List of works - Piotr A Mieczkowski

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

scientific article

A map of open chromatin in human pancreatic islets

scientific article

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma

scientific article published on 4 November 2015

Nucleosome dynamics define transcriptional enhancers

scientific article

Genetic heterogeneity of diffuse large B-cell lymphoma

scientific article published on 4 January 2013

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

scientific article

Practical innovations for high-throughput amplicon sequencing.

scientific article published in September 2013

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

article

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

scholarly article

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on March 2009

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

scientific article

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

scientific article

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

article

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

scientific article (publication date: September 2013)

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

scientific article

Root microbiota drive direct integration of phosphate stress and immunity.

scientific article published on 15 March 2017

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

scientific article

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

scientific article published on 23 June 2006

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

scientific article published on 2 October 2008

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

scientific article

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

scientific article published on 19 July 2016

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

scientific article

Comprehensive Characterization of Cancer Driver Genes and Mutations

article

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

scientific article published on 22 January 2013

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

scientific article

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

scientific article published on 5 November 2015

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

scholarly article

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

scientific article

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

UVA generates pyrimidine dimers in DNA directly

scientific article published on February 2009

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

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

scientific article

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

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

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

scientific article

Antifungal drug resistance evoked via RNAi-dependent epimutations

scientific article published on 27 July 2014

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 10 January 2013

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

article

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

scientific article published on 14 July 2015

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

scientific article

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

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

scientific article (publication date: 19 October 2012)

Essential role for polymerase specialization in cellular nonhomologous end joining.

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

List of works by Piotr A Mieczkowski

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

A map of open chromatin in human pancreatic islets

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma

Nucleosome dynamics define transcriptional enhancers

Genetic heterogeneity of diffuse large B-cell lymphoma

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

Practical innovations for high-throughput amplicon sequencing.

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

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

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

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

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

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

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

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

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

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

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

Root microbiota drive direct integration of phosphate stress and immunity.

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

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

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

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

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

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

Comprehensive Characterization of Cancer Driver Genes and Mutations

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

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

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

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

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

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

UVA generates pyrimidine dimers in DNA directly

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

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

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

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

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

Antifungal drug resistance evoked via RNAi-dependent epimutations

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

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

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

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

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

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

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

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

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

Essential role for polymerase specialization in cellular nonhomologous end joining.

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.