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Resource: Identification of protein features encoded by alternative exons using Exon Ontology
- Léon-Charles Tranchevent,
- Fabien Aubé,
- Louis Dulaurier,
- Clara Benoit-Pilven,
- Amandine Rey,
- Arnaud Poret,
- Emilie Chautard,
- Hussein Mortada,
- François-Olivier Desmet,
- Fatima Zahra Chakrama,
- Maira Alejandra Moreno-Garcia,
- Evelyne Goillot,
- Stéphane Janczarski,
- Franck Mortreux,
- Cyril F. Bourgeois,
- and Didier Auboeuf
Genome Res. June 2017 27: 1087-1097; Published in Advance April 18, 2017, doi:10.1101/gr.212696.116
...-characterized genes while overlooking the poorly characterized ones. In addition, the protein features affected by alternative splicing are currently mostly analyzedmanually in a time-consuming process. The second challenge relies on the identification of processes impacted by coregulated exons. Indeed...
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Method: Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation
- Richa Rashmi,
- Abhinaya Muruganandham,
- Pranita Borkar,
- Sumana Mallick,
- Taylor Hubbs,
- Ari Aviles,
- Daniel Chung,
- and Irtisha Singh
Genome Res. April 13, 2026 gr.281044.125; Published in Advance April 13, 2026, doi:10.1101/gr.281044.125
...-220 10 protein interaction network analysis confirmed a direct functional relationship 221 between ACOT8 and PEX13 (Supplementary Fig. S4A), supporting coordinated regulation of 222 peroxisomal function and lipid metabolism during megakaryopoiesis (Hunt et al. 2012; Lee et al. 223 2018; Plessner et al...
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Research: Comprehensive identification and analysis of human accelerated regulatory DNA
- Rachel M. Gittelman,
- Enna Hun,
- Ferhat Ay,
- Jennifer Madeoy,
- Len Pennacchio,
- William S. Noble,
- R. David Hawkins,
- and Joshua M. Akey
Genome Res. September 2015 25: 1245-1255; Published in Advance June 23, 2015, doi:10.1101/gr.192591.115
...Comprehensive identification and analysis of human accelerated regulatory DNA Rachel M. Gittelman 1 , Enna Hun 2 , Ferhat Ay 1 , Jennifer Madeoy 1 , Len Pennacchio 3 , William S. Noble 1 , R. David Hawkins 1 , 2...
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Research: Yeast genetic interaction screen of human genes associated with amyotrophic lateral sclerosis: identification of MAP2K5 kinase as a potential drug target
- Myungjin Jo,
- Ah Young Chung,
- Nozomu Yachie,
- Minchul Seo,
- Hyejin Jeon,
- Youngpyo Nam,
- Yeojin Seo,
- Eunmi Kim,
- Quan Zhong,
- Marc Vidal,
- Hae Chul Park,
- Frederick P. Roth,
- and Kyoungho Suk
Genome Res. September 2017 27: 1487-1500; Published in Advance June 8, 2017, doi:10.1101/gr.211649.116
...to predict the pathological functions of disease genes. Neurodegenerative diseases are often associated with protein misfolding (Forman et al. 2004; Frost and Diamond 2012; Valastyan and Lindquist 2014). Cytoplasmic inclusions containing tau, transactive response DNA-binding protein (TARDBP), superoxide...
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Method: Proteome-wide discovery of mislocated proteins in cancer
- KiYoung Lee,
- Kyunghee Byun,
- Wonpyo Hong,
- Han-Yu Chuang,
- Chan-Gi Pack,
- Enkhjargal Bayarsaikhan,
- Sun Ha Paek,
- Hyosil Kim,
- Hye Young Shin,
- Trey Ideker,
- and Bonghee Lee
Genome Res. August 2013 23: 1283-1294; Published in Advance May 14, 2013, doi:10.1101/gr.155499.113
...of tissue (Reich and Liu 2006). Changes in protein location are also associated with a host of genetic disorders. For instance, in Zellweger syndrome,mislocation of peroxisomal proteins leads to dysfunctional fatty acid oxidation (Dodt et al. 1995). In model organisms, the location of proteins can...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...function and prognostic value. Notably, LTR7-PLAAT4, present in 29% of tumors, encodes a protein variant transcriptionally regulated by FOXM1 binding to the LTR7 promoter. LTR7-PLAAT4 isoform 2 is associated with increased cholesterol ester accumulation and lipid droplet formation mediated through BSCL2...
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Method: ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies
- Jordan H. Little,
- Guillermo Hoffmann Meyer,
- Aakash Grover,
- Alex Michael Francette,
- Raghavendran Partha,
- Karen M. Arndt,
- Martin Smith,
- Nathan Clark,
- and Maria Chikina
Genome Res. September 2025 35: 2041-2051; Published in Advance August 7, 2025, doi:10.1101/gr.280586.125
...of DNA repair genes. Proc Natl Acad Sci 116: 19593–19599. doi:10.1073/pnas.1906559116 ↵Chen J, Aronow BJ, Jegga AG. 2009. Disease candidate gene identification and prioritization using protein interaction networks. BMC Bioinformatics 10: 73. doi:10.1186/1471-2105-10-73 ↵Clark NL, Alani E, Aquadro CF...
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Research: Natural selection drives the accumulation of amino acid tandem repeats in human proteins
- Loris Mularoni,
- Alice Ledda,
- Macarena Toll-Riera,
- and M. Mar Albà
Genome Res. June 2010 20: 745-754; Published in Advance March 24, 2010, doi:10.1101/gr.101261.109
...140 323 10 10–12 Novel protein (FLJ16611) E ENSG00000066248 ENSP00000264051 NGEF 215 11 4–11 Ephexin-1 E ENSG00000155846 ENSP00000312649 PPARGC1B 433 11 11–14 Peroxisome proliferator-activated receptor g G ENSG00000120093 ENSP00000308252 HOXB3 153 11 7–16 Homeobox protein HOXB3 G ENSG00000153266 ENSP...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...genes, five showed orthology to genes in N2, Caenorhabditis nigoni, or Caenorhabditis remanei. From the 183-gene set, 77 genes encoded a variety of proteins including a G protein-coupled receptor, an MFP2 motility protein, an MPV17 peroxisomal protein, a serine–threonine protein kinase, and a SIR2...
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Methods: Automatic Identification of Subcellular Phenotypes on Human Cell Arrays
- Christian Conrad,
- Holger Erfle,
- Patrick Warnat,
- Nathalie Daigle,
- Thomas Lörch,
- Jan Ellenberg,
- Rainer Pepperkok,
- and Roland Eils
Genome Res. June 2004 14: 1130-1136; doi:10.1101/gr.2383804
...developed a fully automated workflow from cell array production to phenotype analysis. As a case study we chose to phenotype cells by identification of the subcellular localization of marker proteins that can be used as indicators for the cellular state. We achieved a very high overall accuracy of more than...

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