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Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models

Simon Rogers, Mark Girolami, Walter Kolch, Katrina M. Waters, Tao Liu, Brian Thrall, H. Steven Wiley
2008 Computer applications in the biosciences : CABIOS  
A more detailed analysis incorporating information on gene function from the Gene Ontology database shows that a high correlation of mRNA and protein expression is limited to the components of some molecular  ...  Results: Here we have developed a probabilistic clustering model that permits analysis of the links between transcriptomic and proteomic profiles in a sensible and flexible manner.  ...  ACKNOWLEDGEMENTS Portions of this work were conducted at the Environmental Molecular Science Laboratory, a DOE-funded national user facility. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btn553 pmid:18974169 pmcid:PMC4141638 fatcat:ov5e6tctm5g5zdit4ijyjpwpmi

Duplicate gene enrichment and expression pattern diversification in multicellularity

T. Padawer, R. E. Leighty, D. Wang
2012 Nucleic Acids Research  
The budding yeast, Saccharomyces cerevisiae and the nematode, Caenorhabditis elegans, for which the gene sets expressed in specific cells are available, were used as uni and multicellular models, respectively  ...  Furthermore, how much the expression level of a gene fluctuates across different C. elegans cells correlates positively with its paralog count, which is further confirmed by human gene-expression patterns  ...  The authors thank Dr Rickard Sandberg and Mr Daniel Ramskold for providing the human gene-expression dataset (29) .  ... 
doi:10.1093/nar/gks464 pmid:22645319 pmcid:PMC3439886 fatcat:a2oy2nmmxbdorhv257zuou2wyy

Combined Population Dynamics and Entropy Modelling Supports Patient Stratification in Chronic Myeloid Leukemia

Marc Brehme, Steffen Koschmieder, Maryam Montazeri, Mhairi Copland, Vivian G. Oehler, Jerald P. Radich, Tim H. Brümmendorf, Andreas Schuppert
2016 Scientific Reports  
Modelling the parameters of multistep carcinogenesis is key for a better understanding of cancer progression, biomarker identification and the design of individualized therapies.  ...  Using chronic myeloid leukemia (CML) as a paradigm for hierarchical disease evolution we show that combined population dynamic modelling and CML patient biopsy genomic analysis enables patient stratification  ...  Acknowledgements This work was supported by the Interdisciplinary Center for Clinical Research (IZKF) of the Medical Faculty of RWTH Aachen University (O1-2 to SK, and O1-6 to AS and THB) and the Deutsche  ... 
doi:10.1038/srep24057 pmid:27048866 pmcid:PMC4822142 fatcat:w7bo32hefrhcllhezafoxgsuka

An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples

V. K. Yadav, S. De
2014 Briefings in Bioinformatics  
A majority of the cancer genomics and transcriptomics studies do not explicitly consider genetic heterogeneity and impurity, and draw inferences based on mixed populations of cells.  ...  Deconvolution of genomic data from heterogeneous samples provides a powerful tool to address this limitation.  ...  The comparative analysis results published here are in part based upon data generated by The Cancer Genome Atlas pilot project [56] established by the NCI and NHGRI (dbGAP accession ID: phs000178.v8.  ... 
doi:10.1093/bib/bbu002 pmid:24562872 pmcid:PMC4794615 fatcat:mcg7fqdg65gbhnc7okknmpz774

Accelerated Evolutionary Rate of Housekeeping Genes in Tunicates

Georgia Tsagkogeorga, Xavier Turon, Nicolas Galtier, Emmanuel J. P. Douzery, Frédéric Delsuc
2010 Journal of Molecular Evolution  
In order to expand the available genomic data for the group, we used the high-throughput 454 technology to sequence the partial transcriptome of a previously unsampled tunicate, Microcosmus squamiger.  ...  Despite the recurrent interest in the group, the picture of tunicate peculiar evolutionary dynamics is still fragmentary, as it mainly lies in studies focusing on only few model species.  ...  Acknowledgments This work has been supported by the Research Networks Program in Bioinformatics of the High Council for Scientific and Technological Cooperation between France and Israel, and benefited  ... 
doi:10.1007/s00239-010-9372-9 pmid:20697701 fatcat:yxytxegplvgztjdhqvbodkuavy

