Pao‐Yang Chen
Reproducibility track record
1
assessed papers
61/100
mean reproducibility
0
reproduced (C1–C2)
1
flagged
0
total citations
flag rate:
100%
(1/1)
The share of this author’s assessed papers carrying a ⚑ flag. A concentration is a prompt for expert review — never, on its own, a determination about the person.
Authorship role
first author: 1
last author: 0
Topics
—
Funders
—
Frequent co-authors
Matteo Pellegrini 1Marco Morselli 1Wen‐Wei Liao 1Artur Jaroszewicz 1David López 1Barbara Montanini 1Simone Ottonello 1
Institutions
University of California, Los Angeles 1Institute of Plant and Microbial Biology, Academia Sinica 1University of Parma 1
Geography (author institutions)
US 1TW 1IT 1
Co-author network
Collaborators, sized by shared output and coloured by their own reproducibility (green = high, red = low). Click a node to open their card. A pattern is a prompt for review, never a determination.
How this author’s assessed papers reproduced — the outcome of reproduction attempts, not a judgement of the person. Coverage is partial and grows over time.
Assessed papers (1)
Complete publication record (121)
Request a reproduction →1 assessed by us (0 reproduced) · 120 not yet assessed — every PubMed paper on record, linked below.
-
DNA Methylation Dynamics in Rice Regeneration and Transformation ↗IntechOpen eBooks · 2026not yet assessed
-
HOMEODOMAIN-LIKE shapes chromatin architecture and rewires leaf epidermal patterns ↗Nature Communications · 2026not yet assessed
-
Lignocellulose degradation in bacteria and fungi: cellulosomes and industrial relevance ↗Frontiers in Microbiology · 2025 · PMID 40351319not yet assessed
-
Analysing protein complexes in plant science: insights and limitation with AlphaFold 3 ↗Botanical studies · 2025 · PMID 40402396not yet assessed
-
Computational Workflow for Genome-Wide DNA Methylation Profiling and Differential Methylation Analysis ↗BIO-PROTOCOL · 2025 · PMID 41230550not yet assessed
-
Library Preparation for Genome-Wide DNA Methylation Profiling ↗BIO-PROTOCOL · 2025 · PMID 41220974not yet assessed
-
Epigenetic factors direct synergistic and antagonistic regulation of transposable elements in Arabidopsis ↗PLANT PHYSIOLOGY · 2024 · PMID 39041412not yet assessed
-
Establishing an optimized ATAC-seq protocol for the maize ↗Frontiers in Plant Science · 2024 · PMID 38863553not yet assessed
-
Perturbation of periodic spot-generation balance leads to diversified pigmentation patterning of harlequin Phalaenopsis orchids: in silico prediction ↗BMC Plant Biology · 2024 · PMID 39020275not yet assessed
-
Maize unstable factor for orange1 encodes a nuclear protein that affects redox accumulation during kernel development ↗The Plant Cell · 2024 · PMID 39589935not yet assessed
-
Predicting protein synergistic effect in Arabidopsis using epigenome profiling ↗Nature Communications · 2024 · PMID 39448614not yet assessed
-
Perturbation of periodic spot-generation balance leads to diversified pigmentation patterning of harlequin Phalaenopsis orchids: in silico prediction ↗Research Square · 2024not yet assessed
-
Correction: Perturbation of periodic spot-generation balance leads to diversified pigmentation patterning of harlequin Phalaenopsis orchids: in silico prediction ↗BMC Plant Biology · 2024 · PMID 39152386not yet assessed
-
Lignocellulose Degradation in Bacteria and Fungi for Biomass Conversion ↗bioRxiv (Cold Spring Harbor Laboratory) · 2024not yet assessed
-
Estimating genome-wide DNA methylation heterogeneity with methylation patterns ↗Epigenetics & Chromatin · 2023 · PMID 37941029not yet assessed
-
