10 Result(s)

Article

Correction: A common methodological phylogenomics framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones

Filippo Utro, Chaya Levovitz, Kahn Rhrissorrakrai, Laxmi Parida in BMC Genomics (2023)

Article

A common methodological phylogenomics framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones

All diseases containing genetic material undergo genetic evolution and give rise to heterogeneity including cancer and infection. Although these illnesses are biologically very different, the ability for phylo...

Filippo Utro, Chaya Levovitz, Kahn Rhrissorrakrai, Laxmi Parida in BMC Genomics (2021)

Article

Signal enrichment with strain-level resolution in metagenomes using topological data analysis

A metagenome is a collection of genomes, usually in a micro-environment, and sequencing a metagenomic sample en masse is a powerful means for investigating the community of the constituent microorganisms. One of ...

Aldo Guzmán-Sáenz, Niina Haiminen, Saugata Basu, Laxmi Parida in BMC Genomics (2019)

Article

Efficient algorithms for polyploid haplotype phasing

Inference of haplotypes, or the sequence of alleles along the same chromosomes, is a fundamental problem in genetics and is a key component for many analyses including admixture map**, identifying regions of...

Dan He, Subrata Saha, Richard Finkers, Laxmi Parida in BMC Genomics (2018)

Article

Proceedings of The Twelfth Annual RECOMB Comparative Genomics Conference

Laxmi Parida, Gurinder Atwal, Bud Mishra in BMC Genomics (2014)

Article

Comparative exomics of Phalariscultivars under salt stress

Reed canary grass (Phalaris arundinacea) is an economically important forage and bioenergy grass of the temperate regions of the world. Despite its economic importance, it is lacking in public genomic data. We ex...

Niina Haiminen, Manfred Klaas, Zeyu Zhou, Filippo Utro, Paul Cormican… in BMC Genomics (2014)

Article

Sum of parts is greater than the whole: inference of common genetic history of populations

Reconstructability of population history, from genetic information of extant individuals, is studied under a simulation setting. We do not address the issue of accuracy of the reconstruction algorithms: we ass...

Filippo Utro, Marc Pybus, Laxmi Parida in BMC Genomics (2013)

Article

Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes

BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and ...

Frank A Feltus, Christopher A Saski, Keithanne Mockaitis, Niina Haiminen… in BMC Genomics (2011)

Article

Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes

We investigate if pooling BAC clones and sequencing the pools can provide for more accurate assembly of genome sequences than the "whole genome shotgun" (WGS) approach. Furthermore, we quantify this accuracy i...

Niina Haiminen, F Alex Feltus, Laxmi Parida in BMC Genomics (2011)