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

Probabilistic machine learning ensures accurate ambient denoising in droplet-based single-cell omicsPreprint

Sheng, C., Lopes, R., Li, G., Schuierer, S., Waldt, A., Cuttat, R., Dimitrieva, S., Kauffmann, A., Durand, E., Galli, G. G., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.14.476312 · Cited by 37

Accurate and fast graph-based pangenome annotation and clustering with ggCallerPreprint

Horsfield, S., Tonkin‐Hill, G. Q., Croucher, N. J., & Lees, J. A. (2023) · Genome Research · doi:10.1101/gr.277733.123 · Cited by 35

Comparative analysis of multiplexed in situ gene expression profiling technologiesPreprint

Hartman, A., & Satija, R. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.01.11.575135 · Cited by 36

scDREAMER for atlas-level integration of single-cell datasets using deep generative model paired with adversarial classifier

Shree, A., Pavan, M. K., & Zafar, H. (2023) · Nature Communications · doi:10.1038/s41467-023-43590-8 · Cited by 33

ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model

Sashittal, P., Zhang, H., Iacobuzio–Donahue, C. A., & Raphael, B. J. (2023) · Genome biology · doi:10.1186/s13059-023-03106-5 · Cited by 31

Selective whole-genome sequencing of Plasmodium parasites directly from blood samples by nanopore adaptive sampling

Meulenaere, K. D., Cuypers, W. L., Gauglitz, J. M., Guetens, P., Rosanas‐Urgell, A., Laukens, K., & Cuypers, B. (2023) · mBio · doi:10.1128/mbio.01967-23 · Cited by 36

RNA Sequencing in Disease Diagnosis

Smail, C., & Montgomery, S. B. (2024) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-021623-121812 · Cited by 35

Nanopore duplex sequencing as an alternative to Illumina MiSeq sequencing for eDNA-based biomonitoring of coastal aquaculture impacts

Stoeck, T., Katzenmeier, S. N., Breiner, H., & Rubel, V. (2024) · Metabarcoding and Metagenomics · doi:10.3897/mbmg.8.121817 · Cited by 33

From bench to bedside: an interdisciplinary journey through the gut-lung axis with insights into lung cancer and immunotherapy

Dóra, D., Szőcs, E., Soós, Á., Halasy, V., Somodi, C., Mihucz, A., Rostás, M., Mógor, F., Lohinai, Z., & Nagy, N. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1434804 · Cited by 33

Dynamic Nuclear Structure Emerges from Chromatin Cross-Links and Motors

Liu, K., Patteson, A. E., Banigan, E. J., & Schwarz, J. M. (2021) · Physical Review Letters · doi:10.1103/physrevlett.126.158101 · Cited by 33

Evolutionary genetics of skin pigmentation in African populations

Feng, Y., McQuillan, M. A., & Tishkoff, S. A. (2021) · Human Molecular Genetics · doi:10.1093/hmg/ddab007 · Cited by 34

Comparative Analysis of Genotyping by Sequencing and Whole-Genome Sequencing Methods in Diversity Studies of Olea europaea L.

Friel, J., Bombarely, A., Dorca‐Fornell, C., Luque, F., & Fernández-Ocaña, A. M. (2021) · Plants · doi:10.3390/plants10112514 · Cited by 33

Transposable element landscapes in aging Drosophila

Yang, N., Srivastav, S. P., Rahman, R., Ma, Q., Dayama, G., Li, S., Chinen, M., Lei, E. P., Rosbash, M., & Lau, N. C. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010024 · Cited by 33

metaMIC: reference-free misassembly identification and correction of de novo metagenomic assemblies

Lai, S., Pan, S., Sun, C., Coelho, L. P., Chen, W., & Zhao, X. (2022) · Genome biology · doi:10.1186/s13059-022-02810-y · Cited by 33

Next-generation sequencing and bioinformatics in rare movement disorders

Zech, M., & Winkelmann, J. (2024) · Nature Reviews Neurology · doi:10.1038/s41582-023-00909-9 · Cited by 32

CellVoyager: AI CompBio agent generates new insights by autonomously analyzing biological data

