HORmon: automated annotation of human centromeres

Recent advances in long-read sequencing opened a possibility to address the long-standing questions about the architecture and evolution of human centromeres. They also emphasized the need for centromere annotation (partitioning human centromeres into monomers and higher-order repeats (HORs)). Even though there was a half-century-long series of semi-manual studies of centromere architecture, a rigorous centromere annotation algorithm is still lacking. Moreover, an automated centromere annotation is a prerequisite for studies of genetic diseases associated with centromeres, and evolutionary studies of centromeres across multiple species. Although the monomer decomposition (transforming a centromere into a monocentromere written in the monomer alphabet) and the HOR decomposition (representing a monocentromere in the alphabet of HORs) are currently viewed as two separate problems, we demonstrate that they should be integrated into a single framework in such a way that HOR (monomer) inference affects monomer (HOR) inference. We thus developed the HORmon algorithm that integrates the monomer/HOR inference and automatically generates the human monomers/HORs that are largely consistent with the previous semi-manual inference.

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New Work on Speech Acts

10.1093/oso/9780198738831.001.0001 ◽

2018 ◽

Cited By ~ 5

Keyword(s):

Speech Acts ◽

Speech Act ◽

Speech Act Theory ◽

New Work ◽

Half Century ◽

Recent Advances ◽

Current Thinking ◽

Semantics And Pragmatics ◽

Recent Developments ◽

The Relationship

The essays collected in this book represent recent advances in our understanding of speech acts-actions like asserting, asking, and commanding that speakers perform when producing an utterance. The study of speech acts spans disciplines, and embraces both the theoretical and scientific concerns proper to linguistics and philosophy as well as the normative questions that speech acts raise for our politics, our societies, and our ethical lives generally. It is the goal of this book to reflect the diversity of current thinking on speech acts as well as to bring these conversations together, so that they may better inform one another. Topics explored in this book include the relationship between sentence grammar and speech act potential; the fate of traditional frameworks in speech act theory, such as the content-force distinction and the taxonomy of speech acts; and the ways in which speech act theory can illuminate the dynamics of hostile and harmful speech. The book takes stock of well over a half century of thinking about speech acts, bringing this classicwork in linewith recent developments in semantics and pragmatics, and pointing the way forward to further debate and research.

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Recent advances in higher order rotaxane architectures

Chemical Communications ◽

10.1039/d0cc03057k ◽

2020 ◽

Vol 56 (69) ◽

pp. 9916-9936 ◽

Cited By ~ 2

Author(s):

He-Ye Zhou ◽

Qian-Shou Zong ◽

Ying Han ◽

Chuan-Feng Chen

Keyword(s):

Higher Order ◽

Feature Article ◽

Recent Advances

Recent advances in various types of higher order rotaxanes with precisely controlled architectures are summarized in this feature article.

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Recent Advances in the Development of Methods for Detecting Single-base Substitutions Associated with Human Genetic Diseases

Cold Spring Harbor Symposia on Quantitative Biology ◽

10.1101/sqb.1986.051.01.033 ◽

1986 ◽

Vol 51 (0) ◽

pp. 275-284 ◽

Cited By ~ 29

Author(s):

R.M. Myers ◽

T. Maniatis

Keyword(s):

Genetic Diseases ◽

Single Base ◽

Recent Advances ◽

Base Substitutions

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RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes

10.1101/2020.04.17.035287 ◽

2020 ◽

Author(s):

Yuxuan Yuan ◽

Philipp E. Bayer ◽

Robyn Anderson ◽

HueyTyng Lee ◽

Chon-Kit Kenneth Chan ◽

...

Keyword(s):

Genome Assembly ◽

Chinese Spring ◽

Complete Genome ◽

Reference Genome ◽

Computing Time ◽

Link Type ◽

Recent Advances ◽

Long Read ◽

Genome Assemblies

AbstractRecent advances in long-read sequencing have the potential to produce more complete genome assemblies using sequence reads which can span repetitive regions. However, overlap based assembly methods routinely used for this data require significant computing time and resources. Here, we have developed RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel followed by a final bin-stitching step. During benchmarking, we assembled the wheat Chinese Spring (CS) genome using publicly available PacBio reads in parallel in 168 wall hours on a 250 CPU system. The maximum RAM used was 300 Gb and the computing time was 42,000 CPU hours. The approach opens applications for the assembly of other large and complex genomes with much-reduced computing requirements. The RefKA pipeline is available at https://github.com/AppliedBioinformatics/RefKA

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Robust detection of tandem repeat expansions from long DNA reads

10.1101/356931 ◽

2018 ◽

Cited By ~ 1

Author(s):

Satomi Mitsuhashi ◽

Martin C Frith ◽

Takeshi Mizuguchi ◽

Satoko Miyatake ◽

Tomoko Toyota ◽

...

