Explanipedia

Best practices for improving alignment and variant calling on human sex chromosomes Open

Angela M. Taravella Oill, Seema B. Plaisier, Tanya N. Phung, Melissa A. Wilson · 2025

Sex chromosome complement is the largest karyotypic variation observed in humans. X and Y chromosomes were once a pair of homologous autosomes. Although chromosome X and Y differentiated from one another, they still share high levels of se…

Breaking rules: the complex relationship between DNA methylation and X-chromosome inactivation in the human placenta Open

Amy M. Inkster, Allison Matthews, Tanya N. Phung, Seema B. Plaisier, Melissa A. Wilson , et al. · 2025

Background The human placenta is distinct from most organs due to its uniquely low-methylated genome. DNA methylation (DNAme) is particularly depleted in the placenta at partially methylated domains and on the inactive X chromosome (Xi) in…

Genetic Heterogeneity Across Dimensions of Alcohol Use Behaviors Open

Jeanne E. Savage, Peter B. Barr, Tanya N. Phung, Young A Lee, Yingzhe Zhang , et al. · 2024

Deep phenotyping is an important next step to improve understanding of the genetic etiology of AUBs, in addition to increasing sample size. Further effort is required to uncover the genetic heterogeneity underlying AUBs using methods that …

Genetic Heterogeneity Across Dimensions of Alcohol Use Behaviors Open

Jeanne E. Savage, Peter B. Barr, Tanya N. Phung, Young A Lee, Yingzhe Zhang , et al. · 2023

Background Increasingly large samples in genome-wide association studies (GWAS) for alcohol use behaviors (AUBs) have led to an influx of implicated genes, yet the clinical and functional understanding of these associations remains low. Th…

Idiopathic Subglottic Stenosis Is Associated With More Frequent and Abnormal Squamous Metaplasia Open

Yourka D. Tchoukalova, Tanya N. Phung, Maeve M. Kennedy, Danielle Miranda-Grandjean, Emanuel Becquer , et al. · 2023

Objectives: Gain insights into the pathophysiology of idiopathic subglottic stenosis (iSGS) by investigating differences in transcriptome of subglottic mucosal tissue between patients with iSGS and controls, and between tracheal and subglo…

Adaptations to water stress and pastoralism in the Turkana of northwest Kenya Open

AJ Lea, IV Caldas, Kristina M. Garske, J. Echwa, Michael Gurven , et al. · 2023

The Turkana people inhabit arid regions of east Africa—where temperatures are high and water is scarce—and they practice subsistence pastoralism, such that their diet is primarily composed of animal products. Working with Turkana communiti…

Sex differences in early and term placenta are conserved in adult tissues Open

Kimberly C. Olney, Seema B. Plaisier, Tanya N. Phung, Michelle Silasi, Lauren Perley , et al. · 2022

X chromosome inactivation in the human placenta is patchy and distinct from adult tissues Open

Tanya N. Phung, Kimberly C. Olney, Brendan J. Pinto, Michelle Silasi, Lauren Perley , et al. · 2022

Sex differences in early and term placenta are conserved in adult tissues Open

Kimberly C. Olney, Seema B. Plaisier, Tanya N. Phung, Michelle Silasi, Lauren Perley , et al. · 2022

Background Pregnancy complications vary based on the fetus’s genetic sex, which may, in part, be modulated by the placenta. Further, developmental differences early in life can have lifelong health outcomes. Yet, sex differences in gene ex…

X chromosome inactivation in the human placenta is patchy and distinct from adult tissues Open

Tanya N. Phung, Kimberly C. Olney, Brendan J. Pinto, Michelle Silasi, Lauren Perley , et al. · 2022

Unique evolutionary trajectories of breast cancers with distinct genomic and spatial heterogeneity Open

Tanya N. Phung, Timothy H. Webster, Elizabeth Lenkiewicz, Smriti Malasi, Mariacarla Andreozzi , et al. · 2021

Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations Open

Olivera Grujic, Tanya N. Phung, Soo Bin Kwon, A Arneson, Yu‐Ju Lee , et al. · 2020

Unique genomic and neoepitope landscapes across tumors: a study across time, tissues, and space within a single lynch syndrome patient Open

Tanya N. Phung, Elizabeth Lenkiewicz, Smriti Malasi, Amit Sharma, Karen S. Anderson , et al. · 2020

Lynch syndrome (LS) arises in patients with pathogenic germline variants in DNA mismatch repair genes. LS is the most common inherited cancer predisposition condition and confers an elevated lifetime risk of multiple cancers notably colore…

Neoantigen Fitness Model Predicts Lower Immune Recognition of Cutaneous Squamous Cell Carcinomas Than Actinic Keratoses Open

Elizabeth S. Borden, Paul Kang, Heini M. Natri, Tanya N. Phung, Melissa A. Wilson , et al. · 2019

A low percentage of actinic keratoses progress to develop into cutaneous squamous cell carcinoma. The immune mechanisms that successfully control or eliminate the majority of actinic keratoses and the mechanisms of immune escape by invasiv…

