4.8 Article

sgcocaller and comapr: personalised haplotype assembly and comparative crossover map analysis using single-gamete sequencing data

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Multidisciplinary Sciences

Widespread haploid-biased gene expression enables sperm-level natural selection

Kunal Bhutani et al.

Summary: The study found that a large class of mammalian genes are not completely shared across spermatid cytoplasmic bridges, referred to as genoinformative markers (GIMs), with some acting as selfish genetic elements that spread alleles unevenly. GIMs are under evolutionary pressure and are enriched for testis-specific gene expression, paralogs, and isoforms, which may help explain why testis gene expression patterns are an outlier relative to all other tissues.

SCIENCE (2021)

Article Biology

Twelve years of SAMtools and BCFtools

Petr Danecek et al.

Summary: SAMtools and BCFtools are widely used tools for processing high-throughput sequencing data, with a history of 12 years of continuous development and improvement. These packages have been utilized in various software projects and genomic pipelines and are freely available on GitHub.

GIGASCIENCE (2021)

Review Biotechnology & Applied Microbiology

Personalized genome structure via single gamete sequencing

Ruqian Lyu et al.

Summary: Genetic maps are essential for understanding disease genetics and evolutionary processes. Single-cell gamete sequencing has the potential to combine the advantages of short-read sequencing with the ability to build personalized genetic maps, opening up a new space in personalized genetics.

GENOME BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Inference of Chromosome-Length Haplotypes Using Genomic Data of Three or a Few More Single Gametes

Ruidong Li et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Multidisciplinary Sciences

Insights into variation in meiosis from 31,228 human sperm genomes

Avery Davis Bell et al.

NATURE (2020)

Article Multidisciplinary Sciences

Factors influencing meiotic recombination revealed by whole-genome sequencing of single sperm

Anjali Gupta Hinch et al.

SCIENCE (2019)

Article Biochemical Research Methods

hts-nim: scripting high-performance genomic analyses

Brent S. Pedersen et al.

BIOINFORMATICS (2018)

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Article Biochemical Research Methods

fastp: an ultra-fast all-in-one FASTQ preprocessor

Shifu Chen et al.

BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

Peter Edge et al.

GENOME RESEARCH (2017)

Article Multidisciplinary Sciences

Refined genetic maps reveal sexual dimorphism in human meiotic recombination at multiple scales

Claude Bherer et al.

NATURE COMMUNICATIONS (2017)

Review Genetics & Heredity

Haplotype-resolved genome sequencing: experimental methods and applications

Matthew W. Snyder et al.

NATURE REVIEWS GENETICS (2015)

Article Multidisciplinary Sciences

Multiple mechanisms limit meiotic crossovers: TOP3α and two BLM homologs antagonize crossovers in parallel to FANCM

Mathilde Seguela-Arnaud et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Cell Biology

Meiotic Recombination: The Essence of Heredity

Neil Hunter

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2015)

Article Biochemistry & Molecular Biology

Genome Analyses of Single Human Oocytes

Yu Hou et al.

Article Biochemistry & Molecular Biology

Sequencing of isolated sperm cells for direct haplotyping of a human genome

Ewen F. Kirkness et al.

GENOME RESEARCH (2013)

Article Statistics & Probability

An Introduction to Bootstrap Methods with Applications to R by M.R. Chernick and R.A. LaBudde

Michael A. Martin

AUSTRALIAN & NEW ZEALAND JOURNAL OF STATISTICS (2012)

Article Multidisciplinary Sciences

FANCM Limits Meiotic Crossovers

Wayne Crismani et al.

SCIENCE (2012)

Article Genetics & Heredity

Chromosomal Haplotypes by Genetic Phasing of Human Families

Jared C. Roach et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2011)

Article Statistics & Probability

Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models

Simon N. Wood

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY (2011)

Article Multidisciplinary Sciences

The landscape of recombination in African Americans

Anjali G. Hinch et al.

NATURE (2011)

Article Multidisciplinary Sciences

Mouse genomic variation and its effect on phenotypes and gene regulation

Thomas M. Keane et al.

NATURE (2011)

Review Genetics & Heredity

The importance of phase information for human genomics

Ryan Tewhey et al.

NATURE REVIEWS GENETICS (2011)

Article Multidisciplinary Sciences

Variants of the protein PRDM9 differentially regulate a set of human meiotic recombination hotspots highly active in African populations

Ingrid L. Berg et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biochemistry & Molecular Biology

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

Aaron McKenna et al.

GENOME RESEARCH (2010)

Article Multidisciplinary Sciences

Fine-scale recombination rate differences between sexes, populations and individuals

Augustine Kong et al.

NATURE (2010)

Article Multidisciplinary Sciences

Prdm9 Controls Activation of Mammalian Recombination Hotspots

Emil D. Parvanov et al.

SCIENCE (2010)

Article Multidisciplinary Sciences

PRDM9 Is a Major Determinant of Meiotic Recombination Hotspots in Humans and Mice

F. Baudat et al.

SCIENCE (2010)

Article Biochemistry & Molecular Biology

Permutation P-values Should Never Be Zero: Calculating Exact P-values When Permutations Are Randomly Drawn

Belinda Phipson et al.

STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

Abnormal meiotic recombination in infertile men and its association with sperm aneuploidy

Kyle A. Ferguson et al.

HUMAN MOLECULAR GENETICS (2007)