Opportunities and challenges in long-read sequencing data analysis

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106

<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data

Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp616 · Cited by 41,364

limma powers differential expression analyses for RNA-sequencing and microarray studies

Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., & Smyth, G. K. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv007 · Cited by 40,458

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

Liao, Y., Smyth, G. K., & Shi, W. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt656 · Cited by 27,219

Salmon provides fast and bias-aware quantification of transcript expression

Patro, R., Duggal, G., Love, M. I., Irizarry, R. A., & Kingsford, C. (2017) · Nature Methods · doi:10.1038/nmeth.4197 · Cited by 12,700

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C. A., Zeng, Q., Wortman, J. R., Young, S., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0112963 · Cited by 9,130

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

Wick, R. R., Judd, L. M., Gorrie, C. L., & Holt, K. E. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005595 · Cited by 8,728

Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separationPreprint

Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., & Phillippy, A. M. (2017) · Genome Research · doi:10.1101/gr.215087.116 · Cited by 7,260

Assembly of long, error-prone reads using repeat graphs

Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0072-8 · Cited by 5,986

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

McCarthy, D. J., Chen, Y., & Smyth, G. K. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks042 · Cited by 5,195

Genome sequence, phylogenetic analysis, and structure-based annotation reveal metabolic potential of Chlorella sp. SLA-04

Goemann, C. L. C., Wilkinson, R. A., Henriques, W. S., Bui, H., Goemann, H., Carlson, R. P., Viamajala, S., Gerlach, R., & Wiedenheft, B. (2022) · Algal Research · doi:10.1016/j.algal.2022.102943 · Cited by 15

Lost genome segments associate with trait diversity during rice domestication

Zheng, X., Zhong, L., Pang, H., Wen, S., Li, F., Lou, D., Ge, J., Fan, W., Wang, T., Han, Z., et al. (2023) · BMC Biology · doi:10.1186/s12915-023-01512-6 · Cited by 14

Bromodomain-containing Protein 4 regulates innate inflammation via modulation of alternative splicing

Mann, M. W., Fu, Y., Gearhart, R. L., Xu, X., Roberts, D. S., Li, Y., Zhou, J., Ge, Y., & Brasier, A. R. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1212770 · Cited by 18

Report of the third conference on next-generation sequencing for adventitious virus detection in biologics for humans and animals

Khan, A. S., Mallet, L., Blümel, J., Cassart, J.-P., Knežević, I., Ng, S. H. S., Wall, M., Jakava-Viljanen, M., Logvinoff, C., Goios, A., et al. (2023) · Biologicals · doi:10.1016/j.biologicals.2023.101696 · Cited by 16

A practical assembly guideline for genomes with various levels of heterozygosity

Mochizuki, T., Sakamoto, M., Tanizawa, Y., Nakayama, T., Tanifuji, G., Kamikawa, R., & Nakamura, Y. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad337 · Cited by 14

Anemonefishes: A model system for evolutionary genomics

Herrera, M., Ravasi, T., & Laudet, V. (2023) · F1000Research · doi:10.12688/f1000research.130752.1 · Cited by 13

Pasa: leveraging population pangenome graph to scaffold prokaryote genome assemblies

Do, V. H., Nguyen, S. H., Le, D. Q., Nguyen, T. T., Nguyen, C. H., Ho, T. H., Vo, N. S., Nguyen, T. T., Nguyen, S. H., & Cao, M. D. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad1170 · Cited by 13

Long-Read DNA and RNA Sequencing to Streamline Clinical Genetic Testing and Reduce Barriers to Comprehensive Genetic Testing

Damaraju, N., Miller, A. L., & Miller, D. E. (2023) · The Journal of Applied Laboratory Medicine · doi:10.1093/jalm/jfad107 · Cited by 14

Incorporating metabolic activity, taxonomy and community structure to improve microbiome-based predictive models for host phenotype prediction

Monshizadeh, M., & Ye, Y. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2302076 · Cited by 13

Can long-read sequencing tackle the barriers, which the next-generation could not? A review

Szakállas, N., Barták, B. K., Valcz, G., Nagy, Z. B., Takács, I., & Molnar, B. A. (2024) · Pathology & Oncology Research · doi:10.3389/pore.2024.1611676 · Cited by 15

Application of Pan-Omics Technologies in Research on Important Economic Traits for Ruminants

Gao, Z., Lu, Y., Li, M., Chong, Y., Hong, J., Wu, J., Wu, D., Xi, D., & Deng, W. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25179271 · Cited by 15