A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals

Paul Simion, Hervé Philippe, Denis Baurain, Muriel Jager, Daniel J. Richter, Arnaud Di Franco, Béatrice Roure, Nori Satoh, Éric Quéinnec, Alexander Ereskovsky, Pascal Lapébie, Erwan Corre (+4 others)
2017 Current Biology  
We thank the UPMC biological stations of Banyuls-sur-Mer and Villefranche-sur-Mer, as well as Olivier Gros (Universit e des Antilles, Pointe-à -Pitre) for providing lab facilities.  ...  ACKNOWLEDGMENTS We thank Alain Goyeau's diving team for their help collecting antipatharians in Guadeloupe.  ...  In parallel, the pervasive role of epistasis in protein evolution makes modeling of sequence evolution in a site-independent framework (currently a condition for models to remain computationally tractable  ... 
doi:10.1016/j.cub.2017.02.031 pmid:28318975 fatcat:bg5arvrua5edzguol5jx7o2ka4

Novelty by Furcation and Fusion: How tree-like is evolution? [article]

Todd H Oakley
2017 bioRxiv   pre-print
For example, even under the prevailing model of cell-type evolution, the sister-cell-type model, a lack of complete individuation and evolution by co-option will often be involved in forming new cell-types  ...  For one, the central metaphor of a tree of life will often be violated, to the point where we may need a different metaphor, such as economic public goods, or a "web of life".  ...  O'Meara for insightful discussions and comments. Thanks to J. Musser, D. Arendt, and G. Schlosser for organizing the symposium.  ... 
doi:10.1101/113613 fatcat:brvgaqzlpnhfpmdzcqlrmmds3y

Identifying concerted evolution and gene conversion in mammalian gene pairs lasting over 100 million years

Andrew R Carson, Stephen W Scherer
2009 BMC Evolutionary Biology  
Conclusion: The extended duration of concerted evolution in multiple distant lineages suggests that there has been prolonged homogenization of specific segments within these gene pairs.  ...  Our strategy involved the identification of duplicated genes with greater similarity within a species than between species.  ...  Neighbor-joining trees of gene pairs a) BMP8A/B, b) DDX19A/B and c) TUBG1/2 were created in MEGA3 using a Tamura-Nei model of sequence evolution.  ... 
doi:10.1186/1471-2148-9-156 pmid:19583854 pmcid:PMC2720389 fatcat:inozlrszivfffnf3a5u7z6tjee

PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes

Nikolaos Papadopoulos, R Gonzalo Parra, Johannes Söding, Jonathan Wren
2019 Bioinformatics  
PROSSTT can simulate scRNA-seq datasets for differentiation processes with lineage trees of any desired complexity, noise level, noise model and size.  ...  PROSSTT also provides scripts to quantify the quality of predicted lineage trees.  ...  Funding RGP is a long term EMBO postdoctoral fellow (ALTF 212-2016). Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btz078 pmid:30715210 pmcid:PMC6748774 fatcat:nputsb6dbjhifceerxek6lasgu

A Comparative Study of Clustering and Biclustering of Microarray Data[

Haifa Ben Saber, Mourad Elloumi
2014 International Journal of Computer Science & Information Technology (IJCSIT)  
In this paper, we make a new survey on clustering and biclustering of gene expression data, also called microarray data.  ...  That is why, it is of utmost importance to make a simultaneous clustering of genes and conditions to identify clusters of genes that are coexpressed under clusters of conditions.  ...  Finite Mixture Model The finite mixture models underpin a variety of techniques in major areas of statistics including cluster analysis.  ... 
doi:10.5121/ijcsit.2014.6607 fatcat:t7wpao3o6bdyjcdkpkjtntkcri

