Ben Busby
Reproducibility track record
2
assessed papers
55/100
mean reproducibility
0
reproduced (C1–C2)
0
flagged
2
total citations
flag rate:
0%
(0/2)
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: 0
last author: 2
Topics
Funders
—
Frequent co-authors
Tiancheng Xu 1Yilei Fu 1Gaojianyong Wang 1Jędrzej Kubica 1Rajarshi Mondal 1Kimberley J. Billingsley 1Priya Lakra 1Anastasia Illarionova 1Chun-Hsuan Lo 1Sina Majidian 1
Institutions
National Center for Biotechnology Information 2Baylor College of Medicine 1Bayer (United States) 1Helmholtz Institute for Pharmaceutical Research Saarland 1Saarland University 1Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center 1
Geography (author institutions)
US 2DE 1GB 1CN 1TR 1IN 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 (2)
Complete publication record (162)
Request a reproduction →2 assessed by us (0 reproduced) · 160 not yet assessed — every PubMed paper on record, linked below.
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Towards Federated Learning Across Biobanks: Prototype Software from the 2026 Carnegie Mellon University–NVIDIA HackathonBioHackrXiv (OSF Preprints) · 2026not yet assessed
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The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon ↗PLoS Computational Biology · 2025 · PMID 40828848not yet assessed
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Sixth Annual BCM Hackathon on Structural Variation and Pangenomics ↗F1000Research · 2025not yet assessed
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Correction: An international consensus on effective, inclusive, and career-spanning short-format training in the life sciences and beyond ↗PLoS ONE · 2025 · PMID 39977432not yet assessed
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AI for Computational Biology: Highlights from the first BioAI Hackathon at University of Warsaw ↗2025not yet assessed
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The GIAB genomic stratifications resource for human reference genomes ↗Nature Communications · 2024 · PMID 39424793not yet assessed
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Plasma Proteomic Signature Predicts Myeloid Neoplasm Risk ↗Clinical Cancer Research · 2024 · PMID 38446993not yet assessed
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The fifth international hackathon for developing computational cloud-based tools and resources for pan-structural variation and genomics ↗F1000Research · 2024not yet assessed
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A reassessment of Hardy-Weinberg equilibrium filtering in large sample Genomic studies ↗medRxiv · 2024not yet assessed
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Plasma Proteomic Signature Predicts Myeloid Neoplasm Risk ↗Clinical Lymphoma Myeloma & Leukemia · 2024not yet assessed
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MPN-755 Plasma Proteomic Signature Predicts Myeloid Neoplasm Risk ↗Clinical Lymphoma Myeloma & Leukemia · 2024not yet assessed
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33. Customize your variant interpretation workflow with OpenCRAVAT ↗Cancer Genetics · 2024not yet assessed
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The challenge of chromatin model comparison and validation - a project from the first international 4D Nucleome Hackathon ↗bioRxiv (Cold Spring Harbor Laboratory) · 2024not yet assessed
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An international consensus on effective, inclusive, and career-spanning short-format training in the life sciences and beyond ↗PLoS ONE · 2023 · PMID 37943810not yet assessed
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The GIAB genomic stratifications resource for human reference genomes ↗RePEc: Research Papers in Economics · 2023not yet assessed
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Optimizing Short-format Training: an International Consensus on Effective, Inclusive, and Career-spanning Professional Development in the Life Sciences and Beyond ↗bioRxiv (Cold Spring Harbor Laboratory) · 2023not yet assessed
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The GIAB genomic stratifications resource for human reference genomes ↗bioRxiv (Cold Spring Harbor Laboratory) · 2023not yet assessed
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VariantSurvival: a tool to identify genotype–treatment response ↗Frontiers in Bioinformatics · 2023 · PMID 37885757not yet assessed
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Acute and Chronic Pancreatitis Disease Prevalence, Classification, and Comorbidities: A Cohort Study of the UK BioBank ↗Clinical and Translational Gastroenterology · 2022 · PMID 35060944not yet assessed
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iCn3D: From Web-Based 3D Viewer to Structural Analysis Tool in Batch Mode ↗Frontiers in Molecular Biosciences · 2022 · PMID 35252351not yet assessed
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Genetically defined individual reference ranges for tryptase limit unnecessary procedures and unmask myeloid neoplasms ↗Blood Advances · 2022 · PMID 36170795not yet assessed