Intrinsic-dimension analysis for guiding dimensionality reduction and data fusion in multi-omics data processing

Gliozzo, J., Soto-Gomez, M., Guarino, V., Bonometti, A., Cabri, A., Cavalleri, E., Reese, J., Robinson, P. N., Mesiti, M., Valentini, G., et al. (2024) · Artificial Intelligence in Medicine · doi:10.1016/j.artmed.2024.103049 · Cited by 14

Highly accurate Korean draft genomes reveal structural variation highlighting human telomere evolution

Kim, J., Park, J., Yang, J. O., Kim, S., Joe, S., Park, G., Hwang, T., Cho, M.-J., Lee, S. J., Lee, J.-E., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkae1294 · Cited by 14

The widely used Ucp1-Cre transgene elicits complex developmental and metabolic phenotypes

Halurkar, M. S., Inoue, O., Singh, A., Mukherjee, R., Ginugu, M., Ahn, C., Paese, C. L. B., Duszynski, M., Brugmann, S. A., Lim, H., et al. (2025) · Nature Communications · doi:10.1038/s41467-024-54763-4 · Cited by 15

A chromosome-scale and haplotype-resolved genome assembly of tetraploid blackberry (Rubus L. subgenus Rubus Watson)

Paudel, D., Parrish, S. B., Peng, Z., Parajuli, S., & Deng, Z. (2025) · Horticulture Research · doi:10.1093/hr/uhaf052 · Cited by 14

SVHunter: long-read-based structural variation detection through the transformer model

Gao, R., Hu, H. K., Jiang, Z., Cao, S., Wang, G., Zhao, Y., & Jiang, T. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf203 · Cited by 14

A CRISPR/Cas9-based enhancement of high-throughput single-cell transcriptomics

Pandey, A. C., Bezney, J., DeAscanis, D., Kirsch, E., Ahmed, F., Crinklaw, A., Choudhary, K. S., Mandala, T., Deason, J., Hamidi, J., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-59880-2 · Cited by 16

Single-cell compendium of muscle microenvironment in peripheral artery disease reveals altered endothelial diversity and LYVE1+ macrophage activation

Turiel, G., Desgeorges, T., Masschelein, E., Fan, Z., Lussi, D., Capelle, C., Bernardini, G., Ardicoglu, R., Schönberger, K., Birrer, M., et al. (2025) · Nature Cardiovascular Research · doi:10.1038/s44161-025-00709-y · Cited by 15

CoolMPS for robust sequencing of single-nuclear RNAs captured by droplet-based method

Hahn, O., Fehlmann, T., Zhang, H., Munson, C. N., Vest, R. T., Borcherding, A., Liu, S., Villarosa, C., Drmanac, S., Drmanac, R., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1127 · Cited by 16

Towards Integrated Management of Dengue in Mumbai

Paradkar, P. N., Sahasrabudhe, P. R., Sawant, M. G., Mukherjee, S., & Blasdell, K. R. (2021) · Viruses · doi:10.3390/v13122436 · Cited by 14

GCAT|Panel, a comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing

Valls-Margarit, J., Galván‐Femenía, I., Matías-Sánchez, D., Blay, N., Puiggròs, M., Carreras, A., Salvoro, C., Cortés, B., Amela, R., Farré, X., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac076 · Cited by 13

A High-Quality Genome Assembly of Striped Catfish (Pangasianodon hypophthalmus) Based on Highly Accurate Long-Read HiFi Sequencing Data

Hai, D. M., Yên, D. T., Liêm, P. T., Tâm, B. M., Huong, D. T. T., Hằng, B. T. B., Hieu, D. Q., Garigliany, M., Coppieters, W. R., Kestemont, P., et al. (2022) · Genes · doi:10.3390/genes13050923 · Cited by 15

Long-read error correction: a survey and qualitative comparisonPreprint

Morisse, P., Thierry Lecroq, B., & Lefebvre, A. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.03.06.977975 · Cited by 16

Transcriptomic entropy benchmarks stem cell-derived cardiomyocyte maturation against endogenous tissue at single cell levelPreprint

Kannan, S., Farid, M., Lin, B. L., Miyamoto, M., & Kwon, C. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.02.022632 · Cited by 15

Telomere-to-Telomere and Haplotype-Phased Genome Assemblies of the Heterozygous Octoploid ‘Florida Brilliance’ Strawberry (Fragaria × ananassa)Preprint

Han, H., Barbey, C. R., Fan, Z., Verma, S., Whitaker, V., & Lee, S. (2022) · bioRxiv · doi:10.1101/2022.10.05.509768 · Cited by 14