Alber, S., Chen, B., Sun, E., Isakova, A., Wilk, A. J., & Zou, J. (2026) · Nature Methods · doi:10.1038/s41592-026-03029-6 · Cited by 60

A bird-like genome from a frog: Mechanisms of genome size reduction in the ornate burrowing frog, Platyplectrum ornatum

Lamichhaney, S., Catullo, R., Keogh, J. S., Clulow, S., Edwards, S. V., & Ezaz, T. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2011649118 · Cited by 31

Echinococcus granulosus sensu lato Genotypes in Different Hosts Worldwide: A Systematic Review

Manterola, C., Totomoch-Serra, A., Rojas, C., Riffo‐Campos, Á. L., & García-Méndez, N. (2021) · Acta Parasitologica · doi:10.1007/s11686-021-00439-8 · Cited by 32

Throwing away DNA: programmed downsizing in somatic nuclei

Drotos, K. H. I., Zagoskin, M. V., Kess, T., Gregory, T. R., & Wyngaard, G. A. (2022) · Trends in Genetics · doi:10.1016/j.tig.2022.02.003 · Cited by 32

Bridging the splicing gap in human genetics with long-read RNA sequencing: finding the protein isoform drivers of disease

Castaldi, P. J., Abood, A., Farber, C. R., & Sheynkman, G. (2022) · Human Molecular Genetics · doi:10.1093/hmg/ddac196 · Cited by 30

Host-pathogen coevolution drives innate immune response to Aphanomyces astaci infection in freshwater crayfish: transcriptomic evidence

Boštjančić, L. L., Francesconi, C., Rutz, C., Hoffbeck, L., Poidevin, L., Kress, A., Jussila, J., Makkonen, J., Feldmeyer, B., Bálint, M., et al. (2022) · BMC Genomics · doi:10.1186/s12864-022-08571-z · Cited by 32

Towards reliable quantification of cell state velocities

Marot-Lassauzaie, V., Bouman, B. J., Donaghy, F. D., Demerdash, Y., Essers, M. A. G., & Haghverdi, L. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010031 · Cited by 30

In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants

Nguyen, T. V., Jagt, C. J. V., Wang, J., Daetwyler, H. D., Xiang, R., Goddard, M. E., Nguyen, L. T., Ross, E. M., Hayes, B. J., Chamberlain, A. J., et al. (2023) · Genetics Selection Evolution · doi:10.1186/s12711-023-00783-5 · Cited by 34

An integrated Bayesian framework for multi‐omics prediction and classification

Mallick, H., Porwal, A., Saha, S., Basak, P., Svetnik, V., & Paul, E. (2023) · Statistics in Medicine · doi:10.1002/sim.9953 · Cited by 34

Chromosome-scale genome assembly of bread wheat’s wild relative Triticum timopheevii

Grewal, S., Yang, C., Scholefield, D., Ashling, S. S., Ghosh, S., Swarbreck, D., Collins, J., Yao, E., Sen, T. Z., Wilson, M. H., et al. (2024) · Scientific Data · doi:10.1038/s41597-024-03260-w · Cited by 33

Phase Separation and Correlated Motions in Motorized Genome

Jiang, Z., Qi, Y., Kamat, K. D., & Zhang, B. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c03238 · Cited by 29

SpaceX: gene co-expression network estimation for spatial transcriptomics

Acharyya, S., Zhou, X., & Baladandayuthapani, V. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac645 · Cited by 31

Community‐scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing

Cerk, K., Ugalde‐Salas, P., Nedjad, C. G., Lecomte, M., Muller, C., Sherman, D. J., Hildebrand, F., Labarthe, S., & Frioux, C. (2024) · Microbial Biotechnology · doi:10.1111/1751-7915.14396 · Cited by 39

RUBICON: a framework for designing efficient deep learning-based genomic basecallers

Singh, G., Alser, M., Denolf, K., Fırtına, C., Khodamoradi, A., Cavlak, M. B., Corporaal, H., & Mutlu, O. (2024) · Genome biology · doi:10.1186/s13059-024-03181-2 · Cited by 34

Exploring Cereal Metagenomics: Unravelling Microbial Communities for Improved Food Security

