Topics and Trends in Most Cited Genomics and Phylogenetic Studies Papers

Ranked by citations 18 months after publication

Class of 2026 (Papers Published in 2024)

What topics and trends defined most-cited Genomics and Phylogenetic Studies research in the Class of 2026?

The Class of 2026 reveals a strong shift towards AI-driven genomic analysis, with DNA language models and Transformer architectures rising sharply. Concurrently, advanced long-read sequencing technologies like HiFi and Nanopore continue to provide high-resolution data, indicating a deep integration of predictive computational models and cutting-edge sequencing in modern phylogenetics.

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Updated July 17, 2026

At a glance

Field
Genomics and Phylogenetic Studies
Cohort label
Class of 2026 (2024 publications)
Papers analyzed
10,194
Papers ranked
20
Top topics in ranked papers
DNA language model, 16S rRNA gene sequencing, AlphaFold Protein Structure Database, HiFi sequencing, Transformer models
Publication window
Jan 1, 2024 – Dec 31, 2024
Eligibility
Research articles; reviews excluded
Citation window
18 months post-publication
18m citation range
110–1,911
Data source
OpenAlex · Retrieved Jul 2026
License
CC BY 4.0

Rankings

20 papers ranked by 18-month citation count

#1 of 10,194
1,91118m citations

KEGG: biological systems database as a model of the real world

Minoru Kanehisa et al.Nucleic Acids Research202410.1093/nar/gkae909

Minoru KanehisaKyoto University, Japan

KEGGPathway mapsKEGG Orthology (KO)metagenomesTaxonomic assignmentConserved gene ordersVirus ortholog group (VOG)KO sequencesbiological systems databaseMolecular interaction networksKO assigned genomesconserved genesvirus proteinscellular organismsmulti-organism processes
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#2 of 10,194
1,86418m citations

Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool

Ivica Letunic et al.Nucleic Acids Research202410.1093/nar/gkae268

Ivica Letunićbiobyte solutions GmbH, Germany

Interactive Tree of Life (iTOL)Phylogenetic tree visualizationtree annotationcolored/labeled ranges datasetdataset template filessubstring matchingregular expression supportnode metadatabulk label editingmultiple font stylesGenome Taxonomy Database (GTDB)NCBI taxonomyTaxonomic assignmentuser account managementtree sharing
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#3 of 10,194
36918m citations

Sequence modeling and design from molecular to genome scale with Evo

Eric Nguyen, Michael Poli, Matthew G Durrant, Brian Kang, Dhruva Katrekar, David B Li et al.Science202410.1126/science.ado9336

Eric Nguyen, Michael Poli, Matthew G. Durrant, Brian Kang, Dhruva Katrekar, David Li, Patrick D. Hsu, Brian HieArc Institute, United States

Evoprokaryotic genomesPhage genomesscaling laws on DNAZero-shot learningCRISPR-Cas system generationtransposon system generationprotein-RNA codesignprotein-DNA codesignmutation effect predictionwhole-organism fitnessmegabase-scale sequence generationgenomic architecturecross-modality generalizationDNA language modelRNA language modelProtein language model
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#4 of 10,194
34718m citations

Nucleotide Transformer: building and evaluating robust foundation models for human genomics

Hugo Dalla-Torre et al.Nature Methods202410.1038/s41592-024-02523-z

M. Lopez, Thomas PierrotInstaDeep, United Kingdom

Nucleotide Transformerfoundation modelsBiological sequence predictionmolecular phenotype predictionTransformer modelscontext-specific nucleotide representations3,202 human genomes850 diverse species genomesfine-tuninglow-data settingstransfer learninggenetic variant prioritizationattention mechanismsgenomic elements2.5 billion parameterspre-training on DNA sequencesmulti-species genomicsZero-shot learning
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#5 of 10,194
29118m citations

