Daniel J. Gaffney

14.8k total citations · 4 hit papers
53 papers, 7.2k citations indexed

About

Daniel J. Gaffney is a scholar working on Molecular Biology, Genetics and Plant Science. According to data from OpenAlex, Daniel J. Gaffney has authored 53 papers receiving a total of 7.2k indexed citations (citations by other indexed papers that have themselves been cited), including 46 papers in Molecular Biology, 20 papers in Genetics and 10 papers in Plant Science. Recurrent topics in Daniel J. Gaffney's work include Genomics and Chromatin Dynamics (15 papers), Genomics and Phylogenetic Studies (10 papers) and Chromosomal and Genetic Variations (10 papers). Daniel J. Gaffney is often cited by papers focused on Genomics and Chromatin Dynamics (15 papers), Genomics and Phylogenetic Studies (10 papers) and Chromosomal and Genetic Variations (10 papers). Daniel J. Gaffney collaborates with scholars based in United Kingdom, United States and Spain. Daniel J. Gaffney's co-authors include Jonathan K. Pritchard, Yoav Gilad, Roger Piqué-Regi, Athma A. Pai, Jacob F. Degner, Peter D. Keightley, Pedro Madrigal, Andrew McPherson, Michał Wojciech Szcześniak and Xuegong Zhang and has published in prestigious journals such as Nature, Cell and Proceedings of the National Academy of Sciences.

In The Last Decade

Daniel J. Gaffney

53 papers receiving 7.1k citations

Hit Papers

align trajectories

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

A survey of best practices for RNA-seq data analysis

2016 1.7k citations Ana Conesa, Pedro Madrigal et al. Genome biology profile →
DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

2011 633 citations Athma A. Pai, Joseph K. Pickrell et al. Genome biology profile →
DNase I sensitivity QTLs are a major determinant of human expression variation

2012 429 citations Jacob F. Degner, Athma A. Pai et al. Nature profile →
Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer’s disease risk genes

2021 280 citations Jeremy Schwartzentruber, Sarah Cooper et al. Nature Genetics profile →

Peers — A (Enhanced Table)

Peers by citation overlap · career bar shows stage (early→late) cites · hero ref

Name	h						Papers	Cites
Daniel J. Gaffney United Kingdom	35	5.3k	1.8k	803	620	607	53	7.2k
John M. Greally United States	53	6.8k 1.3×	2.3k 1.2×	1.0k 1.3×	615 1.0×	579 1.0×	196	9.1k
Timothy E. Reddy United States	34	6.2k 1.2×	1.7k 0.9×	607 0.8×	441 0.7×	489 0.8×	63	7.5k
Hedi Peterson Estonia	20	3.9k 0.7×	1.0k 0.5×	945 1.2×	896 1.4×	511 0.8×	33	6.5k
Jane Rogers United Kingdom	41	4.2k 0.8×	1.8k 1.0×	611 0.8×	770 1.2×	1.2k 1.9×	72	6.8k
Aaron M. Wenger United States	21	4.2k 0.8×	1.7k 0.9×	818 1.0×	458 0.7×	488 0.8×	33	5.7k
Wei Xie China	36	7.2k 1.3×	1.6k 0.9×	502 0.6×	417 0.7×	1.0k 1.7×	113	8.3k
Victor Guryev Netherlands	36	3.9k 0.7×	1.6k 0.8×	989 1.2×	425 0.7×	646 1.1×	124	5.9k
Zhijin Wu United States	29	4.3k 0.8×	1.0k 0.6×	776 1.0×	440 0.7×	424 0.7×	85	6.3k
Qing‐Yuan Sun China	60	7.9k 1.5×	2.2k 1.2×	717 0.9×	888 1.4×	744 1.2×	467	13.7k
Xiaosong Huang United States	15	4.3k 0.8×	881 0.5×	677 0.8×	579 0.9×	765 1.3×	34	6.7k

Countries citing papers authored by Daniel J. Gaffney

Since Specialization

Citations

This map shows the geographic impact of Daniel J. Gaffney'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 Daniel J. Gaffney with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Daniel J. Gaffney more than expected).

Fields of papers citing papers by Daniel J. Gaffney

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Daniel J. Gaffney. 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 Daniel J. Gaffney. The network helps show where Daniel J. Gaffney may publish in the future.

