Datasets:

NeuML
/

pubmed-highlycited

+---
+language:
+- en
+license: apache-2.0
+---
+# PubMed Highly Cited
+_Current as of December 4, 2025_
+This dataset is metadata (id, publication date, title, link, # citations) for the Top 100 most highly cited PubMed articles. It was created using [paperetl](https://github.com/neuml/paperetl) and the [PubMed Baseline](https://pubmed.ncbi.nlm.nih.gov/download/).
+## Retrieve article abstracts
+The full article abstracts can be retrieved via the [PubMed API](https://www.nlm.nih.gov/dataguide/eutilities/utilities.html#efetch). This method accepts batches of PubMed IDs.

articles.csv ADDED Viewed

	@@ -0,0 +1,101 @@

+"id","published","title","reference","citations"
+11846609,"2001-12-03 00:00:00","Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.","https://pubmed.ncbi.nlm.nih.gov/11846609",89231
+33538338,"2021-05-03 00:00:00","Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries.","https://pubmed.ncbi.nlm.nih.gov/33538338",63310
+25516281,"2014-12-03 00:00:00","Moderated estimation of fold change and  dispersion for RNA-seq data with DESeq2.","https://pubmed.ncbi.nlm.nih.gov/25516281",59613
+30207593,"2018-11-03 00:00:00","Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries.","https://pubmed.ncbi.nlm.nih.gov/30207593",43137
+2231712,"1990-10-05 00:00:00","Basic local alignment search tool.","https://pubmed.ncbi.nlm.nih.gov/2231712",41839
+19505943,"2009-08-15 00:00:00","The Sequence Alignment/Map format and SAMtools.","https://pubmed.ncbi.nlm.nih.gov/19505943",39608
+22743772,"2012-06-28 00:00:00","Fiji: an open-source platform for biological-image analysis.","https://pubmed.ncbi.nlm.nih.gov/22743772",38053
+24695404,"2014-08-01 00:00:00","Trimmomatic: a flexible trimmer for Illumina sequence data.","https://pubmed.ncbi.nlm.nih.gov/24695404",37436
+16199517,"2005-10-25 00:00:00","Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.","https://pubmed.ncbi.nlm.nih.gov/16199517",37326
+21376230,"2011-03-04 00:00:00","Hallmarks of cancer: the next generation.","https://pubmed.ncbi.nlm.nih.gov/21376230",36248
+23104886,"2013-01-01 00:00:00","STAR: ultrafast universal RNA-seq aligner.","https://pubmed.ncbi.nlm.nih.gov/23104886",35851
+22388286,"2012-03-04 00:00:00","Fast gapped-read alignment with Bowtie 2.","https://pubmed.ncbi.nlm.nih.gov/22388286",35156
+19451168,"2009-07-15 00:00:00","Fast and accurate short read alignment with Burrows-Wheeler transform.","https://pubmed.ncbi.nlm.nih.gov/19451168",32244
+18156677,"2008-01-03 00:00:00","A short history of SHELX.","https://pubmed.ncbi.nlm.nih.gov/18156677",30540
+9254694,"1997-09-01 00:00:00","Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.","https://pubmed.ncbi.nlm.nih.gov/9254694",30101
+14597658,"2003-11-03 00:00:00","Cytoscape: a software environment for integrated models of biomolecular interaction networks.","https://pubmed.ncbi.nlm.nih.gov/14597658",29069
+9310563,"1997-09-13 00:00:00","Bias in meta-analysis detected by a simple, graphical test.","https://pubmed.ncbi.nlm.nih.gov/9310563",28851
+18929686,"2009-04-03 00:00:00","Research electronic data capture (REDCap)--a metadata-driven methodology and workflow process for providing translational research informatics support.","https://pubmed.ncbi.nlm.nih.gov/18929686",28450
+22930834,"2012-07-03 00:00:00","NIH Image to ImageJ: 25 years of image analysis.","https://pubmed.ncbi.nlm.nih.gov/22930834",28203
+19910308,"2010-01-01 00:00:00","edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.","https://pubmed.ncbi.nlm.nih.gov/19910308",27564
+15264254,"2004-10-03 00:00:00","UCSF Chimera--a visualization system for exploratory research and analysis.","https://pubmed.ncbi.nlm.nih.gov/15264254",26477
+25605792,"2015-04-20 00:00:00","limma powers differential expression analyses for RNA-sequencing and microarray studies.","https://pubmed.ncbi.nlm.nih.gov/25605792",26023