GENCODE 2025: reference gene annotation for human and mouse

Jonathan M Mudge et al.Nucleic Acids Research202410.1093/nar/gkae1078

Jonathan M MudgeEuropean Molecular Biology Laboratory, United Kingdom

GENCODEreference gene annotationlong-read transcriptome sequencinglong non-coding RNAproteomicsRibo-seqtranslated sequencesmulti-genome alignmentsMANE SelectGENCODE PrimaryPan-genomeEnsembl genome browserUCSC genome browsertranscript modelsannotation workflow
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#6 of 10,194
23718m citations

JCVI: A versatile toolkit for comparative genomics analysis

Haibao Tang et al.iMeta202410.1002/imt2.211

Haibao Tang, Xingtan ZhangFujian Agriculture and Forestry University, China

JCVI librarycomparative genomicsGenome assemblygenome annotationMCScanXALLMAPSPython-based librarysynteny analysisformat parsingPublication-ready figuresQuality controlevolutionary inferenceModular designgenome builds
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#8 of 10,194
21318m citations

OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes

Fredrik Tegenfeldt et al.Nucleic Acids Research202410.1093/nar/gkae987

Fredrik TegenfeldtUniversity of Geneva, Switzerland

OrthoDBBUSCOOrthologous groupshierarchical gene orthologyOrthoLogerODB-mapperSingle-copy orthologsREST APISPARQL/RDFcoding DNA sequencesgene loci coordinatesFunctional annotationevolutionary annotationGenome assemblymetagenomic binstranscriptomesConda packageBioContainersPython APIR Bioconductor
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#9 of 10,194
20318m citations

EzBioCloud: a genome-driven database and platform for microbiome identification and discovery

Mauricio Chalita et al.INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY202410.1099/ijsem.0.006421

Mauricio ChalitaCJ Bioscience Inc, South Korea

EzBioCloud16S rRNA gene sequencinggenome sequence comparisonAverage nucleotide identityANICore gene ANIbacterial core genesTaxonomic assignmentNCBI Assembly DatabaseQuality controlcandidate speciesphylotypesgenomospeciesspecies clustersvalidly published namesBacteria and Archaea classificationmicrobiome identificationGenome assemblyUnderrepresented populations
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#10 of 10,194
19818m citations

Rapid and sensitive detection of genome contamination at scale with FCS-GX

Alexander Astashyn, Eric S Tvedte et al.Genome biology202410.1186/s13059-024-03198-7

Terence D. MurphyNational Institutes of Health, United States

FCS-GXGenome contamination assessmentassembled genome sequencescontaminant sequence removalGenBank assembliesRefSeqartificially fragmented genomesscreening sensitivity and specificitycomputational screening speedGenome quality assessment
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#11 of 10,194
19618m citations

Detection of mosaic and population-level structural variants with Sniffles2

Moritz Smolka, Luis F Paulin et al.Nature Biotechnology202410.1038/s41587-023-02024-y

Fritz J. SedlazeckBaylor College of Medicine, United States

Sniffles2Structural variationlong-read sequencingmosaic structural variantspopulation-level SV callingrepeat-aware clusteringConsensus sequencecoverage-adaptive filteringNanopore sequencingHiFi sequencingMECP2multiple system atrophycingulate cortexgenotyped VCF filesfamily-level SV callingbulk long-read datacomplex genomic alterationsoverlapping SVsbrain tissue mosaicism
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#12 of 10,194
19018m citations

SeqKit2: A Swiss army knife for sequence and alignment processing

Wei Shen et al.iMeta202410.1002/imt2.191

Wei ShenChongqing Medical University, China

SeqKit2sequence analysis toolhigh-throughput sequencingsubcommand architectureamplicon processingerror-tolerant parsingFASTQ formatBinary Alignment/Map formatreal-time analysisstreaming processingcompression methodsperformance optimizationBioawkSeqtkSeqFualignment processingBioinformatics pipelinesequence record parsing
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#13 of 10,194
17418m citations