Masenya, K., Manganyi, M. C., & Dikobe, T. B. (2024) · Microorganisms · doi:10.3390/microorganisms12030510 · Cited by 36

Regulation and function of transposable elements in cancer genomes

Lee, M., Ahmad, S. F., & Xu, J. (2024) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-024-05195-2 · Cited by 34

Mapping lineage-traced cells across time points with moslin

Lange, M., Piran, Z., Klein, M., Spanjaard, B., Klein, D., Junker, J. P., Theis, F. J., & Nitzan, M. (2024) · Genome biology · doi:10.1186/s13059-024-03422-4 · Cited by 32

Improved Gene Annotation of the Fungal Wheat Pathogen Zymoseptoria tritici Based on Combined Iso-Seq and RNA-Seq Evidence

Lapalu, N., Lamothe, L., Petit, Y., Génissel, A., Delude, C., Feurtey, A., Abraham, L., Smith, D. P., King, R., Renwick, A., et al. (2025) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-07-25-0077-ta · Cited by 34

Investigation of the genetic etiology in male infertility with apparently balanced chromosomal structural rearrangements by genome sequencing

Chau, M. H. K., Li, Y., Dai, P., Shi, M., Zhu, X., Chung, J. P. W., Kwok, Y. K. Y., Choy, K. W., Kong, X., & Dong, Z. (2022) · Asian Journal of Andrology · doi:10.4103/aja2021106 · Cited by 31

Population genomic evidence of selection on structural variants in a natural hybrid zone

Zhang, L., Chaturvedi, S., Nice, C. C., Lucas, L. K., & Gompert, Z. (2022) · Molecular Ecology · doi:10.1111/mec.16469 · Cited by 32

Clinical Aspergillus Signatures in COPD and Bronchiectasis

Tiew, P. Y., Thng, K. X., & Chotirmall, S. H. (2022) · Journal of Fungi · doi:10.3390/jof8050480 · Cited by 33

Dynamic Changes in Ascorbic Acid Content during Fruit Development and Ripening of Actinidia latifolia (an Ascorbate-Rich Fruit Crop) and the Associated Molecular Mechanisms

Deng, H., Xia, H., Guo, Y., Liu, X., Lin, L., Wang, J., Xu, K., Lv, X., Hu, R., & Liang, D. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23105808 · Cited by 31

The performance of deep generative models for learning joint embeddings of single-cell multi-omics data

Brombacher, E., Hackenberg, M., Kreutz, C., Binder, H., & Treppner, M. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.962644 · Cited by 30

Historical dispersal and host-switching formed the evolutionary history of a globally distributed multi-host parasite – The Ligula intestinalis species complex

Nazarizadeh, M., Nováková, M., Loot, G., Gabagambi, N. P., Fatemizadeh, F., Osano, O., Presswell, B., Poulin, R., Vitál, Z., Scholz, T., et al. (2022) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2022.107677 · Cited by 32

Comparative analysis of syngeneic mouse models of high-grade serous ovarian cancer

Cook, D. P., Galpin, K. J. C., Rodriguez, G. M., Shakfa, N. E., Wilson‐Sanchez, J., Echaibi, M., Pereira, M., Matuszewska, K., Haagsma, J., Murshed, H., et al. (2023) · Communications Biology · doi:10.1038/s42003-023-05529-z · Cited by 34

Direct RNA sequencing of astronaut blood reveals spaceflight-associated m6A increases and hematopoietic transcriptional responses

Grigorev, K. A., Nelson, T. M., Overbey, E. G., Houerbi, N., Kim, J., Najjar, D., Damle, N., Afshin, E. E., Ryon, K. A., Thierry‐Mieg, J., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-48929-3 · Cited by 32

Evaluating long-read de novo assembly tools for eukaryotic genomes: insights and considerations

Cosma, B.-M., Zade, R. S. H., Jordan, E. N., van Lent, P., Peng, C., Pillay, S., & Abeel, T. (2022) · GigaScience · doi:10.1093/gigascience/giad100 · Cited by 30

