Joint Genome Institute

eScholarship stats: History by Item for February through May, 2025

Item	Title	Total requests	2025-05	2025-04	2025-03	2025-02
1h3515gn	BBMap: A Fast, Accurate, Splice-Aware Aligner	967	272	200	277	218
7vn8q02v	Persistence and plasticity in bacterial gene regulation	579	82	408	59	30
22k9d6k9	Phytozome Comparative Plant Genomics Portal	386	114	114	95	63
57f5059w	Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly	373	65	84	95	129
5fw223fd	Microbial secondary metabolites: advancements to accelerate discovery towards application	316	87	71	86	72
8rk2x6pj	A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome	258	88	57	70	43
4zh090xt	Uncovering Earth’s virome	257	107	44	56	50
0kf9t6gn	Giant viruses with an expanded complement of translation system components	206	153	19	18	16
3n13f2pf	Two decades of bacterial ecology and evolution in a freshwater lake	202	38	37	47	80
7c83j3jr	Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas	180	103	32	25	20
1dc93220	Gain-of-function SOS1 mutations cause a distinctive form of noonan syndrome	143	46	30	33	34
18v6h17b	Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks	137	29	40	27	41
44v0c3r5	Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.	131	38	34	26	33
8fd5q9b2	Next-generation transcriptome assembly	128	39	29	35	25
1549t4d3	Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data	127	86	18	10	13
1r25188f	Fungal Transcriptomics	126	37	26	26	37
9xj0x028	The mole genome reveals regulatory rearrangements associated with adaptive intersexuality	123	40	22	33	28
3dc7454j	The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants	122	26	31	33	32
0s42p998	Multi‐omic analyses of exogenous nutrient bag decomposition by the black morel Morchella importuna reveal sustained carbon acquisition and transferring	121	40	19	37	25
4p25j4tm	Transcriptomics reveal a mechanism of niche defense: two beneficial root endophytes deploy an antimicrobial GH18‐CBM5 chitinase to protect their hosts	121	38	28	33	22
5rv836pk	The western redcedar genome reveals low genetic diversity in a self-compatible conifer	121	11	81	17	12
3z44x6vv	Enhancer redundancy provides phenotypic robustness in mammalian development	115	31	22	22	40
90w6c49d	Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris	114	25	23	29	37
03j415ph	The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism	112	22	30	29	31
2fs841cf	Genome-Based Taxonomic Classification of Bacteroidetes	107	20	32	24	31
2nt21413	CRAGE enables rapid activation of biosynthetic gene clusters in undomesticated bacteria	105	45	18	17	25
57r2q3hw	The Trichoplax Genome and the Nature of Placozoans	105	79	10	5	11
6x297461	A global metagenomic map of urban microbiomes and antimicrobial resistance	105	33	21	31	20
77t1p45r	Separation of life stages within anaerobic fungi (Neocallimastigomycota) highlights differences in global transcription and metabolism	102	34	68
7c96t04w	Mutant phenotypes for thousands of bacterial genes of unknown function	101	31	31	15	24
4b48v7v8	High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk	100	65	7	10	18
5c25c8j1	Characterization of Mammalian In Vivo Enhancers Using Mouse Transgenesis and CRISPR Genome Editing	100	31	27	23	19
7dq3n3h2	The plant cell wall decomposing machinery underlies the functional diversity of forest fungi	100	26	31	20	23
2310v0bv	Vision, challenges and opportunities for a Plant Cell Atlas	99	27	21	19	32
2ms9t9qn	The sequence and analysis of duplication rich human chromosome 16	99	24	16	29	30
7cx5710p	1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life	99	25	26	24	24
2154w19q	Perfect and imperfect views of ultraconserved sequences	98	66	12	8	12
3jj5v0t8	comparative transcriptomics between Synechococcus PCC 7942 and Synechocystis PCC 6803 provide insights into mechanisms of adaptation to stress.	97	17	31	26	23
6p94q2rz	A roadmap for the functional annotation of protein families: a community perspective	97	19	18	26	34
72r3k7s9	The ecoresponsive genome of Daphnia pulex	97	31	23	19	24
8690m3jt	Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes	97	21	21	22	33
8xb4w8w1	Diversity in the soil virosphere: to infinity and beyond?	97	22	20	28	27
0nt655ss	DRAM for distilling microbial metabolism to automate the curation of microbiome function	96	39	19	18	20
6nn6p8db	Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis	95	20	23	23	29
3cr5c1dh	Genome Sequence of the Palaeopolyploid soybean	94	17	18	37	22
5ps719v0	Widespread adenine N6-methylation of active genes in fungi	94	37	19	11	27
2hk138vc	Evolutionary origin and functional diversification of aminotransferases	93	14	54	14	11
7vh845wn	MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes	92	27	27	24	14
0wp465kn	MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies	91	15	19	23	34
5gz6v5q3	Global overview and major challenges of host prediction methods for uncultivated phages	91	26	18	25	22

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