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List of works by Piotr A Mieczkowski

A Case Study of Genomic Instability in an Industrial Strain of

scientific article published on 06 November 2018

A Mutation in the Borcs7 Subunit of the Lysosome Regulatory BORC Complex Results in Motor Deficits and Dystrophic Axonopathy in Mice

scientific article published on 01 July 2018

A dominant mitochondrial mutator phenotype of Saccharomyces cerevisiae conferred by msh1 alleles altered in the sequence encoding the ATP-binding domain.

scientific article published on 15 December 2001

A map of open chromatin in human pancreatic islets

scientific article

A native and an invasive dune grass share similar, patchily distributed, root-associated fungal communities

article

APOBEC3A and APOBEC3B Preferentially Deaminate the Lagging Strand Template during DNA Replication

scientific article

APOBEC3B cytidine deaminase targets the non-transcribed strand of tRNA genes in yeast.

scientific article published on 21 March 2017

Adaptation and selection shape clonal evolution of tumors during residual disease and recurrence

scientific article published on 06 October 2020

An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers

scientific article

Analysis of a food-borne fungal pathogen outbreak: virulence and genome of a Mucor circinelloides isolate from yogurt

scientific article

Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation

scientific article

Antifungal drug resistance evoked via RNAi-dependent epimutations

scientific article published on 27 July 2014

Assessing serotonin receptor mRNA editing frequency by a novel ultra high-throughput sequencing method.

scientific article

Atypical UV Photoproducts Induce Non-canonical Mutation Classes Associated with Driver Mutations in Melanoma

scientific article published on 01 November 2020

BK Polyomavirus Genomic Integration and Large T Antigen Expression: Evolving Paradigms in Human Oncogenesis

scientific article

BK polyomavirus nephropathy with systemic viral spread: Whole genome sequencing data from a fatal case of BKPyV infection

scientific article published on 23 February 2020

Break-induced replication is a source of mutation clusters underlying kataegis

scientific article

Cavitation Enhancing Nanodroplets Mediate Efficient DNA Fragmentation in a Bench Top Ultrasonic Water Bath.

scientific article

Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC).

scientific article published on 17 January 2018

Characterization of a novel DNA damage-inducible gene of Saccharomyces cerevisiae, DIN7, which is a structural homolog of the RAD2 and RAD27 DNA repair genes.

scientific article

Characterization of systemic genomic instability in budding yeast

scientific article published on 26 October 2020

Chromatin architectures at fission yeast transcriptional promoters and replication origins

scientific article

Chromosome fragility at GAA tracts in yeast depends on repeat orientation and requires mismatch repair

scientific article published on 2 October 2008

Chronic oxidative DNA damage due to DNA repair defects causes chromosomal instability in Saccharomyces cerevisiae

scientific article published on 30 June 2008

Clustered mutations in yeast and in human cancers can arise from damaged long single-strand DNA regions.

scientific article

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

article

Comprehensive Characterization of Cancer Driver Genes and Mutations

article

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma

scientific article published on 4 November 2015

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma

article

Congenital Midline Cervical Cleft: First Report and Genetic Analysis of Two Related Patients

scientific article published on 06 February 2020

Contrasting nitrogen fertilization treatments impact xylem gene expression and secondary cell wall lignification in Eucalyptus

scientific article

Correction for Degtyareva et al., "Chronic Oxidative DNA Damage Due to DNA Repair Defects Causes Chromosomal Instability in Saccharomyces cerevisiae"

scientific article published on 11 October 2019

Correction: Repair of multiple simultaneous double-strand breaks causes bursts of genome-wide clustered hypermutation

scientific article published on 06 March 2020

Corrigendum to "APOBEC3B cytidine deaminase targets the non-transcribed strand of tRNA genes in yeast" [DNA Repair 53 (2017) 4-14]

scientific article published on 07 June 2019

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions

scientific article published on 16 April 2021

Cryptococcus gattii VGIII isolates causing infections in HIV/AIDS patients in Southern California: identification of the local environmental source as arboreal

scientific article published in August 2014

Damage-induced localized hypermutability.

scientific article

Dengue type 1 viruses circulating in humans are highly infectious and poorly neutralized by human antibodies

scientific article published on 05 December 2018

Detecting ultraviolet damage in single DNA molecules by atomic force microscopy

scientific article

Double-strand breaks associated with repetitive DNA can reshape the genome

scholarly article

Elucidation of the calcineurin-Crz1 stress response transcriptional network in the human fungal pathogen Cryptococcus neoformans

scientific article

Enhanced expression of the DNA damage-inducible gene DIN7 results in increased mutagenesis of mitochondrial DNA in Saccharomyces cerevisiae

scientific article published on 25 June 2003

Essential Roles for Polymerase θ-Mediated End Joining in the Repair of Chromosome Breaks

scientific article published on 19 July 2016

Essential role for polymerase specialization in cellular nonhomologous end joining.

