List of works - Andrew I. Su

A Comparison of the Celera and Ensembl Predicted Gene Sets Reveals Little Overlap in Novel Genes

article

A Large-scale Drug Repositioning Survey for SARS-CoV-2 Antivirals

scientific article published on 18 April 2020

A common and unstable copy number variant is associated with differences in Glo1 expression and anxiety-like behavior

scientific article

A comprehensive and scalable database search system for metaproteomics

scientific article

A comprehensive and scalable database search system for metaproteomics

A crowdsourcing workflow for extracting chemical-induced disease relations from free text

scientific article (publication date: 2016)

A gene atlas of the mouse and human protein-encoding transcriptomes

scientific article

A gene expression atlas of the domestic pig

scientific article

A gene wiki for community annotation of gene function

scientific article published on 8 July 2008

A genome-wide RNAi screen for modifiers of the circadian clock in human cells

scientific article

A genome-wide survey of mutations in the Jurkat cell line.

scientific article published on 8 May 2018

A novel approach to investigate tissue-specific trinucleotide repeat instability

scientific article

A practical review of gastrointestinal manifestations in Parkinson's disease

scientific article published on 23 February 2017

A protocol for adding knowledge to Wikidata, a case report

scientific article published on 07 April 2020

A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses ⬇️

January 2021 scholarly article

A task-based approach for Gene Ontology evaluation

scientific article published on 15 April 2013

Academics can help shape Wikipedia ⬇️

scientific article published in Science

Advancing computational biology and bioinformatics research through open innovation competitions

scientific article published in 2019

Aligning Needs: Integrating Citizen Science Efforts into Schools Through Service Requirements

scientific article published on 01 January 2019

Aligning interests: Integrating Citizen Science Efforts into Schools Through Service Requirements

An efficient rapid system for profiling the cellular activities of molecular libraries.

scientific article

Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer

scientific article

Applications of a rat multiple tissue gene expression data set.

scientific article

Applying Citizen Science to Gene, Drug, Disease Relationship Extraction from Biomedical Abstracts

bioRxiv article

Applying citizen science to gene, drug and disease relationship extraction from biomedical abstracts

scientific article published on 01 February 2020

Association study of long-term kidney transplant rejection using whole-exome sequencing

Author Correction: A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses

scientific article published in 2023

Author response: Wikidata as a knowledge graph for the life sciences

BioGPS and GXD: mouse gene expression data-the benefits and challenges of data integration

scientific article

BioGPS and MyGene.info: organizing online, gene-centric information

scientific article (publication date: 2013)

BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources

scientific article

BioGPS: building your own mash-up of gene annotations and expression profiles

scientific article

BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs

scientific article published in September 2023

Branch: an interactive, web-based tool for testing hypotheses and developing predictive models

scientific article

Building a biomedical semantic network in Wikipedia with Semantic Wiki Links

scientific article

CAFET algorithm reveals Wnt/PCP signature in lung squamous cell carcinoma

scientific article

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer

scientific article (publication date: 31 January 2017)

CIViC: A knowledgebase for expert-crowdsourcing the clinical interpretation of variants in cancer

Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes

scientific article

ChlamBase: a curated model organism database for the Chlamydia research community

scientific article published on 01 January 2019

ChlamBase: a curated model organism database for the Chlamydia research community.

correction

Citizen Science for Mining the Biomedical Literature

scientific article

Citizen Science for Mining the Biomedical Literature

Clock gene wikis available: join the "long tail"

article

Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text

scientific article

Common PIEZO1 Allele in African Populations Causes RBC Dehydration and Attenuates Plasmodium Infection.

scientific article published on 8 March 2018

Comparative analysis of haplotype association mapping algorithms

scientific article

Coordinated transcription of key pathways in the mouse by the circadian clock

scientific article (publication date: 3 May 2002)

