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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:

CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts
Alison C. Testa, James K. Hane, Simon R. Ellwood, et al.
BMC Genomics (2015) Vol. 16, Iss. 1
Open Access | Times Cited: 177

Showing 1-25 of 177 citing articles:

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS
Katharina J. Hoff, Simone Lange, Alexandre Lomsadze, et al.
Bioinformatics (2015) Vol. 32, Iss. 5, pp. 767-769
Open Access | Times Cited: 1092
GeMoMa: Homology-Based Gene Prediction Utilizing Intron Position Conservation and RNA-seq Data
Jens Keilwagen, Frank Hartung, Jan Grau
Methods in molecular biology (2019), pp. 161-177
Closed Access | Times Cited: 320
Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi
Jens Keilwagen, Frank Hartung, Michael Paulini, et al.
BMC Bioinformatics (2018) Vol. 19, Iss. 1
Open Access | Times Cited: 265
The Complete Genome Sequence of the Phytopathogenic Fungus Sclerotinia sclerotiorum Reveals Insights into the Genome Architecture of Broad Host Range Pathogens
Mark C. Derbyshire, Matthew Denton‐Giles, Dwayne D. Hegedus, et al.
Genome Biology and Evolution (2017) Vol. 9, Iss. 3, pp. 593-618
Open Access | Times Cited: 189
Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation
Feng Li, Narayana M. Upadhyaya, Jana Sperschneider, et al.
Nature Communications (2019) Vol. 10, Iss. 1
Open Access | Times Cited: 151
Environmental gradients reveal stress hubs pre-dating plant terrestrialization
Armin Dadras, Janine M. R. Fürst‐Jansen, Tatyana Darienko, et al.
Nature Plants (2023) Vol. 9, Iss. 9, pp. 1419-1438
Open Access | Times Cited: 48
OcculterCut: A Comprehensive Survey of AT-Rich Regions in Fungal Genomes
Alison C. Testa, Richard P. Oliver, James K. Hane
Genome Biology and Evolution (2016) Vol. 8, Iss. 6, pp. 2044-2064
Open Access | Times Cited: 128
Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing
Bo Wang, Vivek Kumar, Andrew Olson, et al.
Frontiers in Genetics (2019) Vol. 10
Open Access | Times Cited: 125
A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust FungusPuccinia striiformisf. sp.triticiReveals High Interhaplotype Diversity
Benjamin Schwessinger, Jana Sperschneider, William S. Cuddy, et al.
mBio (2018) Vol. 9, Iss. 1
Open Access | Times Cited: 124
Transposon-Mediated Horizontal Transfer of the Host-Specific Virulence Protein ToxA between Three Fungal Wheat Pathogens
Megan C. McDonald, Adam Taranto, Erin Hill, et al.
mBio (2019) Vol. 10, Iss. 5
Open Access | Times Cited: 105
Chromosome-scale genome assembly of sweet cherry (Prunus avium L.) cv. Tieton obtained using long-read and Hi-C sequencing
Jiawei Wang, Weizhen Liu, Dongzi Zhu, et al.
Horticulture Research (2020) Vol. 7, Iss. 1
Open Access | Times Cited: 88
A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms
Nicolas Scalzitti, Anne Jeannin‐Girardon, Pierre Collet, et al.
BMC Genomics (2020) Vol. 21, Iss. 1
Open Access | Times Cited: 79
The pan-genome of Aspergillus fumigatus provides a high-resolution view of its population structure revealing high levels of lineage-specific diversity driven by recombination
Lotus A. Lofgren, Brandon S. Ross, Robert A. Cramer, et al.
PLoS Biology (2022) Vol. 20, Iss. 11, pp. e3001890-e3001890
Open Access | Times Cited: 46
Complexity of the lichen symbiosis revealed by metagenome and transcriptome analysis of Xanthoria parietina
Gulnara Tagirdzhanova, Klara Scharnagl, Neha Sahu, et al.
Current Biology (2025)
Open Access | Times Cited: 1
Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae
Andrew D. Armitage, Andrew Taylor, Maria K. Sobczyk, et al.
Scientific Reports (2018) Vol. 8, Iss. 1
Open Access | Times Cited: 80
Bioinformatic prediction of plant–pathogenicity effector proteins of fungi
Darcy Jones, Stefania Bertazzoni, Chala Turo, et al.
Current Opinion in Microbiology (2018) Vol. 46, pp. 43-49
Closed Access | Times Cited: 76
Evaluation of Secretion Prediction Highlights Differing Approaches Needed for Oomycete and Fungal Effectors
Jana Sperschneider, Angela Williams, James K. Hane, et al.
Frontiers in Plant Science (2015) Vol. 6
Open Access | Times Cited: 73
Curation of the genome annotation ofPichia pastoris(Komagataella phaffii) CBS7435 from gene level to protein function
Minoska Valli, Nadine E. Tatto, Armin Peymann, et al.
FEMS Yeast Research (2016) Vol. 16, Iss. 6, pp. fow051-fow051
Open Access | Times Cited: 68
Seqping: gene prediction pipeline for plant genomes using self-training gene models and transcriptomic data
Kuang‐Lim Chan, Rozana Rosli, Tatiana V. Tatarinova, et al.
BMC Bioinformatics (2017) Vol. 18, Iss. S1, pp. 1-7
Open Access | Times Cited: 66
Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity
Paula Moolhuijzen, Pao Theen See, James K. Hane, et al.
BMC Genomics (2018) Vol. 19, Iss. 1
Open Access | Times Cited: 63
Genomics Evolutionary History and Diagnostics of the Alternaria alternata Species Group Including Apple and Asian Pear Pathotypes
Andrew D. Armitage, Helen M. Cockerton, S. Sreenivasaprasad, et al.
Frontiers in Microbiology (2020) Vol. 10
Open Access | Times Cited: 58
The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome
Michael W. Gray, Gertraud Burger, Romain Derelle, et al.
BMC Biology (2020) Vol. 18, Iss. 1
Open Access | Times Cited: 55
The reuse of public datasets in the life sciences: potential risks and rewards
Katharina Sielemann, Alenka Hafner, Boas Pucker
PeerJ (2020) Vol. 8, pp. e9954-e9954
Open Access | Times Cited: 54
Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection–related chromatin reorganization
Cyril Matthey-Doret, Morgan Colp, Pedro Escoll, et al.
Genome Research (2022) Vol. 32, Iss. 9, pp. 1698-1710
Open Access | Times Cited: 31
TransPi—a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly
Ramón E. Rivera‐Vicéns, Catalina A. García‐Escudero, Nicola Conci, et al.
Molecular Ecology Resources (2022) Vol. 22, Iss. 5, pp. 2070-2086
Open Access | Times Cited: 29
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