Topics and Trends in Most Cited Molecular Biology Techniques and Applications Papers

Ranked by citations 18 months after publication

Class of 2026 (Papers Published in 2024)

What topics and trends defined most-cited Molecular Biology Techniques and Applications research in the Class of 2026?

The Class of 2026 highlights a four-fold rise in genome assembly research and the emergence of direct RNA sequencing, CRISPR-Cas12a diagnostics, and extrachromosomal DNA (ecDNA) structural studies. While spatial transcriptomics remains the leading individual concept despite consolidating from earlier peaks, the field shows accelerating adoption of point-of-care nucleic acid detection.

See details ↓

Updated July 24, 2026

At a glance

Field
Molecular Biology Techniques and Applications
Cohort label
Class of 2026 (2024 publications)
Papers analyzed
3,522
Papers ranked
20
Top topics in ranked papers
Spatial transcriptomics, genome assembly, CRISPR-Cas12a, direct RNA sequencing
Publication window
Jan 1, 2024 – Dec 31, 2024
Eligibility
Research articles; reviews excluded
Citation window
18 months post-publication
18m citation range
30–239
Data source
OpenAlex · Retrieved July 2026
License
CC BY 4.0

Rankings

20 papers ranked by 18-month citation count

#1 of 3,522
23918m citations

NCBI RefSeq: reference sequence standards through 25 years of curation and annotation

Tamara Goldfarb et al.Nucleic Acids Research202410.1093/nar/gkae1038

Tamara GoldfarbNational Institutes of Health, United States

NCBI RefSeqreference sequencesgenome annotationtranscript annotationprotein annotationeukaryotic annotationprokaryotic RefSeqviral RefSeqTranscriptomic dataOrtholog mappingcomparative genomicsexpert curationautomatic annotation processessequencing technologiestaxonomic representationgene function interpretationsequence variationtranscriptomicsproteomicsQuality control
Badge
#2 of 3,522
19718m 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

Foreign Contamination Screen (FCS-GX)genome contamination detectioncontaminant sequence removalGenome assemblyNCBI RefSeqartificially fragmented genomessensitivity and specificity testinghigh-throughput genome screeningcontamination quantificationgenome assembly quality control
Badge
#3 of 3,522
12418m citations

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark Diekhans, Sílvia Carbonell-Sala, Brian Williams, Jane E Loveland, Maite De María et al.Nature Methods202410.1038/s41592-024-02298-3

Ashley M. Brooks, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria Sheynkman, A Mortazavi, Ana Conesa, Angela N. BrooksSpanish National Research Council (CSIC), Spain

long-read RNA-seqIsoform detectiontranscript quantificationTranscript detectioncomplementary DNA sequencingDirect RNA sequencingLong-read RNA-Seq Genome Annotation Assessment ProjectSequencing coverageread lengthread accuracyreference-based transcript assemblyreference-free transcript assemblyMulti-modal integrationtranscriptome benchmarkinggenome annotationsequencing platform comparisonlibrary preparation protocols
Badge
#4 of 3,522
8718m citations

Inferring super-resolution tissue architecture by integrating spatial transcriptomics with histology

Daiwei Zhang et al.Nature Biotechnology202410.1038/s41587-023-02019-9

Daiwei Zhang, Mingyao LiUniversity of Pennsylvania, United States

Spatial transcriptomicsHistology integrationSuper-resolutionTissue morphologyimage registrationTranscriptomic datahistological imagescomputational integrationSpatial mappingGene expression patternsMulti-modal integrationspatial inference
Badge
#5 of 3,522
7518m citations

Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues

Zhiliang Bai et al.Cell202410.1016/j.cell.2024.09.001

Zhiliang Bai, Mingyao Li, Yi Xing, Jun Lü, Mina L. Xu, Rong FanYale University, United States

Patho-DBiTFFPE tissuedeterministic barcoding in tissuein situ polyadenylationSpatial transcriptomicsRNA processingsplicing isoformssingle-nucleotide RNA variantsmalignant subcloneshuman lymphomasmicroRNA regulatory networksRNA splicing dynamicsspatial tumorigenesisSingle-cell spatial transcriptomicstumor clonal architecturespatiotemporal cellular dynamicsclinical tumor tissuesarchival tissue analysis
Badge
#6 of 3,522
7018m citations