Keyword(s):

Tandem Repeat ◽

Tandem Repeats ◽

Genetic Diseases ◽

Error Rates ◽

Robust Detection ◽

Sequencing Errors ◽

Tandem Repeat Sequences ◽

Long Read ◽

Repeat Expansions ◽

The Many

AbstractTandemly repeated sequences are highly mutable and variable features of genomes. Tandem repeat expansions are responsible for a growing list of human diseases, even though it is hard to determine tandem repeat sequences with current DNA sequencing technology. Recent long-read technologies are promising, because the DNA reads are often longer than the repetitive regions, but are hampered by high error rates. Here, we report robust detection of human repeat expansions from careful alignments of long (PacBio and nanopore) reads to a reference genome. Our method (tandem-genotypes) is robust to systematic sequencing errors, inexact repeats with fuzzy boundaries, and low sequencing coverage. By comparing to healthy controls, we can prioritize pathological expansions within the top 10 out of 700000 tandem repeats in the genome. This may help to elucidate the many genetic diseases whose causes remain unknown.

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An Overview of Recent Advances and Clinical Applications of Exon Skipping and Splice Modulation for Muscular Dystrophy and Various Genetic Diseases

Methods in Molecular Biology - Exon Skipping and Inclusion Therapies ◽

10.1007/978-1-4939-8651-4_2 ◽

2018 ◽

pp. 31-55 ◽

Cited By ~ 18

Author(s):

Merryl Rodrigues ◽

Toshifumi Yokota

Keyword(s):

Muscular Dystrophy ◽

Genetic Diseases ◽

Exon Skipping ◽

Clinical Applications ◽

Recent Advances

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The Genome of the North American Brown Bear or Grizzly: Ursus arctos ssp. horribilis

Genes ◽

10.3390/genes9120598 ◽

2018 ◽

Vol 9 (12) ◽

pp. 598 ◽

Cited By ~ 9

Author(s):

Gregory A. Taylor ◽

Heather Kirk ◽

Lauren Coombe ◽

Shaun D. Jackman ◽

Justin Chu ◽

...

Keyword(s):

Ursus Arctos ◽

Brown Bear ◽

Close Relative ◽

Grizzly Bear ◽

Construction Technique ◽

Protein Coding ◽

Automated Annotation ◽

The North ◽

Long Read ◽

Reference Quality

The grizzly bear (Ursus arctos ssp. horribilis) represents the largest population of brown bears in North America. Its genome was sequenced using a microfluidic partitioning library construction technique, and these data were supplemented with sequencing from a nanopore-based long read platform. The final assembly was 2.33 Gb with a scaffold N50 of 36.7 Mb, and the genome is of comparable size to that of its close relative the polar bear (2.30 Gb). An analysis using 4104 highly conserved mammalian genes indicated that 96.1% were found to be complete within the assembly. An automated annotation of the genome identified 19,848 protein coding genes. Our study shows that the combination of the two sequencing modalities that we used is sufficient for the construction of highly contiguous reference quality mammalian genomes. The assembled genome sequence and the supporting raw sequence reads are available from the NCBI (National Center for Biotechnology Information) under the bioproject identifier PRJNA493656, and the assembly described in this paper is version QXTK01000000.

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Cephalopod Biology: At the Intersection Between Genomic and Organismal Novelties

Annual Review of Animal Biosciences ◽

10.1146/annurev-animal-021419-083609 ◽

2020 ◽

Vol 8 (1) ◽

pp. 71-90 ◽

Cited By ~ 2

Author(s):

Caroline B. Albertin ◽

Oleg Simakov

Keyword(s):

Nervous System ◽

Genetic Background ◽

Recent Progress ◽

Significant Progress ◽

The Public ◽

Marine Predators ◽

Molecular Approaches ◽

Recent Advances ◽

Evolutionary Studies

Cephalopods are resourceful marine predators that have fascinated generations of researchers as well as the public owing to their advanced behavior, complex nervous system, and significance in evolutionary studies. Recent advances in genomics have accelerated the pace of cephalopod research. Many traditional areas focusing on evolution, development, behavior, and neurobiology, primarily on the morphological level, are now transitioning to molecular approaches. This review addresses the recent progress and impact of genomic and other molecular resources on research in cephalopods. We outline several key directions in which significant progress in cephalopod research is expected and discuss its impact on our understanding of the genetic background behind cephalopod biology and beyond.

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