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RESEARCH: How to Interpret an Anonymous Bacterial Genome: Machine Learning Approach to Gene Identification
- William S. Hayes and
- Mark Borodovsky
Genome Res. November 1, 1998 8: 1154-1171; doi:10.1101/gr.8.11.1154
...How to Interpret an Anonymous Bacterial Genome: Machine Learning Approach to Gene Identification William S. Hayes and Mark Borodovsky 1 School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0230 USA Abstract In this report we...
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ARTICLE: Gene identification in 1.6-Mb region of the Down syndrome region on chromosome 21.
- M Ohira,
- N Seki,
- T Nagase,
- E Suzuki,
- N Nomura,
- O Ohara,
- M Hattori,
- Y Sakaki,
- T Eki,
- Y Murakami,
- T Saito,
- H Ichikawa,
- and M Ohki
Genome Res. January 1997 7: 47-58; doi:10.1101/gr.7.1.47
...Gene identification in 1.6-Mb region of the Down syndrome region on chromosome 21. M Ohira , N Seki , T Nagase , E Suzuki , N Nomura , O Ohara , M Hattori , Y Sakaki , T Eki , Y Murakami , T Saito...
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ARTICLES: Human chromosome-specific cDNA libraries: new tools for gene identification and genome annotation.
- R G Del Mastro,
- L Wang,
- A D Simmons,
- T D Gallardo,
- G A Clines,
- J A Ashley,
- C J Hilliard,
- J J Wasmuth,
- J D McPherson,
- and M Lovett
Genome Res. September 1995 5: 185-194; doi:10.1101/gr.5.2.185
...Human chromosome-specific cDNA libraries: new tools for gene identification and genome annotation. R G Del Mastro , L Wang , A D Simmons , T D Gallardo , G A Clines , J A Ashley , C J Hilliard , J J Wasmuth , J D Mc...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...applied distinct approaches both to the identification of drivers (i.e., by predicting FIEs) and to their analysis with respect to gene duplication.FunVar was designed to detect mutations with impacts on functional sites, predict rare drivers, and provide insights into the structural and functional...
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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...by expression analysis of host genes. Genome Res 19: 481–490. doi:10.1101/gr.084129.108 ↵Gennarino VA, D'Angelo G, Dharmalingam G, Fernandez S, Russolillo G, Sanges R, Mutarelli M, Belcastro V, Ballabio A, Verde P, et al. 2012. Identification of microRNA-regulated gene networks by expression analysis of target...
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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
...through “premature” polyadenylation are key for cell functions (Singh et al. 2018).Thus, even though the role and the consequences of the host/nested gene organization are starting to be uncovered, an updated -wide analysis is urgently needed. As such, characterization and identification of all possible...
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Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
...) Collection and preprocessing of snRNA-seq and snATAC-seq data sets in physical space. (B) Multiple analysis to identify an AD-associated gene list including differential gene expression analysis; identification of cCRE; cell type–specific, AD-associated risk variants; and peak-to-gene linkages. (C) Two...
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Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
...of the Austrian Academy of Sciences, 1090 Vienna, Austria; 11Eric and Wendy Schmidt Center, The Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA Corresponding author: valentina.boeva@inf.ethz.chAbstractGene signature scoring is integral to single-cell RNA sequencing (scRNA-seq) data analysis...
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Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
- Qinhu Zhang,
- Siguo Wang,
- Zhipeng Li,
- Wenzheng Bao,
- Wenjian Liu,
- and De-Shuang Huang
Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
...@eitech.edu.cnAbstractDeciphering the relationships between cis-regulatory elements (CREs) and target gene expression has been a long-standing unsolved problem in molecular biology, and the dynamics of CREs in different cell types make this problem more challenging. To address this challenge, we propose a scalable computational framework...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...PCR primers designed against nonregulatory regions of the gene when enrichment is not expected, and ensuring DNA shearing with fragments that are not too long in order to prevent nonspecific GOI identification. ChIP has had a revolutionary impact on our understanding of biology and has spearheaded clinical...
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