Activation of human endogenous retroviruses and its physiological consequences
Human endogenous retroviruses (HERVs) are abundant sequences that persist within the
human genome as remnants of ancient retroviral infections. These sequences became fixed …
human genome as remnants of ancient retroviral infections. These sequences became fixed …
The ecology of environmental DNA and implications for conservation genetics
MA Barnes, CR Turner - Conservation genetics, 2016 - Springer
Environmental DNA (eDNA) refers to the genetic material that can be extracted from bulk
environmental samples such as soil, water, and even air. The rapidly expanding study of …
environmental samples such as soil, water, and even air. The rapidly expanding study of …
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this
process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to …
process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to …
A universal SNP and small-indel variant caller using deep neural networks
Despite rapid advances in sequencing technologies, accurately calling genetic variants
present in an individual genome from billions of short, errorful sequence reads remains …
present in an individual genome from billions of short, errorful sequence reads remains …
Scrutinizing key steps for reliable metabarcoding of environmental samples
Metabarcoding of environmental samples has many challenges and limitations that require
carefully considered laboratory and analysis workflows to ensure reliable results. We …
carefully considered laboratory and analysis workflows to ensure reliable results. We …
Tumor cells can follow distinct evolutionary paths to become resistant to epidermal growth factor receptor inhibition
AN Hata, MJ Niederst, HL Archibald… - Nature medicine, 2016 - nature.com
Although mechanisms of acquired resistance of epidermal growth factor receptor (EGFR)-
mutant non-small-cell lung cancers to EGFR inhibitors have been identified, little is known …
mutant non-small-cell lung cancers to EGFR inhibitors have been identified, little is known …
Sequencing pools of individuals—mining genome-wide polymorphism data without big funding
The analysis of polymorphism data is becoming increasingly important as a complementary
tool to classical genetic analyses. Nevertheless, despite plunging sequencing costs …
tool to classical genetic analyses. Nevertheless, despite plunging sequencing costs …
Toward better understanding of artifacts in variant calling from high-coverage samples
H Li - Bioinformatics, 2014 - academic.oup.com
Motivation: Whole-genome high-coverage sequencing has been widely used for personal
and cancer genomics as well as in various research areas. However, in the lack of an …
and cancer genomics as well as in various research areas. However, in the lack of an …
Sequence artifacts in DNA from formalin-fixed tissues: causes and strategies for minimization
H Do, A Dobrovic - Clinical chemistry, 2015 - academic.oup.com
BACKGROUND Precision medicine is dependent on identifying actionable mutations in
tumors. Accurate detection of mutations is often problematic in formalin-fixed paraffin …
tumors. Accurate detection of mutations is often problematic in formalin-fixed paraffin …
Studying clonal dynamics in response to cancer therapy using high-complexity barcoding
HC Bhang, DA Ruddy… - Nature medicine, 2015 - nature.com
Resistance to cancer therapies presents a significant clinical challenge. Recent studies
have revealed intratumoral heterogeneity as a source of therapeutic resistance. However, it …
have revealed intratumoral heterogeneity as a source of therapeutic resistance. However, it …