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

Inference of the Demographic Histories and Selective Effects of Human Gut Commensal Microbiota Over the Course of Human History

Mah, J. C., Lohmueller, K. E., & Garud, N. R. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf010 · Cited by 11

Decoding the fibromelanosis locus complex chromosomal rearrangement of black-bone chicken: genetic differentiation, selective sweeps and protein-coding changes in Kadaknath chicken

Shinde, S. S., Sharma, A., & Vijay, N. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1180658 · Cited by 11

Cell-type annotation with accurate unseen cell-type identification using multiple references

Xiong, Y.-X., Wang, M.-G., Chen, L., & Zhang, X.-F. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011261 · Cited by 11

Deciphering complex breakage-fusion-bridge genome rearrangements with Ambigram

Li, C., Chen, L., Pan, G., Zhang, W., & Li, S. C. (2023) · Nature Communications · doi:10.1038/s41467-023-41259-w · Cited by 11

An updated database of virus circular RNAs provides new insights into the biogenesis mechanism of the molecule

Fu, P., Cai, Z., Zhang, Z., Meng, X., & Peng, Y. (2023) · Emerging Microbes & Infections · doi:10.1080/22221751.2023.2261558 · Cited by 10

Splicing inhibition mediated by reduced splicing factors and helicases is associated with the cellular response of lung cancer cells to cisplatin

Wang, L., Yin, N., Shi, W., Xie, Y., Yi, J., Tang, Z., Tang, J., & Xiang, J. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.12.039 · Cited by 11

PUPpy: a primer design pipeline for substrain-level microbial detection and absolute quantification

Ghezzi, H., Fan, Y. M., Ng, K. M., Burckhardt, J. C., Pepin, D. M., Lin, X., Ziels, R. M., & Tropini, C. (2024) · mSphere · doi:10.1128/msphere.00360-24 · Cited by 11

Long-read transcript sequencing identifies differential isoform expression in the entorhinal cortex in a transgenic model of tau pathology

Leung, S. K., Bamford, R. A., Jeffries, A. R., Castanho, I., Chioza, B. A., Flaxman, C. S., Moore, K., Dempster, E. L., Harvey, J., Brown, J. T., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-50486-8 · Cited by 18

Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing

Henglin, M., Ghareghani, M., Harvey, W. T., Porubskỳ, D., Koren, S., Eichler, E. E., Ebert, P., & Marschall, T. (2024) · Genome biology · doi:10.1186/s13059-024-03409-1 · Cited by 11

Assessing Rapid Adaptation Through Epigenetic Inheritance: A New Experimental Approach

Huber, M., & Chávez, A. (2024) · Plant Cell & Environment · doi:10.1111/pce.15220 · Cited by 11

Genomic characterization of a clonal emergent Salmonella Minnesota lineage in Brazil reveals the presence of a novel megaplasmid of resistance and virulence

dos Santos, A. M. P., Panzenhagen, P., Ferrari, R. G., Portes, A. B., de Jesus, A. C. S., Ochioni, A. C., Rodrigues, D. D. P., Toro, M., Meng, J., Allard, M. W., et al. (2024) · Applied and Environmental Microbiology · doi:10.1128/aem.01579-24 · Cited by 11

Frequent genetic exchanges revealed by a pan-mitogenome graph of a fungal plant pathogen

van Westerhoven, A. C., Dijkstra, J., Palop, J. L. A., Wissink, K., Bell, J., Kema, G. H. J., & Seidl, M. F. (2024) · mBio · doi:10.1128/mbio.02758-24 · Cited by 11

Subfamily evolution analysis using nuclear and chloroplast data from the same reads

Witharana, E. P., Iwasaki, T., San, M. H., Jayawardana, N. U., Kotoda, N., Yamamoto, M., & Nagano, Y. (2025) · Scientific Reports · doi:10.1038/s41598-024-83292-9 · Cited by 12