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The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organismsF1000Research · 2022 · PMID 36262335L1 59/100
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Lessons learned in virulence factor identification and data management from a hackathon on microbial virulence ↗F1000Research · 2022not yet assessed
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Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomes ↗PLoS ONE · 2021 · PMID 33411719not yet assessed
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A strategy for building and using a human reference pangenome ↗F1000Research · 2021 · PMID 34386196not yet assessed
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An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates ↗F1000Research · 2021not yet assessed
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An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates ↗F1000Research · 2021 · PMID 34621504not yet assessed
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iCn3D: From Web-based 3D Viewer to Structural Analysis Tool in Batch Mode ↗bioRxiv (Cold Spring Harbor Laboratory) · 2021not yet assessed
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2021 Bringing Genomics Data to the Clinic Hackathon ↗OSF Preprints (OSF Preprints) · 2021not yet assessed
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Integrated Informatics Analysis of Cancer-Related Variants ↗JCO Clinical Cancer Informatics · 2020 · PMID 32228266not yet assessed
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SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis ↗F1000Research · 2020 · PMID 33014338not yet assessed
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Jupyter notebook-based tools for building structured datasets from the Sequence Read Archive ↗F1000Research · 2020 · PMID 32864105not yet assessed
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NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index ↗Viruses · 2020 · PMID 33322070not yet assessed
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Jupyter notebook-based tools for building structured datasets from the Sequence Read Archive ↗F1000Research · 2020not yet assessed
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39. Integrated informatics analysis of cancer-related variants with OpenCRAVAT ↗Cancer Genetics · 2020not yet assessed
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Methods developed during the first National Center for Biotechnology Information Structural Variation Codeathon at Baylor College of Medicine ↗F1000Research · 2020not yet assessed
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GenerGener/MASQ v0.1.0 ↗Zenodo (CERN European Organization for Nuclear Research) · 2020not yet assessed
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GenerGener/SCANCNV v0.1.0 ↗Zenodo (CERN European Organization for Nuclear Research) · 2020not yet assessed
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GenerGener/DeNovoSV v0.1.0 ↗Zenodo (CERN European Organization for Nuclear Research) · 2020not yet assessed
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GenerGener/SWIGG v0.1.0 ↗Zenodo (CERN European Organization for Nuclear Research) · 2020not yet assessed
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GenerGener/Clouseau v0.1.0 ↗Zenodo (CERN European Organization for Nuclear Research) · 2020not yet assessed
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GenerGener/super-minityper v0.1.0 ↗Zenodo (CERN European Organization for Nuclear Research) · 2020not yet assessed
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GenerGener/ASAP v0.1.0 ↗Zenodo (CERN European Organization for Nuclear Research) · 2020not yet assessed
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Magic-BLAST, an accurate RNA-seq aligner for long and short reads ↗BMC Bioinformatics · 2019 · PMID 31345161not yet assessed
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Box, stalked, and upside-down? Draft genomes from diverse jellyfish (Cnidaria, Acraspeda) lineages: <i>Alatina alata</i> (Cubozoa), <i>Calvadosia cruxmelitensis</i> (Staurozoa), and <i>Cassiopea xamachana</i> (Scyphozoa) ↗GigaScience · 2019 · PMID 31257419not yet assessed
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geneHummus: an R package to define gene families and their expression in legumes and beyond ↗BMC Genomics · 2019 · PMID 31319791not yet assessed
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NCBI’s Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements ↗Genes · 2019 · PMID 31527408not yet assessed
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A strategy for building and using a human reference pangenome ↗F1000Research · 2019not yet assessed
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Iron Hack - A symposium/hackathon focused on porphyrias, Friedreich’s ataxia, and other rare iron-related diseases ↗F1000Research · 2019 · PMID 31824661not yet assessed
