Urminder Singh

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.

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 (2)

• Foster thy young: enhanced prediction of orphan genes in assembled genomes.
  2022 L1 84/100
• pyrpipe: a Python package for RNA-Seq workflows.
  2021 L1 79/100

2 assessed by us (2 reproduced) · 42 not yet assessed — every PubMed paper on record, linked below.

• Importance of De Novo Gene Evolution to Emerging Viral Threats: The ORF10 Strain-Restricted Orphan Gene of SARS-CoV-2 Promotes Pathogenesis ↗

  Molecular Biology and Evolution · 2025 · PMID 41092398
  not yet assessed
• Core mitochondrial genes are down-regulated during SARS-CoV-2 infection of rodent and human hosts ↗

  UNC Libraries · 2025
  not yet assessed
• Space radiation damage rescued by inhibition of key spaceflight associated miRNAs ↗

  Nature Communications · 2024 · PMID 38862542
  not yet assessed
• A pan-tissue, pan-disease compendium of human orphan genes ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2024
  not yet assessed
• SARS-CoV-2 ORF10 Promotes COVID-19 Pathogenesis ↗

  SSRN Electronic Journal · 2024
  not yet assessed
• Core mitochondrial genes are down-regulated during SARS-CoV-2 infection of rodent and human hosts ↗

  Science Translational Medicine · 2023 · PMID 37556555
  not yet assessed
• SARS-CoV-2 Orphan Gene ORF10 Contributes to More Severe COVID-19 Disease ↗

  medRxiv · 2023 · PMID 38076862
  not yet assessed
• So Long, and Thanks for All the Antagomirs: Space Radiation Damage Rescued by Inhibition of Key Spaceflight Associated miRNAs ↗

  Research Square · 2023
  not yet assessed
• 178 Tumor neoantigen prioritization from liquid biopsy whole exome sequencing for selected tumor-infiltrating lymphocyte therapy ↗

  Regular and Young Investigator Award Abstracts · 2023
  not yet assessed
• System-wide transcriptome damage and tissue identity loss in COVID-19 patients ↗

  Cell Reports Medicine · 2022 · PMID 35233546
  not yet assessed
• Targeted Down Regulation Of Core Mitochondrial Genes During SARS-CoV-2 Infection ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2022 · PMID 35233572
  not yet assessed
• System-wide transcriptome damage and tissue identity loss in COVID-19 patients ↗

  UNC Libraries · 2022
  not yet assessed
• Accuracy of functional gene community detection in <i>Saccharomyces cerevisiae</i> by maximizing Generalized Modularity Density ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2022
  not yet assessed
• orfipy: a fast and flexible tool for extracting ORFs ↗

  Bioinformatics · 2021 · PMID 33576786
  not yet assessed
• Role of miR-2392 in driving SARS-CoV-2 infection ↗

  Cell Reports · 2021 · PMID 34624208
  not yet assessed
• Foster thy young: enhanced prediction of orphan genes in assembled genomes

  Nucleic Acids Research · 2021 · PMID 34928390
  L1 84/100
• African Americans and European Americans exhibit distinct gene expression patterns across tissues and tumors associated with immunologic functions and environmental exposures ↗

  Scientific Reports · 2021 · PMID 33972602
  not yet assessed
• Landscape of the Dark Transcriptome Revealed Through Re-mining Massive RNA-Seq Data ↗

  Frontiers in Genetics · 2021 · PMID 34484307
  not yet assessed
• <tt>pyrpipe</tt> : a Python package for RNA-Seq workflows

  NAR Genomics and Bioinformatics · 2021 · PMID 34085037
  L1 79/100
• Systemic Tissue and Cellular Disruption from SARS-CoV-2 Infection revealed in COVID-19 Autopsies and Spatial Omics Tissue Maps ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021 · PMID 33758858
  not yet assessed
• The Great Deceiver: miR-2392’s Hidden Role in Driving SARS-CoV-2 Infection ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021 · PMID 33948587
  not yet assessed
• Corrigendum to: Genome-Wide Transcript Profiling Reveals an Auxin-Responsive Transcription Factor, <i>OsAP2/ERF-40</i>, Promoting Rice Adventitious Root Development ↗

  Plant and Cell Physiology · 2021 · PMID 34893895
  not yet assessed
• Pan-tissue pan-cancer characterization of novel human orphan genes via analysis of RNA-Sequencing data

  Iowa State University Digital Repository (Iowa State University) · 2021
  not yet assessed
• How new genes are born ↗

  eLife · 2020 · PMID 32072921
  not yet assessed
• pyrpipe: a python package for RNA-Seq workflows ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• Differential expression of COVID-19-related genes in European Americans and African Americans ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• orfipy: a fast and flexible tool for extracting ORFs ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• African Americans and European Americans exhibit distinct gene expression patterns across tissues and tumors that are associated with immunologic and infectious functions and environmental exposures ↗

  Research Square · 2020
  not yet assessed
• <tt>phylostratr</tt> : a framework for phylostratigraphy ↗

  Bioinformatics · 2019 · PMID 30873536
  not yet assessed
• Genome-Wide Transcript Profiling Reveals an Auxin-Responsive Transcription Factor, OsAP2/ERF-40, Promoting Rice Adventitious Root Development ↗

  Plant and Cell Physiology · 2019 · PMID 31318417
  not yet assessed
• MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets ↗

  Nucleic Acids Research · 2019 · PMID 31956905
  not yet assessed
• fagin: synteny-based phylostratigraphy and finer classification of young genes ↗

  BMC Bioinformatics · 2019 · PMID 31455236
  not yet assessed
• ORIS: An interactive software tool for prediction of replication origin in prokaryotic genomes ↗

  The Journal of Open Source Software · 2019
  not yet assessed
• Machine Learning-Based Annotation of Long Noncoding RNAs Using PLncPRO ↗

  Methods in molecular biology · 2019 · PMID 31893451
  not yet assessed
• MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• Landscape of the Dark Transcriptome Revealed through Re-mining Massive RNA-Seq Data ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• <tt>synder</tt> : inferring genomic orthologs from synteny maps ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• Additional file 3: of fagin: synteny-based phylostratigraphy and finer classification of young genes ↗

  Figshare · 2019
  not yet assessed
• Additional file 2: of fagin: synteny-based phylostratigraphy and finer classification of young genes ↗

  Figshare · 2019
  not yet assessed
• phylostratr: A framework for phylostratigraphy ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2018
  not yet assessed
• PLncPRO for prediction of long non-coding RNAs (lncRNAs) in plants and its application for discovery of abiotic stress-responsive lncRNAs in rice and chickpea ↗

  Nucleic Acids Research · 2017 · PMID 29036354
  not yet assessed
• Ensemble of deep long short term memory networks for labelling origin of replication sequences ↗

  2015
  not yet assessed
• Fingerprinting the rice isolates of R. solani Kuhn using RAPD markers ↗

  Zenodo (CERN European Organization for Nuclear Research) · 2003
  not yet assessed
• PCR based molecular technique for identification and discrimination of quarantined and non-quarantined Tilletia sps. ↗

  PubMed · 2002 · PMID 12693693
  not yet assessed