+30178033,"2018-10-02 00:00:00","PRISMA Extension for Scoping Reviews (PRISMA-ScR): Checklist and Explanation.","https://pubmed.ncbi.nlm.nih.gov/30178033",25083
+17701901,"2007-09-03 00:00:00","PLINK: a tool set for whole-genome association and population-based linkage analyses.","https://pubmed.ncbi.nlm.nih.gov/17701901",24187
+31986264,"2020-02-15 00:00:00","Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China.","https://pubmed.ncbi.nlm.nih.gov/31986264",23913
+271968,"1977-12-03 00:00:00","DNA sequencing with chain-terminating inhibitors.","https://pubmed.ncbi.nlm.nih.gov/271968",23556
+19131956,"2009-12-03 00:00:00","Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.","https://pubmed.ncbi.nlm.nih.gov/19131956",23417
+34265844,"2021-08-03 00:00:00","Highly accurate protein structure prediction with AlphaFold.","https://pubmed.ncbi.nlm.nih.gov/34265844",23275
+23329690,"2013-04-03 00:00:00","MAFFT multiple sequence alignment software version 7: improvements in performance and usability.","https://pubmed.ncbi.nlm.nih.gov/23329690",22980
+10592173,"2000-01-01 00:00:00","KEGG: kyoto encyclopedia of genes and genomes.","https://pubmed.ncbi.nlm.nih.gov/10592173",22823
+15572765,"2004-12-03 00:00:00","Coot: model-building tools for molecular graphics.","https://pubmed.ncbi.nlm.nih.gov/15572765",22722
+3558716,"1987-12-03 00:00:00","A new method of classifying prognostic comorbidity in longitudinal studies: development and validation.","https://pubmed.ncbi.nlm.nih.gov/3558716",22568
+11556941,"2001-09-03 00:00:00","The PHQ-9: validity of a brief depression severity measure.","https://pubmed.ncbi.nlm.nih.gov/11556941",22451
+15034147,"2004-12-03 00:00:00","MUSCLE: multiple sequence alignment with high accuracy and high throughput.","https://pubmed.ncbi.nlm.nih.gov/15034147",22410
+22455463,"2012-05-03 00:00:00","clusterProfiler: an R package for comparing biological themes among gene clusters.","https://pubmed.ncbi.nlm.nih.gov/22455463",22130
+843571,"1977-03-03 00:00:00","The measurement of observer agreement for categorical data.","https://pubmed.ncbi.nlm.nih.gov/843571",21940
+17695343,"2007-05-03 00:00:00","G*Power 3: a flexible statistical power analysis program for the social, behavioral, and biomedical sciences.","https://pubmed.ncbi.nlm.nih.gov/17695343",21447
+20383002,"2010-04-03 00:00:00","Features and development of Coot.","https://pubmed.ncbi.nlm.nih.gov/20383002",21032
+3802833,"1986-09-03 00:00:00","Meta-analysis in clinical trials.","https://pubmed.ncbi.nlm.nih.gov/3802833",20670
+7984417,"1994-11-11 00:00:00","CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.","https://pubmed.ncbi.nlm.nih.gov/7984417",20559
+8744570,"1996-02-03 00:00:00","VMD: visual molecular dynamics.","https://pubmed.ncbi.nlm.nih.gov/8744570",20064
+17872937,"2007-12-03 00:00:00","Consolidated criteria for reporting qualitative research (COREQ): a 32-item checklist for interviews and focus groups.","https://pubmed.ncbi.nlm.nih.gov/17872937",19325
+20110278,"2010-03-15 00:00:00","BEDTools: a flexible suite of utilities for comparing genomic features.","https://pubmed.ncbi.nlm.nih.gov/20110278",19010
+12111919,"2002-06-15 00:00:00","Quantifying heterogeneity in a meta-analysis.","https://pubmed.ncbi.nlm.nih.gov/12111919",18903
+14744438,"2004-01-23 00:00:00","MicroRNAs: genomics, biogenesis, mechanism, and function.","https://pubmed.ncbi.nlm.nih.gov/14744438",18800
+27004904,"2016-07-03 00:00:00","MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.","https://pubmed.ncbi.nlm.nih.gov/27004904",18220
+25741868,"2015-05-03 00:00:00","Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.","https://pubmed.ncbi.nlm.nih.gov/25741868",18095
+20644199,"2010-09-03 00:00:00","The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.","https://pubmed.ncbi.nlm.nih.gov/20644199",17611