Big data and transformative bioinformatics in genomic diagnostics and beyond

Saparov, A., & Zech, M. (2025) · Parkinsonism & Related Disorders · doi:10.1016/j.parkreldis.2025.107311 · Cited by 11

Gauge fixing for sequence-function relationships

(2025) · doi:10.1371/journal.pcbi.1012818 · Cited by 11

A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona sex chromosomes

Guo, Q., Pan, Y., Dai, W., Guo, F., Zeng, T., Chen, W., Mi, Y., Zhang, Y., Shi, S., Jiang, W., et al. (2025) · GigaScience · doi:10.1093/gigascience/giaf079 · Cited by 13

CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells

Shafighi, S. D., Kiełbasa, S. M., Sepúlveda-Yáñez, J., Monajemi, R., Cats, D., Mei, H., Menafra, R., Kloet, S. L., Veelken, H., van Bergen, C. A. M., et al. (2021) · Genome Medicine · doi:10.1186/s13073-021-00842-w · Cited by 10

Single-Entity Detection With TEM-Fabricated Nanopores

Yang, H., Saqib, M., & Hao, R. (2021) · Frontiers in Chemistry · doi:10.3389/fchem.2021.664820 · Cited by 11

Sincast: a computational framework to predict cell identities in single-cell transcriptomes using bulk atlases as references

Deng, Y., Choi, J., & Cao, K. L. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac088 · Cited by 10

Profiling the Genome-Wide Landscape of Short Tandem Repeats by Long-Read Sequencing

Liu, Z., Zhao, G., Xiao, Y., Zeng, S., Yuan, Y., Zhou, X. C., Fang, Z., He, R., Li, B., Zhao, Y., et al. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.810595 · Cited by 11

Disentangling single-cell omics representation with a power spectral density-based feature extraction

Zandavi, S. M., Koch, F. C., Vijayan, A., Zanini, F., Valdés‐Mora, F., Gallego‐Ortega, D., & Vafaee, F. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac436 · Cited by 11

The impact of single-cell genomics on the field of mycobacterial infection

Geraldes, I., Fernandes, M., Fraga, A. G., & Osório, N. S. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.989464 · Cited by 11

Improvement of large copy number variant detection by whole genome nanopore sequencing

Cuenca-Guardiola, J., de la Morena‐Barrio, B., Garcı́a, J. L., Sanchis‐Juan, A., Corral, J., & Fernández‐Breis, J. T. (2022) · Journal of Advanced Research · doi:10.1016/j.jare.2022.10.012 · Cited by 10

Advanced approaches for the diagnosis and chemoprevention of canine vector-borne pathogens and parasites—Implications for the Asia-Pacific region and beyond

Huggins, L. G., Koehler, A. V. A., Gasser, R. B., & Traub, R. J. (2023) · Advances in Parasitology/Advances in parasitology · doi:10.1016/bs.apar.2022.12.001 · Cited by 11

Draft genome assemblies of the avian louse Brueelia nebulosa and its associates using long-read sequencing from an individual specimen

Sweet, A. D., Browne, D. R., Hernandez, A. G., Johnson, K. P., & Cameron, S. L. (2023) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkad030 · Cited by 11

CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data

Hou, R., Hon, C.-C., & Huang, Y. (2023) · Nature Communications · doi:10.1038/s41467-023-42636-1 · Cited by 13

Dynamic Phytomeric Growth Contributes to Local Adaptation in Barley

Huang, Y.-Y., Maurer, A., Giehl, R., Zhao, S.-S., Golan, G., Thirulogachandar, V., Li, G., Zhao, Y.-S., Trautewig, C., Himmelbach, A., et al. (2024) · Molecular biology and evolution · doi:10.1093/molbev/msae011 · Cited by 6

Co-linear chaining on pangenome graphs

Rajput, J., Chandra, G., & Jain, C. (2024) · Algorithms for Molecular Biology · doi:10.1186/s13015-024-00250-w · Cited by 12

