# Topics and Trends in Most Cited Molecular Biology Techniques and Applications Papers, Class of 2026

*Canonical URL: https://pri.pepkio.com/top-papers/molecular-biology-techniques-and-applications/2026*

## 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.

## At a glance

| Fact | Value |
| --- | --- |
| 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

| Rank | Title | Authors | Corresponding authors | Affiliation | Journal | 18m citations | DOI |
| ---: | --- | --- | --- | --- | --- | ---: | --- |
| 1 | NCBI RefSeq: reference sequence standards through 25 years of curation and annotation | Tamara Goldfarb, Vamsi K Kodali, Shashikant Pujar, Vyacheslav Brover, Barbara Robbertse, Catherine M Farrell, Dong-Ha Oh, Alexander Astashyn, Olga Ermolaeva, Diana Haddad, Wratko Hlavina, Jinna Hoffman, John D Jackson, Vinita S Joardar, David Kristensen, Patrick Masterson, Kelly M McGarvey, Richard McVeigh, Eyal Mozes, Michael R Murphy, Susan S Schafer, Alexander Souvorov, Brett Spurrier, Pooja K Strope, Hanzhen Sun, Anjana R Vatsan, Craig Wallin, David Webb, J Rodney Brister, Eneida Hatcher, Avi Kimchi, William Klimke, Aron Marchler-Bauer, Kim D Pruitt, Françoise Thibaud-Nissen, Terence D Murphy | Tamara Goldfarb | National Institutes of Health, United States | Nucleic Acids Research | 239 | 10.1093/nar/gkae1038 |
| 2 | Rapid and sensitive detection of genome contamination at scale with FCS-GX | Alexander Astashyn, Eric S Tvedte, Deacon Sweeney, Victor Sapojnikov, Nathan Bouk, Victor Joukov, Eyal Mozes, Pooja K Strope, Pape M Sylla, Lukas Wagner, Shelby L Bidwell, Larissa C Brown, Karen Clark, Emily W Davis, Brian Smith-White, Wratko Hlavina, Kim D Pruitt, Valerie A Schneider, Terence D Murphy | Terence D. Murphy | National Institutes of Health, United States | Genome biology | 197 | 10.1186/s13059-024-03198-7 |
| 3 | 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, Matthew S Adams, Gabriela Balderrama-Gutierrez, Amit K Behera, Jose M Gonzalez Martinez, Toby Hunt, Julien Lagarde, Cindy E Liang, Haoran Li, Marcus Jerryd Meade, David A Moraga Amador, Andrey D Prjibelski, Inanc Birol, Hamed Bostan, Ashley M Brooks, Muhammed Hasan Çelik, Ying Chen, Mei R M Du, Colette Felton, Jonathan Göke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, Joseph Lee, Jian-Liang Li, Matthias Lienhard, Alla Mikheenko, Dennis Mulligan, Ka Ming Nip, Mihaela Pertea, Matthew E Ritchie, Andre D Sim, Alison D Tang, Yuk Kei Wan, Changqing Wang, Brandon Y Wong, Chen Yang, If Barnes, Andrew E Berry, Salvador Capella-Gutierrez, Alyssa Cousineau, Namrita Dhillon, Jose M Fernandez-Gonzalez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Götz, Carles Hernández-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M Mudge, Nedka G Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Xingjie Ren, Eric Rouchka, Brandon Saint-John, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid A Youngworth, Piero Carninci, Nancy D Denslow, Roderic Guigó, Margaret E Hunter, Rene Maehr, Yin Shen, Hagen U Tilgner, Barbara J Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M Sheynkman, Ali Mortazavi, Ana Conesa, Angela N Brooks | Ashley M. Brooks, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria Sheynkman, A Mortazavi, Ana Conesa, Angela N. Brooks | Spanish National Research Council (CSIC), Spain | Nature Methods | 124 | 10.1038/s41592-024-02298-3 |
| 4 | Inferring super-resolution tissue architecture by integrating spatial transcriptomics with histology | Daiwei Zhang, Amelia Schroeder, Hanying Yan, Haochen Yang, Jian Hu, Michelle Y Y Lee, Kyung S Cho, Katalin Susztak, George X Xu, Michael D Feldman, Edward B Lee, Emma E Furth, Linghua Wang, Mingyao Li | Daiwei Zhang, Mingyao Li | University of Pennsylvania, United States | Nature Biotechnology | 87 | 10.1038/s41587-023-02019-9 |