MethylC-analyzer: a comprehensive downstream pipeline for the analysis of genome-wide DNA methylation ↗Botanical studies · 2023 · PMID 36607439not yet assessed
-
Rice transformation treatments leave specific epigenome changes beyond tissue culture ↗PLANT PHYSIOLOGY · 2023 · PMID 37394940not yet assessed
-
Methylome Imputation by Methylation Patterns ↗Methods in molecular biology · 2023 · PMID 36723812not yet assessed
-
Bioinformatics of epigenetic data generated from next-generation sequencing ↗Elsevier eBooks · 2023not yet assessed
-
There’s More to it: Uncovering Genomewide DNA Methylation Heterogeneity ↗Epigenomics · 2023 · PMID 37485924not yet assessed
-
Correction: MethylC‑analyzer: a comprehensive downstream pipeline for the analysis of genome‑wide DNA methylation ↗Botanical studies · 2023 · PMID 37249660not yet assessed
-
Contributors ↗Elsevier eBooks · 2023not yet assessed
-
Contributors ↗Elsevier eBooks · 2023not yet assessed
-
HISTONE DEACETYLASE 15 and MOS4-associated complex subunits 3A/3B coregulate intron retention of ABA-responsive genes ↗PLANT PHYSIOLOGY · 2022 · PMID 35670741not yet assessed
-
EED is required for mouse primordial germ cell differentiation in the embryonic gonad ↗Developmental Cell · 2022 · PMID 35679863not yet assessed
-
Aberrant overexpression of HOTAIR inhibits abdominal adipogenesis through remodelling of genome-wide DNA methylation and transcription ↗Molecular Metabolism · 2022 · PMID 35292404not yet assessed
-
Blimp-1 molds the epigenetic architecture of IL-21–mediated autoimmune diseases through an autoregulatory circuit ↗JCI Insight · 2022 · PMID 35503415not yet assessed
-
BSImp: Imputing Partially Observed Methylation Patterns for Evaluating Methylation Heterogeneity ↗Frontiers in Bioinformatics · 2022 · PMID 36304331not yet assessed
-
The histone variant H2A.W cooperates with chromatin modifications and linker histone H1 to maintain transcriptional silencing of transposons in Arabidopsis ↗bioRxiv (Cold Spring Harbor Laboratory) · 2022not yet assessed
-
Diversity of Fungal DNA Methyltransferases and Their Association With DNA Methylation Patterns ↗Frontiers in Microbiology · 2021 · PMID 33552027not yet assessed
-
ATACgraph: Profiling Genome-Wide Chromatin Accessibility From ATAC-seq ↗Frontiers in Genetics · 2021 · PMID 33584814not yet assessed
-
Transcriptome Analysis of Dnmt3l Knock-Out Mice Derived Multipotent Mesenchymal Stem/Stromal Cells During Osteogenic Differentiation ↗Frontiers in Cell and Developmental Biology · 2021 · PMID 33718357not yet assessed
-
BSImp: imputing partially observed methylation patterns for evaluating methylation heterogeneity ↗bioRxiv (Cold Spring Harbor Laboratory) · 2021not yet assessed
-
not yet assessed
-
Thermal-responsive genetic and epigenetic regulation of DAM cluster controlling dormancy and chilling requirement in peach floral buds ↗Horticulture Research · 2020 · PMID 32821397not yet assessed
-
MethGET: web-based bioinformatics software for correlating genome-wide DNA methylation and gene expression ↗BMC Genomics · 2020 · PMID 32471342not yet assessed
-
Mycena genomes resolve the evolution of fungal bioluminescence ↗Proceedings of the National Academy of Sciences · 2020 · PMID 33229585not yet assessed
-
The expression of long non-coding RNAs is associated with H3Ac and H3K4me2 changes regulated by the HDA6-LDL1/2 histone modification complex in Arabidopsis ↗NAR Genomics and Bioinformatics · 2020 · PMID 33575615not yet assessed
-
Construction and characterization of a knock-down RNA interference line of OsNRPD1 in rice ( Oryza sativa ssp japonica cv Nipponbare) ↗Philosophical Transactions of the Royal Society B Biological Sciences · 2020 · PMID 32075556not yet assessed