X chromosome inactivation in the human placenta is patchy and distinct from adult tissues Open

Tanya N. Phung, Kimberly C. Olney, Michelle Silasi, Lauren Perley, Jane O’Bryan , et al. · 2019

One of the X chromosomes in genetic females is silenced by a process called X chromosome inactivation (XCI). Variation in XCI across the placenta may contribute to observed sex differences and variability in pregnancy outcomes. However, XC…

Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations Open

Olivera Grujic, Tanya N. Phung, Soo Bin Kwon, A Arneson, Yu‐Ju Lee , et al. · 2019

Annotations of evolutionarily constraint provide important information for variant prioritization. Genome-wide maps of epigenomic marks and transcription factor binding provide complementary information for interpreting a subset of such pr…

Identifying, understanding, and correcting technical artifacts on the sex chromosomes in next-generation sequencing data Open

Timothy H. Webster, Madeline Couse, Bruno M. Grande, Eric Karlins, Tanya N. Phung , et al. · 2019

Background Mammalian X and Y chromosomes share a common evolutionary origin and retain regions of high sequence similarity. Similar sequence content can confound the mapping of short next-generation sequencing reads to a reference genome. …

Complex patterns of sex-biased demography in canines Open

Tanya N. Phung, Robert K. Wayne, Melissa A. Wilson, Kirk E. Lohmueller · 2019

The demographic history of dogs is complex, involving multiple bottlenecks, admixture events and artificial selection. However, existing genetic studies have not explored variance in the number of reproducing males and females, and whether…

XYalign: Version 1.1.6 Open

Timothy H. Webster, Madeline Couse, Bruno M. Grande, Eric Karlins, Tanya N. Phung , et al. · 2019

The high degree of similarity between gametologous sequences on the sex chromosomes can lead to the misalignment of sequencing reads and substantially affect variant calling. Here we present XYalign, a new tool that (1) quickly infers sex …

Complex patterns of sex-biased demography in canines Open

Tanya N. Phung, Robert K. Wayne, Melissa A. Wilson, Kirk E. Lohmueller · 2018

bottlenecks associated with breed formation during the Victorian era 6 .In addition to bottleneck events, dogs experienced admixture with wolves during the domestication process 7 .Studies have disagreed about the process of domestication,…

Identifying, understanding, and correcting technical biases on the sex chromosomes in next-generation sequencing data Open

Timothy H. Webster, Madeline Couse, Bruno M. Grande, Eric Karlins, Tanya N. Phung , et al. · 2018

Mammalian X and Y chromosomes share a common evolutionary origin and retain regions of high sequence similarity. This sequence homology can cause the mismapping of short sequencing reads derived from the sex chromosomes and affect variant …

Methods and models for the analysis of genetic variation across species using large-scale genomic data Open

Tanya N. Phung · 2018

Understanding how different evolutionary processes shape genetic variation within and between species is an important question in population genetics. The advent of next generation sequencing has allowed for many theories and hypotheses to…

Comparison of Single Genome and Allele Frequency Data Reveals Discordant Demographic Histories Open

Annabel C. Beichman, Tanya N. Phung, Kirk E. Lohmueller · 2017

Inference of demographic history from genetic data is a primary goal of population genetics of model and nonmodel organisms. Whole genome-based approaches such as the pairwise/multiple sequentially Markovian coalescent methods use genomic …

Comparison of single genome and allele frequency data reveals discordant demographic histories Open

Annabel C. Beichman, Tanya N. Phung, Kirk E. Lohmueller · 2017

Inference of demographic history from genetic data is a primary goal of population genetics of model and non-model organisms. Whole genome-based approaches such as the Pairwise/Multiple Sequentially Markovian Coalescent (PSMC/MSMC) methods…

Determining the Effect of Natural Selection on Linked Neutral Divergence across Species Open

Tanya N. Phung, Christian D. Huber, Kirk E. Lohmueller · 2016

A major goal in evolutionary biology is to understand how natural selection has shaped patterns of genetic variation across genomes. Studies in a variety of species have shown that neutral genetic diversity (intra-species differences) has …

XYalign: Inferring and Correcting for Sex Chromosome Ploidy in Next-Generation Sequencing Data Open

T. Preston Webster, Tanya N. Phung, Madeline Couse, Bruno M. Grande, Eric Karlins , et al. · 2016

Sex chromosome aneuploidies are currently estimated to be as common as 1/400 in humans. Atypical ploidy will affect variant calling and measures of genomic variation that are central to most clinical genomic studies. Further, the high degr…

Natural selection reduces linked neutral divergence between distantly related species Open

Tanya N. Phung, Christian D. Huber, Kirk E. Lohmueller · 2015

Much work has been devoted to understanding the evolutionary processes shaping genetic variation across genomes. Studies have found neutral polymorphism is reduced close to genes and in regions of low recombination, suggesting the effects …

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