+24227677,"2014-04-01 00:00:00","featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.","https://pubmed.ncbi.nlm.nih.gov/24227677",17580
+20124702,"2010-02-03 00:00:00","PHENIX: a comprehensive Python-based system for macromolecular structure solution.","https://pubmed.ncbi.nlm.nih.gov/20124702",17363
+6880820,"1983-06-03 00:00:00","The hospital anxiety and depression scale.","https://pubmed.ncbi.nlm.nih.gov/6880820",17208
+3447015,"1987-07-03 00:00:00","The neighbor-joining method: a new method for reconstructing phylogenetic trees.","https://pubmed.ncbi.nlm.nih.gov/3447015",17135
+21296855,"2011-12-03 00:00:00","Global cancer statistics.","https://pubmed.ncbi.nlm.nih.gov/21296855",16612
+11328886,"2001-05-01 00:00:00","A new mathematical model for relative quantification in real-time RT-PCR.","https://pubmed.ncbi.nlm.nih.gov/11328886",16311
+10592235,"2000-01-01 00:00:00","The Protein Data Bank.","https://pubmed.ncbi.nlm.nih.gov/10592235",16256
+29722887,"2018-06-01 00:00:00","MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.","https://pubmed.ncbi.nlm.nih.gov/29722887",16248
+19097774,"2009-01-03 00:00:00","New response evaluation criteria in solid tumours: revised RECIST guideline (version 1.1).","https://pubmed.ncbi.nlm.nih.gov/19097774",16123
+27214047,"2016-07-03 00:00:00","DADA2: High-resolution sample inference from Illumina amplicon data.","https://pubmed.ncbi.nlm.nih.gov/27214047",15840
+16717171,"2006-05-22 00:00:00","A brief measure for assessing generalized anxiety disorder: the GAD-7.","https://pubmed.ncbi.nlm.nih.gov/16717171",15755
+22506599,"2012-05-03 00:00:00","SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.","https://pubmed.ncbi.nlm.nih.gov/22506599",15699
+24451623,"2014-05-01 00:00:00","RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.","https://pubmed.ncbi.nlm.nih.gov/24451623",15694
+19114008,"2008-12-29 00:00:00","WGCNA: an R package for weighted correlation network analysis.","https://pubmed.ncbi.nlm.nih.gov/19114008",15471
+19461840,"2007-08-01 00:00:00","Phaser crystallographic software.","https://pubmed.ncbi.nlm.nih.gov/19461840",15460
+2748771,"1989-05-03 00:00:00","The Pittsburgh Sleep Quality Index: a new instrument for psychiatric practice and research.","https://pubmed.ncbi.nlm.nih.gov/2748771",15419
+25651787,"2015-03-03 00:00:00","Global cancer statistics, 2012.","https://pubmed.ncbi.nlm.nih.gov/25651787",15247
+24132122,"2013-12-03 00:00:00","MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.","https://pubmed.ncbi.nlm.nih.gov/24132122",15174
+23193283,"2013-01-03 00:00:00","The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.","https://pubmed.ncbi.nlm.nih.gov/23193283",14996
+32109013,"2020-04-30 00:00:00","Clinical Characteristics of Coronavirus Disease 2019 in China.","https://pubmed.ncbi.nlm.nih.gov/32109013",14917
+19261174,"2009-12-03 00:00:00","Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.","https://pubmed.ncbi.nlm.nih.gov/19261174",14891
+32171076,"2020-03-28 00:00:00","Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study.","https://pubmed.ncbi.nlm.nih.gov/32171076",14675
+25260700,"2015-01-15 00:00:00","HTSeq--a Python framework to work with high-throughput sequencing data.","https://pubmed.ncbi.nlm.nih.gov/25260700",14628
+21546353,"2011-10-03 00:00:00","MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.","https://pubmed.ncbi.nlm.nih.gov/21546353",14493
+2440339,"1987-04-03 00:00:00","Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction.","https://pubmed.ncbi.nlm.nih.gov/2440339",14455
+2868172,"1986-02-08 00:00:00","Statistical methods for assessing agreement between two methods of clinical measurement.","https://pubmed.ncbi.nlm.nih.gov/2868172",14422
+30423086,"2018-09-01 00:00:00","fastp: an ultra-fast all-in-one FASTQ preprocessor.","https://pubmed.ncbi.nlm.nih.gov/30423086",14420
