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

DNA methylation calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluationPreprint

Liu, Y., Rosikiewicz, W., Pan, Z., Jillette, N., Wang, P., Taghbalout, A., Foox, J., Mason, C. E., Carroll, M. P., Cheng, A. W., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.05.442849 · Cited by 22

Gap-free genome assembly of anadromous Coilia nasus

Ma, F., Wang, Y., Su, B., Zhao, C., Yin, D., Chen, C., Yang, Y., Wang, C., Luo, B., Wang, H., et al. (2023) · Scientific Data · doi:10.1038/s41597-023-02278-w · Cited by 23

Large-scale imputation models for multi-ancestry proteome-wide association analysisPreprint

Wu, C., Zhang, Z., Yang, X., & Zhao, B. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.05.561120 · Cited by 21

Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long readsPreprint

Keşküş, A. G., Bryant, A., Ahmad, T., Yoo, B., Aganezov, S. S., Goretsky, A., Donmez, A., Lansdon, L. A., Rodriguez, I., Park, J., et al. (2024) · medRxiv · doi:10.1101/2024.03.22.24304756 · Cited by 22

Implementation of Exome Sequencing to Identify Rare Genetic Diseases

Udupa, P., & Ghosh, D. K. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-3461-5_5 · Cited by 21

SAILER: scalable and accurate invariant representation learning for single-cell ATAC-seq processing and integration

Cao, Y., Fu, L., Wu, J., Peng, Q., Nie, Q. H., Zhang, J., & Xie, X. S. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab303 · Cited by 18

Reconstructing viral haplotypes using long reads

Cai, D., & Sun, Y. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac089 · Cited by 23

Multi-Omics Strategies for Investigating the Microbiome in Toxicology Research

Morgan, E. W., Perdew, G. H., & Patterson, A. D. (2022) · Toxicological Sciences · doi:10.1093/toxsci/kfac029 · Cited by 23

CMash: fast, multi-resolution estimation of k-mer-based Jaccard and containment indices

Liu, S., & Koslicki, D. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac237 · Cited by 23

Enhanced transcriptional heterogeneity mediated by NF-κB super-enhancers

Wibisana, J. N., Inaba, T., Shinohara, H., Yumoto, N., Hayashi, T., Umeda, M., Ebisawa, M., Nikaido, I., Sako, Y., & Okada, M. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010235 · Cited by 21

Material Engineering in Gut Microbiome and Human Health

Yang, L., Hung, L. Y., Zhu, Y., Ding, S., Margolis, K. G., & Leong, K. W. (2022) · Research · doi:10.34133/2022/9804014 · Cited by 24

VeChat: correcting errors in long reads using variation graphs

Luo, X. L., Kang, X., & Schönhuth, A. (2022) · Nature Communications · doi:10.1038/s41467-022-34381-8 · Cited by 20

SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data

Kang, S., Borgsmüller, N., Valecha, M. V., Kuipers, J., Alves, J. M., Prado‐Lòpez, S., Chantada, D., Beerenwinkel, N., Posada, D., & Szczurek, E. (2022) · Genome biology · doi:10.1186/s13059-022-02813-9 · Cited by 19

Antioxidant prodigiosin-producing cold-adapted Janthinobacterium sp. ERMR3:09 from a glacier moraine: Genomic elucidation of cold adaptation and pigment biosynthesis

Mukhia, S., Kumar, A., V, & Kumar, R. (2023) · Gene · doi:10.1016/j.gene.2023.147178 · Cited by 21

Chimera: The spoiler in multiple displacement amplification

Lü, N., Qiao, Y., Lu, Z., & Tu, J. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.02.034 · Cited by 20

Recovery of 197 eukaryotic bins reveals major challenges for eukaryote genome reconstruction from terrestrial metagenomes

Saraiva, J., Bartholomäus, A., Toscan, R. B., Baldrián, P., & da Rocha, U. N. (2023) · Molecular Ecology Resources · doi:10.1111/1755-0998.13776 · Cited by 22

Sequence-Based Platforms for Discovering Biomarkers in Liquid Biopsy of Non-Small-Cell Lung Cancer

Brockley, L. J., Souza, V. G. P., Forder, A., Pewarchuk, M. E., Erkan, M., Telkar, N., Benard, K., Trejo, J., Stewart, M. D., Stewart, G. L., et al. (2023) · Cancers · doi:10.3390/cancers15082275 · Cited by 22

