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Resource: MPRAbase a Massively Parallel Reporter Assay database
- Jingjing Zhao,
- Fotis A Baltoumas,
- Maxwell A Konnaris,
- Ioannis Mouratidis,
- Zhe Liu,
- Jasmine Sims,
- Vikram Agarwal,
- Georgios A Pavlopoulos,
- Ilias Georgakopoulos-Soares,
- and Nadav Ahituv
Genome Res. April 22, 2025 gr.280387.124; Published in Advance April 22, 2025, doi:10.1101/gr.280387.124
...MPRAbase A Massively Parallel Reporter Assay database Jingjing Zhao1,2,*, Fotis A. Baltoumas3,*, Maxwell A. Konnaris4,5, Ioannis Mouratidis4, Zhe Liu1,2,6, Jasmine Sims1,2, Vikram Agarwal7, Georgios A. Pavlopoulos3, Ilias Georgakopoulos-Soares4,♱, Nadav Ahituv1,2,♱ 1Department of Bioengineering...
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Resource: dbEmbryo multi-omics database for analyses of synergistic regulation in early mammalian embryo development
- Xin Huang,
- Xiaohan Tang,
- Xuemei Bai,
- Honglei Li,
- Huan Tao,
- Junting Wang,
- Yaru Li,
- Yu Sun,
- Yang Zheng,
- Xiang Xu,
- Longteng Wang,
- Yang Ding,
- Meisong Lu,
- Pingkun Zhou,
- Xiaochen Bo,
- Hao Li,
- and Hebing Chen
Genome Res. August 2022 32: 1612-1625; Published in Advance August 17, 2022, doi:10.1101/gr.276744.122
...epigenetic marks undergo reprogramming and play crucial roles in the mediation of gene expression. Currently, several databases provide multi-omics information on early embryos. However, how interconnected epigenetic markers function together to coordinate the expression of the genetic code...
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Resource: The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program
- Olivier Tassy,
- Delphine Dauga,
- Fabrice Daian,
- Daniel Sobral,
- François Robin,
- Pierre Khoueiry,
- David Salgado,
- Vanessa Fox,
- Danièle Caillol,
- Renaud Schiappa,
- Baptiste Laporte,
- Anne Rios,
- Guillaume Luxardi,
- Takehiro Kusakabe,
- Jean-Stéphane Joly,
- Sébastien Darras,
- Lionel Christiaen,
- Magali Contensin,
- Hélène Auger,
- Clément Lamy,
- Clare Hudson,
- Ute Rothbächer,
- Michael J. Gilchrist,
- Kazuhiro W. Makabe,
- Kohji Hotta,
- Shigeki Fujiwara,
- Nori Satoh,
- Yutaka Satou,
- and Patrick Lemaire
Genome Res. October 2010 20: 1459-1468; Published in Advance July 20, 2010, doi:10.1101/gr.108175.110
...The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program Olivier Tassy 1 , 13 , 14 , Delphine Dauga 1 , 13 , Fabrice Daian 1 , 13 , Daniel Sobral 1 , 13 , 15 , François Robin 1...
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Method: Real-time analysis and visualization of nanopore metagenomic samples with MARTi
- Ned Peel,
- Samuel Martin,
- Darren Heavens,
- Douglas W. Yu,
- Matthew D. Clark,
- and Richard M. Leggett
Genome Res. November 2025 35: 2488-2500; Published in Advance October 27, 2025, doi:10.1101/gr.280550.125
..., visualization, and exploration of metagenomic data. MARTi supports various classification methods, including BLAST, Centrifuge, and Kraken2, letting users customize parameters and utilize their own databases for taxonomic classification and antimicrobial resistance analysis. With a user-friendly, browser...