Sex chromosome turnover in hybridizing stickleback lineages

Yi, X., Wang, D., Reid, K., Feng, X., Löytynoja, A., & Merilä, J. (2024) · Evolution Letters · doi:10.1093/evlett/qrae019 · Cited by 11

Meta-colored Compacted de Bruijn Graphs

Pibiri, G. E., Fan, J., & Patro, R. (2024) · Lecture notes in computer science · doi:10.1007/978-1-0716-3989-4_9 · Cited by 11

A hybrid demultiplexing strategy that improves performance and robustness of cell hashing

Li, L., Sun, J., Fu, Y., Changrob, S., McGrath, J. J. C., & Wilson, P. C. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae254 · Cited by 9

A comparison of alternative mRNA splicing in the CD4 and CD8 T cell lineages

Liu, X., Andrews, M. V., Skinner, J. P. J., Johanson, T. M., & Chong, M. M. W. (2021) · Molecular Immunology · doi:10.1016/j.molimm.2021.02.009 · Cited by 11

A variant selection framework for genome graphs

Jain, C., Tavakoli, N., & Aluru, S. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab302 · Cited by 11

GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs

Tognon, M., Bonnici, V., Garrison, E. P., Giugno, R., & Pinello, L. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009444 · Cited by 9

Long RNA-Mediated Chromatin Regulation in Fission Yeast and Mammals

Faber, M. W., & Vo, T. V. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23020968 · Cited by 11

Randomized gates eliminate bias in sort‐seq assays

Trippe, B. L., Huang, B., DeBenedictis, E. A., Coventry, B., Bhattacharya, N., Yang, K., Baker, D. A., & Crawford, L. A. (2022) · Protein Science · doi:10.1002/pro.4401 · Cited by 10

Chromatin-accessibility estimation from single-cell ATAC data with scOpenPreprint

Li, Z., Kuppe, C., Ziegler, S., Cheng, M., Kabgani, N., Menzel, S., Zenke, M., Kramann, R., & Costa, I. G. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/865931 · Cited by 10

Assessing conservation of alternative splicing with evolutionary splicing graphsPreprint

Zea, D. J., Laskina, S., Baudin, A., Richard, H., & Laine, É. (2021) · Genome Research · doi:10.1101/gr.274696.120 · Cited by 15

Accelerating Minimap2 for accurate long read alignment on GPUsPreprint

Sadasivan, H., Maric, M., Dawson, E. T., Iyer, V., Israeli, J., & Narayanasamy, S. (2022) · Research Square · doi:10.21203/rs.3.rs-1523696/v2 · Cited by 11

Benchmarking long-read RNA-sequencing analysis tools using in silico mixturesPreprint

Dong, X., Du, M. R. M., Gouil, Q. A., Tian, L., Jabbari, J. S., Bowden, R. J., Baldoni, P. L., Chen, Y., Smyth, G. K., Amarasinghe, S. L., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.22.501076 · Cited by 11

Editorial: Long-read sequencing—Pitfalls, benefits and success stories

Wohlers, I., Garg, S., & Hehir‐Kwa, J. Y. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2022.1114542 · Cited by 11

A pre-trained large generative model for translating single-cell transcriptome to proteomePreprint

Liu, L., Li, W., Wong, K., Yang, F., & Yao, J. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.04.547619 · Cited by 11

Quality assessment of long read data in multisample lrRNA-seq experiments using SQANTI-readsPreprint

Keil, N., Monzó, C., McIntyre, L. M., & Conesa, A. (2025) · Genome Research · doi:10.1101/gr.280021.124 · Cited by 11

Genome structure mapping with high-resolution 3D genomics and deep learningPreprint

Hong, C. K., Feng, F., Ramanathan, V., Liu, J., & Hansen, A. S. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.06.650874 · Cited by 10

