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OpenAlex Citation Counts

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OpenAlex is a bibliographic catalogue of scientific papers, authors and institutions accessible in open access mode, named after the Library of Alexandria. It's citation coverage is excellent and I hope you will find utility in this listing of citing articles!

If you click the article title, you'll navigate to the article, as listed in CrossRef. If you click the Open Access links, you'll navigate to the "best Open Access location". Clicking the citation count will open this listing for that article. Lastly at the bottom of the page, you'll find basic pagination options.

Requested Article:

IDP-denovo: de novo transcriptome assembly and isoform annotation by hybrid sequencing
Shuhua Fu, Yingke Ma, Hui Yao, et al.
Bioinformatics (2018) Vol. 34, Iss. 13, pp. 2168-2176
Open Access | Times Cited: 46

Showing 1-25 of 46 citing articles:

Nanopore sequencing technology, bioinformatics and applications
Yunhao Wang, Yue Zhao, Audrey Bollas, et al.
Nature Biotechnology (2021) Vol. 39, Iss. 11, pp. 1348-1365
Open Access | Times Cited: 1103
Improved transcriptome assembly using a hybrid of long and short reads with StringTie
Alaina Shumate, Brandon Wong, Geo Pertea, et al.
PLoS Computational Biology (2022) Vol. 18, Iss. 6, pp. e1009730-e1009730
Open Access | Times Cited: 222
Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis
Kristoffer Sahlin, Paul Medvedev
Nature Communications (2021) Vol. 12, Iss. 1
Open Access | Times Cited: 137
Methodologies for Transcript Profiling Using Long-Read Technologies
Spyros Oikonomopoulos, Anthony Bayega, Somayyeh Fahiminiya, et al.
Frontiers in Genetics (2020) Vol. 11
Open Access | Times Cited: 95
RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing
Ivan de la Rubia, Akanksha Srivastava, Wenjing Xue, et al.
Genome biology (2022) Vol. 23, Iss. 1
Open Access | Times Cited: 35
Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data
Leandro Lima, Camille Marchet, Ségolène Caboche, et al.
Briefings in Bioinformatics (2019) Vol. 21, Iss. 4, pp. 1164-1181
Open Access | Times Cited: 39
Multi-Omics Approaches to Study Long Non-coding RNA Function in Atherosclerosis
Adam W. Turner, Doris Wong, Mohammad Daud Khan, et al.
Frontiers in Cardiovascular Medicine (2019) Vol. 6
Open Access | Times Cited: 35
Comparative Transcriptome Analysis of B. oleracea L. var. italica and B. macrocarpa Guss. Genotypes Under Drought Stress: De Novo vs Reference Genome Assembly
Grete Francesca Privitera, Simone Treccarichi, Roberta Nicotra, et al.
Plant Stress (2024), pp. 100657-100657
Open Access | Times Cited: 4
Bioinformatics perspectives on transcriptomics: A comprehensive review of bulk and single‐cell RNA sequencing analyses
Jorge A. Tzec‐Interián, Daianna González‐Padilla, Elsa Góngora‐Castillo
Quantitative Biology (2025) Vol. 13, Iss. 2
Open Access
Extending rnaSPAdes functionality for hybrid transcriptome assembly
Andrey D. Prjibelski, Giuseppe Diego Puglia, Dmitry Antipov, et al.
BMC Bioinformatics (2020) Vol. 21, Iss. S12
Open Access | Times Cited: 31
Hybrid de novo transcriptome assembly of poinsettia (Euphorbia pulcherrima Willd. Ex Klotsch) bracts
Vinicius Vilperte, Calin Lucaciu, Heidi Halbwirth, et al.
BMC Genomics (2019) Vol. 20, Iss. 1
Open Access | Times Cited: 27
Hybrid transcriptome sequencing approach improved assembly and gene annotation in Cynara cardunculus (L.)
Giuseppe Diego Puglia, Andrey D. Prjibelski, Domenico Vitale, et al.
BMC Genomics (2020) Vol. 21, Iss. 1
Open Access | Times Cited: 23
Trans2express – de novo transcriptome assembly pipeline optimized for gene expression analysis
Aleksandra M. Kasianova, Aleksey A. Penin, Mikhail I. Schelkunov, et al.
Plant Methods (2024) Vol. 20, Iss. 1
Open Access | Times Cited: 2
Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis
Kristoffer Sahlin, Botond Sipos, Phillip James, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2020)
Open Access | Times Cited: 19
Utilization of Tissue Ploidy Level Variation in de Novo Transcriptome Assembly of Pinus sylvestris
Darío I. Ojeda, Tiina M. Mattila, Tom Ruttink, et al.
G3 Genes Genomes Genetics (2019) Vol. 9, Iss. 10, pp. 3409-3421
Open Access | Times Cited: 19
TALC: Transcript-level Aware Long-read Correction
Lucile Broseus, Aubin Thomas, Andrew J. Oldfield, et al.
Bioinformatics (2020) Vol. 36, Iss. 20, pp. 5000-5006
Open Access | Times Cited: 16
A Review of Cross-Disciplinary Approaches for the Identification of Novel Industrially Relevant Plastic-Degrading Enzymes
Josephine Herbert, Angela H. Beckett, Samuel C. Robson
Sustainability (2022) Vol. 14, Iss. 23, pp. 15898-15898
Open Access | Times Cited: 10
Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads
Laura H. Tung, Mingfu Shao, Carl Kingsford
Genome biology (2019) Vol. 20, Iss. 1
Open Access | Times Cited: 16
Prospects for the use of third generation sequencers for quantitative profiling of transcriptome
Sergey P. Radko, Leonid K. Kurbatov, K. G. Ptitsyn, et al.
Biomedical Chemistry Research and Methods (2018) Vol. 1, Iss. 4, pp. e00086-e00086
Open Access | Times Cited: 16
Identification of alternatively spliced gene isoforms and novel noncoding RNAs by single-molecule long-read sequencing in Camellia
Zhikang Hu, Tao Lyu, Chao Yan, et al.
RNA Biology (2020) Vol. 17, Iss. 7, pp. 966-976
Open Access | Times Cited: 14
Evolution of gene regulatory network of C4 photosynthesis in the genus Flaveria reveals the evolutionary status of C3-C4 intermediate species
Ming-Ju Amy Lyu, Qiming Tang, Yanjie Wang, et al.
Plant Communications (2022) Vol. 4, Iss. 1, pp. 100426-100426
Open Access | Times Cited: 8
ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning
Angel Ruiz-Reche, Akanksha Srivastava, Joel A. Indi, et al.
Genome biology (2019) Vol. 20, Iss. 1
Open Access | Times Cited: 13
Accurate isoform quantification by joint short- and long-read RNA-sequencing
Michael Apostolides, Man Hung Choi, Albertas Navickas, et al.
(2024)
Open Access | Times Cited: 1
Computational Approaches for Transcriptome Assembly Based on Sequencing Technologies
Yuwen Luo, Xingyu Liao, Fang‐Xiang Wu, et al.
Current Bioinformatics (2019) Vol. 15, Iss. 1, pp. 2-16
Closed Access | Times Cited: 11
AIDE: annotation-assisted isoform discovery with high precision
Wei Vivian Li, Shan Li, Xin Tong, et al.
Genome Research (2019) Vol. 29, Iss. 12, pp. 2056-2072
Open Access | Times Cited: 11
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