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Resource: Mitochondrial DNA variation across 56,434 individuals in gnomAD
- Kristen M. Laricchia,
- Nicole J. Lake,
- Nicholas A. Watts,
- Megan Shand,
- Andrea Haessly,
- Laura Gauthier,
- David Benjamin,
- Eric Banks,
- Jose Soto,
- Kiran Garimella,
- James Emery,
- Genome Aggregation Database Consortium,
- Heidi L. Rehm,
- Daniel G. MacArthur,
- Grace Tiao,
- Monkol Lek,
- Vamsi K. Mootha,
- and Sarah E. Calvo
Genome Res. March 2022 32: 569-582; Published in Advance January 24, 2022, doi:10.1101/gr.276013.121
...Kristen M. Laricchia1,2,8, Nicole J. Lake3,4,8, Nicholas A. Watts1,2, Megan Shand1, Andrea Haessly1, Laura Gauthier1, David Benjamin1, Eric Banks1, Jose Soto1, Kiran Garimella1, James Emery1, Genome Aggregation Database Consortium7, Heidi L. Rehm1,2, Daniel G. MacArthur1,4,5, Grace Tiao1...
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Resource: HistoneHits: A database for histone mutations and their phenotypes
- Hailiang Huang,
- Alexandra M. Maertens,
- Edel M. Hyland,
- Junbiao Dai,
- Anne Norris,
- Jef D. Boeke,
- and Joel S. Bader
Genome Res. April 2009 19: 674-681; Published in Advance February 13, 2009, doi:10.1101/gr.083402.108
...HistoneHits: A database for histone mutations and their phenotypes Hailiang Huang 1 , 2 , Alexandra M. Maertens 2 , 3 , Edel M. Hyland 2 , 4 , Junbiao Dai 2 , 4 , Anne Norris 2 , 4 , Jef D. Boeke 2 , 4 and Joel S...
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RESOURCE: A novel DNA sequence database for analyzing human demographic history
- Jeffrey D. Wall,
- Murray P. Cox,
- Fernando L. Mendez,
- August Woerner,
- Tesa Severson,
- and Michael F. Hammer
Genome Res. August 2008 18: 1354-1361; Published in Advance May 20, 2008, doi:10.1101/gr.075630.107
...A novel DNA sequence database for analyzing human demographic history Jeffrey D. Wall 1 , Murray P. Cox 2 , Fernando L. Mendez 3 , August Woerner 2 , Tesa Severson 2 , and Michael F. Hammer 2 , 3 , 4 1 Institute...
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Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
- Wenhai Zhang,
- Yuansheng Liu,
- Guangyi Li,
- Jialu Xu,
- Enlian Chen,
- Alexander Schönhuth,
- and Xiao Luo
Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
...) evaluates whole s, (2) supports either short-read sequencing or long-read sequencing data, (3) can process multiple species simultaneously, (4) refers to a custom database, which avoids the biases of external databases, and (5) provides estimates on the taxonomic abundances of the involved strains...
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RESOURCE: Database of mRNA gene expression profiles of multiple human organs
- Chang Gue Son,
- Sven Bilke,
- Sean Davis,
- Braden T. Greer,
- Jun S. Wei,
- Craig C. Whiteford,
- Qing-Rong Chen,
- Nicola Cenacchi,
- and Javed Khan
Genome Res. March 2005 15: 443-450; doi:10.1101/gr.3124505
...Database of mRNA gene expression profiles of multiple human organs Chang Gue Son 1 , 2 , 4 , Sven Bilke 1 , 4 , Sean Davis 3 , Braden T. Greer 1 , Jun S. Wei 1 , Craig C. Whiteford 1 , Qing-Rong Chen 1 , Nicola...
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Method: k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants
- Pengju Zhao,
- Jiayi He,
- Chen Peng,
- Yuelang Zhang,
- Chong Wang,
- Dongyou Yu,
- Lingzhao Fang,
- and Zhengguang Wang
Genome Res. March 23, 2026 gr.281289.125; Published in Advance March 23, 2026, doi:10.1101/gr.281289.125
...-dependent techniques for TE phylogenetics. For instance, Hill et al. classified 110 “Starship” elements using k-mer-based clustering, which grouped TEs by host taxonomy 111 without requiring conserved sequence databases (R et al. 2025). This highlights the potential 112 of such approaches for revealing TE expansions...
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