Analyzing single-cell bisulfite sequencing data with MethSCAn

Kremer, L. P. M., Braun, M. M., Ovchinnikova, S., Küchenhoff, L., Cerrizuela, S., Martín-Villalba, A., & Anders, S. (2024) · Nature Methods · doi:10.1038/s41592-024-02347-x · Cited by 28

PlastidHub: An integrated analysis platform for plastid phylogenomics and comparative genomics

Zhang, N.-N., Stull, G. W., Zhang, X., Fan, S., Yi, T., & Qu, X. (2025) · Acta Botanica Yunnanica · doi:10.1016/j.pld.2025.05.005 · Cited by 30

Interactions Between Ticks and Lyme Disease Spirochetes

Pal, U., Kitsou, C., Drecktrah, D., Büyüktanır, Ö., & Fikrig, E. (2020) · Current Issues in Molecular Biology · doi:10.21775/cimb.042.113 · Cited by 30

Minimally overlapping words for sequence similarity search

Frith, M. C., Noé, L., & Kucherov, G. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa1054 · Cited by 30

scMET: Bayesian modeling of DNA methylation heterogeneity at single-cell resolution

Kapourani, C.-A., Argelaguet, R., Sanguinetti, G., & Vallejos, C. A. (2021) · Genome biology · doi:10.1186/s13059-021-02329-8 · Cited by 28

Whole‐genome sequencing and genome regions of special interest: Lessons from major histocompatibility complex, sex determination, and plant self‐incompatibility

Vekemans, X., Castric, V., Hipperson, H., Müller, N. A., Westerdahl, H., & Cronk, Q. (2021) · Molecular Ecology · doi:10.1111/mec.16020 · Cited by 29

Application of third-generation sequencing in cancer research

Chen, Z., & He, X. (2021) · Medical Review · doi:10.1515/mr-2021-0013 · Cited by 35

Challenges and Perspectives in the Epigenetics of Climate Change-Induced Forests Decline

García-García, I., Méndez‐Cea, B., Martín‐Gálvez, D., Seco, J. I., Gallego, F. J., & Linares, J. C. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2021.797958 · Cited by 30

Accurate assembly of multi-end RNA-seq data with Scallop2

Zhang, Q., Shi, Q., & Shao, M. (2022) · Nature Computational Science · doi:10.1038/s43588-022-00216-1 · Cited by 36

Single-cell and long-read sequencing to enhance modelling of splicing and cell-fate determination

Wu, S., & Schmitz, U. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.03.023 · Cited by 31

A phased chromosome-level genome and full mitochondrial sequence for the dikaryotic myrtle rust pathogen, Austropuccinia psidiiPreprint

Edwards, R. J., Dong, C., Park, R., & Tobias, P. A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.04.22.489119 · Cited by 31

Use of whole genome sequencing for surveillance and control of foodborne diseases: status quo and quo vadis

Schadron, T., van den Beld, M. J. C., Mughini‐Gras, L., & Franz, E. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1460335 · Cited by 29

Single cell and spatial alternative splicing analysis with Nanopore long read sequencing

Fu, Y., Kim, H. S., Roy, S., Huang, S., Adams, J. I., Grimes, S. M., Lau, B. T., Sathe, A., Ji, H. P., & Zhang, N. R. (2025) · Nature Communications · doi:10.1038/s41467-025-60902-2 · Cited by 36

Genomic Profiling of Virulence in the Soybean Cyst Nematode Using Single-Nematode Sequencing

Ste‐Croix, D. T., St-Marseille, A.-F. G., Lord, É., Bélanger, R. R., Jacques Brodeur, B., & Mimee, B. (2020) · Phytopathology · doi:10.1094/phyto-08-20-0348-fi · Cited by 29

Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform

Angthong, P., Uengwetwanit, T., Pootakham, W., Sittikankaew, K., Sonthirod, C., Sangsrakru, D., Yoocha, T., Nookaew, I., Wongsurawat, T., Jenjaroenpun, P., et al. (2020) · PeerJ · doi:10.7717/peerj.10340 · Cited by 31

Improved High-Throughput Sequencing of the Human Oral Microbiome: From Illumina to PacBio