Gauge fixing for sequence-function relationships

Posfai, A., Zhou, J., McCandlish, D. M., & Kinney, J. B. (2024) · doi:10.1101/2024.05.12.593772 · Cited by 11

scAGCI: an anchor graph-based method for cell clustering from integrated scRNA-seq and scATAC-seq data

Dong, Y., Zhang, J., Shi, J., Hu, Y., Cao, X., Xing, L., Dong, Y., & Zhang, X. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf244 · Cited by 10

Pangenomics combined with artificial intelligence and precision breeding can accelerate crop improvement

Li, T., Mohamedikbal, S., Bestry, M., Batley, J., & Edwards, D. (2025) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2025.102825 · Cited by 12

DNA barcoding markers: A comprehensive review and taxonomic classification across species

Rani, V., Chauhan, C., & Sengar, R. S. (2025) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2025.108872 · Cited by 10

A practical guide to targeted single-cell RNA sequencing technologies

Moro, G., Brunner, E., & Basler, K. (2026) · Communications Biology · doi:10.1038/s42003-026-09675-y · Cited by 10

Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes

Zhang, T., Li, J., Tang, C., Wu, Y., Wu, H., Xi-Tong, Z., Luo, Z., Qin, H., Ding, L., Zeng, Y., et al. (2026) · iMeta · doi:10.1002/imt2.70136 · Cited by 17

The value of genotype-specific reference for transcriptome analyses in barley

Guo, W., Coulter, M., Waugh, R., & Zhang, R. (2022) · Life Science Alliance · doi:10.26508/lsa.202101255 · Cited by 10

Characterization of a strain-specific CD-1 reference genome reveals potential inter- and intra-strain functional variability

Jung, Y. H., Wang, H. V., Ali, S., Corces, V. G., & Kremsky, I. (2023) · BMC Genomics · doi:10.1186/s12864-023-09523-x · Cited by 10

Detection and discovery of repeat expansions in ataxia enabled by next-generation sequencing: present and future

Rafehi, H., Bennett, M. F., & Bahlo, M. (2023) · Emerging Topics in Life Sciences · doi:10.1042/etls20230018 · Cited by 10

A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X

Jowhar, Z. M., Xu, A., Venkataramanan, S., Dossena, F., Hoye, M. L., Silver, D. L., Floor, S. N., & Calviello, L. (2024) · Molecular Systems Biology · doi:10.1038/s44320-024-00013-0 · Cited by 9

The effect of data transformation on low-dimensional integration of single-cell RNA-seq

Park, Y., & Hauschild, A.-C. (2024) · BMC Bioinformatics · doi:10.1186/s12859-024-05788-5 · Cited by 12

From haystack to high precision: advanced sequencing methods to unraveling circulating tumor DNA mutations

da Silva, T. F., de Azevedo, J. C., Teixeira, E. B., Casseb, S. M. M., Moreira, F. C., de Assumpção, P. P., dos Santos, S. E. B., & Calcagno, D. Q. (2024) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2024.1423470 · Cited by 10

Structural variation discovery in wheat using PacBio high‐fidelity sequencing

Zhang, Z., Zhang, J., Kang, L., Qiu, X., Xu, S., Xu, J. Q., Guo, Y., Niu, Z., Niu, B., Bi, A., et al. (2024) · The Plant Journal · doi:10.1111/tpj.17011 · Cited by 11

4CAC: 4-class classifier of metagenome contigs using machine learning and assembly graphs

Pu, L., & Ron Shamir, A. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae799 · Cited by 11

Where the Patterns Are: Repetition-Aware Compression for Colored de Bruijn Graphs *

Campanelli, A., Pibiri, G. E., Fan, J., & Patro, R. (2024) · Journal of Computational Biology · doi:10.1089/cmb.2024.0714 · Cited by 10

Perturbation of mRNA splicing in liver cancer: insights, opportunities and challenges

Jia, Q., Sun, X., Li, H., Guo, J., Niu, K., Chan, K. M., Bernards, R., Qin, W., & Jin, H. (2024) · Gut · doi:10.1136/gutjnl-2024-333127 · Cited by 10

