Davis J. McCarthy

64.5k citations

40 papers · 35.2k indexed · 5 hit papers · h-index 20

Impact in

Cancer Research top 0.05%
- Cancer-related molecular mechanisms research
- MicroRNA in disease regulation
Molecular Biology top 0.05%
- RNA modifications and cancer
- RNA Research and Splicing
- Single-cell and spatial transcriptomics
- Epigenetics and DNA Methylation
- Gene expression and cancer classification

Papers in

Health Informatics 1
Cancer Research 8
- Cancer Genomics and Diagnostics 6

Co-authors: Gordon K. Smyth Mark D. Robinson Yunshun Chen Aaron T. L. Lun Kieran R. Campbell Quin F. Wills Michał Okoniewski Wolfgang Huber
Journals: Genome biology (10 papers)Bioinformatics (3 papers)Nature Communications (2 papers)Nucleic Acids Research (2 papers)Nature Protocols (2 papers)
Partner nations: Australia United Kingdom United States

In The Last Decade

Davis J. McCarthy

37 papers receiving 35.0k citations

Hit Papers

5 papers align trajectories log scale

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R 2016 · 951 citations

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if any of the following hold:

it has ≥500 total citations;
it reaches ≥1.5× the top-1% citation threshold for papers in the same subfield and year (the threshold is the minimum needed to enter the top 1%, not the average within it);
it reaches the top citation threshold in at least one of its specific research topics.

2016 Bioinformatics
2016 Genome biology
2013 Nature Protocols
2012 Nucleic Acids Research
2009 Bioinformatics

Peers

Countries citing papers authored by Davis J. McCarthy

Since Specialization

Citations

This map shows the geographic impact of Davis J. McCarthy's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Davis J. McCarthy with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Davis J. McCarthy more than expected).

Fields of papers citing papers by Davis J. McCarthy

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Davis J. McCarthy. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Davis J. McCarthy. The network helps show where Davis J. McCarthy may publish in the future.

Co-authors

The 25 scholars most cited alongside Davis J. McCarthy, linked wherever they have co-authored with each other. Click a name or a connecting line to browse the papers they share.

Border = papers with Davis J. McCarthy Line = papers co-authored together Davis J. McCarthy links everyone, so they are left out of the graph.

All Works

Sort: Min cites: Since: Top N: Style:

