A. Ewing

发表

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

Ken Chen, David Haussler, Justin Guinney, 2018, bioRxiv.

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

David Haussler, Justin Guinney, Zechen Chong, 2018, bioRxiv.

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection

Joshua M. Stuart, Adam A. Margolin, Kathleen E. Houlahan, 2015, Nature Methods.

High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes.

H. Kazazian, A. Ewing, Haig H Kazazian, 2010, Genome research.

Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans.

H. Kazazian, A. Ewing, Haig H Kazazian, 2011, Genome research.

Transposable element detection from whole genome sequence data

A. Ewing, 2015, Mobile DNA.

Extensive somatic L1 retrotransposition in colorectal tumors

D. Largaespada, R. Harris, M. Burns, 2012, Genome research.

Germline Contamination and Leakage in Whole Genome Somatic Single Nucleotide Variant Detection

Joshua M. Stuart, Dorota H. Sendorek, Kathleen E. Houlahan, 2017, bioRxiv.

RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection

Joshua M. Stuart, D. Haussler, E. Collisson, 2014, PloS one.

Exon-trapping mediated by the human retrotransposon SVA.

Katsushi Tokunaga, D. C. Hancks, H. Kazazian, 2009, Genome research.

Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis

David Haussler, Colleen M. Bosworth, Adam M. Novak, 2018, Cell.

Genome Sequences of Three Agrobacterium Biovars Help Elucidate the Evolution of Multichromosome Genomes in Bacteria

Steven C. Slater, Jian Sun, Huijun Zhu, 2009, Journal of Bacteriology.

Global optimization of somatic variant identification in cancer genomes with a global community challenge

Joshua M. Stuart, Adam A. Margolin, Kristen K. Dang, 2014, Nature Genetics.

Multiscale imaging of basal cell dynamics in the functionally mature mammary gland

Ethan K. Scott, E. Scott, J. Putney, 2020, Proceedings of the National Academy of Sciences.

No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing

Ira W. Deveson, G. Faulkner, I. Deveson, 2021, Cell Reports.

Single-molecule simultaneous profiling of DNA methylation and DNA-protein interactions with Nanopore-DamID

G. Faulkner, S. Andersen, S. W. Cheetham, 2021, bioRxiv.

Mouse L1s fade with age: a methylation-enforced mechanism for attenuation of L1 retrotransposition potential

G. Faulkner, A. Ewing, Sandra R. Richardson, 2022, bioRxiv.

Arginine to Glutamine Variant in Olfactomedin Like 3 (OLFML3) Is a Candidate for Severe Goniodysgenesis and Glaucoma in the Border Collie Dog Breed

J. Prendergast, A. Ewing, K. Summers, 2019, G3: Genes, Genomes, Genetics.

Sex-dependent differential transcript expression in the placenta of growth restricted infants.

A. Ewing, P. Prentis, E. Pelzer, 2021, Placenta.

Retrotransposition of gene transcripts leads to structural variation in mammalian genomes

Li Ding, David Haussler, Dent Earl, 2013, Genome Biology.

Nanopore Sequencing Enables Comprehensive Transposable Element Epigenomic Profiling.

G. Faulkner, S. W. Cheetham, A. Ewing, 2020, Molecular cell.

Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells

G. Faulkner, R. Lister, A. Ewing, 2022, bioRxiv.

An early proinflammatory transcriptional response to tau pathology is age‐specific and foreshadows reduced tau burden

L. Bodea, G. Faulkner, M. Gearing, 2021, Brain pathology.

Heritable L1 retrotransposition in the mouse primordial germline and early embryo

G. Faulkner, H. Kazazian, J. Jeddeloh, 2017, Genome research.

Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome

G. Faulkner, T. Mercer, S. W. Cheetham, 2021, Genome Biology.

The Mobilisation of Processed Transcripts in Germline and Somatic Tissues

A. Ewing, 2017 .

L1 Retrotransposon Heterogeneity in Ovarian Tumor Cell Evolution.

G. Faulkner, A. Ewing, Patricia E. Carreira, 2018, Cell reports.

L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis

G. Faulkner, D. Samuel, D. J. Gerhardt, 2018, Genome research.

Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme

Jun Wang, G. Faulkner, D. J. Gerhardt, 2016, Mobile DNA.

Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution

Akhilesh Pandey, Christine A Iacobuzio-Donahue, Anthony Gacita, 2015, Genome research.

Ubiquitous L1 Mosaicism in Hippocampal Neurons

Geoffrey J. Faulkner, Adam D. Ewing, Adeline Vanderver, 2015, Cell.

An evolutionary arms race between KRAB zinc finger genes 91/93 and SVA/L1 retrotransposons

David Haussler, Sofie R Salama, Ngan Nguyen, 2014, Nature.

Rare variants in Fanconi anemia genes are enriched in acute myeloid leukemia

Anna L. Brown, Mahmoud A. Bassal, M. Brown, 2018, Blood Cancer Journal.

