# Topics and Trends in Most Cited Genomics and Phylogenetic Studies Papers, Class of 2026

*Canonical URL: https://pri.pepkio.com/top-papers/genomics-and-phylogenetic-studies/2026*

## 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.

## At a glance

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

| Rank | Title | Authors | Corresponding authors | Affiliation | Journal | 18m citations | DOI |
| ---: | --- | --- | --- | --- | --- | ---: | --- |
| 1 | KEGG: biological systems database as a model of the real world | Minoru Kanehisa, Miho Furumichi, Yoko Sato, Yuriko Matsuura, Mari Ishiguro-Watanabe | Minoru Kanehisa | Kyoto University, Japan | Nucleic Acids Research | 1,911 | 10.1093/nar/gkae909 |
| 2 | Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool | Ivica Letunic, Peer Bork | Ivica Letunić | biobyte solutions GmbH, Germany | Nucleic Acids Research | 1,864 | 10.1093/nar/gkae268 |
| 3 | 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, Liam J Bartie, Armin W Thomas, Samuel H King, Garyk Brixi, Jeremy Sullivan, Madelena Y Ng, Ashley Lewis, Aaron Lou, Stefano Ermon, Stephen A Baccus, Tina Hernandez-Boussard, Christopher Ré, Patrick D Hsu, Brian L Hie | Eric Nguyen, Michael Poli, Matthew G. Durrant, Brian Kang, Dhruva Katrekar, David Li, Patrick D. Hsu, Brian Hie | Arc Institute, United States | Science | 369 | 10.1126/science.ado9336 |
| 4 | Nucleotide Transformer: building and evaluating robust foundation models for human genomics | Hugo Dalla-Torre, Liam Gonzalez, Javier Mendoza-Revilla, Nicolas Lopez Carranza, Adam Henryk Grzywaczewski, Francesco Oteri, Christian Dallago, Evan Trop, Bernardo P de Almeida, Hassan Sirelkhatim, Guillaume Richard, Marcin Skwark, Karim Beguir, Marie Lopez, Thomas Pierrot | M. Lopez, Thomas Pierrot | InstaDeep, United Kingdom | Nature Methods | 347 | 10.1038/s41592-024-02523-z |
| 5 | GENCODE 2025: reference gene annotation for human and mouse | Jonathan M Mudge, Sílvia Carbonell-Sala, Mark Diekhans, Jose Gonzalez Martinez, Toby Hunt, Irwin Jungreis, Jane E Loveland, Carme Arnan, If Barnes, Ruth Bennett, Andrew Berry, Alexandra Bignell, Daniel Cerdán-Vélez, Kelly Cochran, Lucas T Cortés, Claire Davidson, Sarah Donaldson, Cagatay Dursun, Reham Fatima, Matthew Hardy, Prajna Hebbar, Zoe Hollis, Benjamin T James, Yunzhe Jiang, Rory Johnson, Gazaldeep Kaur, Mike Kay, Riley J Mangan, Miguel Maquedano, Laura Martínez Gómez, Nourhen Mathlouthi, Ryan Merritt, Pengyu Ni, Emilio Palumbo, Tamara Perteghella, Fernando Pozo, Shriya Raj, Cristina Sisu, Emily Steed, Dulika Sumathipala, Marie-Marthe Suner, Barbara Uszczynska-Ratajczak, Elizabeth Wass, Yucheng T Yang, Dingyao Zhang, Robert D Finn, Mark Gerstein, Roderic Guigó, Tim J P Hubbard, Manolis Kellis, Anshul Kundaje, Benedict Paten, Michael L Tress, Ewan Birney, Fergal J Martin, Adam Frankish | Jonathan M Mudge | European Molecular Biology Laboratory, United Kingdom | Nucleic Acids Research | 291 | 10.1093/nar/gkae1078 |
| 6 | JCVI: A versatile toolkit for comparative genomics analysis | Haibao Tang, Vivek Krishnakumar, Xiaofei Zeng, Zhougeng Xu, Adam Taranto, Johnathan S Lomas, Yixing Zhang, Yumin Huang, Yibin Wang, Won Cheol Yim, Jisen Zhang, Xingtan Zhang | Haibao Tang, Xingtan Zhang | Fujian Agriculture and Forestry University, China | iMeta | 237 | 10.1002/imt2.211 |