| 5 | Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues | Zhiliang Bai, Dingyao Zhang, Yan Gao, Bo Tao, Daiwei Zhang, Shuozhen Bao, Archibald Enninful, Yadong Wang, Haikuo Li, Graham Su, Xiaolong Tian, Ningning Zhang, Yang Xiao, Yang Liu, Mark Gerstein, Mingyao Li, Yi Xing, Jun Lu, Mina L Xu, Rong Fan | Zhiliang Bai, Mingyao Li, Yi Xing, Jun Lü, Mina L. Xu, Rong Fan | Yale University, United States | Cell | 75 | 10.1016/j.cell.2024.09.001 |
| 6 | Global impact of unproductive splicing on human gene expression | Benjamin Fair, Carlos F Buen Abad Najar, Junxing Zhao, Stephanie Lozano, Austin Reilly, Gabriela Mossian, Jonathan P Staley, Jingxin Wang, Yang I Li | Yang Li | University of Chicago, United States | Nature Genetics | 70 | 10.1038/s41588-024-01872-x |
| 7 | Prediction of plasma ctDNA fraction and prognostic implications of liquid biopsy in advanced prostate cancer | Nicolette M Fonseca, Corinne Maurice-Dror, Cameron Herberts, Wilson Tu, William Fan, Andrew J Murtha, Catarina Kollmannsberger, Edmond M Kwan, Karan Parekh, Elena Schönlau, Cecily Q Bernales, Gráinne Donnellan, Sarah W S Ng, Takayuki Sumiyoshi, Joanna Vergidis, Krista Noonan, Daygen L Finch, Muhammad Zulfiqar, Stacy Miller, Sunil Parimi, Jean-Michel Lavoie, Edward Hardy, Maryam Soleimani, Lucia Nappi, Bernhard J Eigl, Christian Kollmannsberger, Sinja Taavitsainen, Matti Nykter, Sofie H Tolmeijer, Emmy Boerrigter, Niven Mehra, Nielka P van Erp, Bram De Laere, Johan Lindberg, Henrik Grönberg, Daniel J Khalaf, Matti Annala, Kim N Chi, Alexander W Wyatt | Matti Annala, Kim N., Alexander W. Wyatt | University of British Columbia, Canada | Nature Communications | 67 | 10.1038/s41467-024-45475-w |
| 8 | Inferring histology-associated gene expression gradients in spatial transcriptomic studies | Jan Kueckelhaus, Simon Frerich, Jasim Kada-Benotmane, Christina Koupourtidou, Jovica Ninkovic, Martin Dichgans, Juergen Beck, Oliver Schnell, Dieter Henrik Heiland | Jan Kueckelhaus, Dieter Henrik Heiland | Freiburg University, Germany | Nature Communications | 59 | 10.1038/s41467-024-50904-x |
| 9 | Whole-brain spatial transcriptional analysis at cellular resolution | Shigeaki Kanatani, Judith C Kreutzmann, Yue Li, Zoe West, Lea Lydolph Larsen, Danai Vougesi Nikou, Ilse Eidhof, Abigail Walton, Songbai Zhang, Leslie Rubio Rodríguez-Kirby, Jacob Lercke Skytte, Casper Gravesen Salinas, Kimiharu Takamatsu, Xiaofei Li, Daisuke H Tanaka, Dagmara Kaczynska, Keishiro Fukumoto, Razieh Karamzadeh, Yujiao Xiang, Naofumi Uesaka, Tsutomu Tanabe, Mikael Adner, Johan Hartman, Ayako Miyakawa, Erik Sundström, Gonçalo Castelo-Branco, Urmas Roostalu, Jacob Hecksher-Sørensen, Per Uhlén | Shigeaki Kanatani, Judith C. Kreutzmann, Yue Li, Zoe West, Per Uhlén | Karolinska Institutet, Sweden | Science | 58 | 10.1126/science.adn9947 |
| 10 | Mapping extrachromosomal DNA amplifications during cancer progression | Hoon Kim, Soyeon Kim, Taylor Wade, Eunchae Yeo, Anuja Lipsa, Anna Golebiewska, Kevin C Johnson, Sepil An, Junyong Ko, Yoonjoo Nam, Hwa Yeon Lee, Seunghyun Kang, Heesuk Chung, Simone P Niclou, Hyo-Eun Moon, Sun Ha Paek, Vineet Bafna, Jens Luebeck, Roel G W Verhaak | Hoon Kim, Roel G.W. Verhaak | Sungkyunkwan University, South Korea | Nature Genetics | 49 | 10.1038/s41588-024-01949-7 |
