19 papers · ranked by Valyu relevance
Fiona J Whelan, Rebecca J Hall, James O McInerney
A pangenome is the complete set of genes (core and accessory) present in a phylogenetic clade. We hypothesize that a pangenome’s accessory gene content is structured and maintained by selection. To test this hypothesis, we interrogated the genomes of 40 Pseudomonas genomes for statistically significant coincident (i.e.…
Maarten Larmuseau, Lieven P. C. Verbeke, Kathleen Marchal
Recent technological evolutions have led to an exponential increase in data in all the omics fields. It is expected that integration of these different data sources, will drastically enhance our knowledge of the biological mechanisms behind genomic diseases such as cancer. However, the integration of different omics…
Pan‐Jun Kim, Nathan D. Price
- 1 Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America - 2 Present addresses: Asia Pacific Center for Theoretical Physics, Pohang, Gyeongbuk, Republic of Korea; Department of Physics, POSTECH, Pohang, Gyeongbuk, Republic of Korea - 3 Department of Chemical and Biomolecular…
Phuong Dao, Yoo-Ah Kim, Damian Wójtowicz, Sanna Madan + 2 more
'Teresa M. Przytycka'] The analysis of the mutational landscape of cancer, including mutual exclusivity and co-occurrence of mutations, has been instrumental in studying the disease. We hypothesized that exploring the interplay between co-occurrence, mutual exclusivity, and functional interactions between genes will…
Diogo M. Ribeiro, Simone Rubinacci, Anna Ramisch, Robin J. Hofmeister + 2 more
Nearby genes are often expressed as a group. Yet, the prevalence, molecular mechanisms and genetic control of local gene co-expression are far from being understood. Here, by leveraging gene expression measurements across 49 human tissues and hundreds of individuals, we found that local gene co-expression occurs in 13%…
Diogo M. Ribeiro, Simone Rubinacci, Anna Ramisch, Robin J. Hofmeister + 2 more
'Robin J. Hofmeister' 'Emmanouil T. Dermitzakis' 'Olivier Delaneau'] Nearby genes are often expressed as a group. Yet, the prevalence, molecular mechanisms and genetic control of local gene co-expression are far from being understood. Here, by leveraging gene expression measurements across 49 human tissues and hundreds…
Georg Kustatscher, Piotr Grabowski, Juri Rappsilber
Genes are not randomly distributed in the genome. In humans, 10% of protein-coding genes are transcribed from bidirectional promoters and many more are organised in larger clusters. Intriguingly, neighbouring genes are frequently coexpressed but rarely functionally related. Here we show that coexpression of…
Simonida Zehr, Sebastian Wolf, Thomas Oellerich, Matthias S. Leisegang + 3 more
Extraction of meaningful biological insight from gene expression profiling often focuses on the identification of statistically enriched terms or pathways. These methods typically use gene sets as input data, and subsequently return overrepresented terms along with associated statistics describing their enrichment.…
Ben-Yang Liao, Andrew Ying-Fei Chang, Jo-Ann L. Stanton
Coexpression has been frequently used to explore modules of functionally related genes in eukaryotic genomes. However, we found that genetically interacting mammalian genes identified through radiation hybrid (RH) genotypes tend not to be coexpressed across tissues. This pattern remained unchanged after controlling for…
Lucia Pannier, Enrique Merino, Kathleen Marchal, Julio Collado-Vides + 1 more
'Akira Ishihama'] In prokaryotes, genomic distance is a feature that in addition to coregulation affects coexpression. Several observations, such as genomic clustering of highly coexpressed small regulons, support the idea that coexpression behavior of coregulated genes is affected by the distance between the…
Jacob L. Steenwyk, Megan A. Phillips, Feng Yang, Swapneeta S. Date + 4 more
Orthologous gene coevolution—which refers to gene pairs whose evolutionary rates covary across speciation events—is often observed among functionally related genes. We present a comprehensive gene coevolution network inferred from the examination of nearly three million orthologous gene pairs from 332 budding yeast…
Yuichi Aoki, Yasunobu Okamura, Shu Tadaka, Kengo Kinoshita + 1 more
'Takeshi Obayashi'] ATTED-II ([http://atted.jp]()) is a coexpression database for plant species with parallel views of multiple coexpression data sets and network analysis tools. The user can efficiently find functional gene relationships and design experiments to identify gene functions by reverse genetics and general…
Om Prakash
Identification of possibility of co-expression or co-performance directly from set of bio-strings as protein sequences represents an important problem of bridging between genotype to phenotype. This algorithm presents above bridging. Algorithm was implemented with proteins known from human hormone signaling system.…
Guillaume Achaz, Julien Y. Dutheil
| 1 | | Introduction | 3 | | --- | --- | --- | --- | | 2 | | Correlated evolution between traits | 5 | | | 2.1 | Species are not independent | 5 | | | 2.2 | The phylogenetically independent contrasts | 6 | | | 2.3 | Extending the linear model to account for phylogeny | 7 | | | 2.4 | Correlation between discrete traits…
Ivan Junier, Paul Frémont, Olivier Rivoire
In condensed matter physics, simplified descriptions are obtained by coarse-graining the features of a system at a certain characteristic length, defined as the typical length beyond which some properties are no longer correlated. From a physics standpoint, in vitro DNA has thus a characteristic length of 300 base…
Erik Wijnker, Geo Velikkakam James, Jia Ding, F. Becker + 13 more
Erik Wijnker 1,2 , Geo Velikkakam James3 , Jia Ding4 , Frank Becker 1 , Jonas R. Klasen3 , Vimal Rawat 3 , Beth A. Rowan5 , Daniël F. de Jong1,6 , C. Bastiaan de Snoo6 , Luis Zapata7 , Bruno Huettel 8 , Hans de Jong1 , Stephan Ossowski 7 , Detlef Weigel 5 , Maarten Koornneef 1,4 , Joost J.B. Keurentjes1 and Korbinian…
Zhiwen Pan, Jan Dellith, Lothar Wondraczek
Understanding the multivariate origin of physical properties is particularly complex for polyionic glasses. As a concept, the term genome has been used to describe the entirety of structure-property relations in solid materials, based on functional genes acting as descriptors for a particular property, for example, for…
Indra Roux, Simon Bowles, John A. Kalaitzis, Daniel Vuong + 3 more
Chemical exploration of the recently described Australian fungus, Aspergillus burnettii, uncovered a new metabolite, burnettiene A. Here, we characterise the structure of burnettiene A as a polyene-decalin polyketide. Bioinformatic analysis of the genome of A. burnettii identified a putative biosynthetic gene cluster…
Authors not listed
Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…