Co-authorship network of co-authors of Daniel J. Gaffney

This figure shows the co-authorship network connecting the top 25 collaborators of Daniel J. Gaffney. A scholar is included among the top collaborators of Daniel J. Gaffney based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Daniel J. Gaffney. Daniel J. Gaffney is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

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20 of 20 papers shown

Panousis, Nikolaos I., Andrew Knights, Natsuhiko Kumasaka, et al.. (2025). Splicing QTL mapping in stimulated macrophages associates low-usage splice junctions with immune-mediated disease risk. Nature Communications. 16(1). 7205–7205. 1 indexed citations

Panousis, Nikolaos I., Andrew Knights, Natsuhiko Kumasaka, et al.. (2025). Gene expression QTL mapping in stimulated iPSC-derived macrophages provides insights into common complex diseases. Nature Communications. 16(1). 7204–7204. 1 indexed citations

Alsinet, Clara, Valentina Lorenzi, Erica Bello, et al.. (2022). Robust temporal map of human in vitro myelopoiesis using single-cell genomics. Nature Communications. 13(1). 13 indexed citations

Rouhani, Foad J., Xueqing Zou, Petr Danecek, et al.. (2022). Substantial somatic genomic variation and selection for BCOR mutations in human induced pluripotent stem cells. Nature Genetics. 54(9). 1406–1416. 47 indexed citations

Schwartzentruber, Jeremy, Sarah Cooper, Jimmy Z. Liu, et al.. (2021). Author Correction: Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer’s disease risk genes. Nature Genetics. 53(4). 585–586. 7 indexed citations

De, Tisham, Ângela Gonçalves, Doug Speed, et al.. (2021). Signatures of TSPAN8 variants associated with human metabolic regulation and diseases. iScience. 24(8). 102893–102893. 5 indexed citations

Heaton, Haynes, Arthur M. Talman, Andrew Knights, et al.. (2020). Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes. Nature Methods. 17(6). 615–620. 183 indexed citations

Conesa, Ana, Pedro Madrigal, Sonia Tarazona, et al.. (2016). A survey of best practices for RNA-seq data analysis. Genome biology. 17(1). 13–13. 1705 indexed citations breakdown →

Aldridge, Sarah, Stephen Watt, Michael A. Quail, et al.. (2013). AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation. Genome biology. 14(11). R124–R124. 31 indexed citations

10.

Gaffney, Daniel J., et al.. (2013). What is the survival after surgery for localized malignant pleural mesothelioma?†. Interactive Cardiovascular and Thoracic Surgery. 16(4). 533–537. 16 indexed citations

11.

Degner, Jacob F., Athma A. Pai, Roger Piqué-Regi, et al.. (2012). DNase I sensitivity QTLs are a major determinant of human expression variation. Nature. 482(7385). 390–394. 429 indexed citations breakdown →

12.

Zullo, Joseph, Ignacio A. Demarco, Roger Piqué-Regi, et al.. (2012). DNA Sequence-Dependent Compartmentalization and Silencing of Chromatin at the Nuclear Lamina. Cell. 149(7). 1474–1487. 342 indexed citations

13.

Veyrieras, Jean‐Baptiste, Daniel J. Gaffney, Joseph K. Pickrell, et al.. (2012). Exon-Specific QTLs Skew the Inferred Distribution of Expression QTLs Detected Using Gene Expression Array Data. PLoS ONE. 7(2). e30629–e30629. 16 indexed citations

14.

Piqué-Regi, Roger, Jacob F. Degner, Athma A. Pai, et al.. (2010). Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Research. 21(3). 447–455. 377 indexed citations

15.

Revil, Timothée, Daniel J. Gaffney, Christel Dias, Jacek Majewski, & Loydie A. Jerome‐Majewska. (2010). Alternative splicing is frequent during early embryonic development in mouse. BMC Genomics. 11(1). 399–399. 65 indexed citations

16.

Gaffney, Daniel J. & Peter D. Keightley. (2008). Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals. BMC Evolutionary Biology. 8(1). 265–265. 12 indexed citations

17.

Keightley, Peter D., Gregory V. Kryukov, Shamil Sunyaev, Daniel L. Halligan, & Daniel J. Gaffney. (2005). Evolutionary constraints in conserved nongenic sequences of mammals. Genome Research. 15(10). 1373–1378. 47 indexed citations

18.

Gaffney, Daniel J., et al.. (2004). DNA Sequence Error Rates in Genbank Records Estimated using the Mouse Genome as a Reference. DNA sequence. 15(5-6). 362–364. 29 indexed citations

19.

Gaffney, Daniel J.. (2004). Unexpected conserved non-coding DNA blocks in mammals. Trends in Genetics. 20(8). 332–337. 16 indexed citations

20.

Eyre‐Walker, Adam, Peter D. Keightley, Nick G.C. Smith, & Daniel J. Gaffney. (2002). Quantifying the Slightly Deleterious Mutation Model of Molecular Evolution. Molecular Biology and Evolution. 19(12). 2142–2149. 161 indexed citations

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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