Data-driven penalty calibration: A case study for Gaussian mixture model selection

Cathy Maugis, Bertrand Michel
2011 E S A I M: Probability & Statistics  
But when a gene subset is studied, all the genes can be non differentially expressed in some experiments.  ...  In the companion paper [C. Maugis and B. Michel, A non asymptotic penalized criterion for Gaussian mixture model selection.  ...  These genes are declared differentially expressed in the two last experiments and non-differentially expressed in five experiments.  ... 
doi:10.1051/ps/2010002 fatcat:u4bxtycngffxzlsfau2jxbzi7y

Molecular paleobiological insights into the origin of the Brachiopoda

Erik A. Sperling, Davide Pisani, Kevin J. Peterson
2011 Evolution & Development  
Analysis of slowly evolving sites results in a robustly supported monophyletic Brachiopoda and Inarticulata (Linguliformea1Craniiformea), which is regarded as the most likely topology for brachiopod interrelationships  ...  Here, these hypotheses were tested with a molecular phylogenetic analysis of seven nuclear housekeeping genes combined with three ribosomal genes.  ...  Near for graciously opening his lab to complete much of the housekeeping gene sequencing, and to the Near/Donoghue labs for stimulating conversations about molecular systematics over 4 years at Yale.  ... 
doi:10.1111/j.1525-142x.2011.00480.x pmid:21535467 fatcat:hzgefzzzyzdu7dbflufjfgqaku

Human gene expression variability and its dependence on methylation and aging

Nasser Bashkeel, Theodore J. Perkins, Mads Kærn, Jonathan M. Lee
2019 BMC Genomics  
The expression variability of a gene is an important functional characteristic of the gene itself and the classification of a gene as one with Hyper-Variability or Hypo-Variability in a human population  ...  Lastly, we find that methylation likely has a key role in controlling expression variability insofar as genes with low expression variability are likely to be non-methylated.  ...  Acknowledgements We thank Stephane Aris-Brosou, Mathieu Lavallee, Martin Pelchat and Redaet Daniel for helpful discussion.  ... 
doi:10.1186/s12864-019-6308-7 pmid:31810449 pmcid:PMC6898959 fatcat:d4isepwq35ex7a7beagz7ro5ee

Toxin expression in snake venom evolves rapidly with constant shifts in evolutionary rates

Agneesh Barua, Alexander S. Mikheyev
2020 Proceedings of the Royal Society of London. Biological Sciences  
Here, we test for patterns of adaptive evolution in venom gene expression data from 52 venomous snake species.  ...  By identifying shifts in tempo and mode of evolution along with models of phenotypic evolution, we show that snake venom exhibits the macroevolutionary dynamics expected of key innovations.  ...  Despite the usefulness of modelling gene expression, relatively few phenotypes can be meaningfully reduced purely to gene expression levels, making the study of gene expression variation in phenotypic  ... 
doi:10.1098/rspb.2020.0613 pmid:32345154 fatcat:6rttassvjzb3lhqt6jaw4edoii

Phylotranscriptomics suggests the jawed vertebrate ancestor could generate diverse helper and regulatory T cell subsets

Anthony K. Redmond, Daniel J. Macqueen, Helen Dooley
2018 BMC Evolutionary Biology  
We searched this, and other newly available sequence datasets, for CD4+ T cell subset-defining genes, aiming to confirm the presence or absence of each subset in cartilaginous fishes.  ...  Results: We generated a new transcriptome based on a normalised, multi-tissue RNA pool, aiming to maximise representation of tissue-specific and lowly expressed genes.  ...  Diane Stewart, and the rest of the Centre for Genome-Enabled Biology and Medicine team at University of Aberdeen for their advice and/or technical assistance. We thank Dr.  ... 
doi:10.1186/s12862-018-1290-2 fatcat:wxzhlnuxsvgurpluxy63wip6di
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