Disentangling shared and group-specific variations in single-cell transcriptomics data with multiGroupVIPreprint

Weinberger, E., Lopez, R., Hütter, J.-C., & Regev, A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.13.520349 · Cited by 13

Single-cell gene expression prediction from DNA sequence at large contextsPreprint

Schweßinger, R., Deasy, J., Woodruff, R. T., Young, S., & Branson, K. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.26.550634 · Cited by 17

The impact of applying various de novo assembly and correction tools on the identification of genome characterization, drug resistance, and virulence factors of clinical isolates using ONT sequencing

Safar, H. A., Alatar, F., Nasser, K., Alajmi, R. Z., Alfouzan, W. A., & Mustafa, A. S. (2023) · BMC Biotechnology · doi:10.1186/s12896-023-00797-3 · Cited by 14

A contextualised protein language model reveals the functional syntax of bacterial evolutionPreprint

Wiatrak, M., Abelson, D. C., Mikhaylenko, R., Torné, R. V., Ntemourtsidou, M., Dinan, A. M., Arora, D., Horsfield, S., Lees, J. A., Brbić, M., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.07.20.665723 · Cited by 19

Best practices for interpretable machine learning in computational biology

Chen, V., Yang, M., Cui, W., Kim, J. S., Talwalkar, A., & Ma, J. (2022) · doi:10.1101/2022.10.28.513978 · Cited by 14

Genomics in plant pathogen identification and control

Ogbuji, N. G., & Agogbua, J. U. (2025) · Frontiers in Plant Science · doi:10.3389/fpls.2025.1661432 · Cited by 15

Assessment of Inter-Laboratory Differences in SARS-CoV-2 Consensus Genome Assemblies between Public Health Laboratories in Australia

Foster, C. S. P., Stelzer‐Braid, S., Deveson, I. W., Bull, R. A., Yeang, M., Au, J.-P., Silva, M. R., van Hal, S. J., Rockett, R. J., Sintchenko, V., et al. (2022) · Viruses · doi:10.3390/v14020185 · Cited by 13

Novel viral and microbial species in a translocated Toutouwai (Petroica longipes) population from Aotearoa/New Zealand

French, R. K., Stone, Z. L., Parker, K. A., & Holmes, E. C. (2022) · One Health Outlook · doi:10.1186/s42522-022-00072-z · Cited by 12

ImmunoTyper-SR: A Computational Approach for Genotyping Immunoglobulin Heavy Chain Variable Genes using Short Read Data

Ford, M., Hari, A., Rodriguez, O. L., Xu, J., Lack, J., Oguz, C., Zhang, Y., Oler, A. J., Delmonte, O., Weber, S., et al. (2022) · Cell Systems · doi:10.1016/j.cels.2022.08.008 · Cited by 11

rcCAE: a convolutional autoencoder method for detecting intra-tumor heterogeneity and single-cell copy number alterations

Yu, Z., Liu, F., Shi, F., & Du, F. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad108 · Cited by 13

Ultrarapid and high-resolution HLA class I typing using transposase-based nanopore sequencing applied in pharmacogenetic testing

Anukul, N., Jenjaroenpun, P., Sirikul, C., Wankaew, N., Nimsamer, P., Roothumnong, E., Pithukpakorn, M., Leetrakool, N., & Wongsurawat, T. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1213457 · Cited by 13

Probabilistic tensor decomposition extracts better latent embeddings from single-cell multiomic data

Wang, R. H., Wang, J., & Li, S. C. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad570 · Cited by 14

Genome-wide methylation patterns from canine nanopore assemblies

Schall, P. Z., Winkler, P. A., Petersen‐Jones, S. M., Yuzbasiyan‐Gurkan, V., & Kidd, J. M. (2023) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkad203 · Cited by 14

Identification and quantification of small exon-containing isoforms in long-read RNA sequencing data

Liu, Z., Zhu, C., Steinmetz, L. M., & Wu, W. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad810 · Cited by 13

Genome sequencing of Syzygium cumini (jamun) reveals adaptive evolution in secondary metabolism pathways associated with its medicinal properties

Chakraborty, A., Mahajan, S., Bisht, M. S., & Sharma, V. K. (2023) · Frontiers in Plant Science · doi:10.3389/fpls.2023.1260414 · Cited by 14

Molecular characterization of blaNDM-harboring plasmids reveal its rapid adaptation and evolution in the Enterobacteriaceae