EIciRNAs in focus: current understanding and future perspectives

Yang, Y., Zhong, Y., & Chen, L. (2024) · RNA Biology · doi:10.1080/15476286.2024.2443876 · Cited by 10

LongReadSum: A fast and flexible quality control and signal summarization tool for long-read sequencing data

Perdomo, J. E., Ahsan, M. U., Liu, Q., Fang, L., & Wang, K. (2025) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2025.01.019 · Cited by 10

Reference-free identification and pangenome analysis of accessory chromosomes in a major fungal plant pathogen

van Westerhoven, A. C., Fokkens, L., Wissink, K., Kema, G. H. J., Rep, M., & Seidl, M. F. (2025) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqaf034 · Cited by 13

Systematic analysis of the effects of splicing on the diversity of post-translational modifications in protein isoforms using PTM-POSE

Crowl, S., Coleman, M. B., Chaphiv, A., Jordan, B. T., & Naegle, K. M. (2025) · Cell Systems · doi:10.1016/j.cels.2025.101318 · Cited by 10

Liquid–liquid phase separation of lamin drives altered chromatin organization in cardiomyopathic mutations of lamin A

Nath, S., Dutta, S., Sarkar, S. D., Sengupta, D., Mitra, M. K., & Sengupta, K. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf615 · Cited by 10

Single-variant genome-wide association study and regional heritability mapping of protein efficiency and performance traits in Large White pigs

Ewaoluwagbemiga, E. O., Lloret‐Villas, A., Nosková, A., Pausch, H., & Kasper, C. (2025) · Genetics Selection Evolution · doi:10.1186/s12711-025-00993-z · Cited by 10

Functional meta-omics provide critical insights into long- and short-read assemblies

Galata, V., Busi, S. B., Kunath, B. J., de Nies, L., Całusińska, M., Halder, R., May, P., Wilmes, P., & Laczny, C. C. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab330 · Cited by 10

Transposable elements and Piwi‑interacting RNAs in hemato‑oncology with a focus on myelodysplastic syndrome (Review)

Merkerová, M. D., & Krejčík, Z. (2021) · International Journal of Oncology · doi:10.3892/ijo.2021.5285 · Cited by 10

High-Throughput Sequencing for Life-History Sorting and for Bridging Reference Sequences in Marine Gerromorpha (Insecta: Heteroptera)

Chang, J. J. M., Ip, Y. C. A., Cheng, L., Kunning, I., Mana, R., Wainwright, B. J., & Huang, D. (2021) · Insect Systematics and Diversity · doi:10.1093/isd/ixab024 · Cited by 10

cfTrack : A Method of Exome-Wide Mutation Analysis of Cell-free DNA to Simultaneously Monitor the Full Spectrum of Cancer Treatment Outcomes Including MRD, Recurrence, and Evolution

Li, S., Zeng, W., Ni, X., Zhou, Y., Stackpole, M. L., Noor, Z. S., Yuan, Z., Neal, A., Memarzadeh, S., Garon, E. B., et al. (2022) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-21-1242 · Cited by 10

Methods to Improve Molecular Diagnosis in Genomic Cold Cases in Pediatric Neurology

Kadlubowska, M. K., & Schrauwen, I. (2022) · Genes · doi:10.3390/genes13020333 · Cited by 12

Prosthecate aerobic anoxygenic phototrophs Photocaulis sulfatitolerans gen. nov. sp. nov. and Photocaulis rubescens sp. nov. isolated from alpine meromictic lakes in British Columbia, Canada

Kuzyk, S. B., Jafri, M., Humphrey, E., Maltman, C., Kyndt, J. A., & Yurkov, V. (2022) · Archives of Microbiology · doi:10.1007/s00203-022-03007-4 · Cited by 10