Genome-Resolved Metagenomics and Metatranscriptomics Reveal Insights into the Ecology and Metabolism of Anaerobic Microbial Communities in PCB-Contaminated Sediments

Dang, H., Ewald, J. M., & Mattes, T. E. (2023) · Environmental Science & Technology · doi:10.1021/acs.est.3c05439 · Cited by 23

Population-level transposable element expression dynamics influence trait evolution in a fungal crop pathogen

Abraham, L., Oggenfuss, U., & Croll, D. (2024) · mBio · doi:10.1128/mbio.02840-23 · Cited by 17

Cell-cycle dependence of bursty gene expression: insights from fitting mechanistic models to single-cell RNA-seq data

Sukys, A., & Grima, R. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf295 · Cited by 22

GraphProt2: A graph neural network-based method for predicting binding sites of RNA-binding proteinsPreprint

Uhl, M., Tran, V. D., Heyl, F., & Backofen, R. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/850024 · Cited by 21

Single-cell multiomics atlas of organoid development uncovers longitudinal molecular programs of cellular diversification of the human cerebral cortexPreprint

Uzquiano, A., Kedaigle, A. J., Pigoni, M., Paulsen, B. D. S., Adiconis, X., Kim, K., Faits, T., Nagaraja, S., Antón-Bolaños, N., Gerhardinger, C., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.17.484798 · Cited by 21

Identifying cell state–associated alternative splicing events and their coregulationPreprint

Najar, C. F. B. A., Burra, P., Yosef, N., & Lareau, L. F. (2022) · Genome Research · doi:10.1101/gr.276109.121 · Cited by 20

CRISPR-Hybrid: A CRISPR-Mediated Intracellular Directed Evolution Platform for RNA Aptamers

Su-Tobon, Q., Fan, J., Goldstein, M., Feeney, K. A., Ren, H., Autissier, P., Wang, P., Huang, Y., Mohanty, U., & Niu, J. (2025) · Nature Communications · doi:10.1038/s41467-025-55957-0 · Cited by 21

Statistical framework for calling allelic imbalance in high-throughput sequencing data

Buyan, A., Meshcheryakov, G., Safronov, V., Abramov, S., Boytsov, A., Nozdrin, V., Baulin, E. F., Kolmykov, S. K., Vierstra, J. D., Kolpakov, F., et al. (2025) · Nature Communications · doi:10.1038/s41467-024-55513-2 · Cited by 23

The RMaP challenge of predicting RNA modifications by nanopore sequencing

Spangenberg, J., Mündnich, S., Busch, A., Pastore, S., Wierczeiko, A., Göettsch, W., Dietrich, V., Pryszcz, L. P., Cruciani, S., Novoa, E. M., et al. (2025) · Communications Chemistry · doi:10.1038/s42004-025-01507-0 · Cited by 20

Advance in the assembly of the plant mitochondrial genomes using high‐throughput DNA sequencing data of total cellular DNAs

Ni, Y., Li, J., Tan, Y. Y., Shen, G., & Liu, C. (2025) · Plant Biotechnology Journal · doi:10.1111/pbi.70249 · Cited by 20

Chromosome‐scale inference of hybrid speciation and admixture with convolutional neural networks

Blischak, P. D., Barker, M. S., & Gutenkunst, R. N. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13355 · Cited by 24

A Chromosome-Scale Assembly of the Wheat Leaf Rust Pathogen Puccinia triticina Provides Insights Into Structural Variations and Genetic Relationships With Haplotype Resolution

Wu, J. Q., Song, L., Ding, Y., Dong, C., Hasan, M. T., & Park, R. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.704253 · Cited by 20

NanoHIV: A Bioinformatics Pipeline for Producing Accurate, Near Full-Length HIV Proviral Genomes Sequenced Using the Oxford Nanopore Technology

Wright, I. A., Delaney, K. E., Katusiime, M. G., Botha, J. C., Engelbrecht, S., Kearney, M. F., & van Zyl, G. U. (2021) · Cells · doi:10.3390/cells10102577 · Cited by 20

CIDER: an interpretable meta-clustering framework for single-cell RNA-seq data integration and evaluation

Hu, Z., Ahmed, A. A., & Yau, C. (2021) · Genome biology · doi:10.1186/s13059-021-02561-2 · Cited by 17

Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets

Mu, W.-C., Sarkar, H., Srivastava, A., Choi, K., Patro, R., & Love, M. (2021) · bioRxiv · doi:10.1093/bioinformatics/btac212 · Cited by 19

Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels

Plaza, J. J. G., Furlan, C., Rijavec, T., Lapanje, A., Barros, R., Tamayo‐Ramos, J. A., & Diez, M. S. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.1006946 · Cited by 20

Genomic characterization of animal genetic resources

Boitard, S., Chikhi, L., da Fonseca, R. R., Ginja, C., Kantanen, J., Lenstra, J. A., Orozco‐terWengel, P., & Pausch, H. (2023) · FAO eBooks · doi:10.4060/cc3079en · Cited by 29

CosTaL: an accurate and scalable graph-based clustering algorithm for high-dimensional single-cell data analysis

Li, Y., Nguyen, J., Anastasiu, D. C., & Arriaga, E. A. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad157 · Cited by 22

Combined genome-wide association studies and expression quantitative trait locus analysis uncovers a genetic regulatory network of floral organ number in a tree peony (Paeonia suffruticosa Andrews) breeding population

Peng, L., Li, Y., Tan, W., Wu, S., Hao, Q., Tong, N., Wang, Z., Liu, Z., & Shu, Q. (2023) · Horticulture Research · doi:10.1093/hr/uhad110 · Cited by 20

Structural variants and short tandem repeats impact gene expression and splicing in bovine testis tissue

Bhati, M., Mapel, X. M., Lloret‐Villas, A., & Pausch, H. (2023) · Genetics · doi:10.1093/genetics/iyad161 · Cited by 21

Merging short and stranded long reads improves transcript assembly

Kainth, A. S., Haddad, G. A., Hall, J. M., & Ruthenburg, A. J. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011576 · Cited by 21

Analytical challenges in omics research on asthma and allergy: A National Institute of Allergy and Infectious Diseases workshop

Bunyavanich, S., Becker, P. M., Altman, M. C., Lasky-Su, J. A., Ober, C., Zengler, K., Berdyshev, E. V., Bonneau, R., Chatila, T. A., Chatterjee, N., et al. (2024) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2024.01.014 · Cited by 19

Predicting A/B compartments from histone modifications using deep learning

Zheng, S., Thakkar, N., Harris, H. L., Liu, S. X., Zhang, M., Gerstein, M., Aiden, E. L., Rowley, M. J., Noble, W. S., Gürsoy, G., et al. (2024) · iScience · doi:10.1016/j.isci.2024.109570 · Cited by 20

TALC: Transcript-level Aware Long-read Correction

Broséus, L., Thomas, A., Oldfield, A., Séverac, D., Dubois, E., & Ritchie, W. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa634 · Cited by 20

GenePert: Leveraging GenePT Embeddings for Gene Perturbation PredictionPreprint

Chen, Y. T., & Zou, J. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.27.620513 · Cited by 24

PmVAE: learning interpretable single-cell representations with pathway modules

Gut, G., Stark, S. G., Rätsch, G., & Davidson, N. R. (2021) · doi:10.1101/2021.01.28.428664 · Cited by 24

Profiling immune cell tissue niches in the spatial -omics era

Lee, C. Y. C., McCaffrey, J., McGovern, D., & Clatworthy, M. R. (2024) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2024.11.001 · Cited by 21

Harnessing the Power of Next-Generation Sequencing in Wastewater-Based Epidemiology and Global Disease Surveillance

Farkas, K., Williams, R. C., Hillary, L. S., Garcia-Delgado, A., Jameson, E., Kevill, J. L., Wade, M. J., Grimsley, J. M. S., & Jones, D. L. (2024) · Food and Environmental Virology · doi:10.1007/s12560-024-09616-0 · Cited by 19

Long-Read Sequencing for the Rapid Response to Infectious Diseases Outbreaks

Oehler, J. B., Burns, K., Warner, J. M., & Schmitz, U. (2025) · Current Clinical Microbiology Reports · doi:10.1007/s40588-025-00247-y · Cited by 19

From DNA Methylation and Histone Modifications to Non-Coding RNAs: Evaluating Tools for Epigenetic Research

Benčik, I., Martinović, L. S., Mladenić, T., Ostojić, S., & Pavlić, S. D. (2025) · Applied Sciences · doi:10.3390/app15189940 · Cited by 19

Next-generation sequencing for the diagnosis of hepatitis B: current status and future prospects

García-García, S., Cortese, M. F., Rodríguez-Algarra, F., Tabernero, D., Rando‐Segura, A., Quer, J., Buti, M., & Rodríguez‐Frias, F. (2021) · Expert Review of Molecular Diagnostics · doi:10.1080/14737159.2021.1913055 · Cited by 19