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OpenCRAVAT, an open source collaborative platform for the annotation of human genetic variation ↗bioRxiv (Cold Spring Harbor Laboratory) · 2019not yet assessed
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Consensus Machine Learning for Gene Target Selection in Pediatric AML Risk ↗bioRxiv (Cold Spring Harbor Laboratory) · 2019not yet assessed
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Session 3: Open Tools and Platforms ↗OSF Preprints (OSF Preprints) · 2019not yet assessed
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Prototype software for machine learning analysis of human genomes, variants, and expression! ↗Faculty of 1000 Research Ltd · 2019not yet assessed
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The Human Pangenome ↗Open MIND · 2019not yet assessed
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A Pipeline to Define Gene Families in Legumes and Beyond [R package geneHummus version 1.0.11]2019not yet assessed
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SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis ↗F1000Research · 2019not yet assessed
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Additional file 1: of Magic-BLAST, an accurate RNA-seq aligner for long and short reads ↗Figshare · 2019not yet assessed
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NovoGraph: Human genome graph construction from multiple long-read de novo assemblies ↗F1000Research · 2018 · PMID 30613392not yet assessed
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NovoGraph: Genome graph construction from multiple long-read de novo assemblies ↗F1000Research · 2018not yet assessed
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SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis ↗F1000Research · 2018not yet assessed
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Matchmaking in Bioinformatics ↗F1000Research · 2018 · PMID 29636898not yet assessed
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SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis ↗F1000Research · 2018not yet assessed
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Reply to the paper: Misunderstood parameters of NCBI BLAST impacts the correctness of bioinformatics workflows ↗Bioinformatics · 2018 · PMID 30590429not yet assessed
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Magic-BLAST, an accurate DNA and RNA-seq aligner for long and short reads ↗bioRxiv (Cold Spring Harbor Laboratory) · 2018not yet assessed
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An ATAC-seq pipeline wrapped in NextFlow that can be run by Jupyter (ATACFlow) ↗OSF Preprints (OSF Preprints) · 2018not yet assessed
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GeneHummus: A pipeline to define gene families and their expression in legumes and beyond ↗bioRxiv (Cold Spring Harbor Laboratory) · 2018not yet assessed
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PhenotypeXpression: sub-classification of disease states using public gene expression data and literature ↗bioRxiv (Cold Spring Harbor Laboratory) · 2018not yet assessed
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Jupyterized Pipeline Generation ProjectOSF Preprints (OSF Preprints) · 2018not yet assessed
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NCBI-Hackathons/NovoGraph: NovoGraph 1.0.0 ↗Zenodo (CERN European Organization for Nuclear Research) · 2018not yet assessed
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Referee report. For: RSEQREP: RNA-Seq Reports, an open-source cloud-enabled framework for reproducible RNA-Seq data processing, analysis, and result reporting [version 1; referees: 2 approved with reservations] ↗Faculty of 1000 Research Ltd · 2018not yet assessed
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Referee report. For: RSEQREP: RNA-Seq Reports, an open-source cloud-enabled framework for reproducible RNA-Seq data processing, analysis, and result reporting [version 2; peer review: 2 approved] ↗Faculty of 1000 Research Ltd · 2018not yet assessed
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PubRunner: A light-weight framework for updating text mining results ↗F1000Research · 2017not yet assessed
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dbVar structural variant cluster set for data analysis and variant comparison ↗F1000Research · 2017 · PMID 28357035not yet assessed
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PubRunner: A light-weight framework for updating text mining results ↗F1000Research · 2017 · PMID 29152221not yet assessed
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DangerTrack: A scoring system to detect difficult-to-assess regions ↗F1000Research · 2017 · PMID 28503299not yet assessed
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Viewing RNA-seq data on the entire human genomeF1000Research · 2017 · PMID 28979763L1 50/100
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Virus Discovery Project ↗Open MIND · 2017not yet assessed