scientific article

Evidence for local regulatory control of escape from imprinted X chromosome inactivation.

scientific article

Expression of UMP1 is inducible by DNA damage and required for resistance of S. cerevisiae cells to UV light

scientific article

Flavonoid supplementation affects the expression of genes involved in cell wall formation and lignification metabolism and increases sugar content and saccharification in the fast-growing eucalyptus hybrid E. urophylla x E. grandis

scientific article

Fragile DNA motifs trigger mutagenesis at distant chromosomal loci in saccharomyces cerevisiae

scientific article

Gene copy-number variation in haploid and diploid strains of the yeast Saccharomyces cerevisiae

scientific article published on 10 January 2013

Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization

scientific article published on March 2009

Genes acquired by horizontal transfer are potentially involved in the evolution of phytopathogenicity in Moniliophthora perniciosa and Moniliophthora roreri, two of the major pathogens of cacao

scientific article published on 23 December 2009

Genetic heterogeneity of diffuse large B-cell lymphoma

scientific article published on 4 January 2013

Genetic regulation of telomere-telomere fusions in the yeast Saccharomyces cerevisae

scientific article

Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases.

scientific article

Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production

scientific article

Genome-wide maps of alkylation damage, repair, and mutagenesis in yeast reveal mechanisms of mutational heterogeneity.

scientific article published on 14 September 2017

Genome-wide model for the normal eukaryotic DNA replication fork.

scientific article

Genomic insights into the atopic eczema-associated skin commensal yeast Malassezia sympodialis

scientific article published on 22 January 2013

Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin

scientific article published on 5 November 2015

Global analyses of Ceratocystis cacaofunesta mitochondria: from genome to proteome

scientific article

Global analysis of genomic instability caused by DNA replication stress in Saccharomyces cerevisiae

scientific article published on 28 November 2016

Global analysis of the relationship between the binding of the Bas1p transcription factor and meiosis-specific double-strand DNA breaks in Saccharomyces cerevisiae

scientific article published on February 2006

Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition.

scientific article

High-resolution genome-wide analysis of irradiated (UV and γ-rays) diploid yeast cells reveals a high frequency of genomic loss of heterozygosity (LOH) events

scientific article published on 20 January 2012

High-resolution transcript profiling of the atypical biotrophic interaction between Theobroma cacao and the fungal pathogen Moniliophthora perniciosa

scientific article published on 4 November 2014

Highly recombinant VGII Cryptococcus gattii population develops clonal outbreak clusters through both sexual macroevolution and asexual microevolution

scientific article

Identification of a Locus in Mice that Regulates the Collateral Damage and Lethality of Virus Infection

Intercellular Communication between Airway Epithelial Cells Is Mediated by Exosome-Like Vesicles

scientific article published on 01 February 2019

Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages

scientific article published on 09 March 2020

Loss of a histone deacetylase dramatically alters the genomic distribution of Spo11p-catalyzed DNA breaks in Saccharomyces cerevisiae.

scholarly article

Low levels of DNA polymerase alpha induce mitotic and meiotic instability in the ribosomal DNA gene cluster of Saccharomyces cerevisiae.

scientific article

MAP3K4/CBP-regulated H2B acetylation controls epithelial-mesenchymal transition in trophoblast stem cells

scientific article

MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.

scientific article

Metabolic Potential, Ecology and Presence of Associated Bacteria Is Reflected in Genomic Diversity of Mucoromycotina

scientific article published on 15 February 2021

Mosaic structure of p1658/97, a 125-kilobase plasmid harboring an active amplicon with the extended-spectrum beta-lactamase gene blaSHV-5.

scientific article published on 12 January 2007

Multiplex amplicon sequencing for microbe identification in community-based culture collections

scientific article published on 12 July 2016

Mutation signatures specific to DNA alkylating agents in yeast and cancers

scientific article published on 01 April 2020

Nanoscale detection of ionizing radiation damage to DNA by atomic force microscopy

scientific article published in February 2008

Nucleosome dynamics define transcriptional enhancers

scientific article

Polyglutamine toxicity is controlled by prion composition and gene dosage in yeast

scientific article

Practical innovations for high-throughput amplicon sequencing.

scientific article published in September 2013

Pre-capture multiplexing provides additional power to detect copy number variation in exome sequencing

scientific article published in 2021

Primer ID Validates Template Sampling Depth and Greatly Reduces the Error Rate of Next-Generation Sequencing of HIV-1 Genomic RNA Populations

scientific article published on 3 June 2015

Pseudomonas syringae Type III Effector HopBB1 Promotes Host Transcriptional Repressor Degradation to Regulate Phytohormone Responses and Virulence.