Li, Y., Yang, Y., Wang, Y., Walsh, T. R., Wang, S., & Cai, C. (2023) · One Health Advances · doi:10.1186/s44280-023-00033-9 · Cited by 13

Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries

Li, W., Miller, D., Liu, X., Tosi, L., Chkaiban, L., Han, M., Hung, P.-H., Parekkadan, B., Sherlock, G., & Levy, S. F. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae332 · Cited by 13

Information‐Distilled Generative Label‐Free Morphological Profiling Encodes Cellular Heterogeneity

Lo, M. C. K., Siu, D. M. D., Lee, K. C. M., Wong, J. S. J., Yeung, M. C. F., Hsin, M. K. Y., Ho, J., & Tsia, K. K. (2024) · Advanced Science · doi:10.1002/advs.202307591 · Cited by 13

Utility analyses of AVITI sequencing chemistry

Liu, S., Obert, C. A., Yu, Y., Zhao, J., Ren, B., Liu, J.-J., Wiseman, K. N., Krajacich, B. J., Wang, W., Metcalfe, K. S., et al. (2024) · BMC Genomics · doi:10.1186/s12864-024-10686-4 · Cited by 14

Targeted long-read sequencing enriches disease-relevant genomic regions of interest to provide complete Mendelian disease diagnostics

Nakamichi, K., Huey, J., Sangermano, R., Place, E., Bujakowska, K. M., Marra, M. H., Everett, L. A., Yang, P. G., Chao, J. R., Gelder, R. N. V., et al. (2024) · JCI Insight · doi:10.1172/jci.insight.183902 · Cited by 13

Integrated functional genomic analysis identifies regulatory variants underlying a major QTL for disease resistance in European sea bass

Mukiibi, R., Ferraresso, S., Franch, R., Peruzza, L., Rovere, G. D., Babbucci, M., Bertotto, D., Toffan, A., Pascoli, F., Faggion, S., et al. (2025) · BMC Biology · doi:10.1186/s12915-025-02180-4 · Cited by 14

Electrical biosensing with synthetic nanopores and nanochannels

Angeli, E., Repetto, L., Firpo, G., & Valbusa, U. (2021) · Current Opinion in Electrochemistry · doi:10.1016/j.coelec.2021.100754 · Cited by 13

Mining the Microbiome and Microbiota-Derived Molecules in Inflammatory Bowel Disease

Bekkers, M., Stojkovic, B., & Kaiko, G. E. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222011243 · Cited by 15

A copula based topology preserving graph convolution network for clustering of single-cell RNA-seq data

Lall, S., Ray, S., & Bandyopadhyay, S. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009600 · Cited by 13

Prediction of transcript isoforms in 19 chicken tissues by Oxford Nanopore long-read sequencing

Guan, D., Halstead, M. M., Islas‐Trejo, A., Goszczynski, D. E., Cheng, H. H., Ross, P. J., & Zhou, H. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.997460 · Cited by 14

The peptide woods are lovely, dark and deep: Hunting for novel cancer antigens

Oreper, D., Klaeger, S., Jhunjhunwala, S., & Delamarre, L. (2023) · Seminars in Immunology · doi:10.1016/j.smim.2023.101758 · Cited by 13

Advantages of Whole Genome Sequencing in Mitigating the Helicobacter pylori Antimicrobial Resistance Problem

Fauzia, K. A., Alfaray, R. I., & Yamaoka, Y. (2023) · Microorganisms · doi:10.3390/microorganisms11051239 · Cited by 13

Miniaturized DNA Sequencers for Personal Use: Unreachable Dreams or Achievable Goals

Huo, W., Ling, W., Wang, Z., Ya, L., Zhou, M., Ren, M., Li, X., Li, J., Xia, Z., Liu, X., et al. (2021) · Frontiers in Nanotechnology · doi:10.3389/fnano.2021.628861 · Cited by 13

Evaluation of nanopore sequencing technology to identify Salmonella enterica Choleraesuis var. Kunzendorf and Orion var. 15+, 34+

Xu, F., Ge, C., Li, S., Tang, S., Wu, X., Luo, H., Deng, X., Zhang, G., Stevenson, A., & Baker, R. C. (2021) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2021.109167 · Cited by 13

Eco-evolutionary significance of domesticated retroelements in microbial genomes

Paul, B. G., & Eren, A. M. (2022) · Mobile DNA · doi:10.1186/s13100-022-00262-6 · Cited by 13

CELLama: Foundation Model for Single Cell and Spatial Transcriptomics by Cell Embedding Leveraging Language Model AbilitiesPreprint