Pacific Biosciences Fusion and Long Isoform Pipeline for Cancer Transcriptome–Based Resolution of Isoform Complexity

Miller, A. R., Wijeratne, S., McGrath, S. D., Schieffer, K. M., Miller, K. E., Lee, K., Mathew, M., LaHaye, S., Fitch, J., Kelly, B., et al. (2022) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2022.09.003 · Cited by 10

Haplotype breeding for unlocking and utilizing plant genomics data

Rai, M., & Tyagi, W. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.1006288 · Cited by 10

Complete genome sequencing of nematode Aphelenchoides besseyi, an economically important pest causing rice white-tip disease

Ji, H., Xie, J., Han, Z., Yang, F., Yu, W., Peng, Y., & Qing, X. (2023) · Phytopathology Research · doi:10.1186/s42483-023-00158-0 · Cited by 11

Lipid metabolism dysfunction following symbiont elimination is linked to altered Kennedy pathway homeostasis

Attardo, G. M., Benoit, J. B., Michalková, V., Kondragunta, A., Baumann, A. A., Weiss, B. L., Malacrida, A., Scolari, F., & Aksoy, S. (2023) · iScience · doi:10.1016/j.isci.2023.107108 · Cited by 10

Functional genomics and small molecules in mitochondrial neurodevelopmental disorders

Calame, D. G., & Emrick, L. (2024) · Neurotherapeutics · doi:10.1016/j.neurot.2024.e00316 · Cited by 11

Self-supervised deep learning of gene–gene interactions for improved gene expression recovery

Wei, Q., Islam, M. T., Zhou, Y., & Xing, L. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae031 · Cited by 11

Genetic score omics regression and multitrait meta-analysis detect widespread cis -regulatory effects shaping bovine complex traits

Xiang, R., Fang, L., Liu, S., Liu, G. E., Tenesa, A., Gao, Y., Mason, B., Chamberlain, A. J., Goddard, M. E., Liu, S., et al. (2025) · PNAS Nexus · doi:10.1093/pnasnexus/pgaf208 · Cited by 11

Personalized genome structure via single gamete sequencing

Lyu, R., Tsui, V., McCarthy, D. J., & Crismani, W. (2021) · Genome biology · doi:10.1186/s13059-021-02327-w · Cited by 12

Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins

Sohrabi-Jahromi, S., & Söding, J. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab300 · Cited by 10

Long-read sequencing-based in silico phage typing of vancomycin-resistant Enterococcus faecium

Lisotto, P., Raangs, E. C., Couto, N., Rosema, S., Lokate, M., Zhou, X. W., Friedrich, A. W., Rossen, J. W. A., Harmsen, H. J. M., Bathoorn, E., et al. (2021) · BMC Genomics · doi:10.1186/s12864-021-08080-5 · Cited by 10

Small investments with big returns: environmental genomic bioprospecting of microbial life

Vuong, P., Wise, M. J., Whiteley, A. S., & Kaur, P. (2022) · Critical Reviews in Microbiology · doi:10.1080/1040841x.2021.2011833 · Cited by 10

CeSpGRN: inferring cell-specific gene regulatory networks from single-cell multi-omics and spatial data

Zhang, Z., Han, J., Song, L., & Zhang, X. (2026) · Bioinformatics · doi:10.1093/bioinformatics/btag324 · Cited by 10

Bookend: precise transcript reconstruction with end-guided assembly

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Variant calling from scRNA-seq data allows the assessment of cellular identity in patient-derived cell lines

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Epigenetic variation in the Lombardy poplar along climatic gradients is independent of genetic structure and persists across clonal reproductionPreprint

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A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxiaPreprint

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SUsPECT: a pipeline for variant effect prediction based on custom long-read transcriptomes for improved clinical variant annotation

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A novel f-divergence based generative adversarial imputation method for scRNA-seq data analysis

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Phenotype versus genotype discordant rifampicin susceptibility testing in tuberculosis: implications for a diagnostic accuracy

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