Correcting the F508del-CFTR variant by modulating eukaryotic translation initiation factor 3-mediated translation initiation

scientific article published in 2018

Correction: Dizeez: An Online Game for Human Gene-Disease Annotation

scientific article published in PLoS ONE

Corrigendum to “Using single cell analysis for translational studies in immune mediated diseases: Opportunities and challenges” [Mol. Immunol. 103 (2018) 191–199]

scientific article published on 04 February 2019

Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration

scientific article published in February 2018

Crowdsourcing and mining crowd data

scientific article

Crowdsourcing for bioinformatics

scientific article

Crowdsourcing in biomedicine: challenges and opportunities

scientific article published in January 2016

Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems

scientific article

Deep sequencing of the murine IgH repertoire reveals complex regulation of nonrandom V gene rearrangement frequencies

scientific article published on 29 July 2013

Design and application of a knowledge network for automatic prioritization of drug mechanisms

scientific article published on 6 April 2022

Destabilization of Ca2+-free gelsolin may not be responsible for proteolysis in Familial Amyloidosis of Finnish Type

scholarly article

Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing

scientific article published on 24 July 2020

Dizeez: an online game for human gene-disease annotation

scientific article (publication date: 2013)

Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation

scientific article published in February 2001

DrugMechDB: A Curated Database of Drug Mechanisms

scientific article published on 16 September 2023

Dysregulated circadian rhythm pathway in human osteoarthritis: NR1D1 and BMAL1 suppression alters TGF-β signaling in chondrocytes.

scientific article published on 21 November 2016

EXPLANe: An Extensible Framework for Poster Annotation with Mobile Devices

Endoscopic Therapies for Gastroparesis

scientific article published on 23 April 2018

Exploring applications of crowdsourcing to cryo-EM.

scientific article

Expression analysis of G Protein-Coupled Receptors in mouse macrophages

scientific article

Extending gene ontology in the context of extracellular RNA and vesicle communication

scientific article published on 12 April 2016

FoxO transcription factors modulate autophagy and proteoglycan 4 in cartilage homeostasis and osteoarthritis.

scientific article published in February 2018

Functional Annotation of the Transcriptome of the Pig, Sus scrofa, Based Upon Network Analysis of an RNAseq Transcriptional Atlas

scientific article published on 01 January 2019

Functional expression of dental plaque microbiota.

scientific article

Games with a scientific purpose

scientific article

Gene Expression Evolves Faster in Narrowly Than in Broadly Expressed Mammalian Genes

article

Gene Expression in Biopsies of Acute Rejection and Interstitial Fibrosis/Tubular Atrophy Reveals Highly Shared Mechanisms That Correlate With Worse Long-Term Outcomes.

scientific article

Gene Profiling and T Cell Receptor Sequencing from Antigen-Specific CD4 T Cells

scientific article published in January 2018

Gene Wiki Reviews: marrying crowdsourcing with traditional peer review

scientific article published on 5 September 2013

Gene Wiki Reviews—Raising the quality and accessibility of information about the human genome

scientific article (publication date: November 2016)

Gene expression during the priming phase of liver regeneration after partial hepatectomy in mice

scientific article

Gene expression profile of murine long-term reconstituting vs. short-term reconstituting hematopoietic stem cells

scientific article

Gene set enrichment in eQTL data identifies novel annotations and pathway regulators

scientific article

Genetical genomics: spotlight on QTL hotspots

scientific article

Genome-Wide Analysis of CREB Target Genes Reveals A Core Promoter Requirement for cAMP Responsiveness

article

Genome-wide analysis of CREB target genes reveals a core promoter requirement for cAMP responsiveness

scientific article

Genome-wide haplotype association mapping in mice identifies a genetic variant in CER1 associated with BMD and fracture in southern Chinese women

scientific article

Genomewide association analysis in diverse inbred mice: power and population structure

scientific article published on 3 April 2007

Genomic effects of polyamide/DNA interactions on mRNA expression

scientific article

Harnessing the heart of big data

scientific article

HierS: hierarchical scaffold clustering using topological chemical graphs

scientific article

High-performance web services for querying gene and variant annotation

scientific article (publication date: 6 May 2016)

IBS bowel habits and associated symptoms: forming a clearer picture

scientific article published on 19 November 2012

Identification of Serum-Derived Sphingosine-1-Phosphate as a Small Molecule Regulator of YAP

Identification of regulatory elements that control PPARγ expression in adipocyte progenitors

scientific article

Identification of transcription factors responsible for dysregulated networks in human osteoarthritis cartilage by global gene expression analysis

article

Increased DNA Methylation and Reduced Expression of Transcription Factors in Human Osteoarthritis Cartilage

scientific article published on 16 February 2016

Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies

scientific article

Integrative analysis of low- and high-resolution eQTL

scientific article

Knowledge.Bio: A Web application for exploring, building and sharing webs of biomedical relationships mined from PubMed

