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Method: Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes
- Philipp Rentzsch,
- Aaron Kollotzek,
- Kaushik Ram Ganapathy,
- Pejman Mohammadi,
- and Tuuli Lappalainen
Genome Res. October 2025 35: 2316-2325; Published in Advance September 17, 2025, doi:10.1101/gr.280360.124
..., University of Washington, Seattle, Washington 98195, USA; 6New York Genome Center, New York, New York 10013, USA; 7Department of Systems Biology, Columbia University, New York, New York 10032, USA Corresponding authors: philipp.rentzsch@scilifelab.se, tuuli.lappalainen@scilifelab.seAbstractDifferential...
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Research: Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation
- Caden J. Martin,
- Elizabeth A. Oser,
- Prabakaran Nagarajan,
- Liudmila V. Popova,
- Benjamin D. Sunkel,
- Benjamin Z. Stanton,
- and Mark R. Parthun
Genome Res. September 2025 35: 1959-1974; Published in Advance August 5, 2025, doi:10.1101/gr.280380.124
...and regulation. One is the large degree of redundancy between tethering mechanisms and the diversity in peripheral proteins which can interact with chromatin, many of which are differentially expressed between different tissues and stages of development. Added to this is the variability of LADs themselves...
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Research: Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites
- João L. Reis-Cunha,
- Samuel A. Pimenta-Carvalho,
- Laila V. Almeida,
- Anderson Coqueiro-dos-Santos,
- Catarina A. Marques,
- Jennifer A. Black,
- Jeziel Damasceno,
- Richard McCulloch,
- Daniella C. Bartholomeu,
- and Daniel C. Jeffares
Genome Res. March 2024 34: 441-453; Published in Advance April 11, 2024, doi:10.1101/gr.278550.123
...Ancestral aneuploidy and stable chromosomal duplication resulting in differential structure and gene expression control in trypanosomatid parasites João L. Reis-Cunha1,5, Samuel A. Pimenta-Carvalho2,5, Laila V. Almeida2, Anderson Coqueiro-dos-Santos2, Catarina A. Marques3, Jennifer A. Black3...
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Research: Allelic diversification after transposable element exaptation promoted gsdf as the master sex determining gene of sablefish
- Amaury Herpin,
- Manfred Schartl,
- Alexandra Depincé,
- Yann Guiguen,
- Julien Bobe,
- Aurélie Hua-Van,
- Edward S. Hayman,
- Anna Octavera,
- Goro Yoshizaki,
- Krista M. Nichols,
- Giles W. Goetz,
- and J. Adam Luckenbach
Genome Res. August 2021 31: 1366-1380; Published in Advance June 28, 2021, doi:10.1101/gr.274266.120
...the sex-determining period only in male sablefish and prior to other genes associated with gonadal sex differentiationSemiquantitative analysis of the tissue distribution of the two gsdf allelic variant mRNAs (PCR targeting both gsdf mRNAs) revealed exclusive gonadal expression in juvenile sablefish (Fig...
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Method: Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change
- Pejman Mohammadi,
- Stephane E. Castel,
- Andrew A. Brown,
- and Tuuli Lappalainen
Genome Res. November 2017 27: 1872-1884; Published in Advance October 11, 2017, doi:10.1101/gr.216747.116
...define log aFC, s1,0 = log2 d1,0, as the relative cis-regulatory strength of the allele v1 versus the reference allele v0. This quantity is similar to thewidely used log expression fold changeof differentially expressedgenes, but defined between two alleles of a genetic variant. The aFC of a biallelic e...
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Method: Detecting differential copy number variation between groups of samples
- Craig B. Lowe,
- Nicelio Sanchez-Luege,
- Timothy R. Howes,
- Shannon D. Brady,
- Rhea R. Daugherty,
- Felicity C. Jones,
- Michael A. Bell,
- and David M. Kingsley
Genome Res. February 2018 28: 256-265; Published in Advance December 11, 2017, doi:10.1101/gr.206938.116
...to this work. ↵6 Present address: Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany Corresponding author: kingsley@stanford.eduAbstractWe present a method to detect copy number variants (CNVs) that are differentially present between two groups of sequenced samples. We use...
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Method: FIND: difFerential chromatin INteractions Detection using a spatial Poisson process
- Mohamed Nadhir Djekidel,
- Yang Chen,
- and Michael Q. Zhang
Genome Res. March 2018 28: 412-422; Published in Advance February 12, 2018, doi:10.1101/gr.212241.116
..., Antosiewicz-Bourget JE, Lee AY, Ye Z, Kim A, Rajagopal N, Xie W, et al. 2015. Chromatin architecture reorganization during stem cell differentiation. Nature 518: 331–336. ↵Du Z, Zheng H, Huang B, Ma R, Wu J, Zhang X, He J, Xiang Y, Wang Q, Li Y, et al. 2017. Allelic reprogramming of 3D chromatin architecture...
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Research: Effects of sequence variation on differential allelic transcription factor occupancy and gene expression
- Timothy E. Reddy,
- Jason Gertz,
- Florencia Pauli,
- Katerina S. Kucera,
- Katherine E. Varley,
- Kimberly M. Newberry,
- Georgi K. Marinov,
- Ali Mortazavi,
- Brian A. Williams,
- Lingyun Song,
- Gregory E. Crawford,
- Barbara Wold,
- Huntington F. Willard,
- and Richard M. Myers
Genome Res. May 2012 22: 860-869; Published in Advance February 2, 2012, doi:10.1101/gr.131201.111
...Effects of sequence variation on differential allelic transcription factor occupancy and gene expression Timothy E. Reddy 1 , 2 , Jason Gertz 1 , Florencia Pauli 1 , Katerina S. Kucera 2 , Katherine E. Varley 1 , Kimberly M. Newberry...
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Research: Genome-wide analysis of differential RNA editing in epilepsy
- Prashant Kumar Srivastava,
- Marta Bagnati,
- Andree Delahaye-Duriez,
- Jeong-Hun Ko,
- Maxime Rotival,
- Sarah R. Langley,
- Kirill Shkura,
- Manuela Mazzuferi,
- Bénédicte Danis,
- Jonathan van Eyll,
- Patrik Foerch,
- Jacques Behmoaras,
- Rafal M. Kaminski,
- Enrico Petretto,
- and Michael R. Johnson
Genome Res. March 2017 27: 440-450; doi:10.1101/gr.210740.116
...for the -wide detection of RNA sites that are differentially edited in disease. Using RNA-sequencing data from 100 hippocampi from mice with epilepsy (pilocarpine–temporal lobe epilepsy model) and 100 healthy control hippocampi, we identified 256 RNA sites (overlapping with 87 genes) that were significantly...
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Research: Confounding factors in assessing the enriched expression of somatic mutant allele in bulk tumor samples
- Kohei Hagiwara,
- Andrew Thrasher,
- Nadezhda V Terekhanova,
- and Jinghui Zhang
Genome Res. March 4, 2026 gr.281003.125; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
...of somatic mutant allele expression relative to its VAFDNA. Tumor and normal 76 tissues are known to exhibit differential gene expressions [Zhang et al. 1997]. For example, the 77 tumor suppressor gene CDKN2A was noted to have significantly higher expression in tumor 78 tissues compared with the matching...
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