-
Epigenomic regulation of OTU5 in Arabidopsis thaliana ↗Genomics · 2020 · PMID 32298708not yet assessed
-
EpiMOLAS: an intuitive web-based framework for genome-wide DNA methylation analysis ↗BMC Genomics · 2020 · PMID 32241255not yet assessed
-
Mycena genomes resolve the evolution of fungal bioluminescence ↗bioRxiv (Cold Spring Harbor Laboratory) · 2020not yet assessed
-
The histone deacetylase HDA15 interacts with MAC3A and MAC3B to regulate intron retention of ABA-responsive genes ↗bioRxiv (Cold Spring Harbor Laboratory) · 2020not yet assessed
-
Directional Polybenzyl Glutamate Biocompatible Scaffold Promotes the Efficiency of Retinal Differentiation toward Retinal Ganglion Cell Lineage from Human-Induced Pluripotent Stem CellsInvestigative Ophthalmology & Visual Science · 2020not yet assessed
-
Detecting and prioritizing biosynthetic gene clusters for bioactive compounds in bacteria and fungi ↗Applied Microbiology and Biotechnology · 2019 · PMID 30859257not yet assessed
-
SWI3B and HDA6 interact and are required for transposon silencing in Arabidopsis ↗The Plant Journal · 2019 · PMID 31883159not yet assessed
-
Polybenzyl Glutamate Biocompatible Scaffold Promotes the Efficiency of Retinal Differentiation toward Retinal Ganglion Cell Lineage from Human-Induced Pluripotent Stem Cells ↗International Journal of Molecular Sciences · 2019 · PMID 30621308not yet assessed
-
Behavioral Epigenetics: Perspectives Based on Experience-Dependent Epigenetic Inheritance ↗Epigenomes · 2019 · PMID 34968228not yet assessed
-
Assessing chromatin accessibility in maize using ATAC-seq ↗bioRxiv (Cold Spring Harbor Laboratory) · 2019not yet assessed
-
EED is Required for Male and Female Primordial Germ Cell Differentiation in the Embryonic Gonad ↗SSRN Electronic Journal · 2019not yet assessed
-
GENOME-WIDE METHYLOME AND TRANSCRIPTOME PROFILES OF MANIC EPISODE IN BIPOLAR DISORDER ↗European Neuropsychopharmacology · 2019not yet assessed
-
双極性障害におけるマニックエピソードのゲノムワイドメチロームおよびトランスクリプトームプロファイル【JST・京大機械翻訳】European Neuropsychopharmacology · 2019not yet assessed
-
not yet assessed
-
not yet assessed
-
Global impacts of chromosomal imbalance on gene expression in Arabidopsis and other taxa ↗Proceedings of the National Academy of Sciences · 2018 · PMID 30429332not yet assessed
-
BS-Seeker3: ultrafast pipeline for bisulfite sequencing ↗BMC Bioinformatics · 2018 · PMID 29614954not yet assessed
-
Bioinformatics of Epigenomic Data Generated From Next-Generation Sequencing ↗Elsevier eBooks · 2018not yet assessed
-
Computational Methods for Assessing Chromatin Hierarchy ↗Computational and Structural Biotechnology Journal · 2018 · PMID 29686798not yet assessed
-
not yet assessed
-
Using Flow Cytometry to Isolate Maize Meiocytes for Next Generation Sequencing: A Time and Labor Efficient Method ↗Current Protocols in Plant Biology · 2018 · PMID 29927118not yet assessed
-
Reduced Representation Bisulfite Sequencing in Maize ↗BIO-PROTOCOL · 2018 · PMID 34179291not yet assessed
-
List of Contributors ↗Elsevier eBooks · 2018not yet assessed
-
Similarity between soybean and Arabidopsis seed methylomes and loss of non-CG methylation does not affect seed development ↗Proceedings of the National Academy of Sciences · 2017 · PMID 29078418not yet assessed
-
Prenatal Growth Patterns and Birthweight Are Associated With Differential DNA Methylation and Gene Expression of Cardiometabolic Risk Genes in Human Placentas: A Discovery-Based Approach ↗Reproductive Sciences · 2017 · PMID 28693373not yet assessed
-