Large scale molecular analysis identifies genes with altered expression in salivary adenoid cystic carcinoma

scientific article

Large-scale analysis of the human and mouse transcriptomes

scientific article

Large-scale profiling of Rab GTPase trafficking networks: the membrome

scientific article

Linking Wikidata to the Rest of the Semantic Web ⬇️

scientific article (publication date: 19 February 2017)

Linking genes to diseases with a SNPedia-Gene Wiki mashup

scientific article

Metaproteomics of colonic microbiota unveils discrete protein functions among colitic mice and control groups

scientific article published on 10 January 2018

Metaproteomics of colonic microbiota unveils discrete protein functions among colitic mice and control groups

Microtask crowdsourcing for disease mention annotation in PubMed abstracts

scientific article

Mining the Gene Wiki for functional genomic knowledge

scientific journal article

Mohawk is a transcription factor that promotes meniscus cell phenotype and tissue repair and reduces osteoarthritis severity

scientific article published on 01 October 2020

Molecular classification of human carcinomas by use of gene expression signatures.

scientific article

Multi-Omics Database Analysis of Aminoacyl-tRNA Synthetases in Cancer

scientific article published on 22 November 2020

MyGene.info and MyVariant.info: Gene and Variant Annotation Query Services

article

MyGene.info: gene annotation query as a service

article

Nonlinear partial differential equations and applications: Genomic analysis of the host response to hepatitis C virus infection

scientific article

Omics Pipe: A Computational Framework for Reproducible Multi-Omics Data Analysis

Omics Pipe: a community-based framework for reproducible multi-omics data analysis

scientific article

OncoRep: An n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing

OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing

scientific article published on 21 May 2015

Opportunities and challenges presented by Wikidata in the context of biocuration ⬇️

scientific article (publication date: 29 November 2016)

Organizing knowledge to enable personalization of medicine in cancer

scientific article

Oxidative stress diverts tRNA synthetase to nucleus for protection against DNA damage

scientific article

Perspectives on tracking data reuse across biodata resources

Phenotypic characterization of a genetically diverse panel of mice for behavioral despair and anxiety

scientific article

Position β57 of I-Ag7 controls early anti-insulin responses in NOD mice, linking an MHC susceptibility allele to type 1 diabetes onset

scientific article published on 01 August 2019

Power-law-like distributions in biomedical publications and research funding

scientific article published on January 2007

Prioritizing Proteomics Assay Development for Clinical Translation

article

Progress toward a universal biomedical data translator

publication published in 2022

Quantitative Metaproteomics and Activity-Based Probe Enrichment Reveals Significant Alterations in Protein Expression from a Mouse Model of Inflammatory Bowel Disease

scientific article

Reply to “Normalization procedures and detection of linkage signal in genetical-genomics experiments”

Right Flank Pain Caused by a Sigmoid Colon Mass

scientific article published on 05 April 2019

Science Game Lab: tool for the unification of biomedical games with a purpose

Screening the mammalian extracellular proteome for regulators of embryonic human stem cell pluripotency

scientific article

SpaCell: integrating tissue morphology and spatial gene expression to predict disease cells

scientific article published on 01 April 2020

Stress-independent activation of XBP1s and/or ATF6 reveals three functionally diverse ER proteostasis environments

scientific article published on 11 April 2013

Structured Reviews for Data and Knowledge Driven Research

Structured reviews for data and knowledge-driven research

scientific article published on 01 January 2020

Suppression of REDD1 in osteoarthritis cartilage, a novel mechanism for dysregulated mTOR signaling and defective autophagy

scientific article published on 23 April 2016

Synthesis and biological evaluation of myoseverin derivatives: microtubule assembly inhibitors.

scientific article published on December 2001

TCLUST: a fast method for clustering genome-scale expression data

scientific article

Ten simple rules for cultivating open science and collaborative R&D;

scientific article (publication date: 2013)

