TRAPR: R Package for Statistical Analysis and Visualization of RNA-Seq Data [PDF]
Genomics & Informatics, 2017 High-throughput transcriptome sequencing, also known as RNA sequencing (RNA-Seq), is a standard technology for measuring gene expression with unprecedented accuracy.
Jae Hyun Lim, Soo Youn Lee, Ju Han Kim
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Bioinformatics, 2022 AbstractMotivationAmplicon sequencing is widely applied to explore heterogeneity and rare variants in genetic populations. Resolving true biological variants and quantifying their abundance is crucial for downstream analyses, but measured abundances are distorted by stochasticity and bias in amplification, plus errors during Polymerase Chain Reaction ...
Xiyu Peng, Karin S Dorman
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Molecular Description of a Novel Orientia Species Causing Scrub Typhus in Chile
Emerging Infectious Diseases, 2020 Scrub typhus is a potentially fatal rickettsiosis caused by Orientia species intracellular bacteria of the genus Orientia. Although considered to be restricted to the Asia Pacific region, scrub typhus has recently been discovered in southern Chile.
Katia Abarca +7 more
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Diversity, 2022 Ideally, the footprint of the evolutionary history of a species is drawn from integrative studies including quantitative and qualitative taxonomy, biogeography, ecology, and molecular genetics.
Wiebke Feindt, Heike Hadrys
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W(h)ither Fossils? Studying Morphological Character Evolution in the Age of Molecular Sequences [PDF]
, 2008 A major challenge in the post-genomics era will be to integrate molecular sequence data from extant organisms with morphological data from fossil and extant taxa into a single, coherent picture of phylogenetic relationships; only then will these ...
Bull J. J. +21 more
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Molecular Epidemiology of O139 Vibrio cholerae: Mutation, Lateral Gene Transfer, and Founder Flush
Emerging Infectious Diseases, 2003 Vibrio cholerae in O-group 139 was first isolated in 1992 and by 1993 had been found throughout the Indian subcontinent. This epidemic expansion probably resulted from a single source after a lateral gene transfer (LGT) event that changed the serotype of
Pallavi Garg +5 more
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A preliminary molecular phylogeny of the family Hydroptilidae (Trichoptera): an exploration of combined targeted enrichment data and legacy sequence data [PDF]
ZooKeys, 2022 Hydroptilidae is an extremely diverse family within Trichoptera, containing over 2,600 known species, that displays a wide array of ecological, morphological, and habitat diversity.
Robin E. Thomson +2 more
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Optimizing nucleic acid sequences for a molecular data recorder [PDF]
Proceedings of the Genetic and Evolutionary Computation Conference, 2017 We recently reported the design for a DNA nano-device that can record and store molecular signals. Here we present an evolutionary algorithm tailored to optimising nucleic acid sequences that predictively fold into our desired target structures. In our approach, a DNA device is first specified abstractly: the topology of the individual strands and ...
Ben Shirt-Ediss +4 more
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Genotyping of Chlamydophila psittaci in Human Samples
Emerging Infectious Diseases, 2006 Chlamydophila (formerly Chlamydia) psittaci genotypes A, B, C, and a new genotype most similar to the 6BC type strain were found in 10 humans with psittacosis by outer membrane protein A gene sequencing.
Edou R. Heddema +4 more
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Congruence of chloroplast- and nuclear-encoded DNA sequence variations used to assess species boundaries in the soil microalga Heterococcus (Stramenopiles, Xanthophyceae). [PDF]
, 2013 BackgroundHeterococcus is a microalgal genus of Xanthophyceae (Stramenopiles) that is common and widespread in soils, especially from cold regions. Species are characterized by extensively branched filaments produced when grown on agarized culture medium.
Andersen, Robert A +3 more
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