Deubiquitinating Enzyme OTU5 Contributes to DNA Methylation Patterns and Is Critical for Phosphate Nutrition Signals ↗PLANT PHYSIOLOGY · 2017 · PMID 29061907not yet assessed
-
TRIM28-Regulated Transposon Repression Is Required for Human Germline Competency and Not Primed or Naive Human Pluripotency ↗Stem Cell Reports · 2017 · PMID 29290627not yet assessed
-
Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize ↗Epigenetics & Chromatin · 2017 · PMID 28854962not yet assessed
-
Vascular hypoperfusion in acute optic neuritis is a potentially new neurovascular model for demyelinating diseases ↗PLoS ONE · 2017 · PMID 28926646not yet assessed
-
A termite symbiotic mushroom maximizing sexual activity at growing tips of vegetative hyphae ↗Botanical studies · 2017 · PMID 28929370not yet assessed
-
H2B ubiquitylation and the histone chaperone Asf1 cooperatively mediate the formation and maintenance of heterochromatin silencing ↗Nucleic Acids Research · 2017 · PMID 28520954not yet assessed
-
Game theory in epigenetic reprogramming ↗Physics of Life Reviews · 2017 · PMID 28109754not yet assessed
-
MOESM8 of Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize ↗Figshare · 2017not yet assessed
-
MOESM6 of Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize ↗Figshare · 2017not yet assessed
-
MOESM1 of A termite symbiotic mushroom maximizing sexual activity at growing tips of vegetative hyphae ↗Figshare · 2017not yet assessed
-
MOESM9 of Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize ↗Figshare · 2017not yet assessed
-
MOESM7 of Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize ↗Figshare · 2017not yet assessed
-
MOESM2 of A termite symbiotic mushroom maximizing sexual activity at growing tips of vegetative hyphae ↗Figshare · 2017not yet assessed
-
MOESM1 of Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize ↗Figshare · 2017not yet assessed
-
MOESM2 of Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize ↗Figshare · 2017not yet assessed
-
MOESM2 of Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize ↗Figshare · 2017not yet assessed
-
MOESM3 of Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize ↗Figshare · 2017not yet assessed
-
MOESM3 of Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize ↗Figshare · 2017not yet assessed
-
MOESM5 of Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize ↗Figshare · 2017not yet assessed
-
MOESM2 of A termite symbiotic mushroom maximizing sexual activity at growing tips of vegetative hyphae ↗Figshare · 2017not yet assessed
-
MOESM4 of Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize ↗Figshare · 2017not yet assessed
-
MOESM4 of Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize ↗Figshare · 2017not yet assessed
-
MOESM1 of Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize ↗Figshare · 2017not yet assessed
-
MOESM5 of Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize ↗Figshare · 2017not yet assessed
-
Profiling genome-wide DNA methylation ↗Epigenetics & Chromatin · 2016 · PMID 27358654not yet assessed
-
Stage-Specific Demethylation in Primordial Germ Cells Safeguards against Precocious Differentiation ↗Developmental Cell · 2016 · PMID 27618282not yet assessed
-
Epigenetic changes mediated by polycomb repressive complex 2 and E2a are associated with drug resistance in a mouse model of lymphoma ↗Genome Medicine · 2016 · PMID 27146673not yet assessed
-
TEA: the epigenome platform for Arabidopsis methylome study ↗BMC Genomics · 2016 · PMID 28155665not yet assessed
-
not yet assessed
-
not yet assessed
-
DNA Demethylation Dynamics in the Human Prenatal Germline ↗Cell · 2015 · PMID 26004067not yet assessed
-