| 7 | SBSM-Pro: support bio-sequence machine for proteins | Yizheng Wang, Yixiao Zhai, Yijie Ding, Quan Zou | Yijie Ding, Quan Zou | University of Electronic Science and Technology of China, China | Science China Information Sciences | 235 | 10.1007/s11432-024-4171-9 |
| 8 | OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes | Fredrik Tegenfeldt, Dmitry Kuznetsov, Mosè Manni, Matthew Berkeley, Evgeny M Zdobnov, Evgenia V Kriventseva | Fredrik Tegenfeldt | University of Geneva, Switzerland | Nucleic Acids Research | 213 | 10.1093/nar/gkae987 |
| 9 | EzBioCloud: a genome-driven database and platform for microbiome identification and discovery | Mauricio Chalita, Yeong Ouk Kim, Sein Park, Hyun-Seok Oh, Jae Hyoung Cho, Jeongsup Moon, Nuga Baek, Changsik Moon, Kihyun Lee, Junwon Yang, Gi Gyun Nam, Yeonjae Jung, Seong-In Na, Michael James Bailey, Jongsik Chun | Mauricio Chalita | CJ Bioscience Inc, South Korea | INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY | 203 | 10.1099/ijsem.0.006421 |
| 10 | 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 | 198 | 10.1186/s13059-024-03198-7 |
| 11 | Detection of mosaic and population-level structural variants with Sniffles2 | Moritz Smolka, Luis F Paulin, Christopher M Grochowski, Dominic W Horner, Medhat Mahmoud, Sairam Behera, Ester Kalef-Ezra, Mira Gandhi, Karl Hong, Davut Pehlivan, Sonja W Scholz, Claudia M B Carvalho, Christos Proukakis, Fritz J Sedlazeck | Fritz J. Sedlazeck | Baylor College of Medicine, United States | Nature Biotechnology | 196 | 10.1038/s41587-023-02024-y |
| 12 | SeqKit2: A Swiss army knife for sequence and alignment processing | Wei Shen, Botond Sipos, Liuyang Zhao | Wei Shen | Chongqing Medical University, China | iMeta | 190 | 10.1002/imt2.191 |
| 13 | Complexity of avian evolution revealed by family-level genomes | Josefin Stiller, Shaohong Feng, Al-Aabid Chowdhury, Iker Rivas-González, David A Duchêne, Qi Fang, Yuan Deng, Alexey Kozlov, Alexandros Stamatakis, Santiago Claramunt, Jacqueline M T Nguyen, Simon Y W Ho, Brant C Faircloth, Julia Haag, Peter Houde, Joel Cracraft, Metin Balaban, Uyen Mai, Guangji Chen, Rongsheng Gao, Chengran Zhou, Yulong Xie, Zijian Huang, Zhen Cao, Zhi Yan, Huw A Ogilvie, Luay Nakhleh, Bent Lindow, Benoit Morel, Jon Fjeldså, Peter A Hosner, Rute R da Fonseca, Bent Petersen, Joseph A Tobias, Tamás Székely, Jonathan David Kennedy, Andrew Hart Reeve, Andras Liker, Martin Stervander, Agostinho Antunes, Dieter Thomas Tietze, Mads F Bertelsen, Fumin Lei, Carsten Rahbek, Gary R Graves, Mikkel H Schierup, Tandy Warnow, Edward L Braun, M Thomas P Gilbert, Erich D Jarvis, Siavash Mirarab, Guojie Zhang | Josefin Stiller, Siavash Mirarab, Guojie Zhang | University of Copenhagen, Denmark | Nature | 174 | 10.1038/s41586-024-07323-1 |