Immunity and lifespan: answering long-standing questions with comparative genomics

O’Connor, E., & Cornwallis, C. K. (2022) · Trends in Genetics · doi:10.1016/j.tig.2022.02.014 · Cited by 19

TT-Mars: structural variants assessment based on haplotype-resolved assemblies

Yang, J., & Chaisson, M. (2022) · Genome biology · doi:10.1186/s13059-022-02666-2 · Cited by 16

Exploring differential exon usage via short- and long-read RNA sequencing strategies

Leshkowitz, D., Kedmi, M., Fried, Y., Pilzer, D., Keren‐Shaul, H., Ainbinder, E., & Dassa, B. (2022) · Open Biology · doi:10.1098/rsob.220206 · Cited by 19

Meta‐analysis of major histocompatibility complex (MHC) class IIA reveals polymorphism and positive selection in many vertebrate species

Dearborn, D. C., Warren, S., & Hailer, F. (2022) · Molecular Ecology · doi:10.1111/mec.16726 · Cited by 19

Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing

Orabi, B., Xie, N., McConeghy, B. J., Dong, X., Chauve, C., & Hach, F. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1112 · Cited by 19

HLA / MHC and KIR characterization in humans and non‐human primates using Oxford Nanopore Technologies and Pacific Biosciences sequencing platforms

Bruijnesteijn, J. (2022) · HLA · doi:10.1111/tan.14957 · Cited by 20

Benchmark study for evaluating the quality of reference genomes and gene annotations in 114 species

Park, S., Lee, J., Kim, J., Kim, D., Lee, J. H., Pack, S. P., & Seo, M. (2023) · Frontiers in Veterinary Science · doi:10.3389/fvets.2023.1128570 · Cited by 20

Trackplot: A flexible toolkit for combinatorial analysis of genomic data

Zhang, Y., Zhou, R., Liu, L., Chen, L., & Wang, Y. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011477 · Cited by 19

SpecHLA enables full-resolution HLA typing from sequencing data

Wang, S., Wang, M., Chen, L., Pan, G., Wang, Y., & Li, S. C. (2023) · Cell Reports Methods · doi:10.1016/j.crmeth.2023.100589 · Cited by 19

Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors

Weber, L. L., Zhang, C., Ochoa, I., & El-Kebir, M. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011544 · Cited by 19

Persistent effects of intramammary ceftiofur treatment on the gut microbiome and antibiotic resistance in dairy cattle

Vasco, K. A., Carbonell, S. L., Sloup, R. E., Bowcutt, B., Colwell, R. R., Graubics, K., Erskine, R. J., Norby, B., Ruegg, P. L., Zhang, L., et al. (2023) · Animal Microbiome · doi:10.1186/s42523-023-00274-4 · Cited by 24

Identification of region-specific gene isoforms in the human brain using long-read transcriptome sequencing

Shimada, M., Omae, Y., Kakita, A., Gabdulkhaev, R., Hitomi, Y., Miyagawa, T., Honda, M., Fujimoto, A., & Tokunaga, K. (2024) · Science Advances · doi:10.1126/sciadv.adj5279 · Cited by 22

Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3′ UTR of FAIM2

Littleton, S. H., Trang, B. K., Volpe, C. M., Cook, K., DeBruyne, N., Maguire, J. A., Weidekamp, M. A., Hodge, K. M., Boehm, K. D., Lu, S., et al. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100556 · Cited by 20

Omics approaches to unravel insecticide resistance mechanism in Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae)

Rosli, M. A. F., Jaafar, S. N. S., Azizan, K. A., Yaakop, S., & Aizat, W. M. (2024) · PeerJ · doi:10.7717/peerj.17843 · Cited by 19

Biophysically interpretable inference of cell types from multimodal sequencing data

Chari, T., Gorin, G., & Pachter, L. S. (2024) · Nature Computational Science · doi:10.1038/s43588-024-00689-2 · Cited by 20

MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication

Cahn, J., Regulski, M., Lynn, J. S., Ernst, E., Alves, C. D. S., Ramakrishnan, S., Chougule, K. M., Wei, S., Lu, Z., Xu, X., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-55195-w · Cited by 21

PacBio Single-Molecule Long-Read Sequencing Provides New Light on the Complexity of Full-Length Transcripts in Cattle

Chang, T., An, B., Liang, M., Duan, X., Du, L., Cai, W., Zhu, B., Gao, X., Chen, Y., Xu, L., et al. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.664974 · Cited by 18