An Rtf2 Domain-Containing Protein Influences Pre-mRNA Splicing and Is Essential for Embryonic Development in Arabidopsis thaliana ↗Genetics · 2015 · PMID 25819795not yet assessed
-
MethGo: a comprehensive tool for analyzing whole-genome bisulfite sequencing data ↗BMC Genomics · 2015 · PMID 26680022not yet assessed
-
Epigenetic reprogramming in the mammalian germline ↗Oncotarget · 2015 · PMID 26506592not yet assessed
-
The effects of perinatal testosterone exposure on the DNA methylome of the mouse brain are late-emerging ↗Biology of Sex Differences · 2014 · PMID 24976947not yet assessed
-
Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content ↗Genome biology · 2014 · PMID 25091826not yet assessed
-
Distinct and concurrent pathways of P ol II ‐ and Pol IV ‐dependent si RNA biogenesis at a repetitive trans‐silencer locus in A rabidopsis thaliana ↗The Plant Journal · 2014 · PMID 24798377not yet assessed
-
A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum⚑GigaScience · 2014 · PMID 25392735L1 61/100 ⚑
-
Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content ↗Genome biology · 2014not yet assessed
-
BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data ↗BMC Genomics · 2013 · PMID 24206606not yet assessed
-
Stage-Specific Roles for Tet1 and Tet2 in DNA Demethylation in Primordial Germ Cells ↗Cell stem cell · 2013 · PMID 23415914not yet assessed
-
Intrauterine calorie restriction affects placental DNA methylation and gene expression ↗Physiological Genomics · 2013 · PMID 23695884not yet assessed
-
Methylomes ↗Encyclopedia of Molecular Cell Biology and Molecular Medicine · 2012not yet assessed
-
A comparative analysis of DNA methylation across human embryonic stem cell lines ↗Genome biology · 2011 · PMID 21733148not yet assessed
-
Precise mapping for reduced representation bisulfite sequencing and paired-end reads2011not yet assessed
-
Conservation and divergence of methylation patterning in plants and animals ↗Proceedings of the National Academy of Sciences · 2010 · PMID 20395551not yet assessed
-
Relationship between nucleosome positioning and DNA methylation ↗Nature · 2010 · PMID 20512117not yet assessed
-
Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli ↗Molecular Systems Biology · 2010 · PMID 21179021not yet assessed
-
BS Seeker: precise mapping for bisulfite sequencing ↗BMC Bioinformatics · 2010 · PMID 20416082not yet assessed
-
Deciphering chemotaxis pathways using cross species comparisons ↗BMC Systems Biology · 2010 · PMID 20064255not yet assessed
-
Predicting and Validating Protein Interactions Using Network Structure ↗PLoS Computational Biology · 2008 · PMID 18654616not yet assessed
-
A statistical approach using network structure in the prediction of protein characteristics ↗Bioinformatics · 2007 · PMID 17599931not yet assessed
-
Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology ↗BMC Bioinformatics · 2006 · PMID 17254302not yet assessed
-
Lung adenocarcinoma and human papillomavirus infection ↗Cancer · 2004 · PMID 15368331not yet assessed
-
hp -DPI: Helicobacter pylori Database of Protein Interactomes—embracing experimental and inferred interactions ↗Bioinformatics · 2004 · PMID 15513991not yet assessed
-
Physical Inactivity is an Important Lifestyle Determinant of Insulin Resistance in Hypertensive Patients ↗Blood Pressure · 2004 · PMID 15771220not yet assessed
-
not yet assessed
Full bibliography from OpenAlex; reproducibility verdicts matched by PMID.
Author attribution follows OpenAlex disambiguation, which is imperfect — a researcher's papers can be split across profiles or mixed with a namesake.
Merged across profiles sharing this ORCID where present. See every “Chen P” paper on PubMed ↗