The Gene Wiki in 2011: community intelligence applied to human gene annotation

scientific article published in 2011

The Gene Wiki: community intelligence applied to human gene annotation

scientific article published in 2009

The Healthy Pregnancy Research Program: Transforming Pregnancy Research Through a ResearchKit App

article published in 2018

The Healthy Pregnancy Research Program: transforming pregnancy research through a ResearchKit app

scientific article published on 05 September 2018

The Implicitome: A Resource for Rationalizing Gene-Disease Associations

scientific article

The ReFRAME library as a comprehensive drug repurposing library and its application to the treatment of cryptosporidiosis

article published in the Proceedings of the National Academy of Sciences of the United States of America

The cure: design and evaluation of a crowdsourcing game for gene selection for breast cancer survival prediction

scientific article

The evolution of dynamin to regulate clathrin-mediated endocytosis: speculations on the evolutionarily late appearance of dynamin relative to clathrin-mediated endocytosis

scientific article published on 16 May 2012

The influence of cholesterol and lipid metabolism on host cell structure and hepatitis C virus replication

scientific article published in February 2006

The nicotinic α6 subunit gene determines variability in chronic pain sensitivity via cross-inhibition of P2X2/3 receptors

scientific article published on May 2015

Time-resolved evaluation of compound repositioning predictions on a text-mined knowledge network

scientific article published on 11 December 2019

Transcriptional profiling of the effects of 25-hydroxycholesterol on human hepatocyte metabolism and the antiviral state it conveys against the hepatitis C virus

scientific article

Triflic Acid Treatment Enables LC-MS/MS Analysis of Insoluble Bacterial Biomass

scientific article published on 08 August 2018

Triflic acid treatment enables LC-MS/MS analysis of insoluble bacterial biomass

Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'.

scientific article

Unifying model for molecular determinants of the preselection Vβ repertoire

scientific article published on 05 August 2013

Use of a dense single nucleotide polymorphism map for in silico mapping in the mouse

scientific article

Using single cell analysis for translational studies in immune mediated diseases: Opportunities and challenges

scientific article published on 06 October 2018

Utility of high-resolution anorectal manometry and wireless motility capsule in the evaluation of patients with Parkinson's disease and chronic constipation

scientific article published on 12 October 2016

Utility of the wireless motility capsule and lactulose breath testing in the evaluation of patients with Parkinson's disease who present with functional gastrointestinal symptoms

scientific article published on 23 February 2017

Visual Artificial Tongue for Quantitative Metal-Cation Analysis by an Off-the-Shelf Dye Array

article

WikiGenomes: an open Web application for community consumption and curation of gene annotation data in Wikidata ⬇️

scientific article

Wikidata as a FAIR knowledge graph for the life sciences

scholarly article

Wikidata as a knowledge graph for the life sciences ⬇️

scientific article published on 17 March 2020

Wikidata as a linked-data hub for Biodiversity data

scientific article published on 18 June 2019

Wikidata as a semantic framework for the Gene Wiki initiative ⬇️

scientific article

Wikidata as a semantic framework for the Gene Wiki initiative

bioRxiv preprint

Wikidata as an intuitive resource towards semantic data modeling in data FAIRification ⬇️

scholarly article by Annika Jacobsen published in December 2018

Wikidata: A platform for data integration and dissemination for the life sciences and beyond ⬇️

2015 scientific article

YY1 plays an essential role at all stages of B-cell differentiation

scientific article published on 22 June 2016

Zone-specific gene expression patterns in articular cartilage

scientific article published on February 2013

exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids

scientific article published on 01 April 2019

List of works by Andrew I. Su

A Comparison of the Celera and Ensembl Predicted Gene Sets Reveals Little Overlap in Novel Genes

A Large-scale Drug Repositioning Survey for SARS-CoV-2 Antivirals

A common and unstable copy number variant is associated with differences in Glo1 expression and anxiety-like behavior

A comprehensive and scalable database search system for metaproteomics

A comprehensive and scalable database search system for metaproteomics

A crowdsourcing workflow for extracting chemical-induced disease relations from free text

A gene atlas of the mouse and human protein-encoding transcriptomes

A gene expression atlas of the domestic pig

A gene wiki for community annotation of gene function

A genome-wide RNAi screen for modifiers of the circadian clock in human cells

A genome-wide survey of mutations in the Jurkat cell line.