Choi, H., Park, J., Kim, S., Kim, J., Lee, D., Bae, S., Shin, H., & Lee, D. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.08.593094 · Cited by 13

HEAL-KGGen: A Hierarchical Multi-Agent LLM Framework with Knowledge Graph Enhancement for Genetic Biomarker-Based Medical DiagnosisPreprint

Zuo, K., Zhong, Z., Huang, P., Tang, S., Chen, Y., & Jiang, Y. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.03.657521 · Cited by 13

Analysis of multi-condition single-cell data with latent embedding multivariate regression

Ahlmann-Eltze, C., & Huber, W. (2025) · Nature Genetics · doi:10.1038/s41588-024-01996-0 · Cited by 15

The Longer, the Better? The Past, Present and the Future of Long Cell‐Free DNA‐Based Liquid Biopsy

Choy, L. Y. L., & Lo, Y. M. D. (2025) · Medicine Bulletin · doi:10.1002/mdb2.70004 · Cited by 13

Ecological Roles and Shared Microbes Differentiate the Plastisphere from Natural Particle-Associated Microbiomes in Urban Rivers

Bao, Y., Ho, Y., Shen, Z., Lam, E. Y. M., Fang, J. K., Leung, K., & Lee, P. K. H. (2025) · Environmental Science & Technology · doi:10.1021/acs.est.5c06538 · Cited by 12

EasyAmplicon 2: Expanding PacBio and Nanopore Long Amplicon Sequencing Analysis Pipeline for Microbiome

Luo, H., Bai, D., Zhu, Z., Yousuf, S., Yang, H., Xun, J., Zeng, M., Wang, Y., Gao, Y., Peng, K., et al. (2025) · Advanced Science · doi:10.1002/advs.202512447 · Cited by 12

New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing reads

González-García, L. N., Guevara-Barrientos, D., Lozano‐Arce, D., Gil, J., Díaz-Riaño, J., Duarte, E., Andrade, G. I., Bojacá, J. C., Sanchez, M. C. H., Chavarro, C., et al. (2023) · Life Science Alliance · doi:10.26508/lsa.202201719 · Cited by 13

INSnet: a method for detecting insertions based on deep learning network

Gao, R., Luo, J., Ding, H., & Zhai, H. (2023) · BMC Bioinformatics · doi:10.1186/s12859-023-05216-0 · Cited by 13

Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths

Arbona, J., Kabalane, H., Barbier, J., Goldar, A., Hyrien, O., & Audit, B. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011138 · Cited by 12

MMDRP: drug response prediction and biomarker discovery using multi-modal deep learning

Taj, F., & Stein, L. D. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbae010 · Cited by 12

When Livestock Genomes Meet Third-Generation Sequencing Technology: From Opportunities to Applications

Liu, X., Zheng, J., Ding, J., Wu, J., Zuo, F., & Zhang, G. (2024) · Genes · doi:10.3390/genes15020245 · Cited by 12

mtDNA analysis using Mitopore

Dobner, J., Nguyen, T. N., Pávez, M., Cyganek, L., Distelmaier, F., Krutmann, J., Prigione, A., & Rossi, A. (2024) · Molecular Therapy — Methods & Clinical Development · doi:10.1016/j.omtm.2024.101231 · Cited by 12

Sex chromosome turnover plays an important role in the maintenance of barriers to post-speciation introgression in willows

Xue, Z., Applequist, W. L., Hörandl, E., & He, L. (2024) · Evolution Letters · doi:10.1093/evlett/qrae013 · Cited by 12

Cross-modality representation and multi-sample integration of spatially resolved omics data

Li, Z., Cui, X., Chen, X., Gao, Z., Liu, Y., Pan, Y., Chen, S., Lv, H., Zhai, L., & Jiang, R. (2026) · Briefings in Bioinformatics · doi:10.1093/bib/bbag214 · Cited by 12

High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing

Shekhar, R., O’Grady, T. M., Keil, N., Feswick, A., Amador, D. A. M., Tibbetts, S. A., Flemington, E. K., & Renne, R. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae540 · Cited by 12

Directly selecting cell-type marker genes for single-cell clustering analyses

Chen, Z., Wang, C., Huang, S., Shi, Y., & Xi, R. (2024) · Cell Reports Methods · doi:10.1016/j.crmeth.2024.100810 · Cited by 11