HIT-scISOseq: High-throughput and High-accuracy Single-cell Full-length Isoform Sequencing for Corneal EpitheliumPreprint

Zheng, Y., Chen, Z.-C., Shi, Z., Hu, K.-H., Zhong, J., Wang, C., Shi, W., Chen, Y., Xie, S., Luo, F., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.27.222349 · Cited by 18

Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cellsPreprint

Karousis, E. D., Gypas, F., Zavolan, M., & Mühlemann, O. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.30.442116 · Cited by 18

Absolute copy number fitting from shallow whole genome sequencing dataPreprint

Sauer, C. M., Eldridge, M., Vias, M., Hall, J. A. M., Boyle, S. E., Macintyre, G., Bradley, T. P., Markowetz, F. M., & Brenton, J. D. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.19.452658 · Cited by 17

Challenges and considerations for reproducibility of STARR-seq assaysPreprint

Das, M., Hossain, A., Banerjee, D., Praul, C. A., & Girirajan, S. (2023) · Genome Research · doi:10.1101/gr.277204.122 · Cited by 18

ADTnorm: Robust Integration of Single-cell Protein Measurement across CITE-seq Datasets

Zheng, Y., Caron, D. P., Kim, J. Y., Jun, S.-H., Tian, Y., Florian, M., Stuart, K. D., Sims, P. A., & Gottardo, R. (2022) · doi:10.1101/2022.04.29.489989 · Cited by 18

tascCODA: Bayesian Tree-Aggregated Analysis of Compositional Amplicon and Single-Cell Data

Ostner, J., Carcy, S., & Müller, C. L. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.766405 · Cited by 19

Applications of CRISPR Technologies in Forestry and Molecular Wood Biotechnology

Cao, H. X., Michels, D., Vu, G. T. H., & Gailing, O. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms252111792 · Cited by 20

Dissecting tumor transcriptional heterogeneity from single-cell RNA-seq data by generalized binary covariance decomposition

Liu, Y., Carbonetto, P. S., Willwerscheid, J., Oakes, S. A., Macleod, K. F., & Stephens, M. (2025) · Nature Genetics · doi:10.1038/s41588-024-01997-z · Cited by 21

Ephedra as a gymnosperm evo‐devo model lineage

Stilio, V. S. D., & Ickert‐Bond, S. M. (2021) · Evolution & Development · doi:10.1111/ede.12370 · Cited by 18

Applications of Deep Mutational Scanning in Virology

Burton, T. D., & Eyre, N. S. (2021) · Viruses · doi:10.3390/v13061020 · Cited by 19

Advancing Genetic Methods in the Study of Parrot Biology and Conservation

Olah, G., Smith, B. T., Joseph, L., Banks, S. C., & Heinsohn, R. (2021) · Diversity · doi:10.3390/d13110521 · Cited by 21

Genion, an accurate tool to detect gene fusion from long transcriptomics reads

Karaoğlanoğlu, F., Chauve, C., & Hach, F. (2022) · BMC Genomics · doi:10.1186/s12864-022-08339-5 · Cited by 18

Quantifying shifts in natural selection on codon usage between protein regions: a population genetics approach

Cope, A. L., & Gilchrist, M. A. (2022) · BMC Genomics · doi:10.1186/s12864-022-08635-0 · Cited by 17

The role of single-cell genomics in human genetics

Sreenivasan, V. K. A., Balachandran, S., & Spielmann, M. (2022) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2022-108588 · Cited by 19

Drosophila insulator proteins exhibit in vivo liquid–liquid phase separation properties

Amankwaa, B., Schoborg, T. A., & Labrador, M. (2022) · Life Science Alliance · doi:10.26508/lsa.202201536 · Cited by 19

Beyond Basic Diversity Estimates—Analytical Tools for Mechanistic Interpretations of Amplicon Sequencing Data

Trego, A. C., Keating, C., Nzeteu, C., Graham, A., O’Flaherty, V., & Ijaz, U. Z. (2022) · Microorganisms · doi:10.3390/microorganisms10101961 · Cited by 17

From the reference human genome to human pangenome: Premise, promise and challenge

Singh, V. K., Pandey, S., & Bhardwaj, A. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.1042550 · Cited by 21

Incorporating cell hierarchy to decipher the functional diversity of single cells

Chen, L., & Li, S. C. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1044 · Cited by 18

DeepPHiC: predicting promoter-centered chromatin interactions using a novel deep learning approach

Agarwal, A., & Chen, L. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac801 · Cited by 18

Single-Cell DNA Methylation Analysis in Cancer

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