A novel approach to investigate tissue-specific trinucleotide repeat instability

A practical review of gastrointestinal manifestations in Parkinson's disease

A protocol for adding knowledge to Wikidata, a case report

A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses ⬇️

A task-based approach for Gene Ontology evaluation

Academics can help shape Wikipedia ⬇️

Advancing computational biology and bioinformatics research through open innovation competitions

Aligning Needs: Integrating Citizen Science Efforts into Schools Through Service Requirements

Aligning interests: Integrating Citizen Science Efforts into Schools Through Service Requirements

An efficient rapid system for profiling the cellular activities of molecular libraries.

Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer

Applications of a rat multiple tissue gene expression data set.

Applying Citizen Science to Gene, Drug, Disease Relationship Extraction from Biomedical Abstracts

Applying citizen science to gene, drug and disease relationship extraction from biomedical abstracts

Association study of long-term kidney transplant rejection using whole-exome sequencing

Author Correction: A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses

Author response: Wikidata as a knowledge graph for the life sciences

BioGPS and GXD: mouse gene expression data-the benefits and challenges of data integration

BioGPS and MyGene.info: organizing online, gene-centric information

BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources

BioGPS: building your own mash-up of gene annotations and expression profiles

BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs

Branch: an interactive, web-based tool for testing hypotheses and developing predictive models

Building a biomedical semantic network in Wikipedia with Semantic Wiki Links

CAFET algorithm reveals Wnt/PCP signature in lung squamous cell carcinoma

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer

CIViC: A knowledgebase for expert-crowdsourcing the clinical interpretation of variants in cancer

Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes

ChlamBase: a curated model organism database for the Chlamydia research community

ChlamBase: a curated model organism database for the Chlamydia research community.

Citizen Science for Mining the Biomedical Literature

Citizen Science for Mining the Biomedical Literature

Clock gene wikis available: join the "long tail"

Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text

Common PIEZO1 Allele in African Populations Causes RBC Dehydration and Attenuates Plasmodium Infection.

Comparative analysis of haplotype association mapping algorithms

Coordinated transcription of key pathways in the mouse by the circadian clock

Correcting the F508del-CFTR variant by modulating eukaryotic translation initiation factor 3-mediated translation initiation

Correction: Dizeez: An Online Game for Human Gene-Disease Annotation

Corrigendum to “Using single cell analysis for translational studies in immune mediated diseases: Opportunities and challenges” [Mol. Immunol. 103 (2018) 191–199]

Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration

Crowdsourcing and mining crowd data

Crowdsourcing for bioinformatics

Crowdsourcing in biomedicine: challenges and opportunities

Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems

Deep sequencing of the murine IgH repertoire reveals complex regulation of nonrandom V gene rearrangement frequencies

Design and application of a knowledge network for automatic prioritization of drug mechanisms

Destabilization of Ca2+-free gelsolin may not be responsible for proteolysis in Familial Amyloidosis of Finnish Type

Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing

Dizeez: an online game for human gene-disease annotation

Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation

DrugMechDB: A Curated Database of Drug Mechanisms

Dysregulated circadian rhythm pathway in human osteoarthritis: NR1D1 and BMAL1 suppression alters TGF-β signaling in chondrocytes.

EXPLANe: An Extensible Framework for Poster Annotation with Mobile Devices

Endoscopic Therapies for Gastroparesis

Exploring applications of crowdsourcing to cryo-EM.

Expression analysis of G Protein-Coupled Receptors in mouse macrophages

Extending gene ontology in the context of extracellular RNA and vesicle communication

FoxO transcription factors modulate autophagy and proteoglycan 4 in cartilage homeostasis and osteoarthritis.

Functional Annotation of the Transcriptome of the Pig, Sus scrofa, Based Upon Network Analysis of an RNAseq Transcriptional Atlas

Functional expression of dental plaque microbiota.

Games with a scientific purpose

Gene Expression Evolves Faster in Narrowly Than in Broadly Expressed Mammalian Genes

Gene Expression in Biopsies of Acute Rejection and Interstitial Fibrosis/Tubular Atrophy Reveals Highly Shared Mechanisms That Correlate With Worse Long-Term Outcomes.

Gene Profiling and T Cell Receptor Sequencing from Antigen-Specific CD4 T Cells

Gene Wiki Reviews: marrying crowdsourcing with traditional peer review

Gene Wiki Reviews—Raising the quality and accessibility of information about the human genome

Gene expression during the priming phase of liver regeneration after partial hepatectomy in mice