Zhang, J., Su, L., Wang, Y., & Deng, S. (2020) · Canadian Journal of Infectious Diseases and Medical Microbiology · doi:10.1155/2020/6678872 · Cited by 27

Oxford Nanopore MinION Direct RNA-Seq for Systems Biology

Pyatnitskiy, M. A., Arzumanian, V. A., Radko, S. P., Ptitsyn, K. G., Vakhrushev, I. V., Poverennaya, E. V., & Ponomarenko, E. A. (2021) · Biology · doi:10.3390/biology10111131 · Cited by 30

Multiplexed Assembly and Annotation of Synthetic Biology Constructs Using Long-Read Nanopore Sequencing

Emiliani, F. E., Hsu, I., & McKenna, A. (2022) · ACS Synthetic Biology · doi:10.1021/acssynbio.2c00126 · Cited by 29

sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network

Xu, Y., Begoli, E., & McCord, R. P. (2022) · npj Systems Biology and Applications · doi:10.1038/s41540-022-00245-6 · Cited by 33

The revised reference genome of the leopard gecko ( Eublepharis macularius ) provides insight into the considerations of genome phasing and assembly

Pinto, B. J., Gamble, T., Smith, C. H., Keating, S. E., Havird, J. C., & Chiari, Y. (2023) · Journal of Heredity · doi:10.1093/jhered/esad016 · Cited by 31

Range-wide differential adaptation and genomic offset in critically endangered Asian rosewoods

Hung, T. H., So, T., Thammavong, B., Chamchumroon, V., Theilade, I., Chhang, P., Bouamanivong, S., Hartvig, I., Gaisberger, H., Jalonen, R., et al. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2301603120 · Cited by 32

Temporally Correlated Active Forces Drive Segregation and Enhanced Dynamics in Chromosome Polymers

Brahmachari, S., Markovich, T., MacKintosh, F. C., & Onuchic, J. N. (2024) · PRX Life · doi:10.1103/prxlife.2.033003 · Cited by 28

Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities

Uffelen, A. V., Posadas, A., Roosens, N. H. C., Marchal, K., Keersmaecker, S. C. J. D., & Vanneste, K. (2024) · Scientific Data · doi:10.1038/s41597-024-03672-8 · Cited by 31

Sexual Dimorphism through the Lens of Genome Manipulation, Forward Genetics, and Spatiotemporal Sequencing

Kasimatis, K. R., Ramirez, S. S., & Stevenson, Z. C. (2020) · Genome Biology and Evolution · doi:10.1093/gbe/evaa243 · Cited by 29

RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy

Ugrina, M., Burkhart, I., Müller, D., Schwalbe, H., & Schwierz, N. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad1065 · Cited by 27

Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues

Degalez, F., Charles, M., Foissac, S., Zhou, H., Guan, D., Fang, L., Klopp, C., Allain, C., Lagoutte, L., Lecerf, F., et al. (2024) · Scientific Reports · doi:10.1038/s41598-024-56705-y · Cited by 28

Standardization in global environmental antibiotic resistance genes (ARGs) surveillance

Mao, X., Yin, X., Yang, Y., Che, Y., Xu, X., Deng, Y., Li, L., & Zhang, T. (2024) · Critical Reviews in Environmental Science and Technology · doi:10.1080/10643389.2024.2344453 · Cited by 28

Biologically informed NeuralODEs for genome-wide regulatory dynamics

Hossain, I., Fanfani, V., Fischer, J., Quackenbush, J. F., & Burkholz, R. (2024) · Genome biology · doi:10.1186/s13059-024-03264-0 · Cited by 44

CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing

Sala, S. C., Perteghella, T., Lagarde, J., Nishiyori, H., Palumbo, E., Arnan, C., Takahashi, H., Carninci, P., Uszczyńska-Ratajczak, B., & Guigó, R. (2024) · Nature Communications · doi:10.1038/s41467-024-49523-3 · Cited by 27

Applications of Nanopore sequencing in precision cancer medicine

Dyshlovoy, S. A., Paigin, S., Afflerbach, A., Lobermeyer, A., Werner, S., Schüller, U., Bokemeyer, C., Schuh, A., Bergmann, L., Amsberg, G. V., et al. (2024) · International Journal of Cancer · doi:10.1002/ijc.35100 · Cited by 31