Web of venom: exploration of big data resources in animal toxin research

Zancolli, G., von Reumont, B. M., Anderluh, G., Çalışkan, F., Chiusano, M. L., Fröhlich, J., Hapeshi, E., Hempel, B.-F., Ikonomopoulou, M. P., Jungo, F., et al. (2024) · GigaScience · doi:10.1093/gigascience/giae054 · Cited by 15

The detection, function, and therapeutic potential of RNA 2'-O-methylation

Wu, K., Li, Y., Yang, Y., Yu, Y., Wang, Y., Zhang, L., Cao, Q., & Chen, K. (2024) · The Innovation Life · doi:10.59717/j.xinn-life.2024.100112 · Cited by 17

Systems biology of Haemonchus contortus – Advancing biotechnology for parasitic nematode control

Zheng, Y., Young, N. D., Wang, T., Chang, B. C. H., Song, J., & Gasser, R. B. (2025) · Biotechnology Advances · doi:10.1016/j.biotechadv.2025.108567 · Cited by 14

Minimizing detection bias of somatic mutations in a highly heterozygous oak genome

Xian, W., Carbonell‐Bejerano, P., Rabanal, F. A., Bezrukov, I., Reymond, P., & Weigel, D. (2025) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkaf143 · Cited by 12

Model-based dimensionality reduction for single-cell RNA-seq using generalized bilinear models

Nicol, P. B., & Miller, J. W. (2024) · Biostatistics · doi:10.1093/biostatistics/kxaf024 · Cited by 12

Temporal dynamics of collateral RNA cleavage by LbuCas13a in human cells

Bot, J. F., Zhao, Z., Li, M., Kammeron, D., Shang, P., & Geijsen, N. (2026) · Communications Biology · doi:10.1038/s42003-026-09511-3 · Cited by 12

Mesoscale Phase Separation of Chromatin in the Nucleus

Bajpai, G., Pavlov, D. A., Lorber, D., Volk, T., & Safran, S. A. (2020) · Biophysical Journal · doi:10.1016/j.bpj.2019.11.3001 · Cited by 12

Bayesian genome-wide analysis of cattle traits using variants with functional and evolutionary significance

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A graphical, interactive and GPU-enabled workflow to process long-read sequencing data

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Genome of the parasitoid wasp Dinocampus coccinellae reveals extensive duplications, accelerated evolution, and independent origins of thelytokous parthenogeny and solitary behavior

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A Chromosome-Scale Genome Assembly of a Helicoverpa zea Strain Resistant to Bacillus thuringiensis Cry1Ac Insecticidal Protein

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Ovine HOXB13: expanding the gene repertoire of sheep tail patterning and implications in genetic improvement

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Unsupervised neural network for single cell Multi-omics INTegration (UMINT): an application to health and disease

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SARS-CoV-2 Co-Infections and Recombinations Identified by Long-Read Single-Molecule Real-Time Sequencing

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Cytogenetic and molecular genetic methods for chromosomal translocations detection with reference to the KMT2A/MLL gene

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De-novo Assembly of Limnospira fusiformis Using Ultra-Long Reads

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DECODE: a De ep-learning framework for Co n de nsing enhancers and refining boundaries with large-scale functional assays

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A pan-cancer landscape of somatic mutations in non-unique regions of the human genome

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Long‐read whole genome sequencing reveals HOXD13 alterations in synpolydactyly

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SRTdb: an omnibus for human tissue and cancer-specific RNA transcripts

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Interactions Between Ticks and Lyme Disease Spirochetes

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Benchmarking small variant detection with ONT reveals high performance in challenging regionsPreprint

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Debiasing FracMinHash and deriving confidence intervals for mutation rates across a wide range of evolutionary distancesPreprint

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CF-Seq, an accessible web application for rapid re-analysis of cystic fibrosis pathogen RNA sequencing studies

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The Evolution of Molecular Genotyping in Plant Breeding

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PhysMAP - interpretable in vivo neuronal cell type identification using multi-modal analysis of electrophysiological dataPreprint

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Closing the gap: Solving complex medically relevant genes at scalePreprint

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Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modificationsPreprint

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Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otterPreprint

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long-read-tools.org: an interactive catalogue of analysis methods for long-read sequencing data

Amarasinghe, S., Ritchie, M., & Gouil, Q. A. (2021) · La Trobe University · doi:10.26181/14337101

A comprehensive evaluation of long read error correction methods

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Long-read error correction: a survey and qualitative comparisonPreprint

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Additional file 1 of Opportunities and challenges in long-read sequencing data analysis

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LoRDEC: a tool for correcting errors in long sequencing reads

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