+388439,"1979-09-03 00:00:00","Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications.","https://pubmed.ncbi.nlm.nih.gov/388439",14415
+19414839,"2009-05-05 00:00:00","A new equation to estimate glomerular filtration rate.","https://pubmed.ncbi.nlm.nih.gov/19414839",14344
+1593914,"1992-06-03 00:00:00","The MOS 36-item short-form health survey (SF-36). I. Conceptual framework and item selection.","https://pubmed.ncbi.nlm.nih.gov/1593914",14214
+25220842,"2015-03-01 00:00:00","Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012.","https://pubmed.ncbi.nlm.nih.gov/25220842",14206
+31978945,"2020-02-20 00:00:00","A Novel Coronavirus from Patients with Pneumonia in China, 2019.","https://pubmed.ncbi.nlm.nih.gov/31978945",14171
+38572751,"2024-12-03 00:00:00","Global cancer statistics 2022: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries.","https://pubmed.ncbi.nlm.nih.gov/38572751",14019
+15273542,"2004-08-03 00:00:00","Classification of surgical complications: a new proposal with evaluation in a cohort of 6336 patients and results of a survey.","https://pubmed.ncbi.nlm.nih.gov/15273542",13883
+18546601,"2008-12-03 00:00:00","Analyzing real-time PCR data by the comparative C(T) method.","https://pubmed.ncbi.nlm.nih.gov/18546601",13612
+18798982,"2008-12-03 00:00:00","Model-based analysis of ChIP-Seq (MACS).","https://pubmed.ncbi.nlm.nih.gov/18798982",13575
+17846036,"2007-11-01 00:00:00","Clustal W and Clustal X version 2.0.","https://pubmed.ncbi.nlm.nih.gov/17846036",13494
+3899825,"1985-07-03 00:00:00","Homeostasis model assessment: insulin resistance and beta-cell function from fasting plasma glucose and insulin concentrations in man.","https://pubmed.ncbi.nlm.nih.gov/3899825",13254
+31078660,"2019-07-03 00:00:00","The REDCap consortium: Building an international community of software platform partners.","https://pubmed.ncbi.nlm.nih.gov/31078660",13236
+25751142,"2015-04-03 00:00:00","HISAT: a fast spliced aligner with low memory requirements.","https://pubmed.ncbi.nlm.nih.gov/25751142",13202
+26903338,"2016-02-23 00:00:00","The Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3).","https://pubmed.ncbi.nlm.nih.gov/26903338",13182
+25371430,"2015-01-03 00:00:00","IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.","https://pubmed.ncbi.nlm.nih.gov/25371430",13153
+25554246,"2015-01-01 00:00:00","Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015 statement.","https://pubmed.ncbi.nlm.nih.gov/25554246",13059
+19499576,"2010-01-30 00:00:00","AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.","https://pubmed.ncbi.nlm.nih.gov/19499576",12971
+16904174,"2006-08-25 00:00:00","Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors.","https://pubmed.ncbi.nlm.nih.gov/16904174",12963
+27919275,"2016-12-05 00:00:00","Rayyan-a web and mobile app for systematic reviews.","https://pubmed.ncbi.nlm.nih.gov/27919275",12824
+21816040,"2011-08-04 00:00:00","RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.","https://pubmed.ncbi.nlm.nih.gov/21816040",12684
+6606682,"1983-12-16 00:00:00","Rapid colorimetric assay for cellular growth and survival: application to proliferation and cytotoxicity assays.","https://pubmed.ncbi.nlm.nih.gov/6606682",12630
+16204405,"2005-11-03 00:00:00","Three approaches to qualitative content analysis.","https://pubmed.ncbi.nlm.nih.gov/16204405",12329
+31912902,"2020-01-03 00:00:00","Cancer statistics, 2020.","https://pubmed.ncbi.nlm.nih.gov/31912902",12328
+32142651,"2020-04-16 00:00:00","SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor.","https://pubmed.ncbi.nlm.nih.gov/32142651",12261
+15817019,"2005-04-03 00:00:00","The Montreal Cognitive Assessment, MoCA: a brief screening tool for mild cognitive impairment.","https://pubmed.ncbi.nlm.nih.gov/15817019",12245