Valid inference for machine learning-assisted genome-wide association studies

Miao, J., Wu, Y., Sun, Z., Miao, X., Lu, T., Zhao, J., & Lu, Q. (2024) · Nature Genetics · doi:10.1038/s41588-024-01934-0 · Cited by 28

Long-Read Sequencing and Structural Variant Detection: Unlocking the Hidden Genome in Rare Genetic Disorders

Moustakli, E., Christopoulos, P., Potiris, A., Zikopoulos, A., Mavrogianni, D., Karampas, G., Kathopoulis, N., Anagnostaki, I., Domali, E., Tzallas, A. T., et al. (2025) · Diagnostics · doi:10.3390/diagnostics15141803 · Cited by 31

Integration and transfer learning of single-cell transcriptomes via cFIT

Peng, M., Li, Y., Wamsley, B., Wei, Y., & Roeder, K. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2024383118 · Cited by 33

High-quality genome assembly of Huazhan and Tianfeng, the parents of an elite rice hybrid Tian-you-hua-zhan

Zhang, H., Wang, Y.-X., Deng, C., Zhao, S., Zhang, P., Feng, J., Huang, W., Kang, S.-J., Qian, Q., Xiong, G., et al. (2021) · Science China Life Sciences · doi:10.1007/s11427-020-1940-9 · Cited by 25

Accuracies of genomic predictions for disease resistance of striped catfish to Edwardsiella ictaluri using artificial intelligence algorithms

Vu, N. T., Phúc, T. H., Oanh, K. T. P., Sáng, N. V., Trang, T. T., & Nguyen, N. H. (2021) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkab361 · Cited by 27

De novo chromosome level assembly of a plant genome from long read sequence data

Sharma, P., Masouleh, A. K., Topp, B. L., Furtado, A., & Henry, R. J. (2021) · The Plant Journal · doi:10.1111/tpj.15583 · Cited by 28

Discovering functional motifs in long noncoding RNAs

Ross, C. J., & Ulitsky, I. (2022) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1708 · Cited by 27

Unravelling the tumour genome: The evolutionary and clinical impacts of structural variants in tumourigenesis

Hamdan, A., & Ewing, A. (2022) · The Journal of Pathology · doi:10.1002/path.5901 · Cited by 29

scINSIGHT for interpreting single-cell gene expression from biologically heterogeneous data

Qian, K., Fu, S., Li, H., & Li, W. V. (2022) · Genome biology · doi:10.1186/s13059-022-02649-3 · Cited by 26

ResPAN: a powerful batch correction model for scRNA-seq data through residual adversarial networks

Wang, Y., Liu, T., & Zhao, H. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac427 · Cited by 25

Genome of tetraploid sour cherry (Prunus cerasus L.) ‘Montmorency’ identifies three distinct ancestral Prunus genomes

Goeckeritz, C. Z., Rhoades, K. E., Childs, K. L., Iezzoni, A. F., VanBuren, R., & Hollender, C. A. (2023) · Horticulture Research · doi:10.1093/hr/uhad097 · Cited by 28

Quantifying transcriptome diversity: a review

Jones, E. F., Haldar, A., Oza, V. H., & Lasseigne, B. N. (2023) · Briefings in Functional Genomics · doi:10.1093/bfgp/elad019 · Cited by 28

Versatile Detection of Diverse Selective Sweeps with Flex-Sweep

Lauterbur, M. E., Munch, K., & Enard, D. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad139 · Cited by 29

RESCUE: a validated Nanopore pipeline to classify bacteria through long-read, 16S-ITS-23S rRNA sequencing

Petrone, J. R., Glusberger, P. R., George, C. D., Milletich, P. L., Ahrens, A. P., Roesch, L. F. W., & Triplett, E. W. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1201064 · Cited by 28

Belayer: Modeling discrete and continuous spatial variation in gene expression from spatially resolved transcriptomics

Ma, C., Chitra, U., Zhang, S., & Raphael, B. J. (2022) · Cell Systems · doi:10.1016/j.cels.2022.09.002 · Cited by 27