| 11 | High resolution long-read telomere sequencing reveals dynamic mechanisms in aging and cancer | Tobias T Schmidt, Carly Tyer, Preeyesh Rughani, Candy Haggblom, Jeffrey R Jones, Xiaoguang Dai, Kelly A Frazer, Fred H Gage, Sissel Juul, Scott Hickey, Jan Karlseder | Scott Hickey, Jan Karlseder | Salk Institute for Biological Studies, United States | Nature Communications | 47 | 10.1038/s41467-024-48917-7 |
| 12 | Phantasus, a web application for visual and interactive gene expression analysis | Maksim Kleverov, Daria Zenkova, Vladislav Kamenev, Margarita Sablina, Maxim N Artyomov, Alexey A Sergushichev | Maksim Kleverov, Daria Zenkova, Vladislav Kamenev | ITMO University, Russia | eLife | 46 | 10.7554/elife.85722 |
| 13 | Extrachromosomal DNA in cancer | Xiaowei Yan, Paul Mischel, Howard Chang | Paul S. Mischel, Howard Y. Chang | Stanford University, United States | Nature reviews. Cancer | 46 | 10.1038/s41568-024-00669-8 |
| 14 | Virtual formalin-fixed and paraffin-embedded staining of fresh brain tissue via stimulated Raman CycleGAN model | Zhijie Liu, Lingchao Chen, Haixia Cheng, Jianpeng Ao, Ji Xiong, Xing Liu, Yaxin Chen, Ying Mao, Minbiao Ji | Zhijie Liu, Lingchao Chen, Haixia Cheng, Minbiao Ji | Fudan University, China | Science Advances | 44 | 10.1126/sciadv.adn3426 |
| 15 | Genetic architecture of telomere length in 462,666 UK Biobank whole-genome sequences | Oliver S Burren, Ryan S Dhindsa, Sri V V Deevi, Sean Wen, Abhishek Nag, Jonathan Mitchell, Fengyuan Hu, Douglas P Loesch, Katherine R Smith, Neetu Razdan, Henric Olsson, Adam Platt, Dimitrios Vitsios, Qiang Wu, AstraZeneca Genomics Initiative, Veryan Codd, Christopher P Nelson, Nilesh J Samani, Ruth E March, Sebastian Wasilewski, Keren Carss, Margarete Fabre, Quanli Wang, Menelas N Pangalos, Slavé Petrovski | Oliver S Burren, Ryan S Dhindsa, Sri V V Deevi | AstraZeneca, United Kingdom | Nature Genetics | 38 | 10.1038/s41588-024-01884-7 |
| 16 | The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics | Ann M Mc Cartney, Giulio Formenti, Alice Mouton, Diego De Panis, Luísa S Marins, Henrique G Leitão, Genevieve Diedericks, Joseph Kirangwa, Marco Morselli, Judit Salces-Ortiz, Nuria Escudero, Alessio Iannucci, Chiara Natali, Hannes Svardal, Rosa Fernández, Tim De Pooter, Geert Joris, Mojca Strazisar, Jonathan M D Wood, Katie E Herron, Ole Seehausen, Phillip C Watts, Felix Shaw, Robert P Davey, Alice Minotto, José M Fernández, Astrid Böhne, Carla Alegria, Tyler Alioto, Paulo C Alves, Isabel R Amorim, Jean-Marc Aury, Niclas Backstrom, Petr Baldrian, Laima Baltrunaite, Endre Barta, Bertrand BedHom, Caroline Belser, Johannes Bergsten, Laurie Bertrand, Helena Bilandija, Mahesh Binzer-Panchal, Iliana Bista, Mark Blaxter, Paulo A V Borges, Guilherme Borges Dias, Mirte Bosse, Tom Brown, Rémy Bruggmann, Elena Buena-Atienza, Josephine Burgin, Elena Buzan, Alessia Cariani, Nicolas Casadei, Matteo Chiara, Sergio Chozas, Fedor Čiampor, Angelica Crottini, Corinne Cruaud, Fernando Cruz, Love Dalen, Alessio De Biase, Javier Del Campo, Teo Delic, Alice B Dennis, Martijn F L Derks, Maria Angela Diroma, Mihajla Djan, Simone Duprat, Klara Eleftheriadi, Philine G D Feulner, Jean-François Flot, Giobbe Forni, Bruno Fosso, Pascal Fournier, Christine Fournier-Chambrillon, Toni Gabaldon, Shilpa Garg, Carmela Gissi, Luca Giupponi, Jessica Gomez-Garrido, Josefa González, Miguel L Grilo, Björn Grüning, Thomas Guerin, Nadege Guiglielmoni, Marta Gut, Marcel P Haesler, Christoph Hahn, Balint Halpern, Peter W Harrison, Julia Heintz, Maris Hindrikson, Jacob Höglund, Kerstin Howe, Graham M Hughes, Benjamin Istace, Mark J Cock, Franc Janžekovič, Zophonias O Jonsson, Sagane Joye-Dind, Janne J Koskimäki, Boris Krystufek, Justyna Kubacka, Heiner Kuhl, Szilvia