Complexity of avian evolution revealed by family-level genomes

Josefin Stiller et al.Nature202410.1038/s41586-024-07323-1

Josefin Stiller, Siavash Mirarab, Guojie ZhangUniversity of Copenhagen, Denmark

avian phylogenyNeoaves363 bird species genomes218 taxonomic familiesintergenic regionsCoalescent theoryPhylogenetic discordanceCretaceous-Paleogene extinction eventAdaptive radiationincomplete lineage sortingancient hybridizationextreme DNA compositionvariable substitution ratesgenomic heterogeneityeffective population sizerelative brain sizetaxon samplingrecalcitrant nodes
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#14 of 10,194
16918m citations

The nature of the last universal common ancestor and its impact on the early Earth system

Edmund R R Moody et al.Nature Ecology & Evolution202410.1038/s41559-024-02461-1

Edmund R. R. Moody, Davide Pisani, Tom A. Williams, Timothy M. Lenton, Philip C. J. DonoghueUniversity of Bristol, United Kingdom

last universal common ancestor (LUCA)Divergence time estimationpre-LUCA gene duplicatescross-bracing calibrationmicrobial fossilsisotope recordsphylogenetic reconciliationgenome size estimationprokaryote-grade organismanaerobic acetogenearly immune systemhydrogen recyclingatmospheric photochemistryearly ecosystem productivitymicrobial community interactions4.2 Ga age estimatecore metabolism reconstructiongeochemistry dependenceArchean Earth system
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#15 of 10,194
14518m citations

Rfam 15: RNA families database in 2025

Nancy Ontiveros-Palacios et al.Nucleic Acids Research202410.1093/nar/gkae1023

Blake SweeneyEuropean Molecular Biology Laboratory, United Kingdom

Rfam databasenon-coding RNA familiesRfamseqUniProt reference proteomesviral genomes3D structure-guided annotationconsensus secondary structureR-scape covariation analysisGene Ontology (GO) annotationSequence OntologyHepatitis C Virus RNA familiesmicroRNA familiesmiRBase synchronizationFULL alignmentsAPICURONgenome annotationRNA structure prediction
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#16 of 10,194
13618m citations

RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments

Sebastian Bittrich et al.Bioinformatics202410.1093/bioinformatics/btae370

Sebastian BittrichUniversity of California, United States

Protein Data Bank (PDB)pairwise structure alignment3D protein structure comparisonFATCATCE algorithmTM-alignSmith-Waterman 3DMol* 3D viewerSequence Annotations viewerModelArchiveAlphaFold Protein Structure DatabaseComputed Structure Modelsbrowser-based alignment tool1D sequence visualization3D structural visualizationalignment APIcustom structure uploadstructural bioinformaticsevolutionary relationship analysis
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#17 of 10,194
12818m citations

Global marine microbial diversity and its potential in bioprospecting

Jianwei Chen, Yangyang Jia, Ying Sun, Kun Liu et al.Nature202410.1038/s41586-024-07891-2

Ying Sun, Thomas Möck, Shengying Li, Wenwei Zhang, Guangyi FanBGI Research, China

marine metagenomesbacterial and archaeal genomesCRISPR–Cas systemsAntimicrobial resistance genesCRISPR–Cas9 systemantimicrobial peptidespolyethylene terephthalate degradation enzymesin silico bioprospectingmarine bacterial genome sizetrade-offs between CRISPR and antibiotic resistance138 distinct phyla43,191 genomesglobal-scale sequencingmarine microbial diversitybiotechnological applicationsbiomedical applications
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#18 of 10,194
11218m citations

<scp>TreeViewer</scp>: Flexible, modular software to visualise and manipulate phylogenetic trees

Giorgio Bianchini et al.Ecology and Evolution202410.1002/ece3.10873

Giorgio BianchiniUniversity of Bristol, United Kingdom

TreeViewerPhylogenetic tree visualizationModular designuser-defined plotting pipelinegraphical user interface (GUI)command-line interfacePublication-ready figuresAGPLv3 licencecross-platform compatibilitycustom modulestree plotting customizationBioinformatics pipelinelarge phylogenetic trees
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#19 of 10,194
11218m citations