An LTR retrotransposon in the promoter of a PsMYB10.2 gene associated with the regulation of fruit flesh color in Japanese plum

Fiol, A., García, S. C., Dujak, C., Pacheco, I., Infante, R., & Aranzana, M. J. (2022) · Horticulture Research · doi:10.1093/hr/uhac206 · Cited by 27

XMAP: Cross-population fine-mapping by leveraging genetic diversity and accounting for confounding bias

Cai, M., Wang, Z., Xiao, J., Hu, X., Chen, G., & Yang, C. (2023) · Nature Communications · doi:10.1038/s41467-023-42614-7 · Cited by 26

From flesh to bones: Multi‐omics approaches in forensic science

Procopio, N., & Bonicelli, A. (2024) · PROTEOMICS · doi:10.1002/pmic.202200335 · Cited by 32

Application of Next-Generation Sequencing (NGS) Techniques for Selected Companion Animals

Domrazek, K., & Jurka, P. (2024) · Animals · doi:10.3390/ani14111578 · Cited by 27

Precision oncology: current and future platforms for treatment selection

Tang, X., Berger, M. F., & Solit, D. B. (2024) · Trends in cancer · doi:10.1016/j.trecan.2024.06.009 · Cited by 32

Genomic Approaches to Plant-Pathogen Epidemiology and Diagnostics

Weisberg, A. J., Grünwald, N. J., Savory, E. A., Putnam, M. L., & Chang, J. H. (2021) · Annual Review of Phytopathology · doi:10.1146/annurev-phyto-020620-121736 · Cited by 27

Precise measurements of chromatin diffusion dynamics by modeling using Gaussian processes

Oliveira, G. M., Oravecz, A., Kobi, D., Maroquenne, M., Bystricky, K., Sexton, T., & Molina, N. (2021) · Nature Communications · doi:10.1038/s41467-021-26466-7 · Cited by 23

RNA Viruses in Aquatic Ecosystems through the Lens of Ecological Genomics and Transcriptomics

Kolundžija, S., Cheng, D.-Q., & Lauro, F. M. (2022) · Viruses · doi:10.3390/v14040702 · Cited by 27

Introduction to the principles and methods underlying the recovery of metagenome‐assembled genomes from metagenomic data

Goussarov, G., Mysara, M., Vandamme, P. A. R., & Houdt, R. V. (2022) · MicrobiologyOpen · doi:10.1002/mbo3.1298 · Cited by 27

Genomic resources and their applications in aquaculture of Asian seabass ( Lates calcarifer )

Yue, G. H., Wang, L., Yang, Z., Sun, F., Tay, Y. X., Wong, J., & Yeo, S. (2022) · Reviews in Aquaculture · doi:10.1111/raq.12764 · Cited by 27

HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph

Rubin, J. D., Vogel, N. A., Gopalakrishnan, S., Sackett, P. W., & Renaud, G. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011148 · Cited by 26

Robust differential expression testing for single-cell CRISPR screens at low multiplicity of infection

Barry, T., Mason, K., Roeder, K., & Katsevich, E. (2024) · Genome Biology · doi:10.1186/s13059-024-03254-2 · Cited by 28

Comparing antimicrobial resistant genes and phenotypes across multiple sequencing platforms and assays for Enterobacterales clinical isolates

Rose, R., Nolan, D. J., Ashcraft, D. S., Feehan, A. K., Velez-Climent, L., Huston, C., Lain, B. N., Rosenthal, S., Miele, L., Fogel, G. B., et al. (2023) · BMC Microbiology · doi:10.1186/s12866-023-02975-x · Cited by 26

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

Zhang, H., Jain, C., & Aluru, S. (2020) · BMC Genomics · doi:10.1186/s12864-020-07227-0 · Cited by 150

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

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

Amarasinghe, S., Su, S., Dong, X., Zappia, L., Ritchie, M., & Gouil, Q. A. (2020) · Figshare · doi:10.6084/m9.figshare.11826234

LoRDEC: a tool for correcting errors in long sequencing reads

Rivals, É. (2015) · HAL