Global impact of unproductive splicing on human gene expression

Benjamin Fair, Carlos F Buen Abad Najar et al.Nature Genetics202410.1038/s41588-024-01872-x

Yang LiUniversity of Chicago, United States

alternative splicingnonsense-mediated decayunproductive splicingunproductive transcriptsAS-NMDproteomic diversitygene expression regulationPopulation-scale sequencingmulti-intronic genesgenetic variation across cell linesGWAS trait-associated lociprotein isoform usagetranscript degradationcytoplasmic decaysteady-state RNANMD-induced expression changes
Badge
#7 of 3,522
6718m citations

Prediction of plasma ctDNA fraction and prognostic implications of liquid biopsy in advanced prostate cancer

Nicolette M Fonseca, Corinne Maurice-Dror, Cameron Herberts et al.Nature Communications202410.1038/s41467-024-45475-w

Matti Annala, Kim N., Alexander W. WyattUniversity of British Columbia, Canada

Circulating tumor DNA fractionMetastatic castration-resistant prostate cancer (mCRPC)liquid biopsyoverall survivalprogression-free survivaltreatment response predictionliver metastasesdisease burden metricsctDNA genotypingrisk stratificationMachine learning prediction modelplasma samplesrandomized phase II trialsblood biobankingclinical prognostic factorsbiomarker testing optimization
Badge
#8 of 3,522
5918m citations

Inferring histology-associated gene expression gradients in spatial transcriptomic studies

Jan Kueckelhaus, Simon Frerich et al.Nature Communications202410.1038/s41467-024-50904-x

Jan Kueckelhaus, Dieter Henrik HeilandFreiburg University, Germany

Spatial Gradient ScreeningSpatial transcriptomicshistology-associated gene expression patternscluster-free detectionCell type deconvolutioninjured mouse cortexTCR-seqbrain tumorsDifferential gene expression analysisspatial architecture of transcriptomesSPATA2supervised detectionTissue morphologyexpression gradientssignature genes
Badge
#9 of 3,522
5818m citations

Whole-brain spatial transcriptional analysis at cellular resolution

Judith C Kreutzmann, Yue Li, Zoe West et al.Science202410.1126/science.adn9947

Shigeaki Kanatani, Judith C. Kreutzmann, Yue Li, Zoe West, Per UhlénKarolinska Institutet, Sweden

TRISCOtissue-clearing methodwhole-brain 3D RNA imagingin situ hybridization chain reactionSpatial transcriptomicsRNA integrity preservationuniform RNA labelingtissue transparency enhancementcell-identity markersNon-coding RNAsactivity-dependent RNAssingle-cell resolutionintact tissue volumesTris buffer-mediated retentioncleared organs
Badge
#10 of 3,522
4918m citations

Mapping extrachromosomal DNA amplifications during cancer progression

Hoon Kim, Soyeon Kim et al.Nature Genetics202410.1038/s41588-024-01949-7

Hoon Kim, Roel G.W. VerhaakSungkyunkwan University, South Korea

Extrachromosomal DNA (ecDNA)Focal amplificationcancer progressionmetastasischemotherapy pretreatmenttubulin inhibitiontreatment responselongitudinally matched tumor sampleschromosomal amplificationsecDNA retentionlocalized hypermutationvariant allele fractionecDNA mutagenesisuntreated metastasesnewly diagnosed primary cancerspretreated tumors
Badge
#11 of 3,522
4718m citations

High resolution long-read telomere sequencing reveals dynamic mechanisms in aging and cancer

Tobias T Schmidt, Carly Tyer, Preeyesh Rughani et al.Nature Communications202410.1038/s41467-024-48917-7

Scott Hickey, Jan KarlsederSalk Institute for Biological Studies, United States

Telo-seqNanopore sequencingDirect RNA sequencingtelomere length measurementchromosome arm-specific telomere lengthallele-specific telomere lengthtelomere length heterogeneitytelomere shorteningpopulation doublingtelomerase-positive cancerALT-positive canceralternative lengthening of telomerestelomere biology
Badge
#12 of 3,522
4618m citations

Phantasus, a web application for visual and interactive gene expression analysis

Maksim Kleverov, Daria Zenkova, Vladislav Kamenev et al.eLife202410.7554/elife.85722