The variation and evolution of complete human centromeres

Glennis A Logsdon et al.Nature202410.1038/s41586-024-07278-3

Evan E. EichlerUniversity of Washington, United States

long-read sequencingcentromere assemblyα-satellite higher-order repeatsHORsSingle nucleotide variantscentromeric size variationDNA methylationCENP-A chromatin immunoprecipitationkinetochore positioncommon chimpanzeeorangutanmacaqueorthologous centromeresα-satellite HOR turnoversaltatory amplificationphylogenetic reconstructionp armq armcentromeric recombinationmonophyletic origin
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#20 of 10,194
11018m citations

Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information

Baptiste Gaborieau, Hugo Vaysset, Florian Tesson et al.Nature Microbiology202410.1038/s41564-024-01832-5

Baptiste GaborieauUniversité Paris Cité, France

phage-host interactionsStrain-level analysisEscherichia genusGenomic dataBacteriophageHost predictioncomputational prediction modelphage receptor binding proteinsbacterial surface receptorsmachine learninggenomic featuresphage infectivityEscherichia coli strainsPhage genomeshost genome sequencescross-strain prediction
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Dominant research themes and year-over-year shifts in Genomics and Phylogenetic Studies

What Topics Define the Class of 2026?

In the Class of 2026, genomics and phylogenetic studies are increasingly defined by the integration of artificial intelligence and advanced sequencing technologies. DNA language models, Transformer architectures, and the AlphaFold Protein Structure Database are among the most prominent topics, indicating a major shift towards computational and predictive modeling in genomics. Concurrently, high-fidelity approaches such as HiFi and Nanopore long-read sequencing maintain a strong presence, enabling unprecedented resolution of complex genomes. This dual focus highlights a field where cutting-edge sequencing provides the high-quality data necessary to train powerful deep learning models, ultimately accelerating sequence analysis, structural prediction, and our understanding of evolutionary relationships.

Leading research themes
Leading research themes

How Did Topics Shift from the Class of 2025 to the Class of 2026?

The transition to the Class of 2026 reveals a distinct pivot toward AI-driven methodologies in genomic analysis. Topics like DNA language models and Transformer models emerged rapidly, reflecting the broader adoption of large language model architectures for interpreting genomic sequences and regulatory elements. Meanwhile, structural prediction tools such as the AlphaFold Protein Structure Database also saw significant growth. Conversely, traditional phylogenetic pipelines and basic genomic assembly approaches experienced relative declines in prominence. This evolution underscores a broader trend in genomics and phylogenetics: researchers are rapidly moving beyond basic sequence assembly to leverage deep learning frameworks that can extract complex, predictive insights from vast genomic datasets.

How topics shifted year over year
How topics shifted year over year
Methodology

PRI identifies high-impact research using a transparent, topic-agnostic framework applied consistently across scientific domains. Bibliographic records are drawn from OpenAlex, including publication dates, citation relationships, and document types.

This ranking covers the Class of 2026 cohort: journal articles published in 2024. Reviews and other non-article document types are excluded to ensure comparability.

Research impact is quantified with an 18-month post-publication citation window—the number of citing works published within 18 months of each paper's publication date. This metric captures early impact while controlling for publication age.

An LLM-based relevance classifier then reviews each candidate's title and abstract to confirm substantive alignment with the target domain. Only papers classified as relevant appear in the final ranking.

Zheng Su, Tinsley Li, Thematic Shifts in Early-High-Impact Cancer Genomics and Diagnostics Research: A Bibliometric and Semantic Analysis. bioRxiv 2026.07.04.736459; doi: https://doi.org/10.64898/2026.07.04.736459

Full methodologyGitHubbioRxiv preprint

Cite this ranking

Pepkio Research Index (PRI). Topics and Trends in Most Cited Genomics and Phylogenetic Studies Papers, Class of 2026. https://pri.pepkio.com/top-papers/genomics-and-phylogenetic-studies/2026. Accessed 2026-07-17.

Zheng Su, Tinsley Li, Thematic Shifts in Early-High-Impact Cancer Genomics and Diagnostics Research: A Bibliometric and Semantic Analysis. bioRxiv 2026.07.04.736459; doi: https://doi.org/10.64898/2026.07.04.736459