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Resource: A comparison of gene expression and DNA methylation patterns across tissues and species
- Lauren E. Blake,
- Julien Roux,
- Irene Hernando-Herraez,
- Nicholas E. Banovich,
- Raquel Garcia Perez,
- Chiaowen Joyce Hsiao,
- Ittai Eres,
- Claudia Cuevas,
- Tomas Marques-Bonet,
- and Yoav Gilad
Genome Res. February 2020 30: 250-262; Published in Advance January 17, 2020, doi:10.1101/gr.254904.119
...confounding effects by using a balanced design with respect to species, tissues, and individuals. We also developed a comparative analysis pipeline that minimizes biases attributable to sequence divergence. Thus, we present the most comprehensive catalog of similarities and differences in gene expression...
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Research: Evolution at two levels of gene expression in yeast
- Carlo G. Artieri and
- Hunter B. Fraser
Genome Res. March 2014 24: 411-421; Published in Advance December 6, 2013, doi:10.1101/gr.165522.113
.... 2008) revealed that orthologs with opposing cisacting divergence were significantly less variable than orthologs with reinforcing differences (Kruskal–Wallis rank sum test, P = 0.030; P = 0.0072 for strongly opposing changes, defined as the 50% of genes with the largest differences in Ribo-mRNA cis...
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Methods: Gene expression profiling by massively parallel sequencing
- Tatiana Teixeira Torres,
- Muralidhar Metta,
- Birgit Ottenwälder,
- and Christian Schlötterer
Genome Res. January 2008 18: 172-177; Published in Advance November 21, 2007, doi:10.1101/gr.6984908
...microarrays reveal the effect of sequence divergence on gene expression profiles . Genome Res. 15 : 674 – 680 . ↵ Kuo, W.P. , Liu, F. , Trimarchi, J. , Punzo, C. , Lombardi, M. , Sarang, J. , Whipple, M.E. , Maysuria, M. , Serikawa, K. , Lee, S.Y. , et al. ( 2006 ) A sequence-oriented comparison of gene...
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Research: Fragile regions and not functional constraints predominate in shaping gene organization in the genus Drosophila
- Marcin von Grotthuss,
- Michael Ashburner,
- and José M. Ranz
Genome Res. August 2010 20: 1084-1096; Published in Advance July 2, 2010, doi:10.1101/gr.103713.109
...of co-expressed genes across species are, if the result of natural selection, firm candidates to be included within a particular HCB. Species-specific microarray experiments have uncovered clusters of co-expressed genes that evolve in a coordinated manner in males of seven species of the D. melanogaster...
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Letter: Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention
- Andrew L. Hufton,
- Susanne Mathia,
- Helene Braun,
- Udo Georgi,
- Hans Lehrach,
- Martin Vingron,
- Albert J. Poustka,
- and Georgia Panopoulou
Genome Res. November 2009 19: 2036-2051; Published in Advance August 24, 2009, doi:10.1101/gr.093237.109
...of the gene functions associated with CNEs and gene duplication. Addressing these issues requires that we are able to identify CNEs sequences deeply in evolution. Previous reports have found many CNE sequences that can be dated back to the divergence of fish and tetrapods, and in some cases all the way back...
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Method: Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules
- Sushmita Roy,
- Ilan Wapinski,
- Jenna Pfiffner,
- Courtney French,
- Amanda Socha,
- Jay Konieczka,
- Naomi Habib,
- Manolis Kellis,
- Dawn Thompson,
- and Aviv Regev
Genome Res. June 2013 23: 1039-1050; Published in Advance May 2, 2013, doi:10.1101/gr.146233.112
...Comparative functional genomics studies the evolution of biological processes by analyzing functional data, such as gene expression profiles, across species. A major challenge is to compare profiles collected in a complex phylogeny. Here, we present Arboretum, a novel scalable computational algorithm...
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12 Drosophila Genomes/Methods: Reliable prediction of regulator targets using 12 Drosophila genomes
- Pouya Kheradpour,
- Alexander Stark,
- Sushmita Roy,
- and Manolis Kellis
Genome Res. December 2007 17: 1919-1931; Published in Advance November 7, 2007, doi:10.1101/gr.7090407
...-wide experimental data, predicted targets are of high quality, matching and surpassing ChIP-chip microarrays and recovering miRNA targets with high sensitivity. The resulting regulatory network suggests significant redundancy between pre- and post-transcriptional regulation of gene expression. Footnotes...
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LETTER: Contrasting evolution of expression differences in the testis between species and subspecies of the house mouse
- Christian Voolstra,
- Diethard Tautz,
- Patrick Farbrother,
- Ludwig Eichinger,
- and Bettina Harr
Genome Res. January 2007 17: 42-49; Published in Advance October 12, 2006, doi:10.1101/gr.5683806
...in the genomic era . Cytogenet. Genome Res. 105 : 385 – 394 . ↵ Gilad, Y. , Rifkin, S.A. , Bertone, P. , Gerstein, M. , White, K.P. ( 2005 ) Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles . Genome Res. 15 : 674 – 680 . ↵ Gilad, Y. , Oshlack, A. , Smyth, G...
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Method: Cross-species analysis of enhancer logic using deep learning
- Liesbeth Minnoye,
- Ibrahim Ihsan Taskiran,
- David Mauduit,
- Maurizio Fazio,
- Linde Van Aerschot,
- Gert Hulselmans,
- Valerie Christiaens,
- Samira Makhzami,
- Monika Seltenhammer,
- Panagiotis Karras,
- Aline Primot,
- Edouard Cadieu,
- Ellen van Rooijen,
- Jean-Christophe Marine,
- Giorgia Egidy,
- Ghanem-Elias Ghanem,
- Leonard Zon,
- Jasper Wouters,
- and Stein Aerts
Genome Res. December 2020 30: 1815-1834; Published in Advance July 30, 2020, doi:10.1101/gr.260844.120
...identity. A better understanding of how enhancers work will improve the interpretation of noncoding variation and empower the generation of cell type–specific drivers for gene therapy. Here, we explore the combination of deep learning and cross-species chromatin accessibility profiling to build explainable...
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Research: Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing
- Yingjia Shen,
- R.C. Venu,
- Kan Nobuta,
- Xiaohui Wu,
- Varun Notibala,
- Caghan Demirci,
- Blake C. Meyers,
- Guo-Liang Wang,
- Guoli Ji,
- and Qingshun Q. Li
Genome Res. September 2011 21: 1478-1486; Published in Advance August 3, 2011, doi:10.1101/gr.114744.110
...sites shared by orthologous genes. This result is indicative of a large amount of conservation among related genes between these two species, representing two groups of evolutionarily divergent plants. To further study whether certain functional gene groups are biased toward APA, we examined...

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