Joint Genome Institute

eScholarship stats: Breakdown by Item for March through June, 2026

Item	Title	Total requests	Download	View-only	%Dnld
1h3515gn	BBMap: A Fast, Accurate, Splice-Aware Aligner	1,461	290	1,171	19.8%
57f5059w	Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly	1,098	678	420	61.7%
96n6w63s	Identification of mobile genetic elements with geNomad	756	515	241	68.1%
7vn8q02v	Persistence and plasticity in bacterial gene regulation	694	505	189	72.8%
5fw223fd	Microbial secondary metabolites: advancements to accelerate discovery towards application	685	359	326	52.4%
0126f84t	Structure, function and diversity of the healthy human microbiome	668	72	596	10.8%
61w6w086	Introduction to Computational Metagenomics	597	370	227	62.0%
8pw2x188	Ancient gene linkages support ctenophores as sister to other animals	582	238	344	40.9%
4zh090xt	Uncovering Earth’s virome	581	356	225	61.3%
6x297461	A global metagenomic map of urban microbiomes and antimicrobial resistance	547	352	195	64.4%
12v5v27c	A call for caution in the biological interpretation of viral auxiliary metabolic genes	534	301	233	56.4%
6rg9n14p	A unified catalog of 204,938 reference genomes from the human gut microbiome	527	279	248	52.9%
8rk2x6pj	A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome	511	209	302	40.9%
2hg7004n	Systematic assessment of long-read RNA-seq methods for transcript identification and quantification	471	359	112	76.2%
5xr3w8d5	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria	466	303	163	65.0%
1r25188f	Fungal Transcriptomics	462	406	56	87.9%
0cf9v4c4	Increased enhancer–promoter interactions during developmental enhancer activation in mammals	447	206	241	46.1%
5gw9r34k	The genome sequence of segmental allotetraploid peanut Arachis hypogaea	446	333	113	74.7%
5wk090j4	A genomic perspective on fungal diversity and evolution	444	214	230	48.2%
3k8311t2	Mapping genome-wide transcription-factor binding sites using DAP-seq	431	69	362	16.0%
43x013sh	Annotation of the Corymbia terpene synthase gene family shows broad conservation but dynamic evolution of physical clusters relative to Eucalyptus	422	342	80	81.0%
2nt21413	CRAGE enables rapid activation of biosynthetic gene clusters in undomesticated bacteria	420	183	237	43.6%
3jj5v0t8	comparative transcriptomics between Synechococcus PCC 7942 and Synechocystis PCC 6803 provide insights into mechanisms of adaptation to stress.	419	189	230	45.1%
4sr1g8sv	Dynamic enhancer landscapes in human craniofacial development	417	197	220	47.2%
4p25j4tm	Transcriptomics reveal a mechanism of niche defense: two beneficial root endophytes deploy an antimicrobial GH18‐CBM5 chitinase to protect their hosts	409	269	140	65.8%
81w457th	XA21-mediated resistance to Xanthomonas oryzae pv. oryzae is dose dependent	399	275	124	68.9%
8dh7k2k4	The complex polyploid genome architecture of sugarcane	386	252	134	65.3%
4391h0zc	Characterisation and comparative analysis of mitochondrial genomes of false, yellow, black and blushing morels provide insights on their structure and evolution	370	258	112	69.7%
9jv4x9mw	Genome-Based Taxonomic Classification of the Phylum Actinobacteria	370	211	159	57.0%
28k88901	Transcription Factor 4 loss-of-function is associated with deficits in progenitor proliferation and cortical neuron content	366	252	114	68.9%
431676dj	Cell-free synthetic biology for natural product biosynthesis and discovery	365	199	166	54.5%
41r662pm	Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem	359	220	139	61.3%
44v0c3r5	Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution	359	168	191	46.8%
8700382s	Unraveling the functional dark matter through global metagenomics	358	212	146	59.2%
13w6f19k	Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria	356	210	146	59.0%
5c25c8j1	Characterization of Mammalian In Vivo Enhancers Using Mouse Transgenesis and CRISPR Genome Editing	352	152	200	43.2%
3n13f2pf	Two decades of bacterial ecology and evolution in a freshwater lake	351	190	161	54.1%
3z44x6vv	Enhancer redundancy provides phenotypic robustness in mammalian development	351	193	158	55.0%
5pg6w486	Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes	350	211	139	60.3%
75w5v2gm	An expanded registry of candidate cis-regulatory elements	350	221	129	63.1%
3g2101xs	A predicted CRISPR-mediated symbiosis between uncultivated archaea	348	196	152	56.3%
4485m01m	The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies	345	227	118	65.8%
0tx6s8g8	Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs	342	189	153	55.3%
2jx454ms	Neurospora intermedia from a traditional fermented food enables waste-to-food conversion	339	199	140	58.7%
7c96t04w	Mutant phenotypes for thousands of bacterial genes of unknown function	339	188	151	55.5%
28w1d3zs	A Korarchael Genome Reveals Insights into the Evolution of the Archaea	338	57	281	16.9%
2n00z5zq	Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass	336	197	139	58.6%
3s14x7d0	CRAGE-RB-PI-seq reveals transcriptional dynamics of plant-associated bacteria during root colonization	336	193	143	57.4%
18v6h17b	Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks	334	121	213	36.2%
513738cv	Secreted Effector Proteins of Poplar Leaf Spot and Stem Canker Pathogen Sphaerulina musiva Manipulate Plant Immunity and Contribute to Virulence in Diverse Ways.	331	236	95	71.3%

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