Most cited papers from Earlham Institute

Earlham Institute

What are the most cited papers from Earlham Institute?

The most cited paper from Earlham Institute is "Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)" (Daniel J. Klionsky et al., 2016), with 6,023 citations. Next come "The zebrafish reference genome sequence and its relationship to the human genome" (5,261) and "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update" (4,017).

Published TypeFieldAccessAuthorsCitations

Showing 50 of 60 papers. Every paper with more than 348 citations is listed.

Most cited papers, sortable by citations and release date
#	Paper
1	Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition) Daniel J. Klionsky et al. · Autophagy Open access2,467 authors	2 Jan 2016	6,023
2	The zebrafish reference genome sequence and its relationship to the human genome Kerstin Howe et al. · Nature Open access177 authors	16 Apr 2013	5,261
3	The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update Enis Afgan, Dannon Baker, Bérénice Batut et al. · Nucleic Acids Research Open access	3 May 2018	4,017
4	The repertoire of mutational signatures in human cancer Ludmil B. Alexandrov et al. · Nature Open access1,384 authors	5 Feb 2020	3,854
5	Shifting the limits in wheat research and breeding using a fully annotated reference genome R. Appels et al. · Science Open access201 authors	17 Aug 2018	3,439
6	Pan-cancer analysis of whole genomes Lauri A. Aaltonen et al. · Nature Open access1,324 authors	5 Feb 2020	3,360
7	Towards complete and error-free genome assemblies of all vertebrate species Arang Rhie et al. · Nature Open access129 authors	28 Apr 2021	3,311
8	Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition) 1 Daniel J. Klionsky et al. · Autophagy Open access2,930 authors	2 Jan 2021	2,743
9	The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update Enis Afgan, Dannon Baker, Marius van den Beek et al. · Nucleic Acids Research Open access	2 May 2016	2,369
10	Mutational Processes Molding the Genomes of 21 Breast Cancers Serena Nik‐Zainal et al. · Cell Open access	May 2012	2,034
11	The landscape of cancer genes and mutational processes in breast cancer Philip J. Stephens et al. · Nature Open access	15 May 2012	1,740
12	A chromosome conformation capture ordered sequence of the barley genome Martin Mascher et al. · Nature Open access	Apr 2017	1,602
13	The Life History of 21 Breast Cancers Serena Nik‐Zainal et al. · Cell Open access	May 2012	1,554
14	A physical, genetic and functional sequence assembly of the barley genome Klaus Mayer et al. · Nature Open access	16 Oct 2012	1,519
15	Analyses of pig genomes provide insight into porcine demography and evolution Martien A. M. Groenen et al. · Nature Open access136 authors	Nov 2012	1,454
16	The Medicago genome provides insight into the evolution of rhizobial symbioses Nevin Dale Young et al. · Nature Open access124 authors	15 Nov 2011	1,319
17	Speed breeding is a powerful tool to accelerate crop research and breeding Amy Watson et al. · Nature Plants Open access	21 Dec 2017	1,257
18	Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia David H. Brann et al. · Science Advances Open access	24 Jul 2020	1,255
19	The Ensembl gene annotation system Bronwen L. Aken et al. · Database Open access	2016	1,242
20	The evolutionary history of 2,658 cancers Moritz Gerstung et al. · Nature Open access1,441 authors	5 Feb 2020	1,149
21	The transcriptional landscape of polyploid wheat R. H. Ramírez-González et al. · Science Open access143 authors	17 Aug 2018	1,132
22	The genomic substrate for adaptive radiation in African cichlid fish David Brawand et al. · Nature Open access	Sep 2014	1,063
23	Multiple wheat genomes reveal global variation in modern breeding Sean Walkowiak et al. · Nature Open access	25 Nov 2020	1,056
24	Patterns of somatic structural variation in human cancer genomes Yilong Li et al. · Nature Open access1,411 authors	5 Feb 2020	1,005
25	The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update The Galaxy Community et al. · Nucleic Acids Research Open access131 authors	3 May 2024	963
26	Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species Thomas C. Mathers et al. · Genome biology Open access	7 Feb 2017	856
