Search results for "Abstract"
showing 10 items of 1959 documents
FastaHerder2: Four Ways to Research Protein Function and Evolution with Clustering and Clustered Databases.
2016
The accelerated growth of protein databases offers great possibilities for the study of protein function using sequence similarity and conservation. However, the huge number of sequences deposited in these databases requires new ways of analyzing and organizing the data. It is necessary to group the many very similar sequences, creating clusters with automated derived annotations useful to understand their function, evolution, and level of experimental evidence. We developed an algorithm called FastaHerder2, which can cluster any protein database, putting together very similar protein sequences based on near-full-length similarity and/or high threshold of sequence identity. We compressed 50…
Fragments of peer review: A quantitative analysis of the literature (1969-2015)
2018
This paper examines research on peer review between 1969 and 2015 by looking at records indexed from the Scopus database. Although it is often argued that peer review has been poorly investigated, we found that the number of publications in this field doubled from 2005. A half of this work was indexed as research articles, a third as editorial notes and literature reviews and the rest were book chapters or letters. We identified the most prolific and influential scholars, the most cited publications and the most important journals in the field. Co-authorship network analysis showed that research on peer review is fragmented, with the largest group of co-authors including only 2.1% of the wh…
Variable Ranking Feature Selection for the Identification of Nucleosome Related Sequences
2018
Several recent works have shown that K-mer sequence representation of a DNA sequence can be used for classification or identification of nucleosome positioning related sequences. This representation can be computationally expensive when k grows, making the complexity in spaces of exponential dimension. This issue effects significantly the classification task computed by a general machine learning algorithm used for the purpose of sequence classification. In this paper, we investigate the advantage offered by the so-called Variable Ranking Feature Selection method to select the most informative k − mers associated to a set of DNA sequences, for the final purpose of nucleosome/linker classifi…
Combining multiple hypothesis testing with machine learning increases the statistical power of genome-wide association studies
2016
Mieth, Bettina et al.
SpaceScanner: COPASI wrapper for automated management of global stochastic optimization experiments
2017
Abstract Motivation Due to their universal applicability, global stochastic optimization methods are popular for designing improvements of biochemical networks. The drawbacks of global stochastic optimization methods are: (i) no guarantee of finding global optima, (ii) no clear optimization run termination criteria and (iii) no criteria to detect stagnation of an optimization run. The impact of these drawbacks can be partly compensated by manual work that becomes inefficient when the solution space is large due to combinatorial explosion of adjustable parameters or for other reasons. Results SpaceScanner uses parallel optimization runs for automatic termination of optimization tasks in case…
Sustained oscillations in the MAP kinase cascade.
2016
Abstract The MAP kinase cascade is a network of enzymatic reactions arranged in layers. In each layer occurs a multiple futile cycle of phosphorylations. The fully phosphorylated substrate then serves as an enzyme for the layer below. This paper focuses on the existence of parameters for which Hopf bifurcations occur and generate periodic orbits. Furthermore it is explained how geometric singular perturbation theory allows to generalize results from simple models to more complex ones.
Identification of control targets in Boolean molecular network models via computational algebra
2015
Motivation: Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biological system into another, more desirable, state through an intervention, such as a drug or other therapeutic treatment. The identification of such strategies is typically based on a mathematical model of the process to be altered through targeted control inputs. This paper focuses on processes at the molecular level that determine the state of an individual cell, involving signaling or gene regulation. The mathematical model type considered is that of Boolean networks. The pot…
CENTENARIANS TRANSCRIPTOME IS UNIQUE AND REVEALS A ROLE OF BCL-XL IN SUCCESSFUL AGING
2017
Centenarians not only enjoy an extraordinary aging, but also show a compression of morbidity. We identified 1721 mRNAs differentially expressed by PMBCs from centenarians when compared with septuagenarians and young people. Sub-network analysis led us to identify Bcl-xL as an important gene up-regulated in centenarians. We found that centenarians display lower plasma cytochrome C levels, higher mitochondrial membrane potential and also less cellular damage accumulation. Immune function is significantly impaired in septuagenarians compared with young people whereas centenarians maintain it. To further ascertain the functional role of Bcl-xL in cellular aging, we found in transduced lymphocyt…
AB052. P-20. Phase 2, open-label study of second-line M7824 treatment in patients with locally advanced or metastatic biliary tract cancer
2019
BACKGROUND: Transforming growth factor β (TGF-β) signaling promotes tumor immunosuppression; its inhibition in the tumor microenvironment may enhance the response to anti-PD-L1 treatment. M7824 is an innovative first-in-class bifunctional fusion protein composed of 2 extracellular domains of TGF-βRII (a TGF-β “trap”) fused to a human IgG1 mAb against PD-L1. Building upon encouraging efficacy observed in a phase 1 study, the present study will evaluate M7824 clinical benefit in patients with pretreated biliary tract cancer (BTC). METHODS: This multicenter, international trial is evaluating M7824 monotherapy in patients with locally advanced or metastatic (LA/M) BTC unselected for tumor PD-L1…
Stability of stationary solutions in models of the Calvin cycle
2017
Abstract In this paper results are obtained concerning the number of positive stationary solutions in simple models of the Calvin cycle of photosynthesis and the stability of these solutions. It is proved that there are open sets of parameters in the model of Zhu et al. (2009) for which there exist two positive stationary solutions. There are never more than two isolated positive stationary solutions but under certain explicit special conditions on the parameters there is a whole continuum of positive stationary solutions. It is also shown that in the set of parameter values for which two isolated positive stationary solutions exist there is an open subset where one of the solutions is asym…