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Extending TCGA queries to automatically identify analogous genomic data from dbGaP ↗F1000Research · 2017 · PMID 28794857not yet assessed
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Screw: tools for building reproducible single-cell epigenomics workflows ↗Faculty of 1000 Research Ltd · 2017not yet assessed
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NastyBugs: A simple method for extracting antimicrobial resistance information from metagenomes ↗F1000Research · 2017not yet assessed
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MeSHgram: An Open Source Tool to Visually Browse Co-occurrence of MeSH Terms in PubMed.AMIA · 2017not yet assessed
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Harmonizing User-defined Phenotypic Variables using Latent Semantic Analysis (LSA) to Improve Data Discoverability in dbGaP.AMIA · 2017not yet assessed
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Stage 3: ViruSpy ↗OSF Preprints (OSF Preprints) · 2017not yet assessed
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Stage 4: EndoVir ↗OSF Preprints (OSF Preprints) · 2017not yet assessed
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Stage 5: VirusFriends ↗OSF Preprints (OSF Preprints) · 2017not yet assessed
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dbVar structural variant cluster set for data analysis and variant comparison ↗F1000Research · 2016not yet assessed
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Mitogen-activated protein kinase signaling causes malignant melanoma cells to differentially alter extracellular matrix biosynthesis to promote cell survival ↗BMC Cancer · 2016 · PMID 26944546not yet assessed
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Closing gaps between open software and public data in a hackathon setting: User-centered software prototyping ↗F1000Research · 2016 · PMID 27134733not yet assessed
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Closing gaps between open software and public data in a hackathon setting: User-centered software prototyping ↗F1000Research · 2016not yet assessed
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MetaNetVar: Pipeline for applying network analysis tools for genomic variants analysis ↗F1000Research · 2016 · PMID 27158457not yet assessed
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A cloud-based learning environment for comparing RNA-seq aligners ↗F1000Research · 2016not yet assessed
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ISMB sequence-structure hackathon 2016! ↗Faculty of 1000 Research Ltd · 2016not yet assessed
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Building Genomic Analysis Pipelines in a Hackathon Setting with Bioinformatician Teams: DNA-seq, Epigenomics, Metagenomics and RNA-seq ↗bioRxiv (Cold Spring Harbor Laboratory) · 2015not yet assessed
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Building Genomic Analysis Pipelines in a Hackathon Setting2015not yet assessed
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Referee report. For: Evidence of polygenic selection on human stature inferred from spatial distribution of allele frequencies [version 1; referees: 1 approved with reservations] ↗Faculty of 1000 Research Ltd · 2015not yet assessed
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Effect of Domestication on the Spread of the [PIN+] Prion in<i>Saccharomyces cerevisiae</i> ↗Genetics · 2014 · PMID 24812307not yet assessed
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Faculty Opinions recommendation of Transcriptome complexity and riboregulation in the human pathogen Helicobacter pylori. ↗Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · 2013not yet assessed
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Contribution of phage‐derived genomic islands to the virulence of facultative bacterial pathogens ↗Environmental Microbiology · 2012 · PMID 23035931not yet assessed
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Referee report. For: Is the pan-genome also a pan-selectome? [v1; indexed, http://f1000r.es/Vl9wKI] ↗Faculty of 1000 Research Ltd · 2012not yet assessed
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Faculty Opinions recommendation of Cellulases: ambiguous nonhomologous enzymes in a genomic perspective. ↗Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · 2011not yet assessed
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Faculty Opinions recommendation of Opportunity and means: horizontal gene transfer from the human host to a bacterial pathogen. ↗Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · 2011not yet assessed
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Faculty Opinions recommendation of A bacterium that can grow by using arsenic instead of phosphorus. ↗Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · 2010not yet assessed
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A global benchmark study using affinity-based biosensors ↗Analytical Biochemistry · 2008 · PMID 19133223not 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 “Busby B” paper on PubMed ↗