20 of 20 papers shown

#	Work
1	Artificial Intelligence-Enabled Devices in Neurology: Mapping the Present and Future Seminars in Neurology ·Елена Васильевна Давыденко, Davis J. McCarthy, Lee H. Schwamm, James Hillis	2025	0
2	A hierarchical, count-based model highlights challenges in scATAC-seq data analysis and points to opportunities to extract finer-resolution information Genome biology ·Eduardo Reyes, Heejung Shim, Davis J. McCarthy	2025	0
3	Profiling genetically driven alternative splicing across the Indonesian archipelago The American Journal of Human Genetics ·Tzung-Shiahn Sheen, Pradiptajati Kusuma, Chelzie Crenna Darusallam, Safarina G. Malik, Herawati Sudoyo, Davis J. McCarthy, Irene Gallego Romero	2024	0
4	Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods Genome biology ·Drew Neavin, Anne Senabouth, JIAN-HUA WANG, Jimmy Tsz Hang Lee, Berta Torruella Trias, Lude Franke, Shyam Prabhakar, Chun Ye, Davis J. McCarthy, Marta Melé, Martin Hemberg, Joseph E. Powell	2024	14
5	Cell-type-specific and disease-associated expression quantitative trait loci in the human lung Nature Genetics ·Heini M. Natri, Christina B. Azodi, Lance Peter, Chase J. Taylor, Gaspare Novara, 由寛内田, Mei-I Chung, David K. Flaherty, Brittany K. Matlock, Carla L. Calvi, Timothy S. Blackwell, Lorraine B. Ware, Matthew Bacchetta, Rajat Walia, Ciara M. Shaver, Jonathan A. Kropski, Davis J. McCarthy, Nicholas E. Banovich	2024	16
6	De novo transcriptome assembly and genome annotation of the fat-tailed dunnart (Sminthopsis crassicaudata) SHILAP Revista de lepidopterología ·Tzung-Shiahn Sheen, Alma Amalia, Stephen Frankenberg, Davis J. McCarthy, Andrew J. Pask, Irene Gallego Romero	2024	2
7	Fancm has dual roles in the limiting of meiotic crossovers and germ cell maintenance in mammals Cell Genomics ·Georgia Farrah, Ruqian Lyu, Paula R. Myslivecek, Jessica M. Stringer, Jessica E. M. Dunleavy, Korotaeva Gn, N.K. Evseeva, Anna L. Leichter, Luciano G. Martelotto, D. Jo Merriner, Ruijie Liu, 森上佳代, Nadeen Zerafa, Eva R. Hoffmann, Moira K. O’Bryan, Karla J. Hutt, Andrew J. Deans, Jörg Heierhorst, Davis J. McCarthy, Wayne Crismani	2023	7
8	sgcocaller and comapr: personalised haplotype assembly and comparative crossover map analysis using single-gamete sequencing data Nucleic Acids Research ·Ruqian Lyu, Georgia Farrah, Wayne Crismani, Ruijie Liu, Heejung Shim, Davis J. McCarthy	2022	5
9	Trade-off between conservation of biological variation and batch effect removal in deep generative modeling for single-cell transcriptomics BMC Bioinformatics ·Hui Li, Davis J. McCarthy, Heejung Shim, Susan Wei	2022	7
10	splatPop: simulating population scale single-cell RNA sequencing data Genome biology ·Christina B. Azodi, Luke Zappia, Alicia Oshlack, Davis J. McCarthy	2021	13
11	Personalized genome structure via single gamete sequencing Genome biology ·Ruqian Lyu, Georgia Farrah, Davis J. McCarthy, Wayne Crismani	2021	9
12	Key signaling networks are dysregulated in patients with the adipose tissue disorder, lipedema International Journal of Obesity ·Bingyu Huo, A Dolle, Camila de Lima Barizão, Cameron J. Nowell, Vainyā Suvannachak, Ruqian Lyu, Davis J. McCarthy, Dovile Anderson, Darren J. Creek, Marc G. Achen, Ramin Shayan, Tara Karnezis	2021	25
13	Optimizing expression quantitative trait locus mapping workflows for single-cell studies Genome biology ·Anna Cuomo, Sophia Beng Hui Lim, Christina B. Azodi, Davis J. McCarthy, Marc Jan Bonder	2021	31
14	Properties of structural variants and short tandem repeats associated with gene expression and complex traits Nature Communications ·David Jakubosky, Matteo D’Antonio, Marc Jan Bonder, Craig Smail, Margaret K. R. Donovan, William W. Greenwald, Hiroko Matsui, Na Cai, Ivan Carcamo‐Orive, Kelly A. Frazer, Joshua W. Knowles, Davis J. McCarthy, Bogdan Mirăuță, Stephen B. Montgomery, Thomas Quertermous, Daniel D. Seaton, Erin N. Smith, Oliver Stegle, Agnieszka D’Antonio‐Chronowska, Christopher DeBoever	2020	57
15	Method to Synchronize Cell Cycle of Human Pluripotent Stem Cells without Affecting Their Fundamental Characteristics Stem Cell Reports ·Loukia Yiangou, Rodrigo A. Grandy, Carola Maria Morell, Rute A. Tomaz, Anna Osnato, Juned Kadiwala, Daniele Muraro, José Garcia‐Bernardo, Shota Nakanoh, William G. Bernard, Daniel Ortmann, Davis J. McCarthy, Ingrid Simonic, Sanjay Sinha, Ludovic Vallier	2018	35
16	Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R Bioinformatics ·Davis J. McCarthy, Kieran R. Campbell, Aaron T. L. Lun, Quin F. Wills Hit paper breakdown →	2016	951
17	Classification of low quality cells from single-cell RNA-seq data Genome biology ·Tomislav Ilicic, Jong Kim, Aleksandra A. Kolodziejczyk, Frederik Otzen Bagger, Davis J. McCarthy, John C. Marioni, Sarah A. Teichmann Hit paper breakdown →	2016	421
18	Choice of transcripts and software has a large effect on variant annotation Genome Medicine ·Davis J. McCarthy, Peter Humburg, Alexander Kanapin, Manuel A. Rivas, Kyle J. Gaulton, Jean‐Baptiste Cazier, Peter Donnelly	2014	128
19	Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates Statistical Applications in Genetics and Molecular Biology ·Steven P. Lund, Dan Nettleton, Davis J. McCarthy, Gordon K. Smyth	2012	212
20	Aliskiren increases bradykinin and tissue kallikrein mRNA levels in the heart Clinical and Experimental Pharmacology and Physiology ·Duncan J. Campbell, Yuan Zhang, Darren J. Kelly, Richard E. Gilbert, Davis J. McCarthy, Wei Shi, Gordon K. Smyth	2011	19

About Davis J. McCarthy

Davis J. McCarthy is a scholar working on Health Informatics, Cancer Research, Biophysics, Molecular Biology and Genetics, having authored 40 papers that have together received 35.2k indexed citations. Recurring topics across this work include Single-cell and spatial transcriptomics (17 papers), Gene expression and cancer classification (10 papers), Molecular Biology Techniques and Applications (7 papers), Genomics and Phylogenetic Studies (6 papers), Cancer Genomics and Diagnostics (6 papers), Extracellular vesicles in disease (3 papers), Gene Regulatory Network Analysis (3 papers) and Cell Image Analysis Techniques (3 papers). The work is most often cited by research in Cancer Research (6.2k citations), Molecular Biology (21.0k citations), Aging (457 citations), Immunology (4.6k citations) and Plant Science (5.6k citations). Davis J. McCarthy has collaborated with scholars based in Australia, United Kingdom and United States. Frequent co-authors include Gordon K. Smyth, Mark D. Robinson, Yunshun Chen, Aaron T. L. Lun, Kieran R. Campbell, Quin F. Wills, Michał Okoniewski, Wolfgang Huber, Simon Anders and John C. Marioni. Their work appears in journals such as Genome biology, Bioinformatics, Nature Communications, Nucleic Acids Research and Nature Protocols.

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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