Joint Genome Institute

eScholarship stats: Breakdown by Item for May through August, 2026

Item	Title	Total requests	Download	View-only	%Dnld
1h3515gn	BBMap: A Fast, Accurate, Splice-Aware Aligner	1,345	250	1,095	18.6%
57f5059w	Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly	1,291	702	589	54.4%
28w1d3zs	A Korarchael Genome Reveals Insights into the Evolution of the Archaea	1,174	30	1,144	2.6%
6rg9n14p	A unified catalog of 204,938 reference genomes from the human gut microbiome	757	326	431	43.1%
7vn8q02v	Persistence and plasticity in bacterial gene regulation	716	480	236	67.0%
5fw223fd	Microbial secondary metabolites: advancements to accelerate discovery towards application	711	384	327	54.0%
96n6w63s	Identification of mobile genetic elements with geNomad	663	492	171	74.2%
12v5v27c	A call for caution in the biological interpretation of viral auxiliary metabolic genes	626	274	352	43.8%
4zh090xt	Uncovering Earth’s virome	592	386	206	65.2%
6x297461	A global metagenomic map of urban microbiomes and antimicrobial resistance	592	411	181	69.4%
5wk090j4	A genomic perspective on fungal diversity and evolution	575	268	307	46.6%
3k8311t2	Mapping genome-wide transcription-factor binding sites using DAP-seq	547	121	426	22.1%
8pw2x188	Ancient gene linkages support ctenophores as sister to other animals	539	216	323	40.1%
0cf9v4c4	Increased enhancer–promoter interactions during developmental enhancer activation in mammals	501	221	280	44.1%
61w6w086	Introduction to Computational Metagenomics	500	307	193	61.4%
0126f84t	Structure, function and diversity of the healthy human microbiome	481	60	421	12.5%
44v0c3r5	Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution	468	123	345	26.3%
8rk2x6pj	A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome	442	159	283	36.0%
2hg7004n	Systematic assessment of long-read RNA-seq methods for transcript identification and quantification	437	349	88	79.9%
0h38397x	High fat intake sustains sorbitol intolerance after antibiotic-mediated Clostridia depletion from the gut microbiota	435	227	208	52.2%
4p25j4tm	Transcriptomics reveal a mechanism of niche defense: two beneficial root endophytes deploy an antimicrobial GH18‐CBM5 chitinase to protect their hosts	429	302	127	70.4%
5gw9r34k	The genome sequence of segmental allotetraploid peanut Arachis hypogaea	420	345	75	82.1%
03b2f02f	Viromics approaches for the study of viral diversity and ecology in microbiomes	411	237	174	57.7%
6n06r0hp	IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata	409	235	174	57.5%
81w457th	XA21-mediated resistance to Xanthomonas oryzae pv. oryzae is dose dependent	398	298	100	74.9%
2nt21413	CRAGE enables rapid activation of biosynthetic gene clusters in undomesticated bacteria	388	194	194	50.0%
43x013sh	Annotation of the Corymbia terpene synthase gene family shows broad conservation but dynamic evolution of physical clusters relative to Eucalyptus	379	327	52	86.3%
8d88b106	Recruitment, rewiring and deep conservation in flowering plant gene regulation	370	309	61	83.5%
5xr3w8d5	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria	365	269	96	73.7%
1h51x8jw	The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools	359	84	275	23.4%
2ms9t9qn	The sequence and analysis of duplication rich human chromosome 16	359	288	71	80.2%
4391h0zc	Characterisation and comparative analysis of mitochondrial genomes of false, yellow, black and blushing morels provide insights on their structure and evolution	357	285	72	79.8%
5c25c8j1	Characterization of Mammalian In Vivo Enhancers Using Mouse Transgenesis and CRISPR Genome Editing	355	157	198	44.2%
0jj595tn	Darling: A Web Application for Detecting Disease-Related Biomedical Entity Associations with Literature Mining	352	72	280	20.5%
41r662pm	Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem	351	256	95	72.9%
1r25188f	Fungal Transcriptomics	350	311	39	88.9%
8dh7k2k4	The complex polyploid genome architecture of sugarcane	349	240	109	68.8%
61k340hk	Comparative genomics of citric-acid producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88	347	83	264	23.9%
3g2101xs	A predicted CRISPR-mediated symbiosis between uncultivated archaea	343	206	137	60.1%
7c96t04w	Mutant phenotypes for thousands of bacterial genes of unknown function	339	228	111	67.3%
64r0m71b	Microbiome Engineering: Synthetic Biology of Plant-Associated Microbiomes in Sustainable Agriculture	336	80	256	23.8%
01j548f4	Perspectives on ENCODE	335	238	97	71.0%
6nn6p8db	Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis	335	177	158	52.8%
75w5v2gm	An expanded registry of candidate cis-regulatory elements	332	225	107	67.8%
4sr1g8sv	Dynamic enhancer landscapes in human craniofacial development	330	187	143	56.7%
1dc93220	Gain-of-function SOS1 mutations cause a distinctive form of noonan syndrome	328	110	218	33.5%
7bd0j5b0	Comparative metagenomics of microbial communities	327	255	72	78.0%
0wp465kn	MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies	326	159	167	48.8%
3101x2rn	The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)	326	84	242	25.8%
7hc8b5xx	IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes	326	247	79	75.8%

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