Joint Genome Institute

eScholarship stats: History by Item for October, 2024 through January, 2025

Item	Title	Total requests	2025-01	2024-12	2024-11	2024-10
1h3515gn	BBMap: A Fast, Accurate, Splice-Aware Aligner	634	163	143	176	152
22k9d6k9	Phytozome Comparative Plant Genomics Portal	430	57	104	104	165
57f5059w	Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly	354	102	63	85	104
7vh845wn	MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes	152	130	7	15
8rk2x6pj	A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome	147	37	36	39	35
4p25j4tm	Transcriptomics reveal a mechanism of niche defense: two beneficial root endophytes deploy an antimicrobial GH18‐CBM5 chitinase to protect their hosts	144	33	71	40
1zx113n5	CTCF-dependent insulation of Hoxb13 and the heterochronic control of tail length.	135	6	12	117
7n8428f3	Genome resources for three modern cotton lines guide future breeding efforts.	124	26	32	33	33
1r25188f	Fungal Transcriptomics	122	56	26	20	20
4zh090xt	Uncovering Earth’s virome	119	23	35	27	34
0r48g3rc	Cultivation of novel Atribacterota from oil well provides new insight into their diversity, ecology, and evolution in anoxic, carbon-rich environments	115	28	26	30	31
8690m3jt	Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes	112	32	24	21	35
3x71c44w	The network makeup artist (NORMA-2.0): distinguishing annotated groups in a network using innovative layout strategies.	110	30	24	29	27
7kt417cw	Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil	110	25	25	31	29
6p94q2rz	A roadmap for the functional annotation of protein families: a community perspective	107	31	16	20	40
2310v0bv	Vision, challenges and opportunities for a Plant Cell Atlas	106	29	23	24	30
2ms9t9qn	The sequence and analysis of duplication rich human chromosome 16	106	32	27	24	23
5630v7q7	Systematic mapping of chromatin state landscapes during mouse development	106	103	2		1
8cw2z936	UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network.	105	27	22	29	27
3z44x6vv	Enhancer redundancy provides phenotypic robustness in mammalian development	104	30	26	20	28
3dc7454j	The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants	103	28	27	25	23
8xb4w8w1	Diversity in the soil virosphere: to infinity and beyond?	102	31	26	15	30
6nn6p8db	Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis	101	20	40	20	21
0wp465kn	MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies	98	32	26	16	24
44v0c3r5	Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.	98	23	21	29	25
9xj0x028	The mole genome reveals regulatory rearrangements associated with adaptive intersexuality	98	27	23	24	24
5663x783	Microbes and Climate Change: a Research Prospectus for the Future	97	30	25	25	17
5gz6v5q3	Global overview and major challenges of host prediction methods for uncultivated phages	96	26	21	21	28
9px708q1	Reactivation of a developmentally silenced embryonic globin gene	96	33	24	18	21
0kf9t6gn	Giant viruses with an expanded complement of translation system components	95	11	25	29	30
2fs841cf	Genome-Based Taxonomic Classification of Bacteroidetes	95	23	19	26	27
59s3224z	Regulatory Dynamics of Midfacial Growth in Evolution and Disease	95	94		1
2x09q87j	Author Correction: Perspectives on ENCODE	94	24	22	23	25
18v6h17b	Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks	93	38	11	16	28
3k8311t2	Mapping genome-wide transcription-factor binding sites using DAP-seq	92	26	24	27	15
51b830z6	Phytozome: A Comparative Platform for Green Plant Genomics	92	22	20	30	20
63h612dp	Sodalis ligni Strain 159R Isolated from an Anaerobic Lignin-Degrading Consortium	92	21	22	19	30
0nm5z1jj	Capturing the genetic makeup of the active microbiome in situ	91	20	25	19	27
35d1h14b	IMG/M: A data management and analysis system for metagenomes	90	27	21	18	24
9bd3z559	The Transcription Factor Roc1 Is a Key Regulator of Cellulose Degradation in the Wood-Decaying Mushroom Schizophyllum commune	90	20	21	23	26
08z8r4ff	101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens	89	22	25	16	26
46z4j35p	Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species	89	26	22	14	27
8n88s2kz	CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping	89	20	23	26	20
0mb8h3r4	Designing and Engineering Methylorubrum extorquens AM1 for Itaconic Acid Production	88	21	24	15	28
0rj32607	Genome sequence of Frateuria aurantia type strain (Kondô 67T), a xanthomonade isolated from Lilium auratium Lindl.	88	26	23	17	22
36g6n553	A fungal transcription factor essential for starch degradation affects integration of carbon and nitrogen metabolism	88	24	28	13	23
7cx5710p	1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life	88	30	14	19	25
2s65v570	Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes	87	30	18	18	21
2zk8j1fx	Genome-wide fetalization of enhancer architecture in heart disease	86	20	22	18	26
8j463183	JGI Plant Genomics Gene Annotation Pipeline	86	23	24	18	21

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