Multiscale activity imaging in mammary gland reveals how oxytocin enables lactation

Ethan K. Scott, E. Scott, J. Putney, 2019, bioRxiv.

LINE-1 Evasion of Epigenetic Repression in Humans.

G. Faulkner, R. Lister, S. W. Cheetham, 2019, Molecular cell.

Dynamic Methylation of an L1 Transduction Family during Reprogramming and Neurodifferentiation

G. Faulkner, E. Wolvetang, A. Ewing, 2019, Molecular and Cellular Biology.

Explorer Extensive somatic L 1 retrotransposition in colorectal tumors

D. Largaespada, G. Faulkner, H. Kazazian, 2017 .

Pathogenic orphan transduction created by a nonreference LINE‐1 retrotransposon

H. Kazazian, Y. Takeshima, M. Matsuo, 2012, Human mutation.

Nanopore sequencing enables comprehensive transposable element epigenomic profiling

G. Faulkner, S. W. Cheetham, A. Ewing, 2020, bioRxiv.

LINE-1 retrotransposon activation intrinsic to interneuron development

Laura R. Fenlon, L. Bodea, A. Hannan, 2022, bioRxiv.

LINE-1 retrotransposition impacts the genome of human pre-implantation embryos and extraembryonic tissues

G. Faulkner, J. L. Cortés, R. Rahbari, 2019, bioRxiv.

A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci

D. Haussler, M. Reinders, J. L. Rosenkrantz, 2022, Genome research.

Analysis of LINE-1 Elements in DNA from Postmortem Brains of Individuals with Schizophrenia

C. Hahn, W. Berrettini, A. Ewing, 2017, Neuropsychopharmacology.

Reading LINEs within the cocaine addicted brain

D. Mash, H. Kazazian, W. Berrettini, 2017, Brain and behavior.

Retrotransposon mobilization in cancer genomes

D. Haussler, Tracy J. Ballinger, A. Ewing, 2015, 1501.04268.

Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles.

H. Kazazian, A. Ewing, P. Mandal, 2013, Human molecular genetics.

A community effort to create standards for evaluating tumor subclonal reconstruction

Nathan M. Wilson, Joshua M. Stuart, Christopher M. Lalansingh, 2019, Nature Biotechnology.

Creating Standards for Evaluating Tumour Subclonal Reconstruction

Nathan M. Wilson, John Chilton, Yuanfang Guan, 2018, bioRxiv.

Living with Genome Instability: the Adaptation of Phytoplasmas to Diverse Environments of Their Insect and Plant Hosts

Alla Lapidus, Sally A. Miller, Adam Ewing, 2006, Journal of bacteriology.

On the role of H3.3 in retroviral silencing

Mohammad M. Karimi, G. Faulkner, K. Ozato, 2017, Nature.

Germline contamination and leakage in whole genome somatic single nucleotide variant detection

Paul C. Boutros, Joshua M. Stuart, J. Christopher Bare, 2017, bioRxiv.

Methylartist: tools for visualizing modified bases from nanopore sequence data

S. W. Cheetham, A. Ewing, Michaela Kindlova, 2021, bioRxiv.

An allele-resolved nanopore-guided tour of the human placental methylome

A. Ewing, S. Steane, Danielle J. Borg, 2023, bioRxiv.

Human-specific NOTCH-like genes in a region linked to neurodevelopmental disorders affect cortical neurogenesis

Colleen M. Bosworth, Adam M. Novak, Ian T. Fiddes, 2017, bioRxiv.

Modulation of Placental Gene Expression in Small-for-Gestational-Age Infants

Y. Miller, A. Ewing, V. Clifton, 2020, Genes.

Microdeletion of 9q22.3: A patient with minimal deletion size associated with a severe phenotype

S. W. Cheetham, A. Ewing, K. Summers, 2021, American journal of medical genetics. Part A.

Whole genome investigation of an atypical autism case identifies a novel ANOS1 mutation with subsequent diagnosis of Kallmann syndrome

P. Dawson, A. Ewing, H. Heussler, 2020, Molecular Genetics and Metabolism Reports.

A community effort to create standards for evaluating tumor subclonal reconstruction

Nathan M. Wilson, Ville Mustonen, Salem Malikic, 2020, Nature Biotechnology.

Resolution of Melanoma to Programmed Death-1 Blockade but Simultaneous Rapid Progression of Concomitant Chronic Lymphocytic Leukemia

M. Gandhi, A. Ewing, D. Gill, 2022, Acta Haematologica.

What We Can Deduce about Metabolism in the Moderate Halophile Chromohalobacter Salexigens from its Genomic Sequence

P. Richardson, A. Lapidus, F. Larimer, 2005 .

Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylation

K. Helin, M. Branco, A. Ewing, 2023, bioRxiv.

CDCP1 enhances Wnt signaling in colorectal cancer promoting nuclear localization of β-catenin and E-cadherin

A. Ewing, M. McGuckin, M. Adams, 2019, Oncogene.