Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer

B Ekim, B Berger, R Chikhi - Cell systems, 2021 - cell.com
DNA sequencing data continue to progress toward longer reads with increasingly lower
sequencing error rates. Here, we define an algorithmic approach, mdBG, that makes use of …

Perspectives on allele-specific expression

S Cleary, C Seoighe - Annual Review of Biomedical Data …, 2021 - annualreviews.org
Diploidy has profound implications for population genetics and susceptibility to genetic
diseases. Although two copies are present for most genes in the human genome, they are …

An efficient genotyper and star-allele caller for pharmacogenomics

A Hari, Q Zhou, N Gonzaludo, J Harting… - Genome …, 2023 - genome.cshlp.org
High-throughput sequencing provides sufficient means for determining genotypes of
clinically important pharmacogenes that can be used to tailor medical decisions to individual …

CYP2C8, CYP2C9, and CYP2C19 characterization using next-generation sequencing and haplotype analysis: a GeT-RM collaborative project

A Gaedigk, EC Boone, SE Scherer, S Lee… - The Journal of Molecular …, 2022 - Elsevier
Pharmacogenetic tests typically target selected sequence variants to identify haplotypes that
are often defined by star (∗) allele nomenclature. Due to their design, these targeted …

A Python-based programming language for high-performance computational genomics

A Shajii, I Numanagić, AT Leighton, H Greenyer… - Nature …, 2021 - nature.com
Fig. 1| The Seq programming language. a, Conceptual comparison of Seq, python and C++.
Seq combines the high performance of C++ with the programming ease and clarity of …

Reconstruction of evolving gene variants and fitness from short sequencing reads

MW Shen, KT Zhao, DR Liu - Nature chemical biology, 2021 - nature.com
Directed evolution can generate proteins with tailor-made activities. However, full-length
genotypes, their frequencies and fitnesses are difficult to measure for evolving gene-length …

Probing molecular excited states by atomic force microscopy

S Fatayer, F Albrecht, I Tavernelli, M Persson, N Moll… - Physical Review Letters, 2021 - APS
By employing single charge injections with an atomic force microscope, we investigated
redox reactions of a molecule on a multilayer insulating film. First, we charged the molecule …

BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies

P Höjer, T Frick, H Siga, P Pourbozorgi… - Nucleic Acids …, 2023 - academic.oup.com
Linked-read sequencing promises a one-method approach for genome-wide insights
including single nucleotide variants (SNVs), structural variants, and haplotyping. We …

Interrogating the Human Diplome: Computational Methods, Emerging Applications, and Challenges

AP Chan, Y Choi, A Rangan, G Zhang… - … : Methods and Protocols, 2022 - Springer
Human DNA sequencing protocols have revolutionized human biology, biomedical science,
and clinical practice, but still have very important limitations. One limitation is that most …

Differential haplotype expression in class I MHC genes during SARS-CoV-2 infection of human lung cell lines

RS Francisco Junior, JR Temerozo… - Frontiers in …, 2023 - frontiersin.org
Introduction Cell entry of SARS-CoV-2 causes genome-wide disruption of the transcriptional
profiles of genes and biological pathways involved in the pathogenesis of COVID-19 …