| 14 | The nature of the last universal common ancestor and its impact on the early Earth system | Edmund R R Moody, Sandra Álvarez-Carretero, Tara A Mahendrarajah, James W Clark, Holly C Betts, Nina Dombrowski, Lénárd L Szánthó, Richard A Boyle, Stuart Daines, Xi Chen, Nick Lane, Ziheng Yang, Graham A Shields, Gergely J Szöllősi, Anja Spang, Davide Pisani, Tom A Williams, Timothy M Lenton, Philip C J Donoghue | Edmund R. R. Moody, Davide Pisani, Tom A. Williams, Timothy M. Lenton, Philip C. J. Donoghue | University of Bristol, United Kingdom | Nature Ecology & Evolution | 169 | 10.1038/s41559-024-02461-1 |
| 15 | Rfam 15: RNA families database in 2025 | Nancy Ontiveros-Palacios, Emma Cooke, Eric P Nawrocki, Sandra Triebel, Manja Marz, Elena Rivas, Sam Griffiths-Jones, Anton I Petrov, Alex Bateman, Blake Sweeney | Blake Sweeney | European Molecular Biology Laboratory, United Kingdom | Nucleic Acids Research | 145 | 10.1093/nar/gkae1023 |
| 16 | RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments | Sebastian Bittrich, Joan Segura, Jose M Duarte, Stephen K Burley, Yana Rose | Sebastian Bittrich | University of California, United States | Bioinformatics | 136 | 10.1093/bioinformatics/btae370 |
| 17 | Global marine microbial diversity and its potential in bioprospecting | Jianwei Chen, Yangyang Jia, Ying Sun, Kun Liu, Changhao Zhou, Chuan Liu, Denghui Li, Guilin Liu, Chengsong Zhang, Tao Yang, Lei Huang, Yunyun Zhuang, Dazhi Wang, Dayou Xu, Qiaoling Zhong, Yang Guo, Anduo Li, Inge Seim, Ling Jiang, Lushan Wang, Simon Ming Yuen Lee, Yujing Liu, Dantong Wang, Guoqiang Zhang, Shanshan Liu, Xiaofeng Wei, Zhen Yue, Shanmin Zheng, Xuechun Shen, Sen Wang, Chen Qi, Jing Chen, Chen Ye, Fang Zhao, Jun Wang, Jie Fan, Baitao Li, Jiahui Sun, Xiaodong Jia, Zhangyong Xia, He Zhang, Junnian Liu, Yue Zheng, Xin Liu, Jian Wang, Huanming Yang, Karsten Kristiansen, Xun Xu, Thomas Mock, Shengying Li, Wenwei Zhang, Guangyi Fan | Ying Sun, Thomas Möck, Shengying Li, Wenwei Zhang, Guangyi Fan | BGI Research, China | Nature | 128 | 10.1038/s41586-024-07891-2 |
| 18 | <scp>TreeViewer</scp>: Flexible, modular software to visualise and manipulate phylogenetic trees | Giorgio Bianchini, Patricia Sánchez-Baracaldo | Giorgio Bianchini | University of Bristol, United Kingdom | Ecology and Evolution | 112 | 10.1002/ece3.10873 |
| 19 | The variation and evolution of complete human centromeres | Glennis A Logsdon, Allison N Rozanski, Fedor Ryabov, Tamara Potapova, Valery A Shepelev, Claudia R Catacchio, David Porubsky, Yafei Mao, DongAhn Yoo, Mikko Rautiainen, Sergey Koren, Sergey Nurk, Julian K Lucas, Kendra Hoekzema, Katherine M Munson, Jennifer L Gerton, Adam M Phillippy, Mario Ventura, Ivan A Alexandrov, Evan E Eichler | Evan E. Eichler | University of Washington, United States | Nature | 112 | 10.1038/s41586-024-07278-3 |
| 20 | Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information | Baptiste Gaborieau, Hugo Vaysset, Florian Tesson, Inès Charachon, Nicolas Dib, Juliette Bernier, Tanguy Dequidt, Héloïse Georjon, Olivier Clermont, Pascal Hersen, Laurent Debarbieux, Jean-Damien Ricard, Erick Denamur, Aude Bernheim | Baptiste Gaborieau | Université Paris Cité, France | Nature Microbiology | 110 | 10.1038/s41564-024-01832-5 |

## Topic trends

### 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*

### 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*

## 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
```