Maksim Kleverov, Daria Zenkova, Vladislav KamenevITMO University, Russia

Phantasusweb applicationgene expression analysisinteractive visualizationGene expression profilingTranscriptomic dataJavaScript-based heatmap interfaceR-based analysis methodsData normalizationdata filteringDifferential gene expression analysisdownstream analysisBioconductoruser-uploaded datasetsstreamlined data access
Badge
#13 of 3,522
4618m citations

Extrachromosomal DNA in cancer

Xiaowei Yan et al.Nature reviews. Cancer202410.1038/s41568-024-00669-8

Paul S. Mischel, Howard Y. ChangStanford University, United States

Extrachromosomal DNA (ecDNA)oncogene amplificationchromothripsisdouble minutescircular DNAFocal amplificationTumor heterogeneityCopy number variationepisomesMYC amplificationEGFR amplificationGenomic instabilityTumor evolutionextrachromosomal circular DNA
Badge
#14 of 3,522
4418m citations

Virtual formalin-fixed and paraffin-embedded staining of fresh brain tissue via stimulated Raman CycleGAN model

Zhijie Liu et al.Science Advances202410.1126/sciadv.adn3426

Zhijie Liu, Lingchao Chen, Haixia Cheng, Minbiao JiFudan University, China

stimulated Raman scattering microscopyCycleGANVirtual histologyformalin-fixed and paraffin-embedded stainingHematoxylin and eosin stainingintraoperative histologyfresh brain tissuefrozen sectionsemi-supervised learningunpaired training datagliomaneuropathologylipid/protein contrastnucleic acid stainingrapid tissue imagingsurgical guidancehistologic subtyping
Badge
#15 of 3,522
3818m citations

Genetic architecture of telomere length in 462,666 UK Biobank whole-genome sequences

Oliver S Burren, Ryan S Dhindsa, Sri V V Deevi et al.Nature Genetics202410.1038/s41588-024-01884-7

Oliver S Burren, Ryan S Dhindsa, Sri V V DeeviAstraZeneca, United Kingdom

telomere lengthUK Biobankwhole-genome sequencingQuantitative PCRjoint telomere length metricSNP heritabilityexome-wide rare-variant associationgene-level collapsing analysisACDRTEL1allelic seriesclonal hematopoiesissomatic mosaicismmyeloid cancersSRSF2somatic variant analysisclonal expansionsrare variantsgene-specific associations
Badge
#16 of 3,522
3618m citations

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Ann M Mc Cartney, Giulio Formenti, Alice Mouton et al.npj Biodiversity202410.1038/s44185-024-00054-6

Ann M. Mc CartneyUniversity of California, United States

Earth BioGenome ProjectEuropean Reference Genome AtlasERGA Pilot ProjectGenome assemblydecentralised genomics infrastructureeukaryotic speciesbiodiversity genomicsequitable genome production modeldistributed infrastructure98 pilot species33 European countriestransnational genomic projectsinclusive genomicsgenome databasescaling genome production
Badge
#17 of 3,522
3118m citations

Comprehensive Impurity Profiling of mRNA: Evaluating Current Technologies and Advanced Analytical Techniques

Julien Camperi et al.Analytical Chemistry202410.1021/acs.analchem.3c05539

Julien Camperi, Axel GuilbaudGenentech, United States

in vitro transcription (IVT)mRNA impuritiesion-pair reversed-phase liquid chromatographyCapillary electrophoresispoly(A) tail length heterogeneitydouble-stranded mRNA (dsRNA)dsRNA 3'-loop back formmass photometrynative mass spectrometrymRNA aggregatesaborted poly(A) additionpartial hydrolysismRNA intact massstability-indicating methodshigh-throughput impurity profilingmRNA therapeutics quality controlmRNA sequence heterogeneity
Badge
#18 of 3,522
3018m citations

Nanoparticle enrichment mass-spectrometry proteomics identifies protein-altering variants for precise pQTL mapping