scientific article published on 21 January 2017

Quantitative analysis of focused a-to-I RNA editing sites by ultra-high-throughput sequencing in psychiatric disorders

scientific article

RIG-I Detects Kaposi's Sarcoma-Associated Herpesvirus Transcripts in a RNA Polymerase III-Independent Manner.

scientific article

Recombination between retrotransposons as a source of chromosome rearrangements in the yeast Saccharomyces cerevisiae

scientific article published on 23 June 2006

Reconstructing genome evolution in historic samples of the Irish potato famine pathogen.

scientific article

Repair of base damage within break-induced replication intermediates promotes kataegis associated with chromosome rearrangements

scientific article published on 01 October 2019

Repair of multiple simultaneous double-strand breaks causes bursts of genome-wide clustered hypermutation

scientific article published on 30 September 2019

Root microbiota drive direct integration of phosphate stress and immunity.

scientific article published on 15 March 2017

Saccharomyces cerevisiae transcriptional reprograming due to bacterial contamination during industrial scale bioethanol production

scientific article published on 30 January 2015

Scattered far and wide: A broadly distributed temperate dune grass finds familiar fungal root associates in its invasive range

scholarly article by Renee B. Johansen et al published September 2017 in Soil Biology and Biochemistry

Separating DNA with different topologies by atomic force microscopy in comparison with gel electrophoresis.

scientific article

Site-specific silencing of regulatory elements as a mechanism of X inactivation

scientific article

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

article

The Shu complex prevents mutagenesis and cytotoxicity of single-strand specific alkylation lesions

scientific article published on 01 November 2021

The compact chromatin structure of a Ty repeated sequence suppresses recombination hotspot activity in Saccharomyces cerevisiae

scientific article

The fidelity of DNA replication, particularly on GC-rich templates, is reduced by defects of the Fe-S cluster in DNA polymerase δ

scientific article published on 01 June 2021

The fidelity of the ligation step determines how ends are resolved during nonhomologous end joining.

scientific article published on 3 July 2014

The fungal pathogen Moniliophthora perniciosa has genes similar to plant PR-1 that are highly expressed during its interaction with cacao

scientific article

The generation of oxidative stress-induced rearrangements in Saccharomyces cerevisiae mtDNA is dependent on the Nuc1 (EndoG/ExoG) nuclease and is enhanced by inactivation of the MRX complex

scientific article published on 28 December 2012

The genome sequence of Leishmania (Leishmania) amazonensis: functional annotation and extended analysis of gene models

scientific article

The genome sequence of Propionibacterium acidipropionici provides insights into its biotechnological and industrial potential

scientific article (publication date: 19 October 2012)

The histone methylase Set2p and the histone deacetylase Rpd3p repress meiotic recombination at the HIS4 meiotic recombination hotspot in Saccharomyces cerevisiae

scientific article

The impact of environmental and endogenous damage on somatic mutation load in human skin fibroblasts

journal article published in 2016

The mitochondrial genome of Moniliophthora roreri, the frosty pod rot pathogen of cacao.

scientific article

The oncogenic potential of BK-polyomavirus is linked to viral integration into the human genome

scientific article published on 14 July 2015

The pattern of gene amplification is determined by the chromosomal location of hairpin-capped breaks

article

The two-faced nature of BK polyomavirus: lytic infection or non-lytic large-T-positive carcinoma

scientific article published on 31 July 2018

Tn-Seq Analysis Identifies Genes Important for Yersinia pestis Adherence during Primary Pneumonic Plague

scientific article published on 05 August 2020

Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation.

scientific article

Tup1 stabilizes promoter nucleosome positioning and occupancy at transcriptionally plastic genes

scientific article

UVA generates pyrimidine dimers in DNA directly

scientific article published on February 2009

Unisexual and heterosexual meiotic reproduction generate aneuploidy and phenotypic diversity de novo in the yeast Cryptococcus neoformans

scientific article (publication date: September 2013)

Unisexual reproduction drives meiotic recombination and phenotypic and karyotypic plasticity in Cryptococcus neoformans

scientific article published on 11 December 2014

Unraveling the complex genome of Saccharum spontaneum using Polyploid Gene Assembler.

scientific article published on 14 February 2019

Variant calling in low-coverage whole genome sequencing of a Native American population sample

scientific article published on 30 January 2014

Whole Genome Sequence Analysis of Mutations Accumulated in rad27Δ Yeast Strains with Defects in the Processing of Okazaki Fragments Indicates Template-Switching Events

scientific article published on 3 October 2017

Xylem transcription profiles indicate potential metabolic responses for economically relevant characteristics of Eucalyptus species.

scientific article

fourSig: a method for determining chromosomal interactions in 4C-Seq data

scientific article

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