Kusza, Karine Labadie, Meri Lähteenaro, Henrik Lantz, Anton Lavrinienko, Lucas Leclère, Ricardo Jorge Lopes, Ole Madsen, Ghislaine Magdelenat, Giulia Magoga, Tereza Manousaki, Tapio Mappes, Joao Pedro Marques, Gemma I Martinez Redondo, Florian Maumus, Shane A McCarthy, Hendrik-Jan Megens, Jose Melo-Ferreira, Sofia L Mendes, Matteo Montagna, Joao Moreno, Mai-Britt Mosbech, Mónica Moura, Zuzana Musilova, Eugene Myers, Will J Nash, Alexander Nater, Pamela Nicholson, Manuel Niell, Reindert Nijland, Benjamin Noel, Karin Noren, Pedro H Oliveira, Remi-Andre Olsen, Lino Ometto, Rebekah A Oomen, Stephan Ossowski, Vaidas Palinauskas, Snaebjorn Palsson, Jerome P Panibe, Joana Pauperio, Martina Pavlek, Emilie Payen, Julia Pawlowska, Jaume Pellicer, Graziano Pesole, Joao Pimenta, Martin Pippel, Anna Maria Pirttilä, Nikos Poulakakis, Jeena Rajan, Rúben M C Rego, Roberto Resendes, Philipp Resl, Ana Riesgo, Patrik Rodin-Morch, Andre E R Soares, Carlos Rodriguez Fernandes, Maria M Romeiras, Guilherme Roxo, Lukas Rüber, Maria Jose Ruiz-Lopez, Urmas Saarma, Luis P da Silva, Manuela Sim-Sim, Lucile Soler, Vitor C Sousa, Carla Sousa Santos, Alberto Spada, Milomir Stefanovic, Viktor Steger, Josefin Stiller, Matthias Stöck, Torsten H Struck, Hiranya Sudasinghe, Riikka Tapanainen, Christian Tellgren-Roth, Helena Trindade, Yevhen Tukalenko, Ilenia Urso, Benoit Vacherie, Steven M Van Belleghem, Kees Van Oers, Carlos Vargas-Chavez, Nevena Velickovic, Noel Vella, Adriana Vella, Cristiano Vernesi, Sara Vicente, Sara Villa, Olga Vinnere Pettersson, Filip A M Volckaert, Judit Voros, Patrick Wincker, Sylke Winkler, Claudio Ciofi, Robert M Waterhouse, Camila J Mazzoni | Ann M. Mc Cartney | University of California, United States | npj Biodiversity | 36 | 10.1038/s44185-024-00054-6 |
| 17 | Comprehensive Impurity Profiling of mRNA: Evaluating Current Technologies and Advanced Analytical Techniques | Julien Camperi, Steffen Lippold, Luladey Ayalew, Brian Roper, Stephanie Shao, Emily Freund, Ariane Nissenbaum, Carolina Galan, Qinjingwen Cao, Feng Yang, Christopher Yu, Axel Guilbaud | Julien Camperi, Axel Guilbaud | Genentech, United States | Analytical Chemistry | 31 | 10.1021/acs.analchem.3c05539 |
| 18 | Nanoparticle enrichment mass-spectrometry proteomics identifies protein-altering variants for precise pQTL mapping | Karsten Suhre, Guhan Ram Venkataraman, Harendra Guturu, Anna Halama, Nisha Stephan, Gaurav Thareja, Hina Sarwath, Khatereh Motamedchaboki, Margaret K R Donovan, Asim Siddiqui, Serafim Batzoglou, Frank Schmidt | Karsten Suhre | Weill Cornell Medicine-Qatar, Qatar | Nature Communications | 30 | 10.1038/s41467-024-45233-y |
| 19 | High-dimensional phenotyping to define the genetic basis of cellular morphology | Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O'Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri | Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri | Broad Institute of MIT and Harvard, United States | Nature Communications | 30 | 10.1038/s41467-023-44045-w |
| 20 | Single-shot 20-fold expansion microscopy | Shiwei Wang, Tay Won Shin, Harley B Yoder, Ryan B McMillan, Hanquan Su, Yixi Liu, Chi Zhang, Kylie S Leung, Peng Yin, Laura L Kiessling, Edward S Boyden | Laura L. Kiessling, Edward S. Boyden | Massachusetts Institute of Technology, United States | Nature Methods | 30 | 10.1038/s41592-024-02454-9 |

## Topic trends

### 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*

### 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*

## 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.

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
```