27	Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing Isidro Cortés-Ciriano et al. · Nature Genetics Open access1,407 authors	5 Feb 2020	793
28	A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life Project Alex D. Twyford et al. · Wellcome Open Research Open access	24 Jun 2024	784
29	OmniPath: guidelines and gateway for literature-curated signaling pathway resources Dénes Türei, Tamas Douglas Korcsmaros, Julio Sáez-Rodríguez · Nature Methods	29 Nov 2016	779
30	Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection Themoula Charalampous, Gemma L. Kay, Hollian Richardson et al. · Nature Biotechnology Open access	24 Jun 2019	754
31	De novo assembly and genotyping of variants using colored de Bruijn graphs Zamin Iqbal, Mario Cáccamo, Isaac Turner et al. · Nature Genetics Open access	8 Jan 2012	731
32	Lag Phase Is a Distinct Growth Phase That Prepares Bacteria for Exponential Growth and Involves Transient Metal Accumulation Matthew D. Rolfe, Christopher J. Rice, Sacha Lucchini et al. · Journal of Bacteriology Open access	3 Dec 2011	729
33	Meta-analysis of the Parkinson’s disease gut microbiome suggests alterations linked to intestinal inflammation Stefano Romano, George M. Savva, Janis R. Bedarf et al. · npj Parkinson s Disease ReviewOpen access	10 Mar 2021	708
34	Analyses of non-coding somatic drivers in 2,658 cancer whole genomes Esther Rheinbay et al. · Nature Open access1,621 authors	5 Feb 2020	674
35	Genomic architecture and introgression shape a butterfly radiation Nathaniel B. Edelman et al. · Science Open access	31 Oct 2019	667
36	Uncovering hidden variation in polyploid wheat Ksenia V. Krasileva, Hans A. Vasquez-Gross, T. A. Howell et al. · Proceedings of the National Academy of Sciences Open access	17 Jan 2017	625
37	KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies Daniel Mapleson, Gonzalo Garcia Accinelli, George Kettleborough et al. · Bioinformatics Open access	17 Oct 2016	618
38	Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants Thomas R. Turner, Ramakrishnan Karunakaran, John Walshaw et al. · The ISME Journal Open access	18 Jul 2013	599
39	Assemblathon 1: A competitive assessment of de novo short read assembly methods Dent A. Earl et al. · Genome Research Open access	16 Sep 2011	547
40	Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification Matthew T Parker, Katarzyna Knop, Anna V. Sherwood et al. · eLife Open access	13 Jan 2020	523
41	Speed breeding in growth chambers and glasshouses for crop breeding and model plant research Sreya Ghosh et al. · Nature Protocols	14 Nov 2018	509
42	Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae Tofazzal Islam et al. · BMC Biology Open access	3 Oct 2016	496
43	expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform Philippa Borrill, Ricardo Humberto Ramirez-Gonzalez, Cristóbal Uauy · PLANT PHYSIOLOGY Open access	11 Feb 2016	493
44	Single-Cell Multiomics: Multiple Measurements from Single Cells Iain C. Macaulay, Chris Paul Ponting, Thierry Voet · Trends in Genetics ReviewOpen access	12 Jan 2017	482
45	Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue the ICGC Prostate Group et al. · Nature Genetics Open access	2 Mar 2015	462
46	A comparative genomics multitool for scientific discovery and conservation Diane P. Genereux et al. · Nature Open access	11 Nov 2020	456
47	An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations Bernardo Clavijo et al. · Genome Research Open access	18 Apr 2017	445
48	Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication Miguel Carneiro et al. · Science Open access	28 Aug 2014	437
49	Genomic innovation for crop improvement Michael Webster Bevan, Cristóbal Uauy, Brande B. H. Wulff et al. · Nature Open access	Mar 2017	436
50	Genomic basis for RNA alterations in cancer PCAWG Transcriptome Core Group et al. · Nature Open access1,461 authors	5 Feb 2020	425

Citations are OpenAlex's own counts, from its 2026-09-23 snapshot, so the ranking can differ from Google Scholar or Web of Science. A paper is listed for an institution when any of its authors gave it as an affiliation; retracted papers and papers whose citation count cannot be traced to citing works are left out, and a preprint and the article it became are shown once. Release dates are OpenAlex's: where a source gave only a month or a year, that is what is shown. How the lists are chosen.