Karsten Suhre et al.Nature Communications202410.1038/s41467-024-45233-y

Karsten SuhreWeill Cornell Medicine-Qatar, Qatar

pQTL mappingproteogenomicsShotgun proteomicsProteograph Product Suitenanoparticle enrichmentNonsynonymous variantspeptide-centric proteomicsmulti-ethnic cohortcis-pQTLepitope affinity bindingvariant peptidesaffinity-based proteomicsdrug target prioritizationblood plasma proteometarget specificity validationcausal protein identification
Badge
#19 of 3,522
3018m citations

High-dimensional phenotyping to define the genetic basis of cellular morphology

Matthew Tegtmeyer, Jatin Arora, Samira Asgari et al.Nature Communications202410.1038/s41467-023-44045-w

Shantanu Singh, Ralda Nehme, Soumya RaychaudhuriBroad Institute of MIT and Harvard, United States

Cell morphological quantitative trait loci (cmQTLs)high-content imagingInduced pluripotent stem cells (iPSCs)rare protein altering variantsWASF2TSPAN15PRLRcell shapenucleic granularitymitochondrial distributionCRISPRi knockdownDeep phenotypingMorphological profilingcommon variant associationsample size predictionGenomic sequencing
Badge
#20 of 3,522
3018m citations

Single-shot 20-fold expansion microscopy

Shiwei Wang, Tay Won Shin et al.Nature Methods202410.1038/s41592-024-02454-9

Laura L. Kiessling, Edward S. BoydenMassachusetts Institute of Technology, United States

Expansion microscopyExpansion microscopy (ExM)20ExMsingle-shot expansion20-fold linear expansionisotropic physical magnificationnanoimagingiterative expansionpostexpansion stainingbrain tissuebiomolecular labeling20-nm resolutionconventional microscopes
Badge

Dominant research themes and year-over-year shifts in Molecular Biology Techniques and Applications

What Topics Define the Class of 2026?

The Class of 2026 in Molecular Biology Techniques and Applications is led by spatial transcriptomics, which remains the single most prominent individual concept in high-impact molecular research, accounting for 12% of ranked publications. High-throughput genomic assembly and long-read sequencing technologies—most notably nanopore sequencing and direct RNA sequencing—form the foundational backbone for high-fidelity genome and epitranscriptome characterization. Concurrently, next-generation point-of-care nucleic acid diagnostic platforms feature heavily, driven by targeted CRISPR-Cas12a enzymatic assays and recombinase polymerase amplification (RPA) for rapid, field-deployable molecular detection. Methodological research also places strong emphasis on complex structural genome variations, particularly extrachromosomal DNA (ecDNA), focal gene amplifications, and genomic instability mechanisms in oncogenic contexts. Furthermore, multi-omics workflows incorporating proteomics, metabolomics, and digital pathology (such as quantitative hematoxylin and eosin staining) continue to expand across disease profiling studies. Collectively, these dominant themes demonstrate a field rapidly converging toward high-resolution spatial single-cell profiling, direct RNA sequencing, and decentralized CRISPR-powered diagnostic tools.

Leading research themes
Leading research themes

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

Comparison between cohorts reveals notable shifts in research momentum across molecular biology methodologies. Direct RNA sequencing and CRISPR-Cas12a diagnostics emerged as major new focal points, surging from zero representation in the Class of 2025 to top-tier frequency in the Class of 2026. Genome assembly methodologies also experienced a four-fold increase in paper frequency, reflecting growing reliance on telomere-to-telomere reference assemblies and pan-genomic tools. Similarly, structural cancer genomics saw sharp rises in extrachromosomal DNA (ecDNA), focal amplification, and genomic instability studies, none of which appeared among top ranked papers in the previous cohort. Point-of-care testing and recombinase polymerase amplification likewise surged from zero to 4% representation. Conversely, while spatial transcriptomics remains the most frequent single concept overall, its relative frequency declined from 26% in 2023 to 12% in 2024, indicating a transition from initial technology demonstration to broader, standardized application across subdisciplines. General long-read sequencing also saw minor consolidation as researchers shifted focus toward specialized direct RNA sequencing workflows. Overall, the cohort transition highlights rapid diversification into targeted RNA modifications, ecDNA structural biology, and field-ready enzymatic detection systems.

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 Molecular Biology Techniques and Applications Papers, Class of 2026. https://pri.pepkio.com/top-papers/molecular-biology-techniques-and-